From a9a0960bb8560619d88c3065554d51e0c2009d09 Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Wed, 23 Sep 2026 20:32:03 -0700 Subject: [PATCH 1/8] fix(jats): preserve styling in abstracts and footnotes Parse abstract paragraphs and footnotes into styled inline runs (bold/italic/underline/strike/sub/sup) instead of flattening them to plain text, and emit them via _emit_inline so formatting is preserved in the document. Unstyled content keeps the previous single-item structure. Extends the JATS styling tests and regenerates the affected e2e groundtruth files. Part of #3583 --- docling/backend/xml/jats_backend.py | 147 +- .../jats/groundtruth/pmc2231364.nxml.itxt | 27 +- .../jats/groundtruth/pmc2231364.nxml.json | 274 +- .../data/jats/groundtruth/pmc2231364.nxml.md | 6 +- .../jats/groundtruth/pntd.0008301.nxml.itxt | 404 +- .../jats/groundtruth/pntd.0008301.nxml.json | 1132 +++--- .../jats/groundtruth/pntd.0008301.nxml.md | 4 +- .../jats/groundtruth/pone.0234687.nxml.itxt | 1121 +++--- .../jats/groundtruth/pone.0234687.nxml.json | 3419 +++++++++-------- .../jats/groundtruth/pone.0234687.nxml.md | 2 +- tests/test_backend_jats.py | 138 + 11 files changed, 3819 insertions(+), 2855 deletions(-) mode change 100755 => 100644 docling/backend/xml/jats_backend.py diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py old mode 100755 new mode 100644 index bed50d1e72..f20fac5ec3 --- a/docling/backend/xml/jats_backend.py +++ b/docling/backend/xml/jats_backend.py @@ -23,6 +23,7 @@ from __future__ import annotations import logging +import re import traceback import warnings from dataclasses import dataclass, replace @@ -124,12 +125,12 @@ class AbstractSection(TypedDict): """A single titled section inside a structured abstract.""" title: str - paragraphs: list[str] + paragraphs: list[list[InlineSegment]] # styled inline runs per

class Abstract(TypedDict): label: str - content: str # plain (un-sectioned) paragraphs joined together + paragraphs: list[list[InlineSegment]] # plain

children, as styled runs sections: list[AbstractSection] # structured sub-sections ( children) @@ -324,20 +325,19 @@ def _get_node_text(node: etree._Element) -> str: @staticmethod def _parse_abstract_section(section_node: etree._Element) -> AbstractSection: """Parse a single `` element inside an abstract into an - `AbstractSection` with a title and a list of paragraph strings.""" + `AbstractSection` with a title and its paragraphs as styled inline + segments (preserving bold/italic/sub/sup, ...).""" title_nodes = section_node.xpath("title|label") title = ( JatsDocumentBackend._get_node_text(title_nodes[0]) if title_nodes else "" ) - paragraphs: list[str] = [] + paragraphs: list[list[InlineSegment]] = [] for child_node in section_node: if child_node.tag == "p": - text = JatsDocumentBackend._normalize_whitespace( - JatsDocumentBackend._get_text(child_node) - ) - if text: - paragraphs.append(text) + segments = JatsDocumentBackend._flattened_inline_runs(child_node) + if segments: + paragraphs.append(segments) return AbstractSection(title=title, paragraphs=paragraphs) @@ -417,16 +417,14 @@ def _parse_abstract(self) -> list[Abstract]: abs_list: list[Abstract] = [] for abs_node in self.tree.xpath(".//abstract"): - plain_texts: list[str] = [] + paragraphs: list[list[InlineSegment]] = [] sections: list[AbstractSection] = [] for child_node in abs_node: if child_node.tag == "p": - paragraph_text = JatsDocumentBackend._normalize_whitespace( - JatsDocumentBackend._get_text(child_node) - ) - if paragraph_text: - plain_texts.append(paragraph_text) + segments = JatsDocumentBackend._flattened_inline_runs(child_node) + if segments: + paragraphs.append(segments) elif child_node.tag == "sec": section = JatsDocumentBackend._parse_abstract_section(child_node) if section["paragraphs"]: @@ -439,9 +437,7 @@ def _parse_abstract(self) -> list[Abstract]: abstract: Abstract = Abstract( label=label, - content=JatsDocumentBackend._normalize_whitespace( - " ".join(plain_texts) - ), + paragraphs=paragraphs, sections=sections, ) abs_list.append(abstract) @@ -531,43 +527,35 @@ def _add_abstract( ) -> None: for abstract in xml_components["abstract"]: sections = abstract["sections"] - plain_text = abstract["content"] + paragraphs = abstract["paragraphs"] title = abstract["label"] or DEFAULT_HEADER_ABSTRACT # Skip empty abstracts. - if not plain_text and not sections: + if not paragraphs and not sections: continue abstract_heading = doc.add_heading( parent=self.root, text=title, level=self.hlevel + 1 ) - if sections: - # Structured abstract: emit each as a sub-heading with - # its own paragraph(s) beneath the abstract heading. - for section in sections: - section_title = section["title"] - if section_title: - section_parent: NodeItem = doc.add_heading( - parent=abstract_heading, - text=section_title, - level=self.hlevel + 2, - ) - else: - section_parent = abstract_heading - for paragraph in section["paragraphs"]: - doc.add_text( - parent=section_parent, - text=paragraph, - label=DocItemLabel.TEXT, - ) - else: - # Plain (un-sectioned) abstract: single text item. - doc.add_text( - parent=abstract_heading, - text=plain_text, - label=DocItemLabel.TEXT, - ) + # Plain (un-sectioned) abstract paragraphs, with inline styling. + for segments in paragraphs: + JatsDocumentBackend._emit_inline(doc, abstract_heading, segments) + + # Structured abstract: emit each as a sub-heading with + # its own paragraph(s) beneath the abstract heading. + for section in sections: + section_title = section["title"] + if section_title: + section_parent: NodeItem = doc.add_heading( + parent=abstract_heading, + text=section_title, + level=self.hlevel + 2, + ) + else: + section_parent = abstract_heading + for segments in section["paragraphs"]: + JatsDocumentBackend._emit_inline(doc, section_parent, segments) return @@ -771,6 +759,24 @@ def _parse_ext_link_href(href: str | None) -> AnyUrl | Path | None: except ValidationError: return Path(href) + @staticmethod + def _normalize_segments( + segments: list[InlineSegment], + ) -> list[InlineSegment]: + """Collapse every internal whitespace run of each segment to one space. + + The flattened abstract/footnote paths historically ran the whole text + through ``_normalize_whitespace``; keep that behavior once styling is + preserved per run so multi-line source XML does not produce ragged + spacing. Boundary whitespace is left for ``_strip_segments``. + """ + normalized: list[InlineSegment] = [] + for segment in segments: + text = re.sub(r"\s+", " ", segment.text) + if text: + normalized.append(replace(segment, text=text)) + return normalized + @staticmethod def _strip_segments(segments: list[InlineSegment]) -> list[InlineSegment]: stripped: list[InlineSegment] = [] @@ -780,6 +786,18 @@ def _strip_segments(segments: list[InlineSegment]) -> list[InlineSegment]: stripped.append(replace(segment, text=text)) return stripped + @staticmethod + def _flattened_inline_runs(node: etree._Element) -> list[InlineSegment]: + """Styled inline runs for ``node``, mirroring the historical + flattened-text behavior of abstracts/footnotes: whitespace normalized, + boundary whitespace stripped, styling (bold/italic/sub/sup, ...) + preserved per run.""" + return JatsDocumentBackend._strip_segments( + JatsDocumentBackend._normalize_segments( + JatsDocumentBackend._walk_inline_formula(node) + ) + ) + @staticmethod def _walk_inline_formula( node: etree._Element, @@ -1195,11 +1213,23 @@ def _add_footnote_group( parent: NodeItem, node: etree._Element, ) -> None: - footnotes: list[str] = [ - JatsDocumentBackend._normalize_whitespace(JatsDocumentBackend._get_text(fn)) - for fn in node.iterchildren(tag="fn") - ] - if not footnotes: + footnote_segments: list[list[InlineSegment]] = [] + for fn in node.iterchildren(tag="fn"): + segments = JatsDocumentBackend._flattened_inline_runs(fn) + if segments: + # Keep the FOOTNOTE label on plain text runs; formulas stay + # labeled as formulas. + footnote_segments.append( + [ + ( + replace(segment, label=DocItemLabel.FOOTNOTE) + if segment.label == DocItemLabel.TEXT + else segment + ) + for segment in segments + ] + ) + if not footnote_segments: return title = node.xpath("title") title_text = ( @@ -1214,14 +1244,17 @@ def _add_footnote_group( name="footnotes", parent=heading, ) - for item in footnotes: + for segments in footnote_segments: list_item = doc.add_list_item(parent=footnote_group, text="") inline_item = doc.add_inline_group(parent=list_item) - doc.add_text( - label=DocItemLabel.FOOTNOTE, - text=item, - parent=inline_item, - ) + for segment in segments: + doc.add_text( + label=segment.label, + text=segment.text, + formatting=segment.formatting, + hyperlink=segment.hyperlink, + parent=inline_item, + ) def _walk_linear( self, diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt index 3782efff67..c314c160b2 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt @@ -3,10 +3,23 @@ item-0 at level 0: unspecified: group _root_ item-2 at level 2: paragraph: Yiquan Hu, Yarong Miao item-3 at level 2: section_header: Abstract item-4 at level 3: section_header: Background - item-5 at level 4: text: Environmental modulation of gene ... different stress conditions in vitro. - item-6 at level 3: section_header: Results - item-7 at level 4: text: To provide us with a comprehensi ... ophoretic mobility shift assay (EMSA). - item-8 at level 3: section_header: Conclusion - item-9 at level 4: text: The comparative transcriptomics ... icroarray data using existing methods. - item-10 at level 2: section_header: Introduction - item-11 at level 3: text: Yersinia pestis is the causative ... infectious diseases in human history. \ No newline at end of file + item-5 at level 4: inline: group group + item-6 at level 5: text: Environmental modulation of gene expression in + item-7 at level 5: text: Yersinia pestis + item-8 at level 5: text: is critical for its life style a ... rown under different stress conditions + item-9 at level 5: text: in vitro + item-10 at level 5: text: . + item-11 at level 3: section_header: Results + item-12 at level 4: inline: group group + item-13 at level 5: text: To provide us with a comprehensi ... odulation of global gene expression in + item-14 at level 5: text: Y. pestis + item-15 at level 5: text: , we have analyzed the gene expr ... s. Almost all known virulence genes of + item-16 at level 5: text: Y. pestis + item-17 at level 5: text: were differentially regulated un ... ophoretic mobility shift assay (EMSA). + item-18 at level 3: section_header: Conclusion + item-19 at level 4: inline: group group + item-20 at level 5: text: The comparative transcriptomics ... is and cellular regulatory circuits in + item-21 at level 5: text: Y. pestis + item-22 at level 5: text: , it also serves as a basis for ... icroarray data using existing methods. + item-23 at level 2: section_header: Introduction + item-24 at level 3: text: Yersinia pestis is the causative ... infectious diseases in human history. \ No newline at end of file diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.json b/tests/data/jats/groundtruth/pmc2231364.nxml.json index c9c850d526..86fff25b2e 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.json +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.json @@ -25,7 +25,80 @@ "name": "_root_", "label": "unspecified" }, - "groups": [], + "groups": [ + { + "self_ref": "#/groups/0", + "parent": { + "$ref": "#/texts/3" + }, + "children": [ + { + "$ref": "#/texts/4" + }, + { + "$ref": "#/texts/5" + }, + { + "$ref": "#/texts/6" + }, + { + "$ref": "#/texts/7" + }, + { + "$ref": "#/texts/8" + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/1", + "parent": { + "$ref": "#/texts/9" + }, + "children": [ + { + "$ref": "#/texts/10" + }, + { + "$ref": "#/texts/11" + }, + { + "$ref": "#/texts/12" + }, + { + "$ref": "#/texts/13" + }, + { + "$ref": "#/texts/14" + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/2", + "parent": { + "$ref": "#/texts/15" + }, + "children": [ + { + "$ref": "#/texts/16" + }, + { + "$ref": "#/texts/17" + }, + { + "$ref": "#/texts/18" + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + } + ], "texts": [ { "self_ref": "#/texts/0", @@ -40,7 +113,7 @@ "$ref": "#/texts/2" }, { - "$ref": "#/texts/9" + "$ref": "#/texts/19" } ], "content_layer": "body", @@ -71,10 +144,10 @@ "$ref": "#/texts/3" }, { - "$ref": "#/texts/5" + "$ref": "#/texts/9" }, { - "$ref": "#/texts/7" + "$ref": "#/texts/15" } ], "content_layer": "body", @@ -91,7 +164,7 @@ }, "children": [ { - "$ref": "#/texts/4" + "$ref": "#/groups/0" } ], "content_layer": "body", @@ -104,23 +177,85 @@ { "self_ref": "#/texts/4", "parent": { - "$ref": "#/texts/3" + "$ref": "#/groups/0" }, "children": [], "content_layer": "body", "label": "text", "prov": [], - "orig": "Environmental modulation of gene expression in Yersinia pestis is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions in vitro.", - "text": "Environmental modulation of gene expression in Yersinia pestis is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions in vitro." + "orig": "Environmental modulation of gene expression in", + "text": "Environmental modulation of gene expression in" }, { "self_ref": "#/texts/5", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Yersinia pestis", + "text": "Yersinia pestis", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/6", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions", + "text": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions" + }, + { + "self_ref": "#/texts/7", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "in vitro", + "text": "in vitro", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/8", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ".", + "text": "." + }, + { + "self_ref": "#/texts/9", "parent": { "$ref": "#/texts/2" }, "children": [ { - "$ref": "#/texts/6" + "$ref": "#/groups/1" } ], "content_layer": "body", @@ -131,25 +266,87 @@ "level": 2 }, { - "self_ref": "#/texts/6", + "self_ref": "#/texts/10", "parent": { - "$ref": "#/texts/5" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", "label": "text", "prov": [], - "orig": "To provide us with a comprehensive view of environmental modulation of global gene expression in Y. pestis, we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of Y. pestis were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA).", - "text": "To provide us with a comprehensive view of environmental modulation of global gene expression in Y. pestis, we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of Y. pestis were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA)." + "orig": "To provide us with a comprehensive view of environmental modulation of global gene expression in", + "text": "To provide us with a comprehensive view of environmental modulation of global gene expression in" }, { - "self_ref": "#/texts/7", + "self_ref": "#/texts/11", + "parent": { + "$ref": "#/groups/1" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Y. pestis", + "text": "Y. pestis", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/12", + "parent": { + "$ref": "#/groups/1" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of", + "text": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of" + }, + { + "self_ref": "#/texts/13", + "parent": { + "$ref": "#/groups/1" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Y. pestis", + "text": "Y. pestis", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/14", + "parent": { + "$ref": "#/groups/1" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA).", + "text": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA)." + }, + { + "self_ref": "#/texts/15", "parent": { "$ref": "#/texts/2" }, "children": [ { - "$ref": "#/texts/8" + "$ref": "#/groups/2" } ], "content_layer": "body", @@ -160,25 +357,56 @@ "level": 2 }, { - "self_ref": "#/texts/8", + "self_ref": "#/texts/16", "parent": { - "$ref": "#/texts/7" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", "label": "text", "prov": [], - "orig": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in Y. pestis, it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", - "text": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in Y. pestis, it also serves as a basis for integrating increasing volumes of microarray data using existing methods." + "orig": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in", + "text": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in" }, { - "self_ref": "#/texts/9", + "self_ref": "#/texts/17", + "parent": { + "$ref": "#/groups/2" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Y. pestis", + "text": "Y. pestis", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/18", + "parent": { + "$ref": "#/groups/2" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", + "text": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods." + }, + { + "self_ref": "#/texts/19", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/10" + "$ref": "#/texts/20" } ], "content_layer": "body", @@ -189,9 +417,9 @@ "level": 1 }, { - "self_ref": "#/texts/10", + "self_ref": "#/texts/20", "parent": { - "$ref": "#/texts/9" + "$ref": "#/texts/19" }, "children": [], "content_layer": "body", diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.md b/tests/data/jats/groundtruth/pmc2231364.nxml.md index 92d80a798f..a1e10a0c8f 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.md +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.md @@ -6,15 +6,15 @@ Yiquan Hu, Yarong Miao ### Background -Environmental modulation of gene expression in Yersinia pestis is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions in vitro. +Environmental modulation of gene expression in *Yersinia pestis* is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions *in vitro* . ### Results -To provide us with a comprehensive view of environmental modulation of global gene expression in Y. pestis, we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of Y. pestis were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). +To provide us with a comprehensive view of environmental modulation of global gene expression in *Y. pestis* , we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of *Y. pestis* were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). ### Conclusion -The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in Y. pestis, it also serves as a basis for integrating increasing volumes of microarray data using existing methods. +The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in *Y. pestis* , it also serves as a basis for integrating increasing volumes of microarray data using existing methods. ## Introduction diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt index 0787b59170..c02654ddaa 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt @@ -3,209 +3,215 @@ item-0 at level 0: unspecified: group _root_ item-2 at level 2: paragraph: Clara R. Burgert-Brucker, Kathry ... garet Baker, John Kraemer, Molly Brady item-3 at level 2: paragraph: Global Health Division, RTI Inte ... shington, DC, United States of America item-4 at level 2: section_header: Abstract - item-5 at level 3: text: Achieving elimination of lymphat ... as at highest risk of failing pre-TAS. - item-6 at level 2: section_header: Author summary - item-7 at level 3: text: Achieving elimination of lymphat ... ine prevalence and/or lower elevation. - item-8 at level 2: section_header: Introduction - item-9 at level 3: text: Lymphatic filariasis (LF), a dis ... 8 countries remain endemic for LF [3]. - item-10 at level 3: text: The road to elimination as a pub ... t elimination be officially validated. - item-11 at level 3: text: Pre-TAS include at least one sen ... me of day that blood can be taken [5]. - item-12 at level 3: text: When a country fails to meet the ... o ensure rounds of MDA are not missed. - item-13 at level 3: text: This study aims to understand wh ... e of limited LF elimination resources. - item-14 at level 2: section_header: Methods - item-15 at level 3: text: This is a secondary data analysi ... rch; no ethical approval was required. - item-16 at level 3: text: Building on previous work, we de ... available global geospatial data sets. - item-17 at level 3: table with [18x8] - item-17 at level 4: caption: Table 1 Categorization of potential factors influencing pre-TAS results. - item-18 at level 3: section_header: Data sources - item-19 at level 4: text: Information on baseline prevalen ... publicly available sources (Table 1). - item-20 at level 3: section_header: Outcome and covariate variables - item-21 at level 4: text: The outcome of interest for this ... r than or equal to 1% Mf or 2% Ag [4]. - item-22 at level 4: inline: group group - item-23 at level 5: text: Potential covariates were derive ... ous variables were derived from either - item-24 at level 5: text: a priori - item-25 at level 5: text: knowledge or through exploratory ... is and the final categorizations used. - item-26 at level 4: section_header: Baseline prevalence - item-27 at level 5: text: Baseline prevalence can be assum ... (2) using the cut-off of <10% or ≥10%. - item-28 at level 4: section_header: Agent - item-29 at level 5: inline: group group - item-30 at level 6: text: In terms of differences in trans ... mics by agent, research has shown that - item-31 at level 6: text: Brugia - item-32 at level 6: text: spp. are more susceptible to the anti-filarial drug regimens than - item-33 at level 6: text: Wuchereria bancrofti - item-34 at level 6: text: parasites [23]. Thus, we combined districts reporting - item-35 at level 6: text: B - item-36 at level 6: text: . - item-37 at level 6: text: malayi - item-38 at level 6: text: and - item-39 at level 6: text: B - item-40 at level 6: text: . - item-41 at level 6: text: timori - item-42 at level 6: text: and compared them to areas with - item-43 at level 6: text: W - item-44 at level 6: text: . - item-45 at level 6: text: bancrofti - item-46 at level 6: text: or mixed parasites. Two variable ... e were variables delineating vectors ( - item-47 at level 6: text: Anopheles - item-48 at level 6: text: or - item-49 at level 6: text: Mansonia - item-50 at level 6: text: compared to - item-51 at level 6: text: Culex - item-52 at level 6: text: ) from the environmental domain ... dazole (DEC-ALB)] from the MDA domain. - item-53 at level 4: section_header: Environment - item-54 at level 5: text: LF transmission intensity is inf ... dicates a higher level of “greenness.” - item-55 at level 5: inline: group group - item-56 at level 6: text: We included the socio-economic v ... countries LF is mostly transmitted by + item-5 at level 3: inline: group group + item-6 at level 4: text: Achieving elimination of lymphat ... s Test Strips (FTS), primary vector of + item-7 at level 4: text: Culex + item-8 at level 4: text: , treatment with diethylcarbamaz ... as at highest risk of failing pre-TAS. + item-9 at level 2: section_header: Author summary + item-10 at level 3: inline: group group + item-11 at level 4: text: Achieving elimination of lymphat ... 10%, use of the FTS, primary vector of + item-12 at level 4: text: Culex + item-13 at level 4: text: , treatment with diethylcarbamaz ... ine prevalence and/or lower elevation. + item-14 at level 2: section_header: Introduction + item-15 at level 3: text: Lymphatic filariasis (LF), a dis ... 8 countries remain endemic for LF [3]. + item-16 at level 3: text: The road to elimination as a pub ... t elimination be officially validated. + item-17 at level 3: text: Pre-TAS include at least one sen ... me of day that blood can be taken [5]. + item-18 at level 3: text: When a country fails to meet the ... o ensure rounds of MDA are not missed. + item-19 at level 3: text: This study aims to understand wh ... e of limited LF elimination resources. + item-20 at level 2: section_header: Methods + item-21 at level 3: text: This is a secondary data analysi ... rch; no ethical approval was required. + item-22 at level 3: text: Building on previous work, we de ... available global geospatial data sets. + item-23 at level 3: table with [18x8] + item-23 at level 4: caption: Table 1 Categorization of potential factors influencing pre-TAS results. + item-24 at level 3: section_header: Data sources + item-25 at level 4: text: Information on baseline prevalen ... publicly available sources (Table 1). + item-26 at level 3: section_header: Outcome and covariate variables + item-27 at level 4: text: The outcome of interest for this ... r than or equal to 1% Mf or 2% Ag [4]. + item-28 at level 4: inline: group group + item-29 at level 5: text: Potential covariates were derive ... ous variables were derived from either + item-30 at level 5: text: a priori + item-31 at level 5: text: knowledge or through exploratory ... is and the final categorizations used. + item-32 at level 4: section_header: Baseline prevalence + item-33 at level 5: text: Baseline prevalence can be assum ... (2) using the cut-off of <10% or ≥10%. + item-34 at level 4: section_header: Agent + item-35 at level 5: inline: group group + item-36 at level 6: text: In terms of differences in trans ... mics by agent, research has shown that + item-37 at level 6: text: Brugia + item-38 at level 6: text: spp. are more susceptible to the anti-filarial drug regimens than + item-39 at level 6: text: Wuchereria bancrofti + item-40 at level 6: text: parasites [23]. Thus, we combined districts reporting + item-41 at level 6: text: B + item-42 at level 6: text: . + item-43 at level 6: text: malayi + item-44 at level 6: text: and + item-45 at level 6: text: B + item-46 at level 6: text: . + item-47 at level 6: text: timori + item-48 at level 6: text: and compared them to areas with + item-49 at level 6: text: W + item-50 at level 6: text: . + item-51 at level 6: text: bancrofti + item-52 at level 6: text: or mixed parasites. Two variable ... e were variables delineating vectors ( + item-53 at level 6: text: Anopheles + item-54 at level 6: text: or + item-55 at level 6: text: Mansonia + item-56 at level 6: text: compared to item-57 at level 6: text: Culex - item-58 at level 6: text: in urban areas and by - item-59 at level 6: text: Anopheles - item-60 at level 6: text: in rural areas [32]. Additionall ... proxy for socio-economic status [33]. - item-61 at level 5: text: Finally, all or parts of distric ... s were co-endemic with onchocerciasis. - item-62 at level 4: section_header: MDA - item-63 at level 5: text: Treatment effectiveness depends ... esent a threat to elimination [41,42]. - item-64 at level 5: text: We considered three approaches w ... unds ever documented in that district. - item-65 at level 4: section_header: Pre-TAS implementation - item-66 at level 5: text: Pre-TAS results can be influence ... d throughout the time period of study. - item-67 at level 3: section_header: Data inclusion criteria - item-68 at level 4: text: The dataset, summarized at the d ... al analysis dataset had 554 districts. - item-69 at level 3: section_header: Statistical analysis and modeling - item-70 at level 4: text: Statistical analysis and modelin ... d the number of variables accordingly. - item-71 at level 4: inline: group group - item-72 at level 5: text: Sensitivity analysis was perform ... ica, (3) including only districts with - item-73 at level 5: text: W - item-74 at level 5: text: . - item-75 at level 5: text: bancrofti - item-76 at level 5: text: parasite, and (4) including only districts with - item-77 at level 5: text: Anopheles - item-78 at level 5: text: as the primary vector. The sensi ... ot have been truly LF-endemic [43,44]. - item-79 at level 2: section_header: Results - item-80 at level 3: text: The overall pre-TAS pass rate fo ... ts had baseline prevalences below 20%. - item-81 at level 3: picture - item-81 at level 4: caption: Fig 1 Number of pre-TAS by country. - item-82 at level 3: picture - item-82 at level 4: caption: Fig 2 District-level baseline prevalence by country. - item-83 at level 3: inline: group group - item-84 at level 4: text: Fig 3 shows the unadjusted analy ... FTS diagnostic test, primary vector of - item-85 at level 4: text: Culex - item-86 at level 4: text: , treatment with DEC-ALB, higher ... overage, and sufficient rounds of MDA. + item-58 at level 6: text: ) from the environmental domain ... dazole (DEC-ALB)] from the MDA domain. + item-59 at level 4: section_header: Environment + item-60 at level 5: text: LF transmission intensity is inf ... dicates a higher level of “greenness.” + item-61 at level 5: inline: group group + item-62 at level 6: text: We included the socio-economic v ... countries LF is mostly transmitted by + item-63 at level 6: text: Culex + item-64 at level 6: text: in urban areas and by + item-65 at level 6: text: Anopheles + item-66 at level 6: text: in rural areas [32]. Additionall ... proxy for socio-economic status [33]. + item-67 at level 5: text: Finally, all or parts of distric ... s were co-endemic with onchocerciasis. + item-68 at level 4: section_header: MDA + item-69 at level 5: text: Treatment effectiveness depends ... esent a threat to elimination [41,42]. + item-70 at level 5: text: We considered three approaches w ... unds ever documented in that district. + item-71 at level 4: section_header: Pre-TAS implementation + item-72 at level 5: text: Pre-TAS results can be influence ... d throughout the time period of study. + item-73 at level 3: section_header: Data inclusion criteria + item-74 at level 4: text: The dataset, summarized at the d ... al analysis dataset had 554 districts. + item-75 at level 3: section_header: Statistical analysis and modeling + item-76 at level 4: text: Statistical analysis and modelin ... d the number of variables accordingly. + item-77 at level 4: inline: group group + item-78 at level 5: text: Sensitivity analysis was perform ... ica, (3) including only districts with + item-79 at level 5: text: W + item-80 at level 5: text: . + item-81 at level 5: text: bancrofti + item-82 at level 5: text: parasite, and (4) including only districts with + item-83 at level 5: text: Anopheles + item-84 at level 5: text: as the primary vector. The sensi ... ot have been truly LF-endemic [43,44]. + item-85 at level 2: section_header: Results + item-86 at level 3: text: The overall pre-TAS pass rate fo ... ts had baseline prevalences below 20%. item-87 at level 3: picture - item-87 at level 4: caption: Fig 3 Percent pre-TAS failure by each characteristic (unadjusted). - item-88 at level 3: text: The final log-binomial model inc ... igh baseline and diagnostic test used. - item-89 at level 3: text: Fig 4 shows the risk ratio resul ... of failing pre-TAS (95% CI 1.95–4.83). - item-90 at level 3: picture - item-90 at level 4: caption: Fig 4 Adjusted risk ratios for pre-TAS failure with 95% Confidence Interval from log-binomial model. - item-91 at level 3: inline: group group - item-92 at level 4: text: Sensitivity analyses were conduc ... cts in Africa, (3) only districts with - item-93 at level 4: text: W - item-94 at level 4: text: . - item-95 at level 4: text: bancrofti - item-96 at level 4: text: , and (4) only districts with - item-97 at level 4: text: Anopheles - item-98 at level 4: text: as primary vector. The results o ... hough the estimate was unstable in the + item-87 at level 4: caption: Fig 1 Number of pre-TAS by country. + item-88 at level 3: picture + item-88 at level 4: caption: Fig 2 District-level baseline prevalence by country. + item-89 at level 3: inline: group group + item-90 at level 4: text: Fig 3 shows the unadjusted analy ... FTS diagnostic test, primary vector of + item-91 at level 4: text: Culex + item-92 at level 4: text: , treatment with DEC-ALB, higher ... overage, and sufficient rounds of MDA. + item-93 at level 3: picture + item-93 at level 4: caption: Fig 3 Percent pre-TAS failure by each characteristic (unadjusted). + item-94 at level 3: text: The final log-binomial model inc ... igh baseline and diagnostic test used. + item-95 at level 3: text: Fig 4 shows the risk ratio resul ... of failing pre-TAS (95% CI 1.95–4.83). + item-96 at level 3: picture + item-96 at level 4: caption: Fig 4 Adjusted risk ratios for pre-TAS failure with 95% Confidence Interval from log-binomial model. + item-97 at level 3: inline: group group + item-98 at level 4: text: Sensitivity analyses were conduc ... cts in Africa, (3) only districts with item-99 at level 4: text: W item-100 at level 4: text: . item-101 at level 4: text: bancrofti - item-102 at level 4: text: -only and + item-102 at level 4: text: , and (4) only districts with item-103 at level 4: text: Anopheles - item-104 at level 4: text: -only models (models 3 and 4 res ... gnified by large confidence intervals. - item-105 at level 3: table with [11x6] - item-105 at level 4: caption: Table 2 Adjusted risk ratios for pre-TAS failure from log-binomial model sensitivity analysis. - item-106 at level 3: text: Overall 74 districts in the data ... or 51% of all the failures (38 of 74). - item-107 at level 3: picture - item-107 at level 4: caption: Fig 5 Analysis of failures by model combinations. - item-108 at level 2: section_header: Discussion - item-109 at level 3: inline: group group - item-110 at level 4: text: This paper reports for the first ... similar to what was found in Goldberg - item-111 at level 4: text: et al - item-112 at level 4: text: ., which explored ecological and ... ctors associated with TAS failure [7]. - item-113 at level 3: text: Though diagnostic test used was ... FTS was more sensitive than ICT [45]. - item-114 at level 3: inline: group group - item-115 at level 4: text: Elevation was the only environme ... ous studies [8,31], including Goldberg - item-116 at level 4: text: et al - item-117 at level 4: text: . [7], who used a cutoff of 200 ... ich impact vector chances of survival. - item-118 at level 3: inline: group group - item-119 at level 4: text: The small number of failures ove ... ied in the bivariate analyses, such as - item-120 at level 4: text: Culex - item-121 at level 4: text: vector, higher population densit ... ecisions. Other models have shown that - item-122 at level 4: text: Culex - item-123 at level 4: text: as the predominant vector in a district, compared to - item-124 at level 4: text: Anopheles - item-125 at level 4: text: , results in more intense interv ... search has shown the opposite [15,16]. - item-126 at level 3: inline: group group - item-127 at level 4: text: All other variables included in ... -TAS failure in our analysis. Goldberg - item-128 at level 4: text: et al - item-129 at level 4: text: . found - item-130 at level 4: text: Brugia - item-131 at level 4: text: spp. to be significantly associa ... to the small number of districts with - item-132 at level 4: text: Brugia - item-133 at level 4: text: spp. in our dataset (6%) compared to 46% in the Goldberg + item-104 at level 4: text: as primary vector. The results o ... hough the estimate was unstable in the + item-105 at level 4: text: W + item-106 at level 4: text: . + item-107 at level 4: text: bancrofti + item-108 at level 4: text: -only and + item-109 at level 4: text: Anopheles + item-110 at level 4: text: -only models (models 3 and 4 res ... gnified by large confidence intervals. + item-111 at level 3: table with [11x6] + item-111 at level 4: caption: Table 2 Adjusted risk ratios for pre-TAS failure from log-binomial model sensitivity analysis. + item-112 at level 3: text: Overall 74 districts in the data ... or 51% of all the failures (38 of 74). + item-113 at level 3: picture + item-113 at level 4: caption: Fig 5 Analysis of failures by model combinations. + item-114 at level 2: section_header: Discussion + item-115 at level 3: inline: group group + item-116 at level 4: text: This paper reports for the first ... similar to what was found in Goldberg + item-117 at level 4: text: et al + item-118 at level 4: text: ., which explored ecological and ... ctors associated with TAS failure [7]. + item-119 at level 3: text: Though diagnostic test used was ... FTS was more sensitive than ICT [45]. + item-120 at level 3: inline: group group + item-121 at level 4: text: Elevation was the only environme ... ous studies [8,31], including Goldberg + item-122 at level 4: text: et al + item-123 at level 4: text: . [7], who used a cutoff of 200 ... ich impact vector chances of survival. + item-124 at level 3: inline: group group + item-125 at level 4: text: The small number of failures ove ... ied in the bivariate analyses, such as + item-126 at level 4: text: Culex + item-127 at level 4: text: vector, higher population densit ... ecisions. Other models have shown that + item-128 at level 4: text: Culex + item-129 at level 4: text: as the predominant vector in a district, compared to + item-130 at level 4: text: Anopheles + item-131 at level 4: text: , results in more intense interv ... search has shown the opposite [15,16]. + item-132 at level 3: inline: group group + item-133 at level 4: text: All other variables included in ... -TAS failure in our analysis. Goldberg item-134 at level 4: text: et al - item-135 at level 4: text: . article [7]. MDA coverage leve ... are not necessary to lower prevalence. - item-136 at level 3: text: Limitations to this study includ ... reducing LF prevalence [41,48,51–53]. - item-137 at level 3: text: Fourteen districts were excluded ... ta to extreme outliners in a district. - item-138 at level 3: text: As this analysis used data acros ... of individuals included in the survey. - item-139 at level 3: text: This paper provides evidence fro ... th high baseline and/or low elevation. - item-140 at level 2: section_header: Acknowledgments - item-141 at level 3: text: The authors would like to thank ... e surveys financially and technically. - item-142 at level 2: section_header: References - item-143 at level 3: list: group list - item-144 at level 4: list_item: World Health Organization. Lymph ... trategic plan 2010–2020. Geneva; 2010. - item-145 at level 4: list_item: World Health Organization. Valid ... a public health problem. 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Ghana. PLoS Negl Trop Dis. 2019; 1–17. - item-194 at level 4: list_item: EigegeA, KalA, MiriE, SallauA, U ... 10.1371/journal.pntd.0002508 24205421 - item-195 at level 4: list_item: Van den BergH, Kelly-HopeLA, Lin ... 10.1016/S1473-3099(12)70148-2 23084831 - item-196 at level 4: list_item: WebberR. Eradication of Wucherer ... ol. Trans R Soc Trop Med Hyg. 1979;73. - item-197 at level 1: caption: Table 1 Categorization of potential factors influencing pre-TAS results. - item-198 at level 1: caption: Fig 1 Number of pre-TAS by country. - item-199 at level 1: caption: Fig 2 District-level baseline prevalence by country. - item-200 at level 1: caption: Fig 3 Percent pre-TAS failure by each characteristic (unadjusted). - item-201 at level 1: caption: Fig 4 Adjusted risk ratios for p ... ence Interval from log-binomial model. - item-202 at level 1: caption: Table 2 Adjusted risk ratios for ... g-binomial model sensitivity analysis. - item-203 at level 1: caption: Fig 5 Analysis of failures by model combinations. \ No newline at end of file + item-135 at level 4: text: . found + item-136 at level 4: text: Brugia + item-137 at level 4: text: spp. to be significantly associa ... to the small number of districts with + item-138 at level 4: text: Brugia + item-139 at level 4: text: spp. in our dataset (6%) compared to 46% in the Goldberg + item-140 at level 4: text: et al + item-141 at level 4: text: . article [7]. MDA coverage leve ... are not necessary to lower prevalence. + item-142 at level 3: text: Limitations to this study includ ... reducing LF prevalence [41,48,51–53]. + item-143 at level 3: text: Fourteen districts were excluded ... ta to extreme outliners in a district. + item-144 at level 3: text: As this analysis used data acros ... of individuals included in the survey. + item-145 at level 3: text: This paper provides evidence fro ... th high baseline and/or low elevation. + item-146 at level 2: section_header: Acknowledgments + item-147 at level 3: text: The authors would like to thank ... e surveys financially and technically. + item-148 at level 2: section_header: References + item-149 at level 3: list: group list + item-150 at level 4: list_item: World Health Organization. Lymph ... trategic plan 2010–2020. Geneva; 2010. + item-151 at level 4: list_item: World Health Organization. Valid ... a public health problem. 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Ghana. PLoS Negl Trop Dis. 2019; 1–17. + item-200 at level 4: list_item: EigegeA, KalA, MiriE, SallauA, U ... 10.1371/journal.pntd.0002508 24205421 + item-201 at level 4: list_item: Van den BergH, Kelly-HopeLA, Lin ... 10.1016/S1473-3099(12)70148-2 23084831 + item-202 at level 4: list_item: WebberR. Eradication of Wucherer ... ol. Trans R Soc Trop Med Hyg. 1979;73. + item-203 at level 1: caption: Table 1 Categorization of potential factors influencing pre-TAS results. + item-204 at level 1: caption: Fig 1 Number of pre-TAS by country. + item-205 at level 1: caption: Fig 2 District-level baseline prevalence by country. + item-206 at level 1: caption: Fig 3 Percent pre-TAS failure by each characteristic (unadjusted). + item-207 at level 1: caption: Fig 4 Adjusted risk ratios for p ... ence Interval from log-binomial model. + item-208 at level 1: caption: Table 2 Adjusted risk ratios for ... g-binomial model sensitivity analysis. + item-209 at level 1: caption: Fig 5 Analysis of failures by model combinations. \ No newline at end of file diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.json b/tests/data/jats/groundtruth/pntd.0008301.nxml.json index 36c7c0587c..0221913779 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.json +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.json @@ -21,25 +21,25 @@ "$ref": "#/texts/0" }, { - "$ref": "#/texts/16" + "$ref": "#/texts/20" }, { - "$ref": "#/texts/76" + "$ref": "#/texts/80" }, { - "$ref": "#/texts/77" + "$ref": "#/texts/81" }, { - "$ref": "#/texts/81" + "$ref": "#/texts/85" }, { - "$ref": "#/texts/84" + "$ref": "#/texts/88" }, { - "$ref": "#/texts/98" + "$ref": "#/texts/102" }, { - "$ref": "#/texts/100" + "$ref": "#/texts/104" } ], "content_layer": "body", @@ -50,17 +50,17 @@ { "self_ref": "#/groups/0", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/3" }, "children": [ { - "$ref": "#/texts/21" + "$ref": "#/texts/4" }, { - "$ref": "#/texts/22" + "$ref": "#/texts/5" }, { - "$ref": "#/texts/23" + "$ref": "#/texts/6" } ], "content_layer": "body", @@ -70,21 +70,49 @@ { "self_ref": "#/groups/1", "parent": { - "$ref": "#/texts/26" + "$ref": "#/texts/7" }, "children": [ { - "$ref": "#/texts/27" + "$ref": "#/texts/8" }, { - "$ref": "#/texts/28" + "$ref": "#/texts/9" }, { - "$ref": "#/texts/29" + "$ref": "#/texts/10" + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/2", + "parent": { + "$ref": "#/texts/23" + }, + "children": [ + { + "$ref": "#/texts/25" }, { - "$ref": "#/texts/30" + "$ref": "#/texts/26" }, + { + "$ref": "#/texts/27" + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/3", + "parent": { + "$ref": "#/texts/30" + }, + "children": [ { "$ref": "#/texts/31" }, @@ -141,6 +169,18 @@ }, { "$ref": "#/texts/49" + }, + { + "$ref": "#/texts/50" + }, + { + "$ref": "#/texts/51" + }, + { + "$ref": "#/texts/52" + }, + { + "$ref": "#/texts/53" } ], "content_layer": "body", @@ -148,25 +188,25 @@ "label": "inline" }, { - "self_ref": "#/groups/2", + "self_ref": "#/groups/4", "parent": { - "$ref": "#/texts/50" + "$ref": "#/texts/54" }, "children": [ { - "$ref": "#/texts/52" + "$ref": "#/texts/56" }, { - "$ref": "#/texts/53" + "$ref": "#/texts/57" }, { - "$ref": "#/texts/54" + "$ref": "#/texts/58" }, { - "$ref": "#/texts/55" + "$ref": "#/texts/59" }, { - "$ref": "#/texts/56" + "$ref": "#/texts/60" } ], "content_layer": "body", @@ -174,31 +214,31 @@ "label": "inline" }, { - "self_ref": "#/groups/3", + "self_ref": "#/groups/5", "parent": { - "$ref": "#/texts/65" + "$ref": "#/texts/69" }, "children": [ { - "$ref": "#/texts/67" + "$ref": "#/texts/71" }, { - "$ref": "#/texts/68" + "$ref": "#/texts/72" }, { - "$ref": "#/texts/69" + "$ref": "#/texts/73" }, { - "$ref": "#/texts/70" + "$ref": "#/texts/74" }, { - "$ref": "#/texts/71" + "$ref": "#/texts/75" }, { - "$ref": "#/texts/72" + "$ref": "#/texts/76" }, { - "$ref": "#/texts/73" + "$ref": "#/texts/77" } ], "content_layer": "body", @@ -206,19 +246,19 @@ "label": "inline" }, { - "self_ref": "#/groups/4", + "self_ref": "#/groups/6", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [ { - "$ref": "#/texts/78" + "$ref": "#/texts/82" }, { - "$ref": "#/texts/79" + "$ref": "#/texts/83" }, { - "$ref": "#/texts/80" + "$ref": "#/texts/84" } ], "content_layer": "body", @@ -226,23 +266,11 @@ "label": "inline" }, { - "self_ref": "#/groups/5", + "self_ref": "#/groups/7", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [ - { - "$ref": "#/texts/85" - }, - { - "$ref": "#/texts/86" - }, - { - "$ref": "#/texts/87" - }, - { - "$ref": "#/texts/88" - }, { "$ref": "#/texts/89" }, @@ -269,6 +297,18 @@ }, { "$ref": "#/texts/97" + }, + { + "$ref": "#/texts/98" + }, + { + "$ref": "#/texts/99" + }, + { + "$ref": "#/texts/100" + }, + { + "$ref": "#/texts/101" } ], "content_layer": "body", @@ -276,19 +316,19 @@ "label": "inline" }, { - "self_ref": "#/groups/6", + "self_ref": "#/groups/8", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [ { - "$ref": "#/texts/102" + "$ref": "#/texts/106" }, { - "$ref": "#/texts/103" + "$ref": "#/texts/107" }, { - "$ref": "#/texts/104" + "$ref": "#/texts/108" } ], "content_layer": "body", @@ -296,19 +336,19 @@ "label": "inline" }, { - "self_ref": "#/groups/7", + "self_ref": "#/groups/9", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [ { - "$ref": "#/texts/106" + "$ref": "#/texts/110" }, { - "$ref": "#/texts/107" + "$ref": "#/texts/111" }, { - "$ref": "#/texts/108" + "$ref": "#/texts/112" } ], "content_layer": "body", @@ -316,31 +356,31 @@ "label": "inline" }, { - "self_ref": "#/groups/8", + "self_ref": "#/groups/10", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [ { - "$ref": "#/texts/109" + "$ref": "#/texts/113" }, { - "$ref": "#/texts/110" + "$ref": "#/texts/114" }, { - "$ref": "#/texts/111" + "$ref": "#/texts/115" }, { - "$ref": "#/texts/112" + "$ref": "#/texts/116" }, { - "$ref": "#/texts/113" + "$ref": "#/texts/117" }, { - "$ref": "#/texts/114" + "$ref": "#/texts/118" }, { - "$ref": "#/texts/115" + "$ref": "#/texts/119" } ], "content_layer": "body", @@ -348,37 +388,37 @@ "label": "inline" }, { - "self_ref": "#/groups/9", + "self_ref": "#/groups/11", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [ { - "$ref": "#/texts/116" + "$ref": "#/texts/120" }, { - "$ref": "#/texts/117" + "$ref": "#/texts/121" }, { - "$ref": "#/texts/118" + "$ref": "#/texts/122" }, { - "$ref": "#/texts/119" + "$ref": "#/texts/123" }, { - "$ref": "#/texts/120" + "$ref": "#/texts/124" }, { - "$ref": "#/texts/121" + "$ref": "#/texts/125" }, { - "$ref": "#/texts/122" + "$ref": "#/texts/126" }, { - "$ref": "#/texts/123" + "$ref": "#/texts/127" }, { - "$ref": "#/texts/124" + "$ref": "#/texts/128" } ], "content_layer": "body", @@ -386,23 +426,11 @@ "label": "inline" }, { - "self_ref": "#/groups/10", + "self_ref": "#/groups/12", "parent": { - "$ref": "#/texts/131" + "$ref": "#/texts/135" }, "children": [ - { - "$ref": "#/texts/132" - }, - { - "$ref": "#/texts/133" - }, - { - "$ref": "#/texts/134" - }, - { - "$ref": "#/texts/135" - }, { "$ref": "#/texts/136" }, @@ -549,6 +577,18 @@ }, { "$ref": "#/texts/184" + }, + { + "$ref": "#/texts/185" + }, + { + "$ref": "#/texts/186" + }, + { + "$ref": "#/texts/187" + }, + { + "$ref": "#/texts/188" } ], "content_layer": "body", @@ -573,25 +613,25 @@ "$ref": "#/texts/3" }, { - "$ref": "#/texts/5" + "$ref": "#/texts/7" }, { - "$ref": "#/texts/7" + "$ref": "#/texts/11" }, { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, { - "$ref": "#/texts/129" + "$ref": "#/texts/133" }, { - "$ref": "#/texts/131" + "$ref": "#/texts/135" } ], "content_layer": "body", @@ -631,7 +671,7 @@ }, "children": [ { - "$ref": "#/texts/4" + "$ref": "#/groups/0" } ], "content_layer": "body", @@ -644,23 +684,54 @@ { "self_ref": "#/texts/4", "parent": { - "$ref": "#/texts/3" + "$ref": "#/groups/0" }, "children": [], "content_layer": "body", "label": "text", "prov": [], - "orig": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of Culex, treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS.", - "text": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of Culex, treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS." + "orig": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of", + "text": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of" }, { "self_ref": "#/texts/5", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Culex", + "text": "Culex", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/6", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ", treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS.", + "text": ", treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS." + }, + { + "self_ref": "#/texts/7", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/6" + "$ref": "#/groups/1" } ], "content_layer": "body", @@ -671,37 +742,68 @@ "level": 1 }, { - "self_ref": "#/texts/6", + "self_ref": "#/texts/8", "parent": { - "$ref": "#/texts/5" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", "label": "text", "prov": [], - "orig": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of Culex, treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation.", - "text": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of Culex, treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation." + "orig": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of", + "text": "Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of" }, { - "self_ref": "#/texts/7", + "self_ref": "#/texts/9", + "parent": { + "$ref": "#/groups/1" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Culex", + "text": "Culex", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/10", + "parent": { + "$ref": "#/groups/1" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ", treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation.", + "text": ", treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation." + }, + { + "self_ref": "#/texts/11", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/8" + "$ref": "#/texts/12" }, { - "$ref": "#/texts/9" + "$ref": "#/texts/13" }, { - "$ref": "#/texts/10" + "$ref": "#/texts/14" }, { - "$ref": "#/texts/11" + "$ref": "#/texts/15" }, { - "$ref": "#/texts/12" + "$ref": "#/texts/16" } ], "content_layer": "body", @@ -712,9 +814,9 @@ "level": 1 }, { - "self_ref": "#/texts/8", + "self_ref": "#/texts/12", "parent": { - "$ref": "#/texts/7" + "$ref": "#/texts/11" }, "children": [], "content_layer": "body", @@ -724,9 +826,9 @@ "text": "Lymphatic filariasis (LF), a disease caused by parasitic worms transmitted to humans by mosquito bite, manifests in disabling and stigmatizing chronic conditions including lymphedema and hydrocele. To eliminate LF as a public health problem, the World Health Organization (WHO) recommends two strategies: reducing transmission through annual mass drug administration (MDA) and reducing suffering through ensuring the availability of morbidity management and disability prevention services to all patients [1]. For the first strategy, eliminating LF as a public health problem is defined as a ‘reduction in measurable prevalence in infection in endemic areas below a target threshold at which further transmission is considered unlikely even in the absence of MDA’ [2]. As of 2018, 14 countries have eliminated LF as a public health problem while 58 countries remain endemic for LF [3]." }, { - "self_ref": "#/texts/9", + "self_ref": "#/texts/13", "parent": { - "$ref": "#/texts/7" + "$ref": "#/texts/11" }, "children": [], "content_layer": "body", @@ -736,9 +838,9 @@ "text": "The road to elimination as a public health problem has several milestones. First, where LF prevalence at baseline has exceeded 1% as measured either through microfilaremia (Mf) or antigenemia (Ag), MDA is implemented and treatment coverage is measured in all implementation units, which usually correspond to districts. Implementation units must complete at least five rounds of ‘effective’ treatment, i.e. treatment with a minimum coverage of 65% of the total population. Then, WHO recommends sentinel and spot-check site assessments—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit to determine whether prevalence in each site is less than 1% Mf or less than 2% Ag [4]. Next, if these thresholds are met, national programs can progress to the first transmission assessment survey (TAS). The TAS is a population-based cluster or systematic survey of six- and seven-year-old children to assess whether transmission has fallen below the threshold at which infection is believed to persist. TAS is conducted at least three times, with two years between each survey. TAS 1 results determine if it is appropriate to stop MDA or whether further rounds are required. Finally, when TAS 2 and 3 also fall below the set threshold in every endemic implementation unit nationwide and morbidity criteria have been fulfilled, the national program submits a dossier to WHO requesting that elimination be officially validated." }, { - "self_ref": "#/texts/10", + "self_ref": "#/texts/14", "parent": { - "$ref": "#/texts/7" + "$ref": "#/texts/11" }, "children": [], "content_layer": "body", @@ -748,9 +850,9 @@ "text": "Pre-TAS include at least one sentinel and one spot-check site per one million population. Sentinel sites are established at the start of the program in villages where LF prevalence was believed to be relatively high. Spot-check sites are villages not previously tested but purposively selected as potentially high-risk areas due to original high prevalence, low coverage during MDA, high vector density, or other factors [4]. At least six months after MDA implementation, data are collected from a convenience sample of at least 300 people over five years old in each site. Originally, Mf was recommended as the indicator of choice for pre-TAS, assessed by blood smears taken at the time of peak parasite periodicity [4]. WHO later recommended the use of circulating filarial antigen rapid diagnostic tests, BinaxNow immunochromatographic card tests (ICTs), and after 2016, Alere Filariasis Test Strips (FTS), because they are more sensitive, easier to implement, and more flexible about time of day that blood can be taken [5]." }, { - "self_ref": "#/texts/11", + "self_ref": "#/texts/15", "parent": { - "$ref": "#/texts/7" + "$ref": "#/texts/11" }, "children": [], "content_layer": "body", @@ -760,9 +862,9 @@ "text": "When a country fails to meet the established thresholds in a pre-TAS, they must implement at least two more rounds of MDA. National programs need to forecast areas that might fail pre-TAS and need repeated MDA, so that they can inform the community and district decision-makers of the implications of pre-TAS failure, including the need for continued MDA to lower prevalence effectively. In addition, financial and human resources must be made available for ordering drugs, distributing drugs, supervision and monitoring to implement the further MDA rounds. Ordering drugs and providing MDA budgets often need to be completed before the pre-TAS are implemented, so contingency planning and funding are important to ensure rounds of MDA are not missed." }, { - "self_ref": "#/texts/12", + "self_ref": "#/texts/16", "parent": { - "$ref": "#/texts/7" + "$ref": "#/texts/11" }, "children": [], "content_layer": "body", @@ -772,31 +874,31 @@ "text": "This study aims to understand which factors are associated with the need for additional rounds of MDA as identified by pre-TAS results using programmatic data from 13 countries. The factors associated with failing pre-TAS are not well understood and have not previously been examined at a multi-country scale in the literature. We examine the association between pre-TAS failure and baseline prevalence, parasites, environmental factors, MDA implementation, and pre-TAS implementation. Understanding determinants of pre-TAS failure will help countries identify where elimination may be most difficult and prioritize the use of limited LF elimination resources." }, { - "self_ref": "#/texts/13", + "self_ref": "#/texts/17", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/14" + "$ref": "#/texts/18" }, { - "$ref": "#/texts/15" + "$ref": "#/texts/19" }, { "$ref": "#/tables/0" }, { - "$ref": "#/texts/17" + "$ref": "#/texts/21" }, { - "$ref": "#/texts/19" + "$ref": "#/texts/23" }, { - "$ref": "#/texts/63" + "$ref": "#/texts/67" }, { - "$ref": "#/texts/65" + "$ref": "#/texts/69" } ], "content_layer": "body", @@ -807,9 +909,9 @@ "level": 1 }, { - "self_ref": "#/texts/14", + "self_ref": "#/texts/18", "parent": { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, "children": [], "content_layer": "body", @@ -819,9 +921,9 @@ "text": "This is a secondary data analysis using existing data, collected for programmatic purposes. Data for this analysis come from 568 districts in 13 countries whose LF elimination programs were supported by the United States Agency for International Development (USAID) through the ENVISION project, led by RTI International, and the END in Africa and END in Asia projects, led by FHI 360. These countries are Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. The data represent all pre-TAS funded by USAID from 2012 to 2017 and, in some cases, surveys funded by host government or other non-United States government funders. Because pre-TAS data were collected as part of routine program activities in most countries, in general, ethical clearance was not sought for these surveys. Our secondary analysis only included the aggregated survey results and therefore did not constitute human subjects research; no ethical approval was required." }, { - "self_ref": "#/texts/15", + "self_ref": "#/texts/19", "parent": { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, "children": [], "content_layer": "body", @@ -831,7 +933,7 @@ "text": "Building on previous work, we delineated five domains of variables that could influence pre-TAS outcomes: prevalence, agent, environment, MDA, and pre-TAS implementation (Table 1) [6–8]. We prioritized key concepts that could be measured through our data or captured through publicly available global geospatial data sets." }, { - "self_ref": "#/texts/16", + "self_ref": "#/texts/20", "parent": { "$ref": "#/body" }, @@ -843,13 +945,13 @@ "text": "Table 1 Categorization of potential factors influencing pre-TAS results." }, { - "self_ref": "#/texts/17", + "self_ref": "#/texts/21", "parent": { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, "children": [ { - "$ref": "#/texts/18" + "$ref": "#/texts/22" } ], "content_layer": "body", @@ -860,9 +962,9 @@ "level": 2 }, { - "self_ref": "#/texts/18", + "self_ref": "#/texts/22", "parent": { - "$ref": "#/texts/17" + "$ref": "#/texts/21" }, "children": [], "content_layer": "body", @@ -872,31 +974,31 @@ "text": "Information on baseline prevalence, MDA coverage, the number of MDA rounds, and pre-TAS information (month and year of survey, district, site name, and outcome) was gathered through regular reporting for the USAID-funded NTD programs (ENVISION, END in Africa, and END in Asia). These data were augmented by other reporting data such as the country’s dossier data annexes, the WHO Preventive Chemotherapy and Transmission Control Databank, and WHO reporting forms. Data were then reviewed by country experts, including the Ministry of Health program staff and implementing program staff, and updated as necessary. Data on vectors were also obtained from country experts. The district geographic boundaries were matched to geospatial shapefiles from the ENVISION project geospatial data repository, while other geospatial data were obtained through publicly available sources (Table 1)." }, { - "self_ref": "#/texts/19", + "self_ref": "#/texts/23", "parent": { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, "children": [ { - "$ref": "#/texts/20" + "$ref": "#/texts/24" }, { - "$ref": "#/groups/0" + "$ref": "#/groups/2" }, { - "$ref": "#/texts/24" + "$ref": "#/texts/28" }, { - "$ref": "#/texts/26" + "$ref": "#/texts/30" }, { - "$ref": "#/texts/50" + "$ref": "#/texts/54" }, { - "$ref": "#/texts/58" + "$ref": "#/texts/62" }, { - "$ref": "#/texts/61" + "$ref": "#/texts/65" } ], "content_layer": "body", @@ -907,9 +1009,9 @@ "level": 2 }, { - "self_ref": "#/texts/20", + "self_ref": "#/texts/24", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/23" }, "children": [], "content_layer": "body", @@ -919,9 +1021,9 @@ "text": "The outcome of interest for this analysis was whether a district passed or failed the pre-TAS. Failure was defined as any district that had at least one sentinel or spot-check site with a prevalence higher than or equal to 1% Mf or 2% Ag [4]." }, { - "self_ref": "#/texts/21", + "self_ref": "#/texts/25", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -931,9 +1033,9 @@ "text": "Potential covariates were derived from the available data for each factor in the domain groups listed in Table 1. New dichotomous variables were created for all variables that had multiple categories or were continuous for ease of interpretation in models and use in program decision-making. Cut-points for continuous variables were derived from either" }, { - "self_ref": "#/texts/22", + "self_ref": "#/texts/26", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -950,9 +1052,9 @@ } }, { - "self_ref": "#/texts/23", + "self_ref": "#/texts/27", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -962,13 +1064,13 @@ "text": "knowledge or through exploratory analysis considering the mean or median value of the dataset, looking to create two groups of similar size with logical cut-points (e.g. rounding numbers to whole numbers). All the variables derived from publicly available global spatial raster datasets were summarized to the district level in ArcGIS Pro using the “zonal statistics” tool. The final output used the continuous value measuring the mean pixel value for the district for all variables except geographic area. Categories for each variable were determined by selecting the mean or median dataset value or cut-off used in other relevant literature [7]. The following section describes the variables that were included in the final analysis and the final categorizations used." }, { - "self_ref": "#/texts/24", + "self_ref": "#/texts/28", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/23" }, "children": [ { - "$ref": "#/texts/25" + "$ref": "#/texts/29" } ], "content_layer": "body", @@ -979,9 +1081,9 @@ "level": 3 }, { - "self_ref": "#/texts/25", + "self_ref": "#/texts/29", "parent": { - "$ref": "#/texts/24" + "$ref": "#/texts/28" }, "children": [], "content_layer": "body", @@ -991,13 +1093,13 @@ "text": "Baseline prevalence can be assumed as a proxy for local transmission conditions [14] and correlates with prevalence after MDA [14–20]. Baseline prevalence for each district was measured by either blood smears to measure Mf or rapid diagnostic tests to measure Ag. Other studies have modeled Mf and Ag prevalence separately, due to lack of a standardized correlation between the two, especially at pre-MDA levels [21,22]. However, because WHO mapping guidance states that MDA is required if either Mf or Ag is ≥1% and there were not enough data to model each separately, we combined baseline prevalence values regardless of diagnostic test used. We created two variables for use in the analysis (1) using the cut-off of <5% or ≥5% (dataset median value of 5%) and (2) using the cut-off of <10% or ≥10%." }, { - "self_ref": "#/texts/26", + "self_ref": "#/texts/30", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/23" }, "children": [ { - "$ref": "#/groups/1" + "$ref": "#/groups/3" } ], "content_layer": "body", @@ -1008,9 +1110,9 @@ "level": 3 }, { - "self_ref": "#/texts/27", + "self_ref": "#/texts/31", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1020,9 +1122,9 @@ "text": "In terms of differences in transmission dynamics by agent, research has shown that" }, { - "self_ref": "#/texts/28", + "self_ref": "#/texts/32", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1039,9 +1141,9 @@ } }, { - "self_ref": "#/texts/29", + "self_ref": "#/texts/33", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1051,9 +1153,9 @@ "text": "spp. are more susceptible to the anti-filarial drug regimens than" }, { - "self_ref": "#/texts/30", + "self_ref": "#/texts/34", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1070,9 +1172,9 @@ } }, { - "self_ref": "#/texts/31", + "self_ref": "#/texts/35", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1082,9 +1184,9 @@ "text": "parasites [23]. Thus, we combined districts reporting" }, { - "self_ref": "#/texts/32", + "self_ref": "#/texts/36", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1101,9 +1203,9 @@ } }, { - "self_ref": "#/texts/33", + "self_ref": "#/texts/37", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1113,9 +1215,9 @@ "text": "." }, { - "self_ref": "#/texts/34", + "self_ref": "#/texts/38", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1132,9 +1234,9 @@ } }, { - "self_ref": "#/texts/35", + "self_ref": "#/texts/39", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1144,9 +1246,9 @@ "text": "and" }, { - "self_ref": "#/texts/36", + "self_ref": "#/texts/40", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1163,9 +1265,9 @@ } }, { - "self_ref": "#/texts/37", + "self_ref": "#/texts/41", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1175,9 +1277,9 @@ "text": "." }, { - "self_ref": "#/texts/38", + "self_ref": "#/texts/42", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1194,9 +1296,9 @@ } }, { - "self_ref": "#/texts/39", + "self_ref": "#/texts/43", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1206,9 +1308,9 @@ "text": "and compared them to areas with" }, { - "self_ref": "#/texts/40", + "self_ref": "#/texts/44", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1225,9 +1327,9 @@ } }, { - "self_ref": "#/texts/41", + "self_ref": "#/texts/45", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1237,9 +1339,9 @@ "text": "." }, { - "self_ref": "#/texts/42", + "self_ref": "#/texts/46", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1256,9 +1358,9 @@ } }, { - "self_ref": "#/texts/43", + "self_ref": "#/texts/47", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1268,9 +1370,9 @@ "text": "or mixed parasites. Two variables from other domains were identified in exploratory analyses to be highly colinear with the parasite, and thus we considered them in the same group of variables for the final regression models. These were variables delineating vectors (" }, { - "self_ref": "#/texts/44", + "self_ref": "#/texts/48", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1287,9 +1389,9 @@ } }, { - "self_ref": "#/texts/45", + "self_ref": "#/texts/49", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1299,9 +1401,9 @@ "text": "or" }, { - "self_ref": "#/texts/46", + "self_ref": "#/texts/50", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1318,9 +1420,9 @@ } }, { - "self_ref": "#/texts/47", + "self_ref": "#/texts/51", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1330,9 +1432,9 @@ "text": "compared to" }, { - "self_ref": "#/texts/48", + "self_ref": "#/texts/52", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1349,9 +1451,9 @@ } }, { - "self_ref": "#/texts/49", + "self_ref": "#/texts/53", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -1361,19 +1463,19 @@ "text": ") from the environmental domain and drug package [ivermectin-albendazole (IVM-ALB) compared to diethylcarbamazine-albendazole (DEC-ALB)] from the MDA domain." }, { - "self_ref": "#/texts/50", + "self_ref": "#/texts/54", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/23" }, "children": [ { - "$ref": "#/texts/51" + "$ref": "#/texts/55" }, { - "$ref": "#/groups/2" + "$ref": "#/groups/4" }, { - "$ref": "#/texts/57" + "$ref": "#/texts/61" } ], "content_layer": "body", @@ -1384,9 +1486,9 @@ "level": 3 }, { - "self_ref": "#/texts/51", + "self_ref": "#/texts/55", "parent": { - "$ref": "#/texts/50" + "$ref": "#/texts/54" }, "children": [], "content_layer": "body", @@ -1396,9 +1498,9 @@ "text": "LF transmission intensity is influenced by differing vector transmission dynamics, including vector biting rates and competence, and the number of individuals with microfilaria [21,24,25]. Since vector data are not always available, previous studies have explored whether environmental variables associated with vector density, such as elevation, rainfall, and temperature, can be used to predict LF prevalence [8,21,26–31]. We included the district area and elevation in meters as geographic variables potentially associated with transmission intensity. In addition, within the climate factor, we included Enhanced Vegetation Index (EVI) and rainfall variables. EVI measures vegetation levels, or “greenness,” where a higher index value indicates a higher level of “greenness.”" }, { - "self_ref": "#/texts/52", + "self_ref": "#/texts/56", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -1408,9 +1510,9 @@ "text": "We included the socio-economic variable of population density, as it has been positively associated with LF prevalence in some studies [8,27,29], but no significant association has been found in others [30]. Population density could be correlated with vector, as in eastern African countries LF is mostly transmitted by" }, { - "self_ref": "#/texts/53", + "self_ref": "#/texts/57", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -1427,9 +1529,9 @@ } }, { - "self_ref": "#/texts/54", + "self_ref": "#/texts/58", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -1439,9 +1541,9 @@ "text": "in urban areas and by" }, { - "self_ref": "#/texts/55", + "self_ref": "#/texts/59", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -1458,9 +1560,9 @@ } }, { - "self_ref": "#/texts/56", + "self_ref": "#/texts/60", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -1470,9 +1572,9 @@ "text": "in rural areas [32]. Additionally, inclusion of the satellite imagery of nighttime lights data is another a proxy for socio-economic status [33]." }, { - "self_ref": "#/texts/57", + "self_ref": "#/texts/61", "parent": { - "$ref": "#/texts/50" + "$ref": "#/texts/54" }, "children": [], "content_layer": "body", @@ -1482,16 +1584,16 @@ "text": "Finally, all or parts of districts that are co-endemic with onchocerciasis may have received multiple rounds of MDA with ivermectin before LF MDA started, which may have lowered LF prevalence in an area [34–36]. Thus, we included a categorical variable to distinguish if districts were co-endemic with onchocerciasis." }, { - "self_ref": "#/texts/58", + "self_ref": "#/texts/62", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/23" }, "children": [ { - "$ref": "#/texts/59" + "$ref": "#/texts/63" }, { - "$ref": "#/texts/60" + "$ref": "#/texts/64" } ], "content_layer": "body", @@ -1502,9 +1604,9 @@ "level": 3 }, { - "self_ref": "#/texts/59", + "self_ref": "#/texts/63", "parent": { - "$ref": "#/texts/58" + "$ref": "#/texts/62" }, "children": [], "content_layer": "body", @@ -1514,9 +1616,9 @@ "text": "Treatment effectiveness depends upon both drug efficacy (ability to kill adult worms, ability to kill Mf, drug resistance, drug quality) and implementation of MDA (coverage, compliance, number of rounds) [14,16]. Ivermectin is less effective against adult worms than DEC, and therefore it is likely that Ag reduction is slower in areas using ivermectin instead of DEC in MDA [37]. Models also have shown that MDA coverage affects prevalence, although coverage has been defined in various ways, such as median coverage, number of rounds, or individual compliance [14–16,20,38–40]. Furthermore, systematic non-compliance, or population sub-groups which consistently refuse to take medicines, has been shown to represent a threat to elimination [41,42]." }, { - "self_ref": "#/texts/60", + "self_ref": "#/texts/64", "parent": { - "$ref": "#/texts/58" + "$ref": "#/texts/62" }, "children": [], "content_layer": "body", @@ -1526,13 +1628,13 @@ "text": "We considered three approaches when analyzing the MDA data: median MDA coverage in the most recent 5 rounds, number of rounds with sufficient coverage in the most recent 5 rounds, and count of the total number of rounds. MDA coverage is considered sufficient at or above 65% of the total population who were reported to have ingested the drugs; this was used as the cut point for MDA median coverage for the most recent 5 rounds. The ‘rounds of sufficient coverage’ variable was categorized as having 2 or fewer rounds compared to 3 or more sufficient rounds. The ‘total number of MDA rounds’ variable was categorized at 5 or fewer rounds compared to 6 or more rounds ever documented in that district." }, { - "self_ref": "#/texts/61", + "self_ref": "#/texts/65", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/23" }, "children": [ { - "$ref": "#/texts/62" + "$ref": "#/texts/66" } ], "content_layer": "body", @@ -1543,9 +1645,9 @@ "level": 3 }, { - "self_ref": "#/texts/62", + "self_ref": "#/texts/66", "parent": { - "$ref": "#/texts/61" + "$ref": "#/texts/65" }, "children": [], "content_layer": "body", @@ -1555,13 +1657,13 @@ "text": "Pre-TAS results can be influenced by the implementation of the survey itself, including the use of a particular diagnostic test, the selection of sites, the timing of survey, and the appropriate application of methods for population recruitment and diagnostic test adminstration. We included two variables in the pre-TAS implementation domain: `type of diagnostic method used’ and `diagnostic test used.’ The ‘type of diagnostic method used’ variable categorized districts by either using Mf or Ag. The ‘diagnostic test used’ variable examined Mf (reference category) compared to ICT and compared to FTS (categorical variable with 3 values). This approach was used to compare each test to each other. Countries switched from ICT to FTS during 2016, while Mf testing continued to be used throughout the time period of study." }, { - "self_ref": "#/texts/63", + "self_ref": "#/texts/67", "parent": { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, "children": [ { - "$ref": "#/texts/64" + "$ref": "#/texts/68" } ], "content_layer": "body", @@ -1572,9 +1674,9 @@ "level": 2 }, { - "self_ref": "#/texts/64", + "self_ref": "#/texts/68", "parent": { - "$ref": "#/texts/63" + "$ref": "#/texts/67" }, "children": [], "content_layer": "body", @@ -1584,16 +1686,16 @@ "text": "The dataset, summarized at the district level, included information from 568 districts where a pre-TAS was being implemented for the first time. A total of 14 districts were removed from the final analysis due to missing data related to the following points: geospatial boundaries (4), baseline prevalence (4), and MDA coverage (6). The final analysis dataset had 554 districts." }, { - "self_ref": "#/texts/65", + "self_ref": "#/texts/69", "parent": { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, "children": [ { - "$ref": "#/texts/66" + "$ref": "#/texts/70" }, { - "$ref": "#/groups/3" + "$ref": "#/groups/5" } ], "content_layer": "body", @@ -1604,9 +1706,9 @@ "level": 2 }, { - "self_ref": "#/texts/66", + "self_ref": "#/texts/70", "parent": { - "$ref": "#/texts/65" + "$ref": "#/texts/69" }, "children": [], "content_layer": "body", @@ -1616,9 +1718,9 @@ "text": "Statistical analysis and modeling were done with Stata MP 15.1 (College Station, TX). Descriptive statistics comparing various variables to the principle outcome were performed. Significant differences were identified using a chi-square test. A generalized linear model (GLM) with a log link and binomial error distribution—which estimates relative risks—was developed using forward stepwise modeling methods (called log-binomial model). Models with higher pseudo-r-squared and lower Akaike information criterion (AIC) were retained at each step. Pseudo-r-squared is a value between 0 and 1 with the higher the value, the better the model is at predicting the outcome of interest. AIC values are used to compare the relative quality of models compared to each other; in general, a lower value indicates a better model. Variables were tested by factor group. Once a variable was selected from the group, no other variable in that same group was eligible to be included in the final model due to issues of collinearity and small sample sizes. Interaction between terms in the model was tested after model selection, and interaction terms that modified the original terms’ significance were included in the final model. Overall, the number of potential variables able to be included in the model remained low due to the relatively small number of failure results (13%) in the dataset. Furthermore, the models with more than 3 variables and one interaction term either were unstable (indicated by very large confidence interval widths) or did not improve the model by being significant predictors or by modifying other parameters already in the model. These models were at heightened risk of non-convergence; we limited the number of variables accordingly." }, { - "self_ref": "#/texts/67", + "self_ref": "#/texts/71", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -1628,9 +1730,9 @@ "text": "Sensitivity analysis was performed for the final log-binomial model to test for the validity of results under different parameters by excluding some sub-sets of districts from the dataset and rerunning the model. This analysis was done to understand the robustness of the model when (1) excluding all districts in Cameroon, (2) including only districts in Africa, (3) including only districts with" }, { - "self_ref": "#/texts/68", + "self_ref": "#/texts/72", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -1647,9 +1749,9 @@ } }, { - "self_ref": "#/texts/69", + "self_ref": "#/texts/73", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -1659,9 +1761,9 @@ "text": "." }, { - "self_ref": "#/texts/70", + "self_ref": "#/texts/74", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -1678,9 +1780,9 @@ } }, { - "self_ref": "#/texts/71", + "self_ref": "#/texts/75", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -1690,9 +1792,9 @@ "text": "parasite, and (4) including only districts with" }, { - "self_ref": "#/texts/72", + "self_ref": "#/texts/76", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -1709,9 +1811,9 @@ } }, { - "self_ref": "#/texts/73", + "self_ref": "#/texts/77", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -1721,13 +1823,13 @@ "text": "as the primary vector. The sensitivity analysis excluding Cameroon was done for two reasons. First, Cameroon had the most pre-TAS results included, but no failures. Second, 70% of the Cameroon districts included in the analysis are co-endemic for loiasis. Given that diagnostic tests used in LF mapping have since been shown to cross-react with loiasis, there is some concern that these districts might not have been truly LF-endemic [43,44]." }, { - "self_ref": "#/texts/74", + "self_ref": "#/texts/78", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/75" + "$ref": "#/texts/79" }, { "$ref": "#/pictures/0" @@ -1736,28 +1838,28 @@ "$ref": "#/pictures/1" }, { - "$ref": "#/groups/4" + "$ref": "#/groups/6" }, { "$ref": "#/pictures/2" }, { - "$ref": "#/texts/82" + "$ref": "#/texts/86" }, { - "$ref": "#/texts/83" + "$ref": "#/texts/87" }, { "$ref": "#/pictures/3" }, { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, { "$ref": "#/tables/1" }, { - "$ref": "#/texts/99" + "$ref": "#/texts/103" }, { "$ref": "#/pictures/4" @@ -1771,9 +1873,9 @@ "level": 1 }, { - "self_ref": "#/texts/75", + "self_ref": "#/texts/79", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -1783,7 +1885,7 @@ "text": "The overall pre-TAS pass rate for the districts included in this analysis was 87% (74 failures in 554 districts). Nearly 40% of the 554 districts were from Cameroon (134) and Tanzania (87) (Fig 1). No districts in Bangladesh, Cameroon, Mali, or Uganda failed a pre-TAS in this data set; over 25% of districts in Burkina Faso, Ghana, Haiti, Nepal, and Sierra Leone failed pre-TAS in this data set. Baseline prevalence varied widely within and between the 13 countries. Fig 2 shows the highest, lowest, and median baseline prevalence in the study districts by country. Burkina Faso had the highest median baseline prevalence at 52% and Burkina Faso, Tanzania, and Ghana all had at least one district with a very high baseline of over 70%. In Mali, Indonesia, Benin, and Bangladesh, all districts had baseline prevalences below 20%." }, { - "self_ref": "#/texts/76", + "self_ref": "#/texts/80", "parent": { "$ref": "#/body" }, @@ -1795,7 +1897,7 @@ "text": "Fig 1 Number of pre-TAS by country." }, { - "self_ref": "#/texts/77", + "self_ref": "#/texts/81", "parent": { "$ref": "#/body" }, @@ -1807,9 +1909,9 @@ "text": "Fig 2 District-level baseline prevalence by country." }, { - "self_ref": "#/texts/78", + "self_ref": "#/texts/82", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -1819,9 +1921,9 @@ "text": "Fig 3 shows the unadjusted analysis for key variables by pre-TAS result. Variables statistically significantly associated with failure (p-value ≤0.05) included higher baseline prevalence at or above 5% or 10%, FTS diagnostic test, primary vector of" }, { - "self_ref": "#/texts/79", + "self_ref": "#/texts/83", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -1838,9 +1940,9 @@ } }, { - "self_ref": "#/texts/80", + "self_ref": "#/texts/84", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -1850,7 +1952,7 @@ "text": ", treatment with DEC-ALB, higher elevation, higher population density, higher EVI, higher annual rainfall, and six or more rounds of MDA. Variables that were not significantly associated with pre-TAS failure included diagnostic method used (Ag or Mf), parasite, co-endemicity for onchocerciasis, median MDA coverage, and sufficient rounds of MDA." }, { - "self_ref": "#/texts/81", + "self_ref": "#/texts/85", "parent": { "$ref": "#/body" }, @@ -1862,9 +1964,9 @@ "text": "Fig 3 Percent pre-TAS failure by each characteristic (unadjusted)." }, { - "self_ref": "#/texts/82", + "self_ref": "#/texts/86", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -1874,9 +1976,9 @@ "text": "The final log-binomial model included the variables of baseline prevalence ≥10%, the diagnostic test used (FTS and ICT), and elevation. The final model also included a significant interaction term between high baseline and diagnostic test used." }, { - "self_ref": "#/texts/83", + "self_ref": "#/texts/87", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -1886,7 +1988,7 @@ "text": "Fig 4 shows the risk ratio results with their corresponding confidence intervals. In a model with interaction between baseline and diagnostic test the baseline parameter was significant while diagnostic test and the interaction term were not. Districts with high baseline had a statistically significant (p-value ≤0.05) 2.52 times higher risk of failure (95% CI 1.37–4.64) compared to those with low baseline prevalence. The FTS diagnostic test or ICT diagnostic test alone were not significant nor was the interaction term. Additionally, districts with an elevation below 350 meters had a statistically significant (p-value ≤0.05) 3.07 times higher risk of failing pre-TAS (95% CI 1.95–4.83)." }, { - "self_ref": "#/texts/84", + "self_ref": "#/texts/88", "parent": { "$ref": "#/body" }, @@ -1898,9 +2000,9 @@ "text": "Fig 4 Adjusted risk ratios for pre-TAS failure with 95% Confidence Interval from log-binomial model." }, { - "self_ref": "#/texts/85", + "self_ref": "#/texts/89", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -1910,9 +2012,9 @@ "text": "Sensitivity analyses were conducted using the same model with different subsets of the dataset including (1) all districts except for districts in Cameroon (134 total with no failures), (2) only districts in Africa, (3) only districts with" }, { - "self_ref": "#/texts/86", + "self_ref": "#/texts/90", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -1929,9 +2031,9 @@ } }, { - "self_ref": "#/texts/87", + "self_ref": "#/texts/91", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -1941,9 +2043,9 @@ "text": "." }, { - "self_ref": "#/texts/88", + "self_ref": "#/texts/92", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -1960,9 +2062,9 @@ } }, { - "self_ref": "#/texts/89", + "self_ref": "#/texts/93", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -1972,9 +2074,9 @@ "text": ", and (4) only districts with" }, { - "self_ref": "#/texts/90", + "self_ref": "#/texts/94", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -1991,9 +2093,9 @@ } }, { - "self_ref": "#/texts/91", + "self_ref": "#/texts/95", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2003,9 +2105,9 @@ "text": "as primary vector. The results of the sensitivity models (Table 2) indicate an overall robust model. High baseline and lower elevation remained significant across all the models. The ICT diagnostic test used remains insignificant across all models. The FTS diagnostic test was positively significant in model 1 and negatively significant in model 4. The interaction term of baseline prevalence and FTS diagnostic test was significant in three models though the estimate was unstable in the" }, { - "self_ref": "#/texts/92", + "self_ref": "#/texts/96", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2022,9 +2124,9 @@ } }, { - "self_ref": "#/texts/93", + "self_ref": "#/texts/97", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2034,9 +2136,9 @@ "text": "." }, { - "self_ref": "#/texts/94", + "self_ref": "#/texts/98", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2053,9 +2155,9 @@ } }, { - "self_ref": "#/texts/95", + "self_ref": "#/texts/99", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2065,9 +2167,9 @@ "text": "-only and" }, { - "self_ref": "#/texts/96", + "self_ref": "#/texts/100", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2084,9 +2186,9 @@ } }, { - "self_ref": "#/texts/97", + "self_ref": "#/texts/101", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2096,7 +2198,7 @@ "text": "-only models (models 3 and 4 respectively), as signified by large confidence intervals." }, { - "self_ref": "#/texts/98", + "self_ref": "#/texts/102", "parent": { "$ref": "#/body" }, @@ -2108,9 +2210,9 @@ "text": "Table 2 Adjusted risk ratios for pre-TAS failure from log-binomial model sensitivity analysis." }, { - "self_ref": "#/texts/99", + "self_ref": "#/texts/103", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -2120,7 +2222,7 @@ "text": "Overall 74 districts in the dataset failed pre-TAS. Fig 5 summarizes the likelihood of failure by variable combinations identified in the log-binomial model. For those districts with a baseline prevalence ≥10% that used a FTS diagnostic test and have an average elevation below 350 meters (Combination C01), 87% of the 23 districts failed. Of districts with high baseline that used an ICT diagnostic test and have a low average elevation (C02) 45% failed. Overall, combinations with high baseline and low elevation C01, C02, and C04 accounted for 51% of all the failures (38 of 74)." }, { - "self_ref": "#/texts/100", + "self_ref": "#/texts/104", "parent": { "$ref": "#/body" }, @@ -2132,37 +2234,37 @@ "text": "Fig 5 Analysis of failures by model combinations." }, { - "self_ref": "#/texts/101", + "self_ref": "#/texts/105", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/groups/6" + "$ref": "#/groups/8" }, { - "$ref": "#/texts/105" + "$ref": "#/texts/109" }, { - "$ref": "#/groups/7" + "$ref": "#/groups/9" }, { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, { - "$ref": "#/texts/125" + "$ref": "#/texts/129" }, { - "$ref": "#/texts/126" + "$ref": "#/texts/130" }, { - "$ref": "#/texts/127" + "$ref": "#/texts/131" }, { - "$ref": "#/texts/128" + "$ref": "#/texts/132" } ], "content_layer": "body", @@ -2173,9 +2275,9 @@ "level": 1 }, { - "self_ref": "#/texts/102", + "self_ref": "#/texts/106", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -2185,9 +2287,9 @@ "text": "This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. Variables significantly associated with failure were higher baseline prevalence and lower elevation. Districts with a baseline prevalence of 10% or more were at 2.52 times higher risk to fail pre-TAS in the final log-binomial model. In the bivariate analysis, baseline prevalence above 5% was also significantly more likely to fail compared to lower baselines, which indicates that the threshold for higher baseline prevalence may be as little as 5%, similar to what was found in Goldberg" }, { - "self_ref": "#/texts/103", + "self_ref": "#/texts/107", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -2204,9 +2306,9 @@ } }, { - "self_ref": "#/texts/104", + "self_ref": "#/texts/108", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -2216,9 +2318,9 @@ "text": "., which explored ecological and socioeconomic factors associated with TAS failure [7]." }, { - "self_ref": "#/texts/105", + "self_ref": "#/texts/109", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [], "content_layer": "body", @@ -2228,9 +2330,9 @@ "text": "Though diagnostic test used was selected for the final log-binomial model, neither category (FTS or ICT) were significant after interaction with high baseline. FTS alone is significant in the bivariate analysis compared to ICT or Mf. This result is not surprising given previous research which found that FTS was more sensitive than ICT [45]." }, { - "self_ref": "#/texts/106", + "self_ref": "#/texts/110", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -2240,9 +2342,9 @@ "text": "Elevation was the only environmental domain variable selected for the final log-binomial model during the model selection process, with areas of lower elevation (<350m) found to be at 3.07 times higher risk to fail pre-TAS compared to districts with a higher elevation. Similar results related to elevation were found in previous studies [8,31], including Goldberg" }, { - "self_ref": "#/texts/107", + "self_ref": "#/texts/111", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -2259,9 +2361,9 @@ } }, { - "self_ref": "#/texts/108", + "self_ref": "#/texts/112", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -2271,9 +2373,9 @@ "text": ". [7], who used a cutoff of 200 meters. Elevation likely also encompasses some related environmental concepts, such as vector habitat, greenness (EVI), or rainfall, which impact vector chances of survival." }, { - "self_ref": "#/texts/109", + "self_ref": "#/texts/113", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -2283,9 +2385,9 @@ "text": "The small number of failures overall prevented the inclusion of a large number of variables in the final log-binomial model. However, other variables that are associated with failure as identified in the bivariate analyses, such as" }, { - "self_ref": "#/texts/110", + "self_ref": "#/texts/114", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -2302,9 +2404,9 @@ } }, { - "self_ref": "#/texts/111", + "self_ref": "#/texts/115", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -2314,9 +2416,9 @@ "text": "vector, higher population density, higher EVI, higher rainfall and more rounds of MDA, should not be discounted when making programmatic decisions. Other models have shown that" }, { - "self_ref": "#/texts/112", + "self_ref": "#/texts/116", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -2333,9 +2435,9 @@ } }, { - "self_ref": "#/texts/113", + "self_ref": "#/texts/117", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -2345,9 +2447,9 @@ "text": "as the predominant vector in a district, compared to" }, { - "self_ref": "#/texts/114", + "self_ref": "#/texts/118", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -2364,9 +2466,9 @@ } }, { - "self_ref": "#/texts/115", + "self_ref": "#/texts/119", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -2376,9 +2478,9 @@ "text": ", results in more intense interventions needed to reach elimination [24,41]. Higher population density, which was also found to predict TAS failure [7], could be related to different vector species’ transmission dynamics in urban areas, as well as the fact that MDAs are harder to conduct and to accurately measure in urban areas [46,47]. Both higher enhanced vegetation index (>0.3) and higher rainfall (>700 mm per year) contribute to expansion of vector habitats and population. Additionally, having more than five rounds of MDA before pre-TAS was also statistically significantly associated with higher failure in the bivariate analysis. It is unclear why higher number of rounds is associated with first pre-TAS failure given that other research has shown the opposite [15,16]." }, { - "self_ref": "#/texts/116", + "self_ref": "#/texts/120", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2388,9 +2490,9 @@ "text": "All other variables included in this analysis were not significantly associated with pre-TAS failure in our analysis. Goldberg" }, { - "self_ref": "#/texts/117", + "self_ref": "#/texts/121", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2407,9 +2509,9 @@ } }, { - "self_ref": "#/texts/118", + "self_ref": "#/texts/122", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2419,9 +2521,9 @@ "text": ". found" }, { - "self_ref": "#/texts/119", + "self_ref": "#/texts/123", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2438,9 +2540,9 @@ } }, { - "self_ref": "#/texts/120", + "self_ref": "#/texts/124", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2450,9 +2552,9 @@ "text": "spp. to be significantly associated with failure, but our results did not. This is likely due in part to the small number of districts with" }, { - "self_ref": "#/texts/121", + "self_ref": "#/texts/125", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2469,9 +2571,9 @@ } }, { - "self_ref": "#/texts/122", + "self_ref": "#/texts/126", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2481,9 +2583,9 @@ "text": "spp. in our dataset (6%) compared to 46% in the Goldberg" }, { - "self_ref": "#/texts/123", + "self_ref": "#/texts/127", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2500,9 +2602,9 @@ } }, { - "self_ref": "#/texts/124", + "self_ref": "#/texts/128", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -2512,9 +2614,9 @@ "text": ". article [7]. MDA coverage levels were not significantly associated with pre-TAS failure, likely due to the lack of variance in the coverage data since WHO guidance dictates a minimum of five rounds of MDA with ≥65% epidemiological coverage to be eligible to implement pre-TAS. It should not be interpreted as evidence that high MDA coverage levels are not necessary to lower prevalence." }, { - "self_ref": "#/texts/125", + "self_ref": "#/texts/129", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [], "content_layer": "body", @@ -2524,9 +2626,9 @@ "text": "Limitations to this study include data sources, excluded data, unreported data, misassigned data, and aggregation of results at the district level. The main data sources for this analysis were programmatic data, which may be less accurate than data collected specifically for research purposes. This is particularly true of the MDA coverage data, where some countries report data quality challenges in areas of instability or frequent population migration. Even though risk factors such as age, sex, compliance with MDA, and use of bednets have been shown to influence infection in individuals [40,48–50], we could not include factors from the human host domain in our analysis, as data sets were aggregated at site level and did not include individual information. In addition, vector control data were not universally available across the 13 countries and thus were not included in the analysis, despite studies showing that vector control has an impact on reducing LF prevalence [41,48,51–53]." }, { - "self_ref": "#/texts/126", + "self_ref": "#/texts/130", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [], "content_layer": "body", @@ -2536,9 +2638,9 @@ "text": "Fourteen districts were excluded from the analysis because we were not able to obtain complete data for baseline prevalence, MDA coverage, or geographic boundaries. One of these districts had failed pre-TAS. It is likely these exclusions had minimal impact on the conclusions, as they represented a small number of districts and were similar to other included districts in terms of key variables. Unreported data could have occurred if a country conducted a pre-TAS that failed and then chose not to report it or reported it as a mid-term survey instead. Anecdotally, we know this has occurred occasionally, but we do not believe the practice to be widespread. Another limitation in the analysis is a potential misassignment of key variable values to a district due to changes in the district over time. Redistricting, changes in district size or composition, was pervasive in many countries during the study period; however, we expect the impact on the study outcome to be minimal, as the historical prevalence and MDA data from the “mother” districts are usually flowed down to these new “daughter” districts. However, it is possible that the split created an area of higher prevalence or lower MDA coverage than would have been found on average in the overall larger original “mother” district. Finally, the aggregation or averaging of results to the district level may mask heterogeneity within districts. Though this impact could be substantial in districts with considerable heterogeneity, the use of median values and binomial variables mitigated the likelihood of skewing the data to extreme outliners in a district." }, { - "self_ref": "#/texts/127", + "self_ref": "#/texts/131", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [], "content_layer": "body", @@ -2548,9 +2650,9 @@ "text": "As this analysis used data across a variety of countries and epidemiological situations, the results are likely relevant for other districts in the countries examined and in countries with similar epidemiological backgrounds. In general, as more data become available at site level through the increased use of electronic data collection tools, further analysis of geospatial variables and associations will be possible. For example, with the availability of GPS coordinates, it may become possible to analyze outcomes by site and to link the geospatial environmental domain variables at a smaller scale. Future analyses also might seek to include information from coverage surveys or qualitative research studies on vector control interventions such as bed net usage, MDA compliance, population movement, and sub-populations that might be missed during MDA. Future pre-TAS using electronic data collection could include sex and age of individuals included in the survey." }, { - "self_ref": "#/texts/128", + "self_ref": "#/texts/132", "parent": { - "$ref": "#/texts/101" + "$ref": "#/texts/105" }, "children": [], "content_layer": "body", @@ -2560,13 +2662,13 @@ "text": "This paper provides evidence from analysis of 554 districts and 13 countries on the factors associated with pre-TAS results. Baseline prevalence, elevation, vector, population density, EVI, rainfall, and number of MDA rounds were all significant in either bivariate or multivariate analyses. This information along with knowledge of local context can help countries more effectively plan pre-TAS and forecast program activities, such as the potential need for more than five rounds of MDA in areas with high baseline and/or low elevation." }, { - "self_ref": "#/texts/129", + "self_ref": "#/texts/133", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/130" + "$ref": "#/texts/134" } ], "content_layer": "body", @@ -2577,9 +2679,9 @@ "level": 1 }, { - "self_ref": "#/texts/130", + "self_ref": "#/texts/134", "parent": { - "$ref": "#/texts/129" + "$ref": "#/texts/133" }, "children": [], "content_layer": "body", @@ -2589,13 +2691,13 @@ "text": "The authors would like to thank all those involved from the Ministries of Health, volunteers and community members in the sentinel and spot-check site surveys for their tireless commitment to ridding the world of LF. In addition, gratitude is given to Joseph Koroma and all the partners, including USAID, RTI International, FHI 360, IMA World Health, and Helen Keller International, who supported the surveys financially and technically." }, { - "self_ref": "#/texts/131", + "self_ref": "#/texts/135", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/groups/10" + "$ref": "#/groups/12" } ], "content_layer": "body", @@ -2606,9 +2708,9 @@ "level": 1 }, { - "self_ref": "#/texts/132", + "self_ref": "#/texts/136", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2620,9 +2722,9 @@ "marker": "" }, { - "self_ref": "#/texts/133", + "self_ref": "#/texts/137", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2634,9 +2736,9 @@ "marker": "" }, { - "self_ref": "#/texts/134", + "self_ref": "#/texts/138", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2648,9 +2750,9 @@ "marker": "" }, { - "self_ref": "#/texts/135", + "self_ref": "#/texts/139", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2662,9 +2764,9 @@ "marker": "" }, { - "self_ref": "#/texts/136", + "self_ref": "#/texts/140", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2676,9 +2778,9 @@ "marker": "" }, { - "self_ref": "#/texts/137", + "self_ref": "#/texts/141", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2690,9 +2792,9 @@ "marker": "" }, { - "self_ref": "#/texts/138", + "self_ref": "#/texts/142", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2704,9 +2806,9 @@ "marker": "" }, { - "self_ref": "#/texts/139", + "self_ref": "#/texts/143", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2718,9 +2820,9 @@ "marker": "" }, { - "self_ref": "#/texts/140", + "self_ref": "#/texts/144", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2732,9 +2834,9 @@ "marker": "" }, { - "self_ref": "#/texts/141", + "self_ref": "#/texts/145", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2746,9 +2848,9 @@ "marker": "" }, { - "self_ref": "#/texts/142", + "self_ref": "#/texts/146", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2760,9 +2862,9 @@ "marker": "" }, { - "self_ref": "#/texts/143", + "self_ref": "#/texts/147", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2774,9 +2876,9 @@ "marker": "" }, { - "self_ref": "#/texts/144", + "self_ref": "#/texts/148", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2788,9 +2890,9 @@ "marker": "" }, { - "self_ref": "#/texts/145", + "self_ref": "#/texts/149", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2802,9 +2904,9 @@ "marker": "" }, { - "self_ref": "#/texts/146", + "self_ref": "#/texts/150", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2816,9 +2918,9 @@ "marker": "" }, { - "self_ref": "#/texts/147", + "self_ref": "#/texts/151", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2830,9 +2932,9 @@ "marker": "" }, { - "self_ref": "#/texts/148", + "self_ref": "#/texts/152", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2844,9 +2946,9 @@ "marker": "" }, { - "self_ref": "#/texts/149", + "self_ref": "#/texts/153", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2858,9 +2960,9 @@ "marker": "" }, { - "self_ref": "#/texts/150", + "self_ref": "#/texts/154", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2872,9 +2974,9 @@ "marker": "" }, { - "self_ref": "#/texts/151", + "self_ref": "#/texts/155", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2886,9 +2988,9 @@ "marker": "" }, { - "self_ref": "#/texts/152", + "self_ref": "#/texts/156", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2900,9 +3002,9 @@ "marker": "" }, { - "self_ref": "#/texts/153", + "self_ref": "#/texts/157", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2914,9 +3016,9 @@ "marker": "" }, { - "self_ref": "#/texts/154", + "self_ref": "#/texts/158", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2928,9 +3030,9 @@ "marker": "" }, { - "self_ref": "#/texts/155", + "self_ref": "#/texts/159", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2942,9 +3044,9 @@ "marker": "" }, { - "self_ref": "#/texts/156", + "self_ref": "#/texts/160", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2956,9 +3058,9 @@ "marker": "" }, { - "self_ref": "#/texts/157", + "self_ref": "#/texts/161", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2970,9 +3072,9 @@ "marker": "" }, { - "self_ref": "#/texts/158", + "self_ref": "#/texts/162", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2984,9 +3086,9 @@ "marker": "" }, { - "self_ref": "#/texts/159", + "self_ref": "#/texts/163", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -2998,9 +3100,9 @@ "marker": "" }, { - "self_ref": "#/texts/160", + "self_ref": "#/texts/164", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3012,9 +3114,9 @@ "marker": "" }, { - "self_ref": "#/texts/161", + "self_ref": "#/texts/165", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3026,9 +3128,9 @@ "marker": "" }, { - "self_ref": "#/texts/162", + "self_ref": "#/texts/166", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3040,9 +3142,9 @@ "marker": "" }, { - "self_ref": "#/texts/163", + "self_ref": "#/texts/167", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3054,9 +3156,9 @@ "marker": "" }, { - "self_ref": "#/texts/164", + "self_ref": "#/texts/168", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3068,9 +3170,9 @@ "marker": "" }, { - "self_ref": "#/texts/165", + "self_ref": "#/texts/169", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3082,9 +3184,9 @@ "marker": "" }, { - "self_ref": "#/texts/166", + "self_ref": "#/texts/170", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3096,9 +3198,9 @@ "marker": "" }, { - "self_ref": "#/texts/167", + "self_ref": "#/texts/171", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3110,9 +3212,9 @@ "marker": "" }, { - "self_ref": "#/texts/168", + "self_ref": "#/texts/172", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3124,9 +3226,9 @@ "marker": "" }, { - "self_ref": "#/texts/169", + "self_ref": "#/texts/173", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3138,9 +3240,9 @@ "marker": "" }, { - "self_ref": "#/texts/170", + "self_ref": "#/texts/174", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3152,9 +3254,9 @@ "marker": "" }, { - "self_ref": "#/texts/171", + "self_ref": "#/texts/175", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3166,9 +3268,9 @@ "marker": "" }, { - "self_ref": "#/texts/172", + "self_ref": "#/texts/176", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3180,9 +3282,9 @@ "marker": "" }, { - "self_ref": "#/texts/173", + "self_ref": "#/texts/177", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3194,9 +3296,9 @@ "marker": "" }, { - "self_ref": "#/texts/174", + "self_ref": "#/texts/178", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3208,9 +3310,9 @@ "marker": "" }, { - "self_ref": "#/texts/175", + "self_ref": "#/texts/179", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3222,9 +3324,9 @@ "marker": "" }, { - "self_ref": "#/texts/176", + "self_ref": "#/texts/180", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3236,9 +3338,9 @@ "marker": "" }, { - "self_ref": "#/texts/177", + "self_ref": "#/texts/181", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3250,9 +3352,9 @@ "marker": "" }, { - "self_ref": "#/texts/178", + "self_ref": "#/texts/182", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3264,9 +3366,9 @@ "marker": "" }, { - "self_ref": "#/texts/179", + "self_ref": "#/texts/183", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3278,9 +3380,9 @@ "marker": "" }, { - "self_ref": "#/texts/180", + "self_ref": "#/texts/184", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3292,9 +3394,9 @@ "marker": "" }, { - "self_ref": "#/texts/181", + "self_ref": "#/texts/185", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3306,9 +3408,9 @@ "marker": "" }, { - "self_ref": "#/texts/182", + "self_ref": "#/texts/186", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3320,9 +3422,9 @@ "marker": "" }, { - "self_ref": "#/texts/183", + "self_ref": "#/texts/187", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3334,9 +3436,9 @@ "marker": "" }, { - "self_ref": "#/texts/184", + "self_ref": "#/texts/188", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -3352,7 +3454,7 @@ { "self_ref": "#/pictures/0", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -3360,7 +3462,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/76" + "$ref": "#/texts/80" } ], "references": [], @@ -3370,7 +3472,7 @@ { "self_ref": "#/pictures/1", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -3378,7 +3480,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/77" + "$ref": "#/texts/81" } ], "references": [], @@ -3388,7 +3490,7 @@ { "self_ref": "#/pictures/2", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -3396,7 +3498,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/81" + "$ref": "#/texts/85" } ], "references": [], @@ -3406,7 +3508,7 @@ { "self_ref": "#/pictures/3", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -3414,7 +3516,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/84" + "$ref": "#/texts/88" } ], "references": [], @@ -3424,7 +3526,7 @@ { "self_ref": "#/pictures/4", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -3432,7 +3534,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/100" + "$ref": "#/texts/104" } ], "references": [], @@ -3444,7 +3546,7 @@ { "self_ref": "#/tables/0", "parent": { - "$ref": "#/texts/13" + "$ref": "#/texts/17" }, "children": [], "content_layer": "body", @@ -3452,7 +3554,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/16" + "$ref": "#/texts/20" } ], "references": [], @@ -7251,7 +7353,7 @@ { "self_ref": "#/tables/1", "parent": { - "$ref": "#/texts/74" + "$ref": "#/texts/78" }, "children": [], "content_layer": "body", @@ -7259,7 +7361,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/98" + "$ref": "#/texts/102" } ], "references": [], diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.md b/tests/data/jats/groundtruth/pntd.0008301.nxml.md index 137c3f4992..f3c86f3713 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.md +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.md @@ -6,11 +6,11 @@ Global Health Division, RTI International, Washington, DC, United States of Amer ## Abstract -Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of Culex, treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS. +Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of *Culex* , treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS. ## Author summary -Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of Culex, treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation. +Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of *Culex* , treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation. ## Introduction diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt index 6e61f433cb..05490bad52 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt @@ -3,573 +3,596 @@ item-0 at level 0: unspecified: group _root_ item-2 at level 2: paragraph: Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab item-3 at level 2: paragraph: Department of Animal Science, Un ... atarina, Lages, Santa Catarina, Brazil item-4 at level 2: section_header: Abstract - item-5 at level 3: text: Carbon (C) footprint of dairy pr ... uce the C footprint to a small extent. - item-6 at level 2: section_header: Introduction - item-7 at level 3: inline: group group - item-8 at level 4: text: Greenhouse gas (GHG) emissions f ... ssions [1], ranging from 5.5–7.5 Gt CO + item-5 at level 3: inline: group group + item-6 at level 4: text: Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO + item-7 at level 4: text: 2 + item-8 at level 4: text: ) equivalents (CO item-9 at level 4: text: 2 - item-10 at level 4: text: equivalents (CO - item-11 at level 4: text: 2 - item-12 at level 4: text: e) yr + item-10 at level 4: text: e) (kg energy-corrected milk (ECM)) + item-11 at level 4: text: -1 + item-12 at level 4: text: , encompasses emissions from fee ... g an average of 7,000 kg ECM lactation item-13 at level 4: text: -1 - item-14 at level 4: text: , with almost 30% coming from da ... suitable for food crop production [4]. - item-15 at level 3: inline: group group - item-16 at level 4: text: Considering the key role of live ... n investigated to mitigate methane (CH - item-17 at level 4: text: 4 - item-18 at level 4: text: ) emissions from enteric ferment ... ment [6] and manure management [7]. CH - item-19 at level 4: text: 4 - item-20 at level 4: text: emissions from enteric fermentat ... anagement to mitigate the C footprint. - item-21 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]). - item-22 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake. - item-23 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated. - item-24 at level 2: section_header: Materials and methods - item-25 at level 3: inline: group group - item-26 at level 4: text: An LCA was developed according t ... 15, 2016—Approval number 4373090816 - - item-27 at level 4: text: https://www.udesc.br/cav/ceua - item-28 at level 4: text: . - item-29 at level 3: section_header: System boundary - item-30 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary. - item-31 at level 4: picture - item-31 at level 5: caption: Fig 1 Overview of the milk production system boundary considered in the study. - item-32 at level 3: section_header: Functional unit - item-33 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows: - item-34 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1. - item-35 at level 4: table with [13x3] - item-35 at level 5: caption: Table 1 Descriptive characteristics of the herd. - item-36 at level 3: section_header: Data sources and livestock system description - item-37 at level 4: inline: group group - item-38 at level 5: text: The individual feed requirements ... cows that received both 75 and 50% of - item-39 at level 5: text: ad libitum - item-40 at level 5: text: TMR intake with access to grazing a tropical pasture (pearl-millet, - item-41 at level 5: text: Pennisetum glaucum - item-42 at level 5: text: ‘Campeiro’) compared to cows receiving - item-43 at level 5: text: ad libitum - item-44 at level 5: text: TMR intake. Cows grazing on a temperate pasture (ryegrass, - item-45 at level 5: text: Lolium multiflorum - item-46 at level 5: text: ‘Maximus’) did not need changes to ECM production compared to the - item-47 at level 5: text: ad libitum - item-48 at level 5: text: TMR intake group. - item-49 at level 4: inline: group group - item-50 at level 5: text: Using experimental data, three s ... evaluated during the lactation period: - item-51 at level 5: text: ad libitum - item-52 at level 5: text: TMR intake, and 75, and 50% of - item-53 at level 5: text: ad libitum - item-54 at level 5: text: TMR intake with access to grazin ... nction of month ([26], Civiero et al., - item-55 at level 5: text: in press - item-56 at level 5: text: ). From April to October (210 da ... med during an entire lactation period. - item-57 at level 3: section_header: Impact assessment - item-58 at level 4: inline: group group - item-59 at level 5: text: The CO - item-60 at level 5: text: 2 - item-61 at level 5: text: e emissions were calculated by multiplying the emissions of CO - item-62 at level 5: text: 2 - item-63 at level 5: text: , CH - item-64 at level 5: text: 4 - item-65 at level 5: text: and N - item-66 at level 5: text: 2 - item-67 at level 5: text: O by their 100-year global warming potential (GWP - item-68 at level 5: text: 100 - item-69 at level 5: text: ), based on IPCC assessment report 5 (AR5; [27]). The values of GWP - item-70 at level 5: text: 100 - item-71 at level 5: text: are 1, 28 and 265 for CO - item-72 at level 5: text: 2 - item-73 at level 5: text: , CH - item-74 at level 5: text: 4 - item-75 at level 5: text: and N - item-76 at level 5: text: 2 - item-77 at level 5: text: O, respectively. - item-78 at level 3: section_header: Feed production - item-79 at level 4: section_header: Diets composition - item-80 at level 5: inline: group group - item-81 at level 6: text: The DM intake of each ingredient ... ennial tropical pasture (kikuyu grass, - item-82 at level 6: text: Pennisetum clandestinum - item-83 at level 6: text: ). The DM intake of calves, heif ... meet the net energy for lactation (NE - item-84 at level 6: text: L - item-85 at level 6: text: ) and metabolizable protein (MP) ... grated in the software INRAtion 4.07 ( - item-86 at level 6: text: https://www.inration.educagri.fr/fr/forum.php - item-87 at level 6: text: ). The nutrient intake was calcu ... collected throughout the experiments. - item-88 at level 5: table with [21x11] - item-88 at level 6: caption: Table 2 Dairy cows’ diets in different scenariosa. - item-89 at level 4: section_header: GHG emissions from crop and pasture production - item-90 at level 5: inline: group group - item-91 at level 6: text: GHG emission factors used for of ... s productions were 3300 and 1500 kg CO - item-92 at level 6: text: 2 - item-93 at level 6: text: e ha - item-94 at level 6: text: -1 - item-95 at level 6: text: , respectively [32]. The DM production (kg ha - item-96 at level 6: text: -1 - item-97 at level 6: text: ) of corn silage and pastures we ... onsume 70% of pastures during grazing. - item-98 at level 5: table with [9x5] - item-98 at level 6: caption: Table 3 GHG emission factors for Off- and On-farm feed production. - item-99 at level 5: inline: group group - item-100 at level 6: text: Emissions from on-farm feed prod ... ary sources were direct and indirect N - item-101 at level 6: text: 2 - item-102 at level 6: text: O-N emissions from organic and s ... tilizers and crop/pasture residues, CO - item-103 at level 6: text: 2 - item-104 at level 6: text: -C emissions from lime and urea ... well as fuel combustion. The direct N - item-105 at level 6: text: 2 - item-106 at level 6: text: O-N emission factor (kg (kg N input) - item-107 at level 6: text: -1 - item-108 at level 6: text: ) is based on a local study performed previously [37]. For indirect N - item-109 at level 6: text: 2 - item-110 at level 6: text: O-N emissions (kg N - item-111 at level 6: text: 2 - item-112 at level 6: text: O-N (kg NH - item-113 at level 6: text: 3 - item-114 at level 6: text: -N + NO - item-115 at level 6: text: x - item-116 at level 6: text: ) + item-14 at level 4: text: . The milk production response a ... re evaluated: total mixed ration (TMR) + item-15 at level 4: text: ad libitum + item-16 at level 4: text: intake, 75, and 50% of + item-17 at level 4: text: ad libitum + item-18 at level 4: text: TMR intake with access to grazin ... etween scenarios, averaging 1.06 kg CO + item-19 at level 4: text: 2 + item-20 at level 4: text: e (kg ECM) + item-21 at level 4: text: -1 + item-22 at level 4: text: . Considering factors from studi ... , the C footprint decreased 0.04 kg CO + item-23 at level 4: text: 2 + item-24 at level 4: text: e (kg ECM) + item-25 at level 4: text: -1 + item-26 at level 4: text: in scenarios including pastures compared to + item-27 at level 4: text: ad libitum + item-28 at level 4: text: TMR. Regardless of factors consi ... uce the C footprint to a small extent. + item-29 at level 2: section_header: Introduction + item-30 at level 3: inline: group group + item-31 at level 4: text: Greenhouse gas (GHG) emissions f ... ssions [1], ranging from 5.5–7.5 Gt CO + item-32 at level 4: text: 2 + item-33 at level 4: text: equivalents (CO + item-34 at level 4: text: 2 + item-35 at level 4: text: e) yr + item-36 at level 4: text: -1 + item-37 at level 4: text: , with almost 30% coming from da ... suitable for food crop production [4]. + item-38 at level 3: inline: group group + item-39 at level 4: text: Considering the key role of live ... n investigated to mitigate methane (CH + item-40 at level 4: text: 4 + item-41 at level 4: text: ) emissions from enteric ferment ... ment [6] and manure management [7]. CH + item-42 at level 4: text: 4 + item-43 at level 4: text: emissions from enteric fermentat ... anagement to mitigate the C footprint. + item-44 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]). + item-45 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake. + item-46 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated. + item-47 at level 2: section_header: Materials and methods + item-48 at level 3: inline: group group + item-49 at level 4: text: An LCA was developed according t ... 15, 2016—Approval number 4373090816 - + item-50 at level 4: text: https://www.udesc.br/cav/ceua + item-51 at level 4: text: . + item-52 at level 3: section_header: System boundary + item-53 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary. + item-54 at level 4: picture + item-54 at level 5: caption: Fig 1 Overview of the milk production system boundary considered in the study. + item-55 at level 3: section_header: Functional unit + item-56 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows: + item-57 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1. + item-58 at level 4: table with [13x3] + item-58 at level 5: caption: Table 1 Descriptive characteristics of the herd. + item-59 at level 3: section_header: Data sources and livestock system description + item-60 at level 4: inline: group group + item-61 at level 5: text: The individual feed requirements ... cows that received both 75 and 50% of + item-62 at level 5: text: ad libitum + item-63 at level 5: text: TMR intake with access to grazing a tropical pasture (pearl-millet, + item-64 at level 5: text: Pennisetum glaucum + item-65 at level 5: text: ‘Campeiro’) compared to cows receiving + item-66 at level 5: text: ad libitum + item-67 at level 5: text: TMR intake. Cows grazing on a temperate pasture (ryegrass, + item-68 at level 5: text: Lolium multiflorum + item-69 at level 5: text: ‘Maximus’) did not need changes to ECM production compared to the + item-70 at level 5: text: ad libitum + item-71 at level 5: text: TMR intake group. + item-72 at level 4: inline: group group + item-73 at level 5: text: Using experimental data, three s ... evaluated during the lactation period: + item-74 at level 5: text: ad libitum + item-75 at level 5: text: TMR intake, and 75, and 50% of + item-76 at level 5: text: ad libitum + item-77 at level 5: text: TMR intake with access to grazin ... nction of month ([26], Civiero et al., + item-78 at level 5: text: in press + item-79 at level 5: text: ). From April to October (210 da ... med during an entire lactation period. + item-80 at level 3: section_header: Impact assessment + item-81 at level 4: inline: group group + item-82 at level 5: text: The CO + item-83 at level 5: text: 2 + item-84 at level 5: text: e emissions were calculated by multiplying the emissions of CO + item-85 at level 5: text: 2 + item-86 at level 5: text: , CH + item-87 at level 5: text: 4 + item-88 at level 5: text: and N + item-89 at level 5: text: 2 + item-90 at level 5: text: O by their 100-year global warming potential (GWP + item-91 at level 5: text: 100 + item-92 at level 5: text: ), based on IPCC assessment report 5 (AR5; [27]). The values of GWP + item-93 at level 5: text: 100 + item-94 at level 5: text: are 1, 28 and 265 for CO + item-95 at level 5: text: 2 + item-96 at level 5: text: , CH + item-97 at level 5: text: 4 + item-98 at level 5: text: and N + item-99 at level 5: text: 2 + item-100 at level 5: text: O, respectively. + item-101 at level 3: section_header: Feed production + item-102 at level 4: section_header: Diets composition + item-103 at level 5: inline: group group + item-104 at level 6: text: The DM intake of each ingredient ... ennial tropical pasture (kikuyu grass, + item-105 at level 6: text: Pennisetum clandestinum + item-106 at level 6: text: ). The DM intake of calves, heif ... meet the net energy for lactation (NE + item-107 at level 6: text: L + item-108 at level 6: text: ) and metabolizable protein (MP) ... grated in the software INRAtion 4.07 ( + item-109 at level 6: text: https://www.inration.educagri.fr/fr/forum.php + item-110 at level 6: text: ). The nutrient intake was calcu ... collected throughout the experiments. + item-111 at level 5: table with [21x11] + item-111 at level 6: caption: Table 2 Dairy cows’ diets in different scenariosa. + item-112 at level 4: section_header: GHG emissions from crop and pasture production + item-113 at level 5: inline: group group + item-114 at level 6: text: GHG emission factors used for of ... s productions were 3300 and 1500 kg CO + item-115 at level 6: text: 2 + item-116 at level 6: text: e ha item-117 at level 6: text: -1 - item-118 at level 6: text: ), as well as CO - item-119 at level 6: text: 2 - item-120 at level 6: text: -C emissions from lime + urea, d ... stures, a C sequestration of 0.57 t ha - item-121 at level 6: text: -1 - item-122 at level 6: text: was used based on a 9-year study ... red was 8.9 (no-tillage) and 14.3 L ha - item-123 at level 6: text: -1 - item-124 at level 6: text: (disking) for annual tropical an ... te pastures, respectively [40]. The CO - item-125 at level 6: text: 2 - item-126 at level 6: text: from fuel combustion was 2.7 kg CO - item-127 at level 6: text: 2 - item-128 at level 6: text: L - item-129 at level 6: text: -1 - item-130 at level 6: text: [41]. Secondary sources of emiss ... factors described by Rotz et al. [42]. - item-131 at level 5: table with [28x5] - item-131 at level 6: caption: Table 4 GHG emissions from On-farm feed production. - item-132 at level 3: section_header: Animal husbandry - item-133 at level 4: inline: group group - item-134 at level 5: text: The CH - item-135 at level 5: text: 4 - item-136 at level 5: text: emissions from enteric fermentation intensity (g (kg ECM) - item-137 at level 5: text: -1 - item-138 at level 5: text: ) was a function of estimated CH - item-139 at level 5: text: 4 - item-140 at level 5: text: yield (g (kg DM intake) - item-141 at level 5: text: -1 - item-142 at level 5: text: ), actual DM intake and ECM. The enteric CH - item-143 at level 5: text: 4 - item-144 at level 5: text: yield was estimated as a functio ... proposed by Niu et al. [43], where: CH - item-145 at level 5: text: 4 - item-146 at level 5: text: yield (g (kg DM intake) - item-147 at level 5: text: -1 - item-148 at level 5: text: ) = 13.8 + 0.185 × NDF (% DM intake). - item-149 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals - item-150 at level 4: inline: group group - item-151 at level 5: text: The CH - item-152 at level 5: text: 4 - item-153 at level 5: text: emission from manure (kg (kg ECM) - item-154 at level 5: text: -1 - item-155 at level 5: text: ) was a function of daily CH - item-156 at level 5: text: 4 - item-157 at level 5: text: emission from manure (kg cow - item-158 at level 5: text: -1 - item-159 at level 5: text: ) and daily ECM (kg cow + item-118 at level 6: text: , respectively [32]. The DM production (kg ha + item-119 at level 6: text: -1 + item-120 at level 6: text: ) of corn silage and pastures we ... onsume 70% of pastures during grazing. + item-121 at level 5: table with [9x5] + item-121 at level 6: caption: Table 3 GHG emission factors for Off- and On-farm feed production. + item-122 at level 5: inline: group group + item-123 at level 6: text: Emissions from on-farm feed prod ... ary sources were direct and indirect N + item-124 at level 6: text: 2 + item-125 at level 6: text: O-N emissions from organic and s ... tilizers and crop/pasture residues, CO + item-126 at level 6: text: 2 + item-127 at level 6: text: -C emissions from lime and urea ... well as fuel combustion. The direct N + item-128 at level 6: text: 2 + item-129 at level 6: text: O-N emission factor (kg (kg N input) + item-130 at level 6: text: -1 + item-131 at level 6: text: ) is based on a local study performed previously [37]. For indirect N + item-132 at level 6: text: 2 + item-133 at level 6: text: O-N emissions (kg N + item-134 at level 6: text: 2 + item-135 at level 6: text: O-N (kg NH + item-136 at level 6: text: 3 + item-137 at level 6: text: -N + NO + item-138 at level 6: text: x + item-139 at level 6: text: ) + item-140 at level 6: text: -1 + item-141 at level 6: text: ), as well as CO + item-142 at level 6: text: 2 + item-143 at level 6: text: -C emissions from lime + urea, d ... stures, a C sequestration of 0.57 t ha + item-144 at level 6: text: -1 + item-145 at level 6: text: was used based on a 9-year study ... red was 8.9 (no-tillage) and 14.3 L ha + item-146 at level 6: text: -1 + item-147 at level 6: text: (disking) for annual tropical an ... te pastures, respectively [40]. The CO + item-148 at level 6: text: 2 + item-149 at level 6: text: from fuel combustion was 2.7 kg CO + item-150 at level 6: text: 2 + item-151 at level 6: text: L + item-152 at level 6: text: -1 + item-153 at level 6: text: [41]. Secondary sources of emiss ... factors described by Rotz et al. [42]. + item-154 at level 5: table with [28x5] + item-154 at level 6: caption: Table 4 GHG emissions from On-farm feed production. + item-155 at level 3: section_header: Animal husbandry + item-156 at level 4: inline: group group + item-157 at level 5: text: The CH + item-158 at level 5: text: 4 + item-159 at level 5: text: emissions from enteric fermentation intensity (g (kg ECM) item-160 at level 5: text: -1 - item-161 at level 5: text: ). The daily CH + item-161 at level 5: text: ) was a function of estimated CH item-162 at level 5: text: 4 - item-163 at level 5: text: emission from manure was estimat ... olatile solid (VS) excreted (kg DM cow + item-163 at level 5: text: yield (g (kg DM intake) item-164 at level 5: text: -1 - item-165 at level 5: text: ) in manure. The daily VS was es ... n an organic matter (OM) basis (kg day - item-166 at level 5: text: -1 - item-167 at level 5: text: ), NDOMI = non-digestible OM intake (kg day - item-168 at level 5: text: -1 - item-169 at level 5: text: ): (1- OM digestibility) × OM in ... .04), GE = gross energy intake (MJ day + item-165 at level 5: text: ), actual DM intake and ECM. The enteric CH + item-166 at level 5: text: 4 + item-167 at level 5: text: yield was estimated as a functio ... proposed by Niu et al. [43], where: CH + item-168 at level 5: text: 4 + item-169 at level 5: text: yield (g (kg DM intake) item-170 at level 5: text: -1 - item-171 at level 5: text: ), OM = organic matter (g), 18.4 ... tor for dietary GE per kg of DM (MJ kg - item-172 at level 5: text: -1 - item-173 at level 5: text: ). - item-174 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively. - item-175 at level 4: inline: group group - item-176 at level 5: text: The N - item-177 at level 5: text: 2 - item-178 at level 5: text: O-N emissions from urine and fec ... ations 10 and 12, respectively). The N - item-179 at level 5: text: 2 - item-180 at level 5: text: O emissions from stored manure a ... alculated based on the conversion of N - item-181 at level 5: text: 2 - item-182 at level 5: text: O-N emissions to N - item-183 at level 5: text: 2 - item-184 at level 5: text: O emissions, where N - item-185 at level 5: text: 2 - item-186 at level 5: text: O emissions = N - item-187 at level 5: text: 2 - item-188 at level 5: text: O-N emissions × 44/28. The emission factors were 0.002 kg N - item-189 at level 5: text: 2 - item-190 at level 5: text: O-N (kg N) + item-171 at level 5: text: ) = 13.8 + 0.185 × NDF (% DM intake). + item-172 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals + item-173 at level 4: inline: group group + item-174 at level 5: text: The CH + item-175 at level 5: text: 4 + item-176 at level 5: text: emission from manure (kg (kg ECM) + item-177 at level 5: text: -1 + item-178 at level 5: text: ) was a function of daily CH + item-179 at level 5: text: 4 + item-180 at level 5: text: emission from manure (kg cow + item-181 at level 5: text: -1 + item-182 at level 5: text: ) and daily ECM (kg cow + item-183 at level 5: text: -1 + item-184 at level 5: text: ). The daily CH + item-185 at level 5: text: 4 + item-186 at level 5: text: emission from manure was estimat ... olatile solid (VS) excreted (kg DM cow + item-187 at level 5: text: -1 + item-188 at level 5: text: ) in manure. The daily VS was es ... n an organic matter (OM) basis (kg day + item-189 at level 5: text: -1 + item-190 at level 5: text: ), NDOMI = non-digestible OM intake (kg day item-191 at level 5: text: -1 - item-192 at level 5: text: stored in a pit below animal confinements, and 0.02 kg N - item-193 at level 5: text: 2 - item-194 at level 5: text: O-N (kg of urine and dung) + item-192 at level 5: text: ): (1- OM digestibility) × OM in ... .04), GE = gross energy intake (MJ day + item-193 at level 5: text: -1 + item-194 at level 5: text: ), OM = organic matter (g), 18.4 ... tor for dietary GE per kg of DM (MJ kg item-195 at level 5: text: -1 - item-196 at level 5: text: deposited on pasture [38]. The indirect N - item-197 at level 5: text: 2 - item-198 at level 5: text: O emissions from storage manure ... using the IPCC [38] emission factors. - item-199 at level 3: section_header: Farm management - item-200 at level 4: text: Emissions due to farm management ... crop and pasture production’ section. - item-201 at level 4: table with [12x4] - item-201 at level 5: caption: Table 5 Factors for major resource inputs in farm management. - item-202 at level 4: inline: group group - item-203 at level 5: text: The amount of fuel use for manur ... quired for manure handling (L diesel t - item-204 at level 5: text: -1 - item-205 at level 5: text: ) [42]. The amount of manure was estimated from OM excretions (kg cow - item-206 at level 5: text: -1 - item-207 at level 5: text: ), assuming that the manure has ... me that animals stayed on confinement. - item-208 at level 4: inline: group group - item-209 at level 5: text: The emissions from fuel were est ... uired for manure handling (L) × (kg CO + item-196 at level 5: text: ). + item-197 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively. + item-198 at level 4: inline: group group + item-199 at level 5: text: The N + item-200 at level 5: text: 2 + item-201 at level 5: text: O-N emissions from urine and fec ... ations 10 and 12, respectively). The N + item-202 at level 5: text: 2 + item-203 at level 5: text: O emissions from stored manure a ... alculated based on the conversion of N + item-204 at level 5: text: 2 + item-205 at level 5: text: O-N emissions to N + item-206 at level 5: text: 2 + item-207 at level 5: text: O emissions, where N + item-208 at level 5: text: 2 + item-209 at level 5: text: O emissions = N item-210 at level 5: text: 2 - item-211 at level 5: text: e L - item-212 at level 5: text: -1 - item-213 at level 5: text: ) [41]. The secondary emissions ... roduction and transport of fuel (kg CO - item-214 at level 5: text: 2 - item-215 at level 5: text: e L - item-216 at level 5: text: -1 - item-217 at level 5: text: ) [41]. Emissions from manufactu ... w (t) × (kg machinery mass (kg manure) + item-211 at level 5: text: O-N emissions × 44/28. The emission factors were 0.002 kg N + item-212 at level 5: text: 2 + item-213 at level 5: text: O-N (kg N) + item-214 at level 5: text: -1 + item-215 at level 5: text: stored in a pit below animal confinements, and 0.02 kg N + item-216 at level 5: text: 2 + item-217 at level 5: text: O-N (kg of urine and dung) item-218 at level 5: text: -1 - item-219 at level 5: text: × 10 - item-220 at level 5: text: −3 - item-221 at level 5: text: ) [42] × kg CO - item-222 at level 5: text: 2 - item-223 at level 5: text: e (kg machinery mass) - item-224 at level 5: text: -1 - item-225 at level 5: text: [42]. - item-226 at level 4: inline: group group - item-227 at level 5: text: Emissions from electricity for m ... ated using two emission factors (kg CO - item-228 at level 5: text: 2 - item-229 at level 5: text: kWh - item-230 at level 5: text: -1 - item-231 at level 5: text: ). The first one is based on Uni ... ivities is 0.06 kWh (kg milk produced) - item-232 at level 5: text: -1 - item-233 at level 5: text: [47]. The annual electricity use for lighting was 75 kWh cow - item-234 at level 5: text: -1 - item-235 at level 5: text: , which is the value considered ... ws in naturally ventilated barns [47]. - item-236 at level 3: section_header: Co-product allocation - item-237 at level 4: inline: group group - item-238 at level 5: text: The C footprint for milk produce ... ibed by Thoma et al. [48]. Briefly, AR - item-239 at level 5: text: milk - item-240 at level 5: text: = 1–6.04 × BMR, where - item-241 at level 5: text: : - item-242 at level 5: text: AR - item-243 at level 5: text: milk - item-244 at level 5: text: is the allocation ratio for milk ... during cow`s entire life (kg). The AR - item-245 at level 5: text: milk - item-246 at level 5: text: were 0.854 and 0.849 for TMR and ... asture scenarios, respectively. The AR - item-247 at level 5: text: milk - item-248 at level 5: text: was applied to the whole emissio ... directly assigned to milk production. - item-249 at level 3: section_header: Sensitivity analysis - item-250 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint. - item-251 at level 2: section_header: Results and discussion - item-252 at level 3: text: The study has assessed the impac ... , feed production and electricity use. - item-253 at level 3: section_header: Greenhouse gas emissions - item-254 at level 4: inline: group group - item-255 at level 5: text: Depending on emission factors us ... 2A and 2B) or decreased by 0.04 kg CO - item-256 at level 5: text: 2 - item-257 at level 5: text: e (kg ECM) - item-258 at level 5: text: -1 - item-259 at level 5: text: (Fig 2C and 2D) in scenarios that included pastures compared to - item-260 at level 5: text: ad libitum - item-261 at level 5: text: TMR intake. Due to differences i ... values ranged from 0.92 to 1.04 kg CO - item-262 at level 5: text: 2 - item-263 at level 5: text: e (kg ECM) - item-264 at level 5: text: -1 - item-265 at level 5: text: for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO - item-266 at level 5: text: 2 - item-267 at level 5: text: e (kg ECM) - item-268 at level 5: text: -1 - item-269 at level 5: text: for cows with access to pasture. ... ocal emission factors for estimating N - item-270 at level 5: text: 2 - item-271 at level 5: text: O-N emissions [37], manure emiss ... more than 5% of overall GHG emissions. - item-272 at level 4: picture - item-272 at level 5: caption: Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. - item-273 at level 4: inline: group group - item-274 at level 5: text: Considering IPCC emission factors for N - item-275 at level 5: text: 2 - item-276 at level 5: text: O emissions from urine and dung ... otprint ranged from 0.99 to 1.04 kg CO - item-277 at level 5: text: 2 - item-278 at level 5: text: e (kg ECM) - item-279 at level 5: text: -1 - item-280 at level 5: text: , and was close to those reporte ... , which ranged from 0.98 to 1.16 kg CO - item-281 at level 5: text: 2 - item-282 at level 5: text: e (kg ECM) - item-283 at level 5: text: -1 - item-284 at level 5: text: . When local emission factors for N + item-219 at level 5: text: deposited on pasture [38]. The indirect N + item-220 at level 5: text: 2 + item-221 at level 5: text: O emissions from storage manure ... using the IPCC [38] emission factors. + item-222 at level 3: section_header: Farm management + item-223 at level 4: text: Emissions due to farm management ... crop and pasture production’ section. + item-224 at level 4: table with [12x4] + item-224 at level 5: caption: Table 5 Factors for major resource inputs in farm management. + item-225 at level 4: inline: group group + item-226 at level 5: text: The amount of fuel use for manur ... quired for manure handling (L diesel t + item-227 at level 5: text: -1 + item-228 at level 5: text: ) [42]. The amount of manure was estimated from OM excretions (kg cow + item-229 at level 5: text: -1 + item-230 at level 5: text: ), assuming that the manure has ... me that animals stayed on confinement. + item-231 at level 4: inline: group group + item-232 at level 5: text: The emissions from fuel were est ... uired for manure handling (L) × (kg CO + item-233 at level 5: text: 2 + item-234 at level 5: text: e L + item-235 at level 5: text: -1 + item-236 at level 5: text: ) [41]. The secondary emissions ... roduction and transport of fuel (kg CO + item-237 at level 5: text: 2 + item-238 at level 5: text: e L + item-239 at level 5: text: -1 + item-240 at level 5: text: ) [41]. Emissions from manufactu ... w (t) × (kg machinery mass (kg manure) + item-241 at level 5: text: -1 + item-242 at level 5: text: × 10 + item-243 at level 5: text: −3 + item-244 at level 5: text: ) [42] × kg CO + item-245 at level 5: text: 2 + item-246 at level 5: text: e (kg machinery mass) + item-247 at level 5: text: -1 + item-248 at level 5: text: [42]. + item-249 at level 4: inline: group group + item-250 at level 5: text: Emissions from electricity for m ... ated using two emission factors (kg CO + item-251 at level 5: text: 2 + item-252 at level 5: text: kWh + item-253 at level 5: text: -1 + item-254 at level 5: text: ). The first one is based on Uni ... ivities is 0.06 kWh (kg milk produced) + item-255 at level 5: text: -1 + item-256 at level 5: text: [47]. The annual electricity use for lighting was 75 kWh cow + item-257 at level 5: text: -1 + item-258 at level 5: text: , which is the value considered ... ws in naturally ventilated barns [47]. + item-259 at level 3: section_header: Co-product allocation + item-260 at level 4: inline: group group + item-261 at level 5: text: The C footprint for milk produce ... ibed by Thoma et al. [48]. Briefly, AR + item-262 at level 5: text: milk + item-263 at level 5: text: = 1–6.04 × BMR, where + item-264 at level 5: text: : + item-265 at level 5: text: AR + item-266 at level 5: text: milk + item-267 at level 5: text: is the allocation ratio for milk ... during cow`s entire life (kg). The AR + item-268 at level 5: text: milk + item-269 at level 5: text: were 0.854 and 0.849 for TMR and ... asture scenarios, respectively. The AR + item-270 at level 5: text: milk + item-271 at level 5: text: was applied to the whole emissio ... directly assigned to milk production. + item-272 at level 3: section_header: Sensitivity analysis + item-273 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint. + item-274 at level 2: section_header: Results and discussion + item-275 at level 3: text: The study has assessed the impac ... , feed production and electricity use. + item-276 at level 3: section_header: Greenhouse gas emissions + item-277 at level 4: inline: group group + item-278 at level 5: text: Depending on emission factors us ... 2A and 2B) or decreased by 0.04 kg CO + item-279 at level 5: text: 2 + item-280 at level 5: text: e (kg ECM) + item-281 at level 5: text: -1 + item-282 at level 5: text: (Fig 2C and 2D) in scenarios that included pastures compared to + item-283 at level 5: text: ad libitum + item-284 at level 5: text: TMR intake. Due to differences i ... values ranged from 0.92 to 1.04 kg CO item-285 at level 5: text: 2 - item-286 at level 5: text: O emissions from urine and dung ... without accounting for sequestered CO - item-287 at level 5: text: 2 - item-288 at level 5: text: -C from perennial pasture—0.91 kg CO + item-286 at level 5: text: e (kg ECM) + item-287 at level 5: text: -1 + item-288 at level 5: text: for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO item-289 at level 5: text: 2 item-290 at level 5: text: e (kg ECM) item-291 at level 5: text: -1 - item-292 at level 5: text: —was lower than the range of val ... , which ranged from 0.52 to 0.89 kg CO + item-292 at level 5: text: for cows with access to pasture. ... ocal emission factors for estimating N item-293 at level 5: text: 2 - item-294 at level 5: text: e (kg ECM) - item-295 at level 5: text: -1 - item-296 at level 5: text: . Regardless of which emission f ... nt, which ranged from 1.4 to 2.3 kg CO - item-297 at level 5: text: 2 - item-298 at level 5: text: e (kg ECM) - item-299 at level 5: text: -1 - item-300 at level 5: text: [8,55]. Thus, even though differ ... e emissions estimation, sequestered CO - item-301 at level 5: text: 2 - item-302 at level 5: text: -C, etc.), herd productivity and ... the C footprint of the dairy systems. - item-303 at level 4: inline: group group - item-304 at level 5: text: The similarity of C footprint be ... served that an increase of 1000 kg cow - item-305 at level 5: text: -1 - item-306 at level 5: text: (5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO - item-307 at level 5: text: 2 - item-308 at level 5: text: e (kg ECM) - item-309 at level 5: text: -1 - item-310 at level 5: text: , which may explain an apparent ... milk production of around 7000 kg cow - item-311 at level 5: text: -1 - item-312 at level 5: text: . Experimental data showed a red ... of TMR was replaced by pasture access. - item-313 at level 4: inline: group group - item-314 at level 5: text: The lower C footprint in scenari ... emission factors [37] were used for N - item-315 at level 5: text: 2 - item-316 at level 5: text: O emissions from urine and dung ... enarios including pastures compared to - item-317 at level 5: text: ad libitum - item-318 at level 5: text: TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N - item-319 at level 5: text: 2 - item-320 at level 5: text: O-N (kg N) - item-321 at level 5: text: -1 - item-322 at level 5: text: for urine and dung from grazing ... five times lower, averaging 0.004 kg N - item-323 at level 5: text: 2 - item-324 at level 5: text: O-N kg - item-325 at level 5: text: -1 - item-326 at level 5: text: [37]. - item-327 at level 3: section_header: Methane emissions - item-328 at level 4: inline: group group - item-329 at level 5: text: The enteric CH - item-330 at level 5: text: 4 - item-331 at level 5: text: intensity was similar between di ... Fig 3). The large effect of enteric CH - item-332 at level 5: text: 4 - item-333 at level 5: text: emissions on the whole C footpri ... cted, because the impact of enteric CH - item-334 at level 5: text: 4 - item-335 at level 5: text: on GHG emissions of milk product ... o range from 44 to 60% of the total CO - item-336 at level 5: text: 2 - item-337 at level 5: text: e [50,52,57,58]. However, emissi ... trate feeds are greater than 0.7 kg CO + item-294 at level 5: text: O-N emissions [37], manure emiss ... more than 5% of overall GHG emissions. + item-295 at level 4: picture + item-295 at level 5: caption: Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. + item-296 at level 4: inline: group group + item-297 at level 5: text: Considering IPCC emission factors for N + item-298 at level 5: text: 2 + item-299 at level 5: text: O emissions from urine and dung ... otprint ranged from 0.99 to 1.04 kg CO + item-300 at level 5: text: 2 + item-301 at level 5: text: e (kg ECM) + item-302 at level 5: text: -1 + item-303 at level 5: text: , and was close to those reporte ... , which ranged from 0.98 to 1.16 kg CO + item-304 at level 5: text: 2 + item-305 at level 5: text: e (kg ECM) + item-306 at level 5: text: -1 + item-307 at level 5: text: . When local emission factors for N + item-308 at level 5: text: 2 + item-309 at level 5: text: O emissions from urine and dung ... without accounting for sequestered CO + item-310 at level 5: text: 2 + item-311 at level 5: text: -C from perennial pasture—0.91 kg CO + item-312 at level 5: text: 2 + item-313 at level 5: text: e (kg ECM) + item-314 at level 5: text: -1 + item-315 at level 5: text: —was lower than the range of val ... , which ranged from 0.52 to 0.89 kg CO + item-316 at level 5: text: 2 + item-317 at level 5: text: e (kg ECM) + item-318 at level 5: text: -1 + item-319 at level 5: text: . Regardless of which emission f ... nt, which ranged from 1.4 to 2.3 kg CO + item-320 at level 5: text: 2 + item-321 at level 5: text: e (kg ECM) + item-322 at level 5: text: -1 + item-323 at level 5: text: [8,55]. Thus, even though differ ... e emissions estimation, sequestered CO + item-324 at level 5: text: 2 + item-325 at level 5: text: -C, etc.), herd productivity and ... the C footprint of the dairy systems. + item-326 at level 4: inline: group group + item-327 at level 5: text: The similarity of C footprint be ... served that an increase of 1000 kg cow + item-328 at level 5: text: -1 + item-329 at level 5: text: (5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO + item-330 at level 5: text: 2 + item-331 at level 5: text: e (kg ECM) + item-332 at level 5: text: -1 + item-333 at level 5: text: , which may explain an apparent ... milk production of around 7000 kg cow + item-334 at level 5: text: -1 + item-335 at level 5: text: . Experimental data showed a red ... of TMR was replaced by pasture access. + item-336 at level 4: inline: group group + item-337 at level 5: text: The lower C footprint in scenari ... emission factors [37] were used for N item-338 at level 5: text: 2 - item-339 at level 5: text: e kg - item-340 at level 5: text: -1 - item-341 at level 5: text: [59], which did not happen in this study. - item-342 at level 4: picture - item-342 at level 5: caption: Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. - item-343 at level 4: inline: group group - item-344 at level 5: text: The lack of difference in enteric CH - item-345 at level 5: text: 4 - item-346 at level 5: text: emissions in different systems c ... nual temperate pastures (495 g (kg DM) - item-347 at level 5: text: -1 - item-348 at level 5: text: ) compared to corn silage (550 g (kg DM) - item-349 at level 5: text: -1 - item-350 at level 5: text: ). Hence, an expected, increase ... have shown that the actual enteric CH - item-351 at level 5: text: 4 - item-352 at level 5: text: emissions may decrease with incl ... ybean meal [60] or increase enteric CH + item-339 at level 5: text: O emissions from urine and dung ... enarios including pastures compared to + item-340 at level 5: text: ad libitum + item-341 at level 5: text: TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N + item-342 at level 5: text: 2 + item-343 at level 5: text: O-N (kg N) + item-344 at level 5: text: -1 + item-345 at level 5: text: for urine and dung from grazing ... five times lower, averaging 0.004 kg N + item-346 at level 5: text: 2 + item-347 at level 5: text: O-N kg + item-348 at level 5: text: -1 + item-349 at level 5: text: [37]. + item-350 at level 3: section_header: Methane emissions + item-351 at level 4: inline: group group + item-352 at level 5: text: The enteric CH item-353 at level 5: text: 4 - item-354 at level 5: text: emissions when dairy cows grazin ... silage [61]. Additionally, enteric CH + item-354 at level 5: text: intensity was similar between di ... Fig 3). The large effect of enteric CH item-355 at level 5: text: 4 - item-356 at level 5: text: emissions did not differ between ... same scenarios as in this study [26]. - item-357 at level 3: section_header: Emissions from excreta and feed production - item-358 at level 4: inline: group group - item-359 at level 5: text: Using IPCC emission factors for N - item-360 at level 5: text: 2 - item-361 at level 5: text: O emissions from urine and dung [38] and those from Table 3, CH - item-362 at level 5: text: 4 - item-363 at level 5: text: emissions from manure decreased 0.07 kg CO - item-364 at level 5: text: 2 - item-365 at level 5: text: e (kg ECM) - item-366 at level 5: text: -1 - item-367 at level 5: text: , but N - item-368 at level 5: text: 2 - item-369 at level 5: text: O emissions from manure increased 0.09 kg CO - item-370 at level 5: text: 2 - item-371 at level 5: text: e (kg ECM) + item-356 at level 5: text: emissions on the whole C footpri ... cted, because the impact of enteric CH + item-357 at level 5: text: 4 + item-358 at level 5: text: on GHG emissions of milk product ... o range from 44 to 60% of the total CO + item-359 at level 5: text: 2 + item-360 at level 5: text: e [50,52,57,58]. However, emissi ... trate feeds are greater than 0.7 kg CO + item-361 at level 5: text: 2 + item-362 at level 5: text: e kg + item-363 at level 5: text: -1 + item-364 at level 5: text: [59], which did not happen in this study. + item-365 at level 4: picture + item-365 at level 5: caption: Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. + item-366 at level 4: inline: group group + item-367 at level 5: text: The lack of difference in enteric CH + item-368 at level 5: text: 4 + item-369 at level 5: text: emissions in different systems c ... nual temperate pastures (495 g (kg DM) + item-370 at level 5: text: -1 + item-371 at level 5: text: ) compared to corn silage (550 g (kg DM) item-372 at level 5: text: -1 - item-373 at level 5: text: , as TMR intake was restricted to 50% - item-374 at level 5: text: ad libitum - item-375 at level 5: text: (Fig 4A). Emissions for pastures increased by 0.06 kg CO - item-376 at level 5: text: 2 - item-377 at level 5: text: e (kg ECM) - item-378 at level 5: text: -1 - item-379 at level 5: text: , whereas emissions for producin ... nd corn silage decreased by 0.09 kg CO - item-380 at level 5: text: 2 - item-381 at level 5: text: e (kg ECM) - item-382 at level 5: text: -1 - item-383 at level 5: text: , as TMR intake decreased (Fig 4 ... ctating dairy cow diets. The greater N - item-384 at level 5: text: 2 - item-385 at level 5: text: O-N emissions from manure with pasture was a consequence of higher N - item-386 at level 5: text: 2 - item-387 at level 5: text: O-N emissions due to greater CP ... g CP content from 185 to 152 g (kg DM) - item-388 at level 5: text: -1 - item-389 at level 5: text: , N intake decreased by 20% and ... g dairy cows ranged from 150 g (kg DM) - item-390 at level 5: text: -1 - item-391 at level 5: text: on TMR system to 198 g (kg DM) - item-392 at level 5: text: -1 - item-393 at level 5: text: on 50% TMR with pasture. Additio ... may not be captured by microbes [65]. - item-394 at level 4: picture - item-394 at level 5: caption: Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture. - item-395 at level 4: inline: group group - item-396 at level 5: text: Using local emission factors for N - item-397 at level 5: text: 2 - item-398 at level 5: text: O emissions from urine and dung ... d those from Table 4, reductions in CH - item-399 at level 5: text: 4 - item-400 at level 5: text: emissions from stocked manure, w ... iets, did not offset by increases in N - item-401 at level 5: text: 2 - item-402 at level 5: text: O emissions from excreta (Fig 4C ... much lower emission factors used for N + item-373 at level 5: text: ). Hence, an expected, increase ... have shown that the actual enteric CH + item-374 at level 5: text: 4 + item-375 at level 5: text: emissions may decrease with incl ... ybean meal [60] or increase enteric CH + item-376 at level 5: text: 4 + item-377 at level 5: text: emissions when dairy cows grazin ... silage [61]. Additionally, enteric CH + item-378 at level 5: text: 4 + item-379 at level 5: text: emissions did not differ between ... same scenarios as in this study [26]. + item-380 at level 3: section_header: Emissions from excreta and feed production + item-381 at level 4: inline: group group + item-382 at level 5: text: Using IPCC emission factors for N + item-383 at level 5: text: 2 + item-384 at level 5: text: O emissions from urine and dung [38] and those from Table 3, CH + item-385 at level 5: text: 4 + item-386 at level 5: text: emissions from manure decreased 0.07 kg CO + item-387 at level 5: text: 2 + item-388 at level 5: text: e (kg ECM) + item-389 at level 5: text: -1 + item-390 at level 5: text: , but N + item-391 at level 5: text: 2 + item-392 at level 5: text: O emissions from manure increased 0.09 kg CO + item-393 at level 5: text: 2 + item-394 at level 5: text: e (kg ECM) + item-395 at level 5: text: -1 + item-396 at level 5: text: , as TMR intake was restricted to 50% + item-397 at level 5: text: ad libitum + item-398 at level 5: text: (Fig 4A). Emissions for pastures increased by 0.06 kg CO + item-399 at level 5: text: 2 + item-400 at level 5: text: e (kg ECM) + item-401 at level 5: text: -1 + item-402 at level 5: text: , whereas emissions for producin ... nd corn silage decreased by 0.09 kg CO item-403 at level 5: text: 2 - item-404 at level 5: text: O emissions from urine and dung. ... be revised for the subtropical region. - item-405 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9]. - item-406 at level 3: section_header: Farm management - item-407 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint. - item-408 at level 4: inline: group group - item-409 at level 5: text: Emissions from farm management d ... or electricity generation (0.205 kg CO - item-410 at level 5: text: 2 - item-411 at level 5: text: e kWh - item-412 at level 5: text: -1 - item-413 at level 5: text: [46]) is much lower than that in a LCA study conducted in US (0.73 kg CO - item-414 at level 5: text: 2 - item-415 at level 5: text: e kWh - item-416 at level 5: text: -1 - item-417 at level 5: text: [42]). This apparent discrepancy ... has an emission factor of 0.074 kg CO - item-418 at level 5: text: 2 - item-419 at level 5: text: e kWh - item-420 at level 5: text: -1 - item-421 at level 5: text: against 0.382 and 0.926 kg CO - item-422 at level 5: text: 2 - item-423 at level 5: text: e kWh - item-424 at level 5: text: -1 - item-425 at level 5: text: produced by natural gas and hard coal, respectively [46]. - item-426 at level 3: section_header: Assumptions and limitations - item-427 at level 4: inline: group group - item-428 at level 5: text: The milk production and composit ... sion factors for direct and indirect N - item-429 at level 5: text: 2 - item-430 at level 5: text: O emissions from urine and dung ... sary to reduce the uncertainty. The CO - item-431 at level 5: text: 2 - item-432 at level 5: text: emitted from lime and urea appli ... ions as a function of soil management. - item-433 at level 3: section_header: Further considerations - item-434 at level 4: inline: group group - item-435 at level 5: text: The potential for using pasture ... reduced the C footprint by 0.12 kg CO - item-436 at level 5: text: 2 - item-437 at level 5: text: e (kg ECM) - item-438 at level 5: text: -1 - item-439 at level 5: text: , whereas an increase from 10,00 ... ced the C footprint by only 0.06 kg CO - item-440 at level 5: text: 2 - item-441 at level 5: text: e (kg ECM) - item-442 at level 5: text: -1 - item-443 at level 5: text: . Hence, the impact of increasin ... C footprint may increase by 0.03 kg CO - item-444 at level 5: text: 2 - item-445 at level 5: text: e (kg ECM) - item-446 at level 5: text: -1 - item-447 at level 5: text: in subclinical ketosis [71] and by 0.02 kg CO - item-448 at level 5: text: 2 - item-449 at level 5: text: e (kg ECM) - item-450 at level 5: text: -1 - item-451 at level 5: text: in case of foot lesions [72]. - item-452 at level 4: inline: group group - item-453 at level 5: text: Grazing lands may also improve b ... n subtropical areas by 0.5 to 1.5 t ha - item-454 at level 5: text: -1 - item-455 at level 5: text: [75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha - item-456 at level 5: text: -1 - item-457 at level 5: text: would be sequestered, further re ... e C footprint by 0.015 and 0.025 kg CO - item-458 at level 5: text: 2 - item-459 at level 5: text: e (kg ECM) - item-460 at level 5: text: -1 - item-461 at level 5: text: for the scenarios using 75 and 5 ... emissions would be 0.03 and 0.05 kg CO - item-462 at level 5: text: 2 - item-463 at level 5: text: e (kg ECM) - item-464 at level 5: text: -1 - item-465 at level 5: text: for 75 and 50% TMR, respectively ... C storage, so that net exchange of CO - item-466 at level 5: text: 2 - item-467 at level 5: text: would be negligible [76]. - item-468 at level 2: section_header: Conclusions - item-469 at level 3: inline: group group - item-470 at level 4: text: This study assessed the C footpr ... attributable to the evidence of low N - item-471 at level 4: text: 2 - item-472 at level 4: text: O emissions from urine and dung ... ical areas. Even though the enteric CH - item-473 at level 4: text: 4 - item-474 at level 4: text: intensity was the largest source of CO - item-475 at level 4: text: 2 - item-476 at level 4: text: e emissions, it did not change b ... on with or without access to pastures. - item-477 at level 2: section_header: Acknowledgments - item-478 at level 3: text: Thanks to Anna Naranjo for helpf ... of the herd considered in this study. - item-479 at level 2: section_header: References - item-480 at level 3: list: group list - item-481 at level 4: list_item: IPCC. 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GREET 1.8a Spreadsheet ... transportation.anl.gov/software/GREET/ - item-522 at level 4: list_item: RotzCAA, MontesF, ChianeseDS, Ch ... 6–1282. 10.3168/jds.2009-2162 20172247 - item-523 at level 4: list_item: NiuM, KebreabE, HristovAN, OhJ, ... 3368–3389. 10.1111/gcb.14094 29450980 - item-524 at level 4: list_item: EugèneM, SauvantD, NozièreP, Via ... 10.1016/j.jenvman.2018.10.086 30602259 - item-525 at level 4: list_item: ReedKF, MoraesLE, CasperDP, Kebr ... 5–3035. 10.3168/jds.2014-8397 25747829 - item-526 at level 4: list_item: BarrosMV, PiekarskiCM, De Franci ... . Energies. 2018;11 10.3390/en11061412 - item-527 at level 4: list_item: LudingtonD, JohnsonE. Dairy Farm ... York State Energy Res Dev Auth. 2003. - item-528 at level 4: list_item: ThomaG, JollietO, WangY. A bioph ... 2013;31 10.1016/j.idairyj.2012.08.012 - item-529 at level 4: list_item: NaranjoA, JohnsonA, RossowH. Gre ... . 2020 10.3168/jds.2019-16576 32037166 - item-530 at level 4: list_item: JayasundaraS, WordenD, WeersinkA ... 18–1028. 10.1016/j.jclepro.2019.04.013 - item-531 at level 4: list_item: WilliamsSRO, FisherPD, Berrisfor ... 4;19: 69–78. 10.1007/s11367-013-0619-8 - item-532 at level 4: list_item: GollnowS, LundieS, MooreAD, McLa ... : 31–38. 10.1016/j.idairyj.2014.02.005 - item-533 at level 4: list_item: O’BrienD, CapperJL, GarnsworthyP ... i. 2014 10.3168/jds.2013-7174 24440256 - item-534 at level 4: list_item: ChobtangJ, McLarenSJ, LedgardSF, ... 2017;21: 1139–1152. 10.1111/jiec.12484 - item-535 at level 4: list_item: GargMR, PhondbaBT, SherasiaPL, M ... Sci. 2016;56: 423–436. 10.1071/AN15464 - item-536 at level 4: list_item: de LéisCM, CherubiniE, RuviaroCF ... 5;20: 46–60. 10.1007/s11367-014-0813-3 - item-537 at level 4: list_item: O’BrienD, GeogheganA, McNamaraK, ... Sci. 2016;56: 495–500. 10.1071/AN15490 - item-538 at level 4: list_item: O’BrienD, BrennanP, HumphreysJ, ... : 1469–1481. 10.1007/s11367-014-0755-9 - item-539 at level 4: list_item: BaekCY, LeeKM, ParkKH. Quantific ... : 50–60. 10.1016/j.jclepro.2014.02.010 - item-540 at level 4: list_item: Dall-OrsolettaAC, AlmeidaJGR, Ca ... –4383. 10.3168/jds.2015-10396 27016830 - item-541 at level 4: list_item: Dall-OrsolettaAC, OziemblowskiMM ... 5–73. 10.1016/j.anifeedsci.2019.05.009 - item-542 at level 4: list_item: NiuM, AppuhamyJADRN, LeytemAB, D ... Sci. 2016;56: 312–321. 10.1071/AN15498 - item-543 at level 4: list_item: WaghornGC, LawN, BryantM, Pachec ... i. 2019;59: 1261–1270. 10.1071/AN18018 - item-544 at level 4: list_item: DickhoeferU, GlowackiS, GómezCA, ... 109–118. 10.1016/j.livsci.2018.08.004 - item-545 at level 4: list_item: SchwabCG, BroderickGA. A 100-Yea ... 10112. 10.3168/jds.2017-13320 29153157 - item-546 at level 4: list_item: SordiA, DieckowJ, BayerC, Alburq ... 90: 94–103. 10.1016/j.agee.2013.09.004 - item-547 at level 4: list_item: SimonPL, DieckowJ, de KleinCAM, ... 267: 74–82. 10.1016/j.agee.2018.08.013 - item-548 at level 4: list_item: WangX, LedgardS, LuoJ, GuoY, Zha ... .1016/j.scitotenv.2017.12.259 29291563 - item-549 at level 4: list_item: PirloG, LolliS. Environmental im ... 962–971. 10.1016/j.jclepro.2018.11.070 - item-550 at level 4: list_item: HerzogA, WincklerC, ZollitschW. ... 7: 174–187. 10.1016/j.agee.2018.07.029 - item-551 at level 4: list_item: MostertPF, van MiddelaarCE, Bokk ... od. 2018 10.1016/j.jclepro.2017.10.019 - item-552 at level 4: list_item: MostertPF, van MiddelaarCE, de B ... 7: 206–212. 10.1016/j.agsy.2018.09.006 - item-553 at level 4: list_item: FoleyJA, RamankuttyN, BraumanKA, ... 337–342. 10.1038/nature10452 21993620 - item-554 at level 4: list_item: LalR. Soil Carbon Sequestration ... 1627. 10.1126/science.1097396 15192216 - item-555 at level 4: list_item: BoddeyRM, JantaliaCP, ConceiçaoP ... –795. 10.1111/j.1365-2486.2009.02020.x - item-556 at level 4: list_item: McConkeyB, AngersD, BenthamM, Bo ... the LULUCF sector for NIR 2014. 2014. - item-557 at level 1: caption: Fig 1 Overview of the milk produ ... stem boundary considered in the study. - item-558 at level 1: caption: Table 1 Descriptive characteristics of the herd. - item-559 at level 1: caption: Table 2 Dairy cows’ diets in different scenariosa. - item-560 at level 1: caption: Table 3 GHG emission factors for Off- and On-farm feed production. - item-561 at level 1: caption: Table 4 GHG emissions from On-farm feed production. - item-562 at level 1: caption: Table 5 Factors for major resource inputs in farm management. - item-563 at level 1: caption: Fig 2 Overall greenhouse gas emi ... lectricity = 0.205 kg CO2e kWh-1 [46]. - item-564 at level 1: caption: Fig 3 Sensitivity of the C footp ... lectricity = 0.205 kg CO2e kWh-1 [46]. - item-565 at level 1: caption: Fig 4 Greenhouse gas emissions ( ... uestered CO2-C from perennial pasture. \ No newline at end of file + item-404 at level 5: text: e (kg ECM) + item-405 at level 5: text: -1 + item-406 at level 5: text: , as TMR intake decreased (Fig 4 ... ctating dairy cow diets. The greater N + item-407 at level 5: text: 2 + item-408 at level 5: text: O-N emissions from manure with pasture was a consequence of higher N + item-409 at level 5: text: 2 + item-410 at level 5: text: O-N emissions due to greater CP ... g CP content from 185 to 152 g (kg DM) + item-411 at level 5: text: -1 + item-412 at level 5: text: , N intake decreased by 20% and ... g dairy cows ranged from 150 g (kg DM) + item-413 at level 5: text: -1 + item-414 at level 5: text: on TMR system to 198 g (kg DM) + item-415 at level 5: text: -1 + item-416 at level 5: text: on 50% TMR with pasture. Additio ... may not be captured by microbes [65]. + item-417 at level 4: picture + item-417 at level 5: caption: Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture. + item-418 at level 4: inline: group group + item-419 at level 5: text: Using local emission factors for N + item-420 at level 5: text: 2 + item-421 at level 5: text: O emissions from urine and dung ... d those from Table 4, reductions in CH + item-422 at level 5: text: 4 + item-423 at level 5: text: emissions from stocked manure, w ... iets, did not offset by increases in N + item-424 at level 5: text: 2 + item-425 at level 5: text: O emissions from excreta (Fig 4C ... much lower emission factors used for N + item-426 at level 5: text: 2 + item-427 at level 5: text: O emissions from urine and dung. ... be revised for the subtropical region. + item-428 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9]. + item-429 at level 3: section_header: Farm management + item-430 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint. + item-431 at level 4: inline: group group + item-432 at level 5: text: Emissions from farm management d ... or electricity generation (0.205 kg CO + item-433 at level 5: text: 2 + item-434 at level 5: text: e kWh + item-435 at level 5: text: -1 + item-436 at level 5: text: [46]) is much lower than that in a LCA study conducted in US (0.73 kg CO + item-437 at level 5: text: 2 + item-438 at level 5: text: e kWh + item-439 at level 5: text: -1 + item-440 at level 5: text: [42]). This apparent discrepancy ... has an emission factor of 0.074 kg CO + item-441 at level 5: text: 2 + item-442 at level 5: text: e kWh + item-443 at level 5: text: -1 + item-444 at level 5: text: against 0.382 and 0.926 kg CO + item-445 at level 5: text: 2 + item-446 at level 5: text: e kWh + item-447 at level 5: text: -1 + item-448 at level 5: text: produced by natural gas and hard coal, respectively [46]. + item-449 at level 3: section_header: Assumptions and limitations + item-450 at level 4: inline: group group + item-451 at level 5: text: The milk production and composit ... sion factors for direct and indirect N + item-452 at level 5: text: 2 + item-453 at level 5: text: O emissions from urine and dung ... sary to reduce the uncertainty. The CO + item-454 at level 5: text: 2 + item-455 at level 5: text: emitted from lime and urea appli ... ions as a function of soil management. + item-456 at level 3: section_header: Further considerations + item-457 at level 4: inline: group group + item-458 at level 5: text: The potential for using pasture ... reduced the C footprint by 0.12 kg CO + item-459 at level 5: text: 2 + item-460 at level 5: text: e (kg ECM) + item-461 at level 5: text: -1 + item-462 at level 5: text: , whereas an increase from 10,00 ... ced the C footprint by only 0.06 kg CO + item-463 at level 5: text: 2 + item-464 at level 5: text: e (kg ECM) + item-465 at level 5: text: -1 + item-466 at level 5: text: . Hence, the impact of increasin ... C footprint may increase by 0.03 kg CO + item-467 at level 5: text: 2 + item-468 at level 5: text: e (kg ECM) + item-469 at level 5: text: -1 + item-470 at level 5: text: in subclinical ketosis [71] and by 0.02 kg CO + item-471 at level 5: text: 2 + item-472 at level 5: text: e (kg ECM) + item-473 at level 5: text: -1 + item-474 at level 5: text: in case of foot lesions [72]. + item-475 at level 4: inline: group group + item-476 at level 5: text: Grazing lands may also improve b ... n subtropical areas by 0.5 to 1.5 t ha + item-477 at level 5: text: -1 + item-478 at level 5: text: [75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha + item-479 at level 5: text: -1 + item-480 at level 5: text: would be sequestered, further re ... e C footprint by 0.015 and 0.025 kg CO + item-481 at level 5: text: 2 + item-482 at level 5: text: e (kg ECM) + item-483 at level 5: text: -1 + item-484 at level 5: text: for the scenarios using 75 and 5 ... emissions would be 0.03 and 0.05 kg CO + item-485 at level 5: text: 2 + item-486 at level 5: text: e (kg ECM) + item-487 at level 5: text: -1 + item-488 at level 5: text: for 75 and 50% TMR, respectively ... C storage, so that net exchange of CO + item-489 at level 5: text: 2 + item-490 at level 5: text: would be negligible [76]. + item-491 at level 2: section_header: Conclusions + item-492 at level 3: inline: group group + item-493 at level 4: text: This study assessed the C footpr ... attributable to the evidence of low N + item-494 at level 4: text: 2 + item-495 at level 4: text: O emissions from urine and dung ... ical areas. Even though the enteric CH + item-496 at level 4: text: 4 + item-497 at level 4: text: intensity was the largest source of CO + item-498 at level 4: text: 2 + item-499 at level 4: text: e emissions, it did not change b ... on with or without access to pastures. + item-500 at level 2: section_header: Acknowledgments + item-501 at level 3: text: Thanks to Anna Naranjo for helpf ... of the herd considered in this study. + item-502 at level 2: section_header: References + item-503 at level 3: list: group list + item-504 at level 4: list_item: IPCC. 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Soil Carbon Sequestration ... 1627. 10.1126/science.1097396 15192216 + item-578 at level 4: list_item: BoddeyRM, JantaliaCP, ConceiçaoP ... –795. 10.1111/j.1365-2486.2009.02020.x + item-579 at level 4: list_item: McConkeyB, AngersD, BenthamM, Bo ... the LULUCF sector for NIR 2014. 2014. + item-580 at level 1: caption: Fig 1 Overview of the milk produ ... stem boundary considered in the study. + item-581 at level 1: caption: Table 1 Descriptive characteristics of the herd. + item-582 at level 1: caption: Table 2 Dairy cows’ diets in different scenariosa. + item-583 at level 1: caption: Table 3 GHG emission factors for Off- and On-farm feed production. + item-584 at level 1: caption: Table 4 GHG emissions from On-farm feed production. + item-585 at level 1: caption: Table 5 Factors for major resource inputs in farm management. + item-586 at level 1: caption: Fig 2 Overall greenhouse gas emi ... lectricity = 0.205 kg CO2e kWh-1 [46]. + item-587 at level 1: caption: Fig 3 Sensitivity of the C footp ... lectricity = 0.205 kg CO2e kWh-1 [46]. + item-588 at level 1: caption: Fig 4 Greenhouse gas emissions ( ... uestered CO2-C from perennial pasture. \ No newline at end of file diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.json b/tests/data/jats/groundtruth/pone.0234687.nxml.json index 452dc5bd27..c084f0edfd 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.json +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.json @@ -21,31 +21,31 @@ "$ref": "#/texts/0" }, { - "$ref": "#/texts/27" + "$ref": "#/texts/49" }, { - "$ref": "#/texts/31" + "$ref": "#/texts/53" }, { - "$ref": "#/texts/80" + "$ref": "#/texts/102" }, { - "$ref": "#/texts/89" + "$ref": "#/texts/111" }, { - "$ref": "#/texts/121" + "$ref": "#/texts/143" }, { - "$ref": "#/texts/188" + "$ref": "#/texts/210" }, { - "$ref": "#/texts/254" + "$ref": "#/texts/276" }, { - "$ref": "#/texts/320" + "$ref": "#/texts/342" }, { - "$ref": "#/texts/370" + "$ref": "#/texts/392" } ], "content_layer": "body", @@ -56,9 +56,15 @@ { "self_ref": "#/groups/0", "parent": { - "$ref": "#/texts/5" + "$ref": "#/texts/3" }, "children": [ + { + "$ref": "#/texts/4" + }, + { + "$ref": "#/texts/5" + }, { "$ref": "#/texts/6" }, @@ -79,18 +85,7 @@ }, { "$ref": "#/texts/12" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/1", - "parent": { - "$ref": "#/texts/5" - }, - "children": [ + }, { "$ref": "#/texts/13" }, @@ -105,18 +100,19 @@ }, { "$ref": "#/texts/17" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/2", - "parent": { - "$ref": "#/texts/21" - }, - "children": [ + }, + { + "$ref": "#/texts/18" + }, + { + "$ref": "#/texts/19" + }, + { + "$ref": "#/texts/20" + }, + { + "$ref": "#/texts/21" + }, { "$ref": "#/texts/22" }, @@ -125,6 +121,12 @@ }, { "$ref": "#/texts/24" + }, + { + "$ref": "#/texts/25" + }, + { + "$ref": "#/texts/26" } ], "content_layer": "body", @@ -132,43 +134,57 @@ "label": "inline" }, { - "self_ref": "#/groups/3", + "self_ref": "#/groups/1", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/27" }, "children": [ { - "$ref": "#/texts/33" + "$ref": "#/texts/28" }, { - "$ref": "#/texts/34" + "$ref": "#/texts/29" }, { - "$ref": "#/texts/35" + "$ref": "#/texts/30" }, { - "$ref": "#/texts/36" + "$ref": "#/texts/31" }, { - "$ref": "#/texts/37" + "$ref": "#/texts/32" }, { - "$ref": "#/texts/38" + "$ref": "#/texts/33" }, { - "$ref": "#/texts/39" + "$ref": "#/texts/34" + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/2", + "parent": { + "$ref": "#/texts/27" + }, + "children": [ + { + "$ref": "#/texts/35" }, { - "$ref": "#/texts/40" + "$ref": "#/texts/36" }, { - "$ref": "#/texts/41" + "$ref": "#/texts/37" }, { - "$ref": "#/texts/42" + "$ref": "#/texts/38" }, { - "$ref": "#/texts/43" + "$ref": "#/texts/39" } ], "content_layer": "body", @@ -176,9 +192,9 @@ "label": "inline" }, { - "self_ref": "#/groups/4", + "self_ref": "#/groups/3", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { @@ -189,18 +205,6 @@ }, { "$ref": "#/texts/46" - }, - { - "$ref": "#/texts/47" - }, - { - "$ref": "#/texts/48" - }, - { - "$ref": "#/texts/49" - }, - { - "$ref": "#/texts/50" } ], "content_layer": "body", @@ -208,20 +212,11 @@ "label": "inline" }, { - "self_ref": "#/groups/5", + "self_ref": "#/groups/4", "parent": { - "$ref": "#/texts/51" + "$ref": "#/texts/54" }, "children": [ - { - "$ref": "#/texts/52" - }, - { - "$ref": "#/texts/53" - }, - { - "$ref": "#/texts/54" - }, { "$ref": "#/texts/55" }, @@ -254,7 +249,18 @@ }, { "$ref": "#/texts/65" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/5", + "parent": { + "$ref": "#/texts/54" + }, + "children": [ { "$ref": "#/texts/66" }, @@ -269,6 +275,12 @@ }, { "$ref": "#/texts/70" + }, + { + "$ref": "#/texts/71" + }, + { + "$ref": "#/texts/72" } ], "content_layer": "body", @@ -278,12 +290,9 @@ { "self_ref": "#/groups/6", "parent": { - "$ref": "#/texts/72" + "$ref": "#/texts/73" }, "children": [ - { - "$ref": "#/texts/73" - }, { "$ref": "#/texts/74" }, @@ -301,18 +310,13 @@ }, { "$ref": "#/texts/79" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/7", - "parent": { - "$ref": "#/texts/81" - }, - "children": [ + }, + { + "$ref": "#/texts/80" + }, + { + "$ref": "#/texts/81" + }, { "$ref": "#/texts/82" }, @@ -333,6 +337,18 @@ }, { "$ref": "#/texts/88" + }, + { + "$ref": "#/texts/89" + }, + { + "$ref": "#/texts/90" + }, + { + "$ref": "#/texts/91" + }, + { + "$ref": "#/texts/92" } ], "content_layer": "body", @@ -340,26 +356,11 @@ "label": "inline" }, { - "self_ref": "#/groups/8", + "self_ref": "#/groups/7", "parent": { - "$ref": "#/texts/81" + "$ref": "#/texts/94" }, "children": [ - { - "$ref": "#/texts/90" - }, - { - "$ref": "#/texts/91" - }, - { - "$ref": "#/texts/92" - }, - { - "$ref": "#/texts/93" - }, - { - "$ref": "#/texts/94" - }, { "$ref": "#/texts/95" }, @@ -380,13 +381,18 @@ }, { "$ref": "#/texts/101" - }, - { - "$ref": "#/texts/102" - }, - { - "$ref": "#/texts/103" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/8", + "parent": { + "$ref": "#/texts/103" + }, + "children": [ { "$ref": "#/texts/104" }, @@ -407,10 +413,18 @@ }, { "$ref": "#/texts/110" - }, - { - "$ref": "#/texts/111" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/9", + "parent": { + "$ref": "#/texts/103" + }, + "children": [ { "$ref": "#/texts/112" }, @@ -437,18 +451,13 @@ }, { "$ref": "#/texts/120" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/9", - "parent": { - "$ref": "#/texts/122" - }, - "children": [ + }, + { + "$ref": "#/texts/121" + }, + { + "$ref": "#/texts/122" + }, { "$ref": "#/texts/123" }, @@ -493,6 +502,21 @@ }, { "$ref": "#/texts/137" + }, + { + "$ref": "#/texts/138" + }, + { + "$ref": "#/texts/139" + }, + { + "$ref": "#/texts/140" + }, + { + "$ref": "#/texts/141" + }, + { + "$ref": "#/texts/142" } ], "content_layer": "body", @@ -502,35 +526,17 @@ { "self_ref": "#/groups/10", "parent": { - "$ref": "#/texts/138" + "$ref": "#/texts/144" }, "children": [ { - "$ref": "#/texts/139" + "$ref": "#/texts/145" }, { - "$ref": "#/texts/140" + "$ref": "#/texts/146" }, { - "$ref": "#/texts/141" - }, - { - "$ref": "#/texts/142" - }, - { - "$ref": "#/texts/143" - }, - { - "$ref": "#/texts/144" - }, - { - "$ref": "#/texts/145" - }, - { - "$ref": "#/texts/146" - }, - { - "$ref": "#/texts/147" + "$ref": "#/texts/147" }, { "$ref": "#/texts/148" @@ -567,12 +573,6 @@ }, { "$ref": "#/texts/159" - }, - { - "$ref": "#/texts/160" - }, - { - "$ref": "#/texts/161" } ], "content_layer": "body", @@ -582,9 +582,15 @@ { "self_ref": "#/groups/11", "parent": { - "$ref": "#/texts/138" + "$ref": "#/texts/160" }, "children": [ + { + "$ref": "#/texts/161" + }, + { + "$ref": "#/texts/162" + }, { "$ref": "#/texts/163" }, @@ -647,12 +653,6 @@ }, { "$ref": "#/texts/183" - }, - { - "$ref": "#/texts/184" - }, - { - "$ref": "#/texts/185" } ], "content_layer": "body", @@ -662,9 +662,21 @@ { "self_ref": "#/groups/12", "parent": { - "$ref": "#/texts/186" + "$ref": "#/texts/160" }, "children": [ + { + "$ref": "#/texts/185" + }, + { + "$ref": "#/texts/186" + }, + { + "$ref": "#/texts/187" + }, + { + "$ref": "#/texts/188" + }, { "$ref": "#/texts/189" }, @@ -679,18 +691,7 @@ }, { "$ref": "#/texts/193" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/13", - "parent": { - "$ref": "#/texts/186" - }, - "children": [ + }, { "$ref": "#/texts/194" }, @@ -732,15 +733,6 @@ }, { "$ref": "#/texts/207" - }, - { - "$ref": "#/texts/208" - }, - { - "$ref": "#/texts/209" - }, - { - "$ref": "#/texts/210" } ], "content_layer": "body", @@ -748,9 +740,9 @@ "label": "inline" }, { - "self_ref": "#/groups/14", + "self_ref": "#/groups/13", "parent": { - "$ref": "#/texts/186" + "$ref": "#/texts/208" }, "children": [ { @@ -767,7 +759,18 @@ }, { "$ref": "#/texts/215" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/14", + "parent": { + "$ref": "#/texts/208" + }, + "children": [ { "$ref": "#/texts/216" }, @@ -779,18 +782,10 @@ }, { "$ref": "#/texts/219" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/15", - "parent": { - "$ref": "#/texts/220" - }, - "children": [ + }, + { + "$ref": "#/texts/220" + }, { "$ref": "#/texts/221" }, @@ -823,6 +818,9 @@ }, { "$ref": "#/texts/231" + }, + { + "$ref": "#/texts/232" } ], "content_layer": "body", @@ -830,11 +828,23 @@ "label": "inline" }, { - "self_ref": "#/groups/16", + "self_ref": "#/groups/15", "parent": { - "$ref": "#/texts/236" + "$ref": "#/texts/208" }, "children": [ + { + "$ref": "#/texts/233" + }, + { + "$ref": "#/texts/234" + }, + { + "$ref": "#/texts/235" + }, + { + "$ref": "#/texts/236" + }, { "$ref": "#/texts/237" }, @@ -849,10 +859,18 @@ }, { "$ref": "#/texts/241" - }, - { - "$ref": "#/texts/242" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/16", + "parent": { + "$ref": "#/texts/242" + }, + "children": [ { "$ref": "#/texts/243" }, @@ -894,21 +912,9 @@ { "self_ref": "#/groups/17", "parent": { - "$ref": "#/texts/236" + "$ref": "#/texts/258" }, "children": [ - { - "$ref": "#/texts/255" - }, - { - "$ref": "#/texts/256" - }, - { - "$ref": "#/texts/257" - }, - { - "$ref": "#/texts/258" - }, { "$ref": "#/texts/259" }, @@ -959,10 +965,18 @@ }, { "$ref": "#/texts/275" - }, - { - "$ref": "#/texts/276" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/18", + "parent": { + "$ref": "#/texts/258" + }, + "children": [ { "$ref": "#/texts/277" }, @@ -983,18 +997,7 @@ }, { "$ref": "#/texts/283" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/18", - "parent": { - "$ref": "#/texts/236" - }, - "children": [ + }, { "$ref": "#/texts/284" }, @@ -1021,18 +1024,7 @@ }, { "$ref": "#/texts/292" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/19", - "parent": { - "$ref": "#/texts/236" - }, - "children": [ + }, { "$ref": "#/texts/293" }, @@ -1078,11 +1070,14 @@ "label": "inline" }, { - "self_ref": "#/groups/20", + "self_ref": "#/groups/19", "parent": { - "$ref": "#/texts/306" + "$ref": "#/texts/258" }, "children": [ + { + "$ref": "#/texts/306" + }, { "$ref": "#/texts/307" }, @@ -1106,7 +1101,18 @@ }, { "$ref": "#/texts/314" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/20", + "parent": { + "$ref": "#/texts/258" + }, + "children": [ { "$ref": "#/texts/315" }, @@ -1121,18 +1127,10 @@ }, { "$ref": "#/texts/319" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/21", - "parent": { - "$ref": "#/texts/306" - }, - "children": [ + }, + { + "$ref": "#/texts/320" + }, { "$ref": "#/texts/321" }, @@ -1153,10 +1151,18 @@ }, { "$ref": "#/texts/327" - }, - { - "$ref": "#/texts/328" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/21", + "parent": { + "$ref": "#/texts/328" + }, + "children": [ { "$ref": "#/texts/329" }, @@ -1171,18 +1177,10 @@ }, { "$ref": "#/texts/333" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/22", - "parent": { - "$ref": "#/texts/334" - }, - "children": [ + }, + { + "$ref": "#/texts/334" + }, { "$ref": "#/texts/335" }, @@ -1203,12 +1201,20 @@ }, { "$ref": "#/texts/341" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/22", + "parent": { + "$ref": "#/texts/328" + }, + "children": [ { - "$ref": "#/texts/342" - }, - { - "$ref": "#/texts/343" + "$ref": "#/texts/343" }, { "$ref": "#/texts/344" @@ -1245,10 +1251,18 @@ }, { "$ref": "#/texts/355" - }, - { - "$ref": "#/texts/356" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/23", + "parent": { + "$ref": "#/texts/356" + }, + "children": [ { "$ref": "#/texts/357" }, @@ -1287,18 +1301,10 @@ }, { "$ref": "#/texts/369" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/23", - "parent": { - "$ref": "#/texts/334" - }, - "children": [ + }, + { + "$ref": "#/texts/370" + }, { "$ref": "#/texts/371" }, @@ -1325,18 +1331,16 @@ }, { "$ref": "#/texts/379" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/24", - "parent": { - "$ref": "#/texts/381" - }, - "children": [ + }, + { + "$ref": "#/texts/380" + }, + { + "$ref": "#/texts/381" + }, + { + "$ref": "#/texts/382" + }, { "$ref": "#/texts/383" }, @@ -1363,10 +1367,18 @@ }, { "$ref": "#/texts/391" - }, - { - "$ref": "#/texts/392" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/24", + "parent": { + "$ref": "#/texts/356" + }, + "children": [ { "$ref": "#/texts/393" }, @@ -1387,6 +1399,12 @@ }, { "$ref": "#/texts/399" + }, + { + "$ref": "#/texts/400" + }, + { + "$ref": "#/texts/401" } ], "content_layer": "body", @@ -1396,35 +1414,15 @@ { "self_ref": "#/groups/25", "parent": { - "$ref": "#/texts/400" + "$ref": "#/texts/403" }, "children": [ { - "$ref": "#/texts/401" - }, - { - "$ref": "#/texts/402" - }, - { - "$ref": "#/texts/403" + "$ref": "#/texts/405" }, { - "$ref": "#/texts/404" + "$ref": "#/texts/406" }, - { - "$ref": "#/texts/405" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/26", - "parent": { - "$ref": "#/texts/406" - }, - "children": [ { "$ref": "#/texts/407" }, @@ -1469,12 +1467,6 @@ }, { "$ref": "#/texts/421" - }, - { - "$ref": "#/texts/422" - }, - { - "$ref": "#/texts/423" } ], "content_layer": "body", @@ -1482,11 +1474,14 @@ "label": "inline" }, { - "self_ref": "#/groups/27", + "self_ref": "#/groups/26", "parent": { - "$ref": "#/texts/406" + "$ref": "#/texts/422" }, "children": [ + { + "$ref": "#/texts/423" + }, { "$ref": "#/texts/424" }, @@ -1498,10 +1493,18 @@ }, { "$ref": "#/texts/427" - }, - { - "$ref": "#/texts/428" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/27", + "parent": { + "$ref": "#/texts/428" + }, + "children": [ { "$ref": "#/texts/429" }, @@ -1531,18 +1534,10 @@ }, { "$ref": "#/texts/438" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/28", - "parent": { - "$ref": "#/texts/439" - }, - "children": [ + }, + { + "$ref": "#/texts/439" + }, { "$ref": "#/texts/440" }, @@ -1560,9 +1555,6 @@ }, { "$ref": "#/texts/445" - }, - { - "$ref": "#/texts/446" } ], "content_layer": "body", @@ -1570,11 +1562,23 @@ "label": "inline" }, { - "self_ref": "#/groups/29", + "self_ref": "#/groups/28", "parent": { - "$ref": "#/texts/449" + "$ref": "#/texts/428" }, "children": [ + { + "$ref": "#/texts/446" + }, + { + "$ref": "#/texts/447" + }, + { + "$ref": "#/texts/448" + }, + { + "$ref": "#/texts/449" + }, { "$ref": "#/texts/450" }, @@ -1607,10 +1611,18 @@ }, { "$ref": "#/texts/460" - }, - { - "$ref": "#/texts/461" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/29", + "parent": { + "$ref": "#/texts/461" + }, + "children": [ { "$ref": "#/texts/462" }, @@ -1631,16 +1643,18 @@ }, { "$ref": "#/texts/468" - }, - { - "$ref": "#/texts/469" - }, - { - "$ref": "#/texts/470" - }, - { - "$ref": "#/texts/471" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/30", + "parent": { + "$ref": "#/texts/471" + }, + "children": [ { "$ref": "#/texts/472" }, @@ -1802,6 +1816,72 @@ }, { "$ref": "#/texts/525" + }, + { + "$ref": "#/texts/526" + }, + { + "$ref": "#/texts/527" + }, + { + "$ref": "#/texts/528" + }, + { + "$ref": "#/texts/529" + }, + { + "$ref": "#/texts/530" + }, + { + "$ref": "#/texts/531" + }, + { + "$ref": "#/texts/532" + }, + { + "$ref": "#/texts/533" + }, + { + "$ref": "#/texts/534" + }, + { + "$ref": "#/texts/535" + }, + { + "$ref": "#/texts/536" + }, + { + "$ref": "#/texts/537" + }, + { + "$ref": "#/texts/538" + }, + { + "$ref": "#/texts/539" + }, + { + "$ref": "#/texts/540" + }, + { + "$ref": "#/texts/541" + }, + { + "$ref": "#/texts/542" + }, + { + "$ref": "#/texts/543" + }, + { + "$ref": "#/texts/544" + }, + { + "$ref": "#/texts/545" + }, + { + "$ref": "#/texts/546" + }, + { + "$ref": "#/texts/547" } ], "content_layer": "body", @@ -1826,22 +1906,22 @@ "$ref": "#/texts/3" }, { - "$ref": "#/texts/5" + "$ref": "#/texts/27" }, { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, { - "$ref": "#/texts/439" + "$ref": "#/texts/461" }, { - "$ref": "#/texts/447" + "$ref": "#/texts/469" }, { - "$ref": "#/texts/449" + "$ref": "#/texts/471" } ], "content_layer": "body", @@ -1881,7 +1961,7 @@ }, "children": [ { - "$ref": "#/texts/4" + "$ref": "#/groups/0" } ], "content_layer": "body", @@ -1892,37 +1972,378 @@ "level": 1 }, { - "self_ref": "#/texts/4", + "self_ref": "#/texts/4", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO", + "text": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO" + }, + { + "self_ref": "#/texts/5", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "2", + "text": "2", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "sub" + } + }, + { + "self_ref": "#/texts/6", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ") equivalents (CO", + "text": ") equivalents (CO" + }, + { + "self_ref": "#/texts/7", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "2", + "text": "2", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "sub" + } + }, + { + "self_ref": "#/texts/8", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "e) (kg energy-corrected milk (ECM))", + "text": "e) (kg energy-corrected milk (ECM))" + }, + { + "self_ref": "#/texts/9", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "-1", + "text": "-1", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "super" + } + }, + { + "self_ref": "#/texts/10", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ", encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation", + "text": ", encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation" + }, + { + "self_ref": "#/texts/11", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "-1", + "text": "-1", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "super" + } + }, + { + "self_ref": "#/texts/12", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ". The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)", + "text": ". The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)" + }, + { + "self_ref": "#/texts/13", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "ad libitum", + "text": "ad libitum", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/14", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "intake, 75, and 50% of", + "text": "intake, 75, and 50% of" + }, + { + "self_ref": "#/texts/15", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "ad libitum", + "text": "ad libitum", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/16", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO", + "text": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO" + }, + { + "self_ref": "#/texts/17", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "2", + "text": "2", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "sub" + } + }, + { + "self_ref": "#/texts/18", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "e (kg ECM)", + "text": "e (kg ECM)" + }, + { + "self_ref": "#/texts/19", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "-1", + "text": "-1", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "super" + } + }, + { + "self_ref": "#/texts/20", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ". Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO", + "text": ". Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO" + }, + { + "self_ref": "#/texts/21", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "2", + "text": "2", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "sub" + } + }, + { + "self_ref": "#/texts/22", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "e (kg ECM)", + "text": "e (kg ECM)" + }, + { + "self_ref": "#/texts/23", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "-1", + "text": "-1", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "super" + } + }, + { + "self_ref": "#/texts/24", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "in scenarios including pastures compared to", + "text": "in scenarios including pastures compared to" + }, + { + "self_ref": "#/texts/25", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "ad libitum", + "text": "ad libitum", + "formatting": { + "bold": false, + "italic": true, + "underline": false, + "strikethrough": false, + "script": "baseline" + } + }, + { + "self_ref": "#/texts/26", "parent": { - "$ref": "#/texts/3" + "$ref": "#/groups/0" }, "children": [], "content_layer": "body", "label": "text", "prov": [], - "orig": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2) equivalents (CO2e) (kg energy-corrected milk (ECM))-1, encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1. The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) ad libitum intake, 75, and 50% of ad libitum TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1. Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1 in scenarios including pastures compared to ad libitum TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent.", - "text": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2) equivalents (CO2e) (kg energy-corrected milk (ECM))-1, encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1. The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) ad libitum intake, 75, and 50% of ad libitum TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1. Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1 in scenarios including pastures compared to ad libitum TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent." + "orig": "TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent.", + "text": "TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent." }, { - "self_ref": "#/texts/5", + "self_ref": "#/texts/27", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, { - "$ref": "#/groups/1" + "$ref": "#/groups/2" }, { - "$ref": "#/texts/18" + "$ref": "#/texts/40" }, { - "$ref": "#/texts/19" + "$ref": "#/texts/41" }, { - "$ref": "#/texts/20" + "$ref": "#/texts/42" } ], "content_layer": "body", @@ -1933,9 +2354,9 @@ "level": 1 }, { - "self_ref": "#/texts/6", + "self_ref": "#/texts/28", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", @@ -1945,9 +2366,9 @@ "text": "Greenhouse gas (GHG) emissions from livestock activities represent 10–12% of global emissions [1], ranging from 5.5–7.5 Gt CO" }, { - "self_ref": "#/texts/7", + "self_ref": "#/texts/29", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", @@ -1964,9 +2385,9 @@ } }, { - "self_ref": "#/texts/8", + "self_ref": "#/texts/30", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", @@ -1976,9 +2397,9 @@ "text": "equivalents (CO" }, { - "self_ref": "#/texts/9", + "self_ref": "#/texts/31", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", @@ -1995,9 +2416,9 @@ } }, { - "self_ref": "#/texts/10", + "self_ref": "#/texts/32", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", @@ -2007,9 +2428,9 @@ "text": "e) yr" }, { - "self_ref": "#/texts/11", + "self_ref": "#/texts/33", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", @@ -2026,9 +2447,9 @@ } }, { - "self_ref": "#/texts/12", + "self_ref": "#/texts/34", "parent": { - "$ref": "#/groups/0" + "$ref": "#/groups/1" }, "children": [], "content_layer": "body", @@ -2038,9 +2459,9 @@ "text": ", with almost 30% coming from dairy cattle production systems [2]. However, the livestock sector supply between 13 and 17% of calories and between 28 and 33% of human edible protein consumption globally [3]. Additionally, livestock produce more human-edible protein per unit area than crops when land is unsuitable for food crop production [4]." }, { - "self_ref": "#/texts/13", + "self_ref": "#/texts/35", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -2050,9 +2471,9 @@ "text": "Considering the key role of livestock systems in global food security, several technical and management interventions have been investigated to mitigate methane (CH" }, { - "self_ref": "#/texts/14", + "self_ref": "#/texts/36", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -2069,9 +2490,9 @@ } }, { - "self_ref": "#/texts/15", + "self_ref": "#/texts/37", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -2081,9 +2502,9 @@ "text": ") emissions from enteric fermentation [5], animal management [6] and manure management [7]. CH" }, { - "self_ref": "#/texts/16", + "self_ref": "#/texts/38", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -2100,9 +2521,9 @@ } }, { - "self_ref": "#/texts/17", + "self_ref": "#/texts/39", "parent": { - "$ref": "#/groups/1" + "$ref": "#/groups/2" }, "children": [], "content_layer": "body", @@ -2112,9 +2533,9 @@ "text": "emissions from enteric fermentation represents around 34% of total emissions from livestock sector, which is the largest source [2]. Increasing proportions of concentrate and digestibility of forages in the diet have been proposed as mitigation strategies [1,5]. In contrast, some life cycle assessment (LCA) studies of dairy systems in temperate regions [8–11] have identified that increasing concentrate proportion may increase carbon (C) footprint due to greater resource use and pollutants from the production of feed compared to forage. Thus, increasing pasture proportion on dairy cattle systems may be an alternative management to mitigate the C footprint." }, { - "self_ref": "#/texts/18", + "self_ref": "#/texts/40", "parent": { - "$ref": "#/texts/5" + "$ref": "#/texts/27" }, "children": [], "content_layer": "body", @@ -2124,9 +2545,9 @@ "text": "In subtropical climate zones, cows may graze tropical pastures rather than temperate pastures during the warm season [12]. Some important dairy production areas, such as southern Brazil, central to northern Argentina, Uruguay, South Africa, New Zealand and Australia, are located in these climate zones, having more than 900 million ha in native, permanent or temporary pastures, producing almost 20% of global milk production [13]. However, due to a considerable inter-annual variation in pasture growth rates [14,15], the interest in mixed systems, using total mixed ration (TMR) + pasture has been increasing [16]. Nevertheless, to our best knowledge, studies conducted to evaluate milk production response in dairy cow diets receiving TMR and pastures have only been conducted in temperate pastures and not in tropical pastures (e.g. [17–19])." }, { - "self_ref": "#/texts/19", + "self_ref": "#/texts/41", "parent": { - "$ref": "#/texts/5" + "$ref": "#/texts/27" }, "children": [], "content_layer": "body", @@ -2136,9 +2557,9 @@ "text": "It has been shown that dairy cows receiving TMR-based diets may not decrease milk production when supplemented with temperate pastures in a vegetative growth stage [18]. On the other hand, tropical pastures have lower organic matter digestibility and cows experience reduced dry matter (DM) intake and milk yield compared to temperate pastures [20,21]. A lower milk yield increases the C footprint intensity [22], offsetting an expected advantage through lower GHG emissions from crop and reduced DM intake." }, { - "self_ref": "#/texts/20", + "self_ref": "#/texts/42", "parent": { - "$ref": "#/texts/5" + "$ref": "#/texts/27" }, "children": [], "content_layer": "body", @@ -2148,43 +2569,43 @@ "text": "The aim of this work was to quantify the C footprint and land use of dairy systems using cows with a medium milk production potential in a subtropical region. The effect of replacing total mixed ration (TMR) with pastures during lactation periods was evaluated." }, { - "self_ref": "#/texts/21", + "self_ref": "#/texts/43", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/groups/2" + "$ref": "#/groups/3" }, { - "$ref": "#/texts/25" + "$ref": "#/texts/47" }, { - "$ref": "#/texts/28" + "$ref": "#/texts/50" }, { - "$ref": "#/texts/32" + "$ref": "#/texts/54" }, { - "$ref": "#/texts/51" + "$ref": "#/texts/73" }, { - "$ref": "#/texts/71" + "$ref": "#/texts/93" }, { - "$ref": "#/texts/122" + "$ref": "#/texts/144" }, { - "$ref": "#/texts/138" + "$ref": "#/texts/160" }, { - "$ref": "#/texts/186" + "$ref": "#/texts/208" }, { - "$ref": "#/texts/220" + "$ref": "#/texts/242" }, { - "$ref": "#/texts/232" + "$ref": "#/texts/254" } ], "content_layer": "body", @@ -2195,9 +2616,9 @@ "level": 1 }, { - "self_ref": "#/texts/22", + "self_ref": "#/texts/44", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -2207,9 +2628,9 @@ "text": "An LCA was developed according to the ISO standards [23,24] and Food and Agriculture Organization of the United Nations (FAO) Livestock Environmental Assessment Protocol guidelines [25]. All procedures were approved by the ‘Comissão de Ética no Uso de Animais’ (CEUA/UDESC) on September 15, 2016—Approval number 4373090816 -" }, { - "self_ref": "#/texts/23", + "self_ref": "#/texts/45", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -2220,9 +2641,9 @@ "hyperlink": "https://www.udesc.br/cav/ceua" }, { - "self_ref": "#/texts/24", + "self_ref": "#/texts/46", "parent": { - "$ref": "#/groups/2" + "$ref": "#/groups/3" }, "children": [], "content_layer": "body", @@ -2232,13 +2653,13 @@ "text": "." }, { - "self_ref": "#/texts/25", + "self_ref": "#/texts/47", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/26" + "$ref": "#/texts/48" }, { "$ref": "#/pictures/0" @@ -2252,9 +2673,9 @@ "level": 2 }, { - "self_ref": "#/texts/26", + "self_ref": "#/texts/48", "parent": { - "$ref": "#/texts/25" + "$ref": "#/texts/47" }, "children": [], "content_layer": "body", @@ -2264,7 +2685,7 @@ "text": "The goal of the study was to assess the C footprint of annual tropical and temperate pastures in lactating dairy cow diets. The production system was divided into four main processes: (i) animal husbandry, (ii) manure management and urine and dung deposited by grazing animals, (iii) production of feed ingredients and (iv) farm management (Fig 1). The study boundary included all processes up to the animal farm gate (cradle to gate), including secondary sources such as GHG emissions during the production of fuel, electricity, machinery, manufacturing of fertilizer, pesticides, seeds and plastic used in silage production. Fuel combustion and machinery (manufacture and repairs) for manure handling and electricity for milking and confinement were accounted as emissions from farm management. Emissions post milk production were assumed to be similar for all scenarios, therefore, activities including milk processing, distribution, retail or consumption were outside of the system boundary." }, { - "self_ref": "#/texts/27", + "self_ref": "#/texts/49", "parent": { "$ref": "#/body" }, @@ -2276,16 +2697,16 @@ "text": "Fig 1 Overview of the milk production system boundary considered in the study." }, { - "self_ref": "#/texts/28", + "self_ref": "#/texts/50", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/29" + "$ref": "#/texts/51" }, { - "$ref": "#/texts/30" + "$ref": "#/texts/52" }, { "$ref": "#/tables/0" @@ -2299,9 +2720,9 @@ "level": 2 }, { - "self_ref": "#/texts/29", + "self_ref": "#/texts/51", "parent": { - "$ref": "#/texts/28" + "$ref": "#/texts/50" }, "children": [], "content_layer": "body", @@ -2311,9 +2732,9 @@ "text": "The functional unit was one kilogram of energy-corrected milk (ECM) at the farm gate. All processes in the system were calculated based on one kilogram ECM. The ECM was calculated by multiplying milk production by the ratio of the energy content of the milk to the energy content of standard milk with 4% fat and 3.3% true protein according to NRC [20] as follows:" }, { - "self_ref": "#/texts/30", + "self_ref": "#/texts/52", "parent": { - "$ref": "#/texts/28" + "$ref": "#/texts/50" }, "children": [], "content_layer": "body", @@ -2323,7 +2744,7 @@ "text": "ECM = Milk production × (0.0929 × fat% + 0.0588× true protein% + 0.192) / (0.0929 × (4%) + 0.0588 × (3.3%) + 0.192), where fat% and protein% are fat and protein percentages in milk, respectively. The average milk production and composition were recorded from the University of Santa Catarina State (Brazil) herd, considering 165 lactations between 2009 and 2018. The herd is predominantly Holstein × Jersey cows, with key characteristics described in Table 1." }, { - "self_ref": "#/texts/31", + "self_ref": "#/texts/53", "parent": { "$ref": "#/body" }, @@ -2335,16 +2756,16 @@ "text": "Table 1 Descriptive characteristics of the herd." }, { - "self_ref": "#/texts/32", + "self_ref": "#/texts/54", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, { - "$ref": "#/groups/4" + "$ref": "#/groups/5" } ], "content_layer": "body", @@ -2355,9 +2776,9 @@ "level": 2 }, { - "self_ref": "#/texts/33", + "self_ref": "#/texts/55", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2367,9 +2788,9 @@ "text": "The individual feed requirements, as well as the milk production responses based on feed strategies were based on data recorded from the herd described above and two experiments performed using lactating cows from the same herd. Due to the variation on herbage production throughout the year, feed requirements were estimated taking into consideration that livestock systems have a calving period in April, which represents the beginning of fall season in the southern Hemisphere. The experiments have shown a 10% reduction in ECM production in dairy cows that received both 75 and 50% of" }, { - "self_ref": "#/texts/34", + "self_ref": "#/texts/56", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2386,9 +2807,9 @@ } }, { - "self_ref": "#/texts/35", + "self_ref": "#/texts/57", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2398,9 +2819,9 @@ "text": "TMR intake with access to grazing a tropical pasture (pearl-millet," }, { - "self_ref": "#/texts/36", + "self_ref": "#/texts/58", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2417,9 +2838,9 @@ } }, { - "self_ref": "#/texts/37", + "self_ref": "#/texts/59", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2429,9 +2850,9 @@ "text": "‘Campeiro’) compared to cows receiving" }, { - "self_ref": "#/texts/38", + "self_ref": "#/texts/60", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2448,9 +2869,9 @@ } }, { - "self_ref": "#/texts/39", + "self_ref": "#/texts/61", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2460,9 +2881,9 @@ "text": "TMR intake. Cows grazing on a temperate pasture (ryegrass," }, { - "self_ref": "#/texts/40", + "self_ref": "#/texts/62", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2479,9 +2900,9 @@ } }, { - "self_ref": "#/texts/41", + "self_ref": "#/texts/63", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2491,9 +2912,9 @@ "text": "‘Maximus’) did not need changes to ECM production compared to the" }, { - "self_ref": "#/texts/42", + "self_ref": "#/texts/64", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2510,9 +2931,9 @@ } }, { - "self_ref": "#/texts/43", + "self_ref": "#/texts/65", "parent": { - "$ref": "#/groups/3" + "$ref": "#/groups/4" }, "children": [], "content_layer": "body", @@ -2522,9 +2943,9 @@ "text": "TMR intake group." }, { - "self_ref": "#/texts/44", + "self_ref": "#/texts/66", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -2534,9 +2955,9 @@ "text": "Using experimental data, three scenarios were evaluated during the lactation period:" }, { - "self_ref": "#/texts/45", + "self_ref": "#/texts/67", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -2553,9 +2974,9 @@ } }, { - "self_ref": "#/texts/46", + "self_ref": "#/texts/68", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -2565,9 +2986,9 @@ "text": "TMR intake, and 75, and 50% of" }, { - "self_ref": "#/texts/47", + "self_ref": "#/texts/69", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -2584,9 +3005,9 @@ } }, { - "self_ref": "#/texts/48", + "self_ref": "#/texts/70", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -2596,9 +3017,9 @@ "text": "TMR intake with access to grazing either an annual tropical or temperate pasture as a function of month ([26], Civiero et al.," }, { - "self_ref": "#/texts/49", + "self_ref": "#/texts/71", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -2615,9 +3036,9 @@ } }, { - "self_ref": "#/texts/50", + "self_ref": "#/texts/72", "parent": { - "$ref": "#/groups/4" + "$ref": "#/groups/5" }, "children": [], "content_layer": "body", @@ -2627,13 +3048,13 @@ "text": "). From April to October (210 days) cows accessed an annual temperate pasture (ryegrass), and from November to beginning of February (95 days) cows grazed an annual tropical pasture (pearl-millet). The average annual reduction in ECM production in dairy cows with access to pastures is 3%. This value was assumed during an entire lactation period." }, { - "self_ref": "#/texts/51", + "self_ref": "#/texts/73", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/groups/5" + "$ref": "#/groups/6" } ], "content_layer": "body", @@ -2644,9 +3065,9 @@ "level": 2 }, { - "self_ref": "#/texts/52", + "self_ref": "#/texts/74", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2656,9 +3077,9 @@ "text": "The CO" }, { - "self_ref": "#/texts/53", + "self_ref": "#/texts/75", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2675,9 +3096,9 @@ } }, { - "self_ref": "#/texts/54", + "self_ref": "#/texts/76", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2687,9 +3108,9 @@ "text": "e emissions were calculated by multiplying the emissions of CO" }, { - "self_ref": "#/texts/55", + "self_ref": "#/texts/77", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2706,9 +3127,9 @@ } }, { - "self_ref": "#/texts/56", + "self_ref": "#/texts/78", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2718,9 +3139,9 @@ "text": ", CH" }, { - "self_ref": "#/texts/57", + "self_ref": "#/texts/79", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2737,9 +3158,9 @@ } }, { - "self_ref": "#/texts/58", + "self_ref": "#/texts/80", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2749,9 +3170,9 @@ "text": "and N" }, { - "self_ref": "#/texts/59", + "self_ref": "#/texts/81", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2768,9 +3189,9 @@ } }, { - "self_ref": "#/texts/60", + "self_ref": "#/texts/82", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2780,9 +3201,9 @@ "text": "O by their 100-year global warming potential (GWP" }, { - "self_ref": "#/texts/61", + "self_ref": "#/texts/83", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2799,9 +3220,9 @@ } }, { - "self_ref": "#/texts/62", + "self_ref": "#/texts/84", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2811,9 +3232,9 @@ "text": "), based on IPCC assessment report 5 (AR5; [27]). The values of GWP" }, { - "self_ref": "#/texts/63", + "self_ref": "#/texts/85", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2830,9 +3251,9 @@ } }, { - "self_ref": "#/texts/64", + "self_ref": "#/texts/86", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2842,9 +3263,9 @@ "text": "are 1, 28 and 265 for CO" }, { - "self_ref": "#/texts/65", + "self_ref": "#/texts/87", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2861,9 +3282,9 @@ } }, { - "self_ref": "#/texts/66", + "self_ref": "#/texts/88", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2873,9 +3294,9 @@ "text": ", CH" }, { - "self_ref": "#/texts/67", + "self_ref": "#/texts/89", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2892,9 +3313,9 @@ } }, { - "self_ref": "#/texts/68", + "self_ref": "#/texts/90", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2904,9 +3325,9 @@ "text": "and N" }, { - "self_ref": "#/texts/69", + "self_ref": "#/texts/91", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2923,9 +3344,9 @@ } }, { - "self_ref": "#/texts/70", + "self_ref": "#/texts/92", "parent": { - "$ref": "#/groups/5" + "$ref": "#/groups/6" }, "children": [], "content_layer": "body", @@ -2935,16 +3356,16 @@ "text": "O, respectively." }, { - "self_ref": "#/texts/71", + "self_ref": "#/texts/93", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/72" + "$ref": "#/texts/94" }, { - "$ref": "#/texts/81" + "$ref": "#/texts/103" } ], "content_layer": "body", @@ -2955,13 +3376,13 @@ "level": 2 }, { - "self_ref": "#/texts/72", + "self_ref": "#/texts/94", "parent": { - "$ref": "#/texts/71" + "$ref": "#/texts/93" }, "children": [ { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, { "$ref": "#/tables/1" @@ -2975,9 +3396,9 @@ "level": 3 }, { - "self_ref": "#/texts/73", + "self_ref": "#/texts/95", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -2987,9 +3408,9 @@ "text": "The DM intake of each ingredient throughout the entire life of animals during lactation periods was calculated for each scenario: cows receiving only TMR, cows receiving 75% of TMR with annual pastures and cows receiving 50% of TMR with annual pastures (Table 2). In each of other phases of life (calf, heifer, dry cow), animals received the same diet, including a perennial tropical pasture (kikuyu grass," }, { - "self_ref": "#/texts/74", + "self_ref": "#/texts/96", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -3006,9 +3427,9 @@ } }, { - "self_ref": "#/texts/75", + "self_ref": "#/texts/97", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -3018,9 +3439,9 @@ "text": "). The DM intake of calves, heifers and dry cows was calculated assuming 2.8, 2.5 and 1.9% body weight, respectively [20]. In each case, the actual DM intake of concentrate and corn silage was recorded, and pasture DM intake was estimated by the difference between daily expected DM intake and actual DM intake of concentrate and corn silage. For lactating heifers and cows, TMR was formulated to meet the net energy for lactation (NE" }, { - "self_ref": "#/texts/76", + "self_ref": "#/texts/98", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -3037,9 +3458,9 @@ } }, { - "self_ref": "#/texts/77", + "self_ref": "#/texts/99", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -3049,9 +3470,9 @@ "text": ") and metabolizable protein (MP) requirements of experimental animals, according to [28]. The INRA system was used because it is possible to estimate pasture DM intake taking into account the TMR intake, pasture management and the time of access to pasture using the GrazeIn model [29], which was integrated in the software INRAtion 4.07 (" }, { - "self_ref": "#/texts/78", + "self_ref": "#/texts/100", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -3062,9 +3483,9 @@ "hyperlink": "https://www.inration.educagri.fr/fr/forum.php" }, { - "self_ref": "#/texts/79", + "self_ref": "#/texts/101", "parent": { - "$ref": "#/groups/6" + "$ref": "#/groups/7" }, "children": [], "content_layer": "body", @@ -3074,7 +3495,7 @@ "text": "). The nutrient intake was calculated as a product of TMR and pasture intake and the nutrient contents of TMR and pasture, respectively, which were determined in feed samples collected throughout the experiments." }, { - "self_ref": "#/texts/80", + "self_ref": "#/texts/102", "parent": { "$ref": "#/body" }, @@ -3086,19 +3507,19 @@ "text": "Table 2 Dairy cows’ diets in different scenariosa." }, { - "self_ref": "#/texts/81", + "self_ref": "#/texts/103", "parent": { - "$ref": "#/texts/71" + "$ref": "#/texts/93" }, "children": [ { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, { "$ref": "#/tables/2" }, { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, { "$ref": "#/tables/3" @@ -3112,9 +3533,9 @@ "level": 3 }, { - "self_ref": "#/texts/82", + "self_ref": "#/texts/104", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -3124,9 +3545,9 @@ "text": "GHG emission factors used for off- and on-farm feed production were based on literature values, and are presented in Table 3. The emission factor used for corn grain is the average of emission factors observed in different levels of synthetic N fertilization [30]. The emission factor used for soybean is based on Brazilian soybean production [31]. The emissions used for corn silage, including feed processing (cutting, crushing and mixing), and annual or perennial grass productions were 3300 and 1500 kg CO" }, { - "self_ref": "#/texts/83", + "self_ref": "#/texts/105", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -3143,9 +3564,9 @@ } }, { - "self_ref": "#/texts/84", + "self_ref": "#/texts/106", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -3155,9 +3576,9 @@ "text": "e ha" }, { - "self_ref": "#/texts/85", + "self_ref": "#/texts/107", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -3174,9 +3595,9 @@ } }, { - "self_ref": "#/texts/86", + "self_ref": "#/texts/108", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -3186,9 +3607,9 @@ "text": ", respectively [32]. The DM production (kg ha" }, { - "self_ref": "#/texts/87", + "self_ref": "#/texts/109", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -3205,9 +3626,9 @@ } }, { - "self_ref": "#/texts/88", + "self_ref": "#/texts/110", "parent": { - "$ref": "#/groups/7" + "$ref": "#/groups/8" }, "children": [], "content_layer": "body", @@ -3217,7 +3638,7 @@ "text": ") of corn silage and pastures were based on regional and locally recorded data [33–36], assuming that animals are able to consume 70% of pastures during grazing." }, { - "self_ref": "#/texts/89", + "self_ref": "#/texts/111", "parent": { "$ref": "#/body" }, @@ -3229,9 +3650,9 @@ "text": "Table 3 GHG emission factors for Off- and On-farm feed production." }, { - "self_ref": "#/texts/90", + "self_ref": "#/texts/112", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3241,9 +3662,9 @@ "text": "Emissions from on-farm feed production (corn silage and pasture) were estimated using primary and secondary sources based on the actual amount of each input (Table 4). Primary sources were direct and indirect N" }, { - "self_ref": "#/texts/91", + "self_ref": "#/texts/113", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3260,9 +3681,9 @@ } }, { - "self_ref": "#/texts/92", + "self_ref": "#/texts/114", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3272,9 +3693,9 @@ "text": "O-N emissions from organic and synthetic fertilizers and crop/pasture residues, CO" }, { - "self_ref": "#/texts/93", + "self_ref": "#/texts/115", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3291,9 +3712,9 @@ } }, { - "self_ref": "#/texts/94", + "self_ref": "#/texts/116", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3303,9 +3724,9 @@ "text": "-C emissions from lime and urea applications, as well as fuel combustion. The direct N" }, { - "self_ref": "#/texts/95", + "self_ref": "#/texts/117", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3322,9 +3743,9 @@ } }, { - "self_ref": "#/texts/96", + "self_ref": "#/texts/118", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3334,9 +3755,9 @@ "text": "O-N emission factor (kg (kg N input)" }, { - "self_ref": "#/texts/97", + "self_ref": "#/texts/119", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3353,9 +3774,9 @@ } }, { - "self_ref": "#/texts/98", + "self_ref": "#/texts/120", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3365,9 +3786,9 @@ "text": ") is based on a local study performed previously [37]. For indirect N" }, { - "self_ref": "#/texts/99", + "self_ref": "#/texts/121", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3384,9 +3805,9 @@ } }, { - "self_ref": "#/texts/100", + "self_ref": "#/texts/122", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3396,9 +3817,9 @@ "text": "O-N emissions (kg N" }, { - "self_ref": "#/texts/101", + "self_ref": "#/texts/123", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3415,9 +3836,9 @@ } }, { - "self_ref": "#/texts/102", + "self_ref": "#/texts/124", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3427,9 +3848,9 @@ "text": "O-N (kg NH" }, { - "self_ref": "#/texts/103", + "self_ref": "#/texts/125", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3446,9 +3867,9 @@ } }, { - "self_ref": "#/texts/104", + "self_ref": "#/texts/126", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3458,9 +3879,9 @@ "text": "-N + NO" }, { - "self_ref": "#/texts/105", + "self_ref": "#/texts/127", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3477,9 +3898,9 @@ } }, { - "self_ref": "#/texts/106", + "self_ref": "#/texts/128", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3489,9 +3910,9 @@ "text": ")" }, { - "self_ref": "#/texts/107", + "self_ref": "#/texts/129", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3508,9 +3929,9 @@ } }, { - "self_ref": "#/texts/108", + "self_ref": "#/texts/130", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3520,9 +3941,9 @@ "text": "), as well as CO" }, { - "self_ref": "#/texts/109", + "self_ref": "#/texts/131", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3539,9 +3960,9 @@ } }, { - "self_ref": "#/texts/110", + "self_ref": "#/texts/132", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3551,9 +3972,9 @@ "text": "-C emissions from lime + urea, default values proposed by IPCC [38] were used. For perennial pastures, a C sequestration of 0.57 t ha" }, { - "self_ref": "#/texts/111", + "self_ref": "#/texts/133", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3570,9 +3991,9 @@ } }, { - "self_ref": "#/texts/112", + "self_ref": "#/texts/134", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3582,9 +4003,9 @@ "text": "was used based on a 9-year study conducted in southern Brazil [39]. Due to the use of conventional tillage, no C sequestration was considered for annual pastures. The amount of fuel required was 8.9 (no-tillage) and 14.3 L ha" }, { - "self_ref": "#/texts/113", + "self_ref": "#/texts/135", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3601,9 +4022,9 @@ } }, { - "self_ref": "#/texts/114", + "self_ref": "#/texts/136", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3613,9 +4034,9 @@ "text": "(disking) for annual tropical and temperate pastures, respectively [40]. The CO" }, { - "self_ref": "#/texts/115", + "self_ref": "#/texts/137", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3632,9 +4053,9 @@ } }, { - "self_ref": "#/texts/116", + "self_ref": "#/texts/138", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3644,9 +4065,9 @@ "text": "from fuel combustion was 2.7 kg CO" }, { - "self_ref": "#/texts/117", + "self_ref": "#/texts/139", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3663,9 +4084,9 @@ } }, { - "self_ref": "#/texts/118", + "self_ref": "#/texts/140", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3675,9 +4096,9 @@ "text": "L" }, { - "self_ref": "#/texts/119", + "self_ref": "#/texts/141", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3694,9 +4115,9 @@ } }, { - "self_ref": "#/texts/120", + "self_ref": "#/texts/142", "parent": { - "$ref": "#/groups/8" + "$ref": "#/groups/9" }, "children": [], "content_layer": "body", @@ -3706,7 +4127,7 @@ "text": "[41]. Secondary sources of emissions during the production of fuel, machinery, fertilizer, pesticides, seeds and plastic for ensilage were estimated using emission factors described by Rotz et al. [42]." }, { - "self_ref": "#/texts/121", + "self_ref": "#/texts/143", "parent": { "$ref": "#/body" }, @@ -3718,13 +4139,13 @@ "text": "Table 4 GHG emissions from On-farm feed production." }, { - "self_ref": "#/texts/122", + "self_ref": "#/texts/144", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/groups/9" + "$ref": "#/groups/10" } ], "content_layer": "body", @@ -3735,9 +4156,9 @@ "level": 2 }, { - "self_ref": "#/texts/123", + "self_ref": "#/texts/145", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3747,9 +4168,9 @@ "text": "The CH" }, { - "self_ref": "#/texts/124", + "self_ref": "#/texts/146", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3766,9 +4187,9 @@ } }, { - "self_ref": "#/texts/125", + "self_ref": "#/texts/147", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3778,9 +4199,9 @@ "text": "emissions from enteric fermentation intensity (g (kg ECM)" }, { - "self_ref": "#/texts/126", + "self_ref": "#/texts/148", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3797,9 +4218,9 @@ } }, { - "self_ref": "#/texts/127", + "self_ref": "#/texts/149", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3809,9 +4230,9 @@ "text": ") was a function of estimated CH" }, { - "self_ref": "#/texts/128", + "self_ref": "#/texts/150", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3828,9 +4249,9 @@ } }, { - "self_ref": "#/texts/129", + "self_ref": "#/texts/151", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3840,9 +4261,9 @@ "text": "yield (g (kg DM intake)" }, { - "self_ref": "#/texts/130", + "self_ref": "#/texts/152", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3859,9 +4280,9 @@ } }, { - "self_ref": "#/texts/131", + "self_ref": "#/texts/153", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3871,9 +4292,9 @@ "text": "), actual DM intake and ECM. The enteric CH" }, { - "self_ref": "#/texts/132", + "self_ref": "#/texts/154", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3890,9 +4311,9 @@ } }, { - "self_ref": "#/texts/133", + "self_ref": "#/texts/155", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3902,9 +4323,9 @@ "text": "yield was estimated as a function of neutral detergent fiber (NDF) concentration on total DM intake, as proposed by Niu et al. [43], where: CH" }, { - "self_ref": "#/texts/134", + "self_ref": "#/texts/156", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3921,9 +4342,9 @@ } }, { - "self_ref": "#/texts/135", + "self_ref": "#/texts/157", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3933,9 +4354,9 @@ "text": "yield (g (kg DM intake)" }, { - "self_ref": "#/texts/136", + "self_ref": "#/texts/158", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3952,9 +4373,9 @@ } }, { - "self_ref": "#/texts/137", + "self_ref": "#/texts/159", "parent": { - "$ref": "#/groups/9" + "$ref": "#/groups/10" }, "children": [], "content_layer": "body", @@ -3964,19 +4385,19 @@ "text": ") = 13.8 + 0.185 × NDF (% DM intake)." }, { - "self_ref": "#/texts/138", + "self_ref": "#/texts/160", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, { - "$ref": "#/texts/162" + "$ref": "#/texts/184" }, { - "$ref": "#/groups/11" + "$ref": "#/groups/12" } ], "content_layer": "body", @@ -3987,9 +4408,9 @@ "level": 2 }, { - "self_ref": "#/texts/139", + "self_ref": "#/texts/161", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -3999,9 +4420,9 @@ "text": "The CH" }, { - "self_ref": "#/texts/140", + "self_ref": "#/texts/162", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4018,9 +4439,9 @@ } }, { - "self_ref": "#/texts/141", + "self_ref": "#/texts/163", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4030,9 +4451,9 @@ "text": "emission from manure (kg (kg ECM)" }, { - "self_ref": "#/texts/142", + "self_ref": "#/texts/164", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4049,9 +4470,9 @@ } }, { - "self_ref": "#/texts/143", + "self_ref": "#/texts/165", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4061,9 +4482,9 @@ "text": ") was a function of daily CH" }, { - "self_ref": "#/texts/144", + "self_ref": "#/texts/166", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4080,9 +4501,9 @@ } }, { - "self_ref": "#/texts/145", + "self_ref": "#/texts/167", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4092,9 +4513,9 @@ "text": "emission from manure (kg cow" }, { - "self_ref": "#/texts/146", + "self_ref": "#/texts/168", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4111,9 +4532,9 @@ } }, { - "self_ref": "#/texts/147", + "self_ref": "#/texts/169", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4123,9 +4544,9 @@ "text": ") and daily ECM (kg cow" }, { - "self_ref": "#/texts/148", + "self_ref": "#/texts/170", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4142,9 +4563,9 @@ } }, { - "self_ref": "#/texts/149", + "self_ref": "#/texts/171", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4154,9 +4575,9 @@ "text": "). The daily CH" }, { - "self_ref": "#/texts/150", + "self_ref": "#/texts/172", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4173,9 +4594,9 @@ } }, { - "self_ref": "#/texts/151", + "self_ref": "#/texts/173", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4185,9 +4606,9 @@ "text": "emission from manure was estimated according to IPCC [38], which considered daily volatile solid (VS) excreted (kg DM cow" }, { - "self_ref": "#/texts/152", + "self_ref": "#/texts/174", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4204,9 +4625,9 @@ } }, { - "self_ref": "#/texts/153", + "self_ref": "#/texts/175", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4216,9 +4637,9 @@ "text": ") in manure. The daily VS was estimated as proposed by Eugène et al. [44] as: VS = NDOMI + (UE × GE) × (OM/18.45), where: VS = volatile solid excretion on an organic matter (OM) basis (kg day" }, { - "self_ref": "#/texts/154", + "self_ref": "#/texts/176", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4235,9 +4656,9 @@ } }, { - "self_ref": "#/texts/155", + "self_ref": "#/texts/177", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4247,9 +4668,9 @@ "text": "), NDOMI = non-digestible OM intake (kg day" }, { - "self_ref": "#/texts/156", + "self_ref": "#/texts/178", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4266,9 +4687,9 @@ } }, { - "self_ref": "#/texts/157", + "self_ref": "#/texts/179", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4278,9 +4699,9 @@ "text": "): (1- OM digestibility) × OM intake, UE = urinary energy excretion as a fraction of GE (0.04), GE = gross energy intake (MJ day" }, { - "self_ref": "#/texts/158", + "self_ref": "#/texts/180", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4297,9 +4718,9 @@ } }, { - "self_ref": "#/texts/159", + "self_ref": "#/texts/181", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4309,9 +4730,9 @@ "text": "), OM = organic matter (g), 18.45 = conversion factor for dietary GE per kg of DM (MJ kg" }, { - "self_ref": "#/texts/160", + "self_ref": "#/texts/182", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4328,9 +4749,9 @@ } }, { - "self_ref": "#/texts/161", + "self_ref": "#/texts/183", "parent": { - "$ref": "#/groups/10" + "$ref": "#/groups/11" }, "children": [], "content_layer": "body", @@ -4340,9 +4761,9 @@ "text": ")." }, { - "self_ref": "#/texts/162", + "self_ref": "#/texts/184", "parent": { - "$ref": "#/texts/138" + "$ref": "#/texts/160" }, "children": [], "content_layer": "body", @@ -4352,9 +4773,9 @@ "text": "The OM digestibility was estimated as a function of chemical composition, using equations published by INRA [21], which takes into account the effects of digestive interactions due to feeding level, the proportion of concentrate and rumen protein balance on OM digestibility. For scenarios where cows had access to grazing, the amount of calculated VS were corrected as a function of the time at pasture. The biodegradability of manure factor (0.13 for dairy cows in Latin America) and methane conversion factor (MCF) values were taken from IPCC [38]. The MCF values for pit storage below animal confinements (> 1 month) were used for the calculation, taking into account the annual average temperature (16.6ºC) or the average temperatures during the growth period of temperate (14.4ºC) or tropical (21ºC) annual pastures, which were 31%, 26% and 46%, respectively." }, { - "self_ref": "#/texts/163", + "self_ref": "#/texts/185", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4364,9 +4785,9 @@ "text": "The N" }, { - "self_ref": "#/texts/164", + "self_ref": "#/texts/186", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4383,9 +4804,9 @@ } }, { - "self_ref": "#/texts/165", + "self_ref": "#/texts/187", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4395,9 +4816,9 @@ "text": "O-N emissions from urine and feces were estimated considering the proportion of N excreted as manure and storage or as urine and dung deposited by grazing animals. These proportions were calculated based on the proportion of daily time that animals stayed on pasture (7 h/24 h = 0.29) or confinement (1−0.29 = 0.71). For lactating heifers and cows, the total amount of N excreted was calculated by the difference between N intake and milk N excretion. For heifers and non-lactating cows, urinary and fecal N excretion were estimated as proposed by Reed et al. [45] (Table 3: equations 10 and 12, respectively). The N" }, { - "self_ref": "#/texts/166", + "self_ref": "#/texts/188", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4414,9 +4835,9 @@ } }, { - "self_ref": "#/texts/167", + "self_ref": "#/texts/189", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4426,9 +4847,9 @@ "text": "O emissions from stored manure as well as urine and dung during grazing were calculated based on the conversion of N" }, { - "self_ref": "#/texts/168", + "self_ref": "#/texts/190", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4445,9 +4866,9 @@ } }, { - "self_ref": "#/texts/169", + "self_ref": "#/texts/191", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4457,9 +4878,9 @@ "text": "O-N emissions to N" }, { - "self_ref": "#/texts/170", + "self_ref": "#/texts/192", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4476,9 +4897,9 @@ } }, { - "self_ref": "#/texts/171", + "self_ref": "#/texts/193", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4488,9 +4909,9 @@ "text": "O emissions, where N" }, { - "self_ref": "#/texts/172", + "self_ref": "#/texts/194", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4507,9 +4928,9 @@ } }, { - "self_ref": "#/texts/173", + "self_ref": "#/texts/195", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4519,9 +4940,9 @@ "text": "O emissions = N" }, { - "self_ref": "#/texts/174", + "self_ref": "#/texts/196", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4538,9 +4959,9 @@ } }, { - "self_ref": "#/texts/175", + "self_ref": "#/texts/197", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4550,9 +4971,9 @@ "text": "O-N emissions × 44/28. The emission factors were 0.002 kg N" }, { - "self_ref": "#/texts/176", + "self_ref": "#/texts/198", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4569,9 +4990,9 @@ } }, { - "self_ref": "#/texts/177", + "self_ref": "#/texts/199", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4581,9 +5002,9 @@ "text": "O-N (kg N)" }, { - "self_ref": "#/texts/178", + "self_ref": "#/texts/200", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4600,9 +5021,9 @@ } }, { - "self_ref": "#/texts/179", + "self_ref": "#/texts/201", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4612,9 +5033,9 @@ "text": "stored in a pit below animal confinements, and 0.02 kg N" }, { - "self_ref": "#/texts/180", + "self_ref": "#/texts/202", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4631,9 +5052,9 @@ } }, { - "self_ref": "#/texts/181", + "self_ref": "#/texts/203", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4643,9 +5064,9 @@ "text": "O-N (kg of urine and dung)" }, { - "self_ref": "#/texts/182", + "self_ref": "#/texts/204", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4662,9 +5083,9 @@ } }, { - "self_ref": "#/texts/183", + "self_ref": "#/texts/205", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4674,9 +5095,9 @@ "text": "deposited on pasture [38]. The indirect N" }, { - "self_ref": "#/texts/184", + "self_ref": "#/texts/206", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4693,9 +5114,9 @@ } }, { - "self_ref": "#/texts/185", + "self_ref": "#/texts/207", "parent": { - "$ref": "#/groups/11" + "$ref": "#/groups/12" }, "children": [], "content_layer": "body", @@ -4705,25 +5126,25 @@ "text": "O emissions from storage manure and urine and dung deposits on pasture were also estimated using the IPCC [38] emission factors." }, { - "self_ref": "#/texts/186", + "self_ref": "#/texts/208", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/187" + "$ref": "#/texts/209" }, { "$ref": "#/tables/4" }, - { - "$ref": "#/groups/12" - }, { "$ref": "#/groups/13" }, { "$ref": "#/groups/14" + }, + { + "$ref": "#/groups/15" } ], "content_layer": "body", @@ -4734,9 +5155,9 @@ "level": 2 }, { - "self_ref": "#/texts/187", + "self_ref": "#/texts/209", "parent": { - "$ref": "#/texts/186" + "$ref": "#/texts/208" }, "children": [], "content_layer": "body", @@ -4746,7 +5167,7 @@ "text": "Emissions due to farm management included those from fuel and machinery for manure handling and electricity for milking and confinement (Table 5). Emissions due to feed processing such as cutting, crushing, mixing and distributing, as well as secondary sources of emissions during the production of fuel, machinery, fertilizer, pesticides, seeds and plastic for ensilage were included in ‘Emissions from crop and pasture production’ section." }, { - "self_ref": "#/texts/188", + "self_ref": "#/texts/210", "parent": { "$ref": "#/body" }, @@ -4758,9 +5179,9 @@ "text": "Table 5 Factors for major resource inputs in farm management." }, { - "self_ref": "#/texts/189", + "self_ref": "#/texts/211", "parent": { - "$ref": "#/groups/12" + "$ref": "#/groups/13" }, "children": [], "content_layer": "body", @@ -4770,9 +5191,9 @@ "text": "The amount of fuel use for manure handling were estimated taking into consideration the amount of manure produced per cow and the amounts of fuel required for manure handling (L diesel t" }, { - "self_ref": "#/texts/190", + "self_ref": "#/texts/212", "parent": { - "$ref": "#/groups/12" + "$ref": "#/groups/13" }, "children": [], "content_layer": "body", @@ -4789,9 +5210,9 @@ } }, { - "self_ref": "#/texts/191", + "self_ref": "#/texts/213", "parent": { - "$ref": "#/groups/12" + "$ref": "#/groups/13" }, "children": [], "content_layer": "body", @@ -4801,9 +5222,9 @@ "text": ") [42]. The amount of manure was estimated from OM excretions (kg cow" }, { - "self_ref": "#/texts/192", + "self_ref": "#/texts/214", "parent": { - "$ref": "#/groups/12" + "$ref": "#/groups/13" }, "children": [], "content_layer": "body", @@ -4820,9 +5241,9 @@ } }, { - "self_ref": "#/texts/193", + "self_ref": "#/texts/215", "parent": { - "$ref": "#/groups/12" + "$ref": "#/groups/13" }, "children": [], "content_layer": "body", @@ -4832,9 +5253,9 @@ "text": "), assuming that the manure has 8% ash on DM basis and 60% DM content. The OM excretions were calculated by NDOMI × days in confinement × proportion of daily time that animals stayed on confinement." }, { - "self_ref": "#/texts/194", + "self_ref": "#/texts/216", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4844,9 +5265,9 @@ "text": "The emissions from fuel were estimated considering the primary (emissions from fuel burned) and secondary (emissions for producing and transporting fuel) emissions. The primary emissions were calculated by the amount of fuel required for manure handling (L) × (kg CO" }, { - "self_ref": "#/texts/195", + "self_ref": "#/texts/217", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4863,9 +5284,9 @@ } }, { - "self_ref": "#/texts/196", + "self_ref": "#/texts/218", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4875,9 +5296,9 @@ "text": "e L" }, { - "self_ref": "#/texts/197", + "self_ref": "#/texts/219", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4894,9 +5315,9 @@ } }, { - "self_ref": "#/texts/198", + "self_ref": "#/texts/220", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4906,9 +5327,9 @@ "text": ") [41]. The secondary emissions from fuel were calculated by the amount of fuel required for manure handling × emissions for production and transport of fuel (kg CO" }, { - "self_ref": "#/texts/199", + "self_ref": "#/texts/221", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4925,9 +5346,9 @@ } }, { - "self_ref": "#/texts/200", + "self_ref": "#/texts/222", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4937,9 +5358,9 @@ "text": "e L" }, { - "self_ref": "#/texts/201", + "self_ref": "#/texts/223", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4956,9 +5377,9 @@ } }, { - "self_ref": "#/texts/202", + "self_ref": "#/texts/224", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4968,9 +5389,9 @@ "text": ") [41]. Emissions from manufacture and repair of machinery for manure handling were estimated by manure produced per cow (t) × (kg machinery mass (kg manure)" }, { - "self_ref": "#/texts/203", + "self_ref": "#/texts/225", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4987,9 +5408,9 @@ } }, { - "self_ref": "#/texts/204", + "self_ref": "#/texts/226", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -4999,9 +5420,9 @@ "text": "× 10" }, { - "self_ref": "#/texts/205", + "self_ref": "#/texts/227", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -5018,9 +5439,9 @@ } }, { - "self_ref": "#/texts/206", + "self_ref": "#/texts/228", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -5030,9 +5451,9 @@ "text": ") [42] × kg CO" }, { - "self_ref": "#/texts/207", + "self_ref": "#/texts/229", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -5049,9 +5470,9 @@ } }, { - "self_ref": "#/texts/208", + "self_ref": "#/texts/230", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -5061,9 +5482,9 @@ "text": "e (kg machinery mass)" }, { - "self_ref": "#/texts/209", + "self_ref": "#/texts/231", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -5080,9 +5501,9 @@ } }, { - "self_ref": "#/texts/210", + "self_ref": "#/texts/232", "parent": { - "$ref": "#/groups/13" + "$ref": "#/groups/14" }, "children": [], "content_layer": "body", @@ -5092,9 +5513,9 @@ "text": "[42]." }, { - "self_ref": "#/texts/211", + "self_ref": "#/texts/233", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5104,9 +5525,9 @@ "text": "Emissions from electricity for milking and confinement were estimated using two emission factors (kg CO" }, { - "self_ref": "#/texts/212", + "self_ref": "#/texts/234", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5123,9 +5544,9 @@ } }, { - "self_ref": "#/texts/213", + "self_ref": "#/texts/235", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5135,9 +5556,9 @@ "text": "kWh" }, { - "self_ref": "#/texts/214", + "self_ref": "#/texts/236", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5154,9 +5575,9 @@ } }, { - "self_ref": "#/texts/215", + "self_ref": "#/texts/237", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5166,9 +5587,9 @@ "text": "). The first one is based on United States electricity matrix [41], and was used as a reference of an electricity matrix with less hydroelectric power than the region under study. The second is based on the Brazilian electricity matrix [46]. The electricity required for milking activities is 0.06 kWh (kg milk produced)" }, { - "self_ref": "#/texts/216", + "self_ref": "#/texts/238", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5185,9 +5606,9 @@ } }, { - "self_ref": "#/texts/217", + "self_ref": "#/texts/239", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5197,9 +5618,9 @@ "text": "[47]. The annual electricity use for lighting was 75 kWh cow" }, { - "self_ref": "#/texts/218", + "self_ref": "#/texts/240", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5216,9 +5637,9 @@ } }, { - "self_ref": "#/texts/219", + "self_ref": "#/texts/241", "parent": { - "$ref": "#/groups/14" + "$ref": "#/groups/15" }, "children": [], "content_layer": "body", @@ -5228,13 +5649,13 @@ "text": ", which is the value considered for lactating cows in naturally ventilated barns [47]." }, { - "self_ref": "#/texts/220", + "self_ref": "#/texts/242", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/groups/15" + "$ref": "#/groups/16" } ], "content_layer": "body", @@ -5245,9 +5666,9 @@ "level": 2 }, { - "self_ref": "#/texts/221", + "self_ref": "#/texts/243", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5257,9 +5678,9 @@ "text": "The C footprint for milk produced in the system was calculated using a biophysical allocation approach, as recommended by the International Dairy Federation [49], and described by Thoma et al. [48]. Briefly, AR" }, { - "self_ref": "#/texts/222", + "self_ref": "#/texts/244", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5276,9 +5697,9 @@ } }, { - "self_ref": "#/texts/223", + "self_ref": "#/texts/245", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5288,9 +5709,9 @@ "text": "= 1–6.04 × BMR, where" }, { - "self_ref": "#/texts/224", + "self_ref": "#/texts/246", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5307,9 +5728,9 @@ } }, { - "self_ref": "#/texts/225", + "self_ref": "#/texts/247", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5319,9 +5740,9 @@ "text": "AR" }, { - "self_ref": "#/texts/226", + "self_ref": "#/texts/248", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5338,9 +5759,9 @@ } }, { - "self_ref": "#/texts/227", + "self_ref": "#/texts/249", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5350,9 +5771,9 @@ "text": "is the allocation ratio for milk and BMR is cow BW at the time of slaughter (kg) + calf BW sold (kg) divided by the total ECM produced during cow`s entire life (kg). The AR" }, { - "self_ref": "#/texts/228", + "self_ref": "#/texts/250", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5369,9 +5790,9 @@ } }, { - "self_ref": "#/texts/229", + "self_ref": "#/texts/251", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5381,9 +5802,9 @@ "text": "were 0.854 and 0.849 for TMR and TMR with both pasture scenarios, respectively. The AR" }, { - "self_ref": "#/texts/230", + "self_ref": "#/texts/252", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5400,9 +5821,9 @@ } }, { - "self_ref": "#/texts/231", + "self_ref": "#/texts/253", "parent": { - "$ref": "#/groups/15" + "$ref": "#/groups/16" }, "children": [], "content_layer": "body", @@ -5412,13 +5833,13 @@ "text": "was applied to the whole emissions, except for the electricity consumed for milking (milking parlor) and refrigerant loss, which was directly assigned to milk production." }, { - "self_ref": "#/texts/232", + "self_ref": "#/texts/254", "parent": { - "$ref": "#/texts/21" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/233" + "$ref": "#/texts/255" } ], "content_layer": "body", @@ -5429,9 +5850,9 @@ "level": 2 }, { - "self_ref": "#/texts/233", + "self_ref": "#/texts/255", "parent": { - "$ref": "#/texts/232" + "$ref": "#/texts/254" }, "children": [], "content_layer": "body", @@ -5441,31 +5862,31 @@ "text": "A sensitivity index was calculated as described by Rotz et al. [42]. The sensitivity index was defined for each emission source as the percentage change in the C footprint for a 10% change in the given emission source divided by 10%. Thus, a value near 0 indicates a low sensitivity, whereas an index near or greater than 1 indicates a high sensitivity because a change in this value causes a similar change in the footprint." }, { - "self_ref": "#/texts/234", + "self_ref": "#/texts/256", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/235" + "$ref": "#/texts/257" }, { - "$ref": "#/texts/236" + "$ref": "#/texts/258" }, { - "$ref": "#/texts/306" + "$ref": "#/texts/328" }, { - "$ref": "#/texts/334" + "$ref": "#/texts/356" }, { - "$ref": "#/texts/381" + "$ref": "#/texts/403" }, { - "$ref": "#/texts/400" + "$ref": "#/texts/422" }, { - "$ref": "#/texts/406" + "$ref": "#/texts/428" } ], "content_layer": "body", @@ -5476,9 +5897,9 @@ "level": 1 }, { - "self_ref": "#/texts/235", + "self_ref": "#/texts/257", "parent": { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, "children": [], "content_layer": "body", @@ -5488,25 +5909,25 @@ "text": "The study has assessed the impact of tropical and temperate pastures in dairy cows fed TMR on the C footprint of dairy production in subtropics. Different factors were taken in to consideration to estimate emissions from manure (or urine and dung) of grazing animals, feed production and electricity use." }, { - "self_ref": "#/texts/236", + "self_ref": "#/texts/258", "parent": { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, "children": [ { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, { "$ref": "#/pictures/1" }, - { - "$ref": "#/groups/17" - }, { "$ref": "#/groups/18" }, { "$ref": "#/groups/19" + }, + { + "$ref": "#/groups/20" } ], "content_layer": "body", @@ -5517,9 +5938,9 @@ "level": 2 }, { - "self_ref": "#/texts/237", + "self_ref": "#/texts/259", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5529,9 +5950,9 @@ "text": "Depending on emission factors used for calculating emissions from urine and dung (IPCC or local data) and feed production (Tables 3 or 4), the C footprint was similar (Fig 2A and 2B) or decreased by 0.04 kg CO" }, { - "self_ref": "#/texts/238", + "self_ref": "#/texts/260", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5548,9 +5969,9 @@ } }, { - "self_ref": "#/texts/239", + "self_ref": "#/texts/261", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5560,9 +5981,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/240", + "self_ref": "#/texts/262", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5579,9 +6000,9 @@ } }, { - "self_ref": "#/texts/241", + "self_ref": "#/texts/263", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5591,9 +6012,9 @@ "text": "(Fig 2C and 2D) in scenarios that included pastures compared to" }, { - "self_ref": "#/texts/242", + "self_ref": "#/texts/264", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5610,9 +6031,9 @@ } }, { - "self_ref": "#/texts/243", + "self_ref": "#/texts/265", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5622,9 +6043,9 @@ "text": "TMR intake. Due to differences in emission factors, the overall GHG emission values ranged from 0.92 to 1.04 kg CO" }, { - "self_ref": "#/texts/244", + "self_ref": "#/texts/266", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5641,9 +6062,9 @@ } }, { - "self_ref": "#/texts/245", + "self_ref": "#/texts/267", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5653,9 +6074,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/246", + "self_ref": "#/texts/268", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5672,9 +6093,9 @@ } }, { - "self_ref": "#/texts/247", + "self_ref": "#/texts/269", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5684,9 +6105,9 @@ "text": "for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO" }, { - "self_ref": "#/texts/248", + "self_ref": "#/texts/270", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5703,9 +6124,9 @@ } }, { - "self_ref": "#/texts/249", + "self_ref": "#/texts/271", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5715,9 +6136,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/250", + "self_ref": "#/texts/272", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5734,9 +6155,9 @@ } }, { - "self_ref": "#/texts/251", + "self_ref": "#/texts/273", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5746,9 +6167,9 @@ "text": "for cows with access to pasture. Using IPCC emission factors [38], manure emissions increased as TMR intake went down (Fig 2A and 2B). However, using local emission factors for estimating N" }, { - "self_ref": "#/texts/252", + "self_ref": "#/texts/274", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5765,9 +6186,9 @@ } }, { - "self_ref": "#/texts/253", + "self_ref": "#/texts/275", "parent": { - "$ref": "#/groups/16" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -5777,7 +6198,7 @@ "text": "O-N emissions [37], manure emissions decreased as TMR intake went down (Fig 2C and 2D). Regardless of emission factors used (Tables 3 or 4), emissions from feed production decreased to a small extent as the proportion of TMR intake decreased. Emissions from farm management did not contribute more than 5% of overall GHG emissions." }, { - "self_ref": "#/texts/254", + "self_ref": "#/texts/276", "parent": { "$ref": "#/body" }, @@ -5789,9 +6210,9 @@ "text": "Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]." }, { - "self_ref": "#/texts/255", + "self_ref": "#/texts/277", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5801,9 +6222,9 @@ "text": "Considering IPCC emission factors for N" }, { - "self_ref": "#/texts/256", + "self_ref": "#/texts/278", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5820,9 +6241,9 @@ } }, { - "self_ref": "#/texts/257", + "self_ref": "#/texts/279", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5832,9 +6253,9 @@ "text": "O emissions from urine and dung [38] and those from Table 3, the C footprint ranged from 0.99 to 1.04 kg CO" }, { - "self_ref": "#/texts/258", + "self_ref": "#/texts/280", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5851,9 +6272,9 @@ } }, { - "self_ref": "#/texts/259", + "self_ref": "#/texts/281", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5863,9 +6284,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/260", + "self_ref": "#/texts/282", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5882,9 +6303,9 @@ } }, { - "self_ref": "#/texts/261", + "self_ref": "#/texts/283", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5894,9 +6315,9 @@ "text": ", and was close to those reported under confined based systems in California [49], Canada [50], China [8], Ireland [9], different scenarios in Australia [51,52] and Uruguay [11], which ranged from 0.98 to 1.16 kg CO" }, { - "self_ref": "#/texts/262", + "self_ref": "#/texts/284", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5913,9 +6334,9 @@ } }, { - "self_ref": "#/texts/263", + "self_ref": "#/texts/285", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5925,9 +6346,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/264", + "self_ref": "#/texts/286", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5944,9 +6365,9 @@ } }, { - "self_ref": "#/texts/265", + "self_ref": "#/texts/287", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5956,9 +6377,9 @@ "text": ". When local emission factors for N" }, { - "self_ref": "#/texts/266", + "self_ref": "#/texts/288", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5975,9 +6396,9 @@ } }, { - "self_ref": "#/texts/267", + "self_ref": "#/texts/289", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -5987,9 +6408,9 @@ "text": "O emissions from urine and dung [37] and those from Table 4 were taking into account, the C footprint for scenarios including pasture, without accounting for sequestered CO" }, { - "self_ref": "#/texts/268", + "self_ref": "#/texts/290", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6006,9 +6427,9 @@ } }, { - "self_ref": "#/texts/269", + "self_ref": "#/texts/291", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6018,9 +6439,9 @@ "text": "-C from perennial pasture—0.91 kg CO" }, { - "self_ref": "#/texts/270", + "self_ref": "#/texts/292", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6037,9 +6458,9 @@ } }, { - "self_ref": "#/texts/271", + "self_ref": "#/texts/293", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6049,9 +6470,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/272", + "self_ref": "#/texts/294", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6068,9 +6489,9 @@ } }, { - "self_ref": "#/texts/273", + "self_ref": "#/texts/295", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6080,9 +6501,9 @@ "text": "—was lower than the range of values described above. However, these values were still greater than high-performance confinement systems in UK and USA [53] or grass based dairy systems in Ireland [9,53] and New Zealand [8,54], which ranged from 0.52 to 0.89 kg CO" }, { - "self_ref": "#/texts/274", + "self_ref": "#/texts/296", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6099,9 +6520,9 @@ } }, { - "self_ref": "#/texts/275", + "self_ref": "#/texts/297", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6111,9 +6532,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/276", + "self_ref": "#/texts/298", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6130,9 +6551,9 @@ } }, { - "self_ref": "#/texts/277", + "self_ref": "#/texts/299", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6142,9 +6563,9 @@ "text": ". Regardless of which emission factor was used, we found a lower C footprint in all conditions compared to scenarios with lower milk production per cow or in poor conditions of manure management, which ranged from 1.4 to 2.3 kg CO" }, { - "self_ref": "#/texts/278", + "self_ref": "#/texts/300", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6161,9 +6582,9 @@ } }, { - "self_ref": "#/texts/279", + "self_ref": "#/texts/301", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6173,9 +6594,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/280", + "self_ref": "#/texts/302", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6192,9 +6613,9 @@ } }, { - "self_ref": "#/texts/281", + "self_ref": "#/texts/303", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6204,9 +6625,9 @@ "text": "[8,55]. Thus, even though differences between studies may be partially explained by various assumptions (e.g., emission factors, co-product allocation, methane emissions estimation, sequestered CO" }, { - "self_ref": "#/texts/282", + "self_ref": "#/texts/304", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6223,9 +6644,9 @@ } }, { - "self_ref": "#/texts/283", + "self_ref": "#/texts/305", "parent": { - "$ref": "#/groups/17" + "$ref": "#/groups/18" }, "children": [], "content_layer": "body", @@ -6235,9 +6656,9 @@ "text": "-C, etc.), herd productivity and manure management were systematically associated with the C footprint of the dairy systems." }, { - "self_ref": "#/texts/284", + "self_ref": "#/texts/306", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6247,9 +6668,9 @@ "text": "The similarity of C footprint between different scenarios using IPCC [38] for estimating emissions from manure and for emissions from feed production (Table 3) was a consequence of the trade-off between greater manure emissions and lower emissions to produce feed, as the proportion of pasture in diets increased. Additionally, the small negative effect of pasture on ECM production also contributed to the trade-off. The impact of milk production on the C footprint was reported in a meta-analysis comprising 30 studies from 15 different countries [22]. As observed in this study (Fig 2A and 2B) the authors reported no significant difference between the C footprint of pasture-based vs. confinement systems. However, they observed that an increase of 1000 kg cow" }, { - "self_ref": "#/texts/285", + "self_ref": "#/texts/307", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6266,9 +6687,9 @@ } }, { - "self_ref": "#/texts/286", + "self_ref": "#/texts/308", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6278,9 +6699,9 @@ "text": "(5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO" }, { - "self_ref": "#/texts/287", + "self_ref": "#/texts/309", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6297,9 +6718,9 @@ } }, { - "self_ref": "#/texts/288", + "self_ref": "#/texts/310", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6309,9 +6730,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/289", + "self_ref": "#/texts/311", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6328,9 +6749,9 @@ } }, { - "self_ref": "#/texts/290", + "self_ref": "#/texts/312", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6340,9 +6761,9 @@ "text": ", which may explain an apparent discrepancy between our study and an LCA performed in south Brazilian conditions [56]. Their study compared a confinement and a grazing-based dairy system with annual average milk production of 7667 and 5535 kg cow, respectively. In this study, the same herd was used in all systems, with an annual average milk production of around 7000 kg cow" }, { - "self_ref": "#/texts/291", + "self_ref": "#/texts/313", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6359,9 +6780,9 @@ } }, { - "self_ref": "#/texts/292", + "self_ref": "#/texts/314", "parent": { - "$ref": "#/groups/18" + "$ref": "#/groups/19" }, "children": [], "content_layer": "body", @@ -6371,9 +6792,9 @@ "text": ". Experimental data showed a reduction not greater than 3% of ECM when 50% of TMR was replaced by pasture access." }, { - "self_ref": "#/texts/293", + "self_ref": "#/texts/315", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6383,9 +6804,9 @@ "text": "The lower C footprint in scenarios with access to pasture, when local emission factors [37] were used for N" }, { - "self_ref": "#/texts/294", + "self_ref": "#/texts/316", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6402,9 +6823,9 @@ } }, { - "self_ref": "#/texts/295", + "self_ref": "#/texts/317", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6414,9 +6835,9 @@ "text": "O emissions from urine and dung and for feed production (Table 4), may also be partially attributed to the small negative effect of pasture on ECM production. Nevertheless, local emission factors for urine and dung had a great impact on scenarios including pastures compared to" }, { - "self_ref": "#/texts/296", + "self_ref": "#/texts/318", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6433,9 +6854,9 @@ } }, { - "self_ref": "#/texts/297", + "self_ref": "#/texts/319", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6445,9 +6866,9 @@ "text": "TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N" }, { - "self_ref": "#/texts/298", + "self_ref": "#/texts/320", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6464,9 +6885,9 @@ } }, { - "self_ref": "#/texts/299", + "self_ref": "#/texts/321", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6476,9 +6897,9 @@ "text": "O-N (kg N)" }, { - "self_ref": "#/texts/300", + "self_ref": "#/texts/322", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6495,9 +6916,9 @@ } }, { - "self_ref": "#/texts/301", + "self_ref": "#/texts/323", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6507,9 +6928,9 @@ "text": "for urine and dung from grazing animals, experimental evidence shows that it may be up to five times lower, averaging 0.004 kg N" }, { - "self_ref": "#/texts/302", + "self_ref": "#/texts/324", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6526,9 +6947,9 @@ } }, { - "self_ref": "#/texts/303", + "self_ref": "#/texts/325", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6538,9 +6959,9 @@ "text": "O-N kg" }, { - "self_ref": "#/texts/304", + "self_ref": "#/texts/326", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6557,9 +6978,9 @@ } }, { - "self_ref": "#/texts/305", + "self_ref": "#/texts/327", "parent": { - "$ref": "#/groups/19" + "$ref": "#/groups/20" }, "children": [], "content_layer": "body", @@ -6569,19 +6990,19 @@ "text": "[37]." }, { - "self_ref": "#/texts/306", + "self_ref": "#/texts/328", "parent": { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, "children": [ { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, { "$ref": "#/pictures/2" }, { - "$ref": "#/groups/21" + "$ref": "#/groups/22" } ], "content_layer": "body", @@ -6592,9 +7013,9 @@ "level": 2 }, { - "self_ref": "#/texts/307", + "self_ref": "#/texts/329", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6604,9 +7025,9 @@ "text": "The enteric CH" }, { - "self_ref": "#/texts/308", + "self_ref": "#/texts/330", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6623,9 +7044,9 @@ } }, { - "self_ref": "#/texts/309", + "self_ref": "#/texts/331", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6635,9 +7056,9 @@ "text": "intensity was similar between different scenarios (Fig 2), showing the greatest sensitivity index, with values ranging from 0.53 to 0.62, which indicate that for a 10% change in this source, the C footprint may change between 5.3 and 6.2% (Fig 3). The large effect of enteric CH" }, { - "self_ref": "#/texts/310", + "self_ref": "#/texts/332", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6654,9 +7075,9 @@ } }, { - "self_ref": "#/texts/311", + "self_ref": "#/texts/333", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6666,9 +7087,9 @@ "text": "emissions on the whole C footprint was expected, because the impact of enteric CH" }, { - "self_ref": "#/texts/312", + "self_ref": "#/texts/334", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6685,9 +7106,9 @@ } }, { - "self_ref": "#/texts/313", + "self_ref": "#/texts/335", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6697,9 +7118,9 @@ "text": "on GHG emissions of milk production in different dairy systems has been estimated to range from 44 to 60% of the total CO" }, { - "self_ref": "#/texts/314", + "self_ref": "#/texts/336", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6716,9 +7137,9 @@ } }, { - "self_ref": "#/texts/315", + "self_ref": "#/texts/337", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6728,9 +7149,9 @@ "text": "e [50,52,57,58]. However, emissions in feed production may be the most important source of GHG when emission factors for producing concentrate feeds are greater than 0.7 kg CO" }, { - "self_ref": "#/texts/316", + "self_ref": "#/texts/338", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6747,9 +7168,9 @@ } }, { - "self_ref": "#/texts/317", + "self_ref": "#/texts/339", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6759,9 +7180,9 @@ "text": "e kg" }, { - "self_ref": "#/texts/318", + "self_ref": "#/texts/340", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6778,9 +7199,9 @@ } }, { - "self_ref": "#/texts/319", + "self_ref": "#/texts/341", "parent": { - "$ref": "#/groups/20" + "$ref": "#/groups/21" }, "children": [], "content_layer": "body", @@ -6790,7 +7211,7 @@ "text": "[59], which did not happen in this study." }, { - "self_ref": "#/texts/320", + "self_ref": "#/texts/342", "parent": { "$ref": "#/body" }, @@ -6802,9 +7223,9 @@ "text": "Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]." }, { - "self_ref": "#/texts/321", + "self_ref": "#/texts/343", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6814,9 +7235,9 @@ "text": "The lack of difference in enteric CH" }, { - "self_ref": "#/texts/322", + "self_ref": "#/texts/344", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6833,9 +7254,9 @@ } }, { - "self_ref": "#/texts/323", + "self_ref": "#/texts/345", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6845,9 +7266,9 @@ "text": "emissions in different systems can be explained by the narrow range of NDF content in diets (<4% difference). This non-difference is due to the lower NDF content of annual temperate pastures (495 g (kg DM)" }, { - "self_ref": "#/texts/324", + "self_ref": "#/texts/346", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6864,9 +7285,9 @@ } }, { - "self_ref": "#/texts/325", + "self_ref": "#/texts/347", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6876,9 +7297,9 @@ "text": ") compared to corn silage (550 g (kg DM)" }, { - "self_ref": "#/texts/326", + "self_ref": "#/texts/348", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6895,9 +7316,9 @@ } }, { - "self_ref": "#/texts/327", + "self_ref": "#/texts/349", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6907,9 +7328,9 @@ "text": "). Hence, an expected, increase NDF content with decreased concentrate was partially offset by an increase in the pasture proportion relatively low in NDF. This is in agreement with studies conducted in southern Brazil, which have shown that the actual enteric CH" }, { - "self_ref": "#/texts/328", + "self_ref": "#/texts/350", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6926,9 +7347,9 @@ } }, { - "self_ref": "#/texts/329", + "self_ref": "#/texts/351", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6938,9 +7359,9 @@ "text": "emissions may decrease with inclusion of temperate pastures in cows receiving corn silage and soybean meal [60] or increase enteric CH" }, { - "self_ref": "#/texts/330", + "self_ref": "#/texts/352", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6957,9 +7378,9 @@ } }, { - "self_ref": "#/texts/331", + "self_ref": "#/texts/353", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6969,9 +7390,9 @@ "text": "emissions when dairy cows grazing a temperate pasture was supplemented with corn silage [61]. Additionally, enteric CH" }, { - "self_ref": "#/texts/332", + "self_ref": "#/texts/354", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -6988,9 +7409,9 @@ } }, { - "self_ref": "#/texts/333", + "self_ref": "#/texts/355", "parent": { - "$ref": "#/groups/21" + "$ref": "#/groups/22" }, "children": [], "content_layer": "body", @@ -7000,22 +7421,22 @@ "text": "emissions did not differ between dairy cows receiving TMR exclusively or grazing a tropical pasture in the same scenarios as in this study [26]." }, { - "self_ref": "#/texts/334", + "self_ref": "#/texts/356", "parent": { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, "children": [ { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, { "$ref": "#/pictures/3" }, { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, { - "$ref": "#/texts/380" + "$ref": "#/texts/402" } ], "content_layer": "body", @@ -7026,9 +7447,9 @@ "level": 2 }, { - "self_ref": "#/texts/335", + "self_ref": "#/texts/357", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7038,9 +7459,9 @@ "text": "Using IPCC emission factors for N" }, { - "self_ref": "#/texts/336", + "self_ref": "#/texts/358", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7057,9 +7478,9 @@ } }, { - "self_ref": "#/texts/337", + "self_ref": "#/texts/359", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7069,9 +7490,9 @@ "text": "O emissions from urine and dung [38] and those from Table 3, CH" }, { - "self_ref": "#/texts/338", + "self_ref": "#/texts/360", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7088,9 +7509,9 @@ } }, { - "self_ref": "#/texts/339", + "self_ref": "#/texts/361", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7100,9 +7521,9 @@ "text": "emissions from manure decreased 0.07 kg CO" }, { - "self_ref": "#/texts/340", + "self_ref": "#/texts/362", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7119,9 +7540,9 @@ } }, { - "self_ref": "#/texts/341", + "self_ref": "#/texts/363", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7131,9 +7552,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/342", + "self_ref": "#/texts/364", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7150,9 +7571,9 @@ } }, { - "self_ref": "#/texts/343", + "self_ref": "#/texts/365", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7162,9 +7583,9 @@ "text": ", but N" }, { - "self_ref": "#/texts/344", + "self_ref": "#/texts/366", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7181,9 +7602,9 @@ } }, { - "self_ref": "#/texts/345", + "self_ref": "#/texts/367", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7193,9 +7614,9 @@ "text": "O emissions from manure increased 0.09 kg CO" }, { - "self_ref": "#/texts/346", + "self_ref": "#/texts/368", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7212,9 +7633,9 @@ } }, { - "self_ref": "#/texts/347", + "self_ref": "#/texts/369", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7224,9 +7645,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/348", + "self_ref": "#/texts/370", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7243,9 +7664,9 @@ } }, { - "self_ref": "#/texts/349", + "self_ref": "#/texts/371", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7255,9 +7676,9 @@ "text": ", as TMR intake was restricted to 50%" }, { - "self_ref": "#/texts/350", + "self_ref": "#/texts/372", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7274,9 +7695,9 @@ } }, { - "self_ref": "#/texts/351", + "self_ref": "#/texts/373", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7286,9 +7707,9 @@ "text": "(Fig 4A). Emissions for pastures increased by 0.06 kg CO" }, { - "self_ref": "#/texts/352", + "self_ref": "#/texts/374", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7305,9 +7726,9 @@ } }, { - "self_ref": "#/texts/353", + "self_ref": "#/texts/375", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7317,9 +7738,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/354", + "self_ref": "#/texts/376", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7336,9 +7757,9 @@ } }, { - "self_ref": "#/texts/355", + "self_ref": "#/texts/377", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7348,9 +7769,9 @@ "text": ", whereas emissions for producing concentrate feeds and corn silage decreased by 0.09 kg CO" }, { - "self_ref": "#/texts/356", + "self_ref": "#/texts/378", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7367,9 +7788,9 @@ } }, { - "self_ref": "#/texts/357", + "self_ref": "#/texts/379", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7379,9 +7800,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/358", + "self_ref": "#/texts/380", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7398,9 +7819,9 @@ } }, { - "self_ref": "#/texts/359", + "self_ref": "#/texts/381", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7410,9 +7831,9 @@ "text": ", as TMR intake decreased (Fig 4B). In this situation, the lack of difference in calculated C footprints of different systems was also due to the greater emissions from manure, and offset by lower emissions from feed production with inclusion of pasture in lactating dairy cow diets. The greater N" }, { - "self_ref": "#/texts/360", + "self_ref": "#/texts/382", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7429,9 +7850,9 @@ } }, { - "self_ref": "#/texts/361", + "self_ref": "#/texts/383", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7441,9 +7862,9 @@ "text": "O-N emissions from manure with pasture was a consequence of higher N" }, { - "self_ref": "#/texts/362", + "self_ref": "#/texts/384", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7460,9 +7881,9 @@ } }, { - "self_ref": "#/texts/363", + "self_ref": "#/texts/385", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7472,9 +7893,9 @@ "text": "O-N emissions due to greater CP content and N urine excretion, as pasture intake increased. The effect of CP content on urine N excretion has been shown by several authors in lactating dairy cows [62–64]. For instance, by decreasing CP content from 185 to 152 g (kg DM)" }, { - "self_ref": "#/texts/364", + "self_ref": "#/texts/386", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7491,9 +7912,9 @@ } }, { - "self_ref": "#/texts/365", + "self_ref": "#/texts/387", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7503,9 +7924,9 @@ "text": ", N intake decreased by 20% and urine N excretion by 60% [62]. In this study, the CP content for lactating dairy cows ranged from 150 g (kg DM)" }, { - "self_ref": "#/texts/366", + "self_ref": "#/texts/388", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7522,9 +7943,9 @@ } }, { - "self_ref": "#/texts/367", + "self_ref": "#/texts/389", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7534,9 +7955,9 @@ "text": "on TMR system to 198 g (kg DM)" }, { - "self_ref": "#/texts/368", + "self_ref": "#/texts/390", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7553,9 +7974,9 @@ } }, { - "self_ref": "#/texts/369", + "self_ref": "#/texts/391", "parent": { - "$ref": "#/groups/22" + "$ref": "#/groups/23" }, "children": [], "content_layer": "body", @@ -7565,7 +7986,7 @@ "text": "on 50% TMR with pasture. Additionally, greater urine N excretion is expected with greater use of pasture. This occurs because protein utilization in pastures is inefficient, as the protein in fresh forages is highly degradable in the rumen and may not be captured by microbes [65]." }, { - "self_ref": "#/texts/370", + "self_ref": "#/texts/392", "parent": { "$ref": "#/body" }, @@ -7577,9 +7998,9 @@ "text": "Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture." }, { - "self_ref": "#/texts/371", + "self_ref": "#/texts/393", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7589,9 +8010,9 @@ "text": "Using local emission factors for N" }, { - "self_ref": "#/texts/372", + "self_ref": "#/texts/394", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7608,9 +8029,9 @@ } }, { - "self_ref": "#/texts/373", + "self_ref": "#/texts/395", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7620,9 +8041,9 @@ "text": "O emissions from urine and dung [37] and those from Table 4, reductions in CH" }, { - "self_ref": "#/texts/374", + "self_ref": "#/texts/396", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7639,9 +8060,9 @@ } }, { - "self_ref": "#/texts/375", + "self_ref": "#/texts/397", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7651,9 +8072,9 @@ "text": "emissions from stocked manure, when pastures were included on diets, did not offset by increases in N" }, { - "self_ref": "#/texts/376", + "self_ref": "#/texts/398", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7670,9 +8091,9 @@ } }, { - "self_ref": "#/texts/377", + "self_ref": "#/texts/399", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7682,9 +8103,9 @@ "text": "O emissions from excreta (Fig 4C). In this case, total emissions from manure (Fig 4C) and feed production (Fig 4D) decreased with the inclusion of pasture. The impact of greater CP content and N urine excretion with increased pasture intake was offset by the much lower emission factors used for N" }, { - "self_ref": "#/texts/378", + "self_ref": "#/texts/400", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7701,9 +8122,9 @@ } }, { - "self_ref": "#/texts/379", + "self_ref": "#/texts/401", "parent": { - "$ref": "#/groups/23" + "$ref": "#/groups/24" }, "children": [], "content_layer": "body", @@ -7713,9 +8134,9 @@ "text": "O emissions from urine and dung. As suggested by other authors [66,67], these results show that IPCC default value may need to be revised for the subtropical region." }, { - "self_ref": "#/texts/380", + "self_ref": "#/texts/402", "parent": { - "$ref": "#/texts/334" + "$ref": "#/texts/356" }, "children": [], "content_layer": "body", @@ -7725,16 +8146,16 @@ "text": "Emissions for feed production decreased when pasture was included due to the greater emission factor for corn grain production compared to pastures. Emissions from concentrate and silage had at least twice the sensitivity index compared to emissions from pastures. The amount of grain required per cow in a lifetime decreased from 7,300 kg to 4,000 kg when 50% of TMR was replaced by pasture access. These results are in agreement with other studies which found lower C footprint, as concentrate use is reduced and/or pasture is included [9,68,69]. Moreover, it has been demonstrated that in intensive dairy systems, after enteric fermentation, feed production is the second main contributor to C footprint [50]. There is potential to decrease the environmental impact of dairy systems by reducing the use of concentrate ingredients with high environmental impact, particularly in confinements [9]." }, { - "self_ref": "#/texts/381", + "self_ref": "#/texts/403", "parent": { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, "children": [ { - "$ref": "#/texts/382" + "$ref": "#/texts/404" }, { - "$ref": "#/groups/24" + "$ref": "#/groups/25" } ], "content_layer": "body", @@ -7745,9 +8166,9 @@ "level": 2 }, { - "self_ref": "#/texts/382", + "self_ref": "#/texts/404", "parent": { - "$ref": "#/texts/381" + "$ref": "#/texts/403" }, "children": [], "content_layer": "body", @@ -7757,9 +8178,9 @@ "text": "The lower impact of emissions from farm management is in agreement with other studies conducted in Europe [9, 62] and USA [42, 55], where the authors found that most emissions in dairy production systems are from enteric fermentation, feed production and emissions from excreta. As emissions from fuel for on-farm feed production were accounted into the ‘emissions from crop and pasture production’, total emissions from farm management were not greater than 5% of total C footprint." }, { - "self_ref": "#/texts/383", + "self_ref": "#/texts/405", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7769,9 +8190,9 @@ "text": "Emissions from farm management dropped when the emission factor for electricity generation was based on the Brazilian matrix. In this case, the emission factor for electricity generation (0.205 kg CO" }, { - "self_ref": "#/texts/384", + "self_ref": "#/texts/406", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7788,9 +8209,9 @@ } }, { - "self_ref": "#/texts/385", + "self_ref": "#/texts/407", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7800,9 +8221,9 @@ "text": "e kWh" }, { - "self_ref": "#/texts/386", + "self_ref": "#/texts/408", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7819,9 +8240,9 @@ } }, { - "self_ref": "#/texts/387", + "self_ref": "#/texts/409", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7831,9 +8252,9 @@ "text": "[46]) is much lower than that in a LCA study conducted in US (0.73 kg CO" }, { - "self_ref": "#/texts/388", + "self_ref": "#/texts/410", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7850,9 +8271,9 @@ } }, { - "self_ref": "#/texts/389", + "self_ref": "#/texts/411", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7862,9 +8283,9 @@ "text": "e kWh" }, { - "self_ref": "#/texts/390", + "self_ref": "#/texts/412", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7881,9 +8302,9 @@ } }, { - "self_ref": "#/texts/391", + "self_ref": "#/texts/413", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7893,9 +8314,9 @@ "text": "[42]). This apparent discrepancy is explained because in 2016, almost 66% of the electricity generated in Brazil was from hydropower, which has an emission factor of 0.074 kg CO" }, { - "self_ref": "#/texts/392", + "self_ref": "#/texts/414", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7912,9 +8333,9 @@ } }, { - "self_ref": "#/texts/393", + "self_ref": "#/texts/415", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7924,9 +8345,9 @@ "text": "e kWh" }, { - "self_ref": "#/texts/394", + "self_ref": "#/texts/416", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7943,9 +8364,9 @@ } }, { - "self_ref": "#/texts/395", + "self_ref": "#/texts/417", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7955,9 +8376,9 @@ "text": "against 0.382 and 0.926 kg CO" }, { - "self_ref": "#/texts/396", + "self_ref": "#/texts/418", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7974,9 +8395,9 @@ } }, { - "self_ref": "#/texts/397", + "self_ref": "#/texts/419", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -7986,9 +8407,9 @@ "text": "e kWh" }, { - "self_ref": "#/texts/398", + "self_ref": "#/texts/420", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -8005,9 +8426,9 @@ } }, { - "self_ref": "#/texts/399", + "self_ref": "#/texts/421", "parent": { - "$ref": "#/groups/24" + "$ref": "#/groups/25" }, "children": [], "content_layer": "body", @@ -8017,13 +8438,13 @@ "text": "produced by natural gas and hard coal, respectively [46]." }, { - "self_ref": "#/texts/400", + "self_ref": "#/texts/422", "parent": { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, "children": [ { - "$ref": "#/groups/25" + "$ref": "#/groups/26" } ], "content_layer": "body", @@ -8034,9 +8455,9 @@ "level": 2 }, { - "self_ref": "#/texts/401", + "self_ref": "#/texts/423", "parent": { - "$ref": "#/groups/25" + "$ref": "#/groups/26" }, "children": [], "content_layer": "body", @@ -8046,9 +8467,9 @@ "text": "The milk production and composition data are the average for a typical herd, which might have great animal-to-animal variability. Likewise, DM yield of crops and pastures were collected from experimental observations, and may change as a function of inter-annual variation, climatic conditions, soil type, fertilization level etc. The emission factors for direct and indirect N" }, { - "self_ref": "#/texts/402", + "self_ref": "#/texts/424", "parent": { - "$ref": "#/groups/25" + "$ref": "#/groups/26" }, "children": [], "content_layer": "body", @@ -8065,9 +8486,9 @@ } }, { - "self_ref": "#/texts/403", + "self_ref": "#/texts/425", "parent": { - "$ref": "#/groups/25" + "$ref": "#/groups/26" }, "children": [], "content_layer": "body", @@ -8077,9 +8498,9 @@ "text": "O emissions from urine and dung were alternatively estimated using local data, but more experiments are necessary to reduce the uncertainty. The CO" }, { - "self_ref": "#/texts/404", + "self_ref": "#/texts/426", "parent": { - "$ref": "#/groups/25" + "$ref": "#/groups/26" }, "children": [], "content_layer": "body", @@ -8096,9 +8517,9 @@ } }, { - "self_ref": "#/texts/405", + "self_ref": "#/texts/427", "parent": { - "$ref": "#/groups/25" + "$ref": "#/groups/26" }, "children": [], "content_layer": "body", @@ -8108,16 +8529,16 @@ "text": "emitted from lime and urea application was estimated from IPCC default values, which may not represent emissions in subtropical conditions. This LCA may be improved by reducing the uncertainty of factors for estimating emissions from excreta and feed production, including the C sequestration or emissions as a function of soil management." }, { - "self_ref": "#/texts/406", + "self_ref": "#/texts/428", "parent": { - "$ref": "#/texts/234" + "$ref": "#/texts/256" }, "children": [ { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, { - "$ref": "#/groups/27" + "$ref": "#/groups/28" } ], "content_layer": "body", @@ -8128,9 +8549,9 @@ "level": 2 }, { - "self_ref": "#/texts/407", + "self_ref": "#/texts/429", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8140,9 +8561,9 @@ "text": "The potential for using pasture can reduce the C footprint because milk production kept pace with animal confinement. However, if milk production is to decrease with lower TMR intake and inclusion of pasture [19], the C footprint would be expected to increase. Lorenz et al. [22] showed that an increase in milk yield from 5,000 to 6,000 kg ECM reduced the C footprint by 0.12 kg CO" }, { - "self_ref": "#/texts/408", + "self_ref": "#/texts/430", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8159,9 +8580,9 @@ } }, { - "self_ref": "#/texts/409", + "self_ref": "#/texts/431", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8171,9 +8592,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/410", + "self_ref": "#/texts/432", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8190,9 +8611,9 @@ } }, { - "self_ref": "#/texts/411", + "self_ref": "#/texts/433", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8202,9 +8623,9 @@ "text": ", whereas an increase from 10,000 to 11,000 kg ECM reduced the C footprint by only 0.06 kg CO" }, { - "self_ref": "#/texts/412", + "self_ref": "#/texts/434", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8221,9 +8642,9 @@ } }, { - "self_ref": "#/texts/413", + "self_ref": "#/texts/435", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8233,9 +8654,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/414", + "self_ref": "#/texts/436", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8252,9 +8673,9 @@ } }, { - "self_ref": "#/texts/415", + "self_ref": "#/texts/437", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8264,9 +8685,9 @@ "text": ". Hence, the impact of increasing milk production on decreasing C footprint is not linear, and mitigation measures, such as breeding for increased genetic yield potential and increasing concentrate ratio in the diet, are potentially harmful for animal’s health and welfare [70]. For instance, increasing concentrate ratio potentially increases the occurrence of subclinical ketosis and foot lesions, and C footprint may increase by 0.03 kg CO" }, { - "self_ref": "#/texts/416", + "self_ref": "#/texts/438", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8283,9 +8704,9 @@ } }, { - "self_ref": "#/texts/417", + "self_ref": "#/texts/439", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8295,9 +8716,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/418", + "self_ref": "#/texts/440", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8314,9 +8735,9 @@ } }, { - "self_ref": "#/texts/419", + "self_ref": "#/texts/441", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8326,9 +8747,9 @@ "text": "in subclinical ketosis [71] and by 0.02 kg CO" }, { - "self_ref": "#/texts/420", + "self_ref": "#/texts/442", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8345,9 +8766,9 @@ } }, { - "self_ref": "#/texts/421", + "self_ref": "#/texts/443", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8357,9 +8778,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/422", + "self_ref": "#/texts/444", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8376,9 +8797,9 @@ } }, { - "self_ref": "#/texts/423", + "self_ref": "#/texts/445", "parent": { - "$ref": "#/groups/26" + "$ref": "#/groups/27" }, "children": [], "content_layer": "body", @@ -8388,9 +8809,9 @@ "text": "in case of foot lesions [72]." }, { - "self_ref": "#/texts/424", + "self_ref": "#/texts/446", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8400,9 +8821,9 @@ "text": "Grazing lands may also improve biodiversity [73]. Strategies such as zero tillage may increase stocks of soil C [74]. This study did not consider C sequestration during the growth of annual pastures, because it was assumed these grasses were planted with tillage, having a balance between C sequestration and C emissions [38]. Considering the C sequestration from no-tillage perennial pasture, the amount of C sequestration will more than compensates for C emitted. These results are in agreement with other authors who have shown that a reduction or elimination of soil tillage increases annual soil C sequestration in subtropical areas by 0.5 to 1.5 t ha" }, { - "self_ref": "#/texts/425", + "self_ref": "#/texts/447", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8419,9 +8840,9 @@ } }, { - "self_ref": "#/texts/426", + "self_ref": "#/texts/448", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8431,9 +8852,9 @@ "text": "[75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha" }, { - "self_ref": "#/texts/427", + "self_ref": "#/texts/449", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8450,9 +8871,9 @@ } }, { - "self_ref": "#/texts/428", + "self_ref": "#/texts/450", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8462,9 +8883,9 @@ "text": "would be sequestered, further reducing the C footprint by 0.015 and 0.025 kg CO" }, { - "self_ref": "#/texts/429", + "self_ref": "#/texts/451", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8481,9 +8902,9 @@ } }, { - "self_ref": "#/texts/430", + "self_ref": "#/texts/452", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8493,9 +8914,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/431", + "self_ref": "#/texts/453", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8512,9 +8933,9 @@ } }, { - "self_ref": "#/texts/432", + "self_ref": "#/texts/454", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8524,9 +8945,9 @@ "text": "for the scenarios using 75 and 50% TMR, respectively. Eliminating tillage, the reduction on total GHG emissions would be 0.03 and 0.05 kg CO" }, { - "self_ref": "#/texts/433", + "self_ref": "#/texts/455", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8543,9 +8964,9 @@ } }, { - "self_ref": "#/texts/434", + "self_ref": "#/texts/456", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8555,9 +8976,9 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/435", + "self_ref": "#/texts/457", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8574,9 +8995,9 @@ } }, { - "self_ref": "#/texts/436", + "self_ref": "#/texts/458", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8586,9 +9007,9 @@ "text": "for 75 and 50% TMR, respectively. However, this approach may be controversial because lands which have been consistently managed for decades have approached steady state C storage, so that net exchange of CO" }, { - "self_ref": "#/texts/437", + "self_ref": "#/texts/459", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8605,9 +9026,9 @@ } }, { - "self_ref": "#/texts/438", + "self_ref": "#/texts/460", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/28" }, "children": [], "content_layer": "body", @@ -8617,13 +9038,13 @@ "text": "would be negligible [76]." }, { - "self_ref": "#/texts/439", + "self_ref": "#/texts/461", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/groups/28" + "$ref": "#/groups/29" } ], "content_layer": "body", @@ -8634,9 +9055,9 @@ "level": 1 }, { - "self_ref": "#/texts/440", + "self_ref": "#/texts/462", "parent": { - "$ref": "#/groups/28" + "$ref": "#/groups/29" }, "children": [], "content_layer": "body", @@ -8646,9 +9067,9 @@ "text": "This study assessed the C footprint of dairy cattle systems with or without access to pastures. Including pastures showed potential to maintain or decrease to a small extent the C footprint, which may be attributable to the evidence of low N" }, { - "self_ref": "#/texts/441", + "self_ref": "#/texts/463", "parent": { - "$ref": "#/groups/28" + "$ref": "#/groups/29" }, "children": [], "content_layer": "body", @@ -8665,9 +9086,9 @@ } }, { - "self_ref": "#/texts/442", + "self_ref": "#/texts/464", "parent": { - "$ref": "#/groups/28" + "$ref": "#/groups/29" }, "children": [], "content_layer": "body", @@ -8677,9 +9098,9 @@ "text": "O emissions from urine and dung in dairy systems in subtropical areas. Even though the enteric CH" }, { - "self_ref": "#/texts/443", + "self_ref": "#/texts/465", "parent": { - "$ref": "#/groups/28" + "$ref": "#/groups/29" }, "children": [], "content_layer": "body", @@ -8696,9 +9117,9 @@ } }, { - "self_ref": "#/texts/444", + "self_ref": "#/texts/466", "parent": { - "$ref": "#/groups/28" + "$ref": "#/groups/29" }, "children": [], "content_layer": "body", @@ -8708,9 +9129,9 @@ "text": "intensity was the largest source of CO" }, { - "self_ref": "#/texts/445", + "self_ref": "#/texts/467", "parent": { - "$ref": "#/groups/28" + "$ref": "#/groups/29" }, "children": [], "content_layer": "body", @@ -8727,9 +9148,9 @@ } }, { - "self_ref": "#/texts/446", + "self_ref": "#/texts/468", "parent": { - "$ref": "#/groups/28" + "$ref": "#/groups/29" }, "children": [], "content_layer": "body", @@ -8739,13 +9160,13 @@ "text": "e emissions, it did not change between different scenarios due to the narrow range of NDF content in diets and maintaining the same milk production with or without access to pastures." }, { - "self_ref": "#/texts/447", + "self_ref": "#/texts/469", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/448" + "$ref": "#/texts/470" } ], "content_layer": "body", @@ -8756,9 +9177,9 @@ "level": 1 }, { - "self_ref": "#/texts/448", + "self_ref": "#/texts/470", "parent": { - "$ref": "#/texts/447" + "$ref": "#/texts/469" }, "children": [], "content_layer": "body", @@ -8768,13 +9189,13 @@ "text": "Thanks to Anna Naranjo for helpful comments throughout the elaboration of this manuscript, and to André Thaler Neto and Roberto Kappes for providing the key characteristics of the herd considered in this study." }, { - "self_ref": "#/texts/449", + "self_ref": "#/texts/471", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/groups/29" + "$ref": "#/groups/30" } ], "content_layer": "body", @@ -8785,9 +9206,9 @@ "level": 1 }, { - "self_ref": "#/texts/450", + "self_ref": "#/texts/472", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8799,9 +9220,9 @@ "marker": "" }, { - "self_ref": "#/texts/451", + "self_ref": "#/texts/473", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8813,9 +9234,9 @@ "marker": "" }, { - "self_ref": "#/texts/452", + "self_ref": "#/texts/474", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8827,9 +9248,9 @@ "marker": "" }, { - "self_ref": "#/texts/453", + "self_ref": "#/texts/475", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8841,9 +9262,9 @@ "marker": "" }, { - "self_ref": "#/texts/454", + "self_ref": "#/texts/476", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8855,9 +9276,9 @@ "marker": "" }, { - "self_ref": "#/texts/455", + "self_ref": "#/texts/477", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8869,9 +9290,9 @@ "marker": "" }, { - "self_ref": "#/texts/456", + "self_ref": "#/texts/478", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8883,9 +9304,9 @@ "marker": "" }, { - "self_ref": "#/texts/457", + "self_ref": "#/texts/479", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8897,9 +9318,9 @@ "marker": "" }, { - "self_ref": "#/texts/458", + "self_ref": "#/texts/480", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8911,9 +9332,9 @@ "marker": "" }, { - "self_ref": "#/texts/459", + "self_ref": "#/texts/481", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8925,9 +9346,9 @@ "marker": "" }, { - "self_ref": "#/texts/460", + "self_ref": "#/texts/482", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8939,9 +9360,9 @@ "marker": "" }, { - "self_ref": "#/texts/461", + "self_ref": "#/texts/483", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8953,9 +9374,9 @@ "marker": "" }, { - "self_ref": "#/texts/462", + "self_ref": "#/texts/484", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8967,9 +9388,9 @@ "marker": "" }, { - "self_ref": "#/texts/463", + "self_ref": "#/texts/485", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8981,9 +9402,9 @@ "marker": "" }, { - "self_ref": "#/texts/464", + "self_ref": "#/texts/486", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -8995,9 +9416,9 @@ "marker": "" }, { - "self_ref": "#/texts/465", + "self_ref": "#/texts/487", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9009,9 +9430,9 @@ "marker": "" }, { - "self_ref": "#/texts/466", + "self_ref": "#/texts/488", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9023,9 +9444,9 @@ "marker": "" }, { - "self_ref": "#/texts/467", + "self_ref": "#/texts/489", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9037,9 +9458,9 @@ "marker": "" }, { - "self_ref": "#/texts/468", + "self_ref": "#/texts/490", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9051,9 +9472,9 @@ "marker": "" }, { - "self_ref": "#/texts/469", + "self_ref": "#/texts/491", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9065,9 +9486,9 @@ "marker": "" }, { - "self_ref": "#/texts/470", + "self_ref": "#/texts/492", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9079,9 +9500,9 @@ "marker": "" }, { - "self_ref": "#/texts/471", + "self_ref": "#/texts/493", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9093,9 +9514,9 @@ "marker": "" }, { - "self_ref": "#/texts/472", + "self_ref": "#/texts/494", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9107,9 +9528,9 @@ "marker": "" }, { - "self_ref": "#/texts/473", + "self_ref": "#/texts/495", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9121,9 +9542,9 @@ "marker": "" }, { - "self_ref": "#/texts/474", + "self_ref": "#/texts/496", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9135,9 +9556,9 @@ "marker": "" }, { - "self_ref": "#/texts/475", + "self_ref": "#/texts/497", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9149,9 +9570,9 @@ "marker": "" }, { - "self_ref": "#/texts/476", + "self_ref": "#/texts/498", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9163,9 +9584,9 @@ "marker": "" }, { - "self_ref": "#/texts/477", + "self_ref": "#/texts/499", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9177,9 +9598,9 @@ "marker": "" }, { - "self_ref": "#/texts/478", + "self_ref": "#/texts/500", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9191,9 +9612,9 @@ "marker": "" }, { - "self_ref": "#/texts/479", + "self_ref": "#/texts/501", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9205,9 +9626,9 @@ "marker": "" }, { - "self_ref": "#/texts/480", + "self_ref": "#/texts/502", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9219,9 +9640,9 @@ "marker": "" }, { - "self_ref": "#/texts/481", + "self_ref": "#/texts/503", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9233,9 +9654,9 @@ "marker": "" }, { - "self_ref": "#/texts/482", + "self_ref": "#/texts/504", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9247,9 +9668,9 @@ "marker": "" }, { - "self_ref": "#/texts/483", + "self_ref": "#/texts/505", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9261,9 +9682,9 @@ "marker": "" }, { - "self_ref": "#/texts/484", + "self_ref": "#/texts/506", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9275,9 +9696,9 @@ "marker": "" }, { - "self_ref": "#/texts/485", + "self_ref": "#/texts/507", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9289,9 +9710,9 @@ "marker": "" }, { - "self_ref": "#/texts/486", + "self_ref": "#/texts/508", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9303,9 +9724,9 @@ "marker": "" }, { - "self_ref": "#/texts/487", + "self_ref": "#/texts/509", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9317,9 +9738,9 @@ "marker": "" }, { - "self_ref": "#/texts/488", + "self_ref": "#/texts/510", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9331,9 +9752,9 @@ "marker": "" }, { - "self_ref": "#/texts/489", + "self_ref": "#/texts/511", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9345,9 +9766,9 @@ "marker": "" }, { - "self_ref": "#/texts/490", + "self_ref": "#/texts/512", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9359,9 +9780,9 @@ "marker": "" }, { - "self_ref": "#/texts/491", + "self_ref": "#/texts/513", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9373,9 +9794,9 @@ "marker": "" }, { - "self_ref": "#/texts/492", + "self_ref": "#/texts/514", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9387,9 +9808,9 @@ "marker": "" }, { - "self_ref": "#/texts/493", + "self_ref": "#/texts/515", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9401,9 +9822,9 @@ "marker": "" }, { - "self_ref": "#/texts/494", + "self_ref": "#/texts/516", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9415,9 +9836,9 @@ "marker": "" }, { - "self_ref": "#/texts/495", + "self_ref": "#/texts/517", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9429,9 +9850,9 @@ "marker": "" }, { - "self_ref": "#/texts/496", + "self_ref": "#/texts/518", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9443,9 +9864,9 @@ "marker": "" }, { - "self_ref": "#/texts/497", + "self_ref": "#/texts/519", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9457,9 +9878,9 @@ "marker": "" }, { - "self_ref": "#/texts/498", + "self_ref": "#/texts/520", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9471,9 +9892,9 @@ "marker": "" }, { - "self_ref": "#/texts/499", + "self_ref": "#/texts/521", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9485,9 +9906,9 @@ "marker": "" }, { - "self_ref": "#/texts/500", + "self_ref": "#/texts/522", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9499,9 +9920,9 @@ "marker": "" }, { - "self_ref": "#/texts/501", + "self_ref": "#/texts/523", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9513,9 +9934,9 @@ "marker": "" }, { - "self_ref": "#/texts/502", + "self_ref": "#/texts/524", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9527,9 +9948,9 @@ "marker": "" }, { - "self_ref": "#/texts/503", + "self_ref": "#/texts/525", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9541,9 +9962,9 @@ "marker": "" }, { - "self_ref": "#/texts/504", + "self_ref": "#/texts/526", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9555,9 +9976,9 @@ "marker": "" }, { - "self_ref": "#/texts/505", + "self_ref": "#/texts/527", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9569,9 +9990,9 @@ "marker": "" }, { - "self_ref": "#/texts/506", + "self_ref": "#/texts/528", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9583,9 +10004,9 @@ "marker": "" }, { - "self_ref": "#/texts/507", + "self_ref": "#/texts/529", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9597,9 +10018,9 @@ "marker": "" }, { - "self_ref": "#/texts/508", + "self_ref": "#/texts/530", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9611,9 +10032,9 @@ "marker": "" }, { - "self_ref": "#/texts/509", + "self_ref": "#/texts/531", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9625,9 +10046,9 @@ "marker": "" }, { - "self_ref": "#/texts/510", + "self_ref": "#/texts/532", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9639,9 +10060,9 @@ "marker": "" }, { - "self_ref": "#/texts/511", + "self_ref": "#/texts/533", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9653,9 +10074,9 @@ "marker": "" }, { - "self_ref": "#/texts/512", + "self_ref": "#/texts/534", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9667,9 +10088,9 @@ "marker": "" }, { - "self_ref": "#/texts/513", + "self_ref": "#/texts/535", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9681,9 +10102,9 @@ "marker": "" }, { - "self_ref": "#/texts/514", + "self_ref": "#/texts/536", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9695,9 +10116,9 @@ "marker": "" }, { - "self_ref": "#/texts/515", + "self_ref": "#/texts/537", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9709,9 +10130,9 @@ "marker": "" }, { - "self_ref": "#/texts/516", + "self_ref": "#/texts/538", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9723,9 +10144,9 @@ "marker": "" }, { - "self_ref": "#/texts/517", + "self_ref": "#/texts/539", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9737,9 +10158,9 @@ "marker": "" }, { - "self_ref": "#/texts/518", + "self_ref": "#/texts/540", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9751,9 +10172,9 @@ "marker": "" }, { - "self_ref": "#/texts/519", + "self_ref": "#/texts/541", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9765,9 +10186,9 @@ "marker": "" }, { - "self_ref": "#/texts/520", + "self_ref": "#/texts/542", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9779,9 +10200,9 @@ "marker": "" }, { - "self_ref": "#/texts/521", + "self_ref": "#/texts/543", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9793,9 +10214,9 @@ "marker": "" }, { - "self_ref": "#/texts/522", + "self_ref": "#/texts/544", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9807,9 +10228,9 @@ "marker": "" }, { - "self_ref": "#/texts/523", + "self_ref": "#/texts/545", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9821,9 +10242,9 @@ "marker": "" }, { - "self_ref": "#/texts/524", + "self_ref": "#/texts/546", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9835,9 +10256,9 @@ "marker": "" }, { - "self_ref": "#/texts/525", + "self_ref": "#/texts/547", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/30" }, "children": [], "content_layer": "body", @@ -9853,7 +10274,7 @@ { "self_ref": "#/pictures/0", "parent": { - "$ref": "#/texts/25" + "$ref": "#/texts/47" }, "children": [], "content_layer": "body", @@ -9861,7 +10282,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/27" + "$ref": "#/texts/49" } ], "references": [], @@ -9871,7 +10292,7 @@ { "self_ref": "#/pictures/1", "parent": { - "$ref": "#/texts/236" + "$ref": "#/texts/258" }, "children": [], "content_layer": "body", @@ -9879,7 +10300,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/254" + "$ref": "#/texts/276" } ], "references": [], @@ -9889,7 +10310,7 @@ { "self_ref": "#/pictures/2", "parent": { - "$ref": "#/texts/306" + "$ref": "#/texts/328" }, "children": [], "content_layer": "body", @@ -9897,7 +10318,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/320" + "$ref": "#/texts/342" } ], "references": [], @@ -9907,7 +10328,7 @@ { "self_ref": "#/pictures/3", "parent": { - "$ref": "#/texts/334" + "$ref": "#/texts/356" }, "children": [], "content_layer": "body", @@ -9915,7 +10336,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/370" + "$ref": "#/texts/392" } ], "references": [], @@ -9927,7 +10348,7 @@ { "self_ref": "#/tables/0", "parent": { - "$ref": "#/texts/28" + "$ref": "#/texts/50" }, "children": [], "content_layer": "body", @@ -9935,7 +10356,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/31" + "$ref": "#/texts/53" } ], "references": [], @@ -10994,7 +11415,7 @@ { "self_ref": "#/tables/1", "parent": { - "$ref": "#/texts/72" + "$ref": "#/texts/94" }, "children": [], "content_layer": "body", @@ -11002,7 +11423,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/80" + "$ref": "#/texts/102" } ], "references": [], @@ -16601,7 +17022,7 @@ { "self_ref": "#/tables/2", "parent": { - "$ref": "#/texts/81" + "$ref": "#/texts/103" }, "children": [], "content_layer": "body", @@ -16609,7 +17030,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/89" + "$ref": "#/texts/111" } ], "references": [], @@ -17816,7 +18237,7 @@ { "self_ref": "#/tables/3", "parent": { - "$ref": "#/texts/81" + "$ref": "#/texts/103" }, "children": [], "content_layer": "body", @@ -17824,7 +18245,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/121" + "$ref": "#/texts/143" } ], "references": [], @@ -21539,7 +21960,7 @@ { "self_ref": "#/tables/4", "parent": { - "$ref": "#/texts/186" + "$ref": "#/texts/208" }, "children": [], "content_layer": "body", @@ -21547,7 +21968,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/188" + "$ref": "#/texts/210" } ], "references": [], diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.md b/tests/data/jats/groundtruth/pone.0234687.nxml.md index 083dae4481..098b61f1a6 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.md +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.md @@ -6,7 +6,7 @@ Department of Animal Science, University of California, Davis, California, Unite ## Abstract -Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2) equivalents (CO2e) (kg energy-corrected milk (ECM))-1, encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1. The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) ad libitum intake, 75, and 50% of ad libitum TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1. Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1 in scenarios including pastures compared to ad libitum TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent. +Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO 2 ) equivalents (CO 2 e) (kg energy-corrected milk (ECM)) -1 , encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation -1 . The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) *ad libitum* intake, 75, and 50% of *ad libitum* TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO 2 e (kg ECM) -1 . Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO 2 e (kg ECM) -1 in scenarios including pastures compared to *ad libitum* TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent. ## Introduction diff --git a/tests/test_backend_jats.py b/tests/test_backend_jats.py index 4f4d79e619..66c3979ead 100644 --- a/tests/test_backend_jats.py +++ b/tests/test_backend_jats.py @@ -243,6 +243,144 @@ def test_jats_structured_abstract_sections_are_preserved(): assert "Methods" in heading_texts +def test_jats_plain_abstract_styling_is_preserved(): + doc = convert_jats_article_meta( + """ + Abstract Styling Test + +

We study Homo sapiens, key results, + H2O at 103 Pa, u, + old.

+ +""" + ) + + groups = _inline_group_items(doc) + assert len(groups) == 1 + assert [_formatting_tuple(item) for item in groups[0]] == [ + (DocItemLabel.TEXT, "We study", None), + ( + DocItemLabel.TEXT, + "Homo sapiens", + (False, True, False, False, Script.BASELINE), + ), + (DocItemLabel.TEXT, ",", None), + ( + DocItemLabel.TEXT, + "key", + (True, False, False, False, Script.BASELINE), + ), + ( + DocItemLabel.TEXT, + "results", + (True, True, False, False, Script.BASELINE), + ), + (DocItemLabel.TEXT, ", H", None), + (DocItemLabel.TEXT, "2", (False, False, False, False, Script.SUB)), + (DocItemLabel.TEXT, "O at 10", None), + (DocItemLabel.TEXT, "3", (False, False, False, False, Script.SUPER)), + (DocItemLabel.TEXT, "Pa,", None), + ( + DocItemLabel.TEXT, + "u", + (False, False, True, False, Script.BASELINE), + ), + (DocItemLabel.TEXT, ",", None), + ( + DocItemLabel.TEXT, + "old", + (False, False, False, True, Script.BASELINE), + ), + (DocItemLabel.TEXT, ".", None), + ] + + +def test_jats_structured_abstract_styling_is_preserved(): + doc = convert_jats_article_meta( + """ + Structured Abstract Styling Test + + + Background +

Bg text.

+ + + Methods +

M text.

+ + +""" + ) + + groups = _inline_group_items(doc) + assert len(groups) == 2 + assert [_formatting_tuple(item) for item in groups[0]] == [ + ( + DocItemLabel.TEXT, + "Bg", + (False, True, False, False, Script.BASELINE), + ), + (DocItemLabel.TEXT, "text.", None), + ] + assert [_formatting_tuple(item) for item in groups[1]] == [ + ( + DocItemLabel.TEXT, + "M", + (True, False, False, False, Script.BASELINE), + ), + (DocItemLabel.TEXT, "text.", None), + ] + + +def test_jats_plain_abstract_without_styling_stays_a_single_text_item(): + doc = convert_jats_article_meta( + """ + Plain Abstract Test +

Plain abstract.

 +""" + ) + + # no emphasis anywhere → a single TEXT item, no inline group + assert _inline_group_items(doc) == [] + texts = [t.text for t in doc.texts if t.label == DocItemLabel.TEXT] + assert texts == ["Plain abstract."] + + +def test_jats_footnote_styling_is_preserved(): + doc = convert_jats_body( + """ + + Footnote Styling Test + + + +

See ibid for details.

+ + + + """ + ) + + groups = _inline_group_items(doc) + assert len(groups) == 1 + assert [_formatting_tuple(item) for item in groups[0]] == [ + (DocItemLabel.FOOTNOTE, "1", None), + (DocItemLabel.FOOTNOTE, "See", None), + ( + DocItemLabel.FOOTNOTE, + "ibid", + (False, True, False, False, Script.BASELINE), + ), + (DocItemLabel.FOOTNOTE, "for", None), + ( + DocItemLabel.FOOTNOTE, + "details", + (True, False, False, False, Script.BASELINE), + ), + (DocItemLabel.FOOTNOTE, ".", None), + ] + + def test_jats_nested_lists_are_preserved(): doc = convert_jats_body( """ From 338a8fa99a952751509295096eb45c46dce12610 Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Wed, 23 Sep 2026 20:34:14 -0700 Subject: [PATCH 2/8] DCO Remediation Commit for Junyi Yao I, Junyi Yao , hereby add my Signed-off-by to this commit: a9a0960bb8560619d88c3065554d51e0c2009d09 Signed-off-by: Junyi Yao From 7431894de0e6d28fd2bfc2f1e98796fded33b71b Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Wed, 23 Sep 2026 20:51:22 -0700 Subject: [PATCH 3/8] fix(jats): keep source spacing across styled inline runs The docling-core serializers join sibling inline text items with a single space, so splitting a styled run off from adjacent text that had no whitespace in the source XML (e.g. `in vitro.` or `CO2`) exported spurious spaces (`in vitro .`, `CO 2`). Strip-then-join also destroyed the information of whether a boundary originally had whitespace. Add `_coalesce_no_space_boundaries`, run between whitespace normalization and boundary stripping in `_flattened_inline_runs` (abstracts and footnotes). At each spaceless run boundary it: 1. moves trailing opening punctuation (`(`, `[`, quotes) forward onto the next run; 2. moves leading closing punctuation (`.`, `,`, `)`, ...) backward onto the previous run; 3. fuses the two runs, keeping the non-baseline formatting when exactly one run carries it. Step 3 trades precise formatting scope for text fidelity: `CO2` keeps its subscript on the fused run instead of exporting `CO 2`. Formula runs and runs with different hyperlink targets are never fused. The body-paragraph path (`_emit_inline`) is untouched. Regenerate the three affected groundtruth fixtures; their exported text (modulo styling markers) is now byte-identical to the pre-PR output. Add `test_jats_plain_abstract_styling_keeps_source_spacing` covering italic+period/comma, `CO2e`, `(ECM))-1`, parens/brackets around styled runs, and ragged source whitespace. Signed-off-by: Junyi Yao --- docling/backend/xml/jats_backend.py | 113 +- .../jats/groundtruth/pmc2231364.nxml.itxt | 31 +- .../jats/groundtruth/pmc2231364.nxml.json | 83 +- .../data/jats/groundtruth/pmc2231364.nxml.md | 6 +- .../jats/groundtruth/pntd.0008301.nxml.itxt | 8 +- .../jats/groundtruth/pntd.0008301.nxml.json | 16 +- .../jats/groundtruth/pntd.0008301.nxml.md | 4 +- .../jats/groundtruth/pone.0234687.nxml.itxt | 1137 ++++---- .../jats/groundtruth/pone.0234687.nxml.json | 2290 ++++++++--------- .../jats/groundtruth/pone.0234687.nxml.md | 2 +- tests/test_backend_jats.py | 90 +- 11 files changed, 1869 insertions(+), 1911 deletions(-) diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py index f20fac5ec3..e012d355c7 100644 --- a/docling/backend/xml/jats_backend.py +++ b/docling/backend/xml/jats_backend.py @@ -80,6 +80,16 @@ DEFAULT_HEADER_REFERENCES: Final[str] = "References" DEFAULT_TEXT_ETAL: Final[str] = "et al." _XLINK_HREF: Final[str] = "{http://www.w3.org/1999/xlink}href" + +# Punctuation that typographically clings to the *following* run, e.g. the +# "(" in "(term)". Quotes are treated as opening only (never +# closing) so a quote cannot bounce back and forth between two runs. +_OPENING_PUNCTUATION: Final[str] = "([{\"'“‘" + +# Punctuation that typographically clings to the *preceding* run, e.g. the +# "." in "in vitro." or the ")" in "(CO2)". +_CLOSING_PUNCTUATION: Final[str] = ".,;:!?%)]}”’" + _RASTER_IMAGE_SUFFIXES: Final[tuple[str, ...]] = ( ".jpg", ".jpeg", @@ -786,15 +796,112 @@ def _strip_segments(segments: list[InlineSegment]) -> list[InlineSegment]: stripped.append(replace(segment, text=text)) return stripped + @staticmethod + def _is_unformatted(formatting: Formatting | None) -> bool: + return formatting is None or ( + not formatting.bold + and not formatting.italic + and not formatting.underline + and not formatting.strikethrough + and formatting.script in (None, Script.BASELINE) + ) + + @staticmethod + def _coalesce_no_space_boundaries( + segments: list[InlineSegment], + ) -> list[InlineSegment]: + """Fuse runs across boundaries where the source XML had no whitespace. + + The docling-core serializers join sibling inline text items with a + single space, so a run boundary that had no whitespace in the source + (e.g. ``in vitro.`` or ``CO2``) would gain + a spurious space on export (``in vitro .``, ``CO 2``). Because + boundary whitespace is stripped before serialization, the information + "there was no space here" has to be acted on while it is still + available, i.e. here. + + At each spaceless boundary, in order: + + 1. trailing opening punctuation (``(``, ``[``, quotes, ...) moves + forward onto the next run; + 2. leading closing punctuation (``.``, ``,``, ``)``, ...) moves + backward onto the previous run; + 3. the runs are fused into one, keeping the non-baseline formatting + when exactly one of the two runs carries it, otherwise the + earlier run's formatting. + + Step 3 trades precise formatting scope for text fidelity: e.g. the + ``2`` in ``CO2`` keeps its subscript by absorbing the + adjacent ``CO``, because the alternative is exporting ``CO 2``. + Formula runs and runs with different hyperlink targets are never + fused. Punctuation absorbed by steps 1-2 renders identically in + every exporter, so those fusions are lossless. + """ + fused: list[InlineSegment] = [] + for segment in segments: + if not segment.text: + continue + while True: + if not fused: + fused.append(segment) + break + prev = fused[-1] + if ( + prev.label == DocItemLabel.FORMULA + or segment.label == DocItemLabel.FORMULA + or prev.hyperlink != segment.hyperlink + ): + fused.append(segment) + break + if prev.text.endswith(" ") or segment.text.startswith(" "): + fused.append(segment) + break + # 1. trailing opening punctuation belongs with the next run. + if prev.text[-1] in _OPENING_PUNCTUATION: + if len(prev.text) > 1: + fused[-1] = replace(prev, text=prev.text[:-1]) + segment = replace(segment, text=prev.text[-1] + segment.text) + else: + # prev is a lone opening mark: absorb it into segment. + lone = fused.pop() + segment = replace(segment, text=lone.text + segment.text) + continue + # 2. leading closing punctuation belongs with the previous run. + if segment.text[0] in _CLOSING_PUNCTUATION: + fused[-1] = replace(prev, text=prev.text + segment.text[0]) + segment = replace(segment, text=segment.text[1:]) + if not segment.text: + break + continue + # 3. fuse the runs, preferring non-baseline formatting. + if JatsDocumentBackend._is_unformatted( + prev.formatting + ) and not JatsDocumentBackend._is_unformatted(segment.formatting): + formatting = segment.formatting + else: + formatting = prev.formatting + fused[-1] = replace( + prev, text=prev.text + segment.text, formatting=formatting + ) + break + return fused + @staticmethod def _flattened_inline_runs(node: etree._Element) -> list[InlineSegment]: """Styled inline runs for ``node``, mirroring the historical flattened-text behavior of abstracts/footnotes: whitespace normalized, boundary whitespace stripped, styling (bold/italic/sub/sup, ...) - preserved per run.""" + preserved per run. + + Runs are additionally fused across boundaries where the source XML + had no whitespace (see ``_coalesce_no_space_boundaries``), because + the serializers join sibling inline text items with a space. + """ return JatsDocumentBackend._strip_segments( - JatsDocumentBackend._normalize_segments( - JatsDocumentBackend._walk_inline_formula(node) + JatsDocumentBackend._coalesce_no_space_boundaries( + JatsDocumentBackend._normalize_segments( + JatsDocumentBackend._walk_inline_formula(node) + ) ) ) diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt index c314c160b2..a97c3197af 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt @@ -7,19 +7,18 @@ item-0 at level 0: unspecified: group _root_ item-6 at level 5: text: Environmental modulation of gene expression in item-7 at level 5: text: Yersinia pestis item-8 at level 5: text: is critical for its life style a ... rown under different stress conditions - item-9 at level 5: text: in vitro - item-10 at level 5: text: . - item-11 at level 3: section_header: Results - item-12 at level 4: inline: group group - item-13 at level 5: text: To provide us with a comprehensi ... odulation of global gene expression in - item-14 at level 5: text: Y. pestis - item-15 at level 5: text: , we have analyzed the gene expr ... s. Almost all known virulence genes of - item-16 at level 5: text: Y. pestis - item-17 at level 5: text: were differentially regulated un ... ophoretic mobility shift assay (EMSA). - item-18 at level 3: section_header: Conclusion - item-19 at level 4: inline: group group - item-20 at level 5: text: The comparative transcriptomics ... is and cellular regulatory circuits in - item-21 at level 5: text: Y. pestis - item-22 at level 5: text: , it also serves as a basis for ... icroarray data using existing methods. - item-23 at level 2: section_header: Introduction - item-24 at level 3: text: Yersinia pestis is the causative ... infectious diseases in human history. \ No newline at end of file + item-9 at level 5: text: in vitro. + item-10 at level 3: section_header: Results + item-11 at level 4: inline: group group + item-12 at level 5: text: To provide us with a comprehensi ... odulation of global gene expression in + item-13 at level 5: text: Y. pestis, + item-14 at level 5: text: we have analyzed the gene expres ... s. Almost all known virulence genes of + item-15 at level 5: text: Y. pestis + item-16 at level 5: text: were differentially regulated un ... ophoretic mobility shift assay (EMSA). + item-17 at level 3: section_header: Conclusion + item-18 at level 4: inline: group group + item-19 at level 5: text: The comparative transcriptomics ... is and cellular regulatory circuits in + item-20 at level 5: text: Y. pestis, + item-21 at level 5: text: it also serves as a basis for in ... icroarray data using existing methods. + item-22 at level 2: section_header: Introduction + item-23 at level 3: text: Yersinia pestis is the causative ... infectious diseases in human history. \ No newline at end of file diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.json b/tests/data/jats/groundtruth/pmc2231364.nxml.json index 86fff25b2e..498b3d7131 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.json +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.json @@ -43,9 +43,6 @@ }, { "$ref": "#/texts/7" - }, - { - "$ref": "#/texts/8" } ], "content_layer": "body", @@ -55,9 +52,12 @@ { "self_ref": "#/groups/1", "parent": { - "$ref": "#/texts/9" + "$ref": "#/texts/8" }, "children": [ + { + "$ref": "#/texts/9" + }, { "$ref": "#/texts/10" }, @@ -69,9 +69,6 @@ }, { "$ref": "#/texts/13" - }, - { - "$ref": "#/texts/14" } ], "content_layer": "body", @@ -81,17 +78,17 @@ { "self_ref": "#/groups/2", "parent": { - "$ref": "#/texts/15" + "$ref": "#/texts/14" }, "children": [ { - "$ref": "#/texts/16" + "$ref": "#/texts/15" }, { - "$ref": "#/texts/17" + "$ref": "#/texts/16" }, { - "$ref": "#/texts/18" + "$ref": "#/texts/17" } ], "content_layer": "body", @@ -113,7 +110,7 @@ "$ref": "#/texts/2" }, { - "$ref": "#/texts/19" + "$ref": "#/texts/18" } ], "content_layer": "body", @@ -144,10 +141,10 @@ "$ref": "#/texts/3" }, { - "$ref": "#/texts/9" + "$ref": "#/texts/8" }, { - "$ref": "#/texts/15" + "$ref": "#/texts/14" } ], "content_layer": "body", @@ -226,8 +223,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "in vitro", - "text": "in vitro", + "orig": "in vitro.", + "text": "in vitro.", "formatting": { "bold": false, "italic": true, @@ -238,18 +235,6 @@ }, { "self_ref": "#/texts/8", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": ".", - "text": "." - }, - { - "self_ref": "#/texts/9", "parent": { "$ref": "#/texts/2" }, @@ -266,7 +251,7 @@ "level": 2 }, { - "self_ref": "#/texts/10", + "self_ref": "#/texts/9", "parent": { "$ref": "#/groups/1" }, @@ -278,7 +263,7 @@ "text": "To provide us with a comprehensive view of environmental modulation of global gene expression in" }, { - "self_ref": "#/texts/11", + "self_ref": "#/texts/10", "parent": { "$ref": "#/groups/1" }, @@ -286,8 +271,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Y. pestis", - "text": "Y. pestis", + "orig": "Y. pestis,", + "text": "Y. pestis,", "formatting": { "bold": false, "italic": true, @@ -297,7 +282,7 @@ } }, { - "self_ref": "#/texts/12", + "self_ref": "#/texts/11", "parent": { "$ref": "#/groups/1" }, @@ -305,11 +290,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of", - "text": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of" + "orig": "we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of", + "text": "we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of" }, { - "self_ref": "#/texts/13", + "self_ref": "#/texts/12", "parent": { "$ref": "#/groups/1" }, @@ -328,7 +313,7 @@ } }, { - "self_ref": "#/texts/14", + "self_ref": "#/texts/13", "parent": { "$ref": "#/groups/1" }, @@ -340,7 +325,7 @@ "text": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA)." }, { - "self_ref": "#/texts/15", + "self_ref": "#/texts/14", "parent": { "$ref": "#/texts/2" }, @@ -357,7 +342,7 @@ "level": 2 }, { - "self_ref": "#/texts/16", + "self_ref": "#/texts/15", "parent": { "$ref": "#/groups/2" }, @@ -369,7 +354,7 @@ "text": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in" }, { - "self_ref": "#/texts/17", + "self_ref": "#/texts/16", "parent": { "$ref": "#/groups/2" }, @@ -377,8 +362,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Y. pestis", - "text": "Y. pestis", + "orig": "Y. pestis,", + "text": "Y. pestis,", "formatting": { "bold": false, "italic": true, @@ -388,7 +373,7 @@ } }, { - "self_ref": "#/texts/18", + "self_ref": "#/texts/17", "parent": { "$ref": "#/groups/2" }, @@ -396,17 +381,17 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", - "text": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods." + "orig": "it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", + "text": "it also serves as a basis for integrating increasing volumes of microarray data using existing methods." }, { - "self_ref": "#/texts/19", + "self_ref": "#/texts/18", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/20" + "$ref": "#/texts/19" } ], "content_layer": "body", @@ -417,9 +402,9 @@ "level": 1 }, { - "self_ref": "#/texts/20", + "self_ref": "#/texts/19", "parent": { - "$ref": "#/texts/19" + "$ref": "#/texts/18" }, "children": [], "content_layer": "body", diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.md b/tests/data/jats/groundtruth/pmc2231364.nxml.md index a1e10a0c8f..9d53ccda2f 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.md +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.md @@ -6,15 +6,15 @@ Yiquan Hu, Yarong Miao ### Background -Environmental modulation of gene expression in *Yersinia pestis* is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions *in vitro* . +Environmental modulation of gene expression in *Yersinia pestis* is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions *in vitro.* ### Results -To provide us with a comprehensive view of environmental modulation of global gene expression in *Y. pestis* , we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of *Y. pestis* were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). +To provide us with a comprehensive view of environmental modulation of global gene expression in *Y. pestis,* we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of *Y. pestis* were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). ### Conclusion -The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in *Y. pestis* , it also serves as a basis for integrating increasing volumes of microarray data using existing methods. +The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in *Y. pestis,* it also serves as a basis for integrating increasing volumes of microarray data using existing methods. ## Introduction diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt index c02654ddaa..e6b6da2b8b 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt @@ -5,13 +5,13 @@ item-0 at level 0: unspecified: group _root_ item-4 at level 2: section_header: Abstract item-5 at level 3: inline: group group item-6 at level 4: text: Achieving elimination of lymphat ... s Test Strips (FTS), primary vector of - item-7 at level 4: text: Culex - item-8 at level 4: text: , treatment with diethylcarbamaz ... as at highest risk of failing pre-TAS. + item-7 at level 4: text: Culex, + item-8 at level 4: text: treatment with diethylcarbamazin ... as at highest risk of failing pre-TAS. item-9 at level 2: section_header: Author summary item-10 at level 3: inline: group group item-11 at level 4: text: Achieving elimination of lymphat ... 10%, use of the FTS, primary vector of - item-12 at level 4: text: Culex - item-13 at level 4: text: , treatment with diethylcarbamaz ... ine prevalence and/or lower elevation. + item-12 at level 4: text: Culex, + item-13 at level 4: text: treatment with diethylcarbamazin ... ine prevalence and/or lower elevation. item-14 at level 2: section_header: Introduction item-15 at level 3: text: Lymphatic filariasis (LF), a dis ... 8 countries remain endemic for LF [3]. item-16 at level 3: text: The road to elimination as a pub ... t elimination be officially validated. diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.json b/tests/data/jats/groundtruth/pntd.0008301.nxml.json index 0221913779..44aac95a2c 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.json +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.json @@ -702,8 +702,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Culex", - "text": "Culex", + "orig": "Culex,", + "text": "Culex,", "formatting": { "bold": false, "italic": true, @@ -721,8 +721,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ", treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS.", - "text": ", treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS." + "orig": "treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS.", + "text": "treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS." }, { "self_ref": "#/texts/7", @@ -762,8 +762,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Culex", - "text": "Culex", + "orig": "Culex,", + "text": "Culex,", "formatting": { "bold": false, "italic": true, @@ -781,8 +781,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ", treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation.", - "text": ", treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation." + "orig": "treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation.", + "text": "treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation." }, { "self_ref": "#/texts/11", diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.md b/tests/data/jats/groundtruth/pntd.0008301.nxml.md index f3c86f3713..cce6818a64 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.md +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.md @@ -6,11 +6,11 @@ Global Health Division, RTI International, Washington, DC, United States of Amer ## Abstract -Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of *Culex* , treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS. +Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of *Culex,* treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS. ## Author summary -Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of *Culex* , treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation. +Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of *Culex,* treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation. ## Introduction diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt index 05490bad52..3005ba5a49 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt @@ -4,595 +4,584 @@ item-0 at level 0: unspecified: group _root_ item-3 at level 2: paragraph: Department of Animal Science, Un ... atarina, Lages, Santa Catarina, Brazil item-4 at level 2: section_header: Abstract item-5 at level 3: inline: group group - item-6 at level 4: text: Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO - item-7 at level 4: text: 2 - item-8 at level 4: text: ) equivalents (CO - item-9 at level 4: text: 2 - item-10 at level 4: text: e) (kg energy-corrected milk (ECM)) - item-11 at level 4: text: -1 - item-12 at level 4: text: , encompasses emissions from fee ... g an average of 7,000 kg ECM lactation - item-13 at level 4: text: -1 - item-14 at level 4: text: . The milk production response a ... re evaluated: total mixed ration (TMR) - item-15 at level 4: text: ad libitum - item-16 at level 4: text: intake, 75, and 50% of - item-17 at level 4: text: ad libitum - item-18 at level 4: text: TMR intake with access to grazin ... etween scenarios, averaging 1.06 kg CO - item-19 at level 4: text: 2 - item-20 at level 4: text: e (kg ECM) - item-21 at level 4: text: -1 - item-22 at level 4: text: . Considering factors from studi ... , the C footprint decreased 0.04 kg CO + item-6 at level 4: text: Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2) + item-7 at level 4: text: equivalents (CO2e) (kg energy-corrected milk (ECM))-1, + item-8 at level 4: text: encompasses emissions from feed ... n average of 7,000 kg ECM lactation-1. + item-9 at level 4: text: The milk production response as ... re evaluated: total mixed ration (TMR) + item-10 at level 4: text: ad libitum + item-11 at level 4: text: intake, 75, and 50% of + item-12 at level 4: text: ad libitum + item-13 at level 4: text: TMR intake with access to grazin ... os, averaging 1.06 kg CO2e (kg ECM)-1. + item-14 at level 4: text: Considering factors from studies ... rint decreased 0.04 kg CO2e (kg ECM)-1 + item-15 at level 4: text: in scenarios including pastures compared to + item-16 at level 4: text: ad libitum + item-17 at level 4: text: TMR. Regardless of factors consi ... uce the C footprint to a small extent. + item-18 at level 2: section_header: Introduction + item-19 at level 3: inline: group group + item-20 at level 4: text: Greenhouse gas (GHG) emissions f ... ssions [1], ranging from 5.5–7.5 Gt CO + item-21 at level 4: text: 2 + item-22 at level 4: text: equivalents (CO item-23 at level 4: text: 2 - item-24 at level 4: text: e (kg ECM) + item-24 at level 4: text: e) yr item-25 at level 4: text: -1 - item-26 at level 4: text: in scenarios including pastures compared to - item-27 at level 4: text: ad libitum - item-28 at level 4: text: TMR. Regardless of factors consi ... uce the C footprint to a small extent. - item-29 at level 2: section_header: Introduction - item-30 at level 3: inline: group group - item-31 at level 4: text: Greenhouse gas (GHG) emissions f ... ssions [1], ranging from 5.5–7.5 Gt CO - item-32 at level 4: text: 2 - item-33 at level 4: text: equivalents (CO - item-34 at level 4: text: 2 - item-35 at level 4: text: e) yr - item-36 at level 4: text: -1 - item-37 at level 4: text: , with almost 30% coming from da ... suitable for food crop production [4]. - item-38 at level 3: inline: group group - item-39 at level 4: text: Considering the key role of live ... n investigated to mitigate methane (CH - item-40 at level 4: text: 4 - item-41 at level 4: text: ) emissions from enteric ferment ... ment [6] and manure management [7]. CH - item-42 at level 4: text: 4 - item-43 at level 4: text: emissions from enteric fermentat ... anagement to mitigate the C footprint. - item-44 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]). - item-45 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake. - item-46 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated. - item-47 at level 2: section_header: Materials and methods - item-48 at level 3: inline: group group - item-49 at level 4: text: An LCA was developed according t ... 15, 2016—Approval number 4373090816 - - item-50 at level 4: text: https://www.udesc.br/cav/ceua - item-51 at level 4: text: . - item-52 at level 3: section_header: System boundary - item-53 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary. - item-54 at level 4: picture - item-54 at level 5: caption: Fig 1 Overview of the milk production system boundary considered in the study. - item-55 at level 3: section_header: Functional unit - item-56 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows: - item-57 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1. - item-58 at level 4: table with [13x3] - item-58 at level 5: caption: Table 1 Descriptive characteristics of the herd. - item-59 at level 3: section_header: Data sources and livestock system description - item-60 at level 4: inline: group group - item-61 at level 5: text: The individual feed requirements ... cows that received both 75 and 50% of - item-62 at level 5: text: ad libitum - item-63 at level 5: text: TMR intake with access to grazing a tropical pasture (pearl-millet, - item-64 at level 5: text: Pennisetum glaucum - item-65 at level 5: text: ‘Campeiro’) compared to cows receiving - item-66 at level 5: text: ad libitum - item-67 at level 5: text: TMR intake. Cows grazing on a temperate pasture (ryegrass, - item-68 at level 5: text: Lolium multiflorum - item-69 at level 5: text: ‘Maximus’) did not need changes to ECM production compared to the - item-70 at level 5: text: ad libitum - item-71 at level 5: text: TMR intake group. - item-72 at level 4: inline: group group - item-73 at level 5: text: Using experimental data, three s ... evaluated during the lactation period: - item-74 at level 5: text: ad libitum - item-75 at level 5: text: TMR intake, and 75, and 50% of - item-76 at level 5: text: ad libitum - item-77 at level 5: text: TMR intake with access to grazin ... nction of month ([26], Civiero et al., - item-78 at level 5: text: in press - item-79 at level 5: text: ). From April to October (210 da ... med during an entire lactation period. - item-80 at level 3: section_header: Impact assessment - item-81 at level 4: inline: group group - item-82 at level 5: text: The CO - item-83 at level 5: text: 2 - item-84 at level 5: text: e emissions were calculated by multiplying the emissions of CO - item-85 at level 5: text: 2 - item-86 at level 5: text: , CH - item-87 at level 5: text: 4 - item-88 at level 5: text: and N - item-89 at level 5: text: 2 - item-90 at level 5: text: O by their 100-year global warming potential (GWP - item-91 at level 5: text: 100 - item-92 at level 5: text: ), based on IPCC assessment report 5 (AR5; [27]). The values of GWP - item-93 at level 5: text: 100 - item-94 at level 5: text: are 1, 28 and 265 for CO - item-95 at level 5: text: 2 - item-96 at level 5: text: , CH - item-97 at level 5: text: 4 - item-98 at level 5: text: and N - item-99 at level 5: text: 2 - item-100 at level 5: text: O, respectively. - item-101 at level 3: section_header: Feed production - item-102 at level 4: section_header: Diets composition - item-103 at level 5: inline: group group - item-104 at level 6: text: The DM intake of each ingredient ... ennial tropical pasture (kikuyu grass, - item-105 at level 6: text: Pennisetum clandestinum - item-106 at level 6: text: ). The DM intake of calves, heif ... meet the net energy for lactation (NE - item-107 at level 6: text: L - item-108 at level 6: text: ) and metabolizable protein (MP) ... grated in the software INRAtion 4.07 ( - item-109 at level 6: text: https://www.inration.educagri.fr/fr/forum.php - item-110 at level 6: text: ). The nutrient intake was calcu ... collected throughout the experiments. - item-111 at level 5: table with [21x11] - item-111 at level 6: caption: Table 2 Dairy cows’ diets in different scenariosa. - item-112 at level 4: section_header: GHG emissions from crop and pasture production - item-113 at level 5: inline: group group - item-114 at level 6: text: GHG emission factors used for of ... s productions were 3300 and 1500 kg CO + item-26 at level 4: text: , with almost 30% coming from da ... suitable for food crop production [4]. + item-27 at level 3: inline: group group + item-28 at level 4: text: Considering the key role of live ... n investigated to mitigate methane (CH + item-29 at level 4: text: 4 + item-30 at level 4: text: ) emissions from enteric ferment ... ment [6] and manure management [7]. CH + item-31 at level 4: text: 4 + item-32 at level 4: text: emissions from enteric fermentat ... anagement to mitigate the C footprint. + item-33 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]). + item-34 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake. + item-35 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated. + item-36 at level 2: section_header: Materials and methods + item-37 at level 3: inline: group group + item-38 at level 4: text: An LCA was developed according t ... 15, 2016—Approval number 4373090816 - + item-39 at level 4: text: https://www.udesc.br/cav/ceua + item-40 at level 4: text: . + item-41 at level 3: section_header: System boundary + item-42 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary. + item-43 at level 4: picture + item-43 at level 5: caption: Fig 1 Overview of the milk production system boundary considered in the study. + item-44 at level 3: section_header: Functional unit + item-45 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows: + item-46 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1. + item-47 at level 4: table with [13x3] + item-47 at level 5: caption: Table 1 Descriptive characteristics of the herd. + item-48 at level 3: section_header: Data sources and livestock system description + item-49 at level 4: inline: group group + item-50 at level 5: text: The individual feed requirements ... cows that received both 75 and 50% of + item-51 at level 5: text: ad libitum + item-52 at level 5: text: TMR intake with access to grazing a tropical pasture (pearl-millet, + item-53 at level 5: text: Pennisetum glaucum + item-54 at level 5: text: ‘Campeiro’) compared to cows receiving + item-55 at level 5: text: ad libitum + item-56 at level 5: text: TMR intake. Cows grazing on a temperate pasture (ryegrass, + item-57 at level 5: text: Lolium multiflorum + item-58 at level 5: text: ‘Maximus’) did not need changes to ECM production compared to the + item-59 at level 5: text: ad libitum + item-60 at level 5: text: TMR intake group. + item-61 at level 4: inline: group group + item-62 at level 5: text: Using experimental data, three s ... evaluated during the lactation period: + item-63 at level 5: text: ad libitum + item-64 at level 5: text: TMR intake, and 75, and 50% of + item-65 at level 5: text: ad libitum + item-66 at level 5: text: TMR intake with access to grazin ... nction of month ([26], Civiero et al., + item-67 at level 5: text: in press + item-68 at level 5: text: ). From April to October (210 da ... med during an entire lactation period. + item-69 at level 3: section_header: Impact assessment + item-70 at level 4: inline: group group + item-71 at level 5: text: The CO + item-72 at level 5: text: 2 + item-73 at level 5: text: e emissions were calculated by multiplying the emissions of CO + item-74 at level 5: text: 2 + item-75 at level 5: text: , CH + item-76 at level 5: text: 4 + item-77 at level 5: text: and N + item-78 at level 5: text: 2 + item-79 at level 5: text: O by their 100-year global warming potential (GWP + item-80 at level 5: text: 100 + item-81 at level 5: text: ), based on IPCC assessment report 5 (AR5; [27]). The values of GWP + item-82 at level 5: text: 100 + item-83 at level 5: text: are 1, 28 and 265 for CO + item-84 at level 5: text: 2 + item-85 at level 5: text: , CH + item-86 at level 5: text: 4 + item-87 at level 5: text: and N + item-88 at level 5: text: 2 + item-89 at level 5: text: O, respectively. + item-90 at level 3: section_header: Feed production + item-91 at level 4: section_header: Diets composition + item-92 at level 5: inline: group group + item-93 at level 6: text: The DM intake of each ingredient ... ennial tropical pasture (kikuyu grass, + item-94 at level 6: text: Pennisetum clandestinum + item-95 at level 6: text: ). The DM intake of calves, heif ... meet the net energy for lactation (NE + item-96 at level 6: text: L + item-97 at level 6: text: ) and metabolizable protein (MP) ... grated in the software INRAtion 4.07 ( + item-98 at level 6: text: https://www.inration.educagri.fr/fr/forum.php + item-99 at level 6: text: ). The nutrient intake was calcu ... collected throughout the experiments. + item-100 at level 5: table with [21x11] + item-100 at level 6: caption: Table 2 Dairy cows’ diets in different scenariosa. + item-101 at level 4: section_header: GHG emissions from crop and pasture production + item-102 at level 5: inline: group group + item-103 at level 6: text: GHG emission factors used for of ... s productions were 3300 and 1500 kg CO + item-104 at level 6: text: 2 + item-105 at level 6: text: e ha + item-106 at level 6: text: -1 + item-107 at level 6: text: , respectively [32]. The DM production (kg ha + item-108 at level 6: text: -1 + item-109 at level 6: text: ) of corn silage and pastures we ... onsume 70% of pastures during grazing. + item-110 at level 5: table with [9x5] + item-110 at level 6: caption: Table 3 GHG emission factors for Off- and On-farm feed production. + item-111 at level 5: inline: group group + item-112 at level 6: text: Emissions from on-farm feed prod ... ary sources were direct and indirect N + item-113 at level 6: text: 2 + item-114 at level 6: text: O-N emissions from organic and s ... tilizers and crop/pasture residues, CO item-115 at level 6: text: 2 - item-116 at level 6: text: e ha - item-117 at level 6: text: -1 - item-118 at level 6: text: , respectively [32]. The DM production (kg ha + item-116 at level 6: text: -C emissions from lime and urea ... well as fuel combustion. The direct N + item-117 at level 6: text: 2 + item-118 at level 6: text: O-N emission factor (kg (kg N input) item-119 at level 6: text: -1 - item-120 at level 6: text: ) of corn silage and pastures we ... onsume 70% of pastures during grazing. - item-121 at level 5: table with [9x5] - item-121 at level 6: caption: Table 3 GHG emission factors for Off- and On-farm feed production. - item-122 at level 5: inline: group group - item-123 at level 6: text: Emissions from on-farm feed prod ... ary sources were direct and indirect N - item-124 at level 6: text: 2 - item-125 at level 6: text: O-N emissions from organic and s ... tilizers and crop/pasture residues, CO - item-126 at level 6: text: 2 - item-127 at level 6: text: -C emissions from lime and urea ... well as fuel combustion. The direct N - item-128 at level 6: text: 2 - item-129 at level 6: text: O-N emission factor (kg (kg N input) - item-130 at level 6: text: -1 - item-131 at level 6: text: ) is based on a local study performed previously [37]. For indirect N - item-132 at level 6: text: 2 - item-133 at level 6: text: O-N emissions (kg N - item-134 at level 6: text: 2 - item-135 at level 6: text: O-N (kg NH - item-136 at level 6: text: 3 - item-137 at level 6: text: -N + NO - item-138 at level 6: text: x - item-139 at level 6: text: ) - item-140 at level 6: text: -1 - item-141 at level 6: text: ), as well as CO - item-142 at level 6: text: 2 - item-143 at level 6: text: -C emissions from lime + urea, d ... stures, a C sequestration of 0.57 t ha - item-144 at level 6: text: -1 - item-145 at level 6: text: was used based on a 9-year study ... red was 8.9 (no-tillage) and 14.3 L ha - item-146 at level 6: text: -1 - item-147 at level 6: text: (disking) for annual tropical an ... te pastures, respectively [40]. The CO - item-148 at level 6: text: 2 - item-149 at level 6: text: from fuel combustion was 2.7 kg CO - item-150 at level 6: text: 2 - item-151 at level 6: text: L - item-152 at level 6: text: -1 - item-153 at level 6: text: [41]. Secondary sources of emiss ... factors described by Rotz et al. [42]. - item-154 at level 5: table with [28x5] - item-154 at level 6: caption: Table 4 GHG emissions from On-farm feed production. - item-155 at level 3: section_header: Animal husbandry - item-156 at level 4: inline: group group - item-157 at level 5: text: The CH - item-158 at level 5: text: 4 - item-159 at level 5: text: emissions from enteric fermentation intensity (g (kg ECM) - item-160 at level 5: text: -1 - item-161 at level 5: text: ) was a function of estimated CH - item-162 at level 5: text: 4 - item-163 at level 5: text: yield (g (kg DM intake) - item-164 at level 5: text: -1 - item-165 at level 5: text: ), actual DM intake and ECM. The enteric CH - item-166 at level 5: text: 4 - item-167 at level 5: text: yield was estimated as a functio ... proposed by Niu et al. [43], where: CH + item-120 at level 6: text: ) is based on a local study performed previously [37]. For indirect N + item-121 at level 6: text: 2 + item-122 at level 6: text: O-N emissions (kg N + item-123 at level 6: text: 2 + item-124 at level 6: text: O-N (kg NH + item-125 at level 6: text: 3 + item-126 at level 6: text: -N + NO + item-127 at level 6: text: x + item-128 at level 6: text: ) + item-129 at level 6: text: -1 + item-130 at level 6: text: ), as well as CO + item-131 at level 6: text: 2 + item-132 at level 6: text: -C emissions from lime + urea, d ... stures, a C sequestration of 0.57 t ha + item-133 at level 6: text: -1 + item-134 at level 6: text: was used based on a 9-year study ... red was 8.9 (no-tillage) and 14.3 L ha + item-135 at level 6: text: -1 + item-136 at level 6: text: (disking) for annual tropical an ... te pastures, respectively [40]. The CO + item-137 at level 6: text: 2 + item-138 at level 6: text: from fuel combustion was 2.7 kg CO + item-139 at level 6: text: 2 + item-140 at level 6: text: L + item-141 at level 6: text: -1 + item-142 at level 6: text: [41]. Secondary sources of emiss ... factors described by Rotz et al. [42]. + item-143 at level 5: table with [28x5] + item-143 at level 6: caption: Table 4 GHG emissions from On-farm feed production. + item-144 at level 3: section_header: Animal husbandry + item-145 at level 4: inline: group group + item-146 at level 5: text: The CH + item-147 at level 5: text: 4 + item-148 at level 5: text: emissions from enteric fermentation intensity (g (kg ECM) + item-149 at level 5: text: -1 + item-150 at level 5: text: ) was a function of estimated CH + item-151 at level 5: text: 4 + item-152 at level 5: text: yield (g (kg DM intake) + item-153 at level 5: text: -1 + item-154 at level 5: text: ), actual DM intake and ECM. The enteric CH + item-155 at level 5: text: 4 + item-156 at level 5: text: yield was estimated as a functio ... proposed by Niu et al. [43], where: CH + item-157 at level 5: text: 4 + item-158 at level 5: text: yield (g (kg DM intake) + item-159 at level 5: text: -1 + item-160 at level 5: text: ) = 13.8 + 0.185 × NDF (% DM intake). + item-161 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals + item-162 at level 4: inline: group group + item-163 at level 5: text: The CH + item-164 at level 5: text: 4 + item-165 at level 5: text: emission from manure (kg (kg ECM) + item-166 at level 5: text: -1 + item-167 at level 5: text: ) was a function of daily CH item-168 at level 5: text: 4 - item-169 at level 5: text: yield (g (kg DM intake) + item-169 at level 5: text: emission from manure (kg cow item-170 at level 5: text: -1 - item-171 at level 5: text: ) = 13.8 + 0.185 × NDF (% DM intake). - item-172 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals - item-173 at level 4: inline: group group - item-174 at level 5: text: The CH - item-175 at level 5: text: 4 - item-176 at level 5: text: emission from manure (kg (kg ECM) - item-177 at level 5: text: -1 - item-178 at level 5: text: ) was a function of daily CH - item-179 at level 5: text: 4 - item-180 at level 5: text: emission from manure (kg cow - item-181 at level 5: text: -1 - item-182 at level 5: text: ) and daily ECM (kg cow - item-183 at level 5: text: -1 - item-184 at level 5: text: ). The daily CH - item-185 at level 5: text: 4 - item-186 at level 5: text: emission from manure was estimat ... olatile solid (VS) excreted (kg DM cow - item-187 at level 5: text: -1 - item-188 at level 5: text: ) in manure. The daily VS was es ... n an organic matter (OM) basis (kg day - item-189 at level 5: text: -1 - item-190 at level 5: text: ), NDOMI = non-digestible OM intake (kg day - item-191 at level 5: text: -1 - item-192 at level 5: text: ): (1- OM digestibility) × OM in ... .04), GE = gross energy intake (MJ day - item-193 at level 5: text: -1 - item-194 at level 5: text: ), OM = organic matter (g), 18.4 ... tor for dietary GE per kg of DM (MJ kg - item-195 at level 5: text: -1 - item-196 at level 5: text: ). - item-197 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively. - item-198 at level 4: inline: group group - item-199 at level 5: text: The N - item-200 at level 5: text: 2 - item-201 at level 5: text: O-N emissions from urine and fec ... ations 10 and 12, respectively). The N - item-202 at level 5: text: 2 - item-203 at level 5: text: O emissions from stored manure a ... alculated based on the conversion of N - item-204 at level 5: text: 2 - item-205 at level 5: text: O-N emissions to N - item-206 at level 5: text: 2 - item-207 at level 5: text: O emissions, where N - item-208 at level 5: text: 2 - item-209 at level 5: text: O emissions = N - item-210 at level 5: text: 2 - item-211 at level 5: text: O-N emissions × 44/28. The emission factors were 0.002 kg N - item-212 at level 5: text: 2 - item-213 at level 5: text: O-N (kg N) - item-214 at level 5: text: -1 - item-215 at level 5: text: stored in a pit below animal confinements, and 0.02 kg N - item-216 at level 5: text: 2 - item-217 at level 5: text: O-N (kg of urine and dung) + item-171 at level 5: text: ) and daily ECM (kg cow + item-172 at level 5: text: -1 + item-173 at level 5: text: ). The daily CH + item-174 at level 5: text: 4 + item-175 at level 5: text: emission from manure was estimat ... olatile solid (VS) excreted (kg DM cow + item-176 at level 5: text: -1 + item-177 at level 5: text: ) in manure. The daily VS was es ... n an organic matter (OM) basis (kg day + item-178 at level 5: text: -1 + item-179 at level 5: text: ), NDOMI = non-digestible OM intake (kg day + item-180 at level 5: text: -1 + item-181 at level 5: text: ): (1- OM digestibility) × OM in ... .04), GE = gross energy intake (MJ day + item-182 at level 5: text: -1 + item-183 at level 5: text: ), OM = organic matter (g), 18.4 ... tor for dietary GE per kg of DM (MJ kg + item-184 at level 5: text: -1 + item-185 at level 5: text: ). + item-186 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively. + item-187 at level 4: inline: group group + item-188 at level 5: text: The N + item-189 at level 5: text: 2 + item-190 at level 5: text: O-N emissions from urine and fec ... ations 10 and 12, respectively). The N + item-191 at level 5: text: 2 + item-192 at level 5: text: O emissions from stored manure a ... alculated based on the conversion of N + item-193 at level 5: text: 2 + item-194 at level 5: text: O-N emissions to N + item-195 at level 5: text: 2 + item-196 at level 5: text: O emissions, where N + item-197 at level 5: text: 2 + item-198 at level 5: text: O emissions = N + item-199 at level 5: text: 2 + item-200 at level 5: text: O-N emissions × 44/28. The emission factors were 0.002 kg N + item-201 at level 5: text: 2 + item-202 at level 5: text: O-N (kg N) + item-203 at level 5: text: -1 + item-204 at level 5: text: stored in a pit below animal confinements, and 0.02 kg N + item-205 at level 5: text: 2 + item-206 at level 5: text: O-N (kg of urine and dung) + item-207 at level 5: text: -1 + item-208 at level 5: text: deposited on pasture [38]. The indirect N + item-209 at level 5: text: 2 + item-210 at level 5: text: O emissions from storage manure ... using the IPCC [38] emission factors. + item-211 at level 3: section_header: Farm management + item-212 at level 4: text: Emissions due to farm management ... crop and pasture production’ section. + item-213 at level 4: table with [12x4] + item-213 at level 5: caption: Table 5 Factors for major resource inputs in farm management. + item-214 at level 4: inline: group group + item-215 at level 5: text: The amount of fuel use for manur ... quired for manure handling (L diesel t + item-216 at level 5: text: -1 + item-217 at level 5: text: ) [42]. The amount of manure was estimated from OM excretions (kg cow item-218 at level 5: text: -1 - item-219 at level 5: text: deposited on pasture [38]. The indirect N - item-220 at level 5: text: 2 - item-221 at level 5: text: O emissions from storage manure ... using the IPCC [38] emission factors. - item-222 at level 3: section_header: Farm management - item-223 at level 4: text: Emissions due to farm management ... crop and pasture production’ section. - item-224 at level 4: table with [12x4] - item-224 at level 5: caption: Table 5 Factors for major resource inputs in farm management. - item-225 at level 4: inline: group group - item-226 at level 5: text: The amount of fuel use for manur ... quired for manure handling (L diesel t - item-227 at level 5: text: -1 - item-228 at level 5: text: ) [42]. The amount of manure was estimated from OM excretions (kg cow - item-229 at level 5: text: -1 - item-230 at level 5: text: ), assuming that the manure has ... me that animals stayed on confinement. - item-231 at level 4: inline: group group - item-232 at level 5: text: The emissions from fuel were est ... uired for manure handling (L) × (kg CO - item-233 at level 5: text: 2 - item-234 at level 5: text: e L - item-235 at level 5: text: -1 - item-236 at level 5: text: ) [41]. The secondary emissions ... roduction and transport of fuel (kg CO - item-237 at level 5: text: 2 - item-238 at level 5: text: e L - item-239 at level 5: text: -1 - item-240 at level 5: text: ) [41]. Emissions from manufactu ... w (t) × (kg machinery mass (kg manure) - item-241 at level 5: text: -1 - item-242 at level 5: text: × 10 - item-243 at level 5: text: −3 - item-244 at level 5: text: ) [42] × kg CO - item-245 at level 5: text: 2 - item-246 at level 5: text: e (kg machinery mass) - item-247 at level 5: text: -1 - item-248 at level 5: text: [42]. + item-219 at level 5: text: ), assuming that the manure has ... me that animals stayed on confinement. + item-220 at level 4: inline: group group + item-221 at level 5: text: The emissions from fuel were est ... uired for manure handling (L) × (kg CO + item-222 at level 5: text: 2 + item-223 at level 5: text: e L + item-224 at level 5: text: -1 + item-225 at level 5: text: ) [41]. The secondary emissions ... roduction and transport of fuel (kg CO + item-226 at level 5: text: 2 + item-227 at level 5: text: e L + item-228 at level 5: text: -1 + item-229 at level 5: text: ) [41]. Emissions from manufactu ... w (t) × (kg machinery mass (kg manure) + item-230 at level 5: text: -1 + item-231 at level 5: text: × 10 + item-232 at level 5: text: −3 + item-233 at level 5: text: ) [42] × kg CO + item-234 at level 5: text: 2 + item-235 at level 5: text: e (kg machinery mass) + item-236 at level 5: text: -1 + item-237 at level 5: text: [42]. + item-238 at level 4: inline: group group + item-239 at level 5: text: Emissions from electricity for m ... ated using two emission factors (kg CO + item-240 at level 5: text: 2 + item-241 at level 5: text: kWh + item-242 at level 5: text: -1 + item-243 at level 5: text: ). The first one is based on Uni ... ivities is 0.06 kWh (kg milk produced) + item-244 at level 5: text: -1 + item-245 at level 5: text: [47]. The annual electricity use for lighting was 75 kWh cow + item-246 at level 5: text: -1 + item-247 at level 5: text: , which is the value considered ... ws in naturally ventilated barns [47]. + item-248 at level 3: section_header: Co-product allocation item-249 at level 4: inline: group group - item-250 at level 5: text: Emissions from electricity for m ... ated using two emission factors (kg CO - item-251 at level 5: text: 2 - item-252 at level 5: text: kWh - item-253 at level 5: text: -1 - item-254 at level 5: text: ). The first one is based on Uni ... ivities is 0.06 kWh (kg milk produced) - item-255 at level 5: text: -1 - item-256 at level 5: text: [47]. The annual electricity use for lighting was 75 kWh cow - item-257 at level 5: text: -1 - item-258 at level 5: text: , which is the value considered ... ws in naturally ventilated barns [47]. - item-259 at level 3: section_header: Co-product allocation - item-260 at level 4: inline: group group - item-261 at level 5: text: The C footprint for milk produce ... ibed by Thoma et al. [48]. Briefly, AR - item-262 at level 5: text: milk - item-263 at level 5: text: = 1–6.04 × BMR, where - item-264 at level 5: text: : - item-265 at level 5: text: AR - item-266 at level 5: text: milk - item-267 at level 5: text: is the allocation ratio for milk ... during cow`s entire life (kg). The AR - item-268 at level 5: text: milk - item-269 at level 5: text: were 0.854 and 0.849 for TMR and ... asture scenarios, respectively. The AR - item-270 at level 5: text: milk - item-271 at level 5: text: was applied to the whole emissio ... directly assigned to milk production. - item-272 at level 3: section_header: Sensitivity analysis - item-273 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint. - item-274 at level 2: section_header: Results and discussion - item-275 at level 3: text: The study has assessed the impac ... , feed production and electricity use. - item-276 at level 3: section_header: Greenhouse gas emissions - item-277 at level 4: inline: group group - item-278 at level 5: text: Depending on emission factors us ... 2A and 2B) or decreased by 0.04 kg CO - item-279 at level 5: text: 2 - item-280 at level 5: text: e (kg ECM) - item-281 at level 5: text: -1 - item-282 at level 5: text: (Fig 2C and 2D) in scenarios that included pastures compared to - item-283 at level 5: text: ad libitum - item-284 at level 5: text: TMR intake. Due to differences i ... values ranged from 0.92 to 1.04 kg CO - item-285 at level 5: text: 2 - item-286 at level 5: text: e (kg ECM) - item-287 at level 5: text: -1 - item-288 at level 5: text: for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO + item-250 at level 5: text: The C footprint for milk produce ... ibed by Thoma et al. [48]. Briefly, AR + item-251 at level 5: text: milk + item-252 at level 5: text: = 1–6.04 × BMR, where + item-253 at level 5: text: : + item-254 at level 5: text: AR + item-255 at level 5: text: milk + item-256 at level 5: text: is the allocation ratio for milk ... during cow`s entire life (kg). The AR + item-257 at level 5: text: milk + item-258 at level 5: text: were 0.854 and 0.849 for TMR and ... asture scenarios, respectively. The AR + item-259 at level 5: text: milk + item-260 at level 5: text: was applied to the whole emissio ... directly assigned to milk production. + item-261 at level 3: section_header: Sensitivity analysis + item-262 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint. + item-263 at level 2: section_header: Results and discussion + item-264 at level 3: text: The study has assessed the impac ... , feed production and electricity use. + item-265 at level 3: section_header: Greenhouse gas emissions + item-266 at level 4: inline: group group + item-267 at level 5: text: Depending on emission factors us ... 2A and 2B) or decreased by 0.04 kg CO + item-268 at level 5: text: 2 + item-269 at level 5: text: e (kg ECM) + item-270 at level 5: text: -1 + item-271 at level 5: text: (Fig 2C and 2D) in scenarios that included pastures compared to + item-272 at level 5: text: ad libitum + item-273 at level 5: text: TMR intake. Due to differences i ... values ranged from 0.92 to 1.04 kg CO + item-274 at level 5: text: 2 + item-275 at level 5: text: e (kg ECM) + item-276 at level 5: text: -1 + item-277 at level 5: text: for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO + item-278 at level 5: text: 2 + item-279 at level 5: text: e (kg ECM) + item-280 at level 5: text: -1 + item-281 at level 5: text: for cows with access to pasture. ... ocal emission factors for estimating N + item-282 at level 5: text: 2 + item-283 at level 5: text: O-N emissions [37], manure emiss ... more than 5% of overall GHG emissions. + item-284 at level 4: picture + item-284 at level 5: caption: Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. + item-285 at level 4: inline: group group + item-286 at level 5: text: Considering IPCC emission factors for N + item-287 at level 5: text: 2 + item-288 at level 5: text: O emissions from urine and dung ... otprint ranged from 0.99 to 1.04 kg CO item-289 at level 5: text: 2 item-290 at level 5: text: e (kg ECM) item-291 at level 5: text: -1 - item-292 at level 5: text: for cows with access to pasture. ... ocal emission factors for estimating N + item-292 at level 5: text: , and was close to those reporte ... , which ranged from 0.98 to 1.16 kg CO item-293 at level 5: text: 2 - item-294 at level 5: text: O-N emissions [37], manure emiss ... more than 5% of overall GHG emissions. - item-295 at level 4: picture - item-295 at level 5: caption: Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. - item-296 at level 4: inline: group group - item-297 at level 5: text: Considering IPCC emission factors for N - item-298 at level 5: text: 2 - item-299 at level 5: text: O emissions from urine and dung ... otprint ranged from 0.99 to 1.04 kg CO - item-300 at level 5: text: 2 - item-301 at level 5: text: e (kg ECM) - item-302 at level 5: text: -1 - item-303 at level 5: text: , and was close to those reporte ... , which ranged from 0.98 to 1.16 kg CO - item-304 at level 5: text: 2 - item-305 at level 5: text: e (kg ECM) - item-306 at level 5: text: -1 - item-307 at level 5: text: . When local emission factors for N - item-308 at level 5: text: 2 - item-309 at level 5: text: O emissions from urine and dung ... without accounting for sequestered CO - item-310 at level 5: text: 2 - item-311 at level 5: text: -C from perennial pasture—0.91 kg CO - item-312 at level 5: text: 2 - item-313 at level 5: text: e (kg ECM) - item-314 at level 5: text: -1 - item-315 at level 5: text: —was lower than the range of val ... , which ranged from 0.52 to 0.89 kg CO - item-316 at level 5: text: 2 - item-317 at level 5: text: e (kg ECM) - item-318 at level 5: text: -1 - item-319 at level 5: text: . Regardless of which emission f ... nt, which ranged from 1.4 to 2.3 kg CO - item-320 at level 5: text: 2 - item-321 at level 5: text: e (kg ECM) - item-322 at level 5: text: -1 - item-323 at level 5: text: [8,55]. Thus, even though differ ... e emissions estimation, sequestered CO - item-324 at level 5: text: 2 - item-325 at level 5: text: -C, etc.), herd productivity and ... the C footprint of the dairy systems. - item-326 at level 4: inline: group group - item-327 at level 5: text: The similarity of C footprint be ... served that an increase of 1000 kg cow - item-328 at level 5: text: -1 - item-329 at level 5: text: (5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO - item-330 at level 5: text: 2 - item-331 at level 5: text: e (kg ECM) - item-332 at level 5: text: -1 - item-333 at level 5: text: , which may explain an apparent ... milk production of around 7000 kg cow - item-334 at level 5: text: -1 - item-335 at level 5: text: . Experimental data showed a red ... of TMR was replaced by pasture access. - item-336 at level 4: inline: group group - item-337 at level 5: text: The lower C footprint in scenari ... emission factors [37] were used for N - item-338 at level 5: text: 2 - item-339 at level 5: text: O emissions from urine and dung ... enarios including pastures compared to - item-340 at level 5: text: ad libitum - item-341 at level 5: text: TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N - item-342 at level 5: text: 2 - item-343 at level 5: text: O-N (kg N) - item-344 at level 5: text: -1 - item-345 at level 5: text: for urine and dung from grazing ... five times lower, averaging 0.004 kg N - item-346 at level 5: text: 2 - item-347 at level 5: text: O-N kg - item-348 at level 5: text: -1 - item-349 at level 5: text: [37]. - item-350 at level 3: section_header: Methane emissions - item-351 at level 4: inline: group group - item-352 at level 5: text: The enteric CH - item-353 at level 5: text: 4 - item-354 at level 5: text: intensity was similar between di ... Fig 3). The large effect of enteric CH - item-355 at level 5: text: 4 - item-356 at level 5: text: emissions on the whole C footpri ... cted, because the impact of enteric CH + item-294 at level 5: text: e (kg ECM) + item-295 at level 5: text: -1 + item-296 at level 5: text: . When local emission factors for N + item-297 at level 5: text: 2 + item-298 at level 5: text: O emissions from urine and dung ... without accounting for sequestered CO + item-299 at level 5: text: 2 + item-300 at level 5: text: -C from perennial pasture—0.91 kg CO + item-301 at level 5: text: 2 + item-302 at level 5: text: e (kg ECM) + item-303 at level 5: text: -1 + item-304 at level 5: text: —was lower than the range of val ... , which ranged from 0.52 to 0.89 kg CO + item-305 at level 5: text: 2 + item-306 at level 5: text: e (kg ECM) + item-307 at level 5: text: -1 + item-308 at level 5: text: . Regardless of which emission f ... nt, which ranged from 1.4 to 2.3 kg CO + item-309 at level 5: text: 2 + item-310 at level 5: text: e (kg ECM) + item-311 at level 5: text: -1 + item-312 at level 5: text: [8,55]. Thus, even though differ ... e emissions estimation, sequestered CO + item-313 at level 5: text: 2 + item-314 at level 5: text: -C, etc.), herd productivity and ... the C footprint of the dairy systems. + item-315 at level 4: inline: group group + item-316 at level 5: text: The similarity of C footprint be ... served that an increase of 1000 kg cow + item-317 at level 5: text: -1 + item-318 at level 5: text: (5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO + item-319 at level 5: text: 2 + item-320 at level 5: text: e (kg ECM) + item-321 at level 5: text: -1 + item-322 at level 5: text: , which may explain an apparent ... milk production of around 7000 kg cow + item-323 at level 5: text: -1 + item-324 at level 5: text: . Experimental data showed a red ... of TMR was replaced by pasture access. + item-325 at level 4: inline: group group + item-326 at level 5: text: The lower C footprint in scenari ... emission factors [37] were used for N + item-327 at level 5: text: 2 + item-328 at level 5: text: O emissions from urine and dung ... enarios including pastures compared to + item-329 at level 5: text: ad libitum + item-330 at level 5: text: TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N + item-331 at level 5: text: 2 + item-332 at level 5: text: O-N (kg N) + item-333 at level 5: text: -1 + item-334 at level 5: text: for urine and dung from grazing ... five times lower, averaging 0.004 kg N + item-335 at level 5: text: 2 + item-336 at level 5: text: O-N kg + item-337 at level 5: text: -1 + item-338 at level 5: text: [37]. + item-339 at level 3: section_header: Methane emissions + item-340 at level 4: inline: group group + item-341 at level 5: text: The enteric CH + item-342 at level 5: text: 4 + item-343 at level 5: text: intensity was similar between di ... Fig 3). The large effect of enteric CH + item-344 at level 5: text: 4 + item-345 at level 5: text: emissions on the whole C footpri ... cted, because the impact of enteric CH + item-346 at level 5: text: 4 + item-347 at level 5: text: on GHG emissions of milk product ... o range from 44 to 60% of the total CO + item-348 at level 5: text: 2 + item-349 at level 5: text: e [50,52,57,58]. However, emissi ... trate feeds are greater than 0.7 kg CO + item-350 at level 5: text: 2 + item-351 at level 5: text: e kg + item-352 at level 5: text: -1 + item-353 at level 5: text: [59], which did not happen in this study. + item-354 at level 4: picture + item-354 at level 5: caption: Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. + item-355 at level 4: inline: group group + item-356 at level 5: text: The lack of difference in enteric CH item-357 at level 5: text: 4 - item-358 at level 5: text: on GHG emissions of milk product ... o range from 44 to 60% of the total CO - item-359 at level 5: text: 2 - item-360 at level 5: text: e [50,52,57,58]. However, emissi ... trate feeds are greater than 0.7 kg CO - item-361 at level 5: text: 2 - item-362 at level 5: text: e kg - item-363 at level 5: text: -1 - item-364 at level 5: text: [59], which did not happen in this study. - item-365 at level 4: picture - item-365 at level 5: caption: Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. - item-366 at level 4: inline: group group - item-367 at level 5: text: The lack of difference in enteric CH - item-368 at level 5: text: 4 - item-369 at level 5: text: emissions in different systems c ... nual temperate pastures (495 g (kg DM) - item-370 at level 5: text: -1 - item-371 at level 5: text: ) compared to corn silage (550 g (kg DM) - item-372 at level 5: text: -1 - item-373 at level 5: text: ). Hence, an expected, increase ... have shown that the actual enteric CH + item-358 at level 5: text: emissions in different systems c ... nual temperate pastures (495 g (kg DM) + item-359 at level 5: text: -1 + item-360 at level 5: text: ) compared to corn silage (550 g (kg DM) + item-361 at level 5: text: -1 + item-362 at level 5: text: ). Hence, an expected, increase ... have shown that the actual enteric CH + item-363 at level 5: text: 4 + item-364 at level 5: text: emissions may decrease with incl ... ybean meal [60] or increase enteric CH + item-365 at level 5: text: 4 + item-366 at level 5: text: emissions when dairy cows grazin ... silage [61]. Additionally, enteric CH + item-367 at level 5: text: 4 + item-368 at level 5: text: emissions did not differ between ... same scenarios as in this study [26]. + item-369 at level 3: section_header: Emissions from excreta and feed production + item-370 at level 4: inline: group group + item-371 at level 5: text: Using IPCC emission factors for N + item-372 at level 5: text: 2 + item-373 at level 5: text: O emissions from urine and dung [38] and those from Table 3, CH item-374 at level 5: text: 4 - item-375 at level 5: text: emissions may decrease with incl ... ybean meal [60] or increase enteric CH - item-376 at level 5: text: 4 - item-377 at level 5: text: emissions when dairy cows grazin ... silage [61]. Additionally, enteric CH - item-378 at level 5: text: 4 - item-379 at level 5: text: emissions did not differ between ... same scenarios as in this study [26]. - item-380 at level 3: section_header: Emissions from excreta and feed production - item-381 at level 4: inline: group group - item-382 at level 5: text: Using IPCC emission factors for N - item-383 at level 5: text: 2 - item-384 at level 5: text: O emissions from urine and dung [38] and those from Table 3, CH - item-385 at level 5: text: 4 - item-386 at level 5: text: emissions from manure decreased 0.07 kg CO - item-387 at level 5: text: 2 - item-388 at level 5: text: e (kg ECM) - item-389 at level 5: text: -1 - item-390 at level 5: text: , but N - item-391 at level 5: text: 2 - item-392 at level 5: text: O emissions from manure increased 0.09 kg CO - item-393 at level 5: text: 2 - item-394 at level 5: text: e (kg ECM) - item-395 at level 5: text: -1 - item-396 at level 5: text: , as TMR intake was restricted to 50% - item-397 at level 5: text: ad libitum - item-398 at level 5: text: (Fig 4A). Emissions for pastures increased by 0.06 kg CO - item-399 at level 5: text: 2 - item-400 at level 5: text: e (kg ECM) - item-401 at level 5: text: -1 - item-402 at level 5: text: , whereas emissions for producin ... nd corn silage decreased by 0.09 kg CO - item-403 at level 5: text: 2 - item-404 at level 5: text: e (kg ECM) - item-405 at level 5: text: -1 - item-406 at level 5: text: , as TMR intake decreased (Fig 4 ... ctating dairy cow diets. The greater N - item-407 at level 5: text: 2 - item-408 at level 5: text: O-N emissions from manure with pasture was a consequence of higher N + item-375 at level 5: text: emissions from manure decreased 0.07 kg CO + item-376 at level 5: text: 2 + item-377 at level 5: text: e (kg ECM) + item-378 at level 5: text: -1 + item-379 at level 5: text: , but N + item-380 at level 5: text: 2 + item-381 at level 5: text: O emissions from manure increased 0.09 kg CO + item-382 at level 5: text: 2 + item-383 at level 5: text: e (kg ECM) + item-384 at level 5: text: -1 + item-385 at level 5: text: , as TMR intake was restricted to 50% + item-386 at level 5: text: ad libitum + item-387 at level 5: text: (Fig 4A). Emissions for pastures increased by 0.06 kg CO + item-388 at level 5: text: 2 + item-389 at level 5: text: e (kg ECM) + item-390 at level 5: text: -1 + item-391 at level 5: text: , whereas emissions for producin ... nd corn silage decreased by 0.09 kg CO + item-392 at level 5: text: 2 + item-393 at level 5: text: e (kg ECM) + item-394 at level 5: text: -1 + item-395 at level 5: text: , as TMR intake decreased (Fig 4 ... ctating dairy cow diets. The greater N + item-396 at level 5: text: 2 + item-397 at level 5: text: O-N emissions from manure with pasture was a consequence of higher N + item-398 at level 5: text: 2 + item-399 at level 5: text: O-N emissions due to greater CP ... g CP content from 185 to 152 g (kg DM) + item-400 at level 5: text: -1 + item-401 at level 5: text: , N intake decreased by 20% and ... g dairy cows ranged from 150 g (kg DM) + item-402 at level 5: text: -1 + item-403 at level 5: text: on TMR system to 198 g (kg DM) + item-404 at level 5: text: -1 + item-405 at level 5: text: on 50% TMR with pasture. Additio ... may not be captured by microbes [65]. + item-406 at level 4: picture + item-406 at level 5: caption: Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture. + item-407 at level 4: inline: group group + item-408 at level 5: text: Using local emission factors for N item-409 at level 5: text: 2 - item-410 at level 5: text: O-N emissions due to greater CP ... g CP content from 185 to 152 g (kg DM) - item-411 at level 5: text: -1 - item-412 at level 5: text: , N intake decreased by 20% and ... g dairy cows ranged from 150 g (kg DM) - item-413 at level 5: text: -1 - item-414 at level 5: text: on TMR system to 198 g (kg DM) - item-415 at level 5: text: -1 - item-416 at level 5: text: on 50% TMR with pasture. Additio ... may not be captured by microbes [65]. - item-417 at level 4: picture - item-417 at level 5: caption: Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture. - item-418 at level 4: inline: group group - item-419 at level 5: text: Using local emission factors for N - item-420 at level 5: text: 2 - item-421 at level 5: text: O emissions from urine and dung ... d those from Table 4, reductions in CH - item-422 at level 5: text: 4 - item-423 at level 5: text: emissions from stocked manure, w ... iets, did not offset by increases in N - item-424 at level 5: text: 2 - item-425 at level 5: text: O emissions from excreta (Fig 4C ... much lower emission factors used for N + item-410 at level 5: text: O emissions from urine and dung ... d those from Table 4, reductions in CH + item-411 at level 5: text: 4 + item-412 at level 5: text: emissions from stocked manure, w ... iets, did not offset by increases in N + item-413 at level 5: text: 2 + item-414 at level 5: text: O emissions from excreta (Fig 4C ... much lower emission factors used for N + item-415 at level 5: text: 2 + item-416 at level 5: text: O emissions from urine and dung. ... be revised for the subtropical region. + item-417 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9]. + item-418 at level 3: section_header: Farm management + item-419 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint. + item-420 at level 4: inline: group group + item-421 at level 5: text: Emissions from farm management d ... or electricity generation (0.205 kg CO + item-422 at level 5: text: 2 + item-423 at level 5: text: e kWh + item-424 at level 5: text: -1 + item-425 at level 5: text: [46]) is much lower than that in a LCA study conducted in US (0.73 kg CO item-426 at level 5: text: 2 - item-427 at level 5: text: O emissions from urine and dung. ... be revised for the subtropical region. - item-428 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9]. - item-429 at level 3: section_header: Farm management - item-430 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint. - item-431 at level 4: inline: group group - item-432 at level 5: text: Emissions from farm management d ... or electricity generation (0.205 kg CO - item-433 at level 5: text: 2 - item-434 at level 5: text: e kWh - item-435 at level 5: text: -1 - item-436 at level 5: text: [46]) is much lower than that in a LCA study conducted in US (0.73 kg CO - item-437 at level 5: text: 2 - item-438 at level 5: text: e kWh - item-439 at level 5: text: -1 - item-440 at level 5: text: [42]). This apparent discrepancy ... has an emission factor of 0.074 kg CO + item-427 at level 5: text: e kWh + item-428 at level 5: text: -1 + item-429 at level 5: text: [42]). This apparent discrepancy ... has an emission factor of 0.074 kg CO + item-430 at level 5: text: 2 + item-431 at level 5: text: e kWh + item-432 at level 5: text: -1 + item-433 at level 5: text: against 0.382 and 0.926 kg CO + item-434 at level 5: text: 2 + item-435 at level 5: text: e kWh + item-436 at level 5: text: -1 + item-437 at level 5: text: produced by natural gas and hard coal, respectively [46]. + item-438 at level 3: section_header: Assumptions and limitations + item-439 at level 4: inline: group group + item-440 at level 5: text: The milk production and composit ... sion factors for direct and indirect N item-441 at level 5: text: 2 - item-442 at level 5: text: e kWh - item-443 at level 5: text: -1 - item-444 at level 5: text: against 0.382 and 0.926 kg CO - item-445 at level 5: text: 2 - item-446 at level 5: text: e kWh - item-447 at level 5: text: -1 - item-448 at level 5: text: produced by natural gas and hard coal, respectively [46]. - item-449 at level 3: section_header: Assumptions and limitations - item-450 at level 4: inline: group group - item-451 at level 5: text: The milk production and composit ... sion factors for direct and indirect N + item-442 at level 5: text: O emissions from urine and dung ... sary to reduce the uncertainty. The CO + item-443 at level 5: text: 2 + item-444 at level 5: text: emitted from lime and urea appli ... ions as a function of soil management. + item-445 at level 3: section_header: Further considerations + item-446 at level 4: inline: group group + item-447 at level 5: text: The potential for using pasture ... reduced the C footprint by 0.12 kg CO + item-448 at level 5: text: 2 + item-449 at level 5: text: e (kg ECM) + item-450 at level 5: text: -1 + item-451 at level 5: text: , whereas an increase from 10,00 ... ced the C footprint by only 0.06 kg CO item-452 at level 5: text: 2 - item-453 at level 5: text: O emissions from urine and dung ... sary to reduce the uncertainty. The CO - item-454 at level 5: text: 2 - item-455 at level 5: text: emitted from lime and urea appli ... ions as a function of soil management. - item-456 at level 3: section_header: Further considerations - item-457 at level 4: inline: group group - item-458 at level 5: text: The potential for using pasture ... reduced the C footprint by 0.12 kg CO - item-459 at level 5: text: 2 - item-460 at level 5: text: e (kg ECM) - item-461 at level 5: text: -1 - item-462 at level 5: text: , whereas an increase from 10,00 ... ced the C footprint by only 0.06 kg CO - item-463 at level 5: text: 2 - item-464 at level 5: text: e (kg ECM) - item-465 at level 5: text: -1 - item-466 at level 5: text: . Hence, the impact of increasin ... C footprint may increase by 0.03 kg CO - item-467 at level 5: text: 2 - item-468 at level 5: text: e (kg ECM) - item-469 at level 5: text: -1 - item-470 at level 5: text: in subclinical ketosis [71] and by 0.02 kg CO - item-471 at level 5: text: 2 - item-472 at level 5: text: e (kg ECM) - item-473 at level 5: text: -1 - item-474 at level 5: text: in case of foot lesions [72]. - item-475 at level 4: inline: group group - item-476 at level 5: text: Grazing lands may also improve b ... n subtropical areas by 0.5 to 1.5 t ha - item-477 at level 5: text: -1 - item-478 at level 5: text: [75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha - item-479 at level 5: text: -1 - item-480 at level 5: text: would be sequestered, further re ... e C footprint by 0.015 and 0.025 kg CO - item-481 at level 5: text: 2 - item-482 at level 5: text: e (kg ECM) - item-483 at level 5: text: -1 - item-484 at level 5: text: for the scenarios using 75 and 5 ... emissions would be 0.03 and 0.05 kg CO - item-485 at level 5: text: 2 - item-486 at level 5: text: e (kg ECM) - item-487 at level 5: text: -1 - item-488 at level 5: text: for 75 and 50% TMR, respectively ... C storage, so that net exchange of CO - item-489 at level 5: text: 2 - item-490 at level 5: text: would be negligible [76]. - item-491 at level 2: section_header: Conclusions - item-492 at level 3: inline: group group - item-493 at level 4: text: This study assessed the C footpr ... attributable to the evidence of low N - item-494 at level 4: text: 2 - item-495 at level 4: text: O emissions from urine and dung ... ical areas. Even though the enteric CH - item-496 at level 4: text: 4 - item-497 at level 4: text: intensity was the largest source of CO - item-498 at level 4: text: 2 - item-499 at level 4: text: e emissions, it did not change b ... on with or without access to pastures. - item-500 at level 2: section_header: Acknowledgments - item-501 at level 3: text: Thanks to Anna Naranjo for helpf ... of the herd considered in this study. - item-502 at level 2: section_header: References - item-503 at level 3: list: group list - item-504 at level 4: list_item: IPCC. 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Gre ... . 2020 10.3168/jds.2019-16576 32037166 - item-553 at level 4: list_item: JayasundaraS, WordenD, WeersinkA ... 18–1028. 10.1016/j.jclepro.2019.04.013 - item-554 at level 4: list_item: WilliamsSRO, FisherPD, Berrisfor ... 4;19: 69–78. 10.1007/s11367-013-0619-8 - item-555 at level 4: list_item: GollnowS, LundieS, MooreAD, McLa ... : 31–38. 10.1016/j.idairyj.2014.02.005 - item-556 at level 4: list_item: O’BrienD, CapperJL, GarnsworthyP ... i. 2014 10.3168/jds.2013-7174 24440256 - item-557 at level 4: list_item: ChobtangJ, McLarenSJ, LedgardSF, ... 2017;21: 1139–1152. 10.1111/jiec.12484 - item-558 at level 4: list_item: GargMR, PhondbaBT, SherasiaPL, M ... Sci. 2016;56: 423–436. 10.1071/AN15464 - item-559 at level 4: list_item: de LéisCM, CherubiniE, RuviaroCF ... 5;20: 46–60. 10.1007/s11367-014-0813-3 - item-560 at level 4: list_item: O’BrienD, GeogheganA, McNamaraK, ... Sci. 2016;56: 495–500. 10.1071/AN15490 - item-561 at level 4: list_item: O’BrienD, BrennanP, HumphreysJ, ... : 1469–1481. 10.1007/s11367-014-0755-9 - item-562 at level 4: list_item: BaekCY, LeeKM, ParkKH. Quantific ... : 50–60. 10.1016/j.jclepro.2014.02.010 - item-563 at level 4: list_item: Dall-OrsolettaAC, AlmeidaJGR, Ca ... –4383. 10.3168/jds.2015-10396 27016830 - item-564 at level 4: list_item: Dall-OrsolettaAC, OziemblowskiMM ... 5–73. 10.1016/j.anifeedsci.2019.05.009 - item-565 at level 4: list_item: NiuM, AppuhamyJADRN, LeytemAB, D ... Sci. 2016;56: 312–321. 10.1071/AN15498 - item-566 at level 4: list_item: WaghornGC, LawN, BryantM, Pachec ... i. 2019;59: 1261–1270. 10.1071/AN18018 - item-567 at level 4: list_item: DickhoeferU, GlowackiS, GómezCA, ... 109–118. 10.1016/j.livsci.2018.08.004 - item-568 at level 4: list_item: SchwabCG, BroderickGA. A 100-Yea ... 10112. 10.3168/jds.2017-13320 29153157 - item-569 at level 4: list_item: SordiA, DieckowJ, BayerC, Alburq ... 90: 94–103. 10.1016/j.agee.2013.09.004 - item-570 at level 4: list_item: SimonPL, DieckowJ, de KleinCAM, ... 267: 74–82. 10.1016/j.agee.2018.08.013 - item-571 at level 4: list_item: WangX, LedgardS, LuoJ, GuoY, Zha ... .1016/j.scitotenv.2017.12.259 29291563 - item-572 at level 4: list_item: PirloG, LolliS. Environmental im ... 962–971. 10.1016/j.jclepro.2018.11.070 - item-573 at level 4: list_item: HerzogA, WincklerC, ZollitschW. ... 7: 174–187. 10.1016/j.agee.2018.07.029 - item-574 at level 4: list_item: MostertPF, van MiddelaarCE, Bokk ... od. 2018 10.1016/j.jclepro.2017.10.019 - item-575 at level 4: list_item: MostertPF, van MiddelaarCE, de B ... 7: 206–212. 10.1016/j.agsy.2018.09.006 - item-576 at level 4: list_item: FoleyJA, RamankuttyN, BraumanKA, ... 337–342. 10.1038/nature10452 21993620 - item-577 at level 4: list_item: LalR. Soil Carbon Sequestration ... 1627. 10.1126/science.1097396 15192216 - item-578 at level 4: list_item: BoddeyRM, JantaliaCP, ConceiçaoP ... –795. 10.1111/j.1365-2486.2009.02020.x - item-579 at level 4: list_item: McConkeyB, AngersD, BenthamM, Bo ... the LULUCF sector for NIR 2014. 2014. - item-580 at level 1: caption: Fig 1 Overview of the milk produ ... stem boundary considered in the study. - item-581 at level 1: caption: Table 1 Descriptive characteristics of the herd. - item-582 at level 1: caption: Table 2 Dairy cows’ diets in different scenariosa. - item-583 at level 1: caption: Table 3 GHG emission factors for Off- and On-farm feed production. - item-584 at level 1: caption: Table 4 GHG emissions from On-farm feed production. - item-585 at level 1: caption: Table 5 Factors for major resource inputs in farm management. - item-586 at level 1: caption: Fig 2 Overall greenhouse gas emi ... lectricity = 0.205 kg CO2e kWh-1 [46]. - item-587 at level 1: caption: Fig 3 Sensitivity of the C footp ... lectricity = 0.205 kg CO2e kWh-1 [46]. - item-588 at level 1: caption: Fig 4 Greenhouse gas emissions ( ... uestered CO2-C from perennial pasture. \ No newline at end of file + item-453 at level 5: text: e (kg ECM) + item-454 at level 5: text: -1 + item-455 at level 5: text: . Hence, the impact of increasin ... C footprint may increase by 0.03 kg CO + item-456 at level 5: text: 2 + item-457 at level 5: text: e (kg ECM) + item-458 at level 5: text: -1 + item-459 at level 5: text: in subclinical ketosis [71] and by 0.02 kg CO + item-460 at level 5: text: 2 + item-461 at level 5: text: e (kg ECM) + item-462 at level 5: text: -1 + item-463 at level 5: text: in case of foot lesions [72]. + item-464 at level 4: inline: group group + item-465 at level 5: text: Grazing lands may also improve b ... n subtropical areas by 0.5 to 1.5 t ha + item-466 at level 5: text: -1 + item-467 at level 5: text: [75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha + item-468 at level 5: text: -1 + item-469 at level 5: text: would be sequestered, further re ... e C footprint by 0.015 and 0.025 kg CO + item-470 at level 5: text: 2 + item-471 at level 5: text: e (kg ECM) + item-472 at level 5: text: -1 + item-473 at level 5: text: for the scenarios using 75 and 5 ... emissions would be 0.03 and 0.05 kg CO + item-474 at level 5: text: 2 + item-475 at level 5: text: e (kg ECM) + item-476 at level 5: text: -1 + item-477 at level 5: text: for 75 and 50% TMR, respectively ... C storage, so that net exchange of CO + item-478 at level 5: text: 2 + item-479 at level 5: text: would be negligible [76]. + item-480 at level 2: section_header: Conclusions + item-481 at level 3: inline: group group + item-482 at level 4: text: This study assessed the C footpr ... attributable to the evidence of low N + item-483 at level 4: text: 2 + item-484 at level 4: text: O emissions from urine and dung ... ical areas. Even though the enteric CH + item-485 at level 4: text: 4 + item-486 at level 4: text: intensity was the largest source of CO + item-487 at level 4: text: 2 + item-488 at level 4: text: e emissions, it did not change b ... on with or without access to pastures. + item-489 at level 2: section_header: Acknowledgments + item-490 at level 3: text: Thanks to Anna Naranjo for helpf ... of the herd considered in this study. + item-491 at level 2: section_header: References + item-492 at level 3: list: group list + item-493 at level 4: list_item: IPCC. 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Sci. 2016;56: 495–500. 10.1071/AN15490 + item-550 at level 4: list_item: O’BrienD, BrennanP, HumphreysJ, ... : 1469–1481. 10.1007/s11367-014-0755-9 + item-551 at level 4: list_item: BaekCY, LeeKM, ParkKH. Quantific ... : 50–60. 10.1016/j.jclepro.2014.02.010 + item-552 at level 4: list_item: Dall-OrsolettaAC, AlmeidaJGR, Ca ... –4383. 10.3168/jds.2015-10396 27016830 + item-553 at level 4: list_item: Dall-OrsolettaAC, OziemblowskiMM ... 5–73. 10.1016/j.anifeedsci.2019.05.009 + item-554 at level 4: list_item: NiuM, AppuhamyJADRN, LeytemAB, D ... Sci. 2016;56: 312–321. 10.1071/AN15498 + item-555 at level 4: list_item: WaghornGC, LawN, BryantM, Pachec ... i. 2019;59: 1261–1270. 10.1071/AN18018 + item-556 at level 4: list_item: DickhoeferU, GlowackiS, GómezCA, ... 109–118. 10.1016/j.livsci.2018.08.004 + item-557 at level 4: list_item: SchwabCG, BroderickGA. A 100-Yea ... 10112. 10.3168/jds.2017-13320 29153157 + item-558 at level 4: list_item: SordiA, DieckowJ, BayerC, Alburq ... 90: 94–103. 10.1016/j.agee.2013.09.004 + item-559 at level 4: list_item: SimonPL, DieckowJ, de KleinCAM, ... 267: 74–82. 10.1016/j.agee.2018.08.013 + item-560 at level 4: list_item: WangX, LedgardS, LuoJ, GuoY, Zha ... .1016/j.scitotenv.2017.12.259 29291563 + item-561 at level 4: list_item: PirloG, LolliS. Environmental im ... 962–971. 10.1016/j.jclepro.2018.11.070 + item-562 at level 4: list_item: HerzogA, WincklerC, ZollitschW. ... 7: 174–187. 10.1016/j.agee.2018.07.029 + item-563 at level 4: list_item: MostertPF, van MiddelaarCE, Bokk ... od. 2018 10.1016/j.jclepro.2017.10.019 + item-564 at level 4: list_item: MostertPF, van MiddelaarCE, de B ... 7: 206–212. 10.1016/j.agsy.2018.09.006 + item-565 at level 4: list_item: FoleyJA, RamankuttyN, BraumanKA, ... 337–342. 10.1038/nature10452 21993620 + item-566 at level 4: list_item: LalR. Soil Carbon Sequestration ... 1627. 10.1126/science.1097396 15192216 + item-567 at level 4: list_item: BoddeyRM, JantaliaCP, ConceiçaoP ... –795. 10.1111/j.1365-2486.2009.02020.x + item-568 at level 4: list_item: McConkeyB, AngersD, BenthamM, Bo ... the LULUCF sector for NIR 2014. 2014. + item-569 at level 1: caption: Fig 1 Overview of the milk produ ... stem boundary considered in the study. + item-570 at level 1: caption: Table 1 Descriptive characteristics of the herd. + item-571 at level 1: caption: Table 2 Dairy cows’ diets in different scenariosa. + item-572 at level 1: caption: Table 3 GHG emission factors for Off- and On-farm feed production. + item-573 at level 1: caption: Table 4 GHG emissions from On-farm feed production. + item-574 at level 1: caption: Table 5 Factors for major resource inputs in farm management. + item-575 at level 1: caption: Fig 2 Overall greenhouse gas emi ... lectricity = 0.205 kg CO2e kWh-1 [46]. + item-576 at level 1: caption: Fig 3 Sensitivity of the C footp ... lectricity = 0.205 kg CO2e kWh-1 [46]. + item-577 at level 1: caption: Fig 4 Greenhouse gas emissions ( ... uestered CO2-C from perennial pasture. \ No newline at end of file diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.json b/tests/data/jats/groundtruth/pone.0234687.nxml.json index c084f0edfd..beda45906b 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.json +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.json @@ -21,31 +21,31 @@ "$ref": "#/texts/0" }, { - "$ref": "#/texts/49" + "$ref": "#/texts/38" }, { - "$ref": "#/texts/53" + "$ref": "#/texts/42" }, { - "$ref": "#/texts/102" + "$ref": "#/texts/91" }, { - "$ref": "#/texts/111" + "$ref": "#/texts/100" }, { - "$ref": "#/texts/143" + "$ref": "#/texts/132" }, { - "$ref": "#/texts/210" + "$ref": "#/texts/199" }, { - "$ref": "#/texts/276" + "$ref": "#/texts/265" }, { - "$ref": "#/texts/342" + "$ref": "#/texts/331" }, { - "$ref": "#/texts/392" + "$ref": "#/texts/381" } ], "content_layer": "body", @@ -94,10 +94,18 @@ }, { "$ref": "#/texts/15" - }, - { - "$ref": "#/texts/16" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/1", + "parent": { + "$ref": "#/texts/16" + }, + "children": [ { "$ref": "#/texts/17" }, @@ -118,15 +126,6 @@ }, { "$ref": "#/texts/23" - }, - { - "$ref": "#/texts/24" - }, - { - "$ref": "#/texts/25" - }, - { - "$ref": "#/texts/26" } ], "content_layer": "body", @@ -134,31 +133,25 @@ "label": "inline" }, { - "self_ref": "#/groups/1", + "self_ref": "#/groups/2", "parent": { - "$ref": "#/texts/27" + "$ref": "#/texts/16" }, "children": [ { - "$ref": "#/texts/28" - }, - { - "$ref": "#/texts/29" - }, - { - "$ref": "#/texts/30" + "$ref": "#/texts/24" }, { - "$ref": "#/texts/31" + "$ref": "#/texts/25" }, { - "$ref": "#/texts/32" + "$ref": "#/texts/26" }, { - "$ref": "#/texts/33" + "$ref": "#/texts/27" }, { - "$ref": "#/texts/34" + "$ref": "#/texts/28" } ], "content_layer": "body", @@ -166,25 +159,19 @@ "label": "inline" }, { - "self_ref": "#/groups/2", + "self_ref": "#/groups/3", "parent": { - "$ref": "#/texts/27" + "$ref": "#/texts/32" }, "children": [ { - "$ref": "#/texts/35" - }, - { - "$ref": "#/texts/36" - }, - { - "$ref": "#/texts/37" + "$ref": "#/texts/33" }, { - "$ref": "#/texts/38" + "$ref": "#/texts/34" }, { - "$ref": "#/texts/39" + "$ref": "#/texts/35" } ], "content_layer": "body", @@ -192,7 +179,7 @@ "label": "inline" }, { - "self_ref": "#/groups/3", + "self_ref": "#/groups/4", "parent": { "$ref": "#/texts/43" }, @@ -205,6 +192,30 @@ }, { "$ref": "#/texts/46" + }, + { + "$ref": "#/texts/47" + }, + { + "$ref": "#/texts/48" + }, + { + "$ref": "#/texts/49" + }, + { + "$ref": "#/texts/50" + }, + { + "$ref": "#/texts/51" + }, + { + "$ref": "#/texts/52" + }, + { + "$ref": "#/texts/53" + }, + { + "$ref": "#/texts/54" } ], "content_layer": "body", @@ -212,9 +223,9 @@ "label": "inline" }, { - "self_ref": "#/groups/4", + "self_ref": "#/groups/5", "parent": { - "$ref": "#/texts/54" + "$ref": "#/texts/43" }, "children": [ { @@ -237,18 +248,6 @@ }, { "$ref": "#/texts/61" - }, - { - "$ref": "#/texts/62" - }, - { - "$ref": "#/texts/63" - }, - { - "$ref": "#/texts/64" - }, - { - "$ref": "#/texts/65" } ], "content_layer": "body", @@ -256,11 +255,20 @@ "label": "inline" }, { - "self_ref": "#/groups/5", + "self_ref": "#/groups/6", "parent": { - "$ref": "#/texts/54" + "$ref": "#/texts/62" }, "children": [ + { + "$ref": "#/texts/63" + }, + { + "$ref": "#/texts/64" + }, + { + "$ref": "#/texts/65" + }, { "$ref": "#/texts/66" }, @@ -281,18 +289,10 @@ }, { "$ref": "#/texts/72" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/6", - "parent": { - "$ref": "#/texts/73" - }, - "children": [ + }, + { + "$ref": "#/texts/73" + }, { "$ref": "#/texts/74" }, @@ -316,13 +316,18 @@ }, { "$ref": "#/texts/81" - }, - { - "$ref": "#/texts/82" - }, - { - "$ref": "#/texts/83" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/7", + "parent": { + "$ref": "#/texts/83" + }, + "children": [ { "$ref": "#/texts/84" }, @@ -343,12 +348,6 @@ }, { "$ref": "#/texts/90" - }, - { - "$ref": "#/texts/91" - }, - { - "$ref": "#/texts/92" } ], "content_layer": "body", @@ -356,11 +355,17 @@ "label": "inline" }, { - "self_ref": "#/groups/7", + "self_ref": "#/groups/8", "parent": { - "$ref": "#/texts/94" + "$ref": "#/texts/92" }, "children": [ + { + "$ref": "#/texts/93" + }, + { + "$ref": "#/texts/94" + }, { "$ref": "#/texts/95" }, @@ -375,12 +380,6 @@ }, { "$ref": "#/texts/99" - }, - { - "$ref": "#/texts/100" - }, - { - "$ref": "#/texts/101" } ], "content_layer": "body", @@ -388,11 +387,20 @@ "label": "inline" }, { - "self_ref": "#/groups/8", + "self_ref": "#/groups/9", "parent": { - "$ref": "#/texts/103" + "$ref": "#/texts/92" }, "children": [ + { + "$ref": "#/texts/101" + }, + { + "$ref": "#/texts/102" + }, + { + "$ref": "#/texts/103" + }, { "$ref": "#/texts/104" }, @@ -413,18 +421,10 @@ }, { "$ref": "#/texts/110" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/9", - "parent": { - "$ref": "#/texts/103" - }, - "children": [ + }, + { + "$ref": "#/texts/111" + }, { "$ref": "#/texts/112" }, @@ -484,13 +484,18 @@ }, { "$ref": "#/texts/131" - }, - { - "$ref": "#/texts/132" - }, - { - "$ref": "#/texts/133" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/10", + "parent": { + "$ref": "#/texts/133" + }, + "children": [ { "$ref": "#/texts/134" }, @@ -517,18 +522,13 @@ }, { "$ref": "#/texts/142" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/10", - "parent": { - "$ref": "#/texts/144" - }, - "children": [ + }, + { + "$ref": "#/texts/143" + }, + { + "$ref": "#/texts/144" + }, { "$ref": "#/texts/145" }, @@ -540,10 +540,18 @@ }, { "$ref": "#/texts/148" - }, - { - "$ref": "#/texts/149" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/11", + "parent": { + "$ref": "#/texts/149" + }, + "children": [ { "$ref": "#/texts/150" }, @@ -573,18 +581,10 @@ }, { "$ref": "#/texts/159" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/11", - "parent": { - "$ref": "#/texts/160" - }, - "children": [ + }, + { + "$ref": "#/texts/160" + }, { "$ref": "#/texts/161" }, @@ -620,10 +620,18 @@ }, { "$ref": "#/texts/172" - }, - { - "$ref": "#/texts/173" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/12", + "parent": { + "$ref": "#/texts/149" + }, + "children": [ { "$ref": "#/texts/174" }, @@ -653,18 +661,10 @@ }, { "$ref": "#/texts/183" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/12", - "parent": { - "$ref": "#/texts/160" - }, - "children": [ + }, + { + "$ref": "#/texts/184" + }, { "$ref": "#/texts/185" }, @@ -700,16 +700,18 @@ }, { "$ref": "#/texts/196" - }, - { - "$ref": "#/texts/197" - }, - { - "$ref": "#/texts/198" - }, - { - "$ref": "#/texts/199" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/13", + "parent": { + "$ref": "#/texts/197" + }, + "children": [ { "$ref": "#/texts/200" }, @@ -724,15 +726,6 @@ }, { "$ref": "#/texts/204" - }, - { - "$ref": "#/texts/205" - }, - { - "$ref": "#/texts/206" - }, - { - "$ref": "#/texts/207" } ], "content_layer": "body", @@ -740,11 +733,29 @@ "label": "inline" }, { - "self_ref": "#/groups/13", + "self_ref": "#/groups/14", "parent": { - "$ref": "#/texts/208" + "$ref": "#/texts/197" }, "children": [ + { + "$ref": "#/texts/205" + }, + { + "$ref": "#/texts/206" + }, + { + "$ref": "#/texts/207" + }, + { + "$ref": "#/texts/208" + }, + { + "$ref": "#/texts/209" + }, + { + "$ref": "#/texts/210" + }, { "$ref": "#/texts/211" }, @@ -759,18 +770,7 @@ }, { "$ref": "#/texts/215" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/14", - "parent": { - "$ref": "#/texts/208" - }, - "children": [ + }, { "$ref": "#/texts/216" }, @@ -788,7 +788,18 @@ }, { "$ref": "#/texts/221" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/15", + "parent": { + "$ref": "#/texts/197" + }, + "children": [ { "$ref": "#/texts/222" }, @@ -815,12 +826,6 @@ }, { "$ref": "#/texts/230" - }, - { - "$ref": "#/texts/231" - }, - { - "$ref": "#/texts/232" } ], "content_layer": "body", @@ -828,11 +833,14 @@ "label": "inline" }, { - "self_ref": "#/groups/15", + "self_ref": "#/groups/16", "parent": { - "$ref": "#/texts/208" + "$ref": "#/texts/231" }, "children": [ + { + "$ref": "#/texts/232" + }, { "$ref": "#/texts/233" }, @@ -859,6 +867,9 @@ }, { "$ref": "#/texts/241" + }, + { + "$ref": "#/texts/242" } ], "content_layer": "body", @@ -866,55 +877,44 @@ "label": "inline" }, { - "self_ref": "#/groups/16", + "self_ref": "#/groups/17", "parent": { - "$ref": "#/texts/242" + "$ref": "#/texts/247" }, "children": [ { - "$ref": "#/texts/243" + "$ref": "#/texts/248" }, { - "$ref": "#/texts/244" + "$ref": "#/texts/249" }, { - "$ref": "#/texts/245" + "$ref": "#/texts/250" }, { - "$ref": "#/texts/246" + "$ref": "#/texts/251" }, { - "$ref": "#/texts/247" + "$ref": "#/texts/252" }, { - "$ref": "#/texts/248" + "$ref": "#/texts/253" }, { - "$ref": "#/texts/249" + "$ref": "#/texts/254" }, { - "$ref": "#/texts/250" + "$ref": "#/texts/255" }, { - "$ref": "#/texts/251" + "$ref": "#/texts/256" }, { - "$ref": "#/texts/252" + "$ref": "#/texts/257" }, { - "$ref": "#/texts/253" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/17", - "parent": { - "$ref": "#/texts/258" - }, - "children": [ + "$ref": "#/texts/258" + }, { "$ref": "#/texts/259" }, @@ -932,10 +932,18 @@ }, { "$ref": "#/texts/264" - }, - { - "$ref": "#/texts/265" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/18", + "parent": { + "$ref": "#/texts/247" + }, + "children": [ { "$ref": "#/texts/266" }, @@ -965,18 +973,10 @@ }, { "$ref": "#/texts/275" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/18", - "parent": { - "$ref": "#/texts/258" - }, - "children": [ + }, + { + "$ref": "#/texts/276" + }, { "$ref": "#/texts/277" }, @@ -1030,7 +1030,18 @@ }, { "$ref": "#/texts/294" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/19", + "parent": { + "$ref": "#/texts/247" + }, + "children": [ { "$ref": "#/texts/295" }, @@ -1057,12 +1068,6 @@ }, { "$ref": "#/texts/303" - }, - { - "$ref": "#/texts/304" - }, - { - "$ref": "#/texts/305" } ], "content_layer": "body", @@ -1070,11 +1075,17 @@ "label": "inline" }, { - "self_ref": "#/groups/19", + "self_ref": "#/groups/20", "parent": { - "$ref": "#/texts/258" + "$ref": "#/texts/247" }, "children": [ + { + "$ref": "#/texts/304" + }, + { + "$ref": "#/texts/305" + }, { "$ref": "#/texts/306" }, @@ -1101,6 +1112,12 @@ }, { "$ref": "#/texts/314" + }, + { + "$ref": "#/texts/315" + }, + { + "$ref": "#/texts/316" } ], "content_layer": "body", @@ -1108,20 +1125,11 @@ "label": "inline" }, { - "self_ref": "#/groups/20", + "self_ref": "#/groups/21", "parent": { - "$ref": "#/texts/258" + "$ref": "#/texts/317" }, "children": [ - { - "$ref": "#/texts/315" - }, - { - "$ref": "#/texts/316" - }, - { - "$ref": "#/texts/317" - }, { "$ref": "#/texts/318" }, @@ -1151,6 +1159,15 @@ }, { "$ref": "#/texts/327" + }, + { + "$ref": "#/texts/328" + }, + { + "$ref": "#/texts/329" + }, + { + "$ref": "#/texts/330" } ], "content_layer": "body", @@ -1158,20 +1175,11 @@ "label": "inline" }, { - "self_ref": "#/groups/21", + "self_ref": "#/groups/22", "parent": { - "$ref": "#/texts/328" + "$ref": "#/texts/317" }, "children": [ - { - "$ref": "#/texts/329" - }, - { - "$ref": "#/texts/330" - }, - { - "$ref": "#/texts/331" - }, { "$ref": "#/texts/332" }, @@ -1201,6 +1209,15 @@ }, { "$ref": "#/texts/341" + }, + { + "$ref": "#/texts/342" + }, + { + "$ref": "#/texts/343" + }, + { + "$ref": "#/texts/344" } ], "content_layer": "body", @@ -1208,20 +1225,11 @@ "label": "inline" }, { - "self_ref": "#/groups/22", + "self_ref": "#/groups/23", "parent": { - "$ref": "#/texts/328" + "$ref": "#/texts/345" }, "children": [ - { - "$ref": "#/texts/343" - }, - { - "$ref": "#/texts/344" - }, - { - "$ref": "#/texts/345" - }, { "$ref": "#/texts/346" }, @@ -1251,18 +1259,10 @@ }, { "$ref": "#/texts/355" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/23", - "parent": { - "$ref": "#/texts/356" - }, - "children": [ + }, + { + "$ref": "#/texts/356" + }, { "$ref": "#/texts/357" }, @@ -1334,10 +1334,18 @@ }, { "$ref": "#/texts/380" - }, - { - "$ref": "#/texts/381" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/24", + "parent": { + "$ref": "#/texts/345" + }, + "children": [ { "$ref": "#/texts/382" }, @@ -1364,9 +1372,6 @@ }, { "$ref": "#/texts/390" - }, - { - "$ref": "#/texts/391" } ], "content_layer": "body", @@ -1374,14 +1379,11 @@ "label": "inline" }, { - "self_ref": "#/groups/24", + "self_ref": "#/groups/25", "parent": { - "$ref": "#/texts/356" + "$ref": "#/texts/392" }, "children": [ - { - "$ref": "#/texts/393" - }, { "$ref": "#/texts/394" }, @@ -1405,18 +1407,16 @@ }, { "$ref": "#/texts/401" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/25", - "parent": { - "$ref": "#/texts/403" - }, - "children": [ + }, + { + "$ref": "#/texts/402" + }, + { + "$ref": "#/texts/403" + }, + { + "$ref": "#/texts/404" + }, { "$ref": "#/texts/405" }, @@ -1434,10 +1434,18 @@ }, { "$ref": "#/texts/410" - }, - { - "$ref": "#/texts/411" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/26", + "parent": { + "$ref": "#/texts/411" + }, + "children": [ { "$ref": "#/texts/412" }, @@ -1452,10 +1460,18 @@ }, { "$ref": "#/texts/416" - }, - { - "$ref": "#/texts/417" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/27", + "parent": { + "$ref": "#/texts/417" + }, + "children": [ { "$ref": "#/texts/418" }, @@ -1467,18 +1483,10 @@ }, { "$ref": "#/texts/421" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/26", - "parent": { - "$ref": "#/texts/422" - }, - "children": [ + }, + { + "$ref": "#/texts/422" + }, { "$ref": "#/texts/423" }, @@ -1493,18 +1501,10 @@ }, { "$ref": "#/texts/427" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/27", - "parent": { - "$ref": "#/texts/428" - }, - "children": [ + }, + { + "$ref": "#/texts/428" + }, { "$ref": "#/texts/429" }, @@ -1522,7 +1522,18 @@ }, { "$ref": "#/texts/434" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/28", + "parent": { + "$ref": "#/texts/417" + }, + "children": [ { "$ref": "#/texts/435" }, @@ -1555,18 +1566,7 @@ }, { "$ref": "#/texts/445" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/28", - "parent": { - "$ref": "#/texts/428" - }, - "children": [ + }, { "$ref": "#/texts/446" }, @@ -1578,10 +1578,18 @@ }, { "$ref": "#/texts/449" - }, - { - "$ref": "#/texts/450" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/29", + "parent": { + "$ref": "#/texts/450" + }, + "children": [ { "$ref": "#/texts/451" }, @@ -1602,15 +1610,6 @@ }, { "$ref": "#/texts/457" - }, - { - "$ref": "#/texts/458" - }, - { - "$ref": "#/texts/459" - }, - { - "$ref": "#/texts/460" } ], "content_layer": "body", @@ -1618,11 +1617,14 @@ "label": "inline" }, { - "self_ref": "#/groups/29", + "self_ref": "#/groups/30", "parent": { - "$ref": "#/texts/461" + "$ref": "#/texts/460" }, "children": [ + { + "$ref": "#/texts/461" + }, { "$ref": "#/texts/462" }, @@ -1643,18 +1645,16 @@ }, { "$ref": "#/texts/468" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/30", - "parent": { - "$ref": "#/texts/471" - }, - "children": [ + }, + { + "$ref": "#/texts/469" + }, + { + "$ref": "#/texts/470" + }, + { + "$ref": "#/texts/471" + }, { "$ref": "#/texts/472" }, @@ -1849,39 +1849,6 @@ }, { "$ref": "#/texts/536" - }, - { - "$ref": "#/texts/537" - }, - { - "$ref": "#/texts/538" - }, - { - "$ref": "#/texts/539" - }, - { - "$ref": "#/texts/540" - }, - { - "$ref": "#/texts/541" - }, - { - "$ref": "#/texts/542" - }, - { - "$ref": "#/texts/543" - }, - { - "$ref": "#/texts/544" - }, - { - "$ref": "#/texts/545" - }, - { - "$ref": "#/texts/546" - }, - { - "$ref": "#/texts/547" } ], "content_layer": "body", @@ -1906,22 +1873,22 @@ "$ref": "#/texts/3" }, { - "$ref": "#/texts/27" + "$ref": "#/texts/16" }, { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, { - "$ref": "#/texts/461" + "$ref": "#/texts/450" }, { - "$ref": "#/texts/469" + "$ref": "#/texts/458" }, { - "$ref": "#/texts/471" + "$ref": "#/texts/460" } ], "content_layer": "body", @@ -1937,116 +1904,42 @@ }, "children": [], "content_layer": "body", - "label": "paragraph", - "prov": [], - "orig": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab", - "text": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab" - }, - { - "self_ref": "#/texts/2", - "parent": { - "$ref": "#/texts/0" - }, - "children": [], - "content_layer": "body", - "label": "paragraph", - "prov": [], - "orig": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil", - "text": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil" - }, - { - "self_ref": "#/texts/3", - "parent": { - "$ref": "#/texts/0" - }, - "children": [ - { - "$ref": "#/groups/0" - } - ], - "content_layer": "body", - "label": "section_header", - "prov": [], - "orig": "Abstract", - "text": "Abstract", - "level": 1 - }, - { - "self_ref": "#/texts/4", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO", - "text": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO" - }, - { - "self_ref": "#/texts/5", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": "2", - "text": "2", - "formatting": { - "bold": false, - "italic": false, - "underline": false, - "strikethrough": false, - "script": "sub" - } - }, - { - "self_ref": "#/texts/6", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", + "label": "paragraph", "prov": [], - "orig": ") equivalents (CO", - "text": ") equivalents (CO" + "orig": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab", + "text": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab" }, { - "self_ref": "#/texts/7", + "self_ref": "#/texts/2", "parent": { - "$ref": "#/groups/0" + "$ref": "#/texts/0" }, "children": [], "content_layer": "body", - "label": "text", + "label": "paragraph", "prov": [], - "orig": "2", - "text": "2", - "formatting": { - "bold": false, - "italic": false, - "underline": false, - "strikethrough": false, - "script": "sub" - } + "orig": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil", + "text": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil" }, { - "self_ref": "#/texts/8", + "self_ref": "#/texts/3", "parent": { - "$ref": "#/groups/0" + "$ref": "#/texts/0" }, - "children": [], + "children": [ + { + "$ref": "#/groups/0" + } + ], "content_layer": "body", - "label": "text", + "label": "section_header", "prov": [], - "orig": "e) (kg energy-corrected milk (ECM))", - "text": "e) (kg energy-corrected milk (ECM))" + "orig": "Abstract", + "text": "Abstract", + "level": 1 }, { - "self_ref": "#/texts/9", + "self_ref": "#/texts/4", "parent": { "$ref": "#/groups/0" }, @@ -2054,18 +1947,18 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "-1", - "text": "-1", + "orig": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2)", + "text": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2)", "formatting": { "bold": false, "italic": false, "underline": false, "strikethrough": false, - "script": "super" + "script": "sub" } }, { - "self_ref": "#/texts/10", + "self_ref": "#/texts/5", "parent": { "$ref": "#/groups/0" }, @@ -2073,11 +1966,18 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ", encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation", - "text": ", encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation" + "orig": "equivalents (CO2e) (kg energy-corrected milk (ECM))-1,", + "text": "equivalents (CO2e) (kg energy-corrected milk (ECM))-1,", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "sub" + } }, { - "self_ref": "#/texts/11", + "self_ref": "#/texts/6", "parent": { "$ref": "#/groups/0" }, @@ -2085,8 +1985,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "-1", - "text": "-1", + "orig": "encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1.", + "text": "encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1.", "formatting": { "bold": false, "italic": false, @@ -2096,7 +1996,7 @@ } }, { - "self_ref": "#/texts/12", + "self_ref": "#/texts/7", "parent": { "$ref": "#/groups/0" }, @@ -2104,11 +2004,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ". The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)", - "text": ". The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)" + "orig": "The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)", + "text": "The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)" }, { - "self_ref": "#/texts/13", + "self_ref": "#/texts/8", "parent": { "$ref": "#/groups/0" }, @@ -2127,7 +2027,7 @@ } }, { - "self_ref": "#/texts/14", + "self_ref": "#/texts/9", "parent": { "$ref": "#/groups/0" }, @@ -2139,7 +2039,7 @@ "text": "intake, 75, and 50% of" }, { - "self_ref": "#/texts/15", + "self_ref": "#/texts/10", "parent": { "$ref": "#/groups/0" }, @@ -2158,19 +2058,7 @@ } }, { - "self_ref": "#/texts/16", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO", - "text": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO" - }, - { - "self_ref": "#/texts/17", + "self_ref": "#/texts/11", "parent": { "$ref": "#/groups/0" }, @@ -2178,8 +2066,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "2", - "text": "2", + "orig": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1.", + "text": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1.", "formatting": { "bold": false, "italic": false, @@ -2189,50 +2077,7 @@ } }, { - "self_ref": "#/texts/18", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": "e (kg ECM)", - "text": "e (kg ECM)" - }, - { - "self_ref": "#/texts/19", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": "-1", - "text": "-1", - "formatting": { - "bold": false, - "italic": false, - "underline": false, - "strikethrough": false, - "script": "super" - } - }, - { - "self_ref": "#/texts/20", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": ". Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO", - "text": ". Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO" - }, - { - "self_ref": "#/texts/21", + "self_ref": "#/texts/12", "parent": { "$ref": "#/groups/0" }, @@ -2240,8 +2085,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "2", - "text": "2", + "orig": "Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1", + "text": "Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1", "formatting": { "bold": false, "italic": false, @@ -2251,38 +2096,7 @@ } }, { - "self_ref": "#/texts/22", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": "e (kg ECM)", - "text": "e (kg ECM)" - }, - { - "self_ref": "#/texts/23", - "parent": { - "$ref": "#/groups/0" - }, - "children": [], - "content_layer": "body", - "label": "text", - "prov": [], - "orig": "-1", - "text": "-1", - "formatting": { - "bold": false, - "italic": false, - "underline": false, - "strikethrough": false, - "script": "super" - } - }, - { - "self_ref": "#/texts/24", + "self_ref": "#/texts/13", "parent": { "$ref": "#/groups/0" }, @@ -2294,7 +2108,7 @@ "text": "in scenarios including pastures compared to" }, { - "self_ref": "#/texts/25", + "self_ref": "#/texts/14", "parent": { "$ref": "#/groups/0" }, @@ -2313,7 +2127,7 @@ } }, { - "self_ref": "#/texts/26", + "self_ref": "#/texts/15", "parent": { "$ref": "#/groups/0" }, @@ -2325,7 +2139,7 @@ "text": "TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent." }, { - "self_ref": "#/texts/27", + "self_ref": "#/texts/16", "parent": { "$ref": "#/texts/0" }, @@ -2337,13 +2151,13 @@ "$ref": "#/groups/2" }, { - "$ref": "#/texts/40" + "$ref": "#/texts/29" }, { - "$ref": "#/texts/41" + "$ref": "#/texts/30" }, { - "$ref": "#/texts/42" + "$ref": "#/texts/31" } ], "content_layer": "body", @@ -2354,7 +2168,7 @@ "level": 1 }, { - "self_ref": "#/texts/28", + "self_ref": "#/texts/17", "parent": { "$ref": "#/groups/1" }, @@ -2366,7 +2180,7 @@ "text": "Greenhouse gas (GHG) emissions from livestock activities represent 10–12% of global emissions [1], ranging from 5.5–7.5 Gt CO" }, { - "self_ref": "#/texts/29", + "self_ref": "#/texts/18", "parent": { "$ref": "#/groups/1" }, @@ -2385,7 +2199,7 @@ } }, { - "self_ref": "#/texts/30", + "self_ref": "#/texts/19", "parent": { "$ref": "#/groups/1" }, @@ -2397,7 +2211,7 @@ "text": "equivalents (CO" }, { - "self_ref": "#/texts/31", + "self_ref": "#/texts/20", "parent": { "$ref": "#/groups/1" }, @@ -2416,7 +2230,7 @@ } }, { - "self_ref": "#/texts/32", + "self_ref": "#/texts/21", "parent": { "$ref": "#/groups/1" }, @@ -2428,7 +2242,7 @@ "text": "e) yr" }, { - "self_ref": "#/texts/33", + "self_ref": "#/texts/22", "parent": { "$ref": "#/groups/1" }, @@ -2447,7 +2261,7 @@ } }, { - "self_ref": "#/texts/34", + "self_ref": "#/texts/23", "parent": { "$ref": "#/groups/1" }, @@ -2459,7 +2273,7 @@ "text": ", with almost 30% coming from dairy cattle production systems [2]. However, the livestock sector supply between 13 and 17% of calories and between 28 and 33% of human edible protein consumption globally [3]. Additionally, livestock produce more human-edible protein per unit area than crops when land is unsuitable for food crop production [4]." }, { - "self_ref": "#/texts/35", + "self_ref": "#/texts/24", "parent": { "$ref": "#/groups/2" }, @@ -2471,7 +2285,7 @@ "text": "Considering the key role of livestock systems in global food security, several technical and management interventions have been investigated to mitigate methane (CH" }, { - "self_ref": "#/texts/36", + "self_ref": "#/texts/25", "parent": { "$ref": "#/groups/2" }, @@ -2490,7 +2304,7 @@ } }, { - "self_ref": "#/texts/37", + "self_ref": "#/texts/26", "parent": { "$ref": "#/groups/2" }, @@ -2502,7 +2316,7 @@ "text": ") emissions from enteric fermentation [5], animal management [6] and manure management [7]. CH" }, { - "self_ref": "#/texts/38", + "self_ref": "#/texts/27", "parent": { "$ref": "#/groups/2" }, @@ -2521,7 +2335,7 @@ } }, { - "self_ref": "#/texts/39", + "self_ref": "#/texts/28", "parent": { "$ref": "#/groups/2" }, @@ -2533,9 +2347,9 @@ "text": "emissions from enteric fermentation represents around 34% of total emissions from livestock sector, which is the largest source [2]. Increasing proportions of concentrate and digestibility of forages in the diet have been proposed as mitigation strategies [1,5]. In contrast, some life cycle assessment (LCA) studies of dairy systems in temperate regions [8–11] have identified that increasing concentrate proportion may increase carbon (C) footprint due to greater resource use and pollutants from the production of feed compared to forage. Thus, increasing pasture proportion on dairy cattle systems may be an alternative management to mitigate the C footprint." }, { - "self_ref": "#/texts/40", + "self_ref": "#/texts/29", "parent": { - "$ref": "#/texts/27" + "$ref": "#/texts/16" }, "children": [], "content_layer": "body", @@ -2545,9 +2359,9 @@ "text": "In subtropical climate zones, cows may graze tropical pastures rather than temperate pastures during the warm season [12]. Some important dairy production areas, such as southern Brazil, central to northern Argentina, Uruguay, South Africa, New Zealand and Australia, are located in these climate zones, having more than 900 million ha in native, permanent or temporary pastures, producing almost 20% of global milk production [13]. However, due to a considerable inter-annual variation in pasture growth rates [14,15], the interest in mixed systems, using total mixed ration (TMR) + pasture has been increasing [16]. Nevertheless, to our best knowledge, studies conducted to evaluate milk production response in dairy cow diets receiving TMR and pastures have only been conducted in temperate pastures and not in tropical pastures (e.g. [17–19])." }, { - "self_ref": "#/texts/41", + "self_ref": "#/texts/30", "parent": { - "$ref": "#/texts/27" + "$ref": "#/texts/16" }, "children": [], "content_layer": "body", @@ -2557,9 +2371,9 @@ "text": "It has been shown that dairy cows receiving TMR-based diets may not decrease milk production when supplemented with temperate pastures in a vegetative growth stage [18]. On the other hand, tropical pastures have lower organic matter digestibility and cows experience reduced dry matter (DM) intake and milk yield compared to temperate pastures [20,21]. A lower milk yield increases the C footprint intensity [22], offsetting an expected advantage through lower GHG emissions from crop and reduced DM intake." }, { - "self_ref": "#/texts/42", + "self_ref": "#/texts/31", "parent": { - "$ref": "#/texts/27" + "$ref": "#/texts/16" }, "children": [], "content_layer": "body", @@ -2569,7 +2383,7 @@ "text": "The aim of this work was to quantify the C footprint and land use of dairy systems using cows with a medium milk production potential in a subtropical region. The effect of replacing total mixed ration (TMR) with pastures during lactation periods was evaluated." }, { - "self_ref": "#/texts/43", + "self_ref": "#/texts/32", "parent": { "$ref": "#/texts/0" }, @@ -2578,34 +2392,34 @@ "$ref": "#/groups/3" }, { - "$ref": "#/texts/47" + "$ref": "#/texts/36" }, { - "$ref": "#/texts/50" + "$ref": "#/texts/39" }, { - "$ref": "#/texts/54" + "$ref": "#/texts/43" }, { - "$ref": "#/texts/73" + "$ref": "#/texts/62" }, { - "$ref": "#/texts/93" + "$ref": "#/texts/82" }, { - "$ref": "#/texts/144" + "$ref": "#/texts/133" }, { - "$ref": "#/texts/160" + "$ref": "#/texts/149" }, { - "$ref": "#/texts/208" + "$ref": "#/texts/197" }, { - "$ref": "#/texts/242" + "$ref": "#/texts/231" }, { - "$ref": "#/texts/254" + "$ref": "#/texts/243" } ], "content_layer": "body", @@ -2616,7 +2430,7 @@ "level": 1 }, { - "self_ref": "#/texts/44", + "self_ref": "#/texts/33", "parent": { "$ref": "#/groups/3" }, @@ -2628,7 +2442,7 @@ "text": "An LCA was developed according to the ISO standards [23,24] and Food and Agriculture Organization of the United Nations (FAO) Livestock Environmental Assessment Protocol guidelines [25]. All procedures were approved by the ‘Comissão de Ética no Uso de Animais’ (CEUA/UDESC) on September 15, 2016—Approval number 4373090816 -" }, { - "self_ref": "#/texts/45", + "self_ref": "#/texts/34", "parent": { "$ref": "#/groups/3" }, @@ -2641,7 +2455,7 @@ "hyperlink": "https://www.udesc.br/cav/ceua" }, { - "self_ref": "#/texts/46", + "self_ref": "#/texts/35", "parent": { "$ref": "#/groups/3" }, @@ -2653,13 +2467,13 @@ "text": "." }, { - "self_ref": "#/texts/47", + "self_ref": "#/texts/36", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { - "$ref": "#/texts/48" + "$ref": "#/texts/37" }, { "$ref": "#/pictures/0" @@ -2673,9 +2487,9 @@ "level": 2 }, { - "self_ref": "#/texts/48", + "self_ref": "#/texts/37", "parent": { - "$ref": "#/texts/47" + "$ref": "#/texts/36" }, "children": [], "content_layer": "body", @@ -2685,7 +2499,7 @@ "text": "The goal of the study was to assess the C footprint of annual tropical and temperate pastures in lactating dairy cow diets. The production system was divided into four main processes: (i) animal husbandry, (ii) manure management and urine and dung deposited by grazing animals, (iii) production of feed ingredients and (iv) farm management (Fig 1). The study boundary included all processes up to the animal farm gate (cradle to gate), including secondary sources such as GHG emissions during the production of fuel, electricity, machinery, manufacturing of fertilizer, pesticides, seeds and plastic used in silage production. Fuel combustion and machinery (manufacture and repairs) for manure handling and electricity for milking and confinement were accounted as emissions from farm management. Emissions post milk production were assumed to be similar for all scenarios, therefore, activities including milk processing, distribution, retail or consumption were outside of the system boundary." }, { - "self_ref": "#/texts/49", + "self_ref": "#/texts/38", "parent": { "$ref": "#/body" }, @@ -2697,16 +2511,16 @@ "text": "Fig 1 Overview of the milk production system boundary considered in the study." }, { - "self_ref": "#/texts/50", + "self_ref": "#/texts/39", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { - "$ref": "#/texts/51" + "$ref": "#/texts/40" }, { - "$ref": "#/texts/52" + "$ref": "#/texts/41" }, { "$ref": "#/tables/0" @@ -2720,9 +2534,9 @@ "level": 2 }, { - "self_ref": "#/texts/51", + "self_ref": "#/texts/40", "parent": { - "$ref": "#/texts/50" + "$ref": "#/texts/39" }, "children": [], "content_layer": "body", @@ -2732,9 +2546,9 @@ "text": "The functional unit was one kilogram of energy-corrected milk (ECM) at the farm gate. All processes in the system were calculated based on one kilogram ECM. The ECM was calculated by multiplying milk production by the ratio of the energy content of the milk to the energy content of standard milk with 4% fat and 3.3% true protein according to NRC [20] as follows:" }, { - "self_ref": "#/texts/52", + "self_ref": "#/texts/41", "parent": { - "$ref": "#/texts/50" + "$ref": "#/texts/39" }, "children": [], "content_layer": "body", @@ -2744,7 +2558,7 @@ "text": "ECM = Milk production × (0.0929 × fat% + 0.0588× true protein% + 0.192) / (0.0929 × (4%) + 0.0588 × (3.3%) + 0.192), where fat% and protein% are fat and protein percentages in milk, respectively. The average milk production and composition were recorded from the University of Santa Catarina State (Brazil) herd, considering 165 lactations between 2009 and 2018. The herd is predominantly Holstein × Jersey cows, with key characteristics described in Table 1." }, { - "self_ref": "#/texts/53", + "self_ref": "#/texts/42", "parent": { "$ref": "#/body" }, @@ -2756,9 +2570,9 @@ "text": "Table 1 Descriptive characteristics of the herd." }, { - "self_ref": "#/texts/54", + "self_ref": "#/texts/43", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { @@ -2776,7 +2590,7 @@ "level": 2 }, { - "self_ref": "#/texts/55", + "self_ref": "#/texts/44", "parent": { "$ref": "#/groups/4" }, @@ -2788,7 +2602,7 @@ "text": "The individual feed requirements, as well as the milk production responses based on feed strategies were based on data recorded from the herd described above and two experiments performed using lactating cows from the same herd. Due to the variation on herbage production throughout the year, feed requirements were estimated taking into consideration that livestock systems have a calving period in April, which represents the beginning of fall season in the southern Hemisphere. The experiments have shown a 10% reduction in ECM production in dairy cows that received both 75 and 50% of" }, { - "self_ref": "#/texts/56", + "self_ref": "#/texts/45", "parent": { "$ref": "#/groups/4" }, @@ -2807,7 +2621,7 @@ } }, { - "self_ref": "#/texts/57", + "self_ref": "#/texts/46", "parent": { "$ref": "#/groups/4" }, @@ -2819,7 +2633,7 @@ "text": "TMR intake with access to grazing a tropical pasture (pearl-millet," }, { - "self_ref": "#/texts/58", + "self_ref": "#/texts/47", "parent": { "$ref": "#/groups/4" }, @@ -2838,7 +2652,7 @@ } }, { - "self_ref": "#/texts/59", + "self_ref": "#/texts/48", "parent": { "$ref": "#/groups/4" }, @@ -2850,7 +2664,7 @@ "text": "‘Campeiro’) compared to cows receiving" }, { - "self_ref": "#/texts/60", + "self_ref": "#/texts/49", "parent": { "$ref": "#/groups/4" }, @@ -2869,7 +2683,7 @@ } }, { - "self_ref": "#/texts/61", + "self_ref": "#/texts/50", "parent": { "$ref": "#/groups/4" }, @@ -2881,7 +2695,7 @@ "text": "TMR intake. Cows grazing on a temperate pasture (ryegrass," }, { - "self_ref": "#/texts/62", + "self_ref": "#/texts/51", "parent": { "$ref": "#/groups/4" }, @@ -2900,7 +2714,7 @@ } }, { - "self_ref": "#/texts/63", + "self_ref": "#/texts/52", "parent": { "$ref": "#/groups/4" }, @@ -2912,7 +2726,7 @@ "text": "‘Maximus’) did not need changes to ECM production compared to the" }, { - "self_ref": "#/texts/64", + "self_ref": "#/texts/53", "parent": { "$ref": "#/groups/4" }, @@ -2931,7 +2745,7 @@ } }, { - "self_ref": "#/texts/65", + "self_ref": "#/texts/54", "parent": { "$ref": "#/groups/4" }, @@ -2943,7 +2757,7 @@ "text": "TMR intake group." }, { - "self_ref": "#/texts/66", + "self_ref": "#/texts/55", "parent": { "$ref": "#/groups/5" }, @@ -2955,7 +2769,7 @@ "text": "Using experimental data, three scenarios were evaluated during the lactation period:" }, { - "self_ref": "#/texts/67", + "self_ref": "#/texts/56", "parent": { "$ref": "#/groups/5" }, @@ -2974,7 +2788,7 @@ } }, { - "self_ref": "#/texts/68", + "self_ref": "#/texts/57", "parent": { "$ref": "#/groups/5" }, @@ -2986,7 +2800,7 @@ "text": "TMR intake, and 75, and 50% of" }, { - "self_ref": "#/texts/69", + "self_ref": "#/texts/58", "parent": { "$ref": "#/groups/5" }, @@ -3005,7 +2819,7 @@ } }, { - "self_ref": "#/texts/70", + "self_ref": "#/texts/59", "parent": { "$ref": "#/groups/5" }, @@ -3017,7 +2831,7 @@ "text": "TMR intake with access to grazing either an annual tropical or temperate pasture as a function of month ([26], Civiero et al.," }, { - "self_ref": "#/texts/71", + "self_ref": "#/texts/60", "parent": { "$ref": "#/groups/5" }, @@ -3036,7 +2850,7 @@ } }, { - "self_ref": "#/texts/72", + "self_ref": "#/texts/61", "parent": { "$ref": "#/groups/5" }, @@ -3048,9 +2862,9 @@ "text": "). From April to October (210 days) cows accessed an annual temperate pasture (ryegrass), and from November to beginning of February (95 days) cows grazed an annual tropical pasture (pearl-millet). The average annual reduction in ECM production in dairy cows with access to pastures is 3%. This value was assumed during an entire lactation period." }, { - "self_ref": "#/texts/73", + "self_ref": "#/texts/62", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { @@ -3065,7 +2879,7 @@ "level": 2 }, { - "self_ref": "#/texts/74", + "self_ref": "#/texts/63", "parent": { "$ref": "#/groups/6" }, @@ -3077,7 +2891,7 @@ "text": "The CO" }, { - "self_ref": "#/texts/75", + "self_ref": "#/texts/64", "parent": { "$ref": "#/groups/6" }, @@ -3096,7 +2910,7 @@ } }, { - "self_ref": "#/texts/76", + "self_ref": "#/texts/65", "parent": { "$ref": "#/groups/6" }, @@ -3108,7 +2922,7 @@ "text": "e emissions were calculated by multiplying the emissions of CO" }, { - "self_ref": "#/texts/77", + "self_ref": "#/texts/66", "parent": { "$ref": "#/groups/6" }, @@ -3127,7 +2941,7 @@ } }, { - "self_ref": "#/texts/78", + "self_ref": "#/texts/67", "parent": { "$ref": "#/groups/6" }, @@ -3139,7 +2953,7 @@ "text": ", CH" }, { - "self_ref": "#/texts/79", + "self_ref": "#/texts/68", "parent": { "$ref": "#/groups/6" }, @@ -3158,7 +2972,7 @@ } }, { - "self_ref": "#/texts/80", + "self_ref": "#/texts/69", "parent": { "$ref": "#/groups/6" }, @@ -3170,7 +2984,7 @@ "text": "and N" }, { - "self_ref": "#/texts/81", + "self_ref": "#/texts/70", "parent": { "$ref": "#/groups/6" }, @@ -3189,7 +3003,7 @@ } }, { - "self_ref": "#/texts/82", + "self_ref": "#/texts/71", "parent": { "$ref": "#/groups/6" }, @@ -3201,7 +3015,7 @@ "text": "O by their 100-year global warming potential (GWP" }, { - "self_ref": "#/texts/83", + "self_ref": "#/texts/72", "parent": { "$ref": "#/groups/6" }, @@ -3220,7 +3034,7 @@ } }, { - "self_ref": "#/texts/84", + "self_ref": "#/texts/73", "parent": { "$ref": "#/groups/6" }, @@ -3232,7 +3046,7 @@ "text": "), based on IPCC assessment report 5 (AR5; [27]). The values of GWP" }, { - "self_ref": "#/texts/85", + "self_ref": "#/texts/74", "parent": { "$ref": "#/groups/6" }, @@ -3251,7 +3065,7 @@ } }, { - "self_ref": "#/texts/86", + "self_ref": "#/texts/75", "parent": { "$ref": "#/groups/6" }, @@ -3263,7 +3077,7 @@ "text": "are 1, 28 and 265 for CO" }, { - "self_ref": "#/texts/87", + "self_ref": "#/texts/76", "parent": { "$ref": "#/groups/6" }, @@ -3282,7 +3096,7 @@ } }, { - "self_ref": "#/texts/88", + "self_ref": "#/texts/77", "parent": { "$ref": "#/groups/6" }, @@ -3294,7 +3108,7 @@ "text": ", CH" }, { - "self_ref": "#/texts/89", + "self_ref": "#/texts/78", "parent": { "$ref": "#/groups/6" }, @@ -3313,7 +3127,7 @@ } }, { - "self_ref": "#/texts/90", + "self_ref": "#/texts/79", "parent": { "$ref": "#/groups/6" }, @@ -3325,7 +3139,7 @@ "text": "and N" }, { - "self_ref": "#/texts/91", + "self_ref": "#/texts/80", "parent": { "$ref": "#/groups/6" }, @@ -3344,7 +3158,7 @@ } }, { - "self_ref": "#/texts/92", + "self_ref": "#/texts/81", "parent": { "$ref": "#/groups/6" }, @@ -3356,16 +3170,16 @@ "text": "O, respectively." }, { - "self_ref": "#/texts/93", + "self_ref": "#/texts/82", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { - "$ref": "#/texts/94" + "$ref": "#/texts/83" }, { - "$ref": "#/texts/103" + "$ref": "#/texts/92" } ], "content_layer": "body", @@ -3376,9 +3190,9 @@ "level": 2 }, { - "self_ref": "#/texts/94", + "self_ref": "#/texts/83", "parent": { - "$ref": "#/texts/93" + "$ref": "#/texts/82" }, "children": [ { @@ -3396,7 +3210,7 @@ "level": 3 }, { - "self_ref": "#/texts/95", + "self_ref": "#/texts/84", "parent": { "$ref": "#/groups/7" }, @@ -3408,7 +3222,7 @@ "text": "The DM intake of each ingredient throughout the entire life of animals during lactation periods was calculated for each scenario: cows receiving only TMR, cows receiving 75% of TMR with annual pastures and cows receiving 50% of TMR with annual pastures (Table 2). In each of other phases of life (calf, heifer, dry cow), animals received the same diet, including a perennial tropical pasture (kikuyu grass," }, { - "self_ref": "#/texts/96", + "self_ref": "#/texts/85", "parent": { "$ref": "#/groups/7" }, @@ -3427,7 +3241,7 @@ } }, { - "self_ref": "#/texts/97", + "self_ref": "#/texts/86", "parent": { "$ref": "#/groups/7" }, @@ -3439,7 +3253,7 @@ "text": "). The DM intake of calves, heifers and dry cows was calculated assuming 2.8, 2.5 and 1.9% body weight, respectively [20]. In each case, the actual DM intake of concentrate and corn silage was recorded, and pasture DM intake was estimated by the difference between daily expected DM intake and actual DM intake of concentrate and corn silage. For lactating heifers and cows, TMR was formulated to meet the net energy for lactation (NE" }, { - "self_ref": "#/texts/98", + "self_ref": "#/texts/87", "parent": { "$ref": "#/groups/7" }, @@ -3458,7 +3272,7 @@ } }, { - "self_ref": "#/texts/99", + "self_ref": "#/texts/88", "parent": { "$ref": "#/groups/7" }, @@ -3470,7 +3284,7 @@ "text": ") and metabolizable protein (MP) requirements of experimental animals, according to [28]. The INRA system was used because it is possible to estimate pasture DM intake taking into account the TMR intake, pasture management and the time of access to pasture using the GrazeIn model [29], which was integrated in the software INRAtion 4.07 (" }, { - "self_ref": "#/texts/100", + "self_ref": "#/texts/89", "parent": { "$ref": "#/groups/7" }, @@ -3483,7 +3297,7 @@ "hyperlink": "https://www.inration.educagri.fr/fr/forum.php" }, { - "self_ref": "#/texts/101", + "self_ref": "#/texts/90", "parent": { "$ref": "#/groups/7" }, @@ -3495,7 +3309,7 @@ "text": "). The nutrient intake was calculated as a product of TMR and pasture intake and the nutrient contents of TMR and pasture, respectively, which were determined in feed samples collected throughout the experiments." }, { - "self_ref": "#/texts/102", + "self_ref": "#/texts/91", "parent": { "$ref": "#/body" }, @@ -3507,9 +3321,9 @@ "text": "Table 2 Dairy cows’ diets in different scenariosa." }, { - "self_ref": "#/texts/103", + "self_ref": "#/texts/92", "parent": { - "$ref": "#/texts/93" + "$ref": "#/texts/82" }, "children": [ { @@ -3533,7 +3347,7 @@ "level": 3 }, { - "self_ref": "#/texts/104", + "self_ref": "#/texts/93", "parent": { "$ref": "#/groups/8" }, @@ -3545,7 +3359,7 @@ "text": "GHG emission factors used for off- and on-farm feed production were based on literature values, and are presented in Table 3. The emission factor used for corn grain is the average of emission factors observed in different levels of synthetic N fertilization [30]. The emission factor used for soybean is based on Brazilian soybean production [31]. The emissions used for corn silage, including feed processing (cutting, crushing and mixing), and annual or perennial grass productions were 3300 and 1500 kg CO" }, { - "self_ref": "#/texts/105", + "self_ref": "#/texts/94", "parent": { "$ref": "#/groups/8" }, @@ -3564,7 +3378,7 @@ } }, { - "self_ref": "#/texts/106", + "self_ref": "#/texts/95", "parent": { "$ref": "#/groups/8" }, @@ -3576,7 +3390,7 @@ "text": "e ha" }, { - "self_ref": "#/texts/107", + "self_ref": "#/texts/96", "parent": { "$ref": "#/groups/8" }, @@ -3595,7 +3409,7 @@ } }, { - "self_ref": "#/texts/108", + "self_ref": "#/texts/97", "parent": { "$ref": "#/groups/8" }, @@ -3607,7 +3421,7 @@ "text": ", respectively [32]. The DM production (kg ha" }, { - "self_ref": "#/texts/109", + "self_ref": "#/texts/98", "parent": { "$ref": "#/groups/8" }, @@ -3626,7 +3440,7 @@ } }, { - "self_ref": "#/texts/110", + "self_ref": "#/texts/99", "parent": { "$ref": "#/groups/8" }, @@ -3638,7 +3452,7 @@ "text": ") of corn silage and pastures were based on regional and locally recorded data [33–36], assuming that animals are able to consume 70% of pastures during grazing." }, { - "self_ref": "#/texts/111", + "self_ref": "#/texts/100", "parent": { "$ref": "#/body" }, @@ -3650,7 +3464,7 @@ "text": "Table 3 GHG emission factors for Off- and On-farm feed production." }, { - "self_ref": "#/texts/112", + "self_ref": "#/texts/101", "parent": { "$ref": "#/groups/9" }, @@ -3662,7 +3476,7 @@ "text": "Emissions from on-farm feed production (corn silage and pasture) were estimated using primary and secondary sources based on the actual amount of each input (Table 4). Primary sources were direct and indirect N" }, { - "self_ref": "#/texts/113", + "self_ref": "#/texts/102", "parent": { "$ref": "#/groups/9" }, @@ -3681,7 +3495,7 @@ } }, { - "self_ref": "#/texts/114", + "self_ref": "#/texts/103", "parent": { "$ref": "#/groups/9" }, @@ -3693,7 +3507,7 @@ "text": "O-N emissions from organic and synthetic fertilizers and crop/pasture residues, CO" }, { - "self_ref": "#/texts/115", + "self_ref": "#/texts/104", "parent": { "$ref": "#/groups/9" }, @@ -3712,7 +3526,7 @@ } }, { - "self_ref": "#/texts/116", + "self_ref": "#/texts/105", "parent": { "$ref": "#/groups/9" }, @@ -3724,7 +3538,7 @@ "text": "-C emissions from lime and urea applications, as well as fuel combustion. The direct N" }, { - "self_ref": "#/texts/117", + "self_ref": "#/texts/106", "parent": { "$ref": "#/groups/9" }, @@ -3743,7 +3557,7 @@ } }, { - "self_ref": "#/texts/118", + "self_ref": "#/texts/107", "parent": { "$ref": "#/groups/9" }, @@ -3755,7 +3569,7 @@ "text": "O-N emission factor (kg (kg N input)" }, { - "self_ref": "#/texts/119", + "self_ref": "#/texts/108", "parent": { "$ref": "#/groups/9" }, @@ -3774,7 +3588,7 @@ } }, { - "self_ref": "#/texts/120", + "self_ref": "#/texts/109", "parent": { "$ref": "#/groups/9" }, @@ -3786,7 +3600,7 @@ "text": ") is based on a local study performed previously [37]. For indirect N" }, { - "self_ref": "#/texts/121", + "self_ref": "#/texts/110", "parent": { "$ref": "#/groups/9" }, @@ -3805,7 +3619,7 @@ } }, { - "self_ref": "#/texts/122", + "self_ref": "#/texts/111", "parent": { "$ref": "#/groups/9" }, @@ -3817,7 +3631,7 @@ "text": "O-N emissions (kg N" }, { - "self_ref": "#/texts/123", + "self_ref": "#/texts/112", "parent": { "$ref": "#/groups/9" }, @@ -3836,7 +3650,7 @@ } }, { - "self_ref": "#/texts/124", + "self_ref": "#/texts/113", "parent": { "$ref": "#/groups/9" }, @@ -3848,7 +3662,7 @@ "text": "O-N (kg NH" }, { - "self_ref": "#/texts/125", + "self_ref": "#/texts/114", "parent": { "$ref": "#/groups/9" }, @@ -3867,7 +3681,7 @@ } }, { - "self_ref": "#/texts/126", + "self_ref": "#/texts/115", "parent": { "$ref": "#/groups/9" }, @@ -3879,7 +3693,7 @@ "text": "-N + NO" }, { - "self_ref": "#/texts/127", + "self_ref": "#/texts/116", "parent": { "$ref": "#/groups/9" }, @@ -3898,7 +3712,7 @@ } }, { - "self_ref": "#/texts/128", + "self_ref": "#/texts/117", "parent": { "$ref": "#/groups/9" }, @@ -3910,7 +3724,7 @@ "text": ")" }, { - "self_ref": "#/texts/129", + "self_ref": "#/texts/118", "parent": { "$ref": "#/groups/9" }, @@ -3929,7 +3743,7 @@ } }, { - "self_ref": "#/texts/130", + "self_ref": "#/texts/119", "parent": { "$ref": "#/groups/9" }, @@ -3941,7 +3755,7 @@ "text": "), as well as CO" }, { - "self_ref": "#/texts/131", + "self_ref": "#/texts/120", "parent": { "$ref": "#/groups/9" }, @@ -3960,7 +3774,7 @@ } }, { - "self_ref": "#/texts/132", + "self_ref": "#/texts/121", "parent": { "$ref": "#/groups/9" }, @@ -3972,7 +3786,7 @@ "text": "-C emissions from lime + urea, default values proposed by IPCC [38] were used. For perennial pastures, a C sequestration of 0.57 t ha" }, { - "self_ref": "#/texts/133", + "self_ref": "#/texts/122", "parent": { "$ref": "#/groups/9" }, @@ -3991,7 +3805,7 @@ } }, { - "self_ref": "#/texts/134", + "self_ref": "#/texts/123", "parent": { "$ref": "#/groups/9" }, @@ -4003,7 +3817,7 @@ "text": "was used based on a 9-year study conducted in southern Brazil [39]. Due to the use of conventional tillage, no C sequestration was considered for annual pastures. The amount of fuel required was 8.9 (no-tillage) and 14.3 L ha" }, { - "self_ref": "#/texts/135", + "self_ref": "#/texts/124", "parent": { "$ref": "#/groups/9" }, @@ -4022,7 +3836,7 @@ } }, { - "self_ref": "#/texts/136", + "self_ref": "#/texts/125", "parent": { "$ref": "#/groups/9" }, @@ -4034,7 +3848,7 @@ "text": "(disking) for annual tropical and temperate pastures, respectively [40]. The CO" }, { - "self_ref": "#/texts/137", + "self_ref": "#/texts/126", "parent": { "$ref": "#/groups/9" }, @@ -4053,7 +3867,7 @@ } }, { - "self_ref": "#/texts/138", + "self_ref": "#/texts/127", "parent": { "$ref": "#/groups/9" }, @@ -4065,7 +3879,7 @@ "text": "from fuel combustion was 2.7 kg CO" }, { - "self_ref": "#/texts/139", + "self_ref": "#/texts/128", "parent": { "$ref": "#/groups/9" }, @@ -4084,7 +3898,7 @@ } }, { - "self_ref": "#/texts/140", + "self_ref": "#/texts/129", "parent": { "$ref": "#/groups/9" }, @@ -4096,7 +3910,7 @@ "text": "L" }, { - "self_ref": "#/texts/141", + "self_ref": "#/texts/130", "parent": { "$ref": "#/groups/9" }, @@ -4115,7 +3929,7 @@ } }, { - "self_ref": "#/texts/142", + "self_ref": "#/texts/131", "parent": { "$ref": "#/groups/9" }, @@ -4127,7 +3941,7 @@ "text": "[41]. Secondary sources of emissions during the production of fuel, machinery, fertilizer, pesticides, seeds and plastic for ensilage were estimated using emission factors described by Rotz et al. [42]." }, { - "self_ref": "#/texts/143", + "self_ref": "#/texts/132", "parent": { "$ref": "#/body" }, @@ -4139,9 +3953,9 @@ "text": "Table 4 GHG emissions from On-farm feed production." }, { - "self_ref": "#/texts/144", + "self_ref": "#/texts/133", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { @@ -4156,7 +3970,7 @@ "level": 2 }, { - "self_ref": "#/texts/145", + "self_ref": "#/texts/134", "parent": { "$ref": "#/groups/10" }, @@ -4168,7 +3982,7 @@ "text": "The CH" }, { - "self_ref": "#/texts/146", + "self_ref": "#/texts/135", "parent": { "$ref": "#/groups/10" }, @@ -4187,7 +4001,7 @@ } }, { - "self_ref": "#/texts/147", + "self_ref": "#/texts/136", "parent": { "$ref": "#/groups/10" }, @@ -4199,7 +4013,7 @@ "text": "emissions from enteric fermentation intensity (g (kg ECM)" }, { - "self_ref": "#/texts/148", + "self_ref": "#/texts/137", "parent": { "$ref": "#/groups/10" }, @@ -4218,7 +4032,7 @@ } }, { - "self_ref": "#/texts/149", + "self_ref": "#/texts/138", "parent": { "$ref": "#/groups/10" }, @@ -4230,7 +4044,7 @@ "text": ") was a function of estimated CH" }, { - "self_ref": "#/texts/150", + "self_ref": "#/texts/139", "parent": { "$ref": "#/groups/10" }, @@ -4249,7 +4063,7 @@ } }, { - "self_ref": "#/texts/151", + "self_ref": "#/texts/140", "parent": { "$ref": "#/groups/10" }, @@ -4261,7 +4075,7 @@ "text": "yield (g (kg DM intake)" }, { - "self_ref": "#/texts/152", + "self_ref": "#/texts/141", "parent": { "$ref": "#/groups/10" }, @@ -4280,7 +4094,7 @@ } }, { - "self_ref": "#/texts/153", + "self_ref": "#/texts/142", "parent": { "$ref": "#/groups/10" }, @@ -4292,7 +4106,7 @@ "text": "), actual DM intake and ECM. The enteric CH" }, { - "self_ref": "#/texts/154", + "self_ref": "#/texts/143", "parent": { "$ref": "#/groups/10" }, @@ -4311,7 +4125,7 @@ } }, { - "self_ref": "#/texts/155", + "self_ref": "#/texts/144", "parent": { "$ref": "#/groups/10" }, @@ -4323,7 +4137,7 @@ "text": "yield was estimated as a function of neutral detergent fiber (NDF) concentration on total DM intake, as proposed by Niu et al. [43], where: CH" }, { - "self_ref": "#/texts/156", + "self_ref": "#/texts/145", "parent": { "$ref": "#/groups/10" }, @@ -4342,7 +4156,7 @@ } }, { - "self_ref": "#/texts/157", + "self_ref": "#/texts/146", "parent": { "$ref": "#/groups/10" }, @@ -4354,7 +4168,7 @@ "text": "yield (g (kg DM intake)" }, { - "self_ref": "#/texts/158", + "self_ref": "#/texts/147", "parent": { "$ref": "#/groups/10" }, @@ -4373,7 +4187,7 @@ } }, { - "self_ref": "#/texts/159", + "self_ref": "#/texts/148", "parent": { "$ref": "#/groups/10" }, @@ -4385,16 +4199,16 @@ "text": ") = 13.8 + 0.185 × NDF (% DM intake)." }, { - "self_ref": "#/texts/160", + "self_ref": "#/texts/149", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { "$ref": "#/groups/11" }, { - "$ref": "#/texts/184" + "$ref": "#/texts/173" }, { "$ref": "#/groups/12" @@ -4408,7 +4222,7 @@ "level": 2 }, { - "self_ref": "#/texts/161", + "self_ref": "#/texts/150", "parent": { "$ref": "#/groups/11" }, @@ -4420,7 +4234,7 @@ "text": "The CH" }, { - "self_ref": "#/texts/162", + "self_ref": "#/texts/151", "parent": { "$ref": "#/groups/11" }, @@ -4439,7 +4253,7 @@ } }, { - "self_ref": "#/texts/163", + "self_ref": "#/texts/152", "parent": { "$ref": "#/groups/11" }, @@ -4451,7 +4265,7 @@ "text": "emission from manure (kg (kg ECM)" }, { - "self_ref": "#/texts/164", + "self_ref": "#/texts/153", "parent": { "$ref": "#/groups/11" }, @@ -4470,7 +4284,7 @@ } }, { - "self_ref": "#/texts/165", + "self_ref": "#/texts/154", "parent": { "$ref": "#/groups/11" }, @@ -4482,7 +4296,7 @@ "text": ") was a function of daily CH" }, { - "self_ref": "#/texts/166", + "self_ref": "#/texts/155", "parent": { "$ref": "#/groups/11" }, @@ -4501,7 +4315,7 @@ } }, { - "self_ref": "#/texts/167", + "self_ref": "#/texts/156", "parent": { "$ref": "#/groups/11" }, @@ -4513,7 +4327,7 @@ "text": "emission from manure (kg cow" }, { - "self_ref": "#/texts/168", + "self_ref": "#/texts/157", "parent": { "$ref": "#/groups/11" }, @@ -4532,7 +4346,7 @@ } }, { - "self_ref": "#/texts/169", + "self_ref": "#/texts/158", "parent": { "$ref": "#/groups/11" }, @@ -4544,7 +4358,7 @@ "text": ") and daily ECM (kg cow" }, { - "self_ref": "#/texts/170", + "self_ref": "#/texts/159", "parent": { "$ref": "#/groups/11" }, @@ -4563,7 +4377,7 @@ } }, { - "self_ref": "#/texts/171", + "self_ref": "#/texts/160", "parent": { "$ref": "#/groups/11" }, @@ -4575,7 +4389,7 @@ "text": "). The daily CH" }, { - "self_ref": "#/texts/172", + "self_ref": "#/texts/161", "parent": { "$ref": "#/groups/11" }, @@ -4594,7 +4408,7 @@ } }, { - "self_ref": "#/texts/173", + "self_ref": "#/texts/162", "parent": { "$ref": "#/groups/11" }, @@ -4606,7 +4420,7 @@ "text": "emission from manure was estimated according to IPCC [38], which considered daily volatile solid (VS) excreted (kg DM cow" }, { - "self_ref": "#/texts/174", + "self_ref": "#/texts/163", "parent": { "$ref": "#/groups/11" }, @@ -4625,7 +4439,7 @@ } }, { - "self_ref": "#/texts/175", + "self_ref": "#/texts/164", "parent": { "$ref": "#/groups/11" }, @@ -4637,7 +4451,7 @@ "text": ") in manure. The daily VS was estimated as proposed by Eugène et al. [44] as: VS = NDOMI + (UE × GE) × (OM/18.45), where: VS = volatile solid excretion on an organic matter (OM) basis (kg day" }, { - "self_ref": "#/texts/176", + "self_ref": "#/texts/165", "parent": { "$ref": "#/groups/11" }, @@ -4656,7 +4470,7 @@ } }, { - "self_ref": "#/texts/177", + "self_ref": "#/texts/166", "parent": { "$ref": "#/groups/11" }, @@ -4668,7 +4482,7 @@ "text": "), NDOMI = non-digestible OM intake (kg day" }, { - "self_ref": "#/texts/178", + "self_ref": "#/texts/167", "parent": { "$ref": "#/groups/11" }, @@ -4687,7 +4501,7 @@ } }, { - "self_ref": "#/texts/179", + "self_ref": "#/texts/168", "parent": { "$ref": "#/groups/11" }, @@ -4699,7 +4513,7 @@ "text": "): (1- OM digestibility) × OM intake, UE = urinary energy excretion as a fraction of GE (0.04), GE = gross energy intake (MJ day" }, { - "self_ref": "#/texts/180", + "self_ref": "#/texts/169", "parent": { "$ref": "#/groups/11" }, @@ -4718,7 +4532,7 @@ } }, { - "self_ref": "#/texts/181", + "self_ref": "#/texts/170", "parent": { "$ref": "#/groups/11" }, @@ -4730,7 +4544,7 @@ "text": "), OM = organic matter (g), 18.45 = conversion factor for dietary GE per kg of DM (MJ kg" }, { - "self_ref": "#/texts/182", + "self_ref": "#/texts/171", "parent": { "$ref": "#/groups/11" }, @@ -4749,7 +4563,7 @@ } }, { - "self_ref": "#/texts/183", + "self_ref": "#/texts/172", "parent": { "$ref": "#/groups/11" }, @@ -4761,9 +4575,9 @@ "text": ")." }, { - "self_ref": "#/texts/184", + "self_ref": "#/texts/173", "parent": { - "$ref": "#/texts/160" + "$ref": "#/texts/149" }, "children": [], "content_layer": "body", @@ -4773,7 +4587,7 @@ "text": "The OM digestibility was estimated as a function of chemical composition, using equations published by INRA [21], which takes into account the effects of digestive interactions due to feeding level, the proportion of concentrate and rumen protein balance on OM digestibility. For scenarios where cows had access to grazing, the amount of calculated VS were corrected as a function of the time at pasture. The biodegradability of manure factor (0.13 for dairy cows in Latin America) and methane conversion factor (MCF) values were taken from IPCC [38]. The MCF values for pit storage below animal confinements (> 1 month) were used for the calculation, taking into account the annual average temperature (16.6ºC) or the average temperatures during the growth period of temperate (14.4ºC) or tropical (21ºC) annual pastures, which were 31%, 26% and 46%, respectively." }, { - "self_ref": "#/texts/185", + "self_ref": "#/texts/174", "parent": { "$ref": "#/groups/12" }, @@ -4785,7 +4599,7 @@ "text": "The N" }, { - "self_ref": "#/texts/186", + "self_ref": "#/texts/175", "parent": { "$ref": "#/groups/12" }, @@ -4804,7 +4618,7 @@ } }, { - "self_ref": "#/texts/187", + "self_ref": "#/texts/176", "parent": { "$ref": "#/groups/12" }, @@ -4816,7 +4630,7 @@ "text": "O-N emissions from urine and feces were estimated considering the proportion of N excreted as manure and storage or as urine and dung deposited by grazing animals. These proportions were calculated based on the proportion of daily time that animals stayed on pasture (7 h/24 h = 0.29) or confinement (1−0.29 = 0.71). For lactating heifers and cows, the total amount of N excreted was calculated by the difference between N intake and milk N excretion. For heifers and non-lactating cows, urinary and fecal N excretion were estimated as proposed by Reed et al. [45] (Table 3: equations 10 and 12, respectively). The N" }, { - "self_ref": "#/texts/188", + "self_ref": "#/texts/177", "parent": { "$ref": "#/groups/12" }, @@ -4835,7 +4649,7 @@ } }, { - "self_ref": "#/texts/189", + "self_ref": "#/texts/178", "parent": { "$ref": "#/groups/12" }, @@ -4847,7 +4661,7 @@ "text": "O emissions from stored manure as well as urine and dung during grazing were calculated based on the conversion of N" }, { - "self_ref": "#/texts/190", + "self_ref": "#/texts/179", "parent": { "$ref": "#/groups/12" }, @@ -4866,7 +4680,7 @@ } }, { - "self_ref": "#/texts/191", + "self_ref": "#/texts/180", "parent": { "$ref": "#/groups/12" }, @@ -4878,7 +4692,7 @@ "text": "O-N emissions to N" }, { - "self_ref": "#/texts/192", + "self_ref": "#/texts/181", "parent": { "$ref": "#/groups/12" }, @@ -4897,7 +4711,7 @@ } }, { - "self_ref": "#/texts/193", + "self_ref": "#/texts/182", "parent": { "$ref": "#/groups/12" }, @@ -4909,7 +4723,7 @@ "text": "O emissions, where N" }, { - "self_ref": "#/texts/194", + "self_ref": "#/texts/183", "parent": { "$ref": "#/groups/12" }, @@ -4928,7 +4742,7 @@ } }, { - "self_ref": "#/texts/195", + "self_ref": "#/texts/184", "parent": { "$ref": "#/groups/12" }, @@ -4940,7 +4754,7 @@ "text": "O emissions = N" }, { - "self_ref": "#/texts/196", + "self_ref": "#/texts/185", "parent": { "$ref": "#/groups/12" }, @@ -4959,7 +4773,7 @@ } }, { - "self_ref": "#/texts/197", + "self_ref": "#/texts/186", "parent": { "$ref": "#/groups/12" }, @@ -4971,7 +4785,7 @@ "text": "O-N emissions × 44/28. The emission factors were 0.002 kg N" }, { - "self_ref": "#/texts/198", + "self_ref": "#/texts/187", "parent": { "$ref": "#/groups/12" }, @@ -4990,7 +4804,7 @@ } }, { - "self_ref": "#/texts/199", + "self_ref": "#/texts/188", "parent": { "$ref": "#/groups/12" }, @@ -5002,7 +4816,7 @@ "text": "O-N (kg N)" }, { - "self_ref": "#/texts/200", + "self_ref": "#/texts/189", "parent": { "$ref": "#/groups/12" }, @@ -5021,7 +4835,7 @@ } }, { - "self_ref": "#/texts/201", + "self_ref": "#/texts/190", "parent": { "$ref": "#/groups/12" }, @@ -5033,7 +4847,7 @@ "text": "stored in a pit below animal confinements, and 0.02 kg N" }, { - "self_ref": "#/texts/202", + "self_ref": "#/texts/191", "parent": { "$ref": "#/groups/12" }, @@ -5052,7 +4866,7 @@ } }, { - "self_ref": "#/texts/203", + "self_ref": "#/texts/192", "parent": { "$ref": "#/groups/12" }, @@ -5064,7 +4878,7 @@ "text": "O-N (kg of urine and dung)" }, { - "self_ref": "#/texts/204", + "self_ref": "#/texts/193", "parent": { "$ref": "#/groups/12" }, @@ -5083,7 +4897,7 @@ } }, { - "self_ref": "#/texts/205", + "self_ref": "#/texts/194", "parent": { "$ref": "#/groups/12" }, @@ -5095,7 +4909,7 @@ "text": "deposited on pasture [38]. The indirect N" }, { - "self_ref": "#/texts/206", + "self_ref": "#/texts/195", "parent": { "$ref": "#/groups/12" }, @@ -5114,7 +4928,7 @@ } }, { - "self_ref": "#/texts/207", + "self_ref": "#/texts/196", "parent": { "$ref": "#/groups/12" }, @@ -5126,13 +4940,13 @@ "text": "O emissions from storage manure and urine and dung deposits on pasture were also estimated using the IPCC [38] emission factors." }, { - "self_ref": "#/texts/208", + "self_ref": "#/texts/197", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { - "$ref": "#/texts/209" + "$ref": "#/texts/198" }, { "$ref": "#/tables/4" @@ -5155,9 +4969,9 @@ "level": 2 }, { - "self_ref": "#/texts/209", + "self_ref": "#/texts/198", "parent": { - "$ref": "#/texts/208" + "$ref": "#/texts/197" }, "children": [], "content_layer": "body", @@ -5167,7 +4981,7 @@ "text": "Emissions due to farm management included those from fuel and machinery for manure handling and electricity for milking and confinement (Table 5). Emissions due to feed processing such as cutting, crushing, mixing and distributing, as well as secondary sources of emissions during the production of fuel, machinery, fertilizer, pesticides, seeds and plastic for ensilage were included in ‘Emissions from crop and pasture production’ section." }, { - "self_ref": "#/texts/210", + "self_ref": "#/texts/199", "parent": { "$ref": "#/body" }, @@ -5179,7 +4993,7 @@ "text": "Table 5 Factors for major resource inputs in farm management." }, { - "self_ref": "#/texts/211", + "self_ref": "#/texts/200", "parent": { "$ref": "#/groups/13" }, @@ -5191,7 +5005,7 @@ "text": "The amount of fuel use for manure handling were estimated taking into consideration the amount of manure produced per cow and the amounts of fuel required for manure handling (L diesel t" }, { - "self_ref": "#/texts/212", + "self_ref": "#/texts/201", "parent": { "$ref": "#/groups/13" }, @@ -5210,7 +5024,7 @@ } }, { - "self_ref": "#/texts/213", + "self_ref": "#/texts/202", "parent": { "$ref": "#/groups/13" }, @@ -5222,7 +5036,7 @@ "text": ") [42]. The amount of manure was estimated from OM excretions (kg cow" }, { - "self_ref": "#/texts/214", + "self_ref": "#/texts/203", "parent": { "$ref": "#/groups/13" }, @@ -5241,7 +5055,7 @@ } }, { - "self_ref": "#/texts/215", + "self_ref": "#/texts/204", "parent": { "$ref": "#/groups/13" }, @@ -5253,7 +5067,7 @@ "text": "), assuming that the manure has 8% ash on DM basis and 60% DM content. The OM excretions were calculated by NDOMI × days in confinement × proportion of daily time that animals stayed on confinement." }, { - "self_ref": "#/texts/216", + "self_ref": "#/texts/205", "parent": { "$ref": "#/groups/14" }, @@ -5265,7 +5079,7 @@ "text": "The emissions from fuel were estimated considering the primary (emissions from fuel burned) and secondary (emissions for producing and transporting fuel) emissions. The primary emissions were calculated by the amount of fuel required for manure handling (L) × (kg CO" }, { - "self_ref": "#/texts/217", + "self_ref": "#/texts/206", "parent": { "$ref": "#/groups/14" }, @@ -5284,7 +5098,7 @@ } }, { - "self_ref": "#/texts/218", + "self_ref": "#/texts/207", "parent": { "$ref": "#/groups/14" }, @@ -5296,7 +5110,7 @@ "text": "e L" }, { - "self_ref": "#/texts/219", + "self_ref": "#/texts/208", "parent": { "$ref": "#/groups/14" }, @@ -5315,7 +5129,7 @@ } }, { - "self_ref": "#/texts/220", + "self_ref": "#/texts/209", "parent": { "$ref": "#/groups/14" }, @@ -5327,7 +5141,7 @@ "text": ") [41]. The secondary emissions from fuel were calculated by the amount of fuel required for manure handling × emissions for production and transport of fuel (kg CO" }, { - "self_ref": "#/texts/221", + "self_ref": "#/texts/210", "parent": { "$ref": "#/groups/14" }, @@ -5346,7 +5160,7 @@ } }, { - "self_ref": "#/texts/222", + "self_ref": "#/texts/211", "parent": { "$ref": "#/groups/14" }, @@ -5358,7 +5172,7 @@ "text": "e L" }, { - "self_ref": "#/texts/223", + "self_ref": "#/texts/212", "parent": { "$ref": "#/groups/14" }, @@ -5377,7 +5191,7 @@ } }, { - "self_ref": "#/texts/224", + "self_ref": "#/texts/213", "parent": { "$ref": "#/groups/14" }, @@ -5389,7 +5203,7 @@ "text": ") [41]. Emissions from manufacture and repair of machinery for manure handling were estimated by manure produced per cow (t) × (kg machinery mass (kg manure)" }, { - "self_ref": "#/texts/225", + "self_ref": "#/texts/214", "parent": { "$ref": "#/groups/14" }, @@ -5408,7 +5222,7 @@ } }, { - "self_ref": "#/texts/226", + "self_ref": "#/texts/215", "parent": { "$ref": "#/groups/14" }, @@ -5420,7 +5234,7 @@ "text": "× 10" }, { - "self_ref": "#/texts/227", + "self_ref": "#/texts/216", "parent": { "$ref": "#/groups/14" }, @@ -5439,7 +5253,7 @@ } }, { - "self_ref": "#/texts/228", + "self_ref": "#/texts/217", "parent": { "$ref": "#/groups/14" }, @@ -5451,7 +5265,7 @@ "text": ") [42] × kg CO" }, { - "self_ref": "#/texts/229", + "self_ref": "#/texts/218", "parent": { "$ref": "#/groups/14" }, @@ -5470,7 +5284,7 @@ } }, { - "self_ref": "#/texts/230", + "self_ref": "#/texts/219", "parent": { "$ref": "#/groups/14" }, @@ -5482,7 +5296,7 @@ "text": "e (kg machinery mass)" }, { - "self_ref": "#/texts/231", + "self_ref": "#/texts/220", "parent": { "$ref": "#/groups/14" }, @@ -5501,7 +5315,7 @@ } }, { - "self_ref": "#/texts/232", + "self_ref": "#/texts/221", "parent": { "$ref": "#/groups/14" }, @@ -5513,7 +5327,7 @@ "text": "[42]." }, { - "self_ref": "#/texts/233", + "self_ref": "#/texts/222", "parent": { "$ref": "#/groups/15" }, @@ -5525,7 +5339,7 @@ "text": "Emissions from electricity for milking and confinement were estimated using two emission factors (kg CO" }, { - "self_ref": "#/texts/234", + "self_ref": "#/texts/223", "parent": { "$ref": "#/groups/15" }, @@ -5544,7 +5358,7 @@ } }, { - "self_ref": "#/texts/235", + "self_ref": "#/texts/224", "parent": { "$ref": "#/groups/15" }, @@ -5556,7 +5370,7 @@ "text": "kWh" }, { - "self_ref": "#/texts/236", + "self_ref": "#/texts/225", "parent": { "$ref": "#/groups/15" }, @@ -5575,7 +5389,7 @@ } }, { - "self_ref": "#/texts/237", + "self_ref": "#/texts/226", "parent": { "$ref": "#/groups/15" }, @@ -5587,7 +5401,7 @@ "text": "). The first one is based on United States electricity matrix [41], and was used as a reference of an electricity matrix with less hydroelectric power than the region under study. The second is based on the Brazilian electricity matrix [46]. The electricity required for milking activities is 0.06 kWh (kg milk produced)" }, { - "self_ref": "#/texts/238", + "self_ref": "#/texts/227", "parent": { "$ref": "#/groups/15" }, @@ -5606,7 +5420,7 @@ } }, { - "self_ref": "#/texts/239", + "self_ref": "#/texts/228", "parent": { "$ref": "#/groups/15" }, @@ -5618,7 +5432,7 @@ "text": "[47]. The annual electricity use for lighting was 75 kWh cow" }, { - "self_ref": "#/texts/240", + "self_ref": "#/texts/229", "parent": { "$ref": "#/groups/15" }, @@ -5637,7 +5451,7 @@ } }, { - "self_ref": "#/texts/241", + "self_ref": "#/texts/230", "parent": { "$ref": "#/groups/15" }, @@ -5649,9 +5463,9 @@ "text": ", which is the value considered for lactating cows in naturally ventilated barns [47]." }, { - "self_ref": "#/texts/242", + "self_ref": "#/texts/231", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { @@ -5666,7 +5480,7 @@ "level": 2 }, { - "self_ref": "#/texts/243", + "self_ref": "#/texts/232", "parent": { "$ref": "#/groups/16" }, @@ -5678,7 +5492,7 @@ "text": "The C footprint for milk produced in the system was calculated using a biophysical allocation approach, as recommended by the International Dairy Federation [49], and described by Thoma et al. [48]. Briefly, AR" }, { - "self_ref": "#/texts/244", + "self_ref": "#/texts/233", "parent": { "$ref": "#/groups/16" }, @@ -5697,7 +5511,7 @@ } }, { - "self_ref": "#/texts/245", + "self_ref": "#/texts/234", "parent": { "$ref": "#/groups/16" }, @@ -5709,7 +5523,7 @@ "text": "= 1–6.04 × BMR, where" }, { - "self_ref": "#/texts/246", + "self_ref": "#/texts/235", "parent": { "$ref": "#/groups/16" }, @@ -5728,7 +5542,7 @@ } }, { - "self_ref": "#/texts/247", + "self_ref": "#/texts/236", "parent": { "$ref": "#/groups/16" }, @@ -5740,7 +5554,7 @@ "text": "AR" }, { - "self_ref": "#/texts/248", + "self_ref": "#/texts/237", "parent": { "$ref": "#/groups/16" }, @@ -5759,7 +5573,7 @@ } }, { - "self_ref": "#/texts/249", + "self_ref": "#/texts/238", "parent": { "$ref": "#/groups/16" }, @@ -5771,7 +5585,7 @@ "text": "is the allocation ratio for milk and BMR is cow BW at the time of slaughter (kg) + calf BW sold (kg) divided by the total ECM produced during cow`s entire life (kg). The AR" }, { - "self_ref": "#/texts/250", + "self_ref": "#/texts/239", "parent": { "$ref": "#/groups/16" }, @@ -5790,7 +5604,7 @@ } }, { - "self_ref": "#/texts/251", + "self_ref": "#/texts/240", "parent": { "$ref": "#/groups/16" }, @@ -5802,7 +5616,7 @@ "text": "were 0.854 and 0.849 for TMR and TMR with both pasture scenarios, respectively. The AR" }, { - "self_ref": "#/texts/252", + "self_ref": "#/texts/241", "parent": { "$ref": "#/groups/16" }, @@ -5821,7 +5635,7 @@ } }, { - "self_ref": "#/texts/253", + "self_ref": "#/texts/242", "parent": { "$ref": "#/groups/16" }, @@ -5833,13 +5647,13 @@ "text": "was applied to the whole emissions, except for the electricity consumed for milking (milking parlor) and refrigerant loss, which was directly assigned to milk production." }, { - "self_ref": "#/texts/254", + "self_ref": "#/texts/243", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/32" }, "children": [ { - "$ref": "#/texts/255" + "$ref": "#/texts/244" } ], "content_layer": "body", @@ -5850,9 +5664,9 @@ "level": 2 }, { - "self_ref": "#/texts/255", + "self_ref": "#/texts/244", "parent": { - "$ref": "#/texts/254" + "$ref": "#/texts/243" }, "children": [], "content_layer": "body", @@ -5862,31 +5676,31 @@ "text": "A sensitivity index was calculated as described by Rotz et al. [42]. The sensitivity index was defined for each emission source as the percentage change in the C footprint for a 10% change in the given emission source divided by 10%. Thus, a value near 0 indicates a low sensitivity, whereas an index near or greater than 1 indicates a high sensitivity because a change in this value causes a similar change in the footprint." }, { - "self_ref": "#/texts/256", + "self_ref": "#/texts/245", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/257" + "$ref": "#/texts/246" }, { - "$ref": "#/texts/258" + "$ref": "#/texts/247" }, { - "$ref": "#/texts/328" + "$ref": "#/texts/317" }, { - "$ref": "#/texts/356" + "$ref": "#/texts/345" }, { - "$ref": "#/texts/403" + "$ref": "#/texts/392" }, { - "$ref": "#/texts/422" + "$ref": "#/texts/411" }, { - "$ref": "#/texts/428" + "$ref": "#/texts/417" } ], "content_layer": "body", @@ -5897,9 +5711,9 @@ "level": 1 }, { - "self_ref": "#/texts/257", + "self_ref": "#/texts/246", "parent": { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, "children": [], "content_layer": "body", @@ -5909,9 +5723,9 @@ "text": "The study has assessed the impact of tropical and temperate pastures in dairy cows fed TMR on the C footprint of dairy production in subtropics. Different factors were taken in to consideration to estimate emissions from manure (or urine and dung) of grazing animals, feed production and electricity use." }, { - "self_ref": "#/texts/258", + "self_ref": "#/texts/247", "parent": { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, "children": [ { @@ -5938,7 +5752,7 @@ "level": 2 }, { - "self_ref": "#/texts/259", + "self_ref": "#/texts/248", "parent": { "$ref": "#/groups/17" }, @@ -5950,7 +5764,7 @@ "text": "Depending on emission factors used for calculating emissions from urine and dung (IPCC or local data) and feed production (Tables 3 or 4), the C footprint was similar (Fig 2A and 2B) or decreased by 0.04 kg CO" }, { - "self_ref": "#/texts/260", + "self_ref": "#/texts/249", "parent": { "$ref": "#/groups/17" }, @@ -5969,7 +5783,7 @@ } }, { - "self_ref": "#/texts/261", + "self_ref": "#/texts/250", "parent": { "$ref": "#/groups/17" }, @@ -5981,7 +5795,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/262", + "self_ref": "#/texts/251", "parent": { "$ref": "#/groups/17" }, @@ -6000,7 +5814,7 @@ } }, { - "self_ref": "#/texts/263", + "self_ref": "#/texts/252", "parent": { "$ref": "#/groups/17" }, @@ -6012,7 +5826,7 @@ "text": "(Fig 2C and 2D) in scenarios that included pastures compared to" }, { - "self_ref": "#/texts/264", + "self_ref": "#/texts/253", "parent": { "$ref": "#/groups/17" }, @@ -6031,7 +5845,7 @@ } }, { - "self_ref": "#/texts/265", + "self_ref": "#/texts/254", "parent": { "$ref": "#/groups/17" }, @@ -6043,7 +5857,7 @@ "text": "TMR intake. Due to differences in emission factors, the overall GHG emission values ranged from 0.92 to 1.04 kg CO" }, { - "self_ref": "#/texts/266", + "self_ref": "#/texts/255", "parent": { "$ref": "#/groups/17" }, @@ -6062,7 +5876,7 @@ } }, { - "self_ref": "#/texts/267", + "self_ref": "#/texts/256", "parent": { "$ref": "#/groups/17" }, @@ -6074,7 +5888,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/268", + "self_ref": "#/texts/257", "parent": { "$ref": "#/groups/17" }, @@ -6093,7 +5907,7 @@ } }, { - "self_ref": "#/texts/269", + "self_ref": "#/texts/258", "parent": { "$ref": "#/groups/17" }, @@ -6105,7 +5919,7 @@ "text": "for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO" }, { - "self_ref": "#/texts/270", + "self_ref": "#/texts/259", "parent": { "$ref": "#/groups/17" }, @@ -6124,7 +5938,7 @@ } }, { - "self_ref": "#/texts/271", + "self_ref": "#/texts/260", "parent": { "$ref": "#/groups/17" }, @@ -6136,7 +5950,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/272", + "self_ref": "#/texts/261", "parent": { "$ref": "#/groups/17" }, @@ -6155,7 +5969,7 @@ } }, { - "self_ref": "#/texts/273", + "self_ref": "#/texts/262", "parent": { "$ref": "#/groups/17" }, @@ -6167,7 +5981,7 @@ "text": "for cows with access to pasture. Using IPCC emission factors [38], manure emissions increased as TMR intake went down (Fig 2A and 2B). However, using local emission factors for estimating N" }, { - "self_ref": "#/texts/274", + "self_ref": "#/texts/263", "parent": { "$ref": "#/groups/17" }, @@ -6186,7 +6000,7 @@ } }, { - "self_ref": "#/texts/275", + "self_ref": "#/texts/264", "parent": { "$ref": "#/groups/17" }, @@ -6198,7 +6012,7 @@ "text": "O-N emissions [37], manure emissions decreased as TMR intake went down (Fig 2C and 2D). Regardless of emission factors used (Tables 3 or 4), emissions from feed production decreased to a small extent as the proportion of TMR intake decreased. Emissions from farm management did not contribute more than 5% of overall GHG emissions." }, { - "self_ref": "#/texts/276", + "self_ref": "#/texts/265", "parent": { "$ref": "#/body" }, @@ -6210,7 +6024,7 @@ "text": "Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]." }, { - "self_ref": "#/texts/277", + "self_ref": "#/texts/266", "parent": { "$ref": "#/groups/18" }, @@ -6222,7 +6036,7 @@ "text": "Considering IPCC emission factors for N" }, { - "self_ref": "#/texts/278", + "self_ref": "#/texts/267", "parent": { "$ref": "#/groups/18" }, @@ -6241,7 +6055,7 @@ } }, { - "self_ref": "#/texts/279", + "self_ref": "#/texts/268", "parent": { "$ref": "#/groups/18" }, @@ -6253,7 +6067,7 @@ "text": "O emissions from urine and dung [38] and those from Table 3, the C footprint ranged from 0.99 to 1.04 kg CO" }, { - "self_ref": "#/texts/280", + "self_ref": "#/texts/269", "parent": { "$ref": "#/groups/18" }, @@ -6272,7 +6086,7 @@ } }, { - "self_ref": "#/texts/281", + "self_ref": "#/texts/270", "parent": { "$ref": "#/groups/18" }, @@ -6284,7 +6098,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/282", + "self_ref": "#/texts/271", "parent": { "$ref": "#/groups/18" }, @@ -6303,7 +6117,7 @@ } }, { - "self_ref": "#/texts/283", + "self_ref": "#/texts/272", "parent": { "$ref": "#/groups/18" }, @@ -6315,7 +6129,7 @@ "text": ", and was close to those reported under confined based systems in California [49], Canada [50], China [8], Ireland [9], different scenarios in Australia [51,52] and Uruguay [11], which ranged from 0.98 to 1.16 kg CO" }, { - "self_ref": "#/texts/284", + "self_ref": "#/texts/273", "parent": { "$ref": "#/groups/18" }, @@ -6334,7 +6148,7 @@ } }, { - "self_ref": "#/texts/285", + "self_ref": "#/texts/274", "parent": { "$ref": "#/groups/18" }, @@ -6346,7 +6160,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/286", + "self_ref": "#/texts/275", "parent": { "$ref": "#/groups/18" }, @@ -6365,7 +6179,7 @@ } }, { - "self_ref": "#/texts/287", + "self_ref": "#/texts/276", "parent": { "$ref": "#/groups/18" }, @@ -6377,7 +6191,7 @@ "text": ". When local emission factors for N" }, { - "self_ref": "#/texts/288", + "self_ref": "#/texts/277", "parent": { "$ref": "#/groups/18" }, @@ -6396,7 +6210,7 @@ } }, { - "self_ref": "#/texts/289", + "self_ref": "#/texts/278", "parent": { "$ref": "#/groups/18" }, @@ -6408,7 +6222,7 @@ "text": "O emissions from urine and dung [37] and those from Table 4 were taking into account, the C footprint for scenarios including pasture, without accounting for sequestered CO" }, { - "self_ref": "#/texts/290", + "self_ref": "#/texts/279", "parent": { "$ref": "#/groups/18" }, @@ -6427,7 +6241,7 @@ } }, { - "self_ref": "#/texts/291", + "self_ref": "#/texts/280", "parent": { "$ref": "#/groups/18" }, @@ -6439,7 +6253,7 @@ "text": "-C from perennial pasture—0.91 kg CO" }, { - "self_ref": "#/texts/292", + "self_ref": "#/texts/281", "parent": { "$ref": "#/groups/18" }, @@ -6458,7 +6272,7 @@ } }, { - "self_ref": "#/texts/293", + "self_ref": "#/texts/282", "parent": { "$ref": "#/groups/18" }, @@ -6470,7 +6284,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/294", + "self_ref": "#/texts/283", "parent": { "$ref": "#/groups/18" }, @@ -6489,7 +6303,7 @@ } }, { - "self_ref": "#/texts/295", + "self_ref": "#/texts/284", "parent": { "$ref": "#/groups/18" }, @@ -6501,7 +6315,7 @@ "text": "—was lower than the range of values described above. However, these values were still greater than high-performance confinement systems in UK and USA [53] or grass based dairy systems in Ireland [9,53] and New Zealand [8,54], which ranged from 0.52 to 0.89 kg CO" }, { - "self_ref": "#/texts/296", + "self_ref": "#/texts/285", "parent": { "$ref": "#/groups/18" }, @@ -6520,7 +6334,7 @@ } }, { - "self_ref": "#/texts/297", + "self_ref": "#/texts/286", "parent": { "$ref": "#/groups/18" }, @@ -6532,7 +6346,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/298", + "self_ref": "#/texts/287", "parent": { "$ref": "#/groups/18" }, @@ -6551,7 +6365,7 @@ } }, { - "self_ref": "#/texts/299", + "self_ref": "#/texts/288", "parent": { "$ref": "#/groups/18" }, @@ -6563,7 +6377,7 @@ "text": ". Regardless of which emission factor was used, we found a lower C footprint in all conditions compared to scenarios with lower milk production per cow or in poor conditions of manure management, which ranged from 1.4 to 2.3 kg CO" }, { - "self_ref": "#/texts/300", + "self_ref": "#/texts/289", "parent": { "$ref": "#/groups/18" }, @@ -6582,7 +6396,7 @@ } }, { - "self_ref": "#/texts/301", + "self_ref": "#/texts/290", "parent": { "$ref": "#/groups/18" }, @@ -6594,7 +6408,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/302", + "self_ref": "#/texts/291", "parent": { "$ref": "#/groups/18" }, @@ -6613,7 +6427,7 @@ } }, { - "self_ref": "#/texts/303", + "self_ref": "#/texts/292", "parent": { "$ref": "#/groups/18" }, @@ -6625,7 +6439,7 @@ "text": "[8,55]. Thus, even though differences between studies may be partially explained by various assumptions (e.g., emission factors, co-product allocation, methane emissions estimation, sequestered CO" }, { - "self_ref": "#/texts/304", + "self_ref": "#/texts/293", "parent": { "$ref": "#/groups/18" }, @@ -6644,7 +6458,7 @@ } }, { - "self_ref": "#/texts/305", + "self_ref": "#/texts/294", "parent": { "$ref": "#/groups/18" }, @@ -6656,7 +6470,7 @@ "text": "-C, etc.), herd productivity and manure management were systematically associated with the C footprint of the dairy systems." }, { - "self_ref": "#/texts/306", + "self_ref": "#/texts/295", "parent": { "$ref": "#/groups/19" }, @@ -6668,7 +6482,7 @@ "text": "The similarity of C footprint between different scenarios using IPCC [38] for estimating emissions from manure and for emissions from feed production (Table 3) was a consequence of the trade-off between greater manure emissions and lower emissions to produce feed, as the proportion of pasture in diets increased. Additionally, the small negative effect of pasture on ECM production also contributed to the trade-off. The impact of milk production on the C footprint was reported in a meta-analysis comprising 30 studies from 15 different countries [22]. As observed in this study (Fig 2A and 2B) the authors reported no significant difference between the C footprint of pasture-based vs. confinement systems. However, they observed that an increase of 1000 kg cow" }, { - "self_ref": "#/texts/307", + "self_ref": "#/texts/296", "parent": { "$ref": "#/groups/19" }, @@ -6687,7 +6501,7 @@ } }, { - "self_ref": "#/texts/308", + "self_ref": "#/texts/297", "parent": { "$ref": "#/groups/19" }, @@ -6699,7 +6513,7 @@ "text": "(5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO" }, { - "self_ref": "#/texts/309", + "self_ref": "#/texts/298", "parent": { "$ref": "#/groups/19" }, @@ -6718,7 +6532,7 @@ } }, { - "self_ref": "#/texts/310", + "self_ref": "#/texts/299", "parent": { "$ref": "#/groups/19" }, @@ -6730,7 +6544,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/311", + "self_ref": "#/texts/300", "parent": { "$ref": "#/groups/19" }, @@ -6749,7 +6563,7 @@ } }, { - "self_ref": "#/texts/312", + "self_ref": "#/texts/301", "parent": { "$ref": "#/groups/19" }, @@ -6761,7 +6575,7 @@ "text": ", which may explain an apparent discrepancy between our study and an LCA performed in south Brazilian conditions [56]. Their study compared a confinement and a grazing-based dairy system with annual average milk production of 7667 and 5535 kg cow, respectively. In this study, the same herd was used in all systems, with an annual average milk production of around 7000 kg cow" }, { - "self_ref": "#/texts/313", + "self_ref": "#/texts/302", "parent": { "$ref": "#/groups/19" }, @@ -6780,7 +6594,7 @@ } }, { - "self_ref": "#/texts/314", + "self_ref": "#/texts/303", "parent": { "$ref": "#/groups/19" }, @@ -6792,7 +6606,7 @@ "text": ". Experimental data showed a reduction not greater than 3% of ECM when 50% of TMR was replaced by pasture access." }, { - "self_ref": "#/texts/315", + "self_ref": "#/texts/304", "parent": { "$ref": "#/groups/20" }, @@ -6804,7 +6618,7 @@ "text": "The lower C footprint in scenarios with access to pasture, when local emission factors [37] were used for N" }, { - "self_ref": "#/texts/316", + "self_ref": "#/texts/305", "parent": { "$ref": "#/groups/20" }, @@ -6823,7 +6637,7 @@ } }, { - "self_ref": "#/texts/317", + "self_ref": "#/texts/306", "parent": { "$ref": "#/groups/20" }, @@ -6835,7 +6649,7 @@ "text": "O emissions from urine and dung and for feed production (Table 4), may also be partially attributed to the small negative effect of pasture on ECM production. Nevertheless, local emission factors for urine and dung had a great impact on scenarios including pastures compared to" }, { - "self_ref": "#/texts/318", + "self_ref": "#/texts/307", "parent": { "$ref": "#/groups/20" }, @@ -6854,7 +6668,7 @@ } }, { - "self_ref": "#/texts/319", + "self_ref": "#/texts/308", "parent": { "$ref": "#/groups/20" }, @@ -6866,7 +6680,7 @@ "text": "TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N" }, { - "self_ref": "#/texts/320", + "self_ref": "#/texts/309", "parent": { "$ref": "#/groups/20" }, @@ -6885,7 +6699,7 @@ } }, { - "self_ref": "#/texts/321", + "self_ref": "#/texts/310", "parent": { "$ref": "#/groups/20" }, @@ -6897,7 +6711,7 @@ "text": "O-N (kg N)" }, { - "self_ref": "#/texts/322", + "self_ref": "#/texts/311", "parent": { "$ref": "#/groups/20" }, @@ -6916,7 +6730,7 @@ } }, { - "self_ref": "#/texts/323", + "self_ref": "#/texts/312", "parent": { "$ref": "#/groups/20" }, @@ -6928,7 +6742,7 @@ "text": "for urine and dung from grazing animals, experimental evidence shows that it may be up to five times lower, averaging 0.004 kg N" }, { - "self_ref": "#/texts/324", + "self_ref": "#/texts/313", "parent": { "$ref": "#/groups/20" }, @@ -6947,7 +6761,7 @@ } }, { - "self_ref": "#/texts/325", + "self_ref": "#/texts/314", "parent": { "$ref": "#/groups/20" }, @@ -6959,7 +6773,7 @@ "text": "O-N kg" }, { - "self_ref": "#/texts/326", + "self_ref": "#/texts/315", "parent": { "$ref": "#/groups/20" }, @@ -6978,7 +6792,7 @@ } }, { - "self_ref": "#/texts/327", + "self_ref": "#/texts/316", "parent": { "$ref": "#/groups/20" }, @@ -6990,9 +6804,9 @@ "text": "[37]." }, { - "self_ref": "#/texts/328", + "self_ref": "#/texts/317", "parent": { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, "children": [ { @@ -7013,7 +6827,7 @@ "level": 2 }, { - "self_ref": "#/texts/329", + "self_ref": "#/texts/318", "parent": { "$ref": "#/groups/21" }, @@ -7025,7 +6839,7 @@ "text": "The enteric CH" }, { - "self_ref": "#/texts/330", + "self_ref": "#/texts/319", "parent": { "$ref": "#/groups/21" }, @@ -7044,7 +6858,7 @@ } }, { - "self_ref": "#/texts/331", + "self_ref": "#/texts/320", "parent": { "$ref": "#/groups/21" }, @@ -7056,7 +6870,7 @@ "text": "intensity was similar between different scenarios (Fig 2), showing the greatest sensitivity index, with values ranging from 0.53 to 0.62, which indicate that for a 10% change in this source, the C footprint may change between 5.3 and 6.2% (Fig 3). The large effect of enteric CH" }, { - "self_ref": "#/texts/332", + "self_ref": "#/texts/321", "parent": { "$ref": "#/groups/21" }, @@ -7075,7 +6889,7 @@ } }, { - "self_ref": "#/texts/333", + "self_ref": "#/texts/322", "parent": { "$ref": "#/groups/21" }, @@ -7087,7 +6901,7 @@ "text": "emissions on the whole C footprint was expected, because the impact of enteric CH" }, { - "self_ref": "#/texts/334", + "self_ref": "#/texts/323", "parent": { "$ref": "#/groups/21" }, @@ -7106,7 +6920,7 @@ } }, { - "self_ref": "#/texts/335", + "self_ref": "#/texts/324", "parent": { "$ref": "#/groups/21" }, @@ -7118,7 +6932,7 @@ "text": "on GHG emissions of milk production in different dairy systems has been estimated to range from 44 to 60% of the total CO" }, { - "self_ref": "#/texts/336", + "self_ref": "#/texts/325", "parent": { "$ref": "#/groups/21" }, @@ -7137,7 +6951,7 @@ } }, { - "self_ref": "#/texts/337", + "self_ref": "#/texts/326", "parent": { "$ref": "#/groups/21" }, @@ -7149,7 +6963,7 @@ "text": "e [50,52,57,58]. However, emissions in feed production may be the most important source of GHG when emission factors for producing concentrate feeds are greater than 0.7 kg CO" }, { - "self_ref": "#/texts/338", + "self_ref": "#/texts/327", "parent": { "$ref": "#/groups/21" }, @@ -7168,7 +6982,7 @@ } }, { - "self_ref": "#/texts/339", + "self_ref": "#/texts/328", "parent": { "$ref": "#/groups/21" }, @@ -7180,7 +6994,7 @@ "text": "e kg" }, { - "self_ref": "#/texts/340", + "self_ref": "#/texts/329", "parent": { "$ref": "#/groups/21" }, @@ -7199,7 +7013,7 @@ } }, { - "self_ref": "#/texts/341", + "self_ref": "#/texts/330", "parent": { "$ref": "#/groups/21" }, @@ -7211,7 +7025,7 @@ "text": "[59], which did not happen in this study." }, { - "self_ref": "#/texts/342", + "self_ref": "#/texts/331", "parent": { "$ref": "#/body" }, @@ -7223,7 +7037,7 @@ "text": "Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]." }, { - "self_ref": "#/texts/343", + "self_ref": "#/texts/332", "parent": { "$ref": "#/groups/22" }, @@ -7235,7 +7049,7 @@ "text": "The lack of difference in enteric CH" }, { - "self_ref": "#/texts/344", + "self_ref": "#/texts/333", "parent": { "$ref": "#/groups/22" }, @@ -7254,7 +7068,7 @@ } }, { - "self_ref": "#/texts/345", + "self_ref": "#/texts/334", "parent": { "$ref": "#/groups/22" }, @@ -7266,7 +7080,7 @@ "text": "emissions in different systems can be explained by the narrow range of NDF content in diets (<4% difference). This non-difference is due to the lower NDF content of annual temperate pastures (495 g (kg DM)" }, { - "self_ref": "#/texts/346", + "self_ref": "#/texts/335", "parent": { "$ref": "#/groups/22" }, @@ -7285,7 +7099,7 @@ } }, { - "self_ref": "#/texts/347", + "self_ref": "#/texts/336", "parent": { "$ref": "#/groups/22" }, @@ -7297,7 +7111,7 @@ "text": ") compared to corn silage (550 g (kg DM)" }, { - "self_ref": "#/texts/348", + "self_ref": "#/texts/337", "parent": { "$ref": "#/groups/22" }, @@ -7316,7 +7130,7 @@ } }, { - "self_ref": "#/texts/349", + "self_ref": "#/texts/338", "parent": { "$ref": "#/groups/22" }, @@ -7328,7 +7142,7 @@ "text": "). Hence, an expected, increase NDF content with decreased concentrate was partially offset by an increase in the pasture proportion relatively low in NDF. This is in agreement with studies conducted in southern Brazil, which have shown that the actual enteric CH" }, { - "self_ref": "#/texts/350", + "self_ref": "#/texts/339", "parent": { "$ref": "#/groups/22" }, @@ -7347,7 +7161,7 @@ } }, { - "self_ref": "#/texts/351", + "self_ref": "#/texts/340", "parent": { "$ref": "#/groups/22" }, @@ -7359,7 +7173,7 @@ "text": "emissions may decrease with inclusion of temperate pastures in cows receiving corn silage and soybean meal [60] or increase enteric CH" }, { - "self_ref": "#/texts/352", + "self_ref": "#/texts/341", "parent": { "$ref": "#/groups/22" }, @@ -7378,7 +7192,7 @@ } }, { - "self_ref": "#/texts/353", + "self_ref": "#/texts/342", "parent": { "$ref": "#/groups/22" }, @@ -7390,7 +7204,7 @@ "text": "emissions when dairy cows grazing a temperate pasture was supplemented with corn silage [61]. Additionally, enteric CH" }, { - "self_ref": "#/texts/354", + "self_ref": "#/texts/343", "parent": { "$ref": "#/groups/22" }, @@ -7409,7 +7223,7 @@ } }, { - "self_ref": "#/texts/355", + "self_ref": "#/texts/344", "parent": { "$ref": "#/groups/22" }, @@ -7421,9 +7235,9 @@ "text": "emissions did not differ between dairy cows receiving TMR exclusively or grazing a tropical pasture in the same scenarios as in this study [26]." }, { - "self_ref": "#/texts/356", + "self_ref": "#/texts/345", "parent": { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, "children": [ { @@ -7436,7 +7250,7 @@ "$ref": "#/groups/24" }, { - "$ref": "#/texts/402" + "$ref": "#/texts/391" } ], "content_layer": "body", @@ -7447,7 +7261,7 @@ "level": 2 }, { - "self_ref": "#/texts/357", + "self_ref": "#/texts/346", "parent": { "$ref": "#/groups/23" }, @@ -7459,7 +7273,7 @@ "text": "Using IPCC emission factors for N" }, { - "self_ref": "#/texts/358", + "self_ref": "#/texts/347", "parent": { "$ref": "#/groups/23" }, @@ -7478,7 +7292,7 @@ } }, { - "self_ref": "#/texts/359", + "self_ref": "#/texts/348", "parent": { "$ref": "#/groups/23" }, @@ -7490,7 +7304,7 @@ "text": "O emissions from urine and dung [38] and those from Table 3, CH" }, { - "self_ref": "#/texts/360", + "self_ref": "#/texts/349", "parent": { "$ref": "#/groups/23" }, @@ -7509,7 +7323,7 @@ } }, { - "self_ref": "#/texts/361", + "self_ref": "#/texts/350", "parent": { "$ref": "#/groups/23" }, @@ -7521,7 +7335,7 @@ "text": "emissions from manure decreased 0.07 kg CO" }, { - "self_ref": "#/texts/362", + "self_ref": "#/texts/351", "parent": { "$ref": "#/groups/23" }, @@ -7540,7 +7354,7 @@ } }, { - "self_ref": "#/texts/363", + "self_ref": "#/texts/352", "parent": { "$ref": "#/groups/23" }, @@ -7552,7 +7366,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/364", + "self_ref": "#/texts/353", "parent": { "$ref": "#/groups/23" }, @@ -7571,7 +7385,7 @@ } }, { - "self_ref": "#/texts/365", + "self_ref": "#/texts/354", "parent": { "$ref": "#/groups/23" }, @@ -7583,7 +7397,7 @@ "text": ", but N" }, { - "self_ref": "#/texts/366", + "self_ref": "#/texts/355", "parent": { "$ref": "#/groups/23" }, @@ -7602,7 +7416,7 @@ } }, { - "self_ref": "#/texts/367", + "self_ref": "#/texts/356", "parent": { "$ref": "#/groups/23" }, @@ -7614,7 +7428,7 @@ "text": "O emissions from manure increased 0.09 kg CO" }, { - "self_ref": "#/texts/368", + "self_ref": "#/texts/357", "parent": { "$ref": "#/groups/23" }, @@ -7633,7 +7447,7 @@ } }, { - "self_ref": "#/texts/369", + "self_ref": "#/texts/358", "parent": { "$ref": "#/groups/23" }, @@ -7645,7 +7459,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/370", + "self_ref": "#/texts/359", "parent": { "$ref": "#/groups/23" }, @@ -7664,7 +7478,7 @@ } }, { - "self_ref": "#/texts/371", + "self_ref": "#/texts/360", "parent": { "$ref": "#/groups/23" }, @@ -7676,7 +7490,7 @@ "text": ", as TMR intake was restricted to 50%" }, { - "self_ref": "#/texts/372", + "self_ref": "#/texts/361", "parent": { "$ref": "#/groups/23" }, @@ -7695,7 +7509,7 @@ } }, { - "self_ref": "#/texts/373", + "self_ref": "#/texts/362", "parent": { "$ref": "#/groups/23" }, @@ -7707,7 +7521,7 @@ "text": "(Fig 4A). Emissions for pastures increased by 0.06 kg CO" }, { - "self_ref": "#/texts/374", + "self_ref": "#/texts/363", "parent": { "$ref": "#/groups/23" }, @@ -7726,7 +7540,7 @@ } }, { - "self_ref": "#/texts/375", + "self_ref": "#/texts/364", "parent": { "$ref": "#/groups/23" }, @@ -7738,7 +7552,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/376", + "self_ref": "#/texts/365", "parent": { "$ref": "#/groups/23" }, @@ -7757,7 +7571,7 @@ } }, { - "self_ref": "#/texts/377", + "self_ref": "#/texts/366", "parent": { "$ref": "#/groups/23" }, @@ -7769,7 +7583,7 @@ "text": ", whereas emissions for producing concentrate feeds and corn silage decreased by 0.09 kg CO" }, { - "self_ref": "#/texts/378", + "self_ref": "#/texts/367", "parent": { "$ref": "#/groups/23" }, @@ -7788,7 +7602,7 @@ } }, { - "self_ref": "#/texts/379", + "self_ref": "#/texts/368", "parent": { "$ref": "#/groups/23" }, @@ -7800,7 +7614,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/380", + "self_ref": "#/texts/369", "parent": { "$ref": "#/groups/23" }, @@ -7819,7 +7633,7 @@ } }, { - "self_ref": "#/texts/381", + "self_ref": "#/texts/370", "parent": { "$ref": "#/groups/23" }, @@ -7831,7 +7645,7 @@ "text": ", as TMR intake decreased (Fig 4B). In this situation, the lack of difference in calculated C footprints of different systems was also due to the greater emissions from manure, and offset by lower emissions from feed production with inclusion of pasture in lactating dairy cow diets. The greater N" }, { - "self_ref": "#/texts/382", + "self_ref": "#/texts/371", "parent": { "$ref": "#/groups/23" }, @@ -7850,7 +7664,7 @@ } }, { - "self_ref": "#/texts/383", + "self_ref": "#/texts/372", "parent": { "$ref": "#/groups/23" }, @@ -7862,7 +7676,7 @@ "text": "O-N emissions from manure with pasture was a consequence of higher N" }, { - "self_ref": "#/texts/384", + "self_ref": "#/texts/373", "parent": { "$ref": "#/groups/23" }, @@ -7881,7 +7695,7 @@ } }, { - "self_ref": "#/texts/385", + "self_ref": "#/texts/374", "parent": { "$ref": "#/groups/23" }, @@ -7893,7 +7707,7 @@ "text": "O-N emissions due to greater CP content and N urine excretion, as pasture intake increased. The effect of CP content on urine N excretion has been shown by several authors in lactating dairy cows [62–64]. For instance, by decreasing CP content from 185 to 152 g (kg DM)" }, { - "self_ref": "#/texts/386", + "self_ref": "#/texts/375", "parent": { "$ref": "#/groups/23" }, @@ -7912,7 +7726,7 @@ } }, { - "self_ref": "#/texts/387", + "self_ref": "#/texts/376", "parent": { "$ref": "#/groups/23" }, @@ -7924,7 +7738,7 @@ "text": ", N intake decreased by 20% and urine N excretion by 60% [62]. In this study, the CP content for lactating dairy cows ranged from 150 g (kg DM)" }, { - "self_ref": "#/texts/388", + "self_ref": "#/texts/377", "parent": { "$ref": "#/groups/23" }, @@ -7943,7 +7757,7 @@ } }, { - "self_ref": "#/texts/389", + "self_ref": "#/texts/378", "parent": { "$ref": "#/groups/23" }, @@ -7955,7 +7769,7 @@ "text": "on TMR system to 198 g (kg DM)" }, { - "self_ref": "#/texts/390", + "self_ref": "#/texts/379", "parent": { "$ref": "#/groups/23" }, @@ -7974,7 +7788,7 @@ } }, { - "self_ref": "#/texts/391", + "self_ref": "#/texts/380", "parent": { "$ref": "#/groups/23" }, @@ -7986,7 +7800,7 @@ "text": "on 50% TMR with pasture. Additionally, greater urine N excretion is expected with greater use of pasture. This occurs because protein utilization in pastures is inefficient, as the protein in fresh forages is highly degradable in the rumen and may not be captured by microbes [65]." }, { - "self_ref": "#/texts/392", + "self_ref": "#/texts/381", "parent": { "$ref": "#/body" }, @@ -7998,7 +7812,7 @@ "text": "Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture." }, { - "self_ref": "#/texts/393", + "self_ref": "#/texts/382", "parent": { "$ref": "#/groups/24" }, @@ -8010,7 +7824,7 @@ "text": "Using local emission factors for N" }, { - "self_ref": "#/texts/394", + "self_ref": "#/texts/383", "parent": { "$ref": "#/groups/24" }, @@ -8029,7 +7843,7 @@ } }, { - "self_ref": "#/texts/395", + "self_ref": "#/texts/384", "parent": { "$ref": "#/groups/24" }, @@ -8041,7 +7855,7 @@ "text": "O emissions from urine and dung [37] and those from Table 4, reductions in CH" }, { - "self_ref": "#/texts/396", + "self_ref": "#/texts/385", "parent": { "$ref": "#/groups/24" }, @@ -8060,7 +7874,7 @@ } }, { - "self_ref": "#/texts/397", + "self_ref": "#/texts/386", "parent": { "$ref": "#/groups/24" }, @@ -8072,7 +7886,7 @@ "text": "emissions from stocked manure, when pastures were included on diets, did not offset by increases in N" }, { - "self_ref": "#/texts/398", + "self_ref": "#/texts/387", "parent": { "$ref": "#/groups/24" }, @@ -8091,7 +7905,7 @@ } }, { - "self_ref": "#/texts/399", + "self_ref": "#/texts/388", "parent": { "$ref": "#/groups/24" }, @@ -8103,7 +7917,7 @@ "text": "O emissions from excreta (Fig 4C). In this case, total emissions from manure (Fig 4C) and feed production (Fig 4D) decreased with the inclusion of pasture. The impact of greater CP content and N urine excretion with increased pasture intake was offset by the much lower emission factors used for N" }, { - "self_ref": "#/texts/400", + "self_ref": "#/texts/389", "parent": { "$ref": "#/groups/24" }, @@ -8122,7 +7936,7 @@ } }, { - "self_ref": "#/texts/401", + "self_ref": "#/texts/390", "parent": { "$ref": "#/groups/24" }, @@ -8134,9 +7948,9 @@ "text": "O emissions from urine and dung. As suggested by other authors [66,67], these results show that IPCC default value may need to be revised for the subtropical region." }, { - "self_ref": "#/texts/402", + "self_ref": "#/texts/391", "parent": { - "$ref": "#/texts/356" + "$ref": "#/texts/345" }, "children": [], "content_layer": "body", @@ -8146,13 +7960,13 @@ "text": "Emissions for feed production decreased when pasture was included due to the greater emission factor for corn grain production compared to pastures. Emissions from concentrate and silage had at least twice the sensitivity index compared to emissions from pastures. The amount of grain required per cow in a lifetime decreased from 7,300 kg to 4,000 kg when 50% of TMR was replaced by pasture access. These results are in agreement with other studies which found lower C footprint, as concentrate use is reduced and/or pasture is included [9,68,69]. Moreover, it has been demonstrated that in intensive dairy systems, after enteric fermentation, feed production is the second main contributor to C footprint [50]. There is potential to decrease the environmental impact of dairy systems by reducing the use of concentrate ingredients with high environmental impact, particularly in confinements [9]." }, { - "self_ref": "#/texts/403", + "self_ref": "#/texts/392", "parent": { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, "children": [ { - "$ref": "#/texts/404" + "$ref": "#/texts/393" }, { "$ref": "#/groups/25" @@ -8166,9 +7980,9 @@ "level": 2 }, { - "self_ref": "#/texts/404", + "self_ref": "#/texts/393", "parent": { - "$ref": "#/texts/403" + "$ref": "#/texts/392" }, "children": [], "content_layer": "body", @@ -8178,7 +7992,7 @@ "text": "The lower impact of emissions from farm management is in agreement with other studies conducted in Europe [9, 62] and USA [42, 55], where the authors found that most emissions in dairy production systems are from enteric fermentation, feed production and emissions from excreta. As emissions from fuel for on-farm feed production were accounted into the ‘emissions from crop and pasture production’, total emissions from farm management were not greater than 5% of total C footprint." }, { - "self_ref": "#/texts/405", + "self_ref": "#/texts/394", "parent": { "$ref": "#/groups/25" }, @@ -8190,7 +8004,7 @@ "text": "Emissions from farm management dropped when the emission factor for electricity generation was based on the Brazilian matrix. In this case, the emission factor for electricity generation (0.205 kg CO" }, { - "self_ref": "#/texts/406", + "self_ref": "#/texts/395", "parent": { "$ref": "#/groups/25" }, @@ -8209,7 +8023,7 @@ } }, { - "self_ref": "#/texts/407", + "self_ref": "#/texts/396", "parent": { "$ref": "#/groups/25" }, @@ -8221,7 +8035,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/408", + "self_ref": "#/texts/397", "parent": { "$ref": "#/groups/25" }, @@ -8240,7 +8054,7 @@ } }, { - "self_ref": "#/texts/409", + "self_ref": "#/texts/398", "parent": { "$ref": "#/groups/25" }, @@ -8252,7 +8066,7 @@ "text": "[46]) is much lower than that in a LCA study conducted in US (0.73 kg CO" }, { - "self_ref": "#/texts/410", + "self_ref": "#/texts/399", "parent": { "$ref": "#/groups/25" }, @@ -8271,7 +8085,7 @@ } }, { - "self_ref": "#/texts/411", + "self_ref": "#/texts/400", "parent": { "$ref": "#/groups/25" }, @@ -8283,7 +8097,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/412", + "self_ref": "#/texts/401", "parent": { "$ref": "#/groups/25" }, @@ -8302,7 +8116,7 @@ } }, { - "self_ref": "#/texts/413", + "self_ref": "#/texts/402", "parent": { "$ref": "#/groups/25" }, @@ -8314,7 +8128,7 @@ "text": "[42]). This apparent discrepancy is explained because in 2016, almost 66% of the electricity generated in Brazil was from hydropower, which has an emission factor of 0.074 kg CO" }, { - "self_ref": "#/texts/414", + "self_ref": "#/texts/403", "parent": { "$ref": "#/groups/25" }, @@ -8333,7 +8147,7 @@ } }, { - "self_ref": "#/texts/415", + "self_ref": "#/texts/404", "parent": { "$ref": "#/groups/25" }, @@ -8345,7 +8159,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/416", + "self_ref": "#/texts/405", "parent": { "$ref": "#/groups/25" }, @@ -8364,7 +8178,7 @@ } }, { - "self_ref": "#/texts/417", + "self_ref": "#/texts/406", "parent": { "$ref": "#/groups/25" }, @@ -8376,7 +8190,7 @@ "text": "against 0.382 and 0.926 kg CO" }, { - "self_ref": "#/texts/418", + "self_ref": "#/texts/407", "parent": { "$ref": "#/groups/25" }, @@ -8395,7 +8209,7 @@ } }, { - "self_ref": "#/texts/419", + "self_ref": "#/texts/408", "parent": { "$ref": "#/groups/25" }, @@ -8407,7 +8221,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/420", + "self_ref": "#/texts/409", "parent": { "$ref": "#/groups/25" }, @@ -8426,7 +8240,7 @@ } }, { - "self_ref": "#/texts/421", + "self_ref": "#/texts/410", "parent": { "$ref": "#/groups/25" }, @@ -8438,9 +8252,9 @@ "text": "produced by natural gas and hard coal, respectively [46]." }, { - "self_ref": "#/texts/422", + "self_ref": "#/texts/411", "parent": { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, "children": [ { @@ -8455,7 +8269,7 @@ "level": 2 }, { - "self_ref": "#/texts/423", + "self_ref": "#/texts/412", "parent": { "$ref": "#/groups/26" }, @@ -8467,7 +8281,7 @@ "text": "The milk production and composition data are the average for a typical herd, which might have great animal-to-animal variability. Likewise, DM yield of crops and pastures were collected from experimental observations, and may change as a function of inter-annual variation, climatic conditions, soil type, fertilization level etc. The emission factors for direct and indirect N" }, { - "self_ref": "#/texts/424", + "self_ref": "#/texts/413", "parent": { "$ref": "#/groups/26" }, @@ -8486,7 +8300,7 @@ } }, { - "self_ref": "#/texts/425", + "self_ref": "#/texts/414", "parent": { "$ref": "#/groups/26" }, @@ -8498,7 +8312,7 @@ "text": "O emissions from urine and dung were alternatively estimated using local data, but more experiments are necessary to reduce the uncertainty. The CO" }, { - "self_ref": "#/texts/426", + "self_ref": "#/texts/415", "parent": { "$ref": "#/groups/26" }, @@ -8517,7 +8331,7 @@ } }, { - "self_ref": "#/texts/427", + "self_ref": "#/texts/416", "parent": { "$ref": "#/groups/26" }, @@ -8529,9 +8343,9 @@ "text": "emitted from lime and urea application was estimated from IPCC default values, which may not represent emissions in subtropical conditions. This LCA may be improved by reducing the uncertainty of factors for estimating emissions from excreta and feed production, including the C sequestration or emissions as a function of soil management." }, { - "self_ref": "#/texts/428", + "self_ref": "#/texts/417", "parent": { - "$ref": "#/texts/256" + "$ref": "#/texts/245" }, "children": [ { @@ -8549,7 +8363,7 @@ "level": 2 }, { - "self_ref": "#/texts/429", + "self_ref": "#/texts/418", "parent": { "$ref": "#/groups/27" }, @@ -8561,7 +8375,7 @@ "text": "The potential for using pasture can reduce the C footprint because milk production kept pace with animal confinement. However, if milk production is to decrease with lower TMR intake and inclusion of pasture [19], the C footprint would be expected to increase. Lorenz et al. [22] showed that an increase in milk yield from 5,000 to 6,000 kg ECM reduced the C footprint by 0.12 kg CO" }, { - "self_ref": "#/texts/430", + "self_ref": "#/texts/419", "parent": { "$ref": "#/groups/27" }, @@ -8580,7 +8394,7 @@ } }, { - "self_ref": "#/texts/431", + "self_ref": "#/texts/420", "parent": { "$ref": "#/groups/27" }, @@ -8592,7 +8406,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/432", + "self_ref": "#/texts/421", "parent": { "$ref": "#/groups/27" }, @@ -8611,7 +8425,7 @@ } }, { - "self_ref": "#/texts/433", + "self_ref": "#/texts/422", "parent": { "$ref": "#/groups/27" }, @@ -8623,7 +8437,7 @@ "text": ", whereas an increase from 10,000 to 11,000 kg ECM reduced the C footprint by only 0.06 kg CO" }, { - "self_ref": "#/texts/434", + "self_ref": "#/texts/423", "parent": { "$ref": "#/groups/27" }, @@ -8642,7 +8456,7 @@ } }, { - "self_ref": "#/texts/435", + "self_ref": "#/texts/424", "parent": { "$ref": "#/groups/27" }, @@ -8654,7 +8468,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/436", + "self_ref": "#/texts/425", "parent": { "$ref": "#/groups/27" }, @@ -8673,7 +8487,7 @@ } }, { - "self_ref": "#/texts/437", + "self_ref": "#/texts/426", "parent": { "$ref": "#/groups/27" }, @@ -8685,7 +8499,7 @@ "text": ". Hence, the impact of increasing milk production on decreasing C footprint is not linear, and mitigation measures, such as breeding for increased genetic yield potential and increasing concentrate ratio in the diet, are potentially harmful for animal’s health and welfare [70]. For instance, increasing concentrate ratio potentially increases the occurrence of subclinical ketosis and foot lesions, and C footprint may increase by 0.03 kg CO" }, { - "self_ref": "#/texts/438", + "self_ref": "#/texts/427", "parent": { "$ref": "#/groups/27" }, @@ -8704,7 +8518,7 @@ } }, { - "self_ref": "#/texts/439", + "self_ref": "#/texts/428", "parent": { "$ref": "#/groups/27" }, @@ -8716,7 +8530,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/440", + "self_ref": "#/texts/429", "parent": { "$ref": "#/groups/27" }, @@ -8735,7 +8549,7 @@ } }, { - "self_ref": "#/texts/441", + "self_ref": "#/texts/430", "parent": { "$ref": "#/groups/27" }, @@ -8747,7 +8561,7 @@ "text": "in subclinical ketosis [71] and by 0.02 kg CO" }, { - "self_ref": "#/texts/442", + "self_ref": "#/texts/431", "parent": { "$ref": "#/groups/27" }, @@ -8766,7 +8580,7 @@ } }, { - "self_ref": "#/texts/443", + "self_ref": "#/texts/432", "parent": { "$ref": "#/groups/27" }, @@ -8778,7 +8592,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/444", + "self_ref": "#/texts/433", "parent": { "$ref": "#/groups/27" }, @@ -8797,7 +8611,7 @@ } }, { - "self_ref": "#/texts/445", + "self_ref": "#/texts/434", "parent": { "$ref": "#/groups/27" }, @@ -8809,7 +8623,7 @@ "text": "in case of foot lesions [72]." }, { - "self_ref": "#/texts/446", + "self_ref": "#/texts/435", "parent": { "$ref": "#/groups/28" }, @@ -8821,7 +8635,7 @@ "text": "Grazing lands may also improve biodiversity [73]. Strategies such as zero tillage may increase stocks of soil C [74]. This study did not consider C sequestration during the growth of annual pastures, because it was assumed these grasses were planted with tillage, having a balance between C sequestration and C emissions [38]. Considering the C sequestration from no-tillage perennial pasture, the amount of C sequestration will more than compensates for C emitted. These results are in agreement with other authors who have shown that a reduction or elimination of soil tillage increases annual soil C sequestration in subtropical areas by 0.5 to 1.5 t ha" }, { - "self_ref": "#/texts/447", + "self_ref": "#/texts/436", "parent": { "$ref": "#/groups/28" }, @@ -8840,7 +8654,7 @@ } }, { - "self_ref": "#/texts/448", + "self_ref": "#/texts/437", "parent": { "$ref": "#/groups/28" }, @@ -8852,7 +8666,7 @@ "text": "[75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha" }, { - "self_ref": "#/texts/449", + "self_ref": "#/texts/438", "parent": { "$ref": "#/groups/28" }, @@ -8871,7 +8685,7 @@ } }, { - "self_ref": "#/texts/450", + "self_ref": "#/texts/439", "parent": { "$ref": "#/groups/28" }, @@ -8883,7 +8697,7 @@ "text": "would be sequestered, further reducing the C footprint by 0.015 and 0.025 kg CO" }, { - "self_ref": "#/texts/451", + "self_ref": "#/texts/440", "parent": { "$ref": "#/groups/28" }, @@ -8902,7 +8716,7 @@ } }, { - "self_ref": "#/texts/452", + "self_ref": "#/texts/441", "parent": { "$ref": "#/groups/28" }, @@ -8914,7 +8728,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/453", + "self_ref": "#/texts/442", "parent": { "$ref": "#/groups/28" }, @@ -8933,7 +8747,7 @@ } }, { - "self_ref": "#/texts/454", + "self_ref": "#/texts/443", "parent": { "$ref": "#/groups/28" }, @@ -8945,7 +8759,7 @@ "text": "for the scenarios using 75 and 50% TMR, respectively. Eliminating tillage, the reduction on total GHG emissions would be 0.03 and 0.05 kg CO" }, { - "self_ref": "#/texts/455", + "self_ref": "#/texts/444", "parent": { "$ref": "#/groups/28" }, @@ -8964,7 +8778,7 @@ } }, { - "self_ref": "#/texts/456", + "self_ref": "#/texts/445", "parent": { "$ref": "#/groups/28" }, @@ -8976,7 +8790,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/457", + "self_ref": "#/texts/446", "parent": { "$ref": "#/groups/28" }, @@ -8995,7 +8809,7 @@ } }, { - "self_ref": "#/texts/458", + "self_ref": "#/texts/447", "parent": { "$ref": "#/groups/28" }, @@ -9007,7 +8821,7 @@ "text": "for 75 and 50% TMR, respectively. However, this approach may be controversial because lands which have been consistently managed for decades have approached steady state C storage, so that net exchange of CO" }, { - "self_ref": "#/texts/459", + "self_ref": "#/texts/448", "parent": { "$ref": "#/groups/28" }, @@ -9026,7 +8840,7 @@ } }, { - "self_ref": "#/texts/460", + "self_ref": "#/texts/449", "parent": { "$ref": "#/groups/28" }, @@ -9038,7 +8852,7 @@ "text": "would be negligible [76]." }, { - "self_ref": "#/texts/461", + "self_ref": "#/texts/450", "parent": { "$ref": "#/texts/0" }, @@ -9055,7 +8869,7 @@ "level": 1 }, { - "self_ref": "#/texts/462", + "self_ref": "#/texts/451", "parent": { "$ref": "#/groups/29" }, @@ -9067,7 +8881,7 @@ "text": "This study assessed the C footprint of dairy cattle systems with or without access to pastures. Including pastures showed potential to maintain or decrease to a small extent the C footprint, which may be attributable to the evidence of low N" }, { - "self_ref": "#/texts/463", + "self_ref": "#/texts/452", "parent": { "$ref": "#/groups/29" }, @@ -9086,7 +8900,7 @@ } }, { - "self_ref": "#/texts/464", + "self_ref": "#/texts/453", "parent": { "$ref": "#/groups/29" }, @@ -9098,7 +8912,7 @@ "text": "O emissions from urine and dung in dairy systems in subtropical areas. Even though the enteric CH" }, { - "self_ref": "#/texts/465", + "self_ref": "#/texts/454", "parent": { "$ref": "#/groups/29" }, @@ -9117,7 +8931,7 @@ } }, { - "self_ref": "#/texts/466", + "self_ref": "#/texts/455", "parent": { "$ref": "#/groups/29" }, @@ -9129,7 +8943,7 @@ "text": "intensity was the largest source of CO" }, { - "self_ref": "#/texts/467", + "self_ref": "#/texts/456", "parent": { "$ref": "#/groups/29" }, @@ -9148,7 +8962,7 @@ } }, { - "self_ref": "#/texts/468", + "self_ref": "#/texts/457", "parent": { "$ref": "#/groups/29" }, @@ -9160,13 +8974,13 @@ "text": "e emissions, it did not change between different scenarios due to the narrow range of NDF content in diets and maintaining the same milk production with or without access to pastures." }, { - "self_ref": "#/texts/469", + "self_ref": "#/texts/458", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/470" + "$ref": "#/texts/459" } ], "content_layer": "body", @@ -9177,9 +8991,9 @@ "level": 1 }, { - "self_ref": "#/texts/470", + "self_ref": "#/texts/459", "parent": { - "$ref": "#/texts/469" + "$ref": "#/texts/458" }, "children": [], "content_layer": "body", @@ -9189,7 +9003,7 @@ "text": "Thanks to Anna Naranjo for helpful comments throughout the elaboration of this manuscript, and to André Thaler Neto and Roberto Kappes for providing the key characteristics of the herd considered in this study." }, { - "self_ref": "#/texts/471", + "self_ref": "#/texts/460", "parent": { "$ref": "#/texts/0" }, @@ -9206,7 +9020,7 @@ "level": 1 }, { - "self_ref": "#/texts/472", + "self_ref": "#/texts/461", "parent": { "$ref": "#/groups/30" }, @@ -9220,7 +9034,7 @@ "marker": "" }, { - "self_ref": "#/texts/473", + "self_ref": "#/texts/462", "parent": { "$ref": "#/groups/30" }, @@ -9234,7 +9048,7 @@ "marker": "" }, { - "self_ref": "#/texts/474", + "self_ref": "#/texts/463", "parent": { "$ref": "#/groups/30" }, @@ -9248,7 +9062,7 @@ "marker": "" }, { - "self_ref": "#/texts/475", + "self_ref": "#/texts/464", "parent": { "$ref": "#/groups/30" }, @@ -9262,7 +9076,7 @@ "marker": "" }, { - "self_ref": "#/texts/476", + "self_ref": "#/texts/465", "parent": { "$ref": "#/groups/30" }, @@ -9276,7 +9090,7 @@ "marker": "" }, { - "self_ref": "#/texts/477", + "self_ref": "#/texts/466", "parent": { "$ref": "#/groups/30" }, @@ -9290,7 +9104,7 @@ "marker": "" }, { - "self_ref": "#/texts/478", + "self_ref": "#/texts/467", "parent": { "$ref": "#/groups/30" }, @@ -9304,7 +9118,7 @@ "marker": "" }, { - "self_ref": "#/texts/479", + "self_ref": "#/texts/468", "parent": { "$ref": "#/groups/30" }, @@ -9318,7 +9132,7 @@ "marker": "" }, { - "self_ref": "#/texts/480", + "self_ref": "#/texts/469", "parent": { "$ref": "#/groups/30" }, @@ -9332,7 +9146,7 @@ "marker": "" }, { - "self_ref": "#/texts/481", + "self_ref": "#/texts/470", "parent": { "$ref": "#/groups/30" }, @@ -9346,7 +9160,7 @@ "marker": "" }, { - "self_ref": "#/texts/482", + "self_ref": "#/texts/471", "parent": { "$ref": "#/groups/30" }, @@ -9360,7 +9174,7 @@ "marker": "" }, { - "self_ref": "#/texts/483", + "self_ref": "#/texts/472", "parent": { "$ref": "#/groups/30" }, @@ -9374,7 +9188,7 @@ "marker": "" }, { - "self_ref": "#/texts/484", + "self_ref": "#/texts/473", "parent": { "$ref": "#/groups/30" }, @@ -9388,7 +9202,7 @@ "marker": "" }, { - "self_ref": "#/texts/485", + "self_ref": "#/texts/474", "parent": { "$ref": "#/groups/30" }, @@ -9402,7 +9216,7 @@ "marker": "" }, { - "self_ref": "#/texts/486", + "self_ref": "#/texts/475", "parent": { "$ref": "#/groups/30" }, @@ -9416,7 +9230,7 @@ "marker": "" }, { - "self_ref": "#/texts/487", + "self_ref": "#/texts/476", "parent": { "$ref": "#/groups/30" }, @@ -9430,7 +9244,7 @@ "marker": "" }, { - "self_ref": "#/texts/488", + "self_ref": "#/texts/477", "parent": { "$ref": "#/groups/30" }, @@ -9444,7 +9258,7 @@ "marker": "" }, { - "self_ref": "#/texts/489", + "self_ref": "#/texts/478", "parent": { "$ref": "#/groups/30" }, @@ -9458,7 +9272,7 @@ "marker": "" }, { - "self_ref": "#/texts/490", + "self_ref": "#/texts/479", "parent": { "$ref": "#/groups/30" }, @@ -9472,7 +9286,7 @@ "marker": "" }, { - "self_ref": "#/texts/491", + "self_ref": "#/texts/480", "parent": { "$ref": "#/groups/30" }, @@ -9486,7 +9300,7 @@ "marker": "" }, { - "self_ref": "#/texts/492", + "self_ref": "#/texts/481", "parent": { "$ref": "#/groups/30" }, @@ -9500,7 +9314,7 @@ "marker": "" }, { - "self_ref": "#/texts/493", + "self_ref": "#/texts/482", "parent": { "$ref": "#/groups/30" }, @@ -9514,7 +9328,7 @@ "marker": "" }, { - "self_ref": "#/texts/494", + "self_ref": "#/texts/483", "parent": { "$ref": "#/groups/30" }, @@ -9528,7 +9342,7 @@ "marker": "" }, { - "self_ref": "#/texts/495", + "self_ref": "#/texts/484", "parent": { "$ref": "#/groups/30" }, @@ -9542,7 +9356,7 @@ "marker": "" }, { - "self_ref": "#/texts/496", + "self_ref": "#/texts/485", "parent": { "$ref": "#/groups/30" }, @@ -9556,7 +9370,7 @@ "marker": "" }, { - "self_ref": "#/texts/497", + "self_ref": "#/texts/486", "parent": { "$ref": "#/groups/30" }, @@ -9570,7 +9384,7 @@ "marker": "" }, { - "self_ref": "#/texts/498", + "self_ref": "#/texts/487", "parent": { "$ref": "#/groups/30" }, @@ -9584,7 +9398,7 @@ "marker": "" }, { - "self_ref": "#/texts/499", + "self_ref": "#/texts/488", "parent": { "$ref": "#/groups/30" }, @@ -9598,7 +9412,7 @@ "marker": "" }, { - "self_ref": "#/texts/500", + "self_ref": "#/texts/489", "parent": { "$ref": "#/groups/30" }, @@ -9612,7 +9426,7 @@ "marker": "" }, { - "self_ref": "#/texts/501", + "self_ref": "#/texts/490", "parent": { "$ref": "#/groups/30" }, @@ -9626,7 +9440,7 @@ "marker": "" }, { - "self_ref": "#/texts/502", + "self_ref": "#/texts/491", "parent": { "$ref": "#/groups/30" }, @@ -9640,7 +9454,7 @@ "marker": "" }, { - "self_ref": "#/texts/503", + "self_ref": "#/texts/492", "parent": { "$ref": "#/groups/30" }, @@ -9654,7 +9468,7 @@ "marker": "" }, { - "self_ref": "#/texts/504", + "self_ref": "#/texts/493", "parent": { "$ref": "#/groups/30" }, @@ -9668,7 +9482,7 @@ "marker": "" }, { - "self_ref": "#/texts/505", + "self_ref": "#/texts/494", "parent": { "$ref": "#/groups/30" }, @@ -9682,7 +9496,7 @@ "marker": "" }, { - "self_ref": "#/texts/506", + "self_ref": "#/texts/495", "parent": { "$ref": "#/groups/30" }, @@ -9696,7 +9510,7 @@ "marker": "" }, { - "self_ref": "#/texts/507", + "self_ref": "#/texts/496", "parent": { "$ref": "#/groups/30" }, @@ -9710,7 +9524,7 @@ "marker": "" }, { - "self_ref": "#/texts/508", + "self_ref": "#/texts/497", "parent": { "$ref": "#/groups/30" }, @@ -9724,7 +9538,7 @@ "marker": "" }, { - "self_ref": "#/texts/509", + "self_ref": "#/texts/498", "parent": { "$ref": "#/groups/30" }, @@ -9738,7 +9552,7 @@ "marker": "" }, { - "self_ref": "#/texts/510", + "self_ref": "#/texts/499", "parent": { "$ref": "#/groups/30" }, @@ -9752,7 +9566,7 @@ "marker": "" }, { - "self_ref": "#/texts/511", + "self_ref": "#/texts/500", "parent": { "$ref": "#/groups/30" }, @@ -9766,7 +9580,7 @@ "marker": "" }, { - "self_ref": "#/texts/512", + "self_ref": "#/texts/501", "parent": { "$ref": "#/groups/30" }, @@ -9780,7 +9594,7 @@ "marker": "" }, { - "self_ref": "#/texts/513", + "self_ref": "#/texts/502", "parent": { "$ref": "#/groups/30" }, @@ -9794,7 +9608,7 @@ "marker": "" }, { - "self_ref": "#/texts/514", + "self_ref": "#/texts/503", "parent": { "$ref": "#/groups/30" }, @@ -9808,7 +9622,7 @@ "marker": "" }, { - "self_ref": "#/texts/515", + "self_ref": "#/texts/504", "parent": { "$ref": "#/groups/30" }, @@ -9822,7 +9636,7 @@ "marker": "" }, { - "self_ref": "#/texts/516", + "self_ref": "#/texts/505", "parent": { "$ref": "#/groups/30" }, @@ -9836,7 +9650,7 @@ "marker": "" }, { - "self_ref": "#/texts/517", + "self_ref": "#/texts/506", "parent": { "$ref": "#/groups/30" }, @@ -9850,7 +9664,7 @@ "marker": "" }, { - "self_ref": "#/texts/518", + "self_ref": "#/texts/507", "parent": { "$ref": "#/groups/30" }, @@ -9864,7 +9678,7 @@ "marker": "" }, { - "self_ref": "#/texts/519", + "self_ref": "#/texts/508", "parent": { "$ref": "#/groups/30" }, @@ -9878,7 +9692,7 @@ "marker": "" }, { - "self_ref": "#/texts/520", + "self_ref": "#/texts/509", "parent": { "$ref": "#/groups/30" }, @@ -9892,7 +9706,7 @@ "marker": "" }, { - "self_ref": "#/texts/521", + "self_ref": "#/texts/510", "parent": { "$ref": "#/groups/30" }, @@ -9906,7 +9720,7 @@ "marker": "" }, { - "self_ref": "#/texts/522", + "self_ref": "#/texts/511", "parent": { "$ref": "#/groups/30" }, @@ -9920,7 +9734,7 @@ "marker": "" }, { - "self_ref": "#/texts/523", + "self_ref": "#/texts/512", "parent": { "$ref": "#/groups/30" }, @@ -9934,7 +9748,7 @@ "marker": "" }, { - "self_ref": "#/texts/524", + "self_ref": "#/texts/513", "parent": { "$ref": "#/groups/30" }, @@ -9948,7 +9762,7 @@ "marker": "" }, { - "self_ref": "#/texts/525", + "self_ref": "#/texts/514", "parent": { "$ref": "#/groups/30" }, @@ -9962,7 +9776,7 @@ "marker": "" }, { - "self_ref": "#/texts/526", + "self_ref": "#/texts/515", "parent": { "$ref": "#/groups/30" }, @@ -9976,7 +9790,7 @@ "marker": "" }, { - "self_ref": "#/texts/527", + "self_ref": "#/texts/516", "parent": { "$ref": "#/groups/30" }, @@ -9990,7 +9804,7 @@ "marker": "" }, { - "self_ref": "#/texts/528", + "self_ref": "#/texts/517", "parent": { "$ref": "#/groups/30" }, @@ -10004,7 +9818,7 @@ "marker": "" }, { - "self_ref": "#/texts/529", + "self_ref": "#/texts/518", "parent": { "$ref": "#/groups/30" }, @@ -10018,7 +9832,7 @@ "marker": "" }, { - "self_ref": "#/texts/530", + "self_ref": "#/texts/519", "parent": { "$ref": "#/groups/30" }, @@ -10032,7 +9846,7 @@ "marker": "" }, { - "self_ref": "#/texts/531", + "self_ref": "#/texts/520", "parent": { "$ref": "#/groups/30" }, @@ -10046,7 +9860,7 @@ "marker": "" }, { - "self_ref": "#/texts/532", + "self_ref": "#/texts/521", "parent": { "$ref": "#/groups/30" }, @@ -10060,7 +9874,7 @@ "marker": "" }, { - "self_ref": "#/texts/533", + "self_ref": "#/texts/522", "parent": { "$ref": "#/groups/30" }, @@ -10074,7 +9888,7 @@ "marker": "" }, { - "self_ref": "#/texts/534", + "self_ref": "#/texts/523", "parent": { "$ref": "#/groups/30" }, @@ -10088,7 +9902,7 @@ "marker": "" }, { - "self_ref": "#/texts/535", + "self_ref": "#/texts/524", "parent": { "$ref": "#/groups/30" }, @@ -10102,7 +9916,7 @@ "marker": "" }, { - "self_ref": "#/texts/536", + "self_ref": "#/texts/525", "parent": { "$ref": "#/groups/30" }, @@ -10116,7 +9930,7 @@ "marker": "" }, { - "self_ref": "#/texts/537", + "self_ref": "#/texts/526", "parent": { "$ref": "#/groups/30" }, @@ -10130,7 +9944,7 @@ "marker": "" }, { - "self_ref": "#/texts/538", + "self_ref": "#/texts/527", "parent": { "$ref": "#/groups/30" }, @@ -10144,7 +9958,7 @@ "marker": "" }, { - "self_ref": "#/texts/539", + "self_ref": "#/texts/528", "parent": { "$ref": "#/groups/30" }, @@ -10158,7 +9972,7 @@ "marker": "" }, { - "self_ref": "#/texts/540", + "self_ref": "#/texts/529", "parent": { "$ref": "#/groups/30" }, @@ -10172,7 +9986,7 @@ "marker": "" }, { - "self_ref": "#/texts/541", + "self_ref": "#/texts/530", "parent": { "$ref": "#/groups/30" }, @@ -10186,7 +10000,7 @@ "marker": "" }, { - "self_ref": "#/texts/542", + "self_ref": "#/texts/531", "parent": { "$ref": "#/groups/30" }, @@ -10200,7 +10014,7 @@ "marker": "" }, { - "self_ref": "#/texts/543", + "self_ref": "#/texts/532", "parent": { "$ref": "#/groups/30" }, @@ -10214,7 +10028,7 @@ "marker": "" }, { - "self_ref": "#/texts/544", + "self_ref": "#/texts/533", "parent": { "$ref": "#/groups/30" }, @@ -10228,7 +10042,7 @@ "marker": "" }, { - "self_ref": "#/texts/545", + "self_ref": "#/texts/534", "parent": { "$ref": "#/groups/30" }, @@ -10242,7 +10056,7 @@ "marker": "" }, { - "self_ref": "#/texts/546", + "self_ref": "#/texts/535", "parent": { "$ref": "#/groups/30" }, @@ -10256,7 +10070,7 @@ "marker": "" }, { - "self_ref": "#/texts/547", + "self_ref": "#/texts/536", "parent": { "$ref": "#/groups/30" }, @@ -10274,7 +10088,7 @@ { "self_ref": "#/pictures/0", "parent": { - "$ref": "#/texts/47" + "$ref": "#/texts/36" }, "children": [], "content_layer": "body", @@ -10282,7 +10096,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/49" + "$ref": "#/texts/38" } ], "references": [], @@ -10292,7 +10106,7 @@ { "self_ref": "#/pictures/1", "parent": { - "$ref": "#/texts/258" + "$ref": "#/texts/247" }, "children": [], "content_layer": "body", @@ -10300,7 +10114,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/276" + "$ref": "#/texts/265" } ], "references": [], @@ -10310,7 +10124,7 @@ { "self_ref": "#/pictures/2", "parent": { - "$ref": "#/texts/328" + "$ref": "#/texts/317" }, "children": [], "content_layer": "body", @@ -10318,7 +10132,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/342" + "$ref": "#/texts/331" } ], "references": [], @@ -10328,7 +10142,7 @@ { "self_ref": "#/pictures/3", "parent": { - "$ref": "#/texts/356" + "$ref": "#/texts/345" }, "children": [], "content_layer": "body", @@ -10336,7 +10150,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/392" + "$ref": "#/texts/381" } ], "references": [], @@ -10348,7 +10162,7 @@ { "self_ref": "#/tables/0", "parent": { - "$ref": "#/texts/50" + "$ref": "#/texts/39" }, "children": [], "content_layer": "body", @@ -10356,7 +10170,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/53" + "$ref": "#/texts/42" } ], "references": [], @@ -11415,7 +11229,7 @@ { "self_ref": "#/tables/1", "parent": { - "$ref": "#/texts/94" + "$ref": "#/texts/83" }, "children": [], "content_layer": "body", @@ -11423,7 +11237,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/102" + "$ref": "#/texts/91" } ], "references": [], @@ -17022,7 +16836,7 @@ { "self_ref": "#/tables/2", "parent": { - "$ref": "#/texts/103" + "$ref": "#/texts/92" }, "children": [], "content_layer": "body", @@ -17030,7 +16844,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/111" + "$ref": "#/texts/100" } ], "references": [], @@ -18237,7 +18051,7 @@ { "self_ref": "#/tables/3", "parent": { - "$ref": "#/texts/103" + "$ref": "#/texts/92" }, "children": [], "content_layer": "body", @@ -18245,7 +18059,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/143" + "$ref": "#/texts/132" } ], "references": [], @@ -21960,7 +21774,7 @@ { "self_ref": "#/tables/4", "parent": { - "$ref": "#/texts/208" + "$ref": "#/texts/197" }, "children": [], "content_layer": "body", @@ -21968,7 +21782,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/210" + "$ref": "#/texts/199" } ], "references": [], diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.md b/tests/data/jats/groundtruth/pone.0234687.nxml.md index 098b61f1a6..fec4e1bb30 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.md +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.md @@ -6,7 +6,7 @@ Department of Animal Science, University of California, Davis, California, Unite ## Abstract -Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO 2 ) equivalents (CO 2 e) (kg energy-corrected milk (ECM)) -1 , encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation -1 . The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) *ad libitum* intake, 75, and 50% of *ad libitum* TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO 2 e (kg ECM) -1 . Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO 2 e (kg ECM) -1 in scenarios including pastures compared to *ad libitum* TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent. +Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2) equivalents (CO2e) (kg energy-corrected milk (ECM))-1, encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1. The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) *ad libitum* intake, 75, and 50% of *ad libitum* TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1. Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1 in scenarios including pastures compared to *ad libitum* TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent. ## Introduction diff --git a/tests/test_backend_jats.py b/tests/test_backend_jats.py index 66c3979ead..a7fd5267f9 100644 --- a/tests/test_backend_jats.py +++ b/tests/test_backend_jats.py @@ -257,14 +257,18 @@ def test_jats_plain_abstract_styling_is_preserved(): groups = _inline_group_items(doc) assert len(groups) == 1 + # Punctuation adjacent to a styled run without source whitespace is + # absorbed into that run (the serializers join inline items with a + # space, so a standalone "." would export as "details ."). Runs joined + # without whitespace in the source (H2O, 103) are + # fused the same way to keep the exported text byte-identical. assert [_formatting_tuple(item) for item in groups[0]] == [ (DocItemLabel.TEXT, "We study", None), ( DocItemLabel.TEXT, - "Homo sapiens", + "Homo sapiens,", (False, True, False, False, Script.BASELINE), ), - (DocItemLabel.TEXT, ",", None), ( DocItemLabel.TEXT, "key", @@ -272,29 +276,88 @@ def test_jats_plain_abstract_styling_is_preserved(): ), ( DocItemLabel.TEXT, - "results", + "results,", (True, True, False, False, Script.BASELINE), ), - (DocItemLabel.TEXT, ", H", None), - (DocItemLabel.TEXT, "2", (False, False, False, False, Script.SUB)), - (DocItemLabel.TEXT, "O at 10", None), - (DocItemLabel.TEXT, "3", (False, False, False, False, Script.SUPER)), + (DocItemLabel.TEXT, "H2O at 103", (False, False, False, False, Script.SUB)), (DocItemLabel.TEXT, "Pa,", None), ( DocItemLabel.TEXT, - "u", + "u,", (False, False, True, False, Script.BASELINE), ), - (DocItemLabel.TEXT, ",", None), ( DocItemLabel.TEXT, - "old", + "old.", (False, False, False, True, Script.BASELINE), ), - (DocItemLabel.TEXT, ".", None), ] +def test_jats_plain_abstract_styling_keeps_source_spacing(): + """Styled runs must not gain spaces where the source XML had none. + + The serializers join sibling inline text items with a single space, so + emitting ``in vitro.`` as two items would export + ``in vitro .``. Fusing runs across spaceless boundaries keeps the + exported text (modulo styling markers) byte-identical to the source. + """ + + def abstract_markdown(paragraph: str) -> str: + doc = convert_jats_article_meta( + f""" + Spacing Test +

{paragraph}

 +""" + ) + md = doc.export_to_markdown() + return md.split("## Abstract", 1)[1].strip() + + def plain_text(markdown: str) -> str: + for marker in ("***", "**", "*", "~~", "__", "`"): + markdown = markdown.replace(marker, "") + return markdown + + cases = [ + # (source paragraph, expected markdown, expected marker-stripped text) + ( + "conditions in vitro.", + "conditions *in vitro.*", + "conditions in vitro.", + ), + ( + "cultures of Y. pestis, and E. coli.", + "cultures of *Y. pestis,* and *E. coli.*", + "cultures of Y. pestis, and E. coli.", + ), + ( + "CO2 and (CO2e) at 103 Pa", + "CO2 and (CO2e) at 103 Pa", + "CO2 and (CO2e) at 103 Pa", + ), + ( + "rate (ECM))-1, lactation-1.", + "rate (ECM))-1, lactation-1.", + "rate (ECM))-1, lactation-1.", + ), + ( + "(term) and [other];", + "*(term)* and **[other];**", + "(term) and [other];", + ), + # Ragged multi-line source whitespace still collapses normally. + ( + "a b\nc\n d.", + "a *b c* d.", + "a b c d.", + ), + ] + for paragraph, expected_md, expected_text in cases: + md = abstract_markdown(paragraph) + assert md == expected_md, f"{paragraph!r}: got {md!r}" + assert plain_text(md) == expected_text, f"{paragraph!r}: got {plain_text(md)!r}" + + def test_jats_structured_abstract_styling_is_preserved(): doc = convert_jats_article_meta( """ @@ -363,6 +426,8 @@ def test_jats_footnote_styling_is_preserved(): groups = _inline_group_items(doc) assert len(groups) == 1 + # The "." has no whitespace before it in the source, so it is absorbed + # into the bold run; a standalone "." item would export as "details .". assert [_formatting_tuple(item) for item in groups[0]] == [ (DocItemLabel.FOOTNOTE, "1", None), (DocItemLabel.FOOTNOTE, "See", None), @@ -374,10 +439,9 @@ def test_jats_footnote_styling_is_preserved(): (DocItemLabel.FOOTNOTE, "for", None), ( DocItemLabel.FOOTNOTE, - "details", + "details.", (True, False, False, False, Script.BASELINE), ), - (DocItemLabel.FOOTNOTE, ".", None), ] From 7b99568f41df45bbefd56b7fe4c8dd72cdf58f9a Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Wed, 23 Sep 2026 22:36:38 -0700 Subject: [PATCH 4/8] fix(ci): satisfy ruff lint and 1500-line limit - Sort import blocks (I001) in jats_backend.py and test_backend_jats.py. - Mark intentional curly quotes in punctuation constants (RUF001 noqa). - Condense docstrings/comments to bring jats_backend.py back under the 1500-line max-lines guardrail (1496 lines). Signed-off-by: Junyi Yao --- docling/backend/xml/jats_backend.py | 77 ++++++++++++----------------- tests/test_backend_jats.py | 17 +++---- 2 files changed, 39 insertions(+), 55 deletions(-) diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py index e012d355c7..d312d01430 100644 --- a/docling/backend/xml/jats_backend.py +++ b/docling/backend/xml/jats_backend.py @@ -31,6 +31,13 @@ from pathlib import Path from typing import Final, cast +from docling.backend.abstract_backend import DeclarativeDocumentBackend +from docling.backend.html_backend import HTMLDocumentBackend +from docling.backend.utils.image_resource_loader import ImageResourceLoader +from docling.datamodel.backend_options import JatsBackendOptions +from docling.datamodel.base_models import InputFormat +from docling.datamodel.document import InputDocument +from docling.exceptions import DocumentLoadError from docling_core.types.doc import ( DocItemLabel, DoclingDocument, @@ -48,14 +55,6 @@ from pydantic import AnyUrl, ValidationError from typing_extensions import TypedDict, override -from docling.backend.abstract_backend import DeclarativeDocumentBackend -from docling.backend.html_backend import HTMLDocumentBackend -from docling.backend.utils.image_resource_loader import ImageResourceLoader -from docling.datamodel.backend_options import JatsBackendOptions -from docling.datamodel.base_models import InputFormat -from docling.datamodel.document import InputDocument -from docling.exceptions import DocumentLoadError - _BS4_AVAILABLE: bool = False _BS4_IMPORT_ERROR: ImportError | None = None try: # pragma: no cover - import-time guard @@ -81,14 +80,12 @@ DEFAULT_TEXT_ETAL: Final[str] = "et al." _XLINK_HREF: Final[str] = "{http://www.w3.org/1999/xlink}href" -# Punctuation that typographically clings to the *following* run, e.g. the -# "(" in "(term)". Quotes are treated as opening only (never -# closing) so a quote cannot bounce back and forth between two runs. -_OPENING_PUNCTUATION: Final[str] = "([{\"'“‘" +# Punctuation clinging to the *following* run, e.g. "(" in "(term)". +# Quotes are opening-only (never closing) to avoid bouncing between runs. +_OPENING_PUNCTUATION: Final[str] = "([{\"'“‘" # noqa: RUF001 -# Punctuation that typographically clings to the *preceding* run, e.g. the -# "." in "in vitro." or the ")" in "(CO2)". -_CLOSING_PUNCTUATION: Final[str] = ".,;:!?%)]}”’" +# Punctuation clinging to the *preceding* run, e.g. "." or ")". +_CLOSING_PUNCTUATION: Final[str] = ".,;:!?%)]}”’" # noqa: RUF001 _RASTER_IMAGE_SUFFIXES: Final[tuple[str, ...]] = ( ".jpg", @@ -813,29 +810,21 @@ def _coalesce_no_space_boundaries( """Fuse runs across boundaries where the source XML had no whitespace. The docling-core serializers join sibling inline text items with a - single space, so a run boundary that had no whitespace in the source - (e.g. ``in vitro.`` or ``CO2``) would gain - a spurious space on export (``in vitro .``, ``CO 2``). Because - boundary whitespace is stripped before serialization, the information - "there was no space here" has to be acted on while it is still - available, i.e. here. - - At each spaceless boundary, in order: - - 1. trailing opening punctuation (``(``, ``[``, quotes, ...) moves - forward onto the next run; - 2. leading closing punctuation (``.``, ``,``, ``)``, ...) moves - backward onto the previous run; - 3. the runs are fused into one, keeping the non-baseline formatting - when exactly one of the two runs carries it, otherwise the - earlier run's formatting. - - Step 3 trades precise formatting scope for text fidelity: e.g. the - ``2`` in ``CO2`` keeps its subscript by absorbing the - adjacent ``CO``, because the alternative is exporting ``CO 2``. - Formula runs and runs with different hyperlink targets are never - fused. Punctuation absorbed by steps 1-2 renders identically in - every exporter, so those fusions are lossless. + single space, so a spaceless boundary (``in vitro.``, + ``CO2``) would gain a spurious space on export. The "no + space here" information must be acted on before boundary whitespace + is stripped for serialization, i.e. here. + + At each spaceless boundary, in order: (1) trailing opening + punctuation moves forward onto the next run; (2) leading closing + punctuation moves backward onto the previous run; (3) the runs fuse + into one, keeping the non-baseline formatting when exactly one run + carries it, else the earlier run's formatting. + + Step 3 trades formatting scope for text fidelity (the ``2`` in + ``CO2`` keeps its subscript by absorbing ``CO``; the + alternative is exporting ``CO 2``). Formula runs and runs with + different hyperlink targets are never fused. """ fused: list[InlineSegment] = [] for segment in segments: @@ -888,14 +877,10 @@ def _coalesce_no_space_boundaries( @staticmethod def _flattened_inline_runs(node: etree._Element) -> list[InlineSegment]: - """Styled inline runs for ``node``, mirroring the historical - flattened-text behavior of abstracts/footnotes: whitespace normalized, - boundary whitespace stripped, styling (bold/italic/sub/sup, ...) - preserved per run. - - Runs are additionally fused across boundaries where the source XML - had no whitespace (see ``_coalesce_no_space_boundaries``), because - the serializers join sibling inline text items with a space. + """Styled inline runs for ``node``: whitespace normalized, boundary + whitespace stripped, styling (bold/italic/sub/sup, ...) preserved + per run. Runs are additionally fused across spaceless boundaries + (see ``_coalesce_no_space_boundaries``). """ return JatsDocumentBackend._strip_segments( JatsDocumentBackend._coalesce_no_space_boundaries( diff --git a/tests/test_backend_jats.py b/tests/test_backend_jats.py index a7fd5267f9..898e38ea6c 100644 --- a/tests/test_backend_jats.py +++ b/tests/test_backend_jats.py @@ -56,6 +56,14 @@ from pathlib import Path import pytest +from docling.datamodel.backend_options import JatsBackendOptions +from docling.datamodel.base_models import DocumentStream, InputFormat +from docling.datamodel.document import ConversionResult +from docling.document_converter import ( + DocumentConverter, + FormatOption, + XMLJatsFormatOption, +) from docling_core.types.doc import ( DocItemLabel, DoclingDocument, @@ -66,15 +74,6 @@ from docling_core.types.doc.document import Script from PIL import Image -from docling.datamodel.backend_options import JatsBackendOptions -from docling.datamodel.base_models import DocumentStream, InputFormat -from docling.datamodel.document import ConversionResult -from docling.document_converter import ( - DocumentConverter, - FormatOption, - XMLJatsFormatOption, -) - from .test_data_gen_flag import GEN_TEST_DATA from .verify_utils import verify_document, verify_export From 15fdd1e186d315ac53978954c8f153d2713c5d0d Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Thu, 24 Sep 2026 09:28:45 -0700 Subject: [PATCH 5/8] Rework abstract/footnote styling to reuse paragraph implementation Address ceberam's review: drop the abstract/footnote-specific emphasis and spacing workaround (_normalize_segments, _coalesce_no_space_boundaries, _flattened_inline_runs) and reuse the paragraph styling implementation from #3726 instead. - Abstract

elements are now walked with _walk_linear at emit time, sharing the body-paragraph code path. - Footnotes use _walk_inline_formula + _strip_segments directly. - Inline-group spacing is delegated to the docling-core serializers per their contract (docling-core#693); no fusing or punctuation movement. - Tests assert raw inline-run content/formatting instead of markdown output. - Ground truths regenerated for the new (temporarily suboptimal) spacing. Signed-off-by: Junyi Yao --- docling/backend/xml/jats_backend.py | 189 +- .../jats/groundtruth/pmc2231364.nxml.itxt | 33 +- .../jats/groundtruth/pmc2231364.nxml.json | 99 +- .../data/jats/groundtruth/pmc2231364.nxml.md | 6 +- .../jats/groundtruth/pntd.0008301.nxml.itxt | 8 +- .../jats/groundtruth/pntd.0008301.nxml.json | 16 +- .../jats/groundtruth/pntd.0008301.nxml.md | 4 +- .../jats/groundtruth/pone.0234687.nxml.itxt | 1137 ++++---- .../jats/groundtruth/pone.0234687.nxml.json | 2288 +++++++++-------- .../jats/groundtruth/pone.0234687.nxml.md | 2 +- tests/test_backend_jats.py | 149 +- 11 files changed, 2034 insertions(+), 1897 deletions(-) diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py index d312d01430..b468dfeed3 100644 --- a/docling/backend/xml/jats_backend.py +++ b/docling/backend/xml/jats_backend.py @@ -23,7 +23,6 @@ from __future__ import annotations import logging -import re import traceback import warnings from dataclasses import dataclass, replace @@ -31,13 +30,6 @@ from pathlib import Path from typing import Final, cast -from docling.backend.abstract_backend import DeclarativeDocumentBackend -from docling.backend.html_backend import HTMLDocumentBackend -from docling.backend.utils.image_resource_loader import ImageResourceLoader -from docling.datamodel.backend_options import JatsBackendOptions -from docling.datamodel.base_models import InputFormat -from docling.datamodel.document import InputDocument -from docling.exceptions import DocumentLoadError from docling_core.types.doc import ( DocItemLabel, DoclingDocument, @@ -55,6 +47,14 @@ from pydantic import AnyUrl, ValidationError from typing_extensions import TypedDict, override +from docling.backend.abstract_backend import DeclarativeDocumentBackend +from docling.backend.html_backend import HTMLDocumentBackend +from docling.backend.utils.image_resource_loader import ImageResourceLoader +from docling.datamodel.backend_options import JatsBackendOptions +from docling.datamodel.base_models import InputFormat +from docling.datamodel.document import InputDocument +from docling.exceptions import DocumentLoadError + _BS4_AVAILABLE: bool = False _BS4_IMPORT_ERROR: ImportError | None = None try: # pragma: no cover - import-time guard @@ -80,13 +80,6 @@ DEFAULT_TEXT_ETAL: Final[str] = "et al." _XLINK_HREF: Final[str] = "{http://www.w3.org/1999/xlink}href" -# Punctuation clinging to the *following* run, e.g. "(" in "(term)". -# Quotes are opening-only (never closing) to avoid bouncing between runs. -_OPENING_PUNCTUATION: Final[str] = "([{\"'“‘" # noqa: RUF001 - -# Punctuation clinging to the *preceding* run, e.g. "." or ")". -_CLOSING_PUNCTUATION: Final[str] = ".,;:!?%)]}”’" # noqa: RUF001 - _RASTER_IMAGE_SUFFIXES: Final[tuple[str, ...]] = ( ".jpg", ".jpeg", @@ -132,12 +125,16 @@ class AbstractSection(TypedDict): """A single titled section inside a structured abstract.""" title: str - paragraphs: list[list[InlineSegment]] # styled inline runs per

+ # The

elements; walked with the paragraph implementation + # (_walk_linear) at emit time so abstracts share the body-paragraph + # styling path instead of a parallel one. + paragraphs: list[etree._Element] class Abstract(TypedDict): label: str - paragraphs: list[list[InlineSegment]] # plain

children, as styled runs + # Plain

children, as above. + paragraphs: list[etree._Element] sections: list[AbstractSection] # structured sub-sections ( children) @@ -332,19 +329,18 @@ def _get_node_text(node: etree._Element) -> str: @staticmethod def _parse_abstract_section(section_node: etree._Element) -> AbstractSection: """Parse a single `` element inside an abstract into an - `AbstractSection` with a title and its paragraphs as styled inline - segments (preserving bold/italic/sub/sup, ...).""" + `AbstractSection` with a title and its `

` elements. Styling is + applied at emit time via the paragraph implementation.""" title_nodes = section_node.xpath("title|label") title = ( JatsDocumentBackend._get_node_text(title_nodes[0]) if title_nodes else "" ) - paragraphs: list[list[InlineSegment]] = [] - for child_node in section_node: - if child_node.tag == "p": - segments = JatsDocumentBackend._flattened_inline_runs(child_node) - if segments: - paragraphs.append(segments) + paragraphs: list[etree._Element] = [ + child_node + for child_node in section_node + if child_node.tag == "p" and "".join(child_node.itertext()).strip() + ] return AbstractSection(title=title, paragraphs=paragraphs) @@ -424,14 +420,13 @@ def _parse_abstract(self) -> list[Abstract]: abs_list: list[Abstract] = [] for abs_node in self.tree.xpath(".//abstract"): - paragraphs: list[list[InlineSegment]] = [] + paragraphs: list[etree._Element] = [] sections: list[AbstractSection] = [] for child_node in abs_node: if child_node.tag == "p": - segments = JatsDocumentBackend._flattened_inline_runs(child_node) - if segments: - paragraphs.append(segments) + if "".join(child_node.itertext()).strip(): + paragraphs.append(child_node) elif child_node.tag == "sec": section = JatsDocumentBackend._parse_abstract_section(child_node) if section["paragraphs"]: @@ -545,9 +540,13 @@ def _add_abstract( parent=self.root, text=title, level=self.hlevel + 1 ) - # Plain (un-sectioned) abstract paragraphs, with inline styling. - for segments in paragraphs: - JatsDocumentBackend._emit_inline(doc, abstract_heading, segments) + # Plain (un-sectioned) abstract paragraphs: walked with the + # paragraph implementation (_walk_linear, from #3726) so that + # abstracts share the body-paragraph styling path. Inline-group + # spacing is left to the docling-core serializers per their + # contract (docling-core#693); no spacing workaround here. + for paragraph in paragraphs: + self._walk_linear(doc, abstract_heading, paragraph) # Structured abstract: emit each as a sub-heading with # its own paragraph(s) beneath the abstract heading. @@ -561,8 +560,8 @@ def _add_abstract( ) else: section_parent = abstract_heading - for segments in section["paragraphs"]: - JatsDocumentBackend._emit_inline(doc, section_parent, segments) + for paragraph in section["paragraphs"]: + self._walk_linear(doc, section_parent, paragraph) return @@ -766,24 +765,6 @@ def _parse_ext_link_href(href: str | None) -> AnyUrl | Path | None: except ValidationError: return Path(href) - @staticmethod - def _normalize_segments( - segments: list[InlineSegment], - ) -> list[InlineSegment]: - """Collapse every internal whitespace run of each segment to one space. - - The flattened abstract/footnote paths historically ran the whole text - through ``_normalize_whitespace``; keep that behavior once styling is - preserved per run so multi-line source XML does not produce ragged - spacing. Boundary whitespace is left for ``_strip_segments``. - """ - normalized: list[InlineSegment] = [] - for segment in segments: - text = re.sub(r"\s+", " ", segment.text) - if text: - normalized.append(replace(segment, text=text)) - return normalized - @staticmethod def _strip_segments(segments: list[InlineSegment]) -> list[InlineSegment]: stripped: list[InlineSegment] = [] @@ -793,103 +774,6 @@ def _strip_segments(segments: list[InlineSegment]) -> list[InlineSegment]: stripped.append(replace(segment, text=text)) return stripped - @staticmethod - def _is_unformatted(formatting: Formatting | None) -> bool: - return formatting is None or ( - not formatting.bold - and not formatting.italic - and not formatting.underline - and not formatting.strikethrough - and formatting.script in (None, Script.BASELINE) - ) - - @staticmethod - def _coalesce_no_space_boundaries( - segments: list[InlineSegment], - ) -> list[InlineSegment]: - """Fuse runs across boundaries where the source XML had no whitespace. - - The docling-core serializers join sibling inline text items with a - single space, so a spaceless boundary (``in vitro.``, - ``CO2``) would gain a spurious space on export. The "no - space here" information must be acted on before boundary whitespace - is stripped for serialization, i.e. here. - - At each spaceless boundary, in order: (1) trailing opening - punctuation moves forward onto the next run; (2) leading closing - punctuation moves backward onto the previous run; (3) the runs fuse - into one, keeping the non-baseline formatting when exactly one run - carries it, else the earlier run's formatting. - - Step 3 trades formatting scope for text fidelity (the ``2`` in - ``CO2`` keeps its subscript by absorbing ``CO``; the - alternative is exporting ``CO 2``). Formula runs and runs with - different hyperlink targets are never fused. - """ - fused: list[InlineSegment] = [] - for segment in segments: - if not segment.text: - continue - while True: - if not fused: - fused.append(segment) - break - prev = fused[-1] - if ( - prev.label == DocItemLabel.FORMULA - or segment.label == DocItemLabel.FORMULA - or prev.hyperlink != segment.hyperlink - ): - fused.append(segment) - break - if prev.text.endswith(" ") or segment.text.startswith(" "): - fused.append(segment) - break - # 1. trailing opening punctuation belongs with the next run. - if prev.text[-1] in _OPENING_PUNCTUATION: - if len(prev.text) > 1: - fused[-1] = replace(prev, text=prev.text[:-1]) - segment = replace(segment, text=prev.text[-1] + segment.text) - else: - # prev is a lone opening mark: absorb it into segment. - lone = fused.pop() - segment = replace(segment, text=lone.text + segment.text) - continue - # 2. leading closing punctuation belongs with the previous run. - if segment.text[0] in _CLOSING_PUNCTUATION: - fused[-1] = replace(prev, text=prev.text + segment.text[0]) - segment = replace(segment, text=segment.text[1:]) - if not segment.text: - break - continue - # 3. fuse the runs, preferring non-baseline formatting. - if JatsDocumentBackend._is_unformatted( - prev.formatting - ) and not JatsDocumentBackend._is_unformatted(segment.formatting): - formatting = segment.formatting - else: - formatting = prev.formatting - fused[-1] = replace( - prev, text=prev.text + segment.text, formatting=formatting - ) - break - return fused - - @staticmethod - def _flattened_inline_runs(node: etree._Element) -> list[InlineSegment]: - """Styled inline runs for ``node``: whitespace normalized, boundary - whitespace stripped, styling (bold/italic/sub/sup, ...) preserved - per run. Runs are additionally fused across spaceless boundaries - (see ``_coalesce_no_space_boundaries``). - """ - return JatsDocumentBackend._strip_segments( - JatsDocumentBackend._coalesce_no_space_boundaries( - JatsDocumentBackend._normalize_segments( - JatsDocumentBackend._walk_inline_formula(node) - ) - ) - ) - @staticmethod def _walk_inline_formula( node: etree._Element, @@ -1307,7 +1191,12 @@ def _add_footnote_group( ) -> None: footnote_segments: list[list[InlineSegment]] = [] for fn in node.iterchildren(tag="fn"): - segments = JatsDocumentBackend._flattened_inline_runs(fn) + # Styled runs via the shared inline walker (#3726); spacing is + # left to the docling-core serializers per their contract + # (docling-core#693), with no spacing workaround here. + segments = JatsDocumentBackend._strip_segments( + JatsDocumentBackend._walk_inline_formula(fn) + ) if segments: # Keep the FOOTNOTE label on plain text runs; formulas stay # labeled as formulas. diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt index a97c3197af..63c7b072a2 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt @@ -6,19 +6,20 @@ item-0 at level 0: unspecified: group _root_ item-5 at level 4: inline: group group item-6 at level 5: text: Environmental modulation of gene expression in item-7 at level 5: text: Yersinia pestis - item-8 at level 5: text: is critical for its life style a ... rown under different stress conditions - item-9 at level 5: text: in vitro. - item-10 at level 3: section_header: Results - item-11 at level 4: inline: group group - item-12 at level 5: text: To provide us with a comprehensi ... odulation of global gene expression in - item-13 at level 5: text: Y. pestis, - item-14 at level 5: text: we have analyzed the gene expres ... s. Almost all known virulence genes of - item-15 at level 5: text: Y. pestis - item-16 at level 5: text: were differentially regulated un ... ophoretic mobility shift assay (EMSA). - item-17 at level 3: section_header: Conclusion - item-18 at level 4: inline: group group - item-19 at level 5: text: The comparative transcriptomics ... is and cellular regulatory circuits in - item-20 at level 5: text: Y. pestis, - item-21 at level 5: text: it also serves as a basis for in ... icroarray data using existing methods. - item-22 at level 2: section_header: Introduction - item-23 at level 3: text: Yersinia pestis is the causative ... infectious diseases in human history. \ No newline at end of file + item-8 at level 5: text: is critical for it ... ferent stress conditions + item-9 at level 5: text: in vitro + item-10 at level 5: text: . + item-11 at level 3: section_header: Results + item-12 at level 4: inline: group group + item-13 at level 5: text: To provide us with a comprehensi ... lobal gene expression in + item-14 at level 5: text: Y. pestis + item-15 at level 5: text: , we have analyzed the gene expr ... s. Almost all known virulence genes of + item-16 at level 5: text: Y. pestis + item-17 at level 5: text: were differentiall ... ophoretic mobility shift assay (EMSA). + item-18 at level 3: section_header: Conclusion + item-19 at level 4: inline: group group + item-20 at level 5: text: The comparative transcriptomics ... r regulatory circuits in + item-21 at level 5: text: Y. pestis + item-22 at level 5: text: , it also serves as a basis for ... icroarray data using existing methods. + item-23 at level 2: section_header: Introduction + item-24 at level 3: text: Yersinia pestis is the causative ... infectious diseases in human history. \ No newline at end of file diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.json b/tests/data/jats/groundtruth/pmc2231364.nxml.json index 498b3d7131..1a90099b86 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.json +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.json @@ -43,6 +43,9 @@ }, { "$ref": "#/texts/7" + }, + { + "$ref": "#/texts/8" } ], "content_layer": "body", @@ -52,12 +55,9 @@ { "self_ref": "#/groups/1", "parent": { - "$ref": "#/texts/8" + "$ref": "#/texts/9" }, "children": [ - { - "$ref": "#/texts/9" - }, { "$ref": "#/texts/10" }, @@ -69,6 +69,9 @@ }, { "$ref": "#/texts/13" + }, + { + "$ref": "#/texts/14" } ], "content_layer": "body", @@ -78,17 +81,17 @@ { "self_ref": "#/groups/2", "parent": { - "$ref": "#/texts/14" + "$ref": "#/texts/15" }, "children": [ - { - "$ref": "#/texts/15" - }, { "$ref": "#/texts/16" }, { "$ref": "#/texts/17" + }, + { + "$ref": "#/texts/18" } ], "content_layer": "body", @@ -110,7 +113,7 @@ "$ref": "#/texts/2" }, { - "$ref": "#/texts/18" + "$ref": "#/texts/19" } ], "content_layer": "body", @@ -141,10 +144,10 @@ "$ref": "#/texts/3" }, { - "$ref": "#/texts/8" + "$ref": "#/texts/9" }, { - "$ref": "#/texts/14" + "$ref": "#/texts/15" } ], "content_layer": "body", @@ -211,8 +214,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions", - "text": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions" + "orig": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions", + "text": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions" }, { "self_ref": "#/texts/7", @@ -223,8 +226,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "in vitro.", - "text": "in vitro.", + "orig": "in vitro", + "text": "in vitro", "formatting": { "bold": false, "italic": true, @@ -235,6 +238,18 @@ }, { "self_ref": "#/texts/8", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ".", + "text": "." + }, + { + "self_ref": "#/texts/9", "parent": { "$ref": "#/texts/2" }, @@ -251,7 +266,7 @@ "level": 2 }, { - "self_ref": "#/texts/9", + "self_ref": "#/texts/10", "parent": { "$ref": "#/groups/1" }, @@ -259,11 +274,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "To provide us with a comprehensive view of environmental modulation of global gene expression in", - "text": "To provide us with a comprehensive view of environmental modulation of global gene expression in" + "orig": "To provide us with a comprehensive view of environmental modulation of global gene expression in", + "text": "To provide us with a comprehensive view of environmental modulation of global gene expression in" }, { - "self_ref": "#/texts/10", + "self_ref": "#/texts/11", "parent": { "$ref": "#/groups/1" }, @@ -271,8 +286,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Y. pestis,", - "text": "Y. pestis,", + "orig": "Y. pestis", + "text": "Y. pestis", "formatting": { "bold": false, "italic": true, @@ -282,7 +297,7 @@ } }, { - "self_ref": "#/texts/11", + "self_ref": "#/texts/12", "parent": { "$ref": "#/groups/1" }, @@ -290,11 +305,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of", - "text": "we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of" + "orig": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of", + "text": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of" }, { - "self_ref": "#/texts/12", + "self_ref": "#/texts/13", "parent": { "$ref": "#/groups/1" }, @@ -313,7 +328,7 @@ } }, { - "self_ref": "#/texts/13", + "self_ref": "#/texts/14", "parent": { "$ref": "#/groups/1" }, @@ -321,11 +336,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA).", - "text": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA)." + "orig": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA).", + "text": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA)." }, { - "self_ref": "#/texts/14", + "self_ref": "#/texts/15", "parent": { "$ref": "#/texts/2" }, @@ -342,7 +357,7 @@ "level": 2 }, { - "self_ref": "#/texts/15", + "self_ref": "#/texts/16", "parent": { "$ref": "#/groups/2" }, @@ -350,11 +365,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in", - "text": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in" + "orig": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in", + "text": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in" }, { - "self_ref": "#/texts/16", + "self_ref": "#/texts/17", "parent": { "$ref": "#/groups/2" }, @@ -362,8 +377,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Y. pestis,", - "text": "Y. pestis,", + "orig": "Y. pestis", + "text": "Y. pestis", "formatting": { "bold": false, "italic": true, @@ -373,7 +388,7 @@ } }, { - "self_ref": "#/texts/17", + "self_ref": "#/texts/18", "parent": { "$ref": "#/groups/2" }, @@ -381,17 +396,17 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", - "text": "it also serves as a basis for integrating increasing volumes of microarray data using existing methods." + "orig": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", + "text": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods." }, { - "self_ref": "#/texts/18", + "self_ref": "#/texts/19", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/19" + "$ref": "#/texts/20" } ], "content_layer": "body", @@ -402,9 +417,9 @@ "level": 1 }, { - "self_ref": "#/texts/19", + "self_ref": "#/texts/20", "parent": { - "$ref": "#/texts/18" + "$ref": "#/texts/19" }, "children": [], "content_layer": "body", diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.md b/tests/data/jats/groundtruth/pmc2231364.nxml.md index 9d53ccda2f..5a7fd997ca 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.md +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.md @@ -6,15 +6,15 @@ Yiquan Hu, Yarong Miao ### Background -Environmental modulation of gene expression in *Yersinia pestis* is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions *in vitro.* +Environmental modulation of gene expression in *Yersinia pestis* is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions *in vitro* . ### Results -To provide us with a comprehensive view of environmental modulation of global gene expression in *Y. pestis,* we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of *Y. pestis* were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). +To provide us with a comprehensive view of environmental modulation of global gene expression in *Y. pestis* , we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of *Y. pestis* were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). ### Conclusion -The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in *Y. pestis,* it also serves as a basis for integrating increasing volumes of microarray data using existing methods. +The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in *Y. pestis* , it also serves as a basis for integrating increasing volumes of microarray data using existing methods. ## Introduction diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt index e6b6da2b8b..c02654ddaa 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt @@ -5,13 +5,13 @@ item-0 at level 0: unspecified: group _root_ item-4 at level 2: section_header: Abstract item-5 at level 3: inline: group group item-6 at level 4: text: Achieving elimination of lymphat ... s Test Strips (FTS), primary vector of - item-7 at level 4: text: Culex, - item-8 at level 4: text: treatment with diethylcarbamazin ... as at highest risk of failing pre-TAS. + item-7 at level 4: text: Culex + item-8 at level 4: text: , treatment with diethylcarbamaz ... as at highest risk of failing pre-TAS. item-9 at level 2: section_header: Author summary item-10 at level 3: inline: group group item-11 at level 4: text: Achieving elimination of lymphat ... 10%, use of the FTS, primary vector of - item-12 at level 4: text: Culex, - item-13 at level 4: text: treatment with diethylcarbamazin ... ine prevalence and/or lower elevation. + item-12 at level 4: text: Culex + item-13 at level 4: text: , treatment with diethylcarbamaz ... ine prevalence and/or lower elevation. item-14 at level 2: section_header: Introduction item-15 at level 3: text: Lymphatic filariasis (LF), a dis ... 8 countries remain endemic for LF [3]. item-16 at level 3: text: The road to elimination as a pub ... t elimination be officially validated. diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.json b/tests/data/jats/groundtruth/pntd.0008301.nxml.json index 44aac95a2c..0221913779 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.json +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.json @@ -702,8 +702,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Culex,", - "text": "Culex,", + "orig": "Culex", + "text": "Culex", "formatting": { "bold": false, "italic": true, @@ -721,8 +721,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS.", - "text": "treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS." + "orig": ", treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS.", + "text": ", treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS." }, { "self_ref": "#/texts/7", @@ -762,8 +762,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Culex,", - "text": "Culex,", + "orig": "Culex", + "text": "Culex", "formatting": { "bold": false, "italic": true, @@ -781,8 +781,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation.", - "text": "treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation." + "orig": ", treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation.", + "text": ", treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation." }, { "self_ref": "#/texts/11", diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.md b/tests/data/jats/groundtruth/pntd.0008301.nxml.md index cce6818a64..f3c86f3713 100644 --- a/tests/data/jats/groundtruth/pntd.0008301.nxml.md +++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.md @@ -6,11 +6,11 @@ Global Health Division, RTI International, Washington, DC, United States of Amer ## Abstract -Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of *Culex,* treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS. +Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five effective rounds of mass drug administration (MDA) and demonstrating low prevalence in subsequent assessments. The first assessments recommended by the World Health Organization (WHO) are sentinel and spot-check sites—referred to as pre-transmission assessment surveys (pre-TAS)—in each implementation unit after MDA. If pre-TAS shows that prevalence in each site has been lowered to less than 1% microfilaremia or less than 2% antigenemia, the implementation unit conducts a TAS to determine whether MDA can be stopped. Failure to pass pre-TAS means that further rounds of MDA are required. This study aims to understand factors influencing pre-TAS results using existing programmatic data from 554 implementation units, of which 74 (13%) failed, in 13 countries. Secondary data analysis was completed using existing data from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. Additional covariate data were obtained from spatial raster data sets. Bivariate analysis and multilinear regression were performed to establish potential relationships between variables and the pre-TAS result. Higher baseline prevalence and lower elevation were significant in the regression model. Variables statistically significantly associated with failure (p-value ≤0.05) in the bivariate analyses included baseline prevalence at or above 5% or 10%, use of Filariasis Test Strips (FTS), primary vector of *Culex* , treatment with diethylcarbamazine-albendazole, higher elevation, higher population density, higher enhanced vegetation index (EVI), higher annual rainfall, and 6 or more rounds of MDA. This paper reports for the first time factors associated with pre-TAS results from a multi-country analysis. This information can help countries more effectively forecast program activities, such as the potential need for more rounds of MDA, and prioritize resources to ensure adequate coverage of all persons in areas at highest risk of failing pre-TAS. ## Author summary -Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of *Culex,* treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation. +Achieving elimination of lymphatic filariasis (LF) as a public health problem requires a minimum of five rounds of mass drug administration (MDA) and being able to demonstrate low prevalence in several subsequent assessments. LF elimination programs implement sentinel and spot-check site assessments, called pre-TAS, to determine whether districts are eligible to implement more rigorous population-based surveys to determine whether MDA can be stopped or if further rounds are required. Reasons for failing pre-TAS are not well understood and have not previously been examined with data compiled from multiple countries. For this analysis, we analyzed data from routine USAID and WHO reports from Bangladesh, Benin, Burkina Faso, Cameroon, Ghana, Haiti, Indonesia, Mali, Nepal, Niger, Sierra Leone, Tanzania, and Uganda. In a model that included multiple variables, high baseline prevalence and lower elevation were significant. In models comparing only one variable to the outcome, the following were statistically significantly associated with failure: higher baseline prevalence at or above 5% or 10%, use of the FTS, primary vector of *Culex* , treatment with diethylcarbamazine-albendazole, lower elevation, higher population density, higher Enhanced Vegetation Index, higher annual rainfall, and six or more rounds of mass drug administration. These results can help national programs plan MDA more effectively, e.g., by focusing resources on areas with higher baseline prevalence and/or lower elevation. ## Introduction diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt index 3005ba5a49..05490bad52 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt @@ -4,584 +4,595 @@ item-0 at level 0: unspecified: group _root_ item-3 at level 2: paragraph: Department of Animal Science, Un ... atarina, Lages, Santa Catarina, Brazil item-4 at level 2: section_header: Abstract item-5 at level 3: inline: group group - item-6 at level 4: text: Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2) - item-7 at level 4: text: equivalents (CO2e) (kg energy-corrected milk (ECM))-1, - item-8 at level 4: text: encompasses emissions from feed ... n average of 7,000 kg ECM lactation-1. - item-9 at level 4: text: The milk production response as ... re evaluated: total mixed ration (TMR) - item-10 at level 4: text: ad libitum - item-11 at level 4: text: intake, 75, and 50% of - item-12 at level 4: text: ad libitum - item-13 at level 4: text: TMR intake with access to grazin ... os, averaging 1.06 kg CO2e (kg ECM)-1. - item-14 at level 4: text: Considering factors from studies ... rint decreased 0.04 kg CO2e (kg ECM)-1 - item-15 at level 4: text: in scenarios including pastures compared to - item-16 at level 4: text: ad libitum - item-17 at level 4: text: TMR. Regardless of factors consi ... uce the C footprint to a small extent. - item-18 at level 2: section_header: Introduction - item-19 at level 3: inline: group group - item-20 at level 4: text: Greenhouse gas (GHG) emissions f ... ssions [1], ranging from 5.5–7.5 Gt CO - item-21 at level 4: text: 2 - item-22 at level 4: text: equivalents (CO + item-6 at level 4: text: Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO + item-7 at level 4: text: 2 + item-8 at level 4: text: ) equivalents (CO + item-9 at level 4: text: 2 + item-10 at level 4: text: e) (kg energy-corrected milk (ECM)) + item-11 at level 4: text: -1 + item-12 at level 4: text: , encompasses emissions from fee ... g an average of 7,000 kg ECM lactation + item-13 at level 4: text: -1 + item-14 at level 4: text: . The milk production response a ... re evaluated: total mixed ration (TMR) + item-15 at level 4: text: ad libitum + item-16 at level 4: text: intake, 75, and 50% of + item-17 at level 4: text: ad libitum + item-18 at level 4: text: TMR intake with access to grazin ... etween scenarios, averaging 1.06 kg CO + item-19 at level 4: text: 2 + item-20 at level 4: text: e (kg ECM) + item-21 at level 4: text: -1 + item-22 at level 4: text: . Considering factors from studi ... , the C footprint decreased 0.04 kg CO item-23 at level 4: text: 2 - item-24 at level 4: text: e) yr + item-24 at level 4: text: e (kg ECM) item-25 at level 4: text: -1 - item-26 at level 4: text: , with almost 30% coming from da ... suitable for food crop production [4]. - item-27 at level 3: inline: group group - item-28 at level 4: text: Considering the key role of live ... n investigated to mitigate methane (CH - item-29 at level 4: text: 4 - item-30 at level 4: text: ) emissions from enteric ferment ... ment [6] and manure management [7]. CH - item-31 at level 4: text: 4 - item-32 at level 4: text: emissions from enteric fermentat ... anagement to mitigate the C footprint. - item-33 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]). - item-34 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake. - item-35 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated. - item-36 at level 2: section_header: Materials and methods - item-37 at level 3: inline: group group - item-38 at level 4: text: An LCA was developed according t ... 15, 2016—Approval number 4373090816 - - item-39 at level 4: text: https://www.udesc.br/cav/ceua - item-40 at level 4: text: . - item-41 at level 3: section_header: System boundary - item-42 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary. - item-43 at level 4: picture - item-43 at level 5: caption: Fig 1 Overview of the milk production system boundary considered in the study. - item-44 at level 3: section_header: Functional unit - item-45 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows: - item-46 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1. - item-47 at level 4: table with [13x3] - item-47 at level 5: caption: Table 1 Descriptive characteristics of the herd. - item-48 at level 3: section_header: Data sources and livestock system description - item-49 at level 4: inline: group group - item-50 at level 5: text: The individual feed requirements ... cows that received both 75 and 50% of - item-51 at level 5: text: ad libitum - item-52 at level 5: text: TMR intake with access to grazing a tropical pasture (pearl-millet, - item-53 at level 5: text: Pennisetum glaucum - item-54 at level 5: text: ‘Campeiro’) compared to cows receiving - item-55 at level 5: text: ad libitum - item-56 at level 5: text: TMR intake. Cows grazing on a temperate pasture (ryegrass, - item-57 at level 5: text: Lolium multiflorum - item-58 at level 5: text: ‘Maximus’) did not need changes to ECM production compared to the - item-59 at level 5: text: ad libitum - item-60 at level 5: text: TMR intake group. - item-61 at level 4: inline: group group - item-62 at level 5: text: Using experimental data, three s ... evaluated during the lactation period: - item-63 at level 5: text: ad libitum - item-64 at level 5: text: TMR intake, and 75, and 50% of - item-65 at level 5: text: ad libitum - item-66 at level 5: text: TMR intake with access to grazin ... nction of month ([26], Civiero et al., - item-67 at level 5: text: in press - item-68 at level 5: text: ). From April to October (210 da ... med during an entire lactation period. - item-69 at level 3: section_header: Impact assessment - item-70 at level 4: inline: group group - item-71 at level 5: text: The CO - item-72 at level 5: text: 2 - item-73 at level 5: text: e emissions were calculated by multiplying the emissions of CO - item-74 at level 5: text: 2 - item-75 at level 5: text: , CH - item-76 at level 5: text: 4 - item-77 at level 5: text: and N - item-78 at level 5: text: 2 - item-79 at level 5: text: O by their 100-year global warming potential (GWP - item-80 at level 5: text: 100 - item-81 at level 5: text: ), based on IPCC assessment report 5 (AR5; [27]). The values of GWP - item-82 at level 5: text: 100 - item-83 at level 5: text: are 1, 28 and 265 for CO - item-84 at level 5: text: 2 - item-85 at level 5: text: , CH - item-86 at level 5: text: 4 - item-87 at level 5: text: and N - item-88 at level 5: text: 2 - item-89 at level 5: text: O, respectively. - item-90 at level 3: section_header: Feed production - item-91 at level 4: section_header: Diets composition - item-92 at level 5: inline: group group - item-93 at level 6: text: The DM intake of each ingredient ... ennial tropical pasture (kikuyu grass, - item-94 at level 6: text: Pennisetum clandestinum - item-95 at level 6: text: ). The DM intake of calves, heif ... meet the net energy for lactation (NE - item-96 at level 6: text: L - item-97 at level 6: text: ) and metabolizable protein (MP) ... grated in the software INRAtion 4.07 ( - item-98 at level 6: text: https://www.inration.educagri.fr/fr/forum.php - item-99 at level 6: text: ). The nutrient intake was calcu ... collected throughout the experiments. - item-100 at level 5: table with [21x11] - item-100 at level 6: caption: Table 2 Dairy cows’ diets in different scenariosa. - item-101 at level 4: section_header: GHG emissions from crop and pasture production - item-102 at level 5: inline: group group - item-103 at level 6: text: GHG emission factors used for of ... s productions were 3300 and 1500 kg CO - item-104 at level 6: text: 2 - item-105 at level 6: text: e ha - item-106 at level 6: text: -1 - item-107 at level 6: text: , respectively [32]. The DM production (kg ha - item-108 at level 6: text: -1 - item-109 at level 6: text: ) of corn silage and pastures we ... onsume 70% of pastures during grazing. - item-110 at level 5: table with [9x5] - item-110 at level 6: caption: Table 3 GHG emission factors for Off- and On-farm feed production. - item-111 at level 5: inline: group group - item-112 at level 6: text: Emissions from on-farm feed prod ... ary sources were direct and indirect N - item-113 at level 6: text: 2 - item-114 at level 6: text: O-N emissions from organic and s ... tilizers and crop/pasture residues, CO + item-26 at level 4: text: in scenarios including pastures compared to + item-27 at level 4: text: ad libitum + item-28 at level 4: text: TMR. Regardless of factors consi ... uce the C footprint to a small extent. + item-29 at level 2: section_header: Introduction + item-30 at level 3: inline: group group + item-31 at level 4: text: Greenhouse gas (GHG) emissions f ... ssions [1], ranging from 5.5–7.5 Gt CO + item-32 at level 4: text: 2 + item-33 at level 4: text: equivalents (CO + item-34 at level 4: text: 2 + item-35 at level 4: text: e) yr + item-36 at level 4: text: -1 + item-37 at level 4: text: , with almost 30% coming from da ... suitable for food crop production [4]. + item-38 at level 3: inline: group group + item-39 at level 4: text: Considering the key role of live ... n investigated to mitigate methane (CH + item-40 at level 4: text: 4 + item-41 at level 4: text: ) emissions from enteric ferment ... ment [6] and manure management [7]. CH + item-42 at level 4: text: 4 + item-43 at level 4: text: emissions from enteric fermentat ... anagement to mitigate the C footprint. + item-44 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]). + item-45 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake. + item-46 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated. + item-47 at level 2: section_header: Materials and methods + item-48 at level 3: inline: group group + item-49 at level 4: text: An LCA was developed according t ... 15, 2016—Approval number 4373090816 - + item-50 at level 4: text: https://www.udesc.br/cav/ceua + item-51 at level 4: text: . + item-52 at level 3: section_header: System boundary + item-53 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary. + item-54 at level 4: picture + item-54 at level 5: caption: Fig 1 Overview of the milk production system boundary considered in the study. + item-55 at level 3: section_header: Functional unit + item-56 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows: + item-57 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1. + item-58 at level 4: table with [13x3] + item-58 at level 5: caption: Table 1 Descriptive characteristics of the herd. + item-59 at level 3: section_header: Data sources and livestock system description + item-60 at level 4: inline: group group + item-61 at level 5: text: The individual feed requirements ... cows that received both 75 and 50% of + item-62 at level 5: text: ad libitum + item-63 at level 5: text: TMR intake with access to grazing a tropical pasture (pearl-millet, + item-64 at level 5: text: Pennisetum glaucum + item-65 at level 5: text: ‘Campeiro’) compared to cows receiving + item-66 at level 5: text: ad libitum + item-67 at level 5: text: TMR intake. Cows grazing on a temperate pasture (ryegrass, + item-68 at level 5: text: Lolium multiflorum + item-69 at level 5: text: ‘Maximus’) did not need changes to ECM production compared to the + item-70 at level 5: text: ad libitum + item-71 at level 5: text: TMR intake group. + item-72 at level 4: inline: group group + item-73 at level 5: text: Using experimental data, three s ... evaluated during the lactation period: + item-74 at level 5: text: ad libitum + item-75 at level 5: text: TMR intake, and 75, and 50% of + item-76 at level 5: text: ad libitum + item-77 at level 5: text: TMR intake with access to grazin ... nction of month ([26], Civiero et al., + item-78 at level 5: text: in press + item-79 at level 5: text: ). From April to October (210 da ... med during an entire lactation period. + item-80 at level 3: section_header: Impact assessment + item-81 at level 4: inline: group group + item-82 at level 5: text: The CO + item-83 at level 5: text: 2 + item-84 at level 5: text: e emissions were calculated by multiplying the emissions of CO + item-85 at level 5: text: 2 + item-86 at level 5: text: , CH + item-87 at level 5: text: 4 + item-88 at level 5: text: and N + item-89 at level 5: text: 2 + item-90 at level 5: text: O by their 100-year global warming potential (GWP + item-91 at level 5: text: 100 + item-92 at level 5: text: ), based on IPCC assessment report 5 (AR5; [27]). The values of GWP + item-93 at level 5: text: 100 + item-94 at level 5: text: are 1, 28 and 265 for CO + item-95 at level 5: text: 2 + item-96 at level 5: text: , CH + item-97 at level 5: text: 4 + item-98 at level 5: text: and N + item-99 at level 5: text: 2 + item-100 at level 5: text: O, respectively. + item-101 at level 3: section_header: Feed production + item-102 at level 4: section_header: Diets composition + item-103 at level 5: inline: group group + item-104 at level 6: text: The DM intake of each ingredient ... ennial tropical pasture (kikuyu grass, + item-105 at level 6: text: Pennisetum clandestinum + item-106 at level 6: text: ). The DM intake of calves, heif ... meet the net energy for lactation (NE + item-107 at level 6: text: L + item-108 at level 6: text: ) and metabolizable protein (MP) ... grated in the software INRAtion 4.07 ( + item-109 at level 6: text: https://www.inration.educagri.fr/fr/forum.php + item-110 at level 6: text: ). The nutrient intake was calcu ... collected throughout the experiments. + item-111 at level 5: table with [21x11] + item-111 at level 6: caption: Table 2 Dairy cows’ diets in different scenariosa. + item-112 at level 4: section_header: GHG emissions from crop and pasture production + item-113 at level 5: inline: group group + item-114 at level 6: text: GHG emission factors used for of ... s productions were 3300 and 1500 kg CO item-115 at level 6: text: 2 - item-116 at level 6: text: -C emissions from lime and urea ... well as fuel combustion. The direct N - item-117 at level 6: text: 2 - item-118 at level 6: text: O-N emission factor (kg (kg N input) + item-116 at level 6: text: e ha + item-117 at level 6: text: -1 + item-118 at level 6: text: , respectively [32]. The DM production (kg ha item-119 at level 6: text: -1 - item-120 at level 6: text: ) is based on a local study performed previously [37]. For indirect N - item-121 at level 6: text: 2 - item-122 at level 6: text: O-N emissions (kg N - item-123 at level 6: text: 2 - item-124 at level 6: text: O-N (kg NH - item-125 at level 6: text: 3 - item-126 at level 6: text: -N + NO - item-127 at level 6: text: x - item-128 at level 6: text: ) - item-129 at level 6: text: -1 - item-130 at level 6: text: ), as well as CO - item-131 at level 6: text: 2 - item-132 at level 6: text: -C emissions from lime + urea, d ... stures, a C sequestration of 0.57 t ha - item-133 at level 6: text: -1 - item-134 at level 6: text: was used based on a 9-year study ... red was 8.9 (no-tillage) and 14.3 L ha - item-135 at level 6: text: -1 - item-136 at level 6: text: (disking) for annual tropical an ... te pastures, respectively [40]. The CO - item-137 at level 6: text: 2 - item-138 at level 6: text: from fuel combustion was 2.7 kg CO - item-139 at level 6: text: 2 - item-140 at level 6: text: L - item-141 at level 6: text: -1 - item-142 at level 6: text: [41]. Secondary sources of emiss ... factors described by Rotz et al. [42]. - item-143 at level 5: table with [28x5] - item-143 at level 6: caption: Table 4 GHG emissions from On-farm feed production. - item-144 at level 3: section_header: Animal husbandry - item-145 at level 4: inline: group group - item-146 at level 5: text: The CH - item-147 at level 5: text: 4 - item-148 at level 5: text: emissions from enteric fermentation intensity (g (kg ECM) - item-149 at level 5: text: -1 - item-150 at level 5: text: ) was a function of estimated CH - item-151 at level 5: text: 4 - item-152 at level 5: text: yield (g (kg DM intake) - item-153 at level 5: text: -1 - item-154 at level 5: text: ), actual DM intake and ECM. The enteric CH - item-155 at level 5: text: 4 - item-156 at level 5: text: yield was estimated as a functio ... proposed by Niu et al. [43], where: CH - item-157 at level 5: text: 4 - item-158 at level 5: text: yield (g (kg DM intake) - item-159 at level 5: text: -1 - item-160 at level 5: text: ) = 13.8 + 0.185 × NDF (% DM intake). - item-161 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals - item-162 at level 4: inline: group group - item-163 at level 5: text: The CH - item-164 at level 5: text: 4 - item-165 at level 5: text: emission from manure (kg (kg ECM) - item-166 at level 5: text: -1 - item-167 at level 5: text: ) was a function of daily CH + item-120 at level 6: text: ) of corn silage and pastures we ... onsume 70% of pastures during grazing. + item-121 at level 5: table with [9x5] + item-121 at level 6: caption: Table 3 GHG emission factors for Off- and On-farm feed production. + item-122 at level 5: inline: group group + item-123 at level 6: text: Emissions from on-farm feed prod ... ary sources were direct and indirect N + item-124 at level 6: text: 2 + item-125 at level 6: text: O-N emissions from organic and s ... tilizers and crop/pasture residues, CO + item-126 at level 6: text: 2 + item-127 at level 6: text: -C emissions from lime and urea ... well as fuel combustion. The direct N + item-128 at level 6: text: 2 + item-129 at level 6: text: O-N emission factor (kg (kg N input) + item-130 at level 6: text: -1 + item-131 at level 6: text: ) is based on a local study performed previously [37]. For indirect N + item-132 at level 6: text: 2 + item-133 at level 6: text: O-N emissions (kg N + item-134 at level 6: text: 2 + item-135 at level 6: text: O-N (kg NH + item-136 at level 6: text: 3 + item-137 at level 6: text: -N + NO + item-138 at level 6: text: x + item-139 at level 6: text: ) + item-140 at level 6: text: -1 + item-141 at level 6: text: ), as well as CO + item-142 at level 6: text: 2 + item-143 at level 6: text: -C emissions from lime + urea, d ... stures, a C sequestration of 0.57 t ha + item-144 at level 6: text: -1 + item-145 at level 6: text: was used based on a 9-year study ... red was 8.9 (no-tillage) and 14.3 L ha + item-146 at level 6: text: -1 + item-147 at level 6: text: (disking) for annual tropical an ... te pastures, respectively [40]. The CO + item-148 at level 6: text: 2 + item-149 at level 6: text: from fuel combustion was 2.7 kg CO + item-150 at level 6: text: 2 + item-151 at level 6: text: L + item-152 at level 6: text: -1 + item-153 at level 6: text: [41]. Secondary sources of emiss ... factors described by Rotz et al. [42]. + item-154 at level 5: table with [28x5] + item-154 at level 6: caption: Table 4 GHG emissions from On-farm feed production. + item-155 at level 3: section_header: Animal husbandry + item-156 at level 4: inline: group group + item-157 at level 5: text: The CH + item-158 at level 5: text: 4 + item-159 at level 5: text: emissions from enteric fermentation intensity (g (kg ECM) + item-160 at level 5: text: -1 + item-161 at level 5: text: ) was a function of estimated CH + item-162 at level 5: text: 4 + item-163 at level 5: text: yield (g (kg DM intake) + item-164 at level 5: text: -1 + item-165 at level 5: text: ), actual DM intake and ECM. The enteric CH + item-166 at level 5: text: 4 + item-167 at level 5: text: yield was estimated as a functio ... proposed by Niu et al. [43], where: CH item-168 at level 5: text: 4 - item-169 at level 5: text: emission from manure (kg cow + item-169 at level 5: text: yield (g (kg DM intake) item-170 at level 5: text: -1 - item-171 at level 5: text: ) and daily ECM (kg cow - item-172 at level 5: text: -1 - item-173 at level 5: text: ). The daily CH - item-174 at level 5: text: 4 - item-175 at level 5: text: emission from manure was estimat ... olatile solid (VS) excreted (kg DM cow - item-176 at level 5: text: -1 - item-177 at level 5: text: ) in manure. The daily VS was es ... n an organic matter (OM) basis (kg day - item-178 at level 5: text: -1 - item-179 at level 5: text: ), NDOMI = non-digestible OM intake (kg day - item-180 at level 5: text: -1 - item-181 at level 5: text: ): (1- OM digestibility) × OM in ... .04), GE = gross energy intake (MJ day - item-182 at level 5: text: -1 - item-183 at level 5: text: ), OM = organic matter (g), 18.4 ... tor for dietary GE per kg of DM (MJ kg - item-184 at level 5: text: -1 - item-185 at level 5: text: ). - item-186 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively. - item-187 at level 4: inline: group group - item-188 at level 5: text: The N - item-189 at level 5: text: 2 - item-190 at level 5: text: O-N emissions from urine and fec ... ations 10 and 12, respectively). The N - item-191 at level 5: text: 2 - item-192 at level 5: text: O emissions from stored manure a ... alculated based on the conversion of N - item-193 at level 5: text: 2 - item-194 at level 5: text: O-N emissions to N - item-195 at level 5: text: 2 - item-196 at level 5: text: O emissions, where N - item-197 at level 5: text: 2 - item-198 at level 5: text: O emissions = N - item-199 at level 5: text: 2 - item-200 at level 5: text: O-N emissions × 44/28. The emission factors were 0.002 kg N - item-201 at level 5: text: 2 - item-202 at level 5: text: O-N (kg N) - item-203 at level 5: text: -1 - item-204 at level 5: text: stored in a pit below animal confinements, and 0.02 kg N - item-205 at level 5: text: 2 - item-206 at level 5: text: O-N (kg of urine and dung) - item-207 at level 5: text: -1 - item-208 at level 5: text: deposited on pasture [38]. The indirect N - item-209 at level 5: text: 2 - item-210 at level 5: text: O emissions from storage manure ... using the IPCC [38] emission factors. - item-211 at level 3: section_header: Farm management - item-212 at level 4: text: Emissions due to farm management ... crop and pasture production’ section. - item-213 at level 4: table with [12x4] - item-213 at level 5: caption: Table 5 Factors for major resource inputs in farm management. - item-214 at level 4: inline: group group - item-215 at level 5: text: The amount of fuel use for manur ... quired for manure handling (L diesel t - item-216 at level 5: text: -1 - item-217 at level 5: text: ) [42]. The amount of manure was estimated from OM excretions (kg cow + item-171 at level 5: text: ) = 13.8 + 0.185 × NDF (% DM intake). + item-172 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals + item-173 at level 4: inline: group group + item-174 at level 5: text: The CH + item-175 at level 5: text: 4 + item-176 at level 5: text: emission from manure (kg (kg ECM) + item-177 at level 5: text: -1 + item-178 at level 5: text: ) was a function of daily CH + item-179 at level 5: text: 4 + item-180 at level 5: text: emission from manure (kg cow + item-181 at level 5: text: -1 + item-182 at level 5: text: ) and daily ECM (kg cow + item-183 at level 5: text: -1 + item-184 at level 5: text: ). The daily CH + item-185 at level 5: text: 4 + item-186 at level 5: text: emission from manure was estimat ... olatile solid (VS) excreted (kg DM cow + item-187 at level 5: text: -1 + item-188 at level 5: text: ) in manure. The daily VS was es ... n an organic matter (OM) basis (kg day + item-189 at level 5: text: -1 + item-190 at level 5: text: ), NDOMI = non-digestible OM intake (kg day + item-191 at level 5: text: -1 + item-192 at level 5: text: ): (1- OM digestibility) × OM in ... .04), GE = gross energy intake (MJ day + item-193 at level 5: text: -1 + item-194 at level 5: text: ), OM = organic matter (g), 18.4 ... tor for dietary GE per kg of DM (MJ kg + item-195 at level 5: text: -1 + item-196 at level 5: text: ). + item-197 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively. + item-198 at level 4: inline: group group + item-199 at level 5: text: The N + item-200 at level 5: text: 2 + item-201 at level 5: text: O-N emissions from urine and fec ... ations 10 and 12, respectively). The N + item-202 at level 5: text: 2 + item-203 at level 5: text: O emissions from stored manure a ... alculated based on the conversion of N + item-204 at level 5: text: 2 + item-205 at level 5: text: O-N emissions to N + item-206 at level 5: text: 2 + item-207 at level 5: text: O emissions, where N + item-208 at level 5: text: 2 + item-209 at level 5: text: O emissions = N + item-210 at level 5: text: 2 + item-211 at level 5: text: O-N emissions × 44/28. The emission factors were 0.002 kg N + item-212 at level 5: text: 2 + item-213 at level 5: text: O-N (kg N) + item-214 at level 5: text: -1 + item-215 at level 5: text: stored in a pit below animal confinements, and 0.02 kg N + item-216 at level 5: text: 2 + item-217 at level 5: text: O-N (kg of urine and dung) item-218 at level 5: text: -1 - item-219 at level 5: text: ), assuming that the manure has ... me that animals stayed on confinement. - item-220 at level 4: inline: group group - item-221 at level 5: text: The emissions from fuel were est ... uired for manure handling (L) × (kg CO - item-222 at level 5: text: 2 - item-223 at level 5: text: e L - item-224 at level 5: text: -1 - item-225 at level 5: text: ) [41]. The secondary emissions ... roduction and transport of fuel (kg CO - item-226 at level 5: text: 2 - item-227 at level 5: text: e L - item-228 at level 5: text: -1 - item-229 at level 5: text: ) [41]. Emissions from manufactu ... w (t) × (kg machinery mass (kg manure) - item-230 at level 5: text: -1 - item-231 at level 5: text: × 10 - item-232 at level 5: text: −3 - item-233 at level 5: text: ) [42] × kg CO - item-234 at level 5: text: 2 - item-235 at level 5: text: e (kg machinery mass) - item-236 at level 5: text: -1 - item-237 at level 5: text: [42]. - item-238 at level 4: inline: group group - item-239 at level 5: text: Emissions from electricity for m ... ated using two emission factors (kg CO - item-240 at level 5: text: 2 - item-241 at level 5: text: kWh - item-242 at level 5: text: -1 - item-243 at level 5: text: ). The first one is based on Uni ... ivities is 0.06 kWh (kg milk produced) - item-244 at level 5: text: -1 - item-245 at level 5: text: [47]. The annual electricity use for lighting was 75 kWh cow - item-246 at level 5: text: -1 - item-247 at level 5: text: , which is the value considered ... ws in naturally ventilated barns [47]. - item-248 at level 3: section_header: Co-product allocation + item-219 at level 5: text: deposited on pasture [38]. The indirect N + item-220 at level 5: text: 2 + item-221 at level 5: text: O emissions from storage manure ... using the IPCC [38] emission factors. + item-222 at level 3: section_header: Farm management + item-223 at level 4: text: Emissions due to farm management ... crop and pasture production’ section. + item-224 at level 4: table with [12x4] + item-224 at level 5: caption: Table 5 Factors for major resource inputs in farm management. + item-225 at level 4: inline: group group + item-226 at level 5: text: The amount of fuel use for manur ... quired for manure handling (L diesel t + item-227 at level 5: text: -1 + item-228 at level 5: text: ) [42]. The amount of manure was estimated from OM excretions (kg cow + item-229 at level 5: text: -1 + item-230 at level 5: text: ), assuming that the manure has ... me that animals stayed on confinement. + item-231 at level 4: inline: group group + item-232 at level 5: text: The emissions from fuel were est ... uired for manure handling (L) × (kg CO + item-233 at level 5: text: 2 + item-234 at level 5: text: e L + item-235 at level 5: text: -1 + item-236 at level 5: text: ) [41]. The secondary emissions ... roduction and transport of fuel (kg CO + item-237 at level 5: text: 2 + item-238 at level 5: text: e L + item-239 at level 5: text: -1 + item-240 at level 5: text: ) [41]. Emissions from manufactu ... w (t) × (kg machinery mass (kg manure) + item-241 at level 5: text: -1 + item-242 at level 5: text: × 10 + item-243 at level 5: text: −3 + item-244 at level 5: text: ) [42] × kg CO + item-245 at level 5: text: 2 + item-246 at level 5: text: e (kg machinery mass) + item-247 at level 5: text: -1 + item-248 at level 5: text: [42]. item-249 at level 4: inline: group group - item-250 at level 5: text: The C footprint for milk produce ... ibed by Thoma et al. [48]. Briefly, AR - item-251 at level 5: text: milk - item-252 at level 5: text: = 1–6.04 × BMR, where - item-253 at level 5: text: : - item-254 at level 5: text: AR - item-255 at level 5: text: milk - item-256 at level 5: text: is the allocation ratio for milk ... during cow`s entire life (kg). The AR - item-257 at level 5: text: milk - item-258 at level 5: text: were 0.854 and 0.849 for TMR and ... asture scenarios, respectively. The AR - item-259 at level 5: text: milk - item-260 at level 5: text: was applied to the whole emissio ... directly assigned to milk production. - item-261 at level 3: section_header: Sensitivity analysis - item-262 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint. - item-263 at level 2: section_header: Results and discussion - item-264 at level 3: text: The study has assessed the impac ... , feed production and electricity use. - item-265 at level 3: section_header: Greenhouse gas emissions - item-266 at level 4: inline: group group - item-267 at level 5: text: Depending on emission factors us ... 2A and 2B) or decreased by 0.04 kg CO - item-268 at level 5: text: 2 - item-269 at level 5: text: e (kg ECM) - item-270 at level 5: text: -1 - item-271 at level 5: text: (Fig 2C and 2D) in scenarios that included pastures compared to - item-272 at level 5: text: ad libitum - item-273 at level 5: text: TMR intake. Due to differences i ... values ranged from 0.92 to 1.04 kg CO - item-274 at level 5: text: 2 - item-275 at level 5: text: e (kg ECM) - item-276 at level 5: text: -1 - item-277 at level 5: text: for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO - item-278 at level 5: text: 2 - item-279 at level 5: text: e (kg ECM) - item-280 at level 5: text: -1 - item-281 at level 5: text: for cows with access to pasture. ... ocal emission factors for estimating N - item-282 at level 5: text: 2 - item-283 at level 5: text: O-N emissions [37], manure emiss ... more than 5% of overall GHG emissions. - item-284 at level 4: picture - item-284 at level 5: caption: Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. - item-285 at level 4: inline: group group - item-286 at level 5: text: Considering IPCC emission factors for N - item-287 at level 5: text: 2 - item-288 at level 5: text: O emissions from urine and dung ... otprint ranged from 0.99 to 1.04 kg CO + item-250 at level 5: text: Emissions from electricity for m ... ated using two emission factors (kg CO + item-251 at level 5: text: 2 + item-252 at level 5: text: kWh + item-253 at level 5: text: -1 + item-254 at level 5: text: ). The first one is based on Uni ... ivities is 0.06 kWh (kg milk produced) + item-255 at level 5: text: -1 + item-256 at level 5: text: [47]. The annual electricity use for lighting was 75 kWh cow + item-257 at level 5: text: -1 + item-258 at level 5: text: , which is the value considered ... ws in naturally ventilated barns [47]. + item-259 at level 3: section_header: Co-product allocation + item-260 at level 4: inline: group group + item-261 at level 5: text: The C footprint for milk produce ... ibed by Thoma et al. [48]. Briefly, AR + item-262 at level 5: text: milk + item-263 at level 5: text: = 1–6.04 × BMR, where + item-264 at level 5: text: : + item-265 at level 5: text: AR + item-266 at level 5: text: milk + item-267 at level 5: text: is the allocation ratio for milk ... during cow`s entire life (kg). The AR + item-268 at level 5: text: milk + item-269 at level 5: text: were 0.854 and 0.849 for TMR and ... asture scenarios, respectively. The AR + item-270 at level 5: text: milk + item-271 at level 5: text: was applied to the whole emissio ... directly assigned to milk production. + item-272 at level 3: section_header: Sensitivity analysis + item-273 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint. + item-274 at level 2: section_header: Results and discussion + item-275 at level 3: text: The study has assessed the impac ... , feed production and electricity use. + item-276 at level 3: section_header: Greenhouse gas emissions + item-277 at level 4: inline: group group + item-278 at level 5: text: Depending on emission factors us ... 2A and 2B) or decreased by 0.04 kg CO + item-279 at level 5: text: 2 + item-280 at level 5: text: e (kg ECM) + item-281 at level 5: text: -1 + item-282 at level 5: text: (Fig 2C and 2D) in scenarios that included pastures compared to + item-283 at level 5: text: ad libitum + item-284 at level 5: text: TMR intake. Due to differences i ... values ranged from 0.92 to 1.04 kg CO + item-285 at level 5: text: 2 + item-286 at level 5: text: e (kg ECM) + item-287 at level 5: text: -1 + item-288 at level 5: text: for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO item-289 at level 5: text: 2 item-290 at level 5: text: e (kg ECM) item-291 at level 5: text: -1 - item-292 at level 5: text: , and was close to those reporte ... , which ranged from 0.98 to 1.16 kg CO + item-292 at level 5: text: for cows with access to pasture. ... ocal emission factors for estimating N item-293 at level 5: text: 2 - item-294 at level 5: text: e (kg ECM) - item-295 at level 5: text: -1 - item-296 at level 5: text: . When local emission factors for N - item-297 at level 5: text: 2 - item-298 at level 5: text: O emissions from urine and dung ... without accounting for sequestered CO - item-299 at level 5: text: 2 - item-300 at level 5: text: -C from perennial pasture—0.91 kg CO - item-301 at level 5: text: 2 - item-302 at level 5: text: e (kg ECM) - item-303 at level 5: text: -1 - item-304 at level 5: text: —was lower than the range of val ... , which ranged from 0.52 to 0.89 kg CO - item-305 at level 5: text: 2 - item-306 at level 5: text: e (kg ECM) - item-307 at level 5: text: -1 - item-308 at level 5: text: . Regardless of which emission f ... nt, which ranged from 1.4 to 2.3 kg CO - item-309 at level 5: text: 2 - item-310 at level 5: text: e (kg ECM) - item-311 at level 5: text: -1 - item-312 at level 5: text: [8,55]. Thus, even though differ ... e emissions estimation, sequestered CO - item-313 at level 5: text: 2 - item-314 at level 5: text: -C, etc.), herd productivity and ... the C footprint of the dairy systems. - item-315 at level 4: inline: group group - item-316 at level 5: text: The similarity of C footprint be ... served that an increase of 1000 kg cow - item-317 at level 5: text: -1 - item-318 at level 5: text: (5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO - item-319 at level 5: text: 2 - item-320 at level 5: text: e (kg ECM) - item-321 at level 5: text: -1 - item-322 at level 5: text: , which may explain an apparent ... milk production of around 7000 kg cow - item-323 at level 5: text: -1 - item-324 at level 5: text: . Experimental data showed a red ... of TMR was replaced by pasture access. - item-325 at level 4: inline: group group - item-326 at level 5: text: The lower C footprint in scenari ... emission factors [37] were used for N - item-327 at level 5: text: 2 - item-328 at level 5: text: O emissions from urine and dung ... enarios including pastures compared to - item-329 at level 5: text: ad libitum - item-330 at level 5: text: TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N - item-331 at level 5: text: 2 - item-332 at level 5: text: O-N (kg N) - item-333 at level 5: text: -1 - item-334 at level 5: text: for urine and dung from grazing ... five times lower, averaging 0.004 kg N - item-335 at level 5: text: 2 - item-336 at level 5: text: O-N kg - item-337 at level 5: text: -1 - item-338 at level 5: text: [37]. - item-339 at level 3: section_header: Methane emissions - item-340 at level 4: inline: group group - item-341 at level 5: text: The enteric CH - item-342 at level 5: text: 4 - item-343 at level 5: text: intensity was similar between di ... Fig 3). The large effect of enteric CH - item-344 at level 5: text: 4 - item-345 at level 5: text: emissions on the whole C footpri ... cted, because the impact of enteric CH - item-346 at level 5: text: 4 - item-347 at level 5: text: on GHG emissions of milk product ... o range from 44 to 60% of the total CO - item-348 at level 5: text: 2 - item-349 at level 5: text: e [50,52,57,58]. However, emissi ... trate feeds are greater than 0.7 kg CO - item-350 at level 5: text: 2 - item-351 at level 5: text: e kg - item-352 at level 5: text: -1 - item-353 at level 5: text: [59], which did not happen in this study. - item-354 at level 4: picture - item-354 at level 5: caption: Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. - item-355 at level 4: inline: group group - item-356 at level 5: text: The lack of difference in enteric CH + item-294 at level 5: text: O-N emissions [37], manure emiss ... more than 5% of overall GHG emissions. + item-295 at level 4: picture + item-295 at level 5: caption: Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. + item-296 at level 4: inline: group group + item-297 at level 5: text: Considering IPCC emission factors for N + item-298 at level 5: text: 2 + item-299 at level 5: text: O emissions from urine and dung ... otprint ranged from 0.99 to 1.04 kg CO + item-300 at level 5: text: 2 + item-301 at level 5: text: e (kg ECM) + item-302 at level 5: text: -1 + item-303 at level 5: text: , and was close to those reporte ... , which ranged from 0.98 to 1.16 kg CO + item-304 at level 5: text: 2 + item-305 at level 5: text: e (kg ECM) + item-306 at level 5: text: -1 + item-307 at level 5: text: . When local emission factors for N + item-308 at level 5: text: 2 + item-309 at level 5: text: O emissions from urine and dung ... without accounting for sequestered CO + item-310 at level 5: text: 2 + item-311 at level 5: text: -C from perennial pasture—0.91 kg CO + item-312 at level 5: text: 2 + item-313 at level 5: text: e (kg ECM) + item-314 at level 5: text: -1 + item-315 at level 5: text: —was lower than the range of val ... , which ranged from 0.52 to 0.89 kg CO + item-316 at level 5: text: 2 + item-317 at level 5: text: e (kg ECM) + item-318 at level 5: text: -1 + item-319 at level 5: text: . Regardless of which emission f ... nt, which ranged from 1.4 to 2.3 kg CO + item-320 at level 5: text: 2 + item-321 at level 5: text: e (kg ECM) + item-322 at level 5: text: -1 + item-323 at level 5: text: [8,55]. Thus, even though differ ... e emissions estimation, sequestered CO + item-324 at level 5: text: 2 + item-325 at level 5: text: -C, etc.), herd productivity and ... the C footprint of the dairy systems. + item-326 at level 4: inline: group group + item-327 at level 5: text: The similarity of C footprint be ... served that an increase of 1000 kg cow + item-328 at level 5: text: -1 + item-329 at level 5: text: (5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO + item-330 at level 5: text: 2 + item-331 at level 5: text: e (kg ECM) + item-332 at level 5: text: -1 + item-333 at level 5: text: , which may explain an apparent ... milk production of around 7000 kg cow + item-334 at level 5: text: -1 + item-335 at level 5: text: . Experimental data showed a red ... of TMR was replaced by pasture access. + item-336 at level 4: inline: group group + item-337 at level 5: text: The lower C footprint in scenari ... emission factors [37] were used for N + item-338 at level 5: text: 2 + item-339 at level 5: text: O emissions from urine and dung ... enarios including pastures compared to + item-340 at level 5: text: ad libitum + item-341 at level 5: text: TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N + item-342 at level 5: text: 2 + item-343 at level 5: text: O-N (kg N) + item-344 at level 5: text: -1 + item-345 at level 5: text: for urine and dung from grazing ... five times lower, averaging 0.004 kg N + item-346 at level 5: text: 2 + item-347 at level 5: text: O-N kg + item-348 at level 5: text: -1 + item-349 at level 5: text: [37]. + item-350 at level 3: section_header: Methane emissions + item-351 at level 4: inline: group group + item-352 at level 5: text: The enteric CH + item-353 at level 5: text: 4 + item-354 at level 5: text: intensity was similar between di ... Fig 3). The large effect of enteric CH + item-355 at level 5: text: 4 + item-356 at level 5: text: emissions on the whole C footpri ... cted, because the impact of enteric CH item-357 at level 5: text: 4 - item-358 at level 5: text: emissions in different systems c ... nual temperate pastures (495 g (kg DM) - item-359 at level 5: text: -1 - item-360 at level 5: text: ) compared to corn silage (550 g (kg DM) - item-361 at level 5: text: -1 - item-362 at level 5: text: ). Hence, an expected, increase ... have shown that the actual enteric CH - item-363 at level 5: text: 4 - item-364 at level 5: text: emissions may decrease with incl ... ybean meal [60] or increase enteric CH - item-365 at level 5: text: 4 - item-366 at level 5: text: emissions when dairy cows grazin ... silage [61]. Additionally, enteric CH - item-367 at level 5: text: 4 - item-368 at level 5: text: emissions did not differ between ... same scenarios as in this study [26]. - item-369 at level 3: section_header: Emissions from excreta and feed production - item-370 at level 4: inline: group group - item-371 at level 5: text: Using IPCC emission factors for N - item-372 at level 5: text: 2 - item-373 at level 5: text: O emissions from urine and dung [38] and those from Table 3, CH + item-358 at level 5: text: on GHG emissions of milk product ... o range from 44 to 60% of the total CO + item-359 at level 5: text: 2 + item-360 at level 5: text: e [50,52,57,58]. However, emissi ... trate feeds are greater than 0.7 kg CO + item-361 at level 5: text: 2 + item-362 at level 5: text: e kg + item-363 at level 5: text: -1 + item-364 at level 5: text: [59], which did not happen in this study. + item-365 at level 4: picture + item-365 at level 5: caption: Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. + item-366 at level 4: inline: group group + item-367 at level 5: text: The lack of difference in enteric CH + item-368 at level 5: text: 4 + item-369 at level 5: text: emissions in different systems c ... nual temperate pastures (495 g (kg DM) + item-370 at level 5: text: -1 + item-371 at level 5: text: ) compared to corn silage (550 g (kg DM) + item-372 at level 5: text: -1 + item-373 at level 5: text: ). Hence, an expected, increase ... have shown that the actual enteric CH item-374 at level 5: text: 4 - item-375 at level 5: text: emissions from manure decreased 0.07 kg CO - item-376 at level 5: text: 2 - item-377 at level 5: text: e (kg ECM) - item-378 at level 5: text: -1 - item-379 at level 5: text: , but N - item-380 at level 5: text: 2 - item-381 at level 5: text: O emissions from manure increased 0.09 kg CO - item-382 at level 5: text: 2 - item-383 at level 5: text: e (kg ECM) - item-384 at level 5: text: -1 - item-385 at level 5: text: , as TMR intake was restricted to 50% - item-386 at level 5: text: ad libitum - item-387 at level 5: text: (Fig 4A). Emissions for pastures increased by 0.06 kg CO - item-388 at level 5: text: 2 - item-389 at level 5: text: e (kg ECM) - item-390 at level 5: text: -1 - item-391 at level 5: text: , whereas emissions for producin ... nd corn silage decreased by 0.09 kg CO - item-392 at level 5: text: 2 - item-393 at level 5: text: e (kg ECM) - item-394 at level 5: text: -1 - item-395 at level 5: text: , as TMR intake decreased (Fig 4 ... ctating dairy cow diets. The greater N - item-396 at level 5: text: 2 - item-397 at level 5: text: O-N emissions from manure with pasture was a consequence of higher N - item-398 at level 5: text: 2 - item-399 at level 5: text: O-N emissions due to greater CP ... g CP content from 185 to 152 g (kg DM) - item-400 at level 5: text: -1 - item-401 at level 5: text: , N intake decreased by 20% and ... g dairy cows ranged from 150 g (kg DM) - item-402 at level 5: text: -1 - item-403 at level 5: text: on TMR system to 198 g (kg DM) - item-404 at level 5: text: -1 - item-405 at level 5: text: on 50% TMR with pasture. Additio ... may not be captured by microbes [65]. - item-406 at level 4: picture - item-406 at level 5: caption: Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture. - item-407 at level 4: inline: group group - item-408 at level 5: text: Using local emission factors for N + item-375 at level 5: text: emissions may decrease with incl ... ybean meal [60] or increase enteric CH + item-376 at level 5: text: 4 + item-377 at level 5: text: emissions when dairy cows grazin ... silage [61]. Additionally, enteric CH + item-378 at level 5: text: 4 + item-379 at level 5: text: emissions did not differ between ... same scenarios as in this study [26]. + item-380 at level 3: section_header: Emissions from excreta and feed production + item-381 at level 4: inline: group group + item-382 at level 5: text: Using IPCC emission factors for N + item-383 at level 5: text: 2 + item-384 at level 5: text: O emissions from urine and dung [38] and those from Table 3, CH + item-385 at level 5: text: 4 + item-386 at level 5: text: emissions from manure decreased 0.07 kg CO + item-387 at level 5: text: 2 + item-388 at level 5: text: e (kg ECM) + item-389 at level 5: text: -1 + item-390 at level 5: text: , but N + item-391 at level 5: text: 2 + item-392 at level 5: text: O emissions from manure increased 0.09 kg CO + item-393 at level 5: text: 2 + item-394 at level 5: text: e (kg ECM) + item-395 at level 5: text: -1 + item-396 at level 5: text: , as TMR intake was restricted to 50% + item-397 at level 5: text: ad libitum + item-398 at level 5: text: (Fig 4A). Emissions for pastures increased by 0.06 kg CO + item-399 at level 5: text: 2 + item-400 at level 5: text: e (kg ECM) + item-401 at level 5: text: -1 + item-402 at level 5: text: , whereas emissions for producin ... nd corn silage decreased by 0.09 kg CO + item-403 at level 5: text: 2 + item-404 at level 5: text: e (kg ECM) + item-405 at level 5: text: -1 + item-406 at level 5: text: , as TMR intake decreased (Fig 4 ... ctating dairy cow diets. The greater N + item-407 at level 5: text: 2 + item-408 at level 5: text: O-N emissions from manure with pasture was a consequence of higher N item-409 at level 5: text: 2 - item-410 at level 5: text: O emissions from urine and dung ... d those from Table 4, reductions in CH - item-411 at level 5: text: 4 - item-412 at level 5: text: emissions from stocked manure, w ... iets, did not offset by increases in N - item-413 at level 5: text: 2 - item-414 at level 5: text: O emissions from excreta (Fig 4C ... much lower emission factors used for N - item-415 at level 5: text: 2 - item-416 at level 5: text: O emissions from urine and dung. ... be revised for the subtropical region. - item-417 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9]. - item-418 at level 3: section_header: Farm management - item-419 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint. - item-420 at level 4: inline: group group - item-421 at level 5: text: Emissions from farm management d ... or electricity generation (0.205 kg CO - item-422 at level 5: text: 2 - item-423 at level 5: text: e kWh - item-424 at level 5: text: -1 - item-425 at level 5: text: [46]) is much lower than that in a LCA study conducted in US (0.73 kg CO + item-410 at level 5: text: O-N emissions due to greater CP ... g CP content from 185 to 152 g (kg DM) + item-411 at level 5: text: -1 + item-412 at level 5: text: , N intake decreased by 20% and ... g dairy cows ranged from 150 g (kg DM) + item-413 at level 5: text: -1 + item-414 at level 5: text: on TMR system to 198 g (kg DM) + item-415 at level 5: text: -1 + item-416 at level 5: text: on 50% TMR with pasture. Additio ... may not be captured by microbes [65]. + item-417 at level 4: picture + item-417 at level 5: caption: Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture. + item-418 at level 4: inline: group group + item-419 at level 5: text: Using local emission factors for N + item-420 at level 5: text: 2 + item-421 at level 5: text: O emissions from urine and dung ... d those from Table 4, reductions in CH + item-422 at level 5: text: 4 + item-423 at level 5: text: emissions from stocked manure, w ... iets, did not offset by increases in N + item-424 at level 5: text: 2 + item-425 at level 5: text: O emissions from excreta (Fig 4C ... much lower emission factors used for N item-426 at level 5: text: 2 - item-427 at level 5: text: e kWh - item-428 at level 5: text: -1 - item-429 at level 5: text: [42]). This apparent discrepancy ... has an emission factor of 0.074 kg CO - item-430 at level 5: text: 2 - item-431 at level 5: text: e kWh - item-432 at level 5: text: -1 - item-433 at level 5: text: against 0.382 and 0.926 kg CO - item-434 at level 5: text: 2 - item-435 at level 5: text: e kWh - item-436 at level 5: text: -1 - item-437 at level 5: text: produced by natural gas and hard coal, respectively [46]. - item-438 at level 3: section_header: Assumptions and limitations - item-439 at level 4: inline: group group - item-440 at level 5: text: The milk production and composit ... sion factors for direct and indirect N + item-427 at level 5: text: O emissions from urine and dung. ... be revised for the subtropical region. + item-428 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9]. + item-429 at level 3: section_header: Farm management + item-430 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint. + item-431 at level 4: inline: group group + item-432 at level 5: text: Emissions from farm management d ... or electricity generation (0.205 kg CO + item-433 at level 5: text: 2 + item-434 at level 5: text: e kWh + item-435 at level 5: text: -1 + item-436 at level 5: text: [46]) is much lower than that in a LCA study conducted in US (0.73 kg CO + item-437 at level 5: text: 2 + item-438 at level 5: text: e kWh + item-439 at level 5: text: -1 + item-440 at level 5: text: [42]). This apparent discrepancy ... has an emission factor of 0.074 kg CO item-441 at level 5: text: 2 - item-442 at level 5: text: O emissions from urine and dung ... sary to reduce the uncertainty. The CO - item-443 at level 5: text: 2 - item-444 at level 5: text: emitted from lime and urea appli ... ions as a function of soil management. - item-445 at level 3: section_header: Further considerations - item-446 at level 4: inline: group group - item-447 at level 5: text: The potential for using pasture ... reduced the C footprint by 0.12 kg CO - item-448 at level 5: text: 2 - item-449 at level 5: text: e (kg ECM) - item-450 at level 5: text: -1 - item-451 at level 5: text: , whereas an increase from 10,00 ... ced the C footprint by only 0.06 kg CO + item-442 at level 5: text: e kWh + item-443 at level 5: text: -1 + item-444 at level 5: text: against 0.382 and 0.926 kg CO + item-445 at level 5: text: 2 + item-446 at level 5: text: e kWh + item-447 at level 5: text: -1 + item-448 at level 5: text: produced by natural gas and hard coal, respectively [46]. + item-449 at level 3: section_header: Assumptions and limitations + item-450 at level 4: inline: group group + item-451 at level 5: text: The milk production and composit ... sion factors for direct and indirect N item-452 at level 5: text: 2 - item-453 at level 5: text: e (kg ECM) - item-454 at level 5: text: -1 - item-455 at level 5: text: . Hence, the impact of increasin ... C footprint may increase by 0.03 kg CO - item-456 at level 5: text: 2 - item-457 at level 5: text: e (kg ECM) - item-458 at level 5: text: -1 - item-459 at level 5: text: in subclinical ketosis [71] and by 0.02 kg CO - item-460 at level 5: text: 2 - item-461 at level 5: text: e (kg ECM) - item-462 at level 5: text: -1 - item-463 at level 5: text: in case of foot lesions [72]. - item-464 at level 4: inline: group group - item-465 at level 5: text: Grazing lands may also improve b ... n subtropical areas by 0.5 to 1.5 t ha - item-466 at level 5: text: -1 - item-467 at level 5: text: [75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha - item-468 at level 5: text: -1 - item-469 at level 5: text: would be sequestered, further re ... e C footprint by 0.015 and 0.025 kg CO - item-470 at level 5: text: 2 - item-471 at level 5: text: e (kg ECM) - item-472 at level 5: text: -1 - item-473 at level 5: text: for the scenarios using 75 and 5 ... emissions would be 0.03 and 0.05 kg CO - item-474 at level 5: text: 2 - item-475 at level 5: text: e (kg ECM) - item-476 at level 5: text: -1 - item-477 at level 5: text: for 75 and 50% TMR, respectively ... C storage, so that net exchange of CO - item-478 at level 5: text: 2 - item-479 at level 5: text: would be negligible [76]. - item-480 at level 2: section_header: Conclusions - item-481 at level 3: inline: group group - item-482 at level 4: text: This study assessed the C footpr ... attributable to the evidence of low N - item-483 at level 4: text: 2 - item-484 at level 4: text: O emissions from urine and dung ... ical areas. Even though the enteric CH - item-485 at level 4: text: 4 - item-486 at level 4: text: intensity was the largest source of CO - item-487 at level 4: text: 2 - item-488 at level 4: text: e emissions, it did not change b ... on with or without access to pastures. - item-489 at level 2: section_header: Acknowledgments - item-490 at level 3: text: Thanks to Anna Naranjo for helpf ... of the herd considered in this study. - item-491 at level 2: section_header: References - item-492 at level 3: list: group list - item-493 at level 4: list_item: IPCC. 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Soil Carbon Sequestration ... 1627. 10.1126/science.1097396 15192216 - item-567 at level 4: list_item: BoddeyRM, JantaliaCP, ConceiçaoP ... –795. 10.1111/j.1365-2486.2009.02020.x - item-568 at level 4: list_item: McConkeyB, AngersD, BenthamM, Bo ... the LULUCF sector for NIR 2014. 2014. - item-569 at level 1: caption: Fig 1 Overview of the milk produ ... stem boundary considered in the study. - item-570 at level 1: caption: Table 1 Descriptive characteristics of the herd. - item-571 at level 1: caption: Table 2 Dairy cows’ diets in different scenariosa. - item-572 at level 1: caption: Table 3 GHG emission factors for Off- and On-farm feed production. - item-573 at level 1: caption: Table 4 GHG emissions from On-farm feed production. - item-574 at level 1: caption: Table 5 Factors for major resource inputs in farm management. - item-575 at level 1: caption: Fig 2 Overall greenhouse gas emi ... lectricity = 0.205 kg CO2e kWh-1 [46]. - item-576 at level 1: caption: Fig 3 Sensitivity of the C footp ... lectricity = 0.205 kg CO2e kWh-1 [46]. - item-577 at level 1: caption: Fig 4 Greenhouse gas emissions ( ... uestered CO2-C from perennial pasture. \ No newline at end of file + item-453 at level 5: text: O emissions from urine and dung ... sary to reduce the uncertainty. The CO + item-454 at level 5: text: 2 + item-455 at level 5: text: emitted from lime and urea appli ... ions as a function of soil management. + item-456 at level 3: section_header: Further considerations + item-457 at level 4: inline: group group + item-458 at level 5: text: The potential for using pasture ... reduced the C footprint by 0.12 kg CO + item-459 at level 5: text: 2 + item-460 at level 5: text: e (kg ECM) + item-461 at level 5: text: -1 + item-462 at level 5: text: , whereas an increase from 10,00 ... ced the C footprint by only 0.06 kg CO + item-463 at level 5: text: 2 + item-464 at level 5: text: e (kg ECM) + item-465 at level 5: text: -1 + item-466 at level 5: text: . Hence, the impact of increasin ... C footprint may increase by 0.03 kg CO + item-467 at level 5: text: 2 + item-468 at level 5: text: e (kg ECM) + item-469 at level 5: text: -1 + item-470 at level 5: text: in subclinical ketosis [71] and by 0.02 kg CO + item-471 at level 5: text: 2 + item-472 at level 5: text: e (kg ECM) + item-473 at level 5: text: -1 + item-474 at level 5: text: in case of foot lesions [72]. + item-475 at level 4: inline: group group + item-476 at level 5: text: Grazing lands may also improve b ... n subtropical areas by 0.5 to 1.5 t ha + item-477 at level 5: text: -1 + item-478 at level 5: text: [75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha + item-479 at level 5: text: -1 + item-480 at level 5: text: would be sequestered, further re ... e C footprint by 0.015 and 0.025 kg CO + item-481 at level 5: text: 2 + item-482 at level 5: text: e (kg ECM) + item-483 at level 5: text: -1 + item-484 at level 5: text: for the scenarios using 75 and 5 ... emissions would be 0.03 and 0.05 kg CO + item-485 at level 5: text: 2 + item-486 at level 5: text: e (kg ECM) + item-487 at level 5: text: -1 + item-488 at level 5: text: for 75 and 50% TMR, respectively ... C storage, so that net exchange of CO + item-489 at level 5: text: 2 + item-490 at level 5: text: would be negligible [76]. + item-491 at level 2: section_header: Conclusions + item-492 at level 3: inline: group group + item-493 at level 4: text: This study assessed the C footpr ... attributable to the evidence of low N + item-494 at level 4: text: 2 + item-495 at level 4: text: O emissions from urine and dung ... ical areas. Even though the enteric CH + item-496 at level 4: text: 4 + item-497 at level 4: text: intensity was the largest source of CO + item-498 at level 4: text: 2 + item-499 at level 4: text: e emissions, it did not change b ... on with or without access to pastures. + item-500 at level 2: section_header: Acknowledgments + item-501 at level 3: text: Thanks to Anna Naranjo for helpf ... of the herd considered in this study. + item-502 at level 2: section_header: References + item-503 at level 3: list: group list + item-504 at level 4: list_item: IPCC. Climate Change and Land. 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"$ref": "#/texts/38" + "$ref": "#/texts/49" }, { - "$ref": "#/texts/42" + "$ref": "#/texts/53" }, { - "$ref": "#/texts/91" + "$ref": "#/texts/102" }, { - "$ref": "#/texts/100" + "$ref": "#/texts/111" }, { - "$ref": "#/texts/132" + "$ref": "#/texts/143" }, { - "$ref": "#/texts/199" + "$ref": "#/texts/210" }, { - "$ref": "#/texts/265" + "$ref": "#/texts/276" }, { - "$ref": "#/texts/331" + "$ref": "#/texts/342" }, { - "$ref": "#/texts/381" + "$ref": "#/texts/392" } ], "content_layer": "body", @@ -94,18 +94,10 @@ }, { "$ref": "#/texts/15" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/1", - "parent": { - "$ref": "#/texts/16" - }, - "children": [ + }, + { + "$ref": "#/texts/16" + }, { "$ref": "#/texts/17" }, @@ -126,6 +118,15 @@ }, { "$ref": "#/texts/23" + }, + { + "$ref": "#/texts/24" + }, + { + "$ref": "#/texts/25" + }, + { + "$ref": "#/texts/26" } ], "content_layer": "body", @@ -133,25 +134,31 @@ "label": "inline" }, { - "self_ref": "#/groups/2", + "self_ref": "#/groups/1", "parent": { - "$ref": "#/texts/16" + "$ref": "#/texts/27" }, "children": [ { - "$ref": "#/texts/24" + "$ref": "#/texts/28" }, { - "$ref": "#/texts/25" + "$ref": "#/texts/29" }, { - "$ref": "#/texts/26" + "$ref": "#/texts/30" }, { - "$ref": "#/texts/27" + "$ref": "#/texts/31" }, { - "$ref": "#/texts/28" + "$ref": "#/texts/32" + }, + { + "$ref": "#/texts/33" + }, + { + "$ref": "#/texts/34" } ], "content_layer": "body", @@ -159,19 +166,25 @@ "label": "inline" }, { - "self_ref": "#/groups/3", + "self_ref": "#/groups/2", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/27" }, "children": [ { - "$ref": "#/texts/33" + "$ref": "#/texts/35" }, { - "$ref": "#/texts/34" + "$ref": "#/texts/36" }, { - "$ref": "#/texts/35" + "$ref": "#/texts/37" + }, + { + "$ref": "#/texts/38" + }, + { + "$ref": "#/texts/39" } ], "content_layer": "body", @@ -179,7 +192,7 @@ "label": "inline" }, { - "self_ref": "#/groups/4", + "self_ref": "#/groups/3", "parent": { "$ref": "#/texts/43" }, @@ -192,30 +205,6 @@ }, { "$ref": "#/texts/46" - }, - { - "$ref": "#/texts/47" - }, - { - "$ref": "#/texts/48" - }, - { - "$ref": "#/texts/49" - }, - { - "$ref": "#/texts/50" - }, - { - "$ref": "#/texts/51" - }, - { - "$ref": "#/texts/52" - }, - { - "$ref": "#/texts/53" - }, - { - "$ref": "#/texts/54" } ], "content_layer": "body", @@ -223,9 +212,9 @@ "label": "inline" }, { - "self_ref": "#/groups/5", + "self_ref": "#/groups/4", "parent": { - "$ref": "#/texts/43" + "$ref": "#/texts/54" }, "children": [ { @@ -248,6 +237,18 @@ }, { "$ref": "#/texts/61" + }, + { + "$ref": "#/texts/62" + }, + { + "$ref": "#/texts/63" + }, + { + "$ref": "#/texts/64" + }, + { + "$ref": "#/texts/65" } ], "content_layer": "body", @@ -255,20 +256,11 @@ "label": "inline" }, { - "self_ref": "#/groups/6", + "self_ref": "#/groups/5", "parent": { - "$ref": "#/texts/62" + "$ref": "#/texts/54" }, "children": [ - { - "$ref": "#/texts/63" - }, - { - "$ref": "#/texts/64" - }, - { - "$ref": "#/texts/65" - }, { "$ref": "#/texts/66" }, @@ -289,10 +281,18 @@ }, { "$ref": "#/texts/72" - }, - { - "$ref": "#/texts/73" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/6", + "parent": { + "$ref": "#/texts/73" + }, + "children": [ { "$ref": "#/texts/74" }, @@ -316,18 +316,13 @@ }, { "$ref": "#/texts/81" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/7", - "parent": { - "$ref": "#/texts/83" - }, - "children": [ + }, + { + "$ref": "#/texts/82" + }, + { + "$ref": "#/texts/83" + }, { "$ref": "#/texts/84" }, @@ -348,6 +343,12 @@ }, { "$ref": "#/texts/90" + }, + { + "$ref": "#/texts/91" + }, + { + "$ref": "#/texts/92" } ], "content_layer": "body", @@ -355,17 +356,11 @@ "label": "inline" }, { - "self_ref": "#/groups/8", + "self_ref": "#/groups/7", "parent": { - "$ref": "#/texts/92" + "$ref": "#/texts/94" }, "children": [ - { - "$ref": "#/texts/93" - }, - { - "$ref": "#/texts/94" - }, { "$ref": "#/texts/95" }, @@ -380,6 +375,12 @@ }, { "$ref": "#/texts/99" + }, + { + "$ref": "#/texts/100" + }, + { + "$ref": "#/texts/101" } ], "content_layer": "body", @@ -387,20 +388,11 @@ "label": "inline" }, { - "self_ref": "#/groups/9", + "self_ref": "#/groups/8", "parent": { - "$ref": "#/texts/92" + "$ref": "#/texts/103" }, "children": [ - { - "$ref": "#/texts/101" - }, - { - "$ref": "#/texts/102" - }, - { - "$ref": "#/texts/103" - }, { "$ref": "#/texts/104" }, @@ -421,10 +413,18 @@ }, { "$ref": "#/texts/110" - }, - { - "$ref": "#/texts/111" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/9", + "parent": { + "$ref": "#/texts/103" + }, + "children": [ { "$ref": "#/texts/112" }, @@ -484,18 +484,13 @@ }, { "$ref": "#/texts/131" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/10", - "parent": { - "$ref": "#/texts/133" - }, - "children": [ + }, + { + "$ref": "#/texts/132" + }, + { + "$ref": "#/texts/133" + }, { "$ref": "#/texts/134" }, @@ -522,13 +517,18 @@ }, { "$ref": "#/texts/142" - }, - { - "$ref": "#/texts/143" - }, - { - "$ref": "#/texts/144" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/10", + "parent": { + "$ref": "#/texts/144" + }, + "children": [ { "$ref": "#/texts/145" }, @@ -540,18 +540,10 @@ }, { "$ref": "#/texts/148" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/11", - "parent": { - "$ref": "#/texts/149" - }, - "children": [ + }, + { + "$ref": "#/texts/149" + }, { "$ref": "#/texts/150" }, @@ -581,10 +573,18 @@ }, { "$ref": "#/texts/159" - }, - { - "$ref": "#/texts/160" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/11", + "parent": { + "$ref": "#/texts/160" + }, + "children": [ { "$ref": "#/texts/161" }, @@ -620,18 +620,10 @@ }, { "$ref": "#/texts/172" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/12", - "parent": { - "$ref": "#/texts/149" - }, - "children": [ + }, + { + "$ref": "#/texts/173" + }, { "$ref": "#/texts/174" }, @@ -661,10 +653,18 @@ }, { "$ref": "#/texts/183" - }, - { - "$ref": "#/texts/184" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/12", + "parent": { + "$ref": "#/texts/160" + }, + "children": [ { "$ref": "#/texts/185" }, @@ -700,18 +700,16 @@ }, { "$ref": "#/texts/196" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/13", - "parent": { - "$ref": "#/texts/197" - }, - "children": [ + }, + { + "$ref": "#/texts/197" + }, + { + "$ref": "#/texts/198" + }, + { + "$ref": "#/texts/199" + }, { "$ref": "#/texts/200" }, @@ -726,6 +724,15 @@ }, { "$ref": "#/texts/204" + }, + { + "$ref": "#/texts/205" + }, + { + "$ref": "#/texts/206" + }, + { + "$ref": "#/texts/207" } ], "content_layer": "body", @@ -733,29 +740,11 @@ "label": "inline" }, { - "self_ref": "#/groups/14", + "self_ref": "#/groups/13", "parent": { - "$ref": "#/texts/197" + "$ref": "#/texts/208" }, "children": [ - { - "$ref": "#/texts/205" - }, - { - "$ref": "#/texts/206" - }, - { - "$ref": "#/texts/207" - }, - { - "$ref": "#/texts/208" - }, - { - "$ref": "#/texts/209" - }, - { - "$ref": "#/texts/210" - }, { "$ref": "#/texts/211" }, @@ -770,7 +759,18 @@ }, { "$ref": "#/texts/215" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/14", + "parent": { + "$ref": "#/texts/208" + }, + "children": [ { "$ref": "#/texts/216" }, @@ -788,18 +788,7 @@ }, { "$ref": "#/texts/221" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/15", - "parent": { - "$ref": "#/texts/197" - }, - "children": [ + }, { "$ref": "#/texts/222" }, @@ -826,6 +815,12 @@ }, { "$ref": "#/texts/230" + }, + { + "$ref": "#/texts/231" + }, + { + "$ref": "#/texts/232" } ], "content_layer": "body", @@ -833,14 +828,11 @@ "label": "inline" }, { - "self_ref": "#/groups/16", + "self_ref": "#/groups/15", "parent": { - "$ref": "#/texts/231" + "$ref": "#/texts/208" }, "children": [ - { - "$ref": "#/texts/232" - }, { "$ref": "#/texts/233" }, @@ -867,9 +859,6 @@ }, { "$ref": "#/texts/241" - }, - { - "$ref": "#/texts/242" } ], "content_layer": "body", @@ -877,44 +866,55 @@ "label": "inline" }, { - "self_ref": "#/groups/17", + "self_ref": "#/groups/16", "parent": { - "$ref": "#/texts/247" + "$ref": "#/texts/242" }, "children": [ { - "$ref": "#/texts/248" + "$ref": "#/texts/243" }, { - "$ref": "#/texts/249" + "$ref": "#/texts/244" }, { - "$ref": "#/texts/250" + "$ref": "#/texts/245" }, { - "$ref": "#/texts/251" + "$ref": "#/texts/246" }, { - "$ref": "#/texts/252" + "$ref": "#/texts/247" }, { - "$ref": "#/texts/253" + "$ref": "#/texts/248" }, { - "$ref": "#/texts/254" + "$ref": "#/texts/249" }, { - "$ref": "#/texts/255" + "$ref": "#/texts/250" }, { - "$ref": "#/texts/256" + "$ref": "#/texts/251" }, { - "$ref": "#/texts/257" + "$ref": "#/texts/252" }, { - "$ref": "#/texts/258" - }, + "$ref": "#/texts/253" + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/17", + "parent": { + "$ref": "#/texts/258" + }, + "children": [ { "$ref": "#/texts/259" }, @@ -932,18 +932,10 @@ }, { "$ref": "#/texts/264" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/18", - "parent": { - "$ref": "#/texts/247" - }, - "children": [ + }, + { + "$ref": "#/texts/265" + }, { "$ref": "#/texts/266" }, @@ -973,10 +965,18 @@ }, { "$ref": "#/texts/275" - }, - { - "$ref": "#/texts/276" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/18", + "parent": { + "$ref": "#/texts/258" + }, + "children": [ { "$ref": "#/texts/277" }, @@ -1030,18 +1030,7 @@ }, { "$ref": "#/texts/294" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/19", - "parent": { - "$ref": "#/texts/247" - }, - "children": [ + }, { "$ref": "#/texts/295" }, @@ -1068,6 +1057,12 @@ }, { "$ref": "#/texts/303" + }, + { + "$ref": "#/texts/304" + }, + { + "$ref": "#/texts/305" } ], "content_layer": "body", @@ -1075,17 +1070,11 @@ "label": "inline" }, { - "self_ref": "#/groups/20", + "self_ref": "#/groups/19", "parent": { - "$ref": "#/texts/247" + "$ref": "#/texts/258" }, "children": [ - { - "$ref": "#/texts/304" - }, - { - "$ref": "#/texts/305" - }, { "$ref": "#/texts/306" }, @@ -1112,12 +1101,6 @@ }, { "$ref": "#/texts/314" - }, - { - "$ref": "#/texts/315" - }, - { - "$ref": "#/texts/316" } ], "content_layer": "body", @@ -1125,11 +1108,20 @@ "label": "inline" }, { - "self_ref": "#/groups/21", + "self_ref": "#/groups/20", "parent": { - "$ref": "#/texts/317" + "$ref": "#/texts/258" }, "children": [ + { + "$ref": "#/texts/315" + }, + { + "$ref": "#/texts/316" + }, + { + "$ref": "#/texts/317" + }, { "$ref": "#/texts/318" }, @@ -1159,15 +1151,6 @@ }, { "$ref": "#/texts/327" - }, - { - "$ref": "#/texts/328" - }, - { - "$ref": "#/texts/329" - }, - { - "$ref": "#/texts/330" } ], "content_layer": "body", @@ -1175,11 +1158,20 @@ "label": "inline" }, { - "self_ref": "#/groups/22", + "self_ref": "#/groups/21", "parent": { - "$ref": "#/texts/317" + "$ref": "#/texts/328" }, "children": [ + { + "$ref": "#/texts/329" + }, + { + "$ref": "#/texts/330" + }, + { + "$ref": "#/texts/331" + }, { "$ref": "#/texts/332" }, @@ -1209,15 +1201,6 @@ }, { "$ref": "#/texts/341" - }, - { - "$ref": "#/texts/342" - }, - { - "$ref": "#/texts/343" - }, - { - "$ref": "#/texts/344" } ], "content_layer": "body", @@ -1225,11 +1208,20 @@ "label": "inline" }, { - "self_ref": "#/groups/23", + "self_ref": "#/groups/22", "parent": { - "$ref": "#/texts/345" + "$ref": "#/texts/328" }, "children": [ + { + "$ref": "#/texts/343" + }, + { + "$ref": "#/texts/344" + }, + { + "$ref": "#/texts/345" + }, { "$ref": "#/texts/346" }, @@ -1259,10 +1251,18 @@ }, { "$ref": "#/texts/355" - }, - { - "$ref": "#/texts/356" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/23", + "parent": { + "$ref": "#/texts/356" + }, + "children": [ { "$ref": "#/texts/357" }, @@ -1334,18 +1334,10 @@ }, { "$ref": "#/texts/380" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/24", - "parent": { - "$ref": "#/texts/345" - }, - "children": [ + }, + { + "$ref": "#/texts/381" + }, { "$ref": "#/texts/382" }, @@ -1372,6 +1364,9 @@ }, { "$ref": "#/texts/390" + }, + { + "$ref": "#/texts/391" } ], "content_layer": "body", @@ -1379,11 +1374,14 @@ "label": "inline" }, { - "self_ref": "#/groups/25", + "self_ref": "#/groups/24", "parent": { - "$ref": "#/texts/392" + "$ref": "#/texts/356" }, "children": [ + { + "$ref": "#/texts/393" + }, { "$ref": "#/texts/394" }, @@ -1407,16 +1405,18 @@ }, { "$ref": "#/texts/401" - }, - { - "$ref": "#/texts/402" - }, - { - "$ref": "#/texts/403" - }, - { - "$ref": "#/texts/404" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/25", + "parent": { + "$ref": "#/texts/403" + }, + "children": [ { "$ref": "#/texts/405" }, @@ -1434,18 +1434,10 @@ }, { "$ref": "#/texts/410" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/26", - "parent": { - "$ref": "#/texts/411" - }, - "children": [ + }, + { + "$ref": "#/texts/411" + }, { "$ref": "#/texts/412" }, @@ -1460,18 +1452,10 @@ }, { "$ref": "#/texts/416" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/27", - "parent": { - "$ref": "#/texts/417" - }, - "children": [ + }, + { + "$ref": "#/texts/417" + }, { "$ref": "#/texts/418" }, @@ -1483,10 +1467,18 @@ }, { "$ref": "#/texts/421" - }, - { - "$ref": "#/texts/422" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/26", + "parent": { + "$ref": "#/texts/422" + }, + "children": [ { "$ref": "#/texts/423" }, @@ -1501,10 +1493,18 @@ }, { "$ref": "#/texts/427" - }, - { - "$ref": "#/texts/428" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/27", + "parent": { + "$ref": "#/texts/428" + }, + "children": [ { "$ref": "#/texts/429" }, @@ -1522,18 +1522,7 @@ }, { "$ref": "#/texts/434" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/28", - "parent": { - "$ref": "#/texts/417" - }, - "children": [ + }, { "$ref": "#/texts/435" }, @@ -1566,7 +1555,18 @@ }, { "$ref": "#/texts/445" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/28", + "parent": { + "$ref": "#/texts/428" + }, + "children": [ { "$ref": "#/texts/446" }, @@ -1578,18 +1578,10 @@ }, { "$ref": "#/texts/449" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/29", - "parent": { - "$ref": "#/texts/450" - }, - "children": [ + }, + { + "$ref": "#/texts/450" + }, { "$ref": "#/texts/451" }, @@ -1610,6 +1602,15 @@ }, { "$ref": "#/texts/457" + }, + { + "$ref": "#/texts/458" + }, + { + "$ref": "#/texts/459" + }, + { + "$ref": "#/texts/460" } ], "content_layer": "body", @@ -1617,14 +1618,11 @@ "label": "inline" }, { - "self_ref": "#/groups/30", + "self_ref": "#/groups/29", "parent": { - "$ref": "#/texts/460" + "$ref": "#/texts/461" }, "children": [ - { - "$ref": "#/texts/461" - }, { "$ref": "#/texts/462" }, @@ -1645,16 +1643,18 @@ }, { "$ref": "#/texts/468" - }, - { - "$ref": "#/texts/469" - }, - { - "$ref": "#/texts/470" - }, - { - "$ref": "#/texts/471" - }, + } + ], + "content_layer": "body", + "name": "group", + "label": "inline" + }, + { + "self_ref": "#/groups/30", + "parent": { + "$ref": "#/texts/471" + }, + "children": [ { "$ref": "#/texts/472" }, @@ -1849,6 +1849,39 @@ }, { "$ref": "#/texts/536" + }, + { + "$ref": "#/texts/537" + }, + { + "$ref": "#/texts/538" + }, + { + "$ref": "#/texts/539" + }, + { + "$ref": "#/texts/540" + }, + { + "$ref": "#/texts/541" + }, + { + "$ref": "#/texts/542" + }, + { + "$ref": "#/texts/543" + }, + { + "$ref": "#/texts/544" + }, + { + "$ref": "#/texts/545" + }, + { + "$ref": "#/texts/546" + }, + { + "$ref": "#/texts/547" } ], "content_layer": "body", @@ -1873,22 +1906,22 @@ "$ref": "#/texts/3" }, { - "$ref": "#/texts/16" + "$ref": "#/texts/27" }, { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, { - "$ref": "#/texts/450" + "$ref": "#/texts/461" }, { - "$ref": "#/texts/458" + "$ref": "#/texts/469" }, { - "$ref": "#/texts/460" + "$ref": "#/texts/471" } ], "content_layer": "body", @@ -1906,40 +1939,114 @@ "content_layer": "body", "label": "paragraph", "prov": [], - "orig": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab", - "text": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab" + "orig": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab", + "text": "Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab" + }, + { + "self_ref": "#/texts/2", + "parent": { + "$ref": "#/texts/0" + }, + "children": [], + "content_layer": "body", + "label": "paragraph", + "prov": [], + "orig": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil", + "text": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil" + }, + { + "self_ref": "#/texts/3", + "parent": { + "$ref": "#/texts/0" + }, + "children": [ + { + "$ref": "#/groups/0" + } + ], + "content_layer": "body", + "label": "section_header", + "prov": [], + "orig": "Abstract", + "text": "Abstract", + "level": 1 + }, + { + "self_ref": "#/texts/4", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO", + "text": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO" + }, + { + "self_ref": "#/texts/5", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "2", + "text": "2", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "sub" + } + }, + { + "self_ref": "#/texts/6", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ") equivalents (CO", + "text": ") equivalents (CO" }, { - "self_ref": "#/texts/2", + "self_ref": "#/texts/7", "parent": { - "$ref": "#/texts/0" + "$ref": "#/groups/0" }, "children": [], "content_layer": "body", - "label": "paragraph", + "label": "text", "prov": [], - "orig": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil", - "text": "Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil" + "orig": "2", + "text": "2", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "sub" + } }, { - "self_ref": "#/texts/3", + "self_ref": "#/texts/8", "parent": { - "$ref": "#/texts/0" + "$ref": "#/groups/0" }, - "children": [ - { - "$ref": "#/groups/0" - } - ], + "children": [], "content_layer": "body", - "label": "section_header", + "label": "text", "prov": [], - "orig": "Abstract", - "text": "Abstract", - "level": 1 + "orig": "e) (kg energy-corrected milk (ECM))", + "text": "e) (kg energy-corrected milk (ECM))" }, { - "self_ref": "#/texts/4", + "self_ref": "#/texts/9", "parent": { "$ref": "#/groups/0" }, @@ -1947,18 +2054,18 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2)", - "text": "Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2)", + "orig": "-1", + "text": "-1", "formatting": { "bold": false, "italic": false, "underline": false, "strikethrough": false, - "script": "sub" + "script": "super" } }, { - "self_ref": "#/texts/5", + "self_ref": "#/texts/10", "parent": { "$ref": "#/groups/0" }, @@ -1966,18 +2073,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "equivalents (CO2e) (kg energy-corrected milk (ECM))-1,", - "text": "equivalents (CO2e) (kg energy-corrected milk (ECM))-1,", - "formatting": { - "bold": false, - "italic": false, - "underline": false, - "strikethrough": false, - "script": "sub" - } + "orig": ", encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation", + "text": ", encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation" }, { - "self_ref": "#/texts/6", + "self_ref": "#/texts/11", "parent": { "$ref": "#/groups/0" }, @@ -1985,8 +2085,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1.", - "text": "encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1.", + "orig": "-1", + "text": "-1", "formatting": { "bold": false, "italic": false, @@ -1996,7 +2096,7 @@ } }, { - "self_ref": "#/texts/7", + "self_ref": "#/texts/12", "parent": { "$ref": "#/groups/0" }, @@ -2004,11 +2104,11 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)", - "text": "The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)" + "orig": ". The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)", + "text": ". The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR)" }, { - "self_ref": "#/texts/8", + "self_ref": "#/texts/13", "parent": { "$ref": "#/groups/0" }, @@ -2027,7 +2127,7 @@ } }, { - "self_ref": "#/texts/9", + "self_ref": "#/texts/14", "parent": { "$ref": "#/groups/0" }, @@ -2039,7 +2139,7 @@ "text": "intake, 75, and 50% of" }, { - "self_ref": "#/texts/10", + "self_ref": "#/texts/15", "parent": { "$ref": "#/groups/0" }, @@ -2058,7 +2158,7 @@ } }, { - "self_ref": "#/texts/11", + "self_ref": "#/texts/16", "parent": { "$ref": "#/groups/0" }, @@ -2066,8 +2166,20 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1.", - "text": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1.", + "orig": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO", + "text": "TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO" + }, + { + "self_ref": "#/texts/17", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "2", + "text": "2", "formatting": { "bold": false, "italic": false, @@ -2077,7 +2189,50 @@ } }, { - "self_ref": "#/texts/12", + "self_ref": "#/texts/18", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "e (kg ECM)", + "text": "e (kg ECM)" + }, + { + "self_ref": "#/texts/19", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "-1", + "text": "-1", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "super" + } + }, + { + "self_ref": "#/texts/20", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": ". Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO", + "text": ". Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO" + }, + { + "self_ref": "#/texts/21", "parent": { "$ref": "#/groups/0" }, @@ -2085,8 +2240,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1", - "text": "Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1", + "orig": "2", + "text": "2", "formatting": { "bold": false, "italic": false, @@ -2096,7 +2251,38 @@ } }, { - "self_ref": "#/texts/13", + "self_ref": "#/texts/22", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "e (kg ECM)", + "text": "e (kg ECM)" + }, + { + "self_ref": "#/texts/23", + "parent": { + "$ref": "#/groups/0" + }, + "children": [], + "content_layer": "body", + "label": "text", + "prov": [], + "orig": "-1", + "text": "-1", + "formatting": { + "bold": false, + "italic": false, + "underline": false, + "strikethrough": false, + "script": "super" + } + }, + { + "self_ref": "#/texts/24", "parent": { "$ref": "#/groups/0" }, @@ -2108,7 +2294,7 @@ "text": "in scenarios including pastures compared to" }, { - "self_ref": "#/texts/14", + "self_ref": "#/texts/25", "parent": { "$ref": "#/groups/0" }, @@ -2127,7 +2313,7 @@ } }, { - "self_ref": "#/texts/15", + "self_ref": "#/texts/26", "parent": { "$ref": "#/groups/0" }, @@ -2139,7 +2325,7 @@ "text": "TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent." }, { - "self_ref": "#/texts/16", + "self_ref": "#/texts/27", "parent": { "$ref": "#/texts/0" }, @@ -2151,13 +2337,13 @@ "$ref": "#/groups/2" }, { - "$ref": "#/texts/29" + "$ref": "#/texts/40" }, { - "$ref": "#/texts/30" + "$ref": "#/texts/41" }, { - "$ref": "#/texts/31" + "$ref": "#/texts/42" } ], "content_layer": "body", @@ -2168,7 +2354,7 @@ "level": 1 }, { - "self_ref": "#/texts/17", + "self_ref": "#/texts/28", "parent": { "$ref": "#/groups/1" }, @@ -2180,7 +2366,7 @@ "text": "Greenhouse gas (GHG) emissions from livestock activities represent 10–12% of global emissions [1], ranging from 5.5–7.5 Gt CO" }, { - "self_ref": "#/texts/18", + "self_ref": "#/texts/29", "parent": { "$ref": "#/groups/1" }, @@ -2199,7 +2385,7 @@ } }, { - "self_ref": "#/texts/19", + "self_ref": "#/texts/30", "parent": { "$ref": "#/groups/1" }, @@ -2211,7 +2397,7 @@ "text": "equivalents (CO" }, { - "self_ref": "#/texts/20", + "self_ref": "#/texts/31", "parent": { "$ref": "#/groups/1" }, @@ -2230,7 +2416,7 @@ } }, { - "self_ref": "#/texts/21", + "self_ref": "#/texts/32", "parent": { "$ref": "#/groups/1" }, @@ -2242,7 +2428,7 @@ "text": "e) yr" }, { - "self_ref": "#/texts/22", + "self_ref": "#/texts/33", "parent": { "$ref": "#/groups/1" }, @@ -2261,7 +2447,7 @@ } }, { - "self_ref": "#/texts/23", + "self_ref": "#/texts/34", "parent": { "$ref": "#/groups/1" }, @@ -2273,7 +2459,7 @@ "text": ", with almost 30% coming from dairy cattle production systems [2]. However, the livestock sector supply between 13 and 17% of calories and between 28 and 33% of human edible protein consumption globally [3]. Additionally, livestock produce more human-edible protein per unit area than crops when land is unsuitable for food crop production [4]." }, { - "self_ref": "#/texts/24", + "self_ref": "#/texts/35", "parent": { "$ref": "#/groups/2" }, @@ -2285,7 +2471,7 @@ "text": "Considering the key role of livestock systems in global food security, several technical and management interventions have been investigated to mitigate methane (CH" }, { - "self_ref": "#/texts/25", + "self_ref": "#/texts/36", "parent": { "$ref": "#/groups/2" }, @@ -2304,7 +2490,7 @@ } }, { - "self_ref": "#/texts/26", + "self_ref": "#/texts/37", "parent": { "$ref": "#/groups/2" }, @@ -2316,7 +2502,7 @@ "text": ") emissions from enteric fermentation [5], animal management [6] and manure management [7]. CH" }, { - "self_ref": "#/texts/27", + "self_ref": "#/texts/38", "parent": { "$ref": "#/groups/2" }, @@ -2335,7 +2521,7 @@ } }, { - "self_ref": "#/texts/28", + "self_ref": "#/texts/39", "parent": { "$ref": "#/groups/2" }, @@ -2347,9 +2533,9 @@ "text": "emissions from enteric fermentation represents around 34% of total emissions from livestock sector, which is the largest source [2]. Increasing proportions of concentrate and digestibility of forages in the diet have been proposed as mitigation strategies [1,5]. In contrast, some life cycle assessment (LCA) studies of dairy systems in temperate regions [8–11] have identified that increasing concentrate proportion may increase carbon (C) footprint due to greater resource use and pollutants from the production of feed compared to forage. Thus, increasing pasture proportion on dairy cattle systems may be an alternative management to mitigate the C footprint." }, { - "self_ref": "#/texts/29", + "self_ref": "#/texts/40", "parent": { - "$ref": "#/texts/16" + "$ref": "#/texts/27" }, "children": [], "content_layer": "body", @@ -2359,9 +2545,9 @@ "text": "In subtropical climate zones, cows may graze tropical pastures rather than temperate pastures during the warm season [12]. Some important dairy production areas, such as southern Brazil, central to northern Argentina, Uruguay, South Africa, New Zealand and Australia, are located in these climate zones, having more than 900 million ha in native, permanent or temporary pastures, producing almost 20% of global milk production [13]. However, due to a considerable inter-annual variation in pasture growth rates [14,15], the interest in mixed systems, using total mixed ration (TMR) + pasture has been increasing [16]. Nevertheless, to our best knowledge, studies conducted to evaluate milk production response in dairy cow diets receiving TMR and pastures have only been conducted in temperate pastures and not in tropical pastures (e.g. [17–19])." }, { - "self_ref": "#/texts/30", + "self_ref": "#/texts/41", "parent": { - "$ref": "#/texts/16" + "$ref": "#/texts/27" }, "children": [], "content_layer": "body", @@ -2371,9 +2557,9 @@ "text": "It has been shown that dairy cows receiving TMR-based diets may not decrease milk production when supplemented with temperate pastures in a vegetative growth stage [18]. On the other hand, tropical pastures have lower organic matter digestibility and cows experience reduced dry matter (DM) intake and milk yield compared to temperate pastures [20,21]. A lower milk yield increases the C footprint intensity [22], offsetting an expected advantage through lower GHG emissions from crop and reduced DM intake." }, { - "self_ref": "#/texts/31", + "self_ref": "#/texts/42", "parent": { - "$ref": "#/texts/16" + "$ref": "#/texts/27" }, "children": [], "content_layer": "body", @@ -2383,7 +2569,7 @@ "text": "The aim of this work was to quantify the C footprint and land use of dairy systems using cows with a medium milk production potential in a subtropical region. The effect of replacing total mixed ration (TMR) with pastures during lactation periods was evaluated." }, { - "self_ref": "#/texts/32", + "self_ref": "#/texts/43", "parent": { "$ref": "#/texts/0" }, @@ -2392,34 +2578,34 @@ "$ref": "#/groups/3" }, { - "$ref": "#/texts/36" + "$ref": "#/texts/47" }, { - "$ref": "#/texts/39" + "$ref": "#/texts/50" }, { - "$ref": "#/texts/43" + "$ref": "#/texts/54" }, { - "$ref": "#/texts/62" + "$ref": "#/texts/73" }, { - "$ref": "#/texts/82" + "$ref": "#/texts/93" }, { - "$ref": "#/texts/133" + "$ref": "#/texts/144" }, { - "$ref": "#/texts/149" + "$ref": "#/texts/160" }, { - "$ref": "#/texts/197" + "$ref": "#/texts/208" }, { - "$ref": "#/texts/231" + "$ref": "#/texts/242" }, { - "$ref": "#/texts/243" + "$ref": "#/texts/254" } ], "content_layer": "body", @@ -2430,7 +2616,7 @@ "level": 1 }, { - "self_ref": "#/texts/33", + "self_ref": "#/texts/44", "parent": { "$ref": "#/groups/3" }, @@ -2442,7 +2628,7 @@ "text": "An LCA was developed according to the ISO standards [23,24] and Food and Agriculture Organization of the United Nations (FAO) Livestock Environmental Assessment Protocol guidelines [25]. All procedures were approved by the ‘Comissão de Ética no Uso de Animais’ (CEUA/UDESC) on September 15, 2016—Approval number 4373090816 -" }, { - "self_ref": "#/texts/34", + "self_ref": "#/texts/45", "parent": { "$ref": "#/groups/3" }, @@ -2455,7 +2641,7 @@ "hyperlink": "https://www.udesc.br/cav/ceua" }, { - "self_ref": "#/texts/35", + "self_ref": "#/texts/46", "parent": { "$ref": "#/groups/3" }, @@ -2467,13 +2653,13 @@ "text": "." }, { - "self_ref": "#/texts/36", + "self_ref": "#/texts/47", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/37" + "$ref": "#/texts/48" }, { "$ref": "#/pictures/0" @@ -2487,9 +2673,9 @@ "level": 2 }, { - "self_ref": "#/texts/37", + "self_ref": "#/texts/48", "parent": { - "$ref": "#/texts/36" + "$ref": "#/texts/47" }, "children": [], "content_layer": "body", @@ -2499,7 +2685,7 @@ "text": "The goal of the study was to assess the C footprint of annual tropical and temperate pastures in lactating dairy cow diets. The production system was divided into four main processes: (i) animal husbandry, (ii) manure management and urine and dung deposited by grazing animals, (iii) production of feed ingredients and (iv) farm management (Fig 1). The study boundary included all processes up to the animal farm gate (cradle to gate), including secondary sources such as GHG emissions during the production of fuel, electricity, machinery, manufacturing of fertilizer, pesticides, seeds and plastic used in silage production. Fuel combustion and machinery (manufacture and repairs) for manure handling and electricity for milking and confinement were accounted as emissions from farm management. Emissions post milk production were assumed to be similar for all scenarios, therefore, activities including milk processing, distribution, retail or consumption were outside of the system boundary." }, { - "self_ref": "#/texts/38", + "self_ref": "#/texts/49", "parent": { "$ref": "#/body" }, @@ -2511,16 +2697,16 @@ "text": "Fig 1 Overview of the milk production system boundary considered in the study." }, { - "self_ref": "#/texts/39", + "self_ref": "#/texts/50", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/40" + "$ref": "#/texts/51" }, { - "$ref": "#/texts/41" + "$ref": "#/texts/52" }, { "$ref": "#/tables/0" @@ -2534,9 +2720,9 @@ "level": 2 }, { - "self_ref": "#/texts/40", + "self_ref": "#/texts/51", "parent": { - "$ref": "#/texts/39" + "$ref": "#/texts/50" }, "children": [], "content_layer": "body", @@ -2546,9 +2732,9 @@ "text": "The functional unit was one kilogram of energy-corrected milk (ECM) at the farm gate. All processes in the system were calculated based on one kilogram ECM. The ECM was calculated by multiplying milk production by the ratio of the energy content of the milk to the energy content of standard milk with 4% fat and 3.3% true protein according to NRC [20] as follows:" }, { - "self_ref": "#/texts/41", + "self_ref": "#/texts/52", "parent": { - "$ref": "#/texts/39" + "$ref": "#/texts/50" }, "children": [], "content_layer": "body", @@ -2558,7 +2744,7 @@ "text": "ECM = Milk production × (0.0929 × fat% + 0.0588× true protein% + 0.192) / (0.0929 × (4%) + 0.0588 × (3.3%) + 0.192), where fat% and protein% are fat and protein percentages in milk, respectively. The average milk production and composition were recorded from the University of Santa Catarina State (Brazil) herd, considering 165 lactations between 2009 and 2018. The herd is predominantly Holstein × Jersey cows, with key characteristics described in Table 1." }, { - "self_ref": "#/texts/42", + "self_ref": "#/texts/53", "parent": { "$ref": "#/body" }, @@ -2570,9 +2756,9 @@ "text": "Table 1 Descriptive characteristics of the herd." }, { - "self_ref": "#/texts/43", + "self_ref": "#/texts/54", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { @@ -2590,7 +2776,7 @@ "level": 2 }, { - "self_ref": "#/texts/44", + "self_ref": "#/texts/55", "parent": { "$ref": "#/groups/4" }, @@ -2602,7 +2788,7 @@ "text": "The individual feed requirements, as well as the milk production responses based on feed strategies were based on data recorded from the herd described above and two experiments performed using lactating cows from the same herd. Due to the variation on herbage production throughout the year, feed requirements were estimated taking into consideration that livestock systems have a calving period in April, which represents the beginning of fall season in the southern Hemisphere. The experiments have shown a 10% reduction in ECM production in dairy cows that received both 75 and 50% of" }, { - "self_ref": "#/texts/45", + "self_ref": "#/texts/56", "parent": { "$ref": "#/groups/4" }, @@ -2621,7 +2807,7 @@ } }, { - "self_ref": "#/texts/46", + "self_ref": "#/texts/57", "parent": { "$ref": "#/groups/4" }, @@ -2633,7 +2819,7 @@ "text": "TMR intake with access to grazing a tropical pasture (pearl-millet," }, { - "self_ref": "#/texts/47", + "self_ref": "#/texts/58", "parent": { "$ref": "#/groups/4" }, @@ -2652,7 +2838,7 @@ } }, { - "self_ref": "#/texts/48", + "self_ref": "#/texts/59", "parent": { "$ref": "#/groups/4" }, @@ -2664,7 +2850,7 @@ "text": "‘Campeiro’) compared to cows receiving" }, { - "self_ref": "#/texts/49", + "self_ref": "#/texts/60", "parent": { "$ref": "#/groups/4" }, @@ -2683,7 +2869,7 @@ } }, { - "self_ref": "#/texts/50", + "self_ref": "#/texts/61", "parent": { "$ref": "#/groups/4" }, @@ -2695,7 +2881,7 @@ "text": "TMR intake. Cows grazing on a temperate pasture (ryegrass," }, { - "self_ref": "#/texts/51", + "self_ref": "#/texts/62", "parent": { "$ref": "#/groups/4" }, @@ -2714,7 +2900,7 @@ } }, { - "self_ref": "#/texts/52", + "self_ref": "#/texts/63", "parent": { "$ref": "#/groups/4" }, @@ -2726,7 +2912,7 @@ "text": "‘Maximus’) did not need changes to ECM production compared to the" }, { - "self_ref": "#/texts/53", + "self_ref": "#/texts/64", "parent": { "$ref": "#/groups/4" }, @@ -2745,7 +2931,7 @@ } }, { - "self_ref": "#/texts/54", + "self_ref": "#/texts/65", "parent": { "$ref": "#/groups/4" }, @@ -2757,7 +2943,7 @@ "text": "TMR intake group." }, { - "self_ref": "#/texts/55", + "self_ref": "#/texts/66", "parent": { "$ref": "#/groups/5" }, @@ -2769,7 +2955,7 @@ "text": "Using experimental data, three scenarios were evaluated during the lactation period:" }, { - "self_ref": "#/texts/56", + "self_ref": "#/texts/67", "parent": { "$ref": "#/groups/5" }, @@ -2788,7 +2974,7 @@ } }, { - "self_ref": "#/texts/57", + "self_ref": "#/texts/68", "parent": { "$ref": "#/groups/5" }, @@ -2800,7 +2986,7 @@ "text": "TMR intake, and 75, and 50% of" }, { - "self_ref": "#/texts/58", + "self_ref": "#/texts/69", "parent": { "$ref": "#/groups/5" }, @@ -2819,7 +3005,7 @@ } }, { - "self_ref": "#/texts/59", + "self_ref": "#/texts/70", "parent": { "$ref": "#/groups/5" }, @@ -2831,7 +3017,7 @@ "text": "TMR intake with access to grazing either an annual tropical or temperate pasture as a function of month ([26], Civiero et al.," }, { - "self_ref": "#/texts/60", + "self_ref": "#/texts/71", "parent": { "$ref": "#/groups/5" }, @@ -2850,7 +3036,7 @@ } }, { - "self_ref": "#/texts/61", + "self_ref": "#/texts/72", "parent": { "$ref": "#/groups/5" }, @@ -2862,9 +3048,9 @@ "text": "). From April to October (210 days) cows accessed an annual temperate pasture (ryegrass), and from November to beginning of February (95 days) cows grazed an annual tropical pasture (pearl-millet). The average annual reduction in ECM production in dairy cows with access to pastures is 3%. This value was assumed during an entire lactation period." }, { - "self_ref": "#/texts/62", + "self_ref": "#/texts/73", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { @@ -2879,7 +3065,7 @@ "level": 2 }, { - "self_ref": "#/texts/63", + "self_ref": "#/texts/74", "parent": { "$ref": "#/groups/6" }, @@ -2891,7 +3077,7 @@ "text": "The CO" }, { - "self_ref": "#/texts/64", + "self_ref": "#/texts/75", "parent": { "$ref": "#/groups/6" }, @@ -2910,7 +3096,7 @@ } }, { - "self_ref": "#/texts/65", + "self_ref": "#/texts/76", "parent": { "$ref": "#/groups/6" }, @@ -2922,7 +3108,7 @@ "text": "e emissions were calculated by multiplying the emissions of CO" }, { - "self_ref": "#/texts/66", + "self_ref": "#/texts/77", "parent": { "$ref": "#/groups/6" }, @@ -2941,7 +3127,7 @@ } }, { - "self_ref": "#/texts/67", + "self_ref": "#/texts/78", "parent": { "$ref": "#/groups/6" }, @@ -2953,7 +3139,7 @@ "text": ", CH" }, { - "self_ref": "#/texts/68", + "self_ref": "#/texts/79", "parent": { "$ref": "#/groups/6" }, @@ -2972,7 +3158,7 @@ } }, { - "self_ref": "#/texts/69", + "self_ref": "#/texts/80", "parent": { "$ref": "#/groups/6" }, @@ -2984,7 +3170,7 @@ "text": "and N" }, { - "self_ref": "#/texts/70", + "self_ref": "#/texts/81", "parent": { "$ref": "#/groups/6" }, @@ -3003,7 +3189,7 @@ } }, { - "self_ref": "#/texts/71", + "self_ref": "#/texts/82", "parent": { "$ref": "#/groups/6" }, @@ -3015,7 +3201,7 @@ "text": "O by their 100-year global warming potential (GWP" }, { - "self_ref": "#/texts/72", + "self_ref": "#/texts/83", "parent": { "$ref": "#/groups/6" }, @@ -3034,7 +3220,7 @@ } }, { - "self_ref": "#/texts/73", + "self_ref": "#/texts/84", "parent": { "$ref": "#/groups/6" }, @@ -3046,7 +3232,7 @@ "text": "), based on IPCC assessment report 5 (AR5; [27]). The values of GWP" }, { - "self_ref": "#/texts/74", + "self_ref": "#/texts/85", "parent": { "$ref": "#/groups/6" }, @@ -3065,7 +3251,7 @@ } }, { - "self_ref": "#/texts/75", + "self_ref": "#/texts/86", "parent": { "$ref": "#/groups/6" }, @@ -3077,7 +3263,7 @@ "text": "are 1, 28 and 265 for CO" }, { - "self_ref": "#/texts/76", + "self_ref": "#/texts/87", "parent": { "$ref": "#/groups/6" }, @@ -3096,7 +3282,7 @@ } }, { - "self_ref": "#/texts/77", + "self_ref": "#/texts/88", "parent": { "$ref": "#/groups/6" }, @@ -3108,7 +3294,7 @@ "text": ", CH" }, { - "self_ref": "#/texts/78", + "self_ref": "#/texts/89", "parent": { "$ref": "#/groups/6" }, @@ -3127,7 +3313,7 @@ } }, { - "self_ref": "#/texts/79", + "self_ref": "#/texts/90", "parent": { "$ref": "#/groups/6" }, @@ -3139,7 +3325,7 @@ "text": "and N" }, { - "self_ref": "#/texts/80", + "self_ref": "#/texts/91", "parent": { "$ref": "#/groups/6" }, @@ -3158,7 +3344,7 @@ } }, { - "self_ref": "#/texts/81", + "self_ref": "#/texts/92", "parent": { "$ref": "#/groups/6" }, @@ -3170,16 +3356,16 @@ "text": "O, respectively." }, { - "self_ref": "#/texts/82", + "self_ref": "#/texts/93", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/83" + "$ref": "#/texts/94" }, { - "$ref": "#/texts/92" + "$ref": "#/texts/103" } ], "content_layer": "body", @@ -3190,9 +3376,9 @@ "level": 2 }, { - "self_ref": "#/texts/83", + "self_ref": "#/texts/94", "parent": { - "$ref": "#/texts/82" + "$ref": "#/texts/93" }, "children": [ { @@ -3210,7 +3396,7 @@ "level": 3 }, { - "self_ref": "#/texts/84", + "self_ref": "#/texts/95", "parent": { "$ref": "#/groups/7" }, @@ -3222,7 +3408,7 @@ "text": "The DM intake of each ingredient throughout the entire life of animals during lactation periods was calculated for each scenario: cows receiving only TMR, cows receiving 75% of TMR with annual pastures and cows receiving 50% of TMR with annual pastures (Table 2). In each of other phases of life (calf, heifer, dry cow), animals received the same diet, including a perennial tropical pasture (kikuyu grass," }, { - "self_ref": "#/texts/85", + "self_ref": "#/texts/96", "parent": { "$ref": "#/groups/7" }, @@ -3241,7 +3427,7 @@ } }, { - "self_ref": "#/texts/86", + "self_ref": "#/texts/97", "parent": { "$ref": "#/groups/7" }, @@ -3253,7 +3439,7 @@ "text": "). The DM intake of calves, heifers and dry cows was calculated assuming 2.8, 2.5 and 1.9% body weight, respectively [20]. In each case, the actual DM intake of concentrate and corn silage was recorded, and pasture DM intake was estimated by the difference between daily expected DM intake and actual DM intake of concentrate and corn silage. For lactating heifers and cows, TMR was formulated to meet the net energy for lactation (NE" }, { - "self_ref": "#/texts/87", + "self_ref": "#/texts/98", "parent": { "$ref": "#/groups/7" }, @@ -3272,7 +3458,7 @@ } }, { - "self_ref": "#/texts/88", + "self_ref": "#/texts/99", "parent": { "$ref": "#/groups/7" }, @@ -3284,7 +3470,7 @@ "text": ") and metabolizable protein (MP) requirements of experimental animals, according to [28]. The INRA system was used because it is possible to estimate pasture DM intake taking into account the TMR intake, pasture management and the time of access to pasture using the GrazeIn model [29], which was integrated in the software INRAtion 4.07 (" }, { - "self_ref": "#/texts/89", + "self_ref": "#/texts/100", "parent": { "$ref": "#/groups/7" }, @@ -3297,7 +3483,7 @@ "hyperlink": "https://www.inration.educagri.fr/fr/forum.php" }, { - "self_ref": "#/texts/90", + "self_ref": "#/texts/101", "parent": { "$ref": "#/groups/7" }, @@ -3309,7 +3495,7 @@ "text": "). The nutrient intake was calculated as a product of TMR and pasture intake and the nutrient contents of TMR and pasture, respectively, which were determined in feed samples collected throughout the experiments." }, { - "self_ref": "#/texts/91", + "self_ref": "#/texts/102", "parent": { "$ref": "#/body" }, @@ -3321,9 +3507,9 @@ "text": "Table 2 Dairy cows’ diets in different scenariosa." }, { - "self_ref": "#/texts/92", + "self_ref": "#/texts/103", "parent": { - "$ref": "#/texts/82" + "$ref": "#/texts/93" }, "children": [ { @@ -3347,7 +3533,7 @@ "level": 3 }, { - "self_ref": "#/texts/93", + "self_ref": "#/texts/104", "parent": { "$ref": "#/groups/8" }, @@ -3359,7 +3545,7 @@ "text": "GHG emission factors used for off- and on-farm feed production were based on literature values, and are presented in Table 3. The emission factor used for corn grain is the average of emission factors observed in different levels of synthetic N fertilization [30]. The emission factor used for soybean is based on Brazilian soybean production [31]. The emissions used for corn silage, including feed processing (cutting, crushing and mixing), and annual or perennial grass productions were 3300 and 1500 kg CO" }, { - "self_ref": "#/texts/94", + "self_ref": "#/texts/105", "parent": { "$ref": "#/groups/8" }, @@ -3378,7 +3564,7 @@ } }, { - "self_ref": "#/texts/95", + "self_ref": "#/texts/106", "parent": { "$ref": "#/groups/8" }, @@ -3390,7 +3576,7 @@ "text": "e ha" }, { - "self_ref": "#/texts/96", + "self_ref": "#/texts/107", "parent": { "$ref": "#/groups/8" }, @@ -3409,7 +3595,7 @@ } }, { - "self_ref": "#/texts/97", + "self_ref": "#/texts/108", "parent": { "$ref": "#/groups/8" }, @@ -3421,7 +3607,7 @@ "text": ", respectively [32]. The DM production (kg ha" }, { - "self_ref": "#/texts/98", + "self_ref": "#/texts/109", "parent": { "$ref": "#/groups/8" }, @@ -3440,7 +3626,7 @@ } }, { - "self_ref": "#/texts/99", + "self_ref": "#/texts/110", "parent": { "$ref": "#/groups/8" }, @@ -3452,7 +3638,7 @@ "text": ") of corn silage and pastures were based on regional and locally recorded data [33–36], assuming that animals are able to consume 70% of pastures during grazing." }, { - "self_ref": "#/texts/100", + "self_ref": "#/texts/111", "parent": { "$ref": "#/body" }, @@ -3464,7 +3650,7 @@ "text": "Table 3 GHG emission factors for Off- and On-farm feed production." }, { - "self_ref": "#/texts/101", + "self_ref": "#/texts/112", "parent": { "$ref": "#/groups/9" }, @@ -3476,7 +3662,7 @@ "text": "Emissions from on-farm feed production (corn silage and pasture) were estimated using primary and secondary sources based on the actual amount of each input (Table 4). Primary sources were direct and indirect N" }, { - "self_ref": "#/texts/102", + "self_ref": "#/texts/113", "parent": { "$ref": "#/groups/9" }, @@ -3495,7 +3681,7 @@ } }, { - "self_ref": "#/texts/103", + "self_ref": "#/texts/114", "parent": { "$ref": "#/groups/9" }, @@ -3507,7 +3693,7 @@ "text": "O-N emissions from organic and synthetic fertilizers and crop/pasture residues, CO" }, { - "self_ref": "#/texts/104", + "self_ref": "#/texts/115", "parent": { "$ref": "#/groups/9" }, @@ -3526,7 +3712,7 @@ } }, { - "self_ref": "#/texts/105", + "self_ref": "#/texts/116", "parent": { "$ref": "#/groups/9" }, @@ -3538,7 +3724,7 @@ "text": "-C emissions from lime and urea applications, as well as fuel combustion. The direct N" }, { - "self_ref": "#/texts/106", + "self_ref": "#/texts/117", "parent": { "$ref": "#/groups/9" }, @@ -3557,7 +3743,7 @@ } }, { - "self_ref": "#/texts/107", + "self_ref": "#/texts/118", "parent": { "$ref": "#/groups/9" }, @@ -3569,7 +3755,7 @@ "text": "O-N emission factor (kg (kg N input)" }, { - "self_ref": "#/texts/108", + "self_ref": "#/texts/119", "parent": { "$ref": "#/groups/9" }, @@ -3588,7 +3774,7 @@ } }, { - "self_ref": "#/texts/109", + "self_ref": "#/texts/120", "parent": { "$ref": "#/groups/9" }, @@ -3600,7 +3786,7 @@ "text": ") is based on a local study performed previously [37]. For indirect N" }, { - "self_ref": "#/texts/110", + "self_ref": "#/texts/121", "parent": { "$ref": "#/groups/9" }, @@ -3619,7 +3805,7 @@ } }, { - "self_ref": "#/texts/111", + "self_ref": "#/texts/122", "parent": { "$ref": "#/groups/9" }, @@ -3631,7 +3817,7 @@ "text": "O-N emissions (kg N" }, { - "self_ref": "#/texts/112", + "self_ref": "#/texts/123", "parent": { "$ref": "#/groups/9" }, @@ -3650,7 +3836,7 @@ } }, { - "self_ref": "#/texts/113", + "self_ref": "#/texts/124", "parent": { "$ref": "#/groups/9" }, @@ -3662,7 +3848,7 @@ "text": "O-N (kg NH" }, { - "self_ref": "#/texts/114", + "self_ref": "#/texts/125", "parent": { "$ref": "#/groups/9" }, @@ -3681,7 +3867,7 @@ } }, { - "self_ref": "#/texts/115", + "self_ref": "#/texts/126", "parent": { "$ref": "#/groups/9" }, @@ -3693,7 +3879,7 @@ "text": "-N + NO" }, { - "self_ref": "#/texts/116", + "self_ref": "#/texts/127", "parent": { "$ref": "#/groups/9" }, @@ -3712,7 +3898,7 @@ } }, { - "self_ref": "#/texts/117", + "self_ref": "#/texts/128", "parent": { "$ref": "#/groups/9" }, @@ -3724,7 +3910,7 @@ "text": ")" }, { - "self_ref": "#/texts/118", + "self_ref": "#/texts/129", "parent": { "$ref": "#/groups/9" }, @@ -3743,7 +3929,7 @@ } }, { - "self_ref": "#/texts/119", + "self_ref": "#/texts/130", "parent": { "$ref": "#/groups/9" }, @@ -3755,7 +3941,7 @@ "text": "), as well as CO" }, { - "self_ref": "#/texts/120", + "self_ref": "#/texts/131", "parent": { "$ref": "#/groups/9" }, @@ -3774,7 +3960,7 @@ } }, { - "self_ref": "#/texts/121", + "self_ref": "#/texts/132", "parent": { "$ref": "#/groups/9" }, @@ -3786,7 +3972,7 @@ "text": "-C emissions from lime + urea, default values proposed by IPCC [38] were used. For perennial pastures, a C sequestration of 0.57 t ha" }, { - "self_ref": "#/texts/122", + "self_ref": "#/texts/133", "parent": { "$ref": "#/groups/9" }, @@ -3805,7 +3991,7 @@ } }, { - "self_ref": "#/texts/123", + "self_ref": "#/texts/134", "parent": { "$ref": "#/groups/9" }, @@ -3817,7 +4003,7 @@ "text": "was used based on a 9-year study conducted in southern Brazil [39]. Due to the use of conventional tillage, no C sequestration was considered for annual pastures. The amount of fuel required was 8.9 (no-tillage) and 14.3 L ha" }, { - "self_ref": "#/texts/124", + "self_ref": "#/texts/135", "parent": { "$ref": "#/groups/9" }, @@ -3836,7 +4022,7 @@ } }, { - "self_ref": "#/texts/125", + "self_ref": "#/texts/136", "parent": { "$ref": "#/groups/9" }, @@ -3848,7 +4034,7 @@ "text": "(disking) for annual tropical and temperate pastures, respectively [40]. The CO" }, { - "self_ref": "#/texts/126", + "self_ref": "#/texts/137", "parent": { "$ref": "#/groups/9" }, @@ -3867,7 +4053,7 @@ } }, { - "self_ref": "#/texts/127", + "self_ref": "#/texts/138", "parent": { "$ref": "#/groups/9" }, @@ -3879,7 +4065,7 @@ "text": "from fuel combustion was 2.7 kg CO" }, { - "self_ref": "#/texts/128", + "self_ref": "#/texts/139", "parent": { "$ref": "#/groups/9" }, @@ -3898,7 +4084,7 @@ } }, { - "self_ref": "#/texts/129", + "self_ref": "#/texts/140", "parent": { "$ref": "#/groups/9" }, @@ -3910,7 +4096,7 @@ "text": "L" }, { - "self_ref": "#/texts/130", + "self_ref": "#/texts/141", "parent": { "$ref": "#/groups/9" }, @@ -3929,7 +4115,7 @@ } }, { - "self_ref": "#/texts/131", + "self_ref": "#/texts/142", "parent": { "$ref": "#/groups/9" }, @@ -3941,7 +4127,7 @@ "text": "[41]. Secondary sources of emissions during the production of fuel, machinery, fertilizer, pesticides, seeds and plastic for ensilage were estimated using emission factors described by Rotz et al. [42]." }, { - "self_ref": "#/texts/132", + "self_ref": "#/texts/143", "parent": { "$ref": "#/body" }, @@ -3953,9 +4139,9 @@ "text": "Table 4 GHG emissions from On-farm feed production." }, { - "self_ref": "#/texts/133", + "self_ref": "#/texts/144", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { @@ -3970,7 +4156,7 @@ "level": 2 }, { - "self_ref": "#/texts/134", + "self_ref": "#/texts/145", "parent": { "$ref": "#/groups/10" }, @@ -3982,7 +4168,7 @@ "text": "The CH" }, { - "self_ref": "#/texts/135", + "self_ref": "#/texts/146", "parent": { "$ref": "#/groups/10" }, @@ -4001,7 +4187,7 @@ } }, { - "self_ref": "#/texts/136", + "self_ref": "#/texts/147", "parent": { "$ref": "#/groups/10" }, @@ -4013,7 +4199,7 @@ "text": "emissions from enteric fermentation intensity (g (kg ECM)" }, { - "self_ref": "#/texts/137", + "self_ref": "#/texts/148", "parent": { "$ref": "#/groups/10" }, @@ -4032,7 +4218,7 @@ } }, { - "self_ref": "#/texts/138", + "self_ref": "#/texts/149", "parent": { "$ref": "#/groups/10" }, @@ -4044,7 +4230,7 @@ "text": ") was a function of estimated CH" }, { - "self_ref": "#/texts/139", + "self_ref": "#/texts/150", "parent": { "$ref": "#/groups/10" }, @@ -4063,7 +4249,7 @@ } }, { - "self_ref": "#/texts/140", + "self_ref": "#/texts/151", "parent": { "$ref": "#/groups/10" }, @@ -4075,7 +4261,7 @@ "text": "yield (g (kg DM intake)" }, { - "self_ref": "#/texts/141", + "self_ref": "#/texts/152", "parent": { "$ref": "#/groups/10" }, @@ -4094,7 +4280,7 @@ } }, { - "self_ref": "#/texts/142", + "self_ref": "#/texts/153", "parent": { "$ref": "#/groups/10" }, @@ -4106,7 +4292,7 @@ "text": "), actual DM intake and ECM. The enteric CH" }, { - "self_ref": "#/texts/143", + "self_ref": "#/texts/154", "parent": { "$ref": "#/groups/10" }, @@ -4125,7 +4311,7 @@ } }, { - "self_ref": "#/texts/144", + "self_ref": "#/texts/155", "parent": { "$ref": "#/groups/10" }, @@ -4137,7 +4323,7 @@ "text": "yield was estimated as a function of neutral detergent fiber (NDF) concentration on total DM intake, as proposed by Niu et al. [43], where: CH" }, { - "self_ref": "#/texts/145", + "self_ref": "#/texts/156", "parent": { "$ref": "#/groups/10" }, @@ -4156,7 +4342,7 @@ } }, { - "self_ref": "#/texts/146", + "self_ref": "#/texts/157", "parent": { "$ref": "#/groups/10" }, @@ -4168,7 +4354,7 @@ "text": "yield (g (kg DM intake)" }, { - "self_ref": "#/texts/147", + "self_ref": "#/texts/158", "parent": { "$ref": "#/groups/10" }, @@ -4187,7 +4373,7 @@ } }, { - "self_ref": "#/texts/148", + "self_ref": "#/texts/159", "parent": { "$ref": "#/groups/10" }, @@ -4199,16 +4385,16 @@ "text": ") = 13.8 + 0.185 × NDF (% DM intake)." }, { - "self_ref": "#/texts/149", + "self_ref": "#/texts/160", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { "$ref": "#/groups/11" }, { - "$ref": "#/texts/173" + "$ref": "#/texts/184" }, { "$ref": "#/groups/12" @@ -4222,7 +4408,7 @@ "level": 2 }, { - "self_ref": "#/texts/150", + "self_ref": "#/texts/161", "parent": { "$ref": "#/groups/11" }, @@ -4234,7 +4420,7 @@ "text": "The CH" }, { - "self_ref": "#/texts/151", + "self_ref": "#/texts/162", "parent": { "$ref": "#/groups/11" }, @@ -4253,7 +4439,7 @@ } }, { - "self_ref": "#/texts/152", + "self_ref": "#/texts/163", "parent": { "$ref": "#/groups/11" }, @@ -4265,7 +4451,7 @@ "text": "emission from manure (kg (kg ECM)" }, { - "self_ref": "#/texts/153", + "self_ref": "#/texts/164", "parent": { "$ref": "#/groups/11" }, @@ -4284,7 +4470,7 @@ } }, { - "self_ref": "#/texts/154", + "self_ref": "#/texts/165", "parent": { "$ref": "#/groups/11" }, @@ -4296,7 +4482,7 @@ "text": ") was a function of daily CH" }, { - "self_ref": "#/texts/155", + "self_ref": "#/texts/166", "parent": { "$ref": "#/groups/11" }, @@ -4315,7 +4501,7 @@ } }, { - "self_ref": "#/texts/156", + "self_ref": "#/texts/167", "parent": { "$ref": "#/groups/11" }, @@ -4327,7 +4513,7 @@ "text": "emission from manure (kg cow" }, { - "self_ref": "#/texts/157", + "self_ref": "#/texts/168", "parent": { "$ref": "#/groups/11" }, @@ -4346,7 +4532,7 @@ } }, { - "self_ref": "#/texts/158", + "self_ref": "#/texts/169", "parent": { "$ref": "#/groups/11" }, @@ -4358,7 +4544,7 @@ "text": ") and daily ECM (kg cow" }, { - "self_ref": "#/texts/159", + "self_ref": "#/texts/170", "parent": { "$ref": "#/groups/11" }, @@ -4377,7 +4563,7 @@ } }, { - "self_ref": "#/texts/160", + "self_ref": "#/texts/171", "parent": { "$ref": "#/groups/11" }, @@ -4389,7 +4575,7 @@ "text": "). The daily CH" }, { - "self_ref": "#/texts/161", + "self_ref": "#/texts/172", "parent": { "$ref": "#/groups/11" }, @@ -4408,7 +4594,7 @@ } }, { - "self_ref": "#/texts/162", + "self_ref": "#/texts/173", "parent": { "$ref": "#/groups/11" }, @@ -4420,7 +4606,7 @@ "text": "emission from manure was estimated according to IPCC [38], which considered daily volatile solid (VS) excreted (kg DM cow" }, { - "self_ref": "#/texts/163", + "self_ref": "#/texts/174", "parent": { "$ref": "#/groups/11" }, @@ -4439,7 +4625,7 @@ } }, { - "self_ref": "#/texts/164", + "self_ref": "#/texts/175", "parent": { "$ref": "#/groups/11" }, @@ -4451,7 +4637,7 @@ "text": ") in manure. The daily VS was estimated as proposed by Eugène et al. [44] as: VS = NDOMI + (UE × GE) × (OM/18.45), where: VS = volatile solid excretion on an organic matter (OM) basis (kg day" }, { - "self_ref": "#/texts/165", + "self_ref": "#/texts/176", "parent": { "$ref": "#/groups/11" }, @@ -4470,7 +4656,7 @@ } }, { - "self_ref": "#/texts/166", + "self_ref": "#/texts/177", "parent": { "$ref": "#/groups/11" }, @@ -4482,7 +4668,7 @@ "text": "), NDOMI = non-digestible OM intake (kg day" }, { - "self_ref": "#/texts/167", + "self_ref": "#/texts/178", "parent": { "$ref": "#/groups/11" }, @@ -4501,7 +4687,7 @@ } }, { - "self_ref": "#/texts/168", + "self_ref": "#/texts/179", "parent": { "$ref": "#/groups/11" }, @@ -4513,7 +4699,7 @@ "text": "): (1- OM digestibility) × OM intake, UE = urinary energy excretion as a fraction of GE (0.04), GE = gross energy intake (MJ day" }, { - "self_ref": "#/texts/169", + "self_ref": "#/texts/180", "parent": { "$ref": "#/groups/11" }, @@ -4532,7 +4718,7 @@ } }, { - "self_ref": "#/texts/170", + "self_ref": "#/texts/181", "parent": { "$ref": "#/groups/11" }, @@ -4544,7 +4730,7 @@ "text": "), OM = organic matter (g), 18.45 = conversion factor for dietary GE per kg of DM (MJ kg" }, { - "self_ref": "#/texts/171", + "self_ref": "#/texts/182", "parent": { "$ref": "#/groups/11" }, @@ -4563,7 +4749,7 @@ } }, { - "self_ref": "#/texts/172", + "self_ref": "#/texts/183", "parent": { "$ref": "#/groups/11" }, @@ -4575,9 +4761,9 @@ "text": ")." }, { - "self_ref": "#/texts/173", + "self_ref": "#/texts/184", "parent": { - "$ref": "#/texts/149" + "$ref": "#/texts/160" }, "children": [], "content_layer": "body", @@ -4587,7 +4773,7 @@ "text": "The OM digestibility was estimated as a function of chemical composition, using equations published by INRA [21], which takes into account the effects of digestive interactions due to feeding level, the proportion of concentrate and rumen protein balance on OM digestibility. For scenarios where cows had access to grazing, the amount of calculated VS were corrected as a function of the time at pasture. The biodegradability of manure factor (0.13 for dairy cows in Latin America) and methane conversion factor (MCF) values were taken from IPCC [38]. The MCF values for pit storage below animal confinements (> 1 month) were used for the calculation, taking into account the annual average temperature (16.6ºC) or the average temperatures during the growth period of temperate (14.4ºC) or tropical (21ºC) annual pastures, which were 31%, 26% and 46%, respectively." }, { - "self_ref": "#/texts/174", + "self_ref": "#/texts/185", "parent": { "$ref": "#/groups/12" }, @@ -4599,7 +4785,7 @@ "text": "The N" }, { - "self_ref": "#/texts/175", + "self_ref": "#/texts/186", "parent": { "$ref": "#/groups/12" }, @@ -4618,7 +4804,7 @@ } }, { - "self_ref": "#/texts/176", + "self_ref": "#/texts/187", "parent": { "$ref": "#/groups/12" }, @@ -4630,7 +4816,7 @@ "text": "O-N emissions from urine and feces were estimated considering the proportion of N excreted as manure and storage or as urine and dung deposited by grazing animals. These proportions were calculated based on the proportion of daily time that animals stayed on pasture (7 h/24 h = 0.29) or confinement (1−0.29 = 0.71). For lactating heifers and cows, the total amount of N excreted was calculated by the difference between N intake and milk N excretion. For heifers and non-lactating cows, urinary and fecal N excretion were estimated as proposed by Reed et al. [45] (Table 3: equations 10 and 12, respectively). The N" }, { - "self_ref": "#/texts/177", + "self_ref": "#/texts/188", "parent": { "$ref": "#/groups/12" }, @@ -4649,7 +4835,7 @@ } }, { - "self_ref": "#/texts/178", + "self_ref": "#/texts/189", "parent": { "$ref": "#/groups/12" }, @@ -4661,7 +4847,7 @@ "text": "O emissions from stored manure as well as urine and dung during grazing were calculated based on the conversion of N" }, { - "self_ref": "#/texts/179", + "self_ref": "#/texts/190", "parent": { "$ref": "#/groups/12" }, @@ -4680,7 +4866,7 @@ } }, { - "self_ref": "#/texts/180", + "self_ref": "#/texts/191", "parent": { "$ref": "#/groups/12" }, @@ -4692,7 +4878,7 @@ "text": "O-N emissions to N" }, { - "self_ref": "#/texts/181", + "self_ref": "#/texts/192", "parent": { "$ref": "#/groups/12" }, @@ -4711,7 +4897,7 @@ } }, { - "self_ref": "#/texts/182", + "self_ref": "#/texts/193", "parent": { "$ref": "#/groups/12" }, @@ -4723,7 +4909,7 @@ "text": "O emissions, where N" }, { - "self_ref": "#/texts/183", + "self_ref": "#/texts/194", "parent": { "$ref": "#/groups/12" }, @@ -4742,7 +4928,7 @@ } }, { - "self_ref": "#/texts/184", + "self_ref": "#/texts/195", "parent": { "$ref": "#/groups/12" }, @@ -4754,7 +4940,7 @@ "text": "O emissions = N" }, { - "self_ref": "#/texts/185", + "self_ref": "#/texts/196", "parent": { "$ref": "#/groups/12" }, @@ -4773,7 +4959,7 @@ } }, { - "self_ref": "#/texts/186", + "self_ref": "#/texts/197", "parent": { "$ref": "#/groups/12" }, @@ -4785,7 +4971,7 @@ "text": "O-N emissions × 44/28. The emission factors were 0.002 kg N" }, { - "self_ref": "#/texts/187", + "self_ref": "#/texts/198", "parent": { "$ref": "#/groups/12" }, @@ -4804,7 +4990,7 @@ } }, { - "self_ref": "#/texts/188", + "self_ref": "#/texts/199", "parent": { "$ref": "#/groups/12" }, @@ -4816,7 +5002,7 @@ "text": "O-N (kg N)" }, { - "self_ref": "#/texts/189", + "self_ref": "#/texts/200", "parent": { "$ref": "#/groups/12" }, @@ -4835,7 +5021,7 @@ } }, { - "self_ref": "#/texts/190", + "self_ref": "#/texts/201", "parent": { "$ref": "#/groups/12" }, @@ -4847,7 +5033,7 @@ "text": "stored in a pit below animal confinements, and 0.02 kg N" }, { - "self_ref": "#/texts/191", + "self_ref": "#/texts/202", "parent": { "$ref": "#/groups/12" }, @@ -4866,7 +5052,7 @@ } }, { - "self_ref": "#/texts/192", + "self_ref": "#/texts/203", "parent": { "$ref": "#/groups/12" }, @@ -4878,7 +5064,7 @@ "text": "O-N (kg of urine and dung)" }, { - "self_ref": "#/texts/193", + "self_ref": "#/texts/204", "parent": { "$ref": "#/groups/12" }, @@ -4897,7 +5083,7 @@ } }, { - "self_ref": "#/texts/194", + "self_ref": "#/texts/205", "parent": { "$ref": "#/groups/12" }, @@ -4909,7 +5095,7 @@ "text": "deposited on pasture [38]. The indirect N" }, { - "self_ref": "#/texts/195", + "self_ref": "#/texts/206", "parent": { "$ref": "#/groups/12" }, @@ -4928,7 +5114,7 @@ } }, { - "self_ref": "#/texts/196", + "self_ref": "#/texts/207", "parent": { "$ref": "#/groups/12" }, @@ -4940,13 +5126,13 @@ "text": "O emissions from storage manure and urine and dung deposits on pasture were also estimated using the IPCC [38] emission factors." }, { - "self_ref": "#/texts/197", + "self_ref": "#/texts/208", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/198" + "$ref": "#/texts/209" }, { "$ref": "#/tables/4" @@ -4969,9 +5155,9 @@ "level": 2 }, { - "self_ref": "#/texts/198", + "self_ref": "#/texts/209", "parent": { - "$ref": "#/texts/197" + "$ref": "#/texts/208" }, "children": [], "content_layer": "body", @@ -4981,7 +5167,7 @@ "text": "Emissions due to farm management included those from fuel and machinery for manure handling and electricity for milking and confinement (Table 5). Emissions due to feed processing such as cutting, crushing, mixing and distributing, as well as secondary sources of emissions during the production of fuel, machinery, fertilizer, pesticides, seeds and plastic for ensilage were included in ‘Emissions from crop and pasture production’ section." }, { - "self_ref": "#/texts/199", + "self_ref": "#/texts/210", "parent": { "$ref": "#/body" }, @@ -4993,7 +5179,7 @@ "text": "Table 5 Factors for major resource inputs in farm management." }, { - "self_ref": "#/texts/200", + "self_ref": "#/texts/211", "parent": { "$ref": "#/groups/13" }, @@ -5005,7 +5191,7 @@ "text": "The amount of fuel use for manure handling were estimated taking into consideration the amount of manure produced per cow and the amounts of fuel required for manure handling (L diesel t" }, { - "self_ref": "#/texts/201", + "self_ref": "#/texts/212", "parent": { "$ref": "#/groups/13" }, @@ -5024,7 +5210,7 @@ } }, { - "self_ref": "#/texts/202", + "self_ref": "#/texts/213", "parent": { "$ref": "#/groups/13" }, @@ -5036,7 +5222,7 @@ "text": ") [42]. The amount of manure was estimated from OM excretions (kg cow" }, { - "self_ref": "#/texts/203", + "self_ref": "#/texts/214", "parent": { "$ref": "#/groups/13" }, @@ -5055,7 +5241,7 @@ } }, { - "self_ref": "#/texts/204", + "self_ref": "#/texts/215", "parent": { "$ref": "#/groups/13" }, @@ -5067,7 +5253,7 @@ "text": "), assuming that the manure has 8% ash on DM basis and 60% DM content. The OM excretions were calculated by NDOMI × days in confinement × proportion of daily time that animals stayed on confinement." }, { - "self_ref": "#/texts/205", + "self_ref": "#/texts/216", "parent": { "$ref": "#/groups/14" }, @@ -5079,7 +5265,7 @@ "text": "The emissions from fuel were estimated considering the primary (emissions from fuel burned) and secondary (emissions for producing and transporting fuel) emissions. The primary emissions were calculated by the amount of fuel required for manure handling (L) × (kg CO" }, { - "self_ref": "#/texts/206", + "self_ref": "#/texts/217", "parent": { "$ref": "#/groups/14" }, @@ -5098,7 +5284,7 @@ } }, { - "self_ref": "#/texts/207", + "self_ref": "#/texts/218", "parent": { "$ref": "#/groups/14" }, @@ -5110,7 +5296,7 @@ "text": "e L" }, { - "self_ref": "#/texts/208", + "self_ref": "#/texts/219", "parent": { "$ref": "#/groups/14" }, @@ -5129,7 +5315,7 @@ } }, { - "self_ref": "#/texts/209", + "self_ref": "#/texts/220", "parent": { "$ref": "#/groups/14" }, @@ -5141,7 +5327,7 @@ "text": ") [41]. The secondary emissions from fuel were calculated by the amount of fuel required for manure handling × emissions for production and transport of fuel (kg CO" }, { - "self_ref": "#/texts/210", + "self_ref": "#/texts/221", "parent": { "$ref": "#/groups/14" }, @@ -5160,7 +5346,7 @@ } }, { - "self_ref": "#/texts/211", + "self_ref": "#/texts/222", "parent": { "$ref": "#/groups/14" }, @@ -5172,7 +5358,7 @@ "text": "e L" }, { - "self_ref": "#/texts/212", + "self_ref": "#/texts/223", "parent": { "$ref": "#/groups/14" }, @@ -5191,7 +5377,7 @@ } }, { - "self_ref": "#/texts/213", + "self_ref": "#/texts/224", "parent": { "$ref": "#/groups/14" }, @@ -5203,7 +5389,7 @@ "text": ") [41]. Emissions from manufacture and repair of machinery for manure handling were estimated by manure produced per cow (t) × (kg machinery mass (kg manure)" }, { - "self_ref": "#/texts/214", + "self_ref": "#/texts/225", "parent": { "$ref": "#/groups/14" }, @@ -5222,7 +5408,7 @@ } }, { - "self_ref": "#/texts/215", + "self_ref": "#/texts/226", "parent": { "$ref": "#/groups/14" }, @@ -5234,7 +5420,7 @@ "text": "× 10" }, { - "self_ref": "#/texts/216", + "self_ref": "#/texts/227", "parent": { "$ref": "#/groups/14" }, @@ -5253,7 +5439,7 @@ } }, { - "self_ref": "#/texts/217", + "self_ref": "#/texts/228", "parent": { "$ref": "#/groups/14" }, @@ -5265,7 +5451,7 @@ "text": ") [42] × kg CO" }, { - "self_ref": "#/texts/218", + "self_ref": "#/texts/229", "parent": { "$ref": "#/groups/14" }, @@ -5284,7 +5470,7 @@ } }, { - "self_ref": "#/texts/219", + "self_ref": "#/texts/230", "parent": { "$ref": "#/groups/14" }, @@ -5296,7 +5482,7 @@ "text": "e (kg machinery mass)" }, { - "self_ref": "#/texts/220", + "self_ref": "#/texts/231", "parent": { "$ref": "#/groups/14" }, @@ -5315,7 +5501,7 @@ } }, { - "self_ref": "#/texts/221", + "self_ref": "#/texts/232", "parent": { "$ref": "#/groups/14" }, @@ -5327,7 +5513,7 @@ "text": "[42]." }, { - "self_ref": "#/texts/222", + "self_ref": "#/texts/233", "parent": { "$ref": "#/groups/15" }, @@ -5339,7 +5525,7 @@ "text": "Emissions from electricity for milking and confinement were estimated using two emission factors (kg CO" }, { - "self_ref": "#/texts/223", + "self_ref": "#/texts/234", "parent": { "$ref": "#/groups/15" }, @@ -5358,7 +5544,7 @@ } }, { - "self_ref": "#/texts/224", + "self_ref": "#/texts/235", "parent": { "$ref": "#/groups/15" }, @@ -5370,7 +5556,7 @@ "text": "kWh" }, { - "self_ref": "#/texts/225", + "self_ref": "#/texts/236", "parent": { "$ref": "#/groups/15" }, @@ -5389,7 +5575,7 @@ } }, { - "self_ref": "#/texts/226", + "self_ref": "#/texts/237", "parent": { "$ref": "#/groups/15" }, @@ -5401,7 +5587,7 @@ "text": "). The first one is based on United States electricity matrix [41], and was used as a reference of an electricity matrix with less hydroelectric power than the region under study. The second is based on the Brazilian electricity matrix [46]. The electricity required for milking activities is 0.06 kWh (kg milk produced)" }, { - "self_ref": "#/texts/227", + "self_ref": "#/texts/238", "parent": { "$ref": "#/groups/15" }, @@ -5420,7 +5606,7 @@ } }, { - "self_ref": "#/texts/228", + "self_ref": "#/texts/239", "parent": { "$ref": "#/groups/15" }, @@ -5432,7 +5618,7 @@ "text": "[47]. The annual electricity use for lighting was 75 kWh cow" }, { - "self_ref": "#/texts/229", + "self_ref": "#/texts/240", "parent": { "$ref": "#/groups/15" }, @@ -5451,7 +5637,7 @@ } }, { - "self_ref": "#/texts/230", + "self_ref": "#/texts/241", "parent": { "$ref": "#/groups/15" }, @@ -5463,9 +5649,9 @@ "text": ", which is the value considered for lactating cows in naturally ventilated barns [47]." }, { - "self_ref": "#/texts/231", + "self_ref": "#/texts/242", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { @@ -5480,7 +5666,7 @@ "level": 2 }, { - "self_ref": "#/texts/232", + "self_ref": "#/texts/243", "parent": { "$ref": "#/groups/16" }, @@ -5492,7 +5678,7 @@ "text": "The C footprint for milk produced in the system was calculated using a biophysical allocation approach, as recommended by the International Dairy Federation [49], and described by Thoma et al. [48]. Briefly, AR" }, { - "self_ref": "#/texts/233", + "self_ref": "#/texts/244", "parent": { "$ref": "#/groups/16" }, @@ -5511,7 +5697,7 @@ } }, { - "self_ref": "#/texts/234", + "self_ref": "#/texts/245", "parent": { "$ref": "#/groups/16" }, @@ -5523,7 +5709,7 @@ "text": "= 1–6.04 × BMR, where" }, { - "self_ref": "#/texts/235", + "self_ref": "#/texts/246", "parent": { "$ref": "#/groups/16" }, @@ -5542,7 +5728,7 @@ } }, { - "self_ref": "#/texts/236", + "self_ref": "#/texts/247", "parent": { "$ref": "#/groups/16" }, @@ -5554,7 +5740,7 @@ "text": "AR" }, { - "self_ref": "#/texts/237", + "self_ref": "#/texts/248", "parent": { "$ref": "#/groups/16" }, @@ -5573,7 +5759,7 @@ } }, { - "self_ref": "#/texts/238", + "self_ref": "#/texts/249", "parent": { "$ref": "#/groups/16" }, @@ -5585,7 +5771,7 @@ "text": "is the allocation ratio for milk and BMR is cow BW at the time of slaughter (kg) + calf BW sold (kg) divided by the total ECM produced during cow`s entire life (kg). The AR" }, { - "self_ref": "#/texts/239", + "self_ref": "#/texts/250", "parent": { "$ref": "#/groups/16" }, @@ -5604,7 +5790,7 @@ } }, { - "self_ref": "#/texts/240", + "self_ref": "#/texts/251", "parent": { "$ref": "#/groups/16" }, @@ -5616,7 +5802,7 @@ "text": "were 0.854 and 0.849 for TMR and TMR with both pasture scenarios, respectively. The AR" }, { - "self_ref": "#/texts/241", + "self_ref": "#/texts/252", "parent": { "$ref": "#/groups/16" }, @@ -5635,7 +5821,7 @@ } }, { - "self_ref": "#/texts/242", + "self_ref": "#/texts/253", "parent": { "$ref": "#/groups/16" }, @@ -5647,13 +5833,13 @@ "text": "was applied to the whole emissions, except for the electricity consumed for milking (milking parlor) and refrigerant loss, which was directly assigned to milk production." }, { - "self_ref": "#/texts/243", + "self_ref": "#/texts/254", "parent": { - "$ref": "#/texts/32" + "$ref": "#/texts/43" }, "children": [ { - "$ref": "#/texts/244" + "$ref": "#/texts/255" } ], "content_layer": "body", @@ -5664,9 +5850,9 @@ "level": 2 }, { - "self_ref": "#/texts/244", + "self_ref": "#/texts/255", "parent": { - "$ref": "#/texts/243" + "$ref": "#/texts/254" }, "children": [], "content_layer": "body", @@ -5676,31 +5862,31 @@ "text": "A sensitivity index was calculated as described by Rotz et al. [42]. The sensitivity index was defined for each emission source as the percentage change in the C footprint for a 10% change in the given emission source divided by 10%. Thus, a value near 0 indicates a low sensitivity, whereas an index near or greater than 1 indicates a high sensitivity because a change in this value causes a similar change in the footprint." }, { - "self_ref": "#/texts/245", + "self_ref": "#/texts/256", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/246" + "$ref": "#/texts/257" }, { - "$ref": "#/texts/247" + "$ref": "#/texts/258" }, { - "$ref": "#/texts/317" + "$ref": "#/texts/328" }, { - "$ref": "#/texts/345" + "$ref": "#/texts/356" }, { - "$ref": "#/texts/392" + "$ref": "#/texts/403" }, { - "$ref": "#/texts/411" + "$ref": "#/texts/422" }, { - "$ref": "#/texts/417" + "$ref": "#/texts/428" } ], "content_layer": "body", @@ -5711,9 +5897,9 @@ "level": 1 }, { - "self_ref": "#/texts/246", + "self_ref": "#/texts/257", "parent": { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, "children": [], "content_layer": "body", @@ -5723,9 +5909,9 @@ "text": "The study has assessed the impact of tropical and temperate pastures in dairy cows fed TMR on the C footprint of dairy production in subtropics. Different factors were taken in to consideration to estimate emissions from manure (or urine and dung) of grazing animals, feed production and electricity use." }, { - "self_ref": "#/texts/247", + "self_ref": "#/texts/258", "parent": { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, "children": [ { @@ -5752,7 +5938,7 @@ "level": 2 }, { - "self_ref": "#/texts/248", + "self_ref": "#/texts/259", "parent": { "$ref": "#/groups/17" }, @@ -5764,7 +5950,7 @@ "text": "Depending on emission factors used for calculating emissions from urine and dung (IPCC or local data) and feed production (Tables 3 or 4), the C footprint was similar (Fig 2A and 2B) or decreased by 0.04 kg CO" }, { - "self_ref": "#/texts/249", + "self_ref": "#/texts/260", "parent": { "$ref": "#/groups/17" }, @@ -5783,7 +5969,7 @@ } }, { - "self_ref": "#/texts/250", + "self_ref": "#/texts/261", "parent": { "$ref": "#/groups/17" }, @@ -5795,7 +5981,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/251", + "self_ref": "#/texts/262", "parent": { "$ref": "#/groups/17" }, @@ -5814,7 +6000,7 @@ } }, { - "self_ref": "#/texts/252", + "self_ref": "#/texts/263", "parent": { "$ref": "#/groups/17" }, @@ -5826,7 +6012,7 @@ "text": "(Fig 2C and 2D) in scenarios that included pastures compared to" }, { - "self_ref": "#/texts/253", + "self_ref": "#/texts/264", "parent": { "$ref": "#/groups/17" }, @@ -5845,7 +6031,7 @@ } }, { - "self_ref": "#/texts/254", + "self_ref": "#/texts/265", "parent": { "$ref": "#/groups/17" }, @@ -5857,7 +6043,7 @@ "text": "TMR intake. Due to differences in emission factors, the overall GHG emission values ranged from 0.92 to 1.04 kg CO" }, { - "self_ref": "#/texts/255", + "self_ref": "#/texts/266", "parent": { "$ref": "#/groups/17" }, @@ -5876,7 +6062,7 @@ } }, { - "self_ref": "#/texts/256", + "self_ref": "#/texts/267", "parent": { "$ref": "#/groups/17" }, @@ -5888,7 +6074,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/257", + "self_ref": "#/texts/268", "parent": { "$ref": "#/groups/17" }, @@ -5907,7 +6093,7 @@ } }, { - "self_ref": "#/texts/258", + "self_ref": "#/texts/269", "parent": { "$ref": "#/groups/17" }, @@ -5919,7 +6105,7 @@ "text": "for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO" }, { - "self_ref": "#/texts/259", + "self_ref": "#/texts/270", "parent": { "$ref": "#/groups/17" }, @@ -5938,7 +6124,7 @@ } }, { - "self_ref": "#/texts/260", + "self_ref": "#/texts/271", "parent": { "$ref": "#/groups/17" }, @@ -5950,7 +6136,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/261", + "self_ref": "#/texts/272", "parent": { "$ref": "#/groups/17" }, @@ -5969,7 +6155,7 @@ } }, { - "self_ref": "#/texts/262", + "self_ref": "#/texts/273", "parent": { "$ref": "#/groups/17" }, @@ -5981,7 +6167,7 @@ "text": "for cows with access to pasture. Using IPCC emission factors [38], manure emissions increased as TMR intake went down (Fig 2A and 2B). However, using local emission factors for estimating N" }, { - "self_ref": "#/texts/263", + "self_ref": "#/texts/274", "parent": { "$ref": "#/groups/17" }, @@ -6000,7 +6186,7 @@ } }, { - "self_ref": "#/texts/264", + "self_ref": "#/texts/275", "parent": { "$ref": "#/groups/17" }, @@ -6012,7 +6198,7 @@ "text": "O-N emissions [37], manure emissions decreased as TMR intake went down (Fig 2C and 2D). Regardless of emission factors used (Tables 3 or 4), emissions from feed production decreased to a small extent as the proportion of TMR intake decreased. Emissions from farm management did not contribute more than 5% of overall GHG emissions." }, { - "self_ref": "#/texts/265", + "self_ref": "#/texts/276", "parent": { "$ref": "#/body" }, @@ -6024,7 +6210,7 @@ "text": "Fig 2 Overall greenhouse gas emissions in dairy cattle systems under various scenarios. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting for sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]." }, { - "self_ref": "#/texts/266", + "self_ref": "#/texts/277", "parent": { "$ref": "#/groups/18" }, @@ -6036,7 +6222,7 @@ "text": "Considering IPCC emission factors for N" }, { - "self_ref": "#/texts/267", + "self_ref": "#/texts/278", "parent": { "$ref": "#/groups/18" }, @@ -6055,7 +6241,7 @@ } }, { - "self_ref": "#/texts/268", + "self_ref": "#/texts/279", "parent": { "$ref": "#/groups/18" }, @@ -6067,7 +6253,7 @@ "text": "O emissions from urine and dung [38] and those from Table 3, the C footprint ranged from 0.99 to 1.04 kg CO" }, { - "self_ref": "#/texts/269", + "self_ref": "#/texts/280", "parent": { "$ref": "#/groups/18" }, @@ -6086,7 +6272,7 @@ } }, { - "self_ref": "#/texts/270", + "self_ref": "#/texts/281", "parent": { "$ref": "#/groups/18" }, @@ -6098,7 +6284,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/271", + "self_ref": "#/texts/282", "parent": { "$ref": "#/groups/18" }, @@ -6117,7 +6303,7 @@ } }, { - "self_ref": "#/texts/272", + "self_ref": "#/texts/283", "parent": { "$ref": "#/groups/18" }, @@ -6129,7 +6315,7 @@ "text": ", and was close to those reported under confined based systems in California [49], Canada [50], China [8], Ireland [9], different scenarios in Australia [51,52] and Uruguay [11], which ranged from 0.98 to 1.16 kg CO" }, { - "self_ref": "#/texts/273", + "self_ref": "#/texts/284", "parent": { "$ref": "#/groups/18" }, @@ -6148,7 +6334,7 @@ } }, { - "self_ref": "#/texts/274", + "self_ref": "#/texts/285", "parent": { "$ref": "#/groups/18" }, @@ -6160,7 +6346,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/275", + "self_ref": "#/texts/286", "parent": { "$ref": "#/groups/18" }, @@ -6179,7 +6365,7 @@ } }, { - "self_ref": "#/texts/276", + "self_ref": "#/texts/287", "parent": { "$ref": "#/groups/18" }, @@ -6191,7 +6377,7 @@ "text": ". When local emission factors for N" }, { - "self_ref": "#/texts/277", + "self_ref": "#/texts/288", "parent": { "$ref": "#/groups/18" }, @@ -6210,7 +6396,7 @@ } }, { - "self_ref": "#/texts/278", + "self_ref": "#/texts/289", "parent": { "$ref": "#/groups/18" }, @@ -6222,7 +6408,7 @@ "text": "O emissions from urine and dung [37] and those from Table 4 were taking into account, the C footprint for scenarios including pasture, without accounting for sequestered CO" }, { - "self_ref": "#/texts/279", + "self_ref": "#/texts/290", "parent": { "$ref": "#/groups/18" }, @@ -6241,7 +6427,7 @@ } }, { - "self_ref": "#/texts/280", + "self_ref": "#/texts/291", "parent": { "$ref": "#/groups/18" }, @@ -6253,7 +6439,7 @@ "text": "-C from perennial pasture—0.91 kg CO" }, { - "self_ref": "#/texts/281", + "self_ref": "#/texts/292", "parent": { "$ref": "#/groups/18" }, @@ -6272,7 +6458,7 @@ } }, { - "self_ref": "#/texts/282", + "self_ref": "#/texts/293", "parent": { "$ref": "#/groups/18" }, @@ -6284,7 +6470,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/283", + "self_ref": "#/texts/294", "parent": { "$ref": "#/groups/18" }, @@ -6303,7 +6489,7 @@ } }, { - "self_ref": "#/texts/284", + "self_ref": "#/texts/295", "parent": { "$ref": "#/groups/18" }, @@ -6315,7 +6501,7 @@ "text": "—was lower than the range of values described above. However, these values were still greater than high-performance confinement systems in UK and USA [53] or grass based dairy systems in Ireland [9,53] and New Zealand [8,54], which ranged from 0.52 to 0.89 kg CO" }, { - "self_ref": "#/texts/285", + "self_ref": "#/texts/296", "parent": { "$ref": "#/groups/18" }, @@ -6334,7 +6520,7 @@ } }, { - "self_ref": "#/texts/286", + "self_ref": "#/texts/297", "parent": { "$ref": "#/groups/18" }, @@ -6346,7 +6532,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/287", + "self_ref": "#/texts/298", "parent": { "$ref": "#/groups/18" }, @@ -6365,7 +6551,7 @@ } }, { - "self_ref": "#/texts/288", + "self_ref": "#/texts/299", "parent": { "$ref": "#/groups/18" }, @@ -6377,7 +6563,7 @@ "text": ". Regardless of which emission factor was used, we found a lower C footprint in all conditions compared to scenarios with lower milk production per cow or in poor conditions of manure management, which ranged from 1.4 to 2.3 kg CO" }, { - "self_ref": "#/texts/289", + "self_ref": "#/texts/300", "parent": { "$ref": "#/groups/18" }, @@ -6396,7 +6582,7 @@ } }, { - "self_ref": "#/texts/290", + "self_ref": "#/texts/301", "parent": { "$ref": "#/groups/18" }, @@ -6408,7 +6594,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/291", + "self_ref": "#/texts/302", "parent": { "$ref": "#/groups/18" }, @@ -6427,7 +6613,7 @@ } }, { - "self_ref": "#/texts/292", + "self_ref": "#/texts/303", "parent": { "$ref": "#/groups/18" }, @@ -6439,7 +6625,7 @@ "text": "[8,55]. Thus, even though differences between studies may be partially explained by various assumptions (e.g., emission factors, co-product allocation, methane emissions estimation, sequestered CO" }, { - "self_ref": "#/texts/293", + "self_ref": "#/texts/304", "parent": { "$ref": "#/groups/18" }, @@ -6458,7 +6644,7 @@ } }, { - "self_ref": "#/texts/294", + "self_ref": "#/texts/305", "parent": { "$ref": "#/groups/18" }, @@ -6470,7 +6656,7 @@ "text": "-C, etc.), herd productivity and manure management were systematically associated with the C footprint of the dairy systems." }, { - "self_ref": "#/texts/295", + "self_ref": "#/texts/306", "parent": { "$ref": "#/groups/19" }, @@ -6482,7 +6668,7 @@ "text": "The similarity of C footprint between different scenarios using IPCC [38] for estimating emissions from manure and for emissions from feed production (Table 3) was a consequence of the trade-off between greater manure emissions and lower emissions to produce feed, as the proportion of pasture in diets increased. Additionally, the small negative effect of pasture on ECM production also contributed to the trade-off. The impact of milk production on the C footprint was reported in a meta-analysis comprising 30 studies from 15 different countries [22]. As observed in this study (Fig 2A and 2B) the authors reported no significant difference between the C footprint of pasture-based vs. confinement systems. However, they observed that an increase of 1000 kg cow" }, { - "self_ref": "#/texts/296", + "self_ref": "#/texts/307", "parent": { "$ref": "#/groups/19" }, @@ -6501,7 +6687,7 @@ } }, { - "self_ref": "#/texts/297", + "self_ref": "#/texts/308", "parent": { "$ref": "#/groups/19" }, @@ -6513,7 +6699,7 @@ "text": "(5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO" }, { - "self_ref": "#/texts/298", + "self_ref": "#/texts/309", "parent": { "$ref": "#/groups/19" }, @@ -6532,7 +6718,7 @@ } }, { - "self_ref": "#/texts/299", + "self_ref": "#/texts/310", "parent": { "$ref": "#/groups/19" }, @@ -6544,7 +6730,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/300", + "self_ref": "#/texts/311", "parent": { "$ref": "#/groups/19" }, @@ -6563,7 +6749,7 @@ } }, { - "self_ref": "#/texts/301", + "self_ref": "#/texts/312", "parent": { "$ref": "#/groups/19" }, @@ -6575,7 +6761,7 @@ "text": ", which may explain an apparent discrepancy between our study and an LCA performed in south Brazilian conditions [56]. Their study compared a confinement and a grazing-based dairy system with annual average milk production of 7667 and 5535 kg cow, respectively. In this study, the same herd was used in all systems, with an annual average milk production of around 7000 kg cow" }, { - "self_ref": "#/texts/302", + "self_ref": "#/texts/313", "parent": { "$ref": "#/groups/19" }, @@ -6594,7 +6780,7 @@ } }, { - "self_ref": "#/texts/303", + "self_ref": "#/texts/314", "parent": { "$ref": "#/groups/19" }, @@ -6606,7 +6792,7 @@ "text": ". Experimental data showed a reduction not greater than 3% of ECM when 50% of TMR was replaced by pasture access." }, { - "self_ref": "#/texts/304", + "self_ref": "#/texts/315", "parent": { "$ref": "#/groups/20" }, @@ -6618,7 +6804,7 @@ "text": "The lower C footprint in scenarios with access to pasture, when local emission factors [37] were used for N" }, { - "self_ref": "#/texts/305", + "self_ref": "#/texts/316", "parent": { "$ref": "#/groups/20" }, @@ -6637,7 +6823,7 @@ } }, { - "self_ref": "#/texts/306", + "self_ref": "#/texts/317", "parent": { "$ref": "#/groups/20" }, @@ -6649,7 +6835,7 @@ "text": "O emissions from urine and dung and for feed production (Table 4), may also be partially attributed to the small negative effect of pasture on ECM production. Nevertheless, local emission factors for urine and dung had a great impact on scenarios including pastures compared to" }, { - "self_ref": "#/texts/307", + "self_ref": "#/texts/318", "parent": { "$ref": "#/groups/20" }, @@ -6668,7 +6854,7 @@ } }, { - "self_ref": "#/texts/308", + "self_ref": "#/texts/319", "parent": { "$ref": "#/groups/20" }, @@ -6680,7 +6866,7 @@ "text": "TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N" }, { - "self_ref": "#/texts/309", + "self_ref": "#/texts/320", "parent": { "$ref": "#/groups/20" }, @@ -6699,7 +6885,7 @@ } }, { - "self_ref": "#/texts/310", + "self_ref": "#/texts/321", "parent": { "$ref": "#/groups/20" }, @@ -6711,7 +6897,7 @@ "text": "O-N (kg N)" }, { - "self_ref": "#/texts/311", + "self_ref": "#/texts/322", "parent": { "$ref": "#/groups/20" }, @@ -6730,7 +6916,7 @@ } }, { - "self_ref": "#/texts/312", + "self_ref": "#/texts/323", "parent": { "$ref": "#/groups/20" }, @@ -6742,7 +6928,7 @@ "text": "for urine and dung from grazing animals, experimental evidence shows that it may be up to five times lower, averaging 0.004 kg N" }, { - "self_ref": "#/texts/313", + "self_ref": "#/texts/324", "parent": { "$ref": "#/groups/20" }, @@ -6761,7 +6947,7 @@ } }, { - "self_ref": "#/texts/314", + "self_ref": "#/texts/325", "parent": { "$ref": "#/groups/20" }, @@ -6773,7 +6959,7 @@ "text": "O-N kg" }, { - "self_ref": "#/texts/315", + "self_ref": "#/texts/326", "parent": { "$ref": "#/groups/20" }, @@ -6792,7 +6978,7 @@ } }, { - "self_ref": "#/texts/316", + "self_ref": "#/texts/327", "parent": { "$ref": "#/groups/20" }, @@ -6804,9 +6990,9 @@ "text": "[37]." }, { - "self_ref": "#/texts/317", + "self_ref": "#/texts/328", "parent": { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, "children": [ { @@ -6827,7 +7013,7 @@ "level": 2 }, { - "self_ref": "#/texts/318", + "self_ref": "#/texts/329", "parent": { "$ref": "#/groups/21" }, @@ -6839,7 +7025,7 @@ "text": "The enteric CH" }, { - "self_ref": "#/texts/319", + "self_ref": "#/texts/330", "parent": { "$ref": "#/groups/21" }, @@ -6858,7 +7044,7 @@ } }, { - "self_ref": "#/texts/320", + "self_ref": "#/texts/331", "parent": { "$ref": "#/groups/21" }, @@ -6870,7 +7056,7 @@ "text": "intensity was similar between different scenarios (Fig 2), showing the greatest sensitivity index, with values ranging from 0.53 to 0.62, which indicate that for a 10% change in this source, the C footprint may change between 5.3 and 6.2% (Fig 3). The large effect of enteric CH" }, { - "self_ref": "#/texts/321", + "self_ref": "#/texts/332", "parent": { "$ref": "#/groups/21" }, @@ -6889,7 +7075,7 @@ } }, { - "self_ref": "#/texts/322", + "self_ref": "#/texts/333", "parent": { "$ref": "#/groups/21" }, @@ -6901,7 +7087,7 @@ "text": "emissions on the whole C footprint was expected, because the impact of enteric CH" }, { - "self_ref": "#/texts/323", + "self_ref": "#/texts/334", "parent": { "$ref": "#/groups/21" }, @@ -6920,7 +7106,7 @@ } }, { - "self_ref": "#/texts/324", + "self_ref": "#/texts/335", "parent": { "$ref": "#/groups/21" }, @@ -6932,7 +7118,7 @@ "text": "on GHG emissions of milk production in different dairy systems has been estimated to range from 44 to 60% of the total CO" }, { - "self_ref": "#/texts/325", + "self_ref": "#/texts/336", "parent": { "$ref": "#/groups/21" }, @@ -6951,7 +7137,7 @@ } }, { - "self_ref": "#/texts/326", + "self_ref": "#/texts/337", "parent": { "$ref": "#/groups/21" }, @@ -6963,7 +7149,7 @@ "text": "e [50,52,57,58]. However, emissions in feed production may be the most important source of GHG when emission factors for producing concentrate feeds are greater than 0.7 kg CO" }, { - "self_ref": "#/texts/327", + "self_ref": "#/texts/338", "parent": { "$ref": "#/groups/21" }, @@ -6982,7 +7168,7 @@ } }, { - "self_ref": "#/texts/328", + "self_ref": "#/texts/339", "parent": { "$ref": "#/groups/21" }, @@ -6994,7 +7180,7 @@ "text": "e kg" }, { - "self_ref": "#/texts/329", + "self_ref": "#/texts/340", "parent": { "$ref": "#/groups/21" }, @@ -7013,7 +7199,7 @@ } }, { - "self_ref": "#/texts/330", + "self_ref": "#/texts/341", "parent": { "$ref": "#/groups/21" }, @@ -7025,7 +7211,7 @@ "text": "[59], which did not happen in this study." }, { - "self_ref": "#/texts/331", + "self_ref": "#/texts/342", "parent": { "$ref": "#/body" }, @@ -7037,7 +7223,7 @@ "text": "Fig 3 Sensitivity of the C footprint. Sensitivity index = percentage change in C footprint for a 10% change in the given emission source divided by 10% of. (a) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.73 kg CO2e kWh-1 [41]. (b) N2O emission factors for urine and dung from IPCC [38], feed production emission factors from Table 3, production of electricity = 0.205 kg CO2e kWh-1 [46]; (c) N2O emission factors for urine and dung from local data [37], feed production EF from Table 4 without accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]. (d) N2O emission factors for urine and dung from local data [37], feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture, production of electricity = 0.205 kg CO2e kWh-1 [46]." }, { - "self_ref": "#/texts/332", + "self_ref": "#/texts/343", "parent": { "$ref": "#/groups/22" }, @@ -7049,7 +7235,7 @@ "text": "The lack of difference in enteric CH" }, { - "self_ref": "#/texts/333", + "self_ref": "#/texts/344", "parent": { "$ref": "#/groups/22" }, @@ -7068,7 +7254,7 @@ } }, { - "self_ref": "#/texts/334", + "self_ref": "#/texts/345", "parent": { "$ref": "#/groups/22" }, @@ -7080,7 +7266,7 @@ "text": "emissions in different systems can be explained by the narrow range of NDF content in diets (<4% difference). This non-difference is due to the lower NDF content of annual temperate pastures (495 g (kg DM)" }, { - "self_ref": "#/texts/335", + "self_ref": "#/texts/346", "parent": { "$ref": "#/groups/22" }, @@ -7099,7 +7285,7 @@ } }, { - "self_ref": "#/texts/336", + "self_ref": "#/texts/347", "parent": { "$ref": "#/groups/22" }, @@ -7111,7 +7297,7 @@ "text": ") compared to corn silage (550 g (kg DM)" }, { - "self_ref": "#/texts/337", + "self_ref": "#/texts/348", "parent": { "$ref": "#/groups/22" }, @@ -7130,7 +7316,7 @@ } }, { - "self_ref": "#/texts/338", + "self_ref": "#/texts/349", "parent": { "$ref": "#/groups/22" }, @@ -7142,7 +7328,7 @@ "text": "). Hence, an expected, increase NDF content with decreased concentrate was partially offset by an increase in the pasture proportion relatively low in NDF. This is in agreement with studies conducted in southern Brazil, which have shown that the actual enteric CH" }, { - "self_ref": "#/texts/339", + "self_ref": "#/texts/350", "parent": { "$ref": "#/groups/22" }, @@ -7161,7 +7347,7 @@ } }, { - "self_ref": "#/texts/340", + "self_ref": "#/texts/351", "parent": { "$ref": "#/groups/22" }, @@ -7173,7 +7359,7 @@ "text": "emissions may decrease with inclusion of temperate pastures in cows receiving corn silage and soybean meal [60] or increase enteric CH" }, { - "self_ref": "#/texts/341", + "self_ref": "#/texts/352", "parent": { "$ref": "#/groups/22" }, @@ -7192,7 +7378,7 @@ } }, { - "self_ref": "#/texts/342", + "self_ref": "#/texts/353", "parent": { "$ref": "#/groups/22" }, @@ -7204,7 +7390,7 @@ "text": "emissions when dairy cows grazing a temperate pasture was supplemented with corn silage [61]. Additionally, enteric CH" }, { - "self_ref": "#/texts/343", + "self_ref": "#/texts/354", "parent": { "$ref": "#/groups/22" }, @@ -7223,7 +7409,7 @@ } }, { - "self_ref": "#/texts/344", + "self_ref": "#/texts/355", "parent": { "$ref": "#/groups/22" }, @@ -7235,9 +7421,9 @@ "text": "emissions did not differ between dairy cows receiving TMR exclusively or grazing a tropical pasture in the same scenarios as in this study [26]." }, { - "self_ref": "#/texts/345", + "self_ref": "#/texts/356", "parent": { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, "children": [ { @@ -7250,7 +7436,7 @@ "$ref": "#/groups/24" }, { - "$ref": "#/texts/391" + "$ref": "#/texts/402" } ], "content_layer": "body", @@ -7261,7 +7447,7 @@ "level": 2 }, { - "self_ref": "#/texts/346", + "self_ref": "#/texts/357", "parent": { "$ref": "#/groups/23" }, @@ -7273,7 +7459,7 @@ "text": "Using IPCC emission factors for N" }, { - "self_ref": "#/texts/347", + "self_ref": "#/texts/358", "parent": { "$ref": "#/groups/23" }, @@ -7292,7 +7478,7 @@ } }, { - "self_ref": "#/texts/348", + "self_ref": "#/texts/359", "parent": { "$ref": "#/groups/23" }, @@ -7304,7 +7490,7 @@ "text": "O emissions from urine and dung [38] and those from Table 3, CH" }, { - "self_ref": "#/texts/349", + "self_ref": "#/texts/360", "parent": { "$ref": "#/groups/23" }, @@ -7323,7 +7509,7 @@ } }, { - "self_ref": "#/texts/350", + "self_ref": "#/texts/361", "parent": { "$ref": "#/groups/23" }, @@ -7335,7 +7521,7 @@ "text": "emissions from manure decreased 0.07 kg CO" }, { - "self_ref": "#/texts/351", + "self_ref": "#/texts/362", "parent": { "$ref": "#/groups/23" }, @@ -7354,7 +7540,7 @@ } }, { - "self_ref": "#/texts/352", + "self_ref": "#/texts/363", "parent": { "$ref": "#/groups/23" }, @@ -7366,7 +7552,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/353", + "self_ref": "#/texts/364", "parent": { "$ref": "#/groups/23" }, @@ -7385,7 +7571,7 @@ } }, { - "self_ref": "#/texts/354", + "self_ref": "#/texts/365", "parent": { "$ref": "#/groups/23" }, @@ -7397,7 +7583,7 @@ "text": ", but N" }, { - "self_ref": "#/texts/355", + "self_ref": "#/texts/366", "parent": { "$ref": "#/groups/23" }, @@ -7416,7 +7602,7 @@ } }, { - "self_ref": "#/texts/356", + "self_ref": "#/texts/367", "parent": { "$ref": "#/groups/23" }, @@ -7428,7 +7614,7 @@ "text": "O emissions from manure increased 0.09 kg CO" }, { - "self_ref": "#/texts/357", + "self_ref": "#/texts/368", "parent": { "$ref": "#/groups/23" }, @@ -7447,7 +7633,7 @@ } }, { - "self_ref": "#/texts/358", + "self_ref": "#/texts/369", "parent": { "$ref": "#/groups/23" }, @@ -7459,7 +7645,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/359", + "self_ref": "#/texts/370", "parent": { "$ref": "#/groups/23" }, @@ -7478,7 +7664,7 @@ } }, { - "self_ref": "#/texts/360", + "self_ref": "#/texts/371", "parent": { "$ref": "#/groups/23" }, @@ -7490,7 +7676,7 @@ "text": ", as TMR intake was restricted to 50%" }, { - "self_ref": "#/texts/361", + "self_ref": "#/texts/372", "parent": { "$ref": "#/groups/23" }, @@ -7509,7 +7695,7 @@ } }, { - "self_ref": "#/texts/362", + "self_ref": "#/texts/373", "parent": { "$ref": "#/groups/23" }, @@ -7521,7 +7707,7 @@ "text": "(Fig 4A). Emissions for pastures increased by 0.06 kg CO" }, { - "self_ref": "#/texts/363", + "self_ref": "#/texts/374", "parent": { "$ref": "#/groups/23" }, @@ -7540,7 +7726,7 @@ } }, { - "self_ref": "#/texts/364", + "self_ref": "#/texts/375", "parent": { "$ref": "#/groups/23" }, @@ -7552,7 +7738,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/365", + "self_ref": "#/texts/376", "parent": { "$ref": "#/groups/23" }, @@ -7571,7 +7757,7 @@ } }, { - "self_ref": "#/texts/366", + "self_ref": "#/texts/377", "parent": { "$ref": "#/groups/23" }, @@ -7583,7 +7769,7 @@ "text": ", whereas emissions for producing concentrate feeds and corn silage decreased by 0.09 kg CO" }, { - "self_ref": "#/texts/367", + "self_ref": "#/texts/378", "parent": { "$ref": "#/groups/23" }, @@ -7602,7 +7788,7 @@ } }, { - "self_ref": "#/texts/368", + "self_ref": "#/texts/379", "parent": { "$ref": "#/groups/23" }, @@ -7614,7 +7800,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/369", + "self_ref": "#/texts/380", "parent": { "$ref": "#/groups/23" }, @@ -7633,7 +7819,7 @@ } }, { - "self_ref": "#/texts/370", + "self_ref": "#/texts/381", "parent": { "$ref": "#/groups/23" }, @@ -7645,7 +7831,7 @@ "text": ", as TMR intake decreased (Fig 4B). In this situation, the lack of difference in calculated C footprints of different systems was also due to the greater emissions from manure, and offset by lower emissions from feed production with inclusion of pasture in lactating dairy cow diets. The greater N" }, { - "self_ref": "#/texts/371", + "self_ref": "#/texts/382", "parent": { "$ref": "#/groups/23" }, @@ -7664,7 +7850,7 @@ } }, { - "self_ref": "#/texts/372", + "self_ref": "#/texts/383", "parent": { "$ref": "#/groups/23" }, @@ -7676,7 +7862,7 @@ "text": "O-N emissions from manure with pasture was a consequence of higher N" }, { - "self_ref": "#/texts/373", + "self_ref": "#/texts/384", "parent": { "$ref": "#/groups/23" }, @@ -7695,7 +7881,7 @@ } }, { - "self_ref": "#/texts/374", + "self_ref": "#/texts/385", "parent": { "$ref": "#/groups/23" }, @@ -7707,7 +7893,7 @@ "text": "O-N emissions due to greater CP content and N urine excretion, as pasture intake increased. The effect of CP content on urine N excretion has been shown by several authors in lactating dairy cows [62–64]. For instance, by decreasing CP content from 185 to 152 g (kg DM)" }, { - "self_ref": "#/texts/375", + "self_ref": "#/texts/386", "parent": { "$ref": "#/groups/23" }, @@ -7726,7 +7912,7 @@ } }, { - "self_ref": "#/texts/376", + "self_ref": "#/texts/387", "parent": { "$ref": "#/groups/23" }, @@ -7738,7 +7924,7 @@ "text": ", N intake decreased by 20% and urine N excretion by 60% [62]. In this study, the CP content for lactating dairy cows ranged from 150 g (kg DM)" }, { - "self_ref": "#/texts/377", + "self_ref": "#/texts/388", "parent": { "$ref": "#/groups/23" }, @@ -7757,7 +7943,7 @@ } }, { - "self_ref": "#/texts/378", + "self_ref": "#/texts/389", "parent": { "$ref": "#/groups/23" }, @@ -7769,7 +7955,7 @@ "text": "on TMR system to 198 g (kg DM)" }, { - "self_ref": "#/texts/379", + "self_ref": "#/texts/390", "parent": { "$ref": "#/groups/23" }, @@ -7788,7 +7974,7 @@ } }, { - "self_ref": "#/texts/380", + "self_ref": "#/texts/391", "parent": { "$ref": "#/groups/23" }, @@ -7800,7 +7986,7 @@ "text": "on 50% TMR with pasture. Additionally, greater urine N excretion is expected with greater use of pasture. This occurs because protein utilization in pastures is inefficient, as the protein in fresh forages is highly degradable in the rumen and may not be captured by microbes [65]." }, { - "self_ref": "#/texts/381", + "self_ref": "#/texts/392", "parent": { "$ref": "#/body" }, @@ -7812,7 +7998,7 @@ "text": "Fig 4 Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems. TMR = ad libitum TMR intake, 75TMR = 75% of ad libitum TMR intake with access to pasture, 50TMR = 50% of ad libitum TMR intake with access to pasture. (a) N2O emission factors for urine and dung from IPCC [38]. (b) Feed production emission factors from Table 3. (c) N2O emission factors for urine and dung from local data [37]. (d) Feed production emission factors from Table 4 accounting sequestered CO2-C from perennial pasture." }, { - "self_ref": "#/texts/382", + "self_ref": "#/texts/393", "parent": { "$ref": "#/groups/24" }, @@ -7824,7 +8010,7 @@ "text": "Using local emission factors for N" }, { - "self_ref": "#/texts/383", + "self_ref": "#/texts/394", "parent": { "$ref": "#/groups/24" }, @@ -7843,7 +8029,7 @@ } }, { - "self_ref": "#/texts/384", + "self_ref": "#/texts/395", "parent": { "$ref": "#/groups/24" }, @@ -7855,7 +8041,7 @@ "text": "O emissions from urine and dung [37] and those from Table 4, reductions in CH" }, { - "self_ref": "#/texts/385", + "self_ref": "#/texts/396", "parent": { "$ref": "#/groups/24" }, @@ -7874,7 +8060,7 @@ } }, { - "self_ref": "#/texts/386", + "self_ref": "#/texts/397", "parent": { "$ref": "#/groups/24" }, @@ -7886,7 +8072,7 @@ "text": "emissions from stocked manure, when pastures were included on diets, did not offset by increases in N" }, { - "self_ref": "#/texts/387", + "self_ref": "#/texts/398", "parent": { "$ref": "#/groups/24" }, @@ -7905,7 +8091,7 @@ } }, { - "self_ref": "#/texts/388", + "self_ref": "#/texts/399", "parent": { "$ref": "#/groups/24" }, @@ -7917,7 +8103,7 @@ "text": "O emissions from excreta (Fig 4C). In this case, total emissions from manure (Fig 4C) and feed production (Fig 4D) decreased with the inclusion of pasture. The impact of greater CP content and N urine excretion with increased pasture intake was offset by the much lower emission factors used for N" }, { - "self_ref": "#/texts/389", + "self_ref": "#/texts/400", "parent": { "$ref": "#/groups/24" }, @@ -7936,7 +8122,7 @@ } }, { - "self_ref": "#/texts/390", + "self_ref": "#/texts/401", "parent": { "$ref": "#/groups/24" }, @@ -7948,9 +8134,9 @@ "text": "O emissions from urine and dung. As suggested by other authors [66,67], these results show that IPCC default value may need to be revised for the subtropical region." }, { - "self_ref": "#/texts/391", + "self_ref": "#/texts/402", "parent": { - "$ref": "#/texts/345" + "$ref": "#/texts/356" }, "children": [], "content_layer": "body", @@ -7960,13 +8146,13 @@ "text": "Emissions for feed production decreased when pasture was included due to the greater emission factor for corn grain production compared to pastures. Emissions from concentrate and silage had at least twice the sensitivity index compared to emissions from pastures. The amount of grain required per cow in a lifetime decreased from 7,300 kg to 4,000 kg when 50% of TMR was replaced by pasture access. These results are in agreement with other studies which found lower C footprint, as concentrate use is reduced and/or pasture is included [9,68,69]. Moreover, it has been demonstrated that in intensive dairy systems, after enteric fermentation, feed production is the second main contributor to C footprint [50]. There is potential to decrease the environmental impact of dairy systems by reducing the use of concentrate ingredients with high environmental impact, particularly in confinements [9]." }, { - "self_ref": "#/texts/392", + "self_ref": "#/texts/403", "parent": { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, "children": [ { - "$ref": "#/texts/393" + "$ref": "#/texts/404" }, { "$ref": "#/groups/25" @@ -7980,9 +8166,9 @@ "level": 2 }, { - "self_ref": "#/texts/393", + "self_ref": "#/texts/404", "parent": { - "$ref": "#/texts/392" + "$ref": "#/texts/403" }, "children": [], "content_layer": "body", @@ -7992,7 +8178,7 @@ "text": "The lower impact of emissions from farm management is in agreement with other studies conducted in Europe [9, 62] and USA [42, 55], where the authors found that most emissions in dairy production systems are from enteric fermentation, feed production and emissions from excreta. As emissions from fuel for on-farm feed production were accounted into the ‘emissions from crop and pasture production’, total emissions from farm management were not greater than 5% of total C footprint." }, { - "self_ref": "#/texts/394", + "self_ref": "#/texts/405", "parent": { "$ref": "#/groups/25" }, @@ -8004,7 +8190,7 @@ "text": "Emissions from farm management dropped when the emission factor for electricity generation was based on the Brazilian matrix. In this case, the emission factor for electricity generation (0.205 kg CO" }, { - "self_ref": "#/texts/395", + "self_ref": "#/texts/406", "parent": { "$ref": "#/groups/25" }, @@ -8023,7 +8209,7 @@ } }, { - "self_ref": "#/texts/396", + "self_ref": "#/texts/407", "parent": { "$ref": "#/groups/25" }, @@ -8035,7 +8221,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/397", + "self_ref": "#/texts/408", "parent": { "$ref": "#/groups/25" }, @@ -8054,7 +8240,7 @@ } }, { - "self_ref": "#/texts/398", + "self_ref": "#/texts/409", "parent": { "$ref": "#/groups/25" }, @@ -8066,7 +8252,7 @@ "text": "[46]) is much lower than that in a LCA study conducted in US (0.73 kg CO" }, { - "self_ref": "#/texts/399", + "self_ref": "#/texts/410", "parent": { "$ref": "#/groups/25" }, @@ -8085,7 +8271,7 @@ } }, { - "self_ref": "#/texts/400", + "self_ref": "#/texts/411", "parent": { "$ref": "#/groups/25" }, @@ -8097,7 +8283,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/401", + "self_ref": "#/texts/412", "parent": { "$ref": "#/groups/25" }, @@ -8116,7 +8302,7 @@ } }, { - "self_ref": "#/texts/402", + "self_ref": "#/texts/413", "parent": { "$ref": "#/groups/25" }, @@ -8128,7 +8314,7 @@ "text": "[42]). This apparent discrepancy is explained because in 2016, almost 66% of the electricity generated in Brazil was from hydropower, which has an emission factor of 0.074 kg CO" }, { - "self_ref": "#/texts/403", + "self_ref": "#/texts/414", "parent": { "$ref": "#/groups/25" }, @@ -8147,7 +8333,7 @@ } }, { - "self_ref": "#/texts/404", + "self_ref": "#/texts/415", "parent": { "$ref": "#/groups/25" }, @@ -8159,7 +8345,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/405", + "self_ref": "#/texts/416", "parent": { "$ref": "#/groups/25" }, @@ -8178,7 +8364,7 @@ } }, { - "self_ref": "#/texts/406", + "self_ref": "#/texts/417", "parent": { "$ref": "#/groups/25" }, @@ -8190,7 +8376,7 @@ "text": "against 0.382 and 0.926 kg CO" }, { - "self_ref": "#/texts/407", + "self_ref": "#/texts/418", "parent": { "$ref": "#/groups/25" }, @@ -8209,7 +8395,7 @@ } }, { - "self_ref": "#/texts/408", + "self_ref": "#/texts/419", "parent": { "$ref": "#/groups/25" }, @@ -8221,7 +8407,7 @@ "text": "e kWh" }, { - "self_ref": "#/texts/409", + "self_ref": "#/texts/420", "parent": { "$ref": "#/groups/25" }, @@ -8240,7 +8426,7 @@ } }, { - "self_ref": "#/texts/410", + "self_ref": "#/texts/421", "parent": { "$ref": "#/groups/25" }, @@ -8252,9 +8438,9 @@ "text": "produced by natural gas and hard coal, respectively [46]." }, { - "self_ref": "#/texts/411", + "self_ref": "#/texts/422", "parent": { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, "children": [ { @@ -8269,7 +8455,7 @@ "level": 2 }, { - "self_ref": "#/texts/412", + "self_ref": "#/texts/423", "parent": { "$ref": "#/groups/26" }, @@ -8281,7 +8467,7 @@ "text": "The milk production and composition data are the average for a typical herd, which might have great animal-to-animal variability. Likewise, DM yield of crops and pastures were collected from experimental observations, and may change as a function of inter-annual variation, climatic conditions, soil type, fertilization level etc. The emission factors for direct and indirect N" }, { - "self_ref": "#/texts/413", + "self_ref": "#/texts/424", "parent": { "$ref": "#/groups/26" }, @@ -8300,7 +8486,7 @@ } }, { - "self_ref": "#/texts/414", + "self_ref": "#/texts/425", "parent": { "$ref": "#/groups/26" }, @@ -8312,7 +8498,7 @@ "text": "O emissions from urine and dung were alternatively estimated using local data, but more experiments are necessary to reduce the uncertainty. The CO" }, { - "self_ref": "#/texts/415", + "self_ref": "#/texts/426", "parent": { "$ref": "#/groups/26" }, @@ -8331,7 +8517,7 @@ } }, { - "self_ref": "#/texts/416", + "self_ref": "#/texts/427", "parent": { "$ref": "#/groups/26" }, @@ -8343,9 +8529,9 @@ "text": "emitted from lime and urea application was estimated from IPCC default values, which may not represent emissions in subtropical conditions. This LCA may be improved by reducing the uncertainty of factors for estimating emissions from excreta and feed production, including the C sequestration or emissions as a function of soil management." }, { - "self_ref": "#/texts/417", + "self_ref": "#/texts/428", "parent": { - "$ref": "#/texts/245" + "$ref": "#/texts/256" }, "children": [ { @@ -8363,7 +8549,7 @@ "level": 2 }, { - "self_ref": "#/texts/418", + "self_ref": "#/texts/429", "parent": { "$ref": "#/groups/27" }, @@ -8375,7 +8561,7 @@ "text": "The potential for using pasture can reduce the C footprint because milk production kept pace with animal confinement. However, if milk production is to decrease with lower TMR intake and inclusion of pasture [19], the C footprint would be expected to increase. Lorenz et al. [22] showed that an increase in milk yield from 5,000 to 6,000 kg ECM reduced the C footprint by 0.12 kg CO" }, { - "self_ref": "#/texts/419", + "self_ref": "#/texts/430", "parent": { "$ref": "#/groups/27" }, @@ -8394,7 +8580,7 @@ } }, { - "self_ref": "#/texts/420", + "self_ref": "#/texts/431", "parent": { "$ref": "#/groups/27" }, @@ -8406,7 +8592,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/421", + "self_ref": "#/texts/432", "parent": { "$ref": "#/groups/27" }, @@ -8425,7 +8611,7 @@ } }, { - "self_ref": "#/texts/422", + "self_ref": "#/texts/433", "parent": { "$ref": "#/groups/27" }, @@ -8437,7 +8623,7 @@ "text": ", whereas an increase from 10,000 to 11,000 kg ECM reduced the C footprint by only 0.06 kg CO" }, { - "self_ref": "#/texts/423", + "self_ref": "#/texts/434", "parent": { "$ref": "#/groups/27" }, @@ -8456,7 +8642,7 @@ } }, { - "self_ref": "#/texts/424", + "self_ref": "#/texts/435", "parent": { "$ref": "#/groups/27" }, @@ -8468,7 +8654,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/425", + "self_ref": "#/texts/436", "parent": { "$ref": "#/groups/27" }, @@ -8487,7 +8673,7 @@ } }, { - "self_ref": "#/texts/426", + "self_ref": "#/texts/437", "parent": { "$ref": "#/groups/27" }, @@ -8499,7 +8685,7 @@ "text": ". Hence, the impact of increasing milk production on decreasing C footprint is not linear, and mitigation measures, such as breeding for increased genetic yield potential and increasing concentrate ratio in the diet, are potentially harmful for animal’s health and welfare [70]. For instance, increasing concentrate ratio potentially increases the occurrence of subclinical ketosis and foot lesions, and C footprint may increase by 0.03 kg CO" }, { - "self_ref": "#/texts/427", + "self_ref": "#/texts/438", "parent": { "$ref": "#/groups/27" }, @@ -8518,7 +8704,7 @@ } }, { - "self_ref": "#/texts/428", + "self_ref": "#/texts/439", "parent": { "$ref": "#/groups/27" }, @@ -8530,7 +8716,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/429", + "self_ref": "#/texts/440", "parent": { "$ref": "#/groups/27" }, @@ -8549,7 +8735,7 @@ } }, { - "self_ref": "#/texts/430", + "self_ref": "#/texts/441", "parent": { "$ref": "#/groups/27" }, @@ -8561,7 +8747,7 @@ "text": "in subclinical ketosis [71] and by 0.02 kg CO" }, { - "self_ref": "#/texts/431", + "self_ref": "#/texts/442", "parent": { "$ref": "#/groups/27" }, @@ -8580,7 +8766,7 @@ } }, { - "self_ref": "#/texts/432", + "self_ref": "#/texts/443", "parent": { "$ref": "#/groups/27" }, @@ -8592,7 +8778,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/433", + "self_ref": "#/texts/444", "parent": { "$ref": "#/groups/27" }, @@ -8611,7 +8797,7 @@ } }, { - "self_ref": "#/texts/434", + "self_ref": "#/texts/445", "parent": { "$ref": "#/groups/27" }, @@ -8623,7 +8809,7 @@ "text": "in case of foot lesions [72]." }, { - "self_ref": "#/texts/435", + "self_ref": "#/texts/446", "parent": { "$ref": "#/groups/28" }, @@ -8635,7 +8821,7 @@ "text": "Grazing lands may also improve biodiversity [73]. Strategies such as zero tillage may increase stocks of soil C [74]. This study did not consider C sequestration during the growth of annual pastures, because it was assumed these grasses were planted with tillage, having a balance between C sequestration and C emissions [38]. Considering the C sequestration from no-tillage perennial pasture, the amount of C sequestration will more than compensates for C emitted. These results are in agreement with other authors who have shown that a reduction or elimination of soil tillage increases annual soil C sequestration in subtropical areas by 0.5 to 1.5 t ha" }, { - "self_ref": "#/texts/436", + "self_ref": "#/texts/447", "parent": { "$ref": "#/groups/28" }, @@ -8654,7 +8840,7 @@ } }, { - "self_ref": "#/texts/437", + "self_ref": "#/texts/448", "parent": { "$ref": "#/groups/28" }, @@ -8666,7 +8852,7 @@ "text": "[75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha" }, { - "self_ref": "#/texts/438", + "self_ref": "#/texts/449", "parent": { "$ref": "#/groups/28" }, @@ -8685,7 +8871,7 @@ } }, { - "self_ref": "#/texts/439", + "self_ref": "#/texts/450", "parent": { "$ref": "#/groups/28" }, @@ -8697,7 +8883,7 @@ "text": "would be sequestered, further reducing the C footprint by 0.015 and 0.025 kg CO" }, { - "self_ref": "#/texts/440", + "self_ref": "#/texts/451", "parent": { "$ref": "#/groups/28" }, @@ -8716,7 +8902,7 @@ } }, { - "self_ref": "#/texts/441", + "self_ref": "#/texts/452", "parent": { "$ref": "#/groups/28" }, @@ -8728,7 +8914,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/442", + "self_ref": "#/texts/453", "parent": { "$ref": "#/groups/28" }, @@ -8747,7 +8933,7 @@ } }, { - "self_ref": "#/texts/443", + "self_ref": "#/texts/454", "parent": { "$ref": "#/groups/28" }, @@ -8759,7 +8945,7 @@ "text": "for the scenarios using 75 and 50% TMR, respectively. Eliminating tillage, the reduction on total GHG emissions would be 0.03 and 0.05 kg CO" }, { - "self_ref": "#/texts/444", + "self_ref": "#/texts/455", "parent": { "$ref": "#/groups/28" }, @@ -8778,7 +8964,7 @@ } }, { - "self_ref": "#/texts/445", + "self_ref": "#/texts/456", "parent": { "$ref": "#/groups/28" }, @@ -8790,7 +8976,7 @@ "text": "e (kg ECM)" }, { - "self_ref": "#/texts/446", + "self_ref": "#/texts/457", "parent": { "$ref": "#/groups/28" }, @@ -8809,7 +8995,7 @@ } }, { - "self_ref": "#/texts/447", + "self_ref": "#/texts/458", "parent": { "$ref": "#/groups/28" }, @@ -8821,7 +9007,7 @@ "text": "for 75 and 50% TMR, respectively. However, this approach may be controversial because lands which have been consistently managed for decades have approached steady state C storage, so that net exchange of CO" }, { - "self_ref": "#/texts/448", + "self_ref": "#/texts/459", "parent": { "$ref": "#/groups/28" }, @@ -8840,7 +9026,7 @@ } }, { - "self_ref": "#/texts/449", + "self_ref": "#/texts/460", "parent": { "$ref": "#/groups/28" }, @@ -8852,7 +9038,7 @@ "text": "would be negligible [76]." }, { - "self_ref": "#/texts/450", + "self_ref": "#/texts/461", "parent": { "$ref": "#/texts/0" }, @@ -8869,7 +9055,7 @@ "level": 1 }, { - "self_ref": "#/texts/451", + "self_ref": "#/texts/462", "parent": { "$ref": "#/groups/29" }, @@ -8881,7 +9067,7 @@ "text": "This study assessed the C footprint of dairy cattle systems with or without access to pastures. Including pastures showed potential to maintain or decrease to a small extent the C footprint, which may be attributable to the evidence of low N" }, { - "self_ref": "#/texts/452", + "self_ref": "#/texts/463", "parent": { "$ref": "#/groups/29" }, @@ -8900,7 +9086,7 @@ } }, { - "self_ref": "#/texts/453", + "self_ref": "#/texts/464", "parent": { "$ref": "#/groups/29" }, @@ -8912,7 +9098,7 @@ "text": "O emissions from urine and dung in dairy systems in subtropical areas. Even though the enteric CH" }, { - "self_ref": "#/texts/454", + "self_ref": "#/texts/465", "parent": { "$ref": "#/groups/29" }, @@ -8931,7 +9117,7 @@ } }, { - "self_ref": "#/texts/455", + "self_ref": "#/texts/466", "parent": { "$ref": "#/groups/29" }, @@ -8943,7 +9129,7 @@ "text": "intensity was the largest source of CO" }, { - "self_ref": "#/texts/456", + "self_ref": "#/texts/467", "parent": { "$ref": "#/groups/29" }, @@ -8962,7 +9148,7 @@ } }, { - "self_ref": "#/texts/457", + "self_ref": "#/texts/468", "parent": { "$ref": "#/groups/29" }, @@ -8974,13 +9160,13 @@ "text": "e emissions, it did not change between different scenarios due to the narrow range of NDF content in diets and maintaining the same milk production with or without access to pastures." }, { - "self_ref": "#/texts/458", + "self_ref": "#/texts/469", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/459" + "$ref": "#/texts/470" } ], "content_layer": "body", @@ -8991,9 +9177,9 @@ "level": 1 }, { - "self_ref": "#/texts/459", + "self_ref": "#/texts/470", "parent": { - "$ref": "#/texts/458" + "$ref": "#/texts/469" }, "children": [], "content_layer": "body", @@ -9003,7 +9189,7 @@ "text": "Thanks to Anna Naranjo for helpful comments throughout the elaboration of this manuscript, and to André Thaler Neto and Roberto Kappes for providing the key characteristics of the herd considered in this study." }, { - "self_ref": "#/texts/460", + "self_ref": "#/texts/471", "parent": { "$ref": "#/texts/0" }, @@ -9020,7 +9206,7 @@ "level": 1 }, { - "self_ref": "#/texts/461", + "self_ref": "#/texts/472", "parent": { "$ref": "#/groups/30" }, @@ -9034,7 +9220,7 @@ "marker": "" }, { - "self_ref": "#/texts/462", + "self_ref": "#/texts/473", "parent": { "$ref": "#/groups/30" }, @@ -9048,7 +9234,7 @@ "marker": "" }, { - "self_ref": "#/texts/463", + "self_ref": "#/texts/474", "parent": { "$ref": "#/groups/30" }, @@ -9062,7 +9248,7 @@ "marker": "" }, { - "self_ref": "#/texts/464", + "self_ref": "#/texts/475", "parent": { "$ref": "#/groups/30" }, @@ -9076,7 +9262,7 @@ "marker": "" }, { - "self_ref": "#/texts/465", + "self_ref": "#/texts/476", "parent": { "$ref": "#/groups/30" }, @@ -9090,7 +9276,7 @@ "marker": "" }, { - "self_ref": "#/texts/466", + "self_ref": "#/texts/477", "parent": { "$ref": "#/groups/30" }, @@ -9104,7 +9290,7 @@ "marker": "" }, { - "self_ref": "#/texts/467", + "self_ref": "#/texts/478", "parent": { "$ref": "#/groups/30" }, @@ -9118,7 +9304,7 @@ "marker": "" }, { - "self_ref": "#/texts/468", + "self_ref": "#/texts/479", "parent": { "$ref": "#/groups/30" }, @@ -9132,7 +9318,7 @@ "marker": "" }, { - "self_ref": "#/texts/469", + "self_ref": "#/texts/480", "parent": { "$ref": "#/groups/30" }, @@ -9146,7 +9332,7 @@ "marker": "" }, { - "self_ref": "#/texts/470", + "self_ref": "#/texts/481", "parent": { "$ref": "#/groups/30" }, @@ -9160,7 +9346,7 @@ "marker": "" }, { - "self_ref": "#/texts/471", + "self_ref": "#/texts/482", "parent": { "$ref": "#/groups/30" }, @@ -9174,7 +9360,7 @@ "marker": "" }, { - "self_ref": "#/texts/472", + "self_ref": "#/texts/483", "parent": { "$ref": "#/groups/30" }, @@ -9188,7 +9374,7 @@ "marker": "" }, { - "self_ref": "#/texts/473", + "self_ref": "#/texts/484", "parent": { "$ref": "#/groups/30" }, @@ -9202,7 +9388,7 @@ "marker": "" }, { - "self_ref": "#/texts/474", + "self_ref": "#/texts/485", "parent": { "$ref": "#/groups/30" }, @@ -9216,7 +9402,7 @@ "marker": "" }, { - "self_ref": "#/texts/475", + "self_ref": "#/texts/486", "parent": { "$ref": "#/groups/30" }, @@ -9230,7 +9416,7 @@ "marker": "" }, { - "self_ref": "#/texts/476", + "self_ref": "#/texts/487", "parent": { "$ref": "#/groups/30" }, @@ -9244,7 +9430,7 @@ "marker": "" }, { - "self_ref": "#/texts/477", + "self_ref": "#/texts/488", "parent": { "$ref": "#/groups/30" }, @@ -9258,7 +9444,7 @@ "marker": "" }, { - "self_ref": "#/texts/478", + "self_ref": "#/texts/489", "parent": { "$ref": "#/groups/30" }, @@ -9272,7 +9458,7 @@ "marker": "" }, { - "self_ref": "#/texts/479", + "self_ref": "#/texts/490", "parent": { "$ref": "#/groups/30" }, @@ -9286,7 +9472,7 @@ "marker": "" }, { - "self_ref": "#/texts/480", + "self_ref": "#/texts/491", "parent": { "$ref": "#/groups/30" }, @@ -9300,7 +9486,7 @@ "marker": "" }, { - "self_ref": "#/texts/481", + "self_ref": "#/texts/492", "parent": { "$ref": "#/groups/30" }, @@ -9314,7 +9500,7 @@ "marker": "" }, { - "self_ref": "#/texts/482", + "self_ref": "#/texts/493", "parent": { "$ref": "#/groups/30" }, @@ -9328,7 +9514,7 @@ "marker": "" }, { - "self_ref": "#/texts/483", + "self_ref": "#/texts/494", "parent": { "$ref": "#/groups/30" }, @@ -9342,7 +9528,7 @@ "marker": "" }, { - "self_ref": "#/texts/484", + "self_ref": "#/texts/495", "parent": { "$ref": "#/groups/30" }, @@ -9356,7 +9542,7 @@ "marker": "" }, { - "self_ref": "#/texts/485", + "self_ref": "#/texts/496", "parent": { "$ref": "#/groups/30" }, @@ -9370,7 +9556,7 @@ "marker": "" }, { - "self_ref": "#/texts/486", + "self_ref": "#/texts/497", "parent": { "$ref": "#/groups/30" }, @@ -9384,7 +9570,7 @@ "marker": "" }, { - "self_ref": "#/texts/487", + "self_ref": "#/texts/498", "parent": { "$ref": "#/groups/30" }, @@ -9398,7 +9584,7 @@ "marker": "" }, { - "self_ref": "#/texts/488", + "self_ref": "#/texts/499", "parent": { "$ref": "#/groups/30" }, @@ -9412,7 +9598,7 @@ "marker": "" }, { - "self_ref": "#/texts/489", + "self_ref": "#/texts/500", "parent": { "$ref": "#/groups/30" }, @@ -9426,7 +9612,7 @@ "marker": "" }, { - "self_ref": "#/texts/490", + "self_ref": "#/texts/501", "parent": { "$ref": "#/groups/30" }, @@ -9440,7 +9626,7 @@ "marker": "" }, { - "self_ref": "#/texts/491", + "self_ref": "#/texts/502", "parent": { "$ref": "#/groups/30" }, @@ -9454,7 +9640,7 @@ "marker": "" }, { - "self_ref": "#/texts/492", + "self_ref": "#/texts/503", "parent": { "$ref": "#/groups/30" }, @@ -9468,7 +9654,7 @@ "marker": "" }, { - "self_ref": "#/texts/493", + "self_ref": "#/texts/504", "parent": { "$ref": "#/groups/30" }, @@ -9482,7 +9668,7 @@ "marker": "" }, { - "self_ref": "#/texts/494", + "self_ref": "#/texts/505", "parent": { "$ref": "#/groups/30" }, @@ -9496,7 +9682,7 @@ "marker": "" }, { - "self_ref": "#/texts/495", + "self_ref": "#/texts/506", "parent": { "$ref": "#/groups/30" }, @@ -9510,7 +9696,7 @@ "marker": "" }, { - "self_ref": "#/texts/496", + "self_ref": "#/texts/507", "parent": { "$ref": "#/groups/30" }, @@ -9524,7 +9710,7 @@ "marker": "" }, { - "self_ref": "#/texts/497", + "self_ref": "#/texts/508", "parent": { "$ref": "#/groups/30" }, @@ -9538,7 +9724,7 @@ "marker": "" }, { - "self_ref": "#/texts/498", + "self_ref": "#/texts/509", "parent": { "$ref": "#/groups/30" }, @@ -9552,7 +9738,7 @@ "marker": "" }, { - "self_ref": "#/texts/499", + "self_ref": "#/texts/510", "parent": { "$ref": "#/groups/30" }, @@ -9566,7 +9752,7 @@ "marker": "" }, { - "self_ref": "#/texts/500", + "self_ref": "#/texts/511", "parent": { "$ref": "#/groups/30" }, @@ -9580,7 +9766,7 @@ "marker": "" }, { - "self_ref": "#/texts/501", + "self_ref": "#/texts/512", "parent": { "$ref": "#/groups/30" }, @@ -9594,7 +9780,7 @@ "marker": "" }, { - "self_ref": "#/texts/502", + "self_ref": "#/texts/513", "parent": { "$ref": "#/groups/30" }, @@ -9608,7 +9794,7 @@ "marker": "" }, { - "self_ref": "#/texts/503", + "self_ref": "#/texts/514", "parent": { "$ref": "#/groups/30" }, @@ -9622,7 +9808,7 @@ "marker": "" }, { - "self_ref": "#/texts/504", + "self_ref": "#/texts/515", "parent": { "$ref": "#/groups/30" }, @@ -9636,7 +9822,7 @@ "marker": "" }, { - "self_ref": "#/texts/505", + "self_ref": "#/texts/516", "parent": { "$ref": "#/groups/30" }, @@ -9650,7 +9836,7 @@ "marker": "" }, { - "self_ref": "#/texts/506", + "self_ref": "#/texts/517", "parent": { "$ref": "#/groups/30" }, @@ -9664,7 +9850,7 @@ "marker": "" }, { - "self_ref": "#/texts/507", + "self_ref": "#/texts/518", "parent": { "$ref": "#/groups/30" }, @@ -9678,7 +9864,7 @@ "marker": "" }, { - "self_ref": "#/texts/508", + "self_ref": "#/texts/519", "parent": { "$ref": "#/groups/30" }, @@ -9692,7 +9878,7 @@ "marker": "" }, { - "self_ref": "#/texts/509", + "self_ref": "#/texts/520", "parent": { "$ref": "#/groups/30" }, @@ -9706,7 +9892,7 @@ "marker": "" }, { - "self_ref": "#/texts/510", + "self_ref": "#/texts/521", "parent": { "$ref": "#/groups/30" }, @@ -9720,7 +9906,7 @@ "marker": "" }, { - "self_ref": "#/texts/511", + "self_ref": "#/texts/522", "parent": { "$ref": "#/groups/30" }, @@ -9734,7 +9920,7 @@ "marker": "" }, { - "self_ref": "#/texts/512", + "self_ref": "#/texts/523", "parent": { "$ref": "#/groups/30" }, @@ -9748,7 +9934,7 @@ "marker": "" }, { - "self_ref": "#/texts/513", + "self_ref": "#/texts/524", "parent": { "$ref": "#/groups/30" }, @@ -9762,7 +9948,7 @@ "marker": "" }, { - "self_ref": "#/texts/514", + "self_ref": "#/texts/525", "parent": { "$ref": "#/groups/30" }, @@ -9776,7 +9962,7 @@ "marker": "" }, { - "self_ref": "#/texts/515", + "self_ref": "#/texts/526", "parent": { "$ref": "#/groups/30" }, @@ -9790,7 +9976,7 @@ "marker": "" }, { - "self_ref": "#/texts/516", + "self_ref": "#/texts/527", "parent": { "$ref": "#/groups/30" }, @@ -9804,7 +9990,7 @@ "marker": "" }, { - "self_ref": "#/texts/517", + "self_ref": "#/texts/528", "parent": { "$ref": "#/groups/30" }, @@ -9818,7 +10004,7 @@ "marker": "" }, { - "self_ref": "#/texts/518", + "self_ref": "#/texts/529", "parent": { "$ref": "#/groups/30" }, @@ -9832,7 +10018,7 @@ "marker": "" }, { - "self_ref": "#/texts/519", + "self_ref": "#/texts/530", "parent": { "$ref": "#/groups/30" }, @@ -9846,7 +10032,7 @@ "marker": "" }, { - "self_ref": "#/texts/520", + "self_ref": "#/texts/531", "parent": { "$ref": "#/groups/30" }, @@ -9860,7 +10046,7 @@ "marker": "" }, { - "self_ref": "#/texts/521", + "self_ref": "#/texts/532", "parent": { "$ref": "#/groups/30" }, @@ -9874,7 +10060,7 @@ "marker": "" }, { - "self_ref": "#/texts/522", + "self_ref": "#/texts/533", "parent": { "$ref": "#/groups/30" }, @@ -9888,7 +10074,7 @@ "marker": "" }, { - "self_ref": "#/texts/523", + "self_ref": "#/texts/534", "parent": { "$ref": "#/groups/30" }, @@ -9902,7 +10088,7 @@ "marker": "" }, { - "self_ref": "#/texts/524", + "self_ref": "#/texts/535", "parent": { "$ref": "#/groups/30" }, @@ -9916,7 +10102,7 @@ "marker": "" }, { - "self_ref": "#/texts/525", + "self_ref": "#/texts/536", "parent": { "$ref": "#/groups/30" }, @@ -9930,7 +10116,7 @@ "marker": "" }, { - "self_ref": "#/texts/526", + "self_ref": "#/texts/537", "parent": { "$ref": "#/groups/30" }, @@ -9944,7 +10130,7 @@ "marker": "" }, { - "self_ref": "#/texts/527", + "self_ref": "#/texts/538", "parent": { "$ref": "#/groups/30" }, @@ -9958,7 +10144,7 @@ "marker": "" }, { - "self_ref": "#/texts/528", + "self_ref": "#/texts/539", "parent": { "$ref": "#/groups/30" }, @@ -9972,7 +10158,7 @@ "marker": "" }, { - "self_ref": "#/texts/529", + "self_ref": "#/texts/540", "parent": { "$ref": "#/groups/30" }, @@ -9986,7 +10172,7 @@ "marker": "" }, { - "self_ref": "#/texts/530", + "self_ref": "#/texts/541", "parent": { "$ref": "#/groups/30" }, @@ -10000,7 +10186,7 @@ "marker": "" }, { - "self_ref": "#/texts/531", + "self_ref": "#/texts/542", "parent": { "$ref": "#/groups/30" }, @@ -10014,7 +10200,7 @@ "marker": "" }, { - "self_ref": "#/texts/532", + "self_ref": "#/texts/543", "parent": { "$ref": "#/groups/30" }, @@ -10028,7 +10214,7 @@ "marker": "" }, { - "self_ref": "#/texts/533", + "self_ref": "#/texts/544", "parent": { "$ref": "#/groups/30" }, @@ -10042,7 +10228,7 @@ "marker": "" }, { - "self_ref": "#/texts/534", + "self_ref": "#/texts/545", "parent": { "$ref": "#/groups/30" }, @@ -10056,7 +10242,7 @@ "marker": "" }, { - "self_ref": "#/texts/535", + "self_ref": "#/texts/546", "parent": { "$ref": "#/groups/30" }, @@ -10070,7 +10256,7 @@ "marker": "" }, { - "self_ref": "#/texts/536", + "self_ref": "#/texts/547", "parent": { "$ref": "#/groups/30" }, @@ -10088,7 +10274,7 @@ { "self_ref": "#/pictures/0", "parent": { - "$ref": "#/texts/36" + "$ref": "#/texts/47" }, "children": [], "content_layer": "body", @@ -10096,7 +10282,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/38" + "$ref": "#/texts/49" } ], "references": [], @@ -10106,7 +10292,7 @@ { "self_ref": "#/pictures/1", "parent": { - "$ref": "#/texts/247" + "$ref": "#/texts/258" }, "children": [], "content_layer": "body", @@ -10114,7 +10300,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/265" + "$ref": "#/texts/276" } ], "references": [], @@ -10124,7 +10310,7 @@ { "self_ref": "#/pictures/2", "parent": { - "$ref": "#/texts/317" + "$ref": "#/texts/328" }, "children": [], "content_layer": "body", @@ -10132,7 +10318,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/331" + "$ref": "#/texts/342" } ], "references": [], @@ -10142,7 +10328,7 @@ { "self_ref": "#/pictures/3", "parent": { - "$ref": "#/texts/345" + "$ref": "#/texts/356" }, "children": [], "content_layer": "body", @@ -10150,7 +10336,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/381" + "$ref": "#/texts/392" } ], "references": [], @@ -10162,7 +10348,7 @@ { "self_ref": "#/tables/0", "parent": { - "$ref": "#/texts/39" + "$ref": "#/texts/50" }, "children": [], "content_layer": "body", @@ -10170,7 +10356,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/42" + "$ref": "#/texts/53" } ], "references": [], @@ -11229,7 +11415,7 @@ { "self_ref": "#/tables/1", "parent": { - "$ref": "#/texts/83" + "$ref": "#/texts/94" }, "children": [], "content_layer": "body", @@ -11237,7 +11423,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/91" + "$ref": "#/texts/102" } ], "references": [], @@ -16836,7 +17022,7 @@ { "self_ref": "#/tables/2", "parent": { - "$ref": "#/texts/92" + "$ref": "#/texts/103" }, "children": [], "content_layer": "body", @@ -16844,7 +17030,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/100" + "$ref": "#/texts/111" } ], "references": [], @@ -18051,7 +18237,7 @@ { "self_ref": "#/tables/3", "parent": { - "$ref": "#/texts/92" + "$ref": "#/texts/103" }, "children": [], "content_layer": "body", @@ -18059,7 +18245,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/132" + "$ref": "#/texts/143" } ], "references": [], @@ -21774,7 +21960,7 @@ { "self_ref": "#/tables/4", "parent": { - "$ref": "#/texts/197" + "$ref": "#/texts/208" }, "children": [], "content_layer": "body", @@ -21782,7 +21968,7 @@ "prov": [], "captions": [ { - "$ref": "#/texts/199" + "$ref": "#/texts/210" } ], "references": [], diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.md b/tests/data/jats/groundtruth/pone.0234687.nxml.md index fec4e1bb30..098b61f1a6 100644 --- a/tests/data/jats/groundtruth/pone.0234687.nxml.md +++ b/tests/data/jats/groundtruth/pone.0234687.nxml.md @@ -6,7 +6,7 @@ Department of Animal Science, University of California, Davis, California, Unite ## Abstract -Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO2) equivalents (CO2e) (kg energy-corrected milk (ECM))-1, encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation-1. The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) *ad libitum* intake, 75, and 50% of *ad libitum* TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO2e (kg ECM)-1. Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO2e (kg ECM)-1 in scenarios including pastures compared to *ad libitum* TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent. +Carbon (C) footprint of dairy production, expressed in kg C dioxide (CO 2 ) equivalents (CO 2 e) (kg energy-corrected milk (ECM)) -1 , encompasses emissions from feed production, diet management and total product output. The proportion of pasture on diets may affect all these factors, mainly in subtropical climate zones, where cows may access tropical and temperate pastures during warm and cold seasons, respectively. The aim of the study was to assess the C footprint of a dairy system with annual tropical and temperate pastures in a subtropical region. The system boundary included all processes up to the animal farm gate. Feed requirement during the entire life of each cow was based on data recorded from Holstein × Jersey cow herds producing an average of 7,000 kg ECM lactation -1 . The milk production response as consequence of feed strategies (scenarios) was based on results from two experiments (warm and cold seasons) using lactating cows from the same herd. Three scenarios were evaluated: total mixed ration (TMR) *ad libitum* intake, 75, and 50% of *ad libitum* TMR intake with access to grazing either a tropical or temperate pasture during lactation periods. Considering IPCC and international literature values to estimate emissions from urine/dung, feed production and electricity, the C footprint was similar between scenarios, averaging 1.06 kg CO 2 e (kg ECM) -1 . Considering factors from studies conducted in subtropical conditions and actual inputs for on-farm feed production, the C footprint decreased 0.04 kg CO 2 e (kg ECM) -1 in scenarios including pastures compared to *ad libitum* TMR. Regardless of factors considered, emissions from feed production decreased as the proportion of pasture went up. In conclusion, decreasing TMR intake and including pastures in dairy cow diets in subtropical conditions have the potential to maintain or reduce the C footprint to a small extent. ## Introduction diff --git a/tests/test_backend_jats.py b/tests/test_backend_jats.py index 898e38ea6c..c7912435af 100644 --- a/tests/test_backend_jats.py +++ b/tests/test_backend_jats.py @@ -56,14 +56,6 @@ from pathlib import Path import pytest -from docling.datamodel.backend_options import JatsBackendOptions -from docling.datamodel.base_models import DocumentStream, InputFormat -from docling.datamodel.document import ConversionResult -from docling.document_converter import ( - DocumentConverter, - FormatOption, - XMLJatsFormatOption, -) from docling_core.types.doc import ( DocItemLabel, DoclingDocument, @@ -74,6 +66,15 @@ from docling_core.types.doc.document import Script from PIL import Image +from docling.datamodel.backend_options import JatsBackendOptions +from docling.datamodel.base_models import DocumentStream, InputFormat +from docling.datamodel.document import ConversionResult +from docling.document_converter import ( + DocumentConverter, + FormatOption, + XMLJatsFormatOption, +) + from .test_data_gen_flag import GEN_TEST_DATA from .verify_utils import verify_document, verify_export @@ -246,28 +247,25 @@ def test_jats_plain_abstract_styling_is_preserved(): doc = convert_jats_article_meta( """ Abstract Styling Test - -

We study Homo sapiens, key results, - H2O at 103 Pa, u, - old.

- +

We study Homo sapiens, key results, H2O at 103 Pa, u, old.

 """ ) groups = _inline_group_items(doc) assert len(groups) == 1 - # Punctuation adjacent to a styled run without source whitespace is - # absorbed into that run (the serializers join inline items with a - # space, so a standalone "." would export as "details ."). Runs joined - # without whitespace in the source (H2O, 103) are - # fused the same way to keep the exported text byte-identical. + # Abstract paragraphs go through the paragraph implementation + # (_walk_linear, from #3726): one inline run per styled span, boundary + # whitespace stripped per run. Spacing on markdown export is delegated + # to the docling-core serializers (docling-core#693); runs are not fused + # across spaceless boundaries here. assert [_formatting_tuple(item) for item in groups[0]] == [ (DocItemLabel.TEXT, "We study", None), ( DocItemLabel.TEXT, - "Homo sapiens,", + "Homo sapiens", (False, True, False, False, Script.BASELINE), ), + (DocItemLabel.TEXT, ",", None), ( DocItemLabel.TEXT, "key", @@ -275,86 +273,121 @@ def test_jats_plain_abstract_styling_is_preserved(): ), ( DocItemLabel.TEXT, - "results,", + "results", (True, True, False, False, Script.BASELINE), ), - (DocItemLabel.TEXT, "H2O at 103", (False, False, False, False, Script.SUB)), + (DocItemLabel.TEXT, ", H", None), + ( + DocItemLabel.TEXT, + "2", + (False, False, False, False, Script.SUB), + ), + (DocItemLabel.TEXT, "O at 10", None), + ( + DocItemLabel.TEXT, + "3", + (False, False, False, False, Script.SUPER), + ), (DocItemLabel.TEXT, "Pa,", None), ( DocItemLabel.TEXT, - "u,", + "u", (False, False, True, False, Script.BASELINE), ), + (DocItemLabel.TEXT, ",", None), ( DocItemLabel.TEXT, - "old.", + "old", (False, False, False, True, Script.BASELINE), ), + (DocItemLabel.TEXT, ".", None), ] -def test_jats_plain_abstract_styling_keeps_source_spacing(): - """Styled runs must not gain spaces where the source XML had none. +def test_jats_abstract_styling_preserves_inline_runs(): + """Styled spans become their own inline runs; nothing is fused or dropped. - The serializers join sibling inline text items with a single space, so - emitting ``in vitro.`` as two items would export - ``in vitro .``. Fusing runs across spaceless boundaries keeps the - exported text (modulo styling markers) byte-identical to the source. + Per the docling-core serializer contract (docling-core#693), spacing on + export is the serializers' job: the backend must not fuse runs across + spaceless boundaries (``CO2`` stays three runs) nor invent + whitespace. Markdown export is therefore not asserted here — it is + suboptimal until #693 lands and is deliberately out of scope. """ - def abstract_markdown(paragraph: str) -> str: + def abstract_runs(paragraph: str) -> list: doc = convert_jats_article_meta( f""" Spacing Test

{paragraph}

 """ ) - md = doc.export_to_markdown() - return md.split("## Abstract", 1)[1].strip() + groups = _inline_group_items(doc) + assert len(groups) == 1 + return [_formatting_tuple(item) for item in groups[0]] - def plain_text(markdown: str) -> str: - for marker in ("***", "**", "*", "~~", "__", "`"): - markdown = markdown.replace(marker, "") - return markdown + italic = (False, True, False, False, Script.BASELINE) + bold = (True, False, False, False, Script.BASELINE) + sub = (False, False, False, False, Script.SUB) + sup = (False, False, False, False, Script.SUPER) + T = DocItemLabel.TEXT cases = [ - # (source paragraph, expected markdown, expected marker-stripped text) + # (source paragraph, expected inline runs) ( "conditions in vitro.", - "conditions *in vitro.*", - "conditions in vitro.", + [(T, "conditions", None), (T, "in vitro", italic), (T, ".", None)], ), ( "cultures of Y. pestis, and E. coli.", - "cultures of *Y. pestis,* and *E. coli.*", - "cultures of Y. pestis, and E. coli.", + [ + (T, "cultures of", None), + (T, "Y. pestis", italic), + (T, ", and", None), + (T, "E. coli", italic), + (T, ".", None), + ], ), ( "CO2 and (CO2e) at 103 Pa", - "CO2 and (CO2e) at 103 Pa", - "CO2 and (CO2e) at 103 Pa", + [ + (T, "CO", None), + (T, "2", sub), + (T, "and (CO", None), + (T, "2", sub), + (T, "e) at 10", None), + (T, "3", sup), + (T, "Pa", None), + ], ), ( "rate (ECM))-1, lactation-1.", - "rate (ECM))-1, lactation-1.", - "rate (ECM))-1, lactation-1.", + [ + (T, "rate (ECM))", None), + (T, "-1", sup), + (T, ", lactation", None), + (T, "-1", sup), + (T, ".", None), + ], ), ( "(term) and [other];", - "*(term)* and **[other];**", - "(term) and [other];", + [ + (T, "(", None), + (T, "term", italic), + (T, ") and [", None), + (T, "other", bold), + (T, "];", None), + ], ), - # Ragged multi-line source whitespace still collapses normally. + # Newlines in source XML become spaces; other whitespace is kept + # as authored (no collapsing, no stripping of interior blanks). ( "a b\nc\n d.", - "a *b c* d.", - "a b c d.", + [(T, "a", None), (T, "b c", italic), (T, "d.", None)], ), ] - for paragraph, expected_md, expected_text in cases: - md = abstract_markdown(paragraph) - assert md == expected_md, f"{paragraph!r}: got {md!r}" - assert plain_text(md) == expected_text, f"{paragraph!r}: got {plain_text(md)!r}" + for paragraph, expected in cases: + assert abstract_runs(paragraph) == expected, f"{paragraph!r}" def test_jats_structured_abstract_styling_is_preserved(): @@ -425,8 +458,9 @@ def test_jats_footnote_styling_is_preserved(): groups = _inline_group_items(doc) assert len(groups) == 1 - # The "." has no whitespace before it in the source, so it is absorbed - # into the bold run; a standalone "." item would export as "details .". + # No workaround: the "." after the bold run stays its own inline run, + # and the bold scope ends before it. Spacing on export is delegated to + # the docling-core serializers (docling-core#693). assert [_formatting_tuple(item) for item in groups[0]] == [ (DocItemLabel.FOOTNOTE, "1", None), (DocItemLabel.FOOTNOTE, "See", None), @@ -438,9 +472,10 @@ def test_jats_footnote_styling_is_preserved(): (DocItemLabel.FOOTNOTE, "for", None), ( DocItemLabel.FOOTNOTE, - "details.", + "details", (True, False, False, False, Script.BASELINE), ), + (DocItemLabel.FOOTNOTE, ".", None), ] From c50b37b6be6d1dd6a90c32c4076e536869e8baf1 Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Fri, 2 Oct 2026 11:30:00 -0700 Subject: [PATCH 6/8] fix(jats): normalize XML line-break indentation Signed-off-by: Junyi Yao --- docling/backend/xml/jats_backend.py | 20 +++++++++++-- .../jats/groundtruth/pmc2231364.nxml.itxt | 8 +++--- .../jats/groundtruth/pmc2231364.nxml.json | 28 +++++++++---------- .../data/jats/groundtruth/pmc2231364.nxml.md | 8 +++--- tests/test_backend_jats.py | 25 +++++++++++++++++ 5 files changed, 64 insertions(+), 25 deletions(-) mode change 100644 => 100755 docling/backend/xml/jats_backend.py diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py old mode 100644 new mode 100755 index b468dfeed3..060995b60f --- a/docling/backend/xml/jats_backend.py +++ b/docling/backend/xml/jats_backend.py @@ -23,6 +23,7 @@ from __future__ import annotations import logging +import re import traceback import warnings from dataclasses import dataclass, replace @@ -79,6 +80,9 @@ DEFAULT_HEADER_REFERENCES: Final[str] = "References" DEFAULT_TEXT_ETAL: Final[str] = "et al." _XLINK_HREF: Final[str] = "{http://www.w3.org/1999/xlink}href" +_XML_INDENTED_LINE_BREAK_RE: Final[re.Pattern[str]] = re.compile( + r"[^\S\r\n]*(?:\r\n?|\n)(?:[^\S\r\n]*(?:\r\n?|\n))*[^\S\r\n]*" +) _RASTER_IMAGE_SUFFIXES: Final[tuple[str, ...]] = ( ".jpg", @@ -783,7 +787,7 @@ def _walk_inline_formula( current = JatsDocumentBackend._merge_formatting(formatting, node.tag) segments: list[InlineSegment] = [] if node.text: - text = node.text.replace("\n", " ") + text = JatsDocumentBackend._normalize_xml_line_breaks(node.text) if text: segments.append( InlineSegment( @@ -813,7 +817,7 @@ def _walk_inline_formula( JatsDocumentBackend._walk_inline_formula(child, current, hyperlink) ) if child.tail: - tail = child.tail.replace("\n", " ") + tail = JatsDocumentBackend._normalize_xml_line_breaks(child.tail) if tail: segments.append( InlineSegment( @@ -825,6 +829,16 @@ def _walk_inline_formula( ) return segments + @staticmethod + def _normalize_xml_line_breaks(text: str) -> str: + """Remove XML formatting indentation around line breaks. + + Same-line whitespace is significant and remains untouched. A run of + line breaks and its surrounding indentation, however, comes from the + source XML layout and represents a single word boundary. + """ + return _XML_INDENTED_LINE_BREAK_RE.sub(" ", text) + @staticmethod def _append_run( segments: list[InlineSegment], @@ -833,7 +847,7 @@ def _append_run( hyperlink: AnyUrl | Path | None = None, ) -> None: """Append text, coalescing when formatting and hyperlink both match.""" - text = text.replace("\n", " ") + text = JatsDocumentBackend._normalize_xml_line_breaks(text) if not text: return if ( diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt index 63c7b072a2..c314c160b2 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.itxt +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.itxt @@ -6,19 +6,19 @@ item-0 at level 0: unspecified: group _root_ item-5 at level 4: inline: group group item-6 at level 5: text: Environmental modulation of gene expression in item-7 at level 5: text: Yersinia pestis - item-8 at level 5: text: is critical for it ... ferent stress conditions + item-8 at level 5: text: is critical for its life style a ... rown under different stress conditions item-9 at level 5: text: in vitro item-10 at level 5: text: . item-11 at level 3: section_header: Results item-12 at level 4: inline: group group - item-13 at level 5: text: To provide us with a comprehensi ... lobal gene expression in + item-13 at level 5: text: To provide us with a comprehensi ... odulation of global gene expression in item-14 at level 5: text: Y. pestis item-15 at level 5: text: , we have analyzed the gene expr ... s. Almost all known virulence genes of item-16 at level 5: text: Y. pestis - item-17 at level 5: text: were differentiall ... ophoretic mobility shift assay (EMSA). + item-17 at level 5: text: were differentially regulated un ... ophoretic mobility shift assay (EMSA). item-18 at level 3: section_header: Conclusion item-19 at level 4: inline: group group - item-20 at level 5: text: The comparative transcriptomics ... r regulatory circuits in + item-20 at level 5: text: The comparative transcriptomics ... is and cellular regulatory circuits in item-21 at level 5: text: Y. pestis item-22 at level 5: text: , it also serves as a basis for ... icroarray data using existing methods. item-23 at level 2: section_header: Introduction diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.json b/tests/data/jats/groundtruth/pmc2231364.nxml.json index 1a90099b86..62b9c859bf 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.json +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.json @@ -214,8 +214,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions", - "text": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions" + "orig": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions", + "text": "is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions" }, { "self_ref": "#/texts/7", @@ -274,8 +274,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "To provide us with a comprehensive view of environmental modulation of global gene expression in", - "text": "To provide us with a comprehensive view of environmental modulation of global gene expression in" + "orig": "To provide us with a comprehensive view of environmental modulation of global gene expression in", + "text": "To provide us with a comprehensive view of environmental modulation of global gene expression in" }, { "self_ref": "#/texts/11", @@ -305,8 +305,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of", - "text": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of" + "orig": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of", + "text": ", we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of" }, { "self_ref": "#/texts/13", @@ -336,8 +336,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA).", - "text": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA)." + "orig": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA).", + "text": "were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA)." }, { "self_ref": "#/texts/15", @@ -365,8 +365,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in", - "text": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in" + "orig": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in", + "text": "The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in" }, { "self_ref": "#/texts/17", @@ -396,8 +396,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", - "text": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods." + "orig": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods.", + "text": ", it also serves as a basis for integrating increasing volumes of microarray data using existing methods." }, { "self_ref": "#/texts/19", @@ -425,8 +425,8 @@ "content_layer": "body", "label": "text", "prov": [], - "orig": "Yersinia pestis is the causative agent of plague, one of the most devastating infectious diseases in human history.", - "text": "Yersinia pestis is the causative agent of plague, one of the most devastating infectious diseases in human history." + "orig": "Yersinia pestis is the causative agent of plague, one of the most devastating infectious diseases in human history.", + "text": "Yersinia pestis is the causative agent of plague, one of the most devastating infectious diseases in human history." } ], "pictures": [], diff --git a/tests/data/jats/groundtruth/pmc2231364.nxml.md b/tests/data/jats/groundtruth/pmc2231364.nxml.md index 5a7fd997ca..d67a234765 100644 --- a/tests/data/jats/groundtruth/pmc2231364.nxml.md +++ b/tests/data/jats/groundtruth/pmc2231364.nxml.md @@ -6,16 +6,16 @@ Yiquan Hu, Yarong Miao ### Background -Environmental modulation of gene expression in *Yersinia pestis* is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions *in vitro* . +Environmental modulation of gene expression in *Yersinia pestis* is critical for its life style and pathogenesis. Using cDNA microarray technology, we have analyzed the global gene expression of this deadly pathogen when grown under different stress conditions *in vitro* . ### Results -To provide us with a comprehensive view of environmental modulation of global gene expression in *Y. pestis* , we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of *Y. pestis* were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). +To provide us with a comprehensive view of environmental modulation of global gene expression in *Y. pestis* , we have analyzed the gene expression profiles of 25 different stress conditions. Almost all known virulence genes of *Y. pestis* were differentially regulated under multiple environmental perturbations. Clustering enabled us to functionally classify co-expressed genes, including some uncharacterized genes. Collections of operons were predicted from the microarray data, and some of these were confirmed by reverse-transcription polymerase chain reaction (RT-PCR). Several regulatory DNA motifs, probably recognized by the regulatory protein Fur, PurR, or Fnr, were predicted from the clustered genes, and a Fur binding site in the corresponding promoter regions was verified by electrophoretic mobility shift assay (EMSA). ### Conclusion -The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in *Y. pestis* , it also serves as a basis for integrating increasing volumes of microarray data using existing methods. +The comparative transcriptomics analysis we present here not only benefits our understanding of the molecular determinants of pathogenesis and cellular regulatory circuits in *Y. pestis* , it also serves as a basis for integrating increasing volumes of microarray data using existing methods. ## Introduction -Yersinia pestis is the causative agent of plague, one of the most devastating infectious diseases in human history. \ No newline at end of file +Yersinia pestis is the causative agent of plague, one of the most devastating infectious diseases in human history. \ No newline at end of file diff --git a/tests/test_backend_jats.py b/tests/test_backend_jats.py index c7912435af..147ed08c50 100644 --- a/tests/test_backend_jats.py +++ b/tests/test_backend_jats.py @@ -390,6 +390,31 @@ def abstract_runs(paragraph: str) -> list: assert abstract_runs(paragraph) == expected, f"{paragraph!r}" +def test_jats_inline_runs_drop_xml_indentation_but_keep_same_line_whitespace(): + paragraph = """

Alpha beta Yersinia pestis is + critical here.

""" + documents = [ + convert_jats_article_meta( + f""" + Abstract Spacing Test + {paragraph} +""" + ), + convert_jats_body(f"Body Spacing Test{paragraph}"), + ] + + italic = (False, True, False, False, Script.BASELINE) + expected = [ + (DocItemLabel.TEXT, "Alpha beta", None), + (DocItemLabel.TEXT, "Yersinia pestis", italic), + (DocItemLabel.TEXT, "is critical here.", None), + ] + for doc in documents: + groups = _inline_group_items(doc) + assert len(groups) == 1 + assert [_formatting_tuple(item) for item in groups[0]] == expected + + def test_jats_structured_abstract_styling_is_preserved(): doc = convert_jats_article_meta( """ From 5ac1b45adead1e371b90500c9c0d5c30057d98f0 Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Mon, 5 Oct 2026 13:15:07 -0700 Subject: [PATCH 7/8] fix(jats): address abstract review feedback Signed-off-by: Junyi Yao --- docling/backend/xml/jats_backend.py | 54 +- .../jats/groundtruth/elife-56337.nxml.itxt | 206 ++--- .../jats/groundtruth/elife-56337.nxml.json | 846 +++++------------- tests/test_backend_jats.py | 53 +- 4 files changed, 393 insertions(+), 766 deletions(-) mode change 100755 => 100644 docling/backend/xml/jats_backend.py diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py old mode 100755 new mode 100644 index 060995b60f..cc4dd4e751 --- a/docling/backend/xml/jats_backend.py +++ b/docling/backend/xml/jats_backend.py @@ -23,7 +23,6 @@ from __future__ import annotations import logging -import re import traceback import warnings from dataclasses import dataclass, replace @@ -80,9 +79,6 @@ DEFAULT_HEADER_REFERENCES: Final[str] = "References" DEFAULT_TEXT_ETAL: Final[str] = "et al." _XLINK_HREF: Final[str] = "{http://www.w3.org/1999/xlink}href" -_XML_INDENTED_LINE_BREAK_RE: Final[re.Pattern[str]] = re.compile( - r"[^\S\r\n]*(?:\r\n?|\n)(?:[^\S\r\n]*(?:\r\n?|\n))*[^\S\r\n]*" -) _RASTER_IMAGE_SUFFIXES: Final[tuple[str, ...]] = ( ".jpg", @@ -129,15 +125,12 @@ class AbstractSection(TypedDict): """A single titled section inside a structured abstract.""" title: str - # The

elements; walked with the paragraph implementation - # (_walk_linear) at emit time so abstracts share the body-paragraph - # styling path instead of a parallel one. + # Raw

nodes are walked at emit time to preserve inline styling. paragraphs: list[etree._Element] class Abstract(TypedDict): label: str - # Plain

children, as above. paragraphs: list[etree._Element] sections: list[AbstractSection] # structured sub-sections ( children) @@ -332,9 +325,7 @@ def _get_node_text(node: etree._Element) -> str: @staticmethod def _parse_abstract_section(section_node: etree._Element) -> AbstractSection: - """Parse a single `` element inside an abstract into an - `AbstractSection` with a title and its `

` elements. Styling is - applied at emit time via the paragraph implementation.""" + """Parse an abstract section while retaining its paragraph nodes.""" title_nodes = section_node.xpath("title|label") title = ( JatsDocumentBackend._get_node_text(title_nodes[0]) if title_nodes else "" @@ -544,11 +535,7 @@ def _add_abstract( parent=self.root, text=title, level=self.hlevel + 1 ) - # Plain (un-sectioned) abstract paragraphs: walked with the - # paragraph implementation (_walk_linear, from #3726) so that - # abstracts share the body-paragraph styling path. Inline-group - # spacing is left to the docling-core serializers per their - # contract (docling-core#693); no spacing workaround here. + # Inline-group serializer spacing is tracked in docling-core#693. for paragraph in paragraphs: self._walk_linear(doc, abstract_heading, paragraph) @@ -831,13 +818,18 @@ def _walk_inline_formula( @staticmethod def _normalize_xml_line_breaks(text: str) -> str: - """Remove XML formatting indentation around line breaks. - - Same-line whitespace is significant and remains untouched. A run of - line breaks and its surrounding indentation, however, comes from the - source XML layout and represents a single word boundary. - """ - return _XML_INDENTED_LINE_BREAK_RE.sub(" ", text) + """Collapse XML formatting whitespace around line breaks.""" + if "\n" not in text: + return text + + chunks = text.split("\n") + middle = [chunk.strip(" \t") for chunk in chunks[1:-1]] + normalized = [ + chunks[0].rstrip(" \t"), + *(chunk for chunk in middle if chunk), + chunks[-1].lstrip(" \t"), + ] + return " ".join(normalized) @staticmethod def _append_run( @@ -1205,9 +1197,6 @@ def _add_footnote_group( ) -> None: footnote_segments: list[list[InlineSegment]] = [] for fn in node.iterchildren(tag="fn"): - # Styled runs via the shared inline walker (#3726); spacing is - # left to the docling-core serializers per their contract - # (docling-core#693), with no spacing workaround here. segments = JatsDocumentBackend._strip_segments( JatsDocumentBackend._walk_inline_formula(fn) ) @@ -1240,16 +1229,17 @@ def _add_footnote_group( parent=heading, ) for segments in footnote_segments: - list_item = doc.add_list_item(parent=footnote_group, text="") - inline_item = doc.add_inline_group(parent=list_item) - for segment in segments: - doc.add_text( - label=segment.label, + if len(segments) == 1 and segments[0].label == DocItemLabel.FOOTNOTE: + segment = segments[0] + doc.add_list_item( + parent=footnote_group, text=segment.text, formatting=segment.formatting, hyperlink=segment.hyperlink, - parent=inline_item, ) + continue + list_item = doc.add_list_item(parent=footnote_group, text="") + JatsDocumentBackend._emit_inline(doc, list_item, segments) def _walk_linear( self, diff --git a/tests/data/jats/groundtruth/elife-56337.nxml.itxt b/tests/data/jats/groundtruth/elife-56337.nxml.itxt index e1065521fb..c7f0689cba 100644 --- a/tests/data/jats/groundtruth/elife-56337.nxml.itxt +++ b/tests/data/jats/groundtruth/elife-56337.nxml.itxt @@ -159,118 +159,94 @@ item-0 at level 0: unspecified: group _root_ item-152 at level 2: section_header: Additional information item-153 at level 3: section_header: Competing interests item-154 at level 4: list: group footnotes - item-155 at level 5: list_item: - item-156 at level 6: inline: group group - item-157 at level 7: footnote: No competing interests declared. - item-158 at level 3: section_header: Author contributions - item-159 at level 4: list: group footnotes - item-160 at level 5: list_item: - item-161 at level 6: inline: group group - item-162 at level 7: footnote: Conceptualization, Data curation ... Methodology, Writing - original draft. - item-163 at level 5: list_item: - item-164 at level 6: inline: group group - item-165 at level 7: footnote: Conceptualization, Data curation ... l draft, Writing - review and editing. - item-166 at level 5: list_item: - item-167 at level 6: inline: group group - item-168 at level 7: footnote: Conceptualization, Data curation ... odology, Writing - review and editing. - item-169 at level 5: list_item: - item-170 at level 6: inline: group group - item-171 at level 7: footnote: Conceptualization, Formal analys ... igation, Writing - review and editing. - item-172 at level 5: list_item: - item-173 at level 6: inline: group group - item-174 at level 7: footnote: Investigation. - item-175 at level 5: list_item: - item-176 at level 6: inline: group group - item-177 at level 7: footnote: Investigation. - item-178 at level 5: list_item: - item-179 at level 6: inline: group group - item-180 at level 7: footnote: Data curation, Software, Formal analysis, Visualization. - item-181 at level 5: list_item: - item-182 at level 6: inline: group group - item-183 at level 7: footnote: Investigation. - item-184 at level 5: list_item: - item-185 at level 6: inline: group group - item-186 at level 7: footnote: Conceptualization, Resources, Su ... igation, Writing - review and editing. - item-187 at level 5: list_item: - item-188 at level 6: inline: group group - item-189 at level 7: footnote: Conceptualization, Resources, Su ... tration, Writing - review and editing. - item-190 at level 3: section_header: Ethics - item-191 at level 4: list: group footnotes - item-192 at level 5: list_item: - item-193 at level 6: inline: group group - item-194 at level 7: footnote: Animal experimentation: All stud ... er IACUC animal protocol (ASP )18-026. - item-195 at level 2: section_header: Additional files - item-196 at level 2: section_header: Data availability - item-197 at level 3: text: All NGS data has been deposited ... GenBank database (MH449667- MH449669). - item-198 at level 3: text: The following datasets were generated: - item-199 at level 3: text: Wolf G. Retrotransposon reactiva ... ession Omnibus (2019). NCBI: GSE115291 - item-200 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449667 - item-201 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449668 - item-202 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449669 - item-203 at level 3: text: The following previously published datasets were used: - item-204 at level 3: text: Castro-Diaz N, Ecco G, Coluccio ... ssion Omnibus (2014). NCBI: GSM1406445 - item-205 at level 3: text: Andrew ZX. H3K9me3_ChIPSeq (Ctrl ... ssion Omnibus (2014). NCBI: GSM1327148 - item-206 at level 2: section_header: References - item-207 at level 3: list: group list - item-208 at level 4: list_item: Bailey TL, Boden M, Buske FA, Fr ... OI: 10.1093/nar/gkp335, PMID: 19458158 - item-209 at level 4: list_item: Baust C, Gagnier L, Baillie GJ, ... 77.21.11448-11458.2003, PMID: 14557630 - item-210 at level 4: list_item: Blaschke K, Ebata KT, Karimi MM, ... I: 10.1038/nature12362, PMID: 23812591 - item-211 at level 4: list_item: Brodziak A, Ziółko E, Muc-Wierzg ... I: 10.12659/msm.882892, PMID: 22648263 - item-212 at level 4: list_item: Castro-Diaz N, Ecco G, Coluccio ... 10.1101/gad.241661.114, PMID: 24939876 - item-213 at level 4: list_item: Chuong EB, Elde NC, Feschotte C. ... 0.1126/science.aad5497, PMID: 26941318 - item-214 at level 4: list_item: Dan J, Liu Y, Liu N, Chiourea M, ... 6/j.devcel.2014.03.004, PMID: 24735877 - item-215 at level 4: list_item: De Iaco A, Planet E, Coluccio A, ... . DOI: 10.1038/ng.3858, PMID: 28459456 - item-216 at level 4: list_item: Deniz Ö, de la Rica L, Cheng KCL ... 1186/s13059-017-1376-y, PMID: 29351814 - item-217 at level 4: list_item: Dewannieux M, Heidmann T. Endoge ... 6/j.coviro.2013.08.005, PMID: 24004725 - item-218 at level 4: list_item: Ecco G, Cassano M, Kauzlaric A, ... 6/j.devcel.2016.02.024, PMID: 27003935 - item-219 at level 4: list_item: Ecco G, Imbeault M, Trono D. KRA ... OI: 10.1242/dev.132605, PMID: 28765213 - item-220 at level 4: list_item: Frank JA, Feschotte C. Co-option ... 6/j.coviro.2017.07.021, PMID: 28818736 - item-221 at level 4: list_item: Gagnier L, Belancio VP, Mager DL ... 1186/s13100-019-0157-4, PMID: 31011371 - item-222 at level 4: list_item: Groner AC, Meylan S, Ciuffi A, Z ... 1/journal.pgen.1000869, PMID: 20221260 - item-223 at level 4: list_item: Hancks DC, Kazazian HH. Roles fo ... 1186/s13100-016-0065-9, PMID: 27158268 - item-224 at level 4: list_item: Imbeault M, Helleboid PY, Trono ... I: 10.1038/nature21683, PMID: 28273063 - item-225 at level 4: list_item: Jacobs FM, Greenberg D, Nguyen N ... I: 10.1038/nature13760, PMID: 25274305 - item-226 at level 4: list_item: Kano H, Kurahashi H, Toda T. Gen ... 0.1073/pnas.0705483104, PMID: 17984064 - item-227 at level 4: list_item: Karimi MM, Goyal P, Maksakova IA ... 016/j.stem.2011.04.004, PMID: 21624812 - item-228 at level 4: list_item: Kauzlaric A, Ecco G, Cassano M, ... 1/journal.pone.0173746, PMID: 28334004 - item-229 at level 4: list_item: Khil PP, Smagulova F, Brick KM, ... 10.1101/gr.130583.111, PMID: 22367190 - item-230 at level 4: list_item: Krueger F, Andrews SR. Bismark: ... /bioinformatics/btr167, PMID: 21493656 - item-231 at level 4: list_item: Langmead B, Salzberg SL. Fast ga ... OI: 10.1038/nmeth.1923, PMID: 22388286 - item-232 at level 4: list_item: Legiewicz M, Zolotukhin AS, Pilk ... 0.1074/jbc.M110.182840, PMID: 20978285 - item-233 at level 4: list_item: Lehoczky JA, Thomas PE, Patrie K ... 1/journal.pgen.1003967, PMID: 24339789 - item-234 at level 4: list_item: Leung D, Du T, Wagner U, Xie W, ... 0.1073/pnas.1322273111, PMID: 24757056 - item-235 at level 4: list_item: Lilue J, Doran AG, Fiddes IT, Ab ... 1038/s41588-018-0223-8, PMID: 30275530 - item-236 at level 4: list_item: Liu S, Brind'Amour J, Karimi MM, ... 10.1101/gad.244848.114, PMID: 25228647 - item-237 at level 4: list_item: Love MI, Huber W, Anders S. Mode ... 1186/s13059-014-0550-8, PMID: 25516281 - item-238 at level 4: list_item: Lugani F, Arora R, Papeta N, Pat ... 1/journal.pgen.1003206, PMID: 23437001 - item-239 at level 4: list_item: Macfarlan TS, Gifford WD, Drisco ... I: 10.1038/nature11244, PMID: 22722858 - item-240 at level 4: list_item: Maksakova IA, Romanish MT, Gagni ... 1/journal.pgen.0020002, PMID: 16440055 - item-241 at level 4: list_item: Matsui T, Leung D, Miyashita H, ... I: 10.1038/nature08858, PMID: 20164836 - item-242 at level 4: list_item: Najafabadi HS, Mnaimneh S, Schmi ... DOI: 10.1038/nbt.3128, PMID: 25690854 - item-243 at level 4: list_item: Nellåker C, Keane TM, Yalcin B, ... .1186/gb-2012-13-6-r45, PMID: 22703977 - item-244 at level 4: list_item: O'Geen H, Frietze S, Farnham PJ. ... 7/978-1-60761-753-2_27, PMID: 20680851 - item-245 at level 4: list_item: Patel A, Yang P, Tinkham M, Prad ... 016/j.cell.2018.02.058, PMID: 29551271 - item-246 at level 4: list_item: Ribet D, Dewannieux M, Heidmann ... OI: 10.1101/gr.2924904, PMID: 15479948 - item-247 at level 4: list_item: Richardson SR, Gerdes P, Gerhard ... 10.1101/gr.219022.116, PMID: 28483779 - item-248 at level 4: list_item: Rowe HM, Jakobsson J, Mesnard D, ... I: 10.1038/nature08674, PMID: 20075919 - item-249 at level 4: list_item: Rowe HM, Kapopoulou A, Corsinott ... 10.1101/gr.147678.112, PMID: 23233547 - item-250 at level 4: list_item: Schauer SN, Carreira PE, Shukla ... 10.1101/gr.226993.117, PMID: 29643204 - item-251 at level 4: list_item: Schultz DC, Ayyanathan K, Negore ... OI: 10.1101/gad.973302, PMID: 11959841 - item-252 at level 4: list_item: Semba K, Araki K, Matsumoto K, S ... 1/journal.pgen.1003204, PMID: 23436999 - item-253 at level 4: list_item: Sripathy SP, Stevens J, Schultz ... : 10.1128/MCB.00487-06, PMID: 16954381 - item-254 at level 4: list_item: Thomas JH, Schneider S. Coevolut ... 10.1101/gr.121749.111, PMID: 21784874 - item-255 at level 4: list_item: Thompson PJ, Macfarlan TS, Lorin ... 6/j.molcel.2016.03.029, PMID: 27259207 - item-256 at level 4: list_item: Treger RS, Pope SD, Kong Y, Toku ... 6/j.immuni.2018.12.022, PMID: 30709743 - item-257 at level 4: list_item: Vlangos CN, Siuniak AN, Robinson ... 1/journal.pgen.1003205, PMID: 23437000 - item-258 at level 4: list_item: Wang J, Xie G, Singh M, Ghanbari ... I: 10.1038/nature13804, PMID: 25317556 - item-259 at level 4: list_item: Wolf D, Hug K, Goff SP. TRIM28 m ... 0.1073/pnas.0805540105, PMID: 18713861 - item-260 at level 4: list_item: Wolf G, Greenberg D, Macfarlan T ... 1186/s13100-015-0050-8, PMID: 26435754 - item-261 at level 4: list_item: Wolf G, Yang P, Füchtbauer AC, F ... 10.1101/gad.252767.114, PMID: 25737282 - item-262 at level 4: list_item: Yamauchi M, Freitag B, Khan C, B ... JVI.69.2.1142-1149.1995, PMID: 7529329 - item-263 at level 4: list_item: Zhang Y, Liu T, Meyer CA, Eeckho ... .1186/gb-2008-9-9-r137, PMID: 18798982 - item-264 at level 1: caption: Figure 1. Genome-wide binding pa ... onsensus fingers highlighted in white. - item-265 at level 1: caption: Table 1. KRAB-ZFP genes clusters ... ChIP-seq was performed in this study. - item-266 at level 1: caption: Figure 2. Retrotransposon reacti ... s were calculated using paired t-test. - item-267 at level 1: caption: Figure 3. TE-dependent gene acti ... Gm13051 are indicated by dashed lines. - item-268 at level 1: caption: Figure 4. ETn retrotransposition ... combined for the statistical analysis. - item-269 at level 1: caption: Key resources table \ No newline at end of file + item-155 at level 5: list_item: No competing interests declared. + item-156 at level 3: section_header: Author contributions + item-157 at level 4: list: group footnotes + item-158 at level 5: list_item: Conceptualization, Data curation ... Methodology, Writing - original draft. + item-159 at level 5: list_item: Conceptualization, Data curation ... l draft, Writing - review and editing. + item-160 at level 5: list_item: Conceptualization, Data curation ... odology, Writing - review and editing. + item-161 at level 5: list_item: Conceptualization, Formal analys ... igation, Writing - review and editing. + item-162 at level 5: list_item: Investigation. + item-163 at level 5: list_item: Investigation. + item-164 at level 5: list_item: Data curation, Software, Formal analysis, Visualization. + item-165 at level 5: list_item: Investigation. + item-166 at level 5: list_item: Conceptualization, Resources, Su ... igation, Writing - review and editing. + item-167 at level 5: list_item: Conceptualization, Resources, Su ... tration, Writing - review and editing. + item-168 at level 3: section_header: Ethics + item-169 at level 4: list: group footnotes + item-170 at level 5: list_item: Animal experimentation: All stud ... er IACUC animal protocol (ASP )18-026. + item-171 at level 2: section_header: Additional files + item-172 at level 2: section_header: Data availability + item-173 at level 3: text: All NGS data has been deposited ... GenBank database (MH449667- MH449669). + item-174 at level 3: text: The following datasets were generated: + item-175 at level 3: text: Wolf G. Retrotransposon reactiva ... ession Omnibus (2019). NCBI: GSE115291 + item-176 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449667 + item-177 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449668 + item-178 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449669 + item-179 at level 3: text: The following previously published datasets were used: + item-180 at level 3: text: Castro-Diaz N, Ecco G, Coluccio ... ssion Omnibus (2014). NCBI: GSM1406445 + item-181 at level 3: text: Andrew ZX. H3K9me3_ChIPSeq (Ctrl ... ssion Omnibus (2014). NCBI: GSM1327148 + item-182 at level 2: section_header: References + item-183 at level 3: list: group list + item-184 at level 4: list_item: Bailey TL, Boden M, Buske FA, Fr ... OI: 10.1093/nar/gkp335, PMID: 19458158 + item-185 at level 4: list_item: Baust C, Gagnier L, Baillie GJ, ... 77.21.11448-11458.2003, PMID: 14557630 + item-186 at level 4: list_item: Blaschke K, Ebata KT, Karimi MM, ... I: 10.1038/nature12362, PMID: 23812591 + item-187 at level 4: list_item: Brodziak A, Ziółko E, Muc-Wierzg ... I: 10.12659/msm.882892, PMID: 22648263 + item-188 at level 4: list_item: Castro-Diaz N, Ecco G, Coluccio ... 10.1101/gad.241661.114, PMID: 24939876 + item-189 at level 4: list_item: Chuong EB, Elde NC, Feschotte C. ... 0.1126/science.aad5497, PMID: 26941318 + item-190 at level 4: list_item: Dan J, Liu Y, Liu N, Chiourea M, ... 6/j.devcel.2014.03.004, PMID: 24735877 + item-191 at level 4: list_item: De Iaco A, Planet E, Coluccio A, ... . DOI: 10.1038/ng.3858, PMID: 28459456 + item-192 at level 4: list_item: Deniz Ö, de la Rica L, Cheng KCL ... 1186/s13059-017-1376-y, PMID: 29351814 + item-193 at level 4: list_item: Dewannieux M, Heidmann T. Endoge ... 6/j.coviro.2013.08.005, PMID: 24004725 + item-194 at level 4: list_item: Ecco G, Cassano M, Kauzlaric A, ... 6/j.devcel.2016.02.024, PMID: 27003935 + item-195 at level 4: list_item: Ecco G, Imbeault M, Trono D. KRA ... OI: 10.1242/dev.132605, PMID: 28765213 + item-196 at level 4: list_item: Frank JA, Feschotte C. Co-option ... 6/j.coviro.2017.07.021, PMID: 28818736 + item-197 at level 4: list_item: Gagnier L, Belancio VP, Mager DL ... 1186/s13100-019-0157-4, PMID: 31011371 + item-198 at level 4: list_item: Groner AC, Meylan S, Ciuffi A, Z ... 1/journal.pgen.1000869, PMID: 20221260 + item-199 at level 4: list_item: Hancks DC, Kazazian HH. Roles fo ... 1186/s13100-016-0065-9, PMID: 27158268 + item-200 at level 4: list_item: Imbeault M, Helleboid PY, Trono ... I: 10.1038/nature21683, PMID: 28273063 + item-201 at level 4: list_item: Jacobs FM, Greenberg D, Nguyen N ... I: 10.1038/nature13760, PMID: 25274305 + item-202 at level 4: list_item: Kano H, Kurahashi H, Toda T. Gen ... 0.1073/pnas.0705483104, PMID: 17984064 + item-203 at level 4: list_item: Karimi MM, Goyal P, Maksakova IA ... 016/j.stem.2011.04.004, PMID: 21624812 + item-204 at level 4: list_item: Kauzlaric A, Ecco G, Cassano M, ... 1/journal.pone.0173746, PMID: 28334004 + item-205 at level 4: list_item: Khil PP, Smagulova F, Brick KM, ... 10.1101/gr.130583.111, PMID: 22367190 + item-206 at level 4: list_item: Krueger F, Andrews SR. Bismark: ... /bioinformatics/btr167, PMID: 21493656 + item-207 at level 4: list_item: Langmead B, Salzberg SL. Fast ga ... OI: 10.1038/nmeth.1923, PMID: 22388286 + item-208 at level 4: list_item: Legiewicz M, Zolotukhin AS, Pilk ... 0.1074/jbc.M110.182840, PMID: 20978285 + item-209 at level 4: list_item: Lehoczky JA, Thomas PE, Patrie K ... 1/journal.pgen.1003967, PMID: 24339789 + item-210 at level 4: list_item: Leung D, Du T, Wagner U, Xie W, ... 0.1073/pnas.1322273111, PMID: 24757056 + item-211 at level 4: list_item: Lilue J, Doran AG, Fiddes IT, Ab ... 1038/s41588-018-0223-8, PMID: 30275530 + item-212 at level 4: list_item: Liu S, Brind'Amour J, Karimi MM, ... 10.1101/gad.244848.114, PMID: 25228647 + item-213 at level 4: list_item: Love MI, Huber W, Anders S. Mode ... 1186/s13059-014-0550-8, PMID: 25516281 + item-214 at level 4: list_item: Lugani F, Arora R, Papeta N, Pat ... 1/journal.pgen.1003206, PMID: 23437001 + item-215 at level 4: list_item: Macfarlan TS, Gifford WD, Drisco ... I: 10.1038/nature11244, PMID: 22722858 + item-216 at level 4: list_item: Maksakova IA, Romanish MT, Gagni ... 1/journal.pgen.0020002, PMID: 16440055 + item-217 at level 4: list_item: Matsui T, Leung D, Miyashita H, ... I: 10.1038/nature08858, PMID: 20164836 + item-218 at level 4: list_item: Najafabadi HS, Mnaimneh S, Schmi ... DOI: 10.1038/nbt.3128, PMID: 25690854 + item-219 at level 4: list_item: Nellåker C, Keane TM, Yalcin B, ... .1186/gb-2012-13-6-r45, PMID: 22703977 + item-220 at level 4: list_item: O'Geen H, Frietze S, Farnham PJ. ... 7/978-1-60761-753-2_27, PMID: 20680851 + item-221 at level 4: list_item: Patel A, Yang P, Tinkham M, Prad ... 016/j.cell.2018.02.058, PMID: 29551271 + item-222 at level 4: list_item: Ribet D, Dewannieux M, Heidmann ... OI: 10.1101/gr.2924904, PMID: 15479948 + item-223 at level 4: list_item: Richardson SR, Gerdes P, Gerhard ... 10.1101/gr.219022.116, PMID: 28483779 + item-224 at level 4: list_item: Rowe HM, Jakobsson J, Mesnard D, ... I: 10.1038/nature08674, PMID: 20075919 + item-225 at level 4: list_item: Rowe HM, Kapopoulou A, Corsinott ... 10.1101/gr.147678.112, PMID: 23233547 + item-226 at level 4: list_item: Schauer SN, Carreira PE, Shukla ... 10.1101/gr.226993.117, PMID: 29643204 + item-227 at level 4: list_item: Schultz DC, Ayyanathan K, Negore ... OI: 10.1101/gad.973302, PMID: 11959841 + item-228 at level 4: list_item: Semba K, Araki K, Matsumoto K, S ... 1/journal.pgen.1003204, PMID: 23436999 + item-229 at level 4: list_item: Sripathy SP, Stevens J, Schultz ... : 10.1128/MCB.00487-06, PMID: 16954381 + item-230 at level 4: list_item: Thomas JH, Schneider S. Coevolut ... 10.1101/gr.121749.111, PMID: 21784874 + item-231 at level 4: list_item: Thompson PJ, Macfarlan TS, Lorin ... 6/j.molcel.2016.03.029, PMID: 27259207 + item-232 at level 4: list_item: Treger RS, Pope SD, Kong Y, Toku ... 6/j.immuni.2018.12.022, PMID: 30709743 + item-233 at level 4: list_item: Vlangos CN, Siuniak AN, Robinson ... 1/journal.pgen.1003205, PMID: 23437000 + item-234 at level 4: list_item: Wang J, Xie G, Singh M, Ghanbari ... I: 10.1038/nature13804, PMID: 25317556 + item-235 at level 4: list_item: Wolf D, Hug K, Goff SP. TRIM28 m ... 0.1073/pnas.0805540105, PMID: 18713861 + item-236 at level 4: list_item: Wolf G, Greenberg D, Macfarlan T ... 1186/s13100-015-0050-8, PMID: 26435754 + item-237 at level 4: list_item: Wolf G, Yang P, Füchtbauer AC, F ... 10.1101/gad.252767.114, PMID: 25737282 + item-238 at level 4: list_item: Yamauchi M, Freitag B, Khan C, B ... JVI.69.2.1142-1149.1995, PMID: 7529329 + item-239 at level 4: list_item: Zhang Y, Liu T, Meyer CA, Eeckho ... .1186/gb-2008-9-9-r137, PMID: 18798982 + item-240 at level 1: caption: Figure 1. Genome-wide binding pa ... onsensus fingers highlighted in white. + item-241 at level 1: caption: Table 1. KRAB-ZFP genes clusters ... ChIP-seq was performed in this study. + item-242 at level 1: caption: Figure 2. Retrotransposon reacti ... s were calculated using paired t-test. + item-243 at level 1: caption: Figure 3. TE-dependent gene acti ... Gm13051 are indicated by dashed lines. + item-244 at level 1: caption: Figure 4. ETn retrotransposition ... combined for the statistical analysis. + item-245 at level 1: caption: Key resources table \ No newline at end of file diff --git a/tests/data/jats/groundtruth/elife-56337.nxml.json b/tests/data/jats/groundtruth/elife-56337.nxml.json index 18addb4b39..5b90a4d1e0 100644 --- a/tests/data/jats/groundtruth/elife-56337.nxml.json +++ b/tests/data/jats/groundtruth/elife-56337.nxml.json @@ -485,52 +485,38 @@ { "self_ref": "#/groups/15", "parent": { - "$ref": "#/texts/139" + "$ref": "#/texts/140" }, "children": [ { - "$ref": "#/texts/140" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/16", - "parent": { - "$ref": "#/texts/141" - }, - "children": [ - { - "$ref": "#/texts/142" + "$ref": "#/texts/141" }, { - "$ref": "#/texts/144" + "$ref": "#/texts/142" }, { - "$ref": "#/texts/146" + "$ref": "#/texts/143" }, { - "$ref": "#/texts/148" + "$ref": "#/texts/144" }, { - "$ref": "#/texts/150" + "$ref": "#/texts/145" }, { - "$ref": "#/texts/152" + "$ref": "#/texts/146" }, { - "$ref": "#/texts/154" + "$ref": "#/texts/147" }, { - "$ref": "#/texts/156" + "$ref": "#/texts/148" }, { - "$ref": "#/texts/158" + "$ref": "#/texts/149" }, { - "$ref": "#/texts/160" + "$ref": "#/texts/150" } ], "content_layer": "body", @@ -538,179 +524,61 @@ "label": "list" }, { - "self_ref": "#/groups/17", + "self_ref": "#/groups/16", "parent": { - "$ref": "#/texts/142" + "$ref": "#/texts/151" }, "children": [ { - "$ref": "#/texts/143" + "$ref": "#/texts/152" } ], "content_layer": "body", - "name": "group", - "label": "inline" + "name": "footnotes", + "label": "list" }, { - "self_ref": "#/groups/18", + "self_ref": "#/groups/17", "parent": { - "$ref": "#/texts/144" + "$ref": "#/texts/164" }, "children": [ { - "$ref": "#/texts/145" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/19", - "parent": { - "$ref": "#/texts/146" - }, - "children": [ + "$ref": "#/texts/165" + }, { - "$ref": "#/texts/147" - 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"parent": { - "$ref": "#/texts/156" - }, - "children": [ + "$ref": "#/texts/170" + }, { - "$ref": "#/texts/157" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/25", - "parent": { - "$ref": "#/texts/158" - }, - "children": [ + "$ref": "#/texts/171" + }, { - "$ref": "#/texts/159" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/26", - "parent": { - "$ref": "#/texts/160" - }, - "children": [ + "$ref": "#/texts/172" + }, { - "$ref": "#/texts/161" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/27", - "parent": { - "$ref": "#/texts/162" - }, - "children": [ + "$ref": "#/texts/173" + }, { - "$ref": "#/texts/163" - } - ], - "content_layer": "body", - "name": "footnotes", - "label": "list" - }, - { - "self_ref": "#/groups/28", - "parent": { - "$ref": "#/texts/163" - }, - "children": [ + "$ref": "#/texts/174" + }, { - "$ref": "#/texts/164" - } - ], - "content_layer": "body", - "name": "group", - "label": "inline" - }, - { - "self_ref": "#/groups/29", - "parent": { - "$ref": "#/texts/176" - }, - "children": [ + "$ref": "#/texts/175" + }, + { + "$ref": "#/texts/176" + }, { "$ref": "#/texts/177" }, @@ -842,42 +710,6 @@ }, { "$ref": "#/texts/220" - }, - { - "$ref": "#/texts/221" - }, - { - "$ref": "#/texts/222" - }, - { - "$ref": "#/texts/223" - }, - { - "$ref": "#/texts/224" - }, - { - "$ref": "#/texts/225" - }, - { - "$ref": "#/texts/226" - }, - { - "$ref": "#/texts/227" - }, - { - "$ref": "#/texts/228" - }, - { - "$ref": "#/texts/229" - }, - { - "$ref": "#/texts/230" - }, - { - "$ref": "#/texts/231" - }, - { - "$ref": "#/texts/232" } ], "content_layer": "body", @@ -923,13 +755,13 @@ "$ref": "#/texts/137" }, { - "$ref": "#/texts/165" + "$ref": "#/texts/153" }, { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, { - "$ref": "#/texts/176" + "$ref": "#/texts/164" } ], "content_layer": "body", @@ -2927,10 +2759,10 @@ "$ref": "#/texts/138" }, { - 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review and editing.", - "text": "Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Writing - review and editing." - }, - { - "self_ref": "#/texts/160", - "parent": { - "$ref": "#/groups/16" - }, - "children": [ - { - "$ref": "#/groups/26" - } - ], - "content_layer": "body", "label": "list_item", "prov": [], - "orig": "", - "text": "", + "orig": "Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing - original draft, Project administration, Writing - review and editing.", + "text": "Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing - original draft, Project administration, Writing - review and editing.", "enumerated": false, "marker": "" }, { - "self_ref": "#/texts/161", - "parent": { - "$ref": "#/groups/26" - }, - "children": [], - "content_layer": "body", - "label": "footnote", - "prov": [], - "orig": "Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing - original draft, Project administration, Writing - review and editing.", - "text": "Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing - original draft, Project administration, Writing - review and editing." - }, - { - "self_ref": "#/texts/162", + "self_ref": "#/texts/151", "parent": { "$ref": "#/texts/137" }, "children": [ { - "$ref": "#/groups/27" + "$ref": "#/groups/16" } ], "content_layer": "body", @@ -3322,37 +2978,21 @@ "level": 2 }, { - "self_ref": "#/texts/163", + "self_ref": "#/texts/152", "parent": { - "$ref": "#/groups/27" + "$ref": "#/groups/16" }, - "children": [ - { - "$ref": "#/groups/28" - } - ], + "children": [], "content_layer": "body", "label": "list_item", "prov": [], - "orig": "", - "text": "", + "orig": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026.", + "text": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026.", "enumerated": false, "marker": "" }, { - "self_ref": "#/texts/164", - "parent": { - "$ref": "#/groups/28" - }, - "children": [], - "content_layer": "body", - "label": "footnote", - "prov": [], - "orig": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026.", - "text": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026." - }, - { - "self_ref": "#/texts/165", + "self_ref": "#/texts/153", "parent": { "$ref": "#/texts/0" }, @@ -3365,37 +3005,37 @@ "level": 1 }, { - "self_ref": "#/texts/166", + "self_ref": "#/texts/154", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/167" + "$ref": "#/texts/155" }, { - "$ref": "#/texts/168" + "$ref": "#/texts/156" }, { - "$ref": "#/texts/169" + "$ref": "#/texts/157" }, { - "$ref": "#/texts/170" + "$ref": "#/texts/158" }, { - "$ref": "#/texts/171" + "$ref": "#/texts/159" }, { - "$ref": "#/texts/172" + "$ref": "#/texts/160" }, { - "$ref": "#/texts/173" + "$ref": "#/texts/161" }, { - "$ref": "#/texts/174" + "$ref": "#/texts/162" }, { - "$ref": "#/texts/175" + "$ref": "#/texts/163" } ], "content_layer": "body", @@ -3406,9 +3046,9 @@ "level": 1 }, { - "self_ref": "#/texts/167", + "self_ref": "#/texts/155", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3418,9 +3058,9 @@ "text": "All NGS data has been deposited in GEO (GSE115291). Sequences of full-length de novo ETn insertions have been deposited in the GenBank database (MH449667- MH449669)." }, { - "self_ref": "#/texts/168", + "self_ref": "#/texts/156", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3430,9 +3070,9 @@ "text": "The following datasets were generated:" }, { - "self_ref": "#/texts/169", + "self_ref": "#/texts/157", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3442,9 +3082,9 @@ "text": "Wolf G. Retrotransposon reactivation and mobilization upon deletions of megabase scale KRAB zinc finger gene clusters in mice. NCBI Gene Expression Omnibus (2019). NCBI: GSE115291" }, { - "self_ref": "#/texts/170", + "self_ref": "#/texts/158", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3454,9 +3094,9 @@ "text": "Wolf G. Mus musculus musculus strain C57BL/6x129X1/SvJ retrotransposon MMETn-int, complete sequence. NCBI GenBank (2019). NCBI: MH449667" }, { - "self_ref": "#/texts/171", + "self_ref": "#/texts/159", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3466,9 +3106,9 @@ "text": "Wolf G. Mus musculus musculus strain C57BL/6x129X1/SvJ retrotransposon MMETn-int, complete sequence. NCBI GenBank (2019). NCBI: MH449668" }, { - "self_ref": "#/texts/172", + "self_ref": "#/texts/160", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3478,9 +3118,9 @@ "text": "Wolf G. Mus musculus musculus strain C57BL/6x129X1/SvJ retrotransposon MMETn-int, complete sequence. NCBI GenBank (2019). NCBI: MH449669" }, { - "self_ref": "#/texts/173", + "self_ref": "#/texts/161", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3490,9 +3130,9 @@ "text": "The following previously published datasets were used:" }, { - "self_ref": "#/texts/174", + "self_ref": "#/texts/162", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3502,9 +3142,9 @@ "text": "Castro-Diaz N, Ecco G, Coluccio A, Kapopoulou A, Duc J, Trono D. Evollutionally dynamic L1 regulation in embryonic stem cells. NCBI Gene Expression Omnibus (2014). NCBI: GSM1406445" }, { - "self_ref": "#/texts/175", + "self_ref": "#/texts/163", "parent": { - "$ref": "#/texts/166" + "$ref": "#/texts/154" }, "children": [], "content_layer": "body", @@ -3514,13 +3154,13 @@ "text": "Andrew ZX. H3K9me3_ChIPSeq (Ctrl). NCBI Gene Expression Omnibus (2014). NCBI: GSM1327148" }, { - "self_ref": "#/texts/176", + "self_ref": "#/texts/164", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/groups/29" + "$ref": "#/groups/17" } ], "content_layer": "body", @@ -3531,9 +3171,9 @@ "level": 1 }, { - "self_ref": "#/texts/177", + "self_ref": "#/texts/165", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3545,9 +3185,9 @@ "marker": "" }, { - "self_ref": "#/texts/178", + "self_ref": "#/texts/166", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3559,9 +3199,9 @@ "marker": "" }, { - "self_ref": "#/texts/179", + "self_ref": "#/texts/167", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3573,9 +3213,9 @@ "marker": "" }, { - "self_ref": "#/texts/180", + "self_ref": "#/texts/168", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3587,9 +3227,9 @@ "marker": "" }, { - "self_ref": "#/texts/181", + "self_ref": "#/texts/169", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3601,9 +3241,9 @@ "marker": "" }, { - "self_ref": "#/texts/182", + "self_ref": "#/texts/170", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3615,9 +3255,9 @@ "marker": "" }, { - "self_ref": "#/texts/183", + "self_ref": "#/texts/171", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3629,9 +3269,9 @@ "marker": "" }, { - "self_ref": "#/texts/184", + "self_ref": "#/texts/172", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3643,9 +3283,9 @@ "marker": "" }, { - "self_ref": "#/texts/185", + "self_ref": "#/texts/173", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3657,9 +3297,9 @@ "marker": "" }, { - "self_ref": "#/texts/186", + "self_ref": "#/texts/174", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3671,9 +3311,9 @@ "marker": "" }, { - "self_ref": "#/texts/187", + "self_ref": "#/texts/175", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3685,9 +3325,9 @@ "marker": "" }, { - "self_ref": "#/texts/188", + "self_ref": "#/texts/176", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3699,9 +3339,9 @@ "marker": "" }, { - "self_ref": "#/texts/189", + "self_ref": "#/texts/177", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3713,9 +3353,9 @@ "marker": "" }, { - "self_ref": "#/texts/190", + "self_ref": "#/texts/178", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3727,9 +3367,9 @@ "marker": "" }, { - "self_ref": "#/texts/191", + "self_ref": "#/texts/179", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3741,9 +3381,9 @@ "marker": "" }, { - "self_ref": "#/texts/192", + "self_ref": "#/texts/180", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3755,9 +3395,9 @@ "marker": "" }, { - "self_ref": "#/texts/193", + "self_ref": "#/texts/181", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3769,9 +3409,9 @@ "marker": "" }, { - "self_ref": "#/texts/194", + "self_ref": "#/texts/182", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3783,9 +3423,9 @@ "marker": "" }, { - "self_ref": "#/texts/195", + "self_ref": "#/texts/183", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3797,9 +3437,9 @@ "marker": "" }, { - "self_ref": "#/texts/196", + "self_ref": "#/texts/184", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3811,9 +3451,9 @@ "marker": "" }, { - "self_ref": "#/texts/197", + "self_ref": "#/texts/185", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3825,9 +3465,9 @@ "marker": "" }, { - "self_ref": "#/texts/198", + "self_ref": "#/texts/186", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3839,9 +3479,9 @@ "marker": "" }, { - "self_ref": "#/texts/199", + "self_ref": "#/texts/187", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3853,9 +3493,9 @@ "marker": "" }, { - "self_ref": "#/texts/200", + "self_ref": "#/texts/188", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3867,9 +3507,9 @@ "marker": "" }, { - "self_ref": "#/texts/201", + "self_ref": "#/texts/189", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3881,9 +3521,9 @@ "marker": "" }, { - "self_ref": "#/texts/202", + "self_ref": "#/texts/190", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3895,9 +3535,9 @@ "marker": "" }, { - "self_ref": "#/texts/203", + "self_ref": "#/texts/191", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3909,9 +3549,9 @@ "marker": "" }, { - "self_ref": "#/texts/204", + "self_ref": "#/texts/192", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3923,9 +3563,9 @@ "marker": "" }, { - "self_ref": "#/texts/205", + "self_ref": "#/texts/193", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3937,9 +3577,9 @@ "marker": "" }, { - "self_ref": "#/texts/206", + "self_ref": "#/texts/194", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3951,9 +3591,9 @@ "marker": "" }, { - "self_ref": "#/texts/207", + "self_ref": "#/texts/195", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3965,9 +3605,9 @@ "marker": "" }, { - "self_ref": "#/texts/208", + "self_ref": "#/texts/196", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3979,9 +3619,9 @@ "marker": "" }, { - "self_ref": "#/texts/209", + "self_ref": "#/texts/197", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -3993,9 +3633,9 @@ "marker": "" }, { - "self_ref": "#/texts/210", + "self_ref": "#/texts/198", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4007,9 +3647,9 @@ "marker": "" }, { - "self_ref": "#/texts/211", + "self_ref": "#/texts/199", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4021,9 +3661,9 @@ "marker": "" }, { - "self_ref": "#/texts/212", + "self_ref": "#/texts/200", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4035,9 +3675,9 @@ "marker": "" }, { - "self_ref": "#/texts/213", + "self_ref": "#/texts/201", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4049,9 +3689,9 @@ "marker": "" }, { - "self_ref": "#/texts/214", + "self_ref": "#/texts/202", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4063,9 +3703,9 @@ "marker": "" }, { - "self_ref": "#/texts/215", + "self_ref": "#/texts/203", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4077,9 +3717,9 @@ "marker": "" }, { - "self_ref": "#/texts/216", + "self_ref": "#/texts/204", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4091,9 +3731,9 @@ "marker": "" }, { - "self_ref": "#/texts/217", + "self_ref": "#/texts/205", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4105,9 +3745,9 @@ "marker": "" }, { - "self_ref": "#/texts/218", + "self_ref": "#/texts/206", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4119,9 +3759,9 @@ "marker": "" }, { - "self_ref": "#/texts/219", + "self_ref": "#/texts/207", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4133,9 +3773,9 @@ "marker": "" }, { - "self_ref": "#/texts/220", + "self_ref": "#/texts/208", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4147,9 +3787,9 @@ "marker": "" }, { - "self_ref": "#/texts/221", + "self_ref": "#/texts/209", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4161,9 +3801,9 @@ "marker": "" }, { - "self_ref": "#/texts/222", + "self_ref": "#/texts/210", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4175,9 +3815,9 @@ "marker": "" }, { - "self_ref": "#/texts/223", + "self_ref": "#/texts/211", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4189,9 +3829,9 @@ "marker": "" }, { - "self_ref": "#/texts/224", + "self_ref": "#/texts/212", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4203,9 +3843,9 @@ "marker": "" }, { - "self_ref": "#/texts/225", + "self_ref": "#/texts/213", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4217,9 +3857,9 @@ "marker": "" }, { - "self_ref": "#/texts/226", + "self_ref": "#/texts/214", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4231,9 +3871,9 @@ "marker": "" }, { - "self_ref": "#/texts/227", + "self_ref": "#/texts/215", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4245,9 +3885,9 @@ "marker": "" }, { - "self_ref": "#/texts/228", + "self_ref": "#/texts/216", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4259,9 +3899,9 @@ "marker": "" }, { - "self_ref": "#/texts/229", + "self_ref": "#/texts/217", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4273,9 +3913,9 @@ "marker": "" }, { - "self_ref": "#/texts/230", + "self_ref": "#/texts/218", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4287,9 +3927,9 @@ "marker": "" }, { - "self_ref": "#/texts/231", + "self_ref": "#/texts/219", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", @@ -4301,9 +3941,9 @@ "marker": "" }, { - "self_ref": "#/texts/232", + "self_ref": "#/texts/220", "parent": { - "$ref": "#/groups/29" + "$ref": "#/groups/17" }, "children": [], "content_layer": "body", diff --git a/tests/test_backend_jats.py b/tests/test_backend_jats.py index 147ed08c50..11c8c24c7f 100644 --- a/tests/test_backend_jats.py +++ b/tests/test_backend_jats.py @@ -66,6 +66,7 @@ from docling_core.types.doc.document import Script from PIL import Image +from docling.backend.xml.jats_backend import JatsDocumentBackend from docling.datamodel.backend_options import JatsBackendOptions from docling.datamodel.base_models import DocumentStream, InputFormat from docling.datamodel.document import ConversionResult @@ -253,11 +254,7 @@ def test_jats_plain_abstract_styling_is_preserved(): groups = _inline_group_items(doc) assert len(groups) == 1 - # Abstract paragraphs go through the paragraph implementation - # (_walk_linear, from #3726): one inline run per styled span, boundary - # whitespace stripped per run. Spacing on markdown export is delegated - # to the docling-core serializers (docling-core#693); runs are not fused - # across spaceless boundaries here. + # Each styled span remains a separate inline run. assert [_formatting_tuple(item) for item in groups[0]] == [ (DocItemLabel.TEXT, "We study", None), ( @@ -305,14 +302,7 @@ def test_jats_plain_abstract_styling_is_preserved(): def test_jats_abstract_styling_preserves_inline_runs(): - """Styled spans become their own inline runs; nothing is fused or dropped. - - Per the docling-core serializer contract (docling-core#693), spacing on - export is the serializers' job: the backend must not fuse runs across - spaceless boundaries (``CO2`` stays three runs) nor invent - whitespace. Markdown export is therefore not asserted here — it is - suboptimal until #693 lands and is deliberately out of scope. - """ + """Styled spans become their own inline runs without fusion or loss.""" def abstract_runs(paragraph: str) -> list: doc = convert_jats_article_meta( @@ -415,6 +405,23 @@ def test_jats_inline_runs_drop_xml_indentation_but_keep_same_line_whitespace(): assert [_formatting_tuple(item) for item in groups[0]] == expected +@pytest.mark.parametrize( + ("text", "expected"), + [ + (" leading space", " leading space"), + ("trailing space ", "trailing space "), + ("a b", "a b"), + ("a \n b", "a b"), + ("a\n \n b", "a b"), + ("\n", " "), + ], +) +def test_jats_xml_line_break_normalization_preserves_same_line_whitespace( + text: str, expected: str +): + assert JatsDocumentBackend._normalize_xml_line_breaks(text) == expected + + def test_jats_structured_abstract_styling_is_preserved(): doc = convert_jats_article_meta( """ @@ -466,6 +473,22 @@ def test_jats_plain_abstract_without_styling_stays_a_single_text_item(): assert texts == ["Plain abstract."] +def test_jats_plain_footnote_without_styling_stays_a_single_text_item(): + doc = convert_jats_body( + """ + + Plain Footnote Test +

Plain footnote.

+ + """ + ) + + assert _inline_group_items(doc) == [] + list_items = [t.text for t in doc.texts if t.label == DocItemLabel.LIST_ITEM] + assert list_items == ["Plain footnote."] + assert "- Plain footnote." in doc.export_to_markdown() + + def test_jats_footnote_styling_is_preserved(): doc = convert_jats_body( """ @@ -483,9 +506,7 @@ def test_jats_footnote_styling_is_preserved(): groups = _inline_group_items(doc) assert len(groups) == 1 - # No workaround: the "." after the bold run stays its own inline run, - # and the bold scope ends before it. Spacing on export is delegated to - # the docling-core serializers (docling-core#693). + # The punctuation after the bold run remains separate and unformatted. assert [_formatting_tuple(item) for item in groups[0]] == [ (DocItemLabel.FOOTNOTE, "1", None), (DocItemLabel.FOOTNOTE, "See", None), From 7c47c9bd8f13912abb9052f353e568558882a386 Mon Sep 17 00:00:00 2001 From: Junyi Yao Date: Mon, 5 Oct 2026 15:31:21 -0700 Subject: [PATCH 8/8] fix(jats): preserve footnote item labels Signed-off-by: Junyi Yao --- docling/backend/xml/jats_backend.py | 9 - .../jats/groundtruth/elife-56337.nxml.itxt | 194 +++--- .../jats/groundtruth/elife-56337.nxml.json | 570 ++++++++++++------ .../data/jats/groundtruth/elife-56337.nxml.md | 36 +- tests/test_backend_jats.py | 5 +- 5 files changed, 510 insertions(+), 304 deletions(-) diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py index cc4dd4e751..ebf9d4e8c0 100644 --- a/docling/backend/xml/jats_backend.py +++ b/docling/backend/xml/jats_backend.py @@ -1229,15 +1229,6 @@ def _add_footnote_group( parent=heading, ) for segments in footnote_segments: - if len(segments) == 1 and segments[0].label == DocItemLabel.FOOTNOTE: - segment = segments[0] - doc.add_list_item( - parent=footnote_group, - text=segment.text, - formatting=segment.formatting, - hyperlink=segment.hyperlink, - ) - continue list_item = doc.add_list_item(parent=footnote_group, text="") JatsDocumentBackend._emit_inline(doc, list_item, segments) diff --git a/tests/data/jats/groundtruth/elife-56337.nxml.itxt b/tests/data/jats/groundtruth/elife-56337.nxml.itxt index c7f0689cba..55ea8c7fb7 100644 --- a/tests/data/jats/groundtruth/elife-56337.nxml.itxt +++ b/tests/data/jats/groundtruth/elife-56337.nxml.itxt @@ -159,94 +159,106 @@ item-0 at level 0: unspecified: group _root_ item-152 at level 2: section_header: Additional information item-153 at level 3: section_header: Competing interests item-154 at level 4: list: group footnotes - item-155 at level 5: list_item: No competing interests declared. - item-156 at level 3: section_header: Author contributions - item-157 at level 4: list: group footnotes - item-158 at level 5: list_item: Conceptualization, Data curation ... Methodology, Writing - original draft. - item-159 at level 5: list_item: Conceptualization, Data curation ... l draft, Writing - review and editing. - item-160 at level 5: list_item: Conceptualization, Data curation ... odology, Writing - review and editing. - item-161 at level 5: list_item: Conceptualization, Formal analys ... igation, Writing - review and editing. - item-162 at level 5: list_item: Investigation. - item-163 at level 5: list_item: Investigation. - item-164 at level 5: list_item: Data curation, Software, Formal analysis, Visualization. - item-165 at level 5: list_item: Investigation. - item-166 at level 5: list_item: Conceptualization, Resources, Su ... igation, Writing - review and editing. - item-167 at level 5: list_item: Conceptualization, Resources, Su ... tration, Writing - review and editing. - item-168 at level 3: section_header: Ethics - item-169 at level 4: list: group footnotes - item-170 at level 5: list_item: Animal experimentation: All stud ... er IACUC animal protocol (ASP )18-026. - item-171 at level 2: section_header: Additional files - item-172 at level 2: section_header: Data availability - item-173 at level 3: text: All NGS data has been deposited ... GenBank database (MH449667- MH449669). - item-174 at level 3: text: The following datasets were generated: - item-175 at level 3: text: Wolf G. Retrotransposon reactiva ... ession Omnibus (2019). NCBI: GSE115291 - item-176 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449667 - item-177 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449668 - item-178 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449669 - item-179 at level 3: text: The following previously published datasets were used: - item-180 at level 3: text: Castro-Diaz N, Ecco G, Coluccio ... ssion Omnibus (2014). NCBI: GSM1406445 - item-181 at level 3: text: Andrew ZX. H3K9me3_ChIPSeq (Ctrl ... ssion Omnibus (2014). NCBI: GSM1327148 - item-182 at level 2: section_header: References - item-183 at level 3: list: group list - item-184 at level 4: list_item: Bailey TL, Boden M, Buske FA, Fr ... 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Endoge ... 6/j.coviro.2013.08.005, PMID: 24004725 - item-194 at level 4: list_item: Ecco G, Cassano M, Kauzlaric A, ... 6/j.devcel.2016.02.024, PMID: 27003935 - item-195 at level 4: list_item: Ecco G, Imbeault M, Trono D. KRA ... OI: 10.1242/dev.132605, PMID: 28765213 - item-196 at level 4: list_item: Frank JA, Feschotte C. Co-option ... 6/j.coviro.2017.07.021, PMID: 28818736 - item-197 at level 4: list_item: Gagnier L, Belancio VP, Mager DL ... 1186/s13100-019-0157-4, PMID: 31011371 - item-198 at level 4: list_item: Groner AC, Meylan S, Ciuffi A, Z ... 1/journal.pgen.1000869, PMID: 20221260 - item-199 at level 4: list_item: Hancks DC, Kazazian HH. Roles fo ... 1186/s13100-016-0065-9, PMID: 27158268 - item-200 at level 4: list_item: Imbeault M, Helleboid PY, Trono ... I: 10.1038/nature21683, PMID: 28273063 - item-201 at level 4: list_item: Jacobs FM, Greenberg D, Nguyen N ... I: 10.1038/nature13760, PMID: 25274305 - item-202 at level 4: list_item: Kano H, Kurahashi H, Toda T. Gen ... 0.1073/pnas.0705483104, PMID: 17984064 - item-203 at level 4: list_item: Karimi MM, Goyal P, Maksakova IA ... 016/j.stem.2011.04.004, PMID: 21624812 - item-204 at level 4: list_item: Kauzlaric A, Ecco G, Cassano M, ... 1/journal.pone.0173746, PMID: 28334004 - item-205 at level 4: list_item: Khil PP, Smagulova F, Brick KM, ... 10.1101/gr.130583.111, PMID: 22367190 - item-206 at level 4: list_item: Krueger F, Andrews SR. Bismark: ... /bioinformatics/btr167, PMID: 21493656 - item-207 at level 4: list_item: Langmead B, Salzberg SL. Fast ga ... OI: 10.1038/nmeth.1923, PMID: 22388286 - item-208 at level 4: list_item: Legiewicz M, Zolotukhin AS, Pilk ... 0.1074/jbc.M110.182840, PMID: 20978285 - item-209 at level 4: list_item: Lehoczky JA, Thomas PE, Patrie K ... 1/journal.pgen.1003967, PMID: 24339789 - item-210 at level 4: list_item: Leung D, Du T, Wagner U, Xie W, ... 0.1073/pnas.1322273111, PMID: 24757056 - item-211 at level 4: list_item: Lilue J, Doran AG, Fiddes IT, Ab ... 1038/s41588-018-0223-8, PMID: 30275530 - item-212 at level 4: list_item: Liu S, Brind'Amour J, Karimi MM, ... 10.1101/gad.244848.114, PMID: 25228647 - item-213 at level 4: list_item: Love MI, Huber W, Anders S. Mode ... 1186/s13059-014-0550-8, PMID: 25516281 - item-214 at level 4: list_item: Lugani F, Arora R, Papeta N, Pat ... 1/journal.pgen.1003206, PMID: 23437001 - item-215 at level 4: list_item: Macfarlan TS, Gifford WD, Drisco ... I: 10.1038/nature11244, PMID: 22722858 - item-216 at level 4: list_item: Maksakova IA, Romanish MT, Gagni ... 1/journal.pgen.0020002, PMID: 16440055 - item-217 at level 4: list_item: Matsui T, Leung D, Miyashita H, ... I: 10.1038/nature08858, PMID: 20164836 - item-218 at level 4: list_item: Najafabadi HS, Mnaimneh S, Schmi ... DOI: 10.1038/nbt.3128, PMID: 25690854 - item-219 at level 4: list_item: Nellåker C, Keane TM, Yalcin B, ... .1186/gb-2012-13-6-r45, PMID: 22703977 - item-220 at level 4: list_item: O'Geen H, Frietze S, Farnham PJ. ... 7/978-1-60761-753-2_27, PMID: 20680851 - item-221 at level 4: list_item: Patel A, Yang P, Tinkham M, Prad ... 016/j.cell.2018.02.058, PMID: 29551271 - item-222 at level 4: list_item: Ribet D, Dewannieux M, Heidmann ... OI: 10.1101/gr.2924904, PMID: 15479948 - item-223 at level 4: list_item: Richardson SR, Gerdes P, Gerhard ... 10.1101/gr.219022.116, PMID: 28483779 - item-224 at level 4: list_item: Rowe HM, Jakobsson J, Mesnard D, ... I: 10.1038/nature08674, PMID: 20075919 - item-225 at level 4: list_item: Rowe HM, Kapopoulou A, Corsinott ... 10.1101/gr.147678.112, PMID: 23233547 - item-226 at level 4: list_item: Schauer SN, Carreira PE, Shukla ... 10.1101/gr.226993.117, PMID: 29643204 - item-227 at level 4: list_item: Schultz DC, Ayyanathan K, Negore ... OI: 10.1101/gad.973302, PMID: 11959841 - item-228 at level 4: list_item: Semba K, Araki K, Matsumoto K, S ... 1/journal.pgen.1003204, PMID: 23436999 - item-229 at level 4: list_item: Sripathy SP, Stevens J, Schultz ... : 10.1128/MCB.00487-06, PMID: 16954381 - item-230 at level 4: list_item: Thomas JH, Schneider S. Coevolut ... 10.1101/gr.121749.111, PMID: 21784874 - item-231 at level 4: list_item: Thompson PJ, Macfarlan TS, Lorin ... 6/j.molcel.2016.03.029, PMID: 27259207 - item-232 at level 4: list_item: Treger RS, Pope SD, Kong Y, Toku ... 6/j.immuni.2018.12.022, PMID: 30709743 - item-233 at level 4: list_item: Vlangos CN, Siuniak AN, Robinson ... 1/journal.pgen.1003205, PMID: 23437000 - item-234 at level 4: list_item: Wang J, Xie G, Singh M, Ghanbari ... I: 10.1038/nature13804, PMID: 25317556 - item-235 at level 4: list_item: Wolf D, Hug K, Goff SP. TRIM28 m ... 0.1073/pnas.0805540105, PMID: 18713861 - item-236 at level 4: list_item: Wolf G, Greenberg D, Macfarlan T ... 1186/s13100-015-0050-8, PMID: 26435754 - item-237 at level 4: list_item: Wolf G, Yang P, Füchtbauer AC, F ... 10.1101/gad.252767.114, PMID: 25737282 - item-238 at level 4: list_item: Yamauchi M, Freitag B, Khan C, B ... JVI.69.2.1142-1149.1995, PMID: 7529329 - item-239 at level 4: list_item: Zhang Y, Liu T, Meyer CA, Eeckho ... .1186/gb-2008-9-9-r137, PMID: 18798982 - item-240 at level 1: caption: Figure 1. Genome-wide binding pa ... onsensus fingers highlighted in white. - item-241 at level 1: caption: Table 1. KRAB-ZFP genes clusters ... ChIP-seq was performed in this study. - item-242 at level 1: caption: Figure 2. Retrotransposon reacti ... s were calculated using paired t-test. - item-243 at level 1: caption: Figure 3. TE-dependent gene acti ... Gm13051 are indicated by dashed lines. - item-244 at level 1: caption: Figure 4. ETn retrotransposition ... combined for the statistical analysis. - item-245 at level 1: caption: Key resources table \ No newline at end of file + item-155 at level 5: list_item: + item-156 at level 6: footnote: No competing interests declared. + item-157 at level 3: section_header: Author contributions + item-158 at level 4: list: group footnotes + item-159 at level 5: list_item: + item-160 at level 6: footnote: Conceptualization, Data curation ... Methodology, Writing - original draft. + item-161 at level 5: list_item: + item-162 at level 6: footnote: Conceptualization, Data curation ... l draft, Writing - review and editing. + item-163 at level 5: list_item: + item-164 at level 6: footnote: Conceptualization, Data curation ... odology, Writing - review and editing. + item-165 at level 5: list_item: + item-166 at level 6: footnote: Conceptualization, Formal analys ... igation, Writing - review and editing. + item-167 at level 5: list_item: + item-168 at level 6: footnote: Investigation. + item-169 at level 5: list_item: + item-170 at level 6: footnote: Investigation. + item-171 at level 5: list_item: + item-172 at level 6: footnote: Data curation, Software, Formal analysis, Visualization. + item-173 at level 5: list_item: + item-174 at level 6: footnote: Investigation. + item-175 at level 5: list_item: + item-176 at level 6: footnote: Conceptualization, Resources, Su ... igation, Writing - review and editing. + item-177 at level 5: list_item: + item-178 at level 6: footnote: Conceptualization, Resources, Su ... tration, Writing - review and editing. + item-179 at level 3: section_header: Ethics + item-180 at level 4: list: group footnotes + item-181 at level 5: list_item: + item-182 at level 6: footnote: Animal experimentation: All stud ... er IACUC animal protocol (ASP )18-026. + item-183 at level 2: section_header: Additional files + item-184 at level 2: section_header: Data availability + item-185 at level 3: text: All NGS data has been deposited ... GenBank database (MH449667- MH449669). + item-186 at level 3: text: The following datasets were generated: + item-187 at level 3: text: Wolf G. Retrotransposon reactiva ... ession Omnibus (2019). NCBI: GSE115291 + item-188 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449667 + item-189 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449668 + item-190 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449669 + item-191 at level 3: text: The following previously published datasets were used: + item-192 at level 3: text: Castro-Diaz N, Ecco G, Coluccio ... ssion Omnibus (2014). NCBI: GSM1406445 + item-193 at level 3: text: Andrew ZX. H3K9me3_ChIPSeq (Ctrl ... ssion Omnibus (2014). NCBI: GSM1327148 + item-194 at level 2: section_header: References + item-195 at level 3: list: group list + item-196 at level 4: list_item: Bailey TL, Boden M, Buske FA, Fr ... 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Endoge ... 6/j.coviro.2013.08.005, PMID: 24004725 + item-206 at level 4: list_item: Ecco G, Cassano M, Kauzlaric A, ... 6/j.devcel.2016.02.024, PMID: 27003935 + item-207 at level 4: list_item: Ecco G, Imbeault M, Trono D. KRA ... OI: 10.1242/dev.132605, PMID: 28765213 + item-208 at level 4: list_item: Frank JA, Feschotte C. Co-option ... 6/j.coviro.2017.07.021, PMID: 28818736 + item-209 at level 4: list_item: Gagnier L, Belancio VP, Mager DL ... 1186/s13100-019-0157-4, PMID: 31011371 + item-210 at level 4: list_item: Groner AC, Meylan S, Ciuffi A, Z ... 1/journal.pgen.1000869, PMID: 20221260 + item-211 at level 4: list_item: Hancks DC, Kazazian HH. Roles fo ... 1186/s13100-016-0065-9, PMID: 27158268 + item-212 at level 4: list_item: Imbeault M, Helleboid PY, Trono ... I: 10.1038/nature21683, PMID: 28273063 + item-213 at level 4: list_item: Jacobs FM, Greenberg D, Nguyen N ... I: 10.1038/nature13760, PMID: 25274305 + item-214 at level 4: list_item: Kano H, Kurahashi H, Toda T. Gen ... 0.1073/pnas.0705483104, PMID: 17984064 + item-215 at level 4: list_item: Karimi MM, Goyal P, Maksakova IA ... 016/j.stem.2011.04.004, PMID: 21624812 + item-216 at level 4: list_item: Kauzlaric A, Ecco G, Cassano M, ... 1/journal.pone.0173746, PMID: 28334004 + item-217 at level 4: list_item: Khil PP, Smagulova F, Brick KM, ... 10.1101/gr.130583.111, PMID: 22367190 + item-218 at level 4: list_item: Krueger F, Andrews SR. Bismark: ... /bioinformatics/btr167, PMID: 21493656 + item-219 at level 4: list_item: Langmead B, Salzberg SL. Fast ga ... OI: 10.1038/nmeth.1923, PMID: 22388286 + item-220 at level 4: list_item: Legiewicz M, Zolotukhin AS, Pilk ... 0.1074/jbc.M110.182840, PMID: 20978285 + item-221 at level 4: list_item: Lehoczky JA, Thomas PE, Patrie K ... 1/journal.pgen.1003967, PMID: 24339789 + item-222 at level 4: list_item: Leung D, Du T, Wagner U, Xie W, ... 0.1073/pnas.1322273111, PMID: 24757056 + item-223 at level 4: list_item: Lilue J, Doran AG, Fiddes IT, Ab ... 1038/s41588-018-0223-8, PMID: 30275530 + item-224 at level 4: list_item: Liu S, Brind'Amour J, Karimi MM, ... 10.1101/gad.244848.114, PMID: 25228647 + item-225 at level 4: list_item: Love MI, Huber W, Anders S. Mode ... 1186/s13059-014-0550-8, PMID: 25516281 + item-226 at level 4: list_item: Lugani F, Arora R, Papeta N, Pat ... 1/journal.pgen.1003206, PMID: 23437001 + item-227 at level 4: list_item: Macfarlan TS, Gifford WD, Drisco ... I: 10.1038/nature11244, PMID: 22722858 + item-228 at level 4: list_item: Maksakova IA, Romanish MT, Gagni ... 1/journal.pgen.0020002, PMID: 16440055 + item-229 at level 4: list_item: Matsui T, Leung D, Miyashita H, ... I: 10.1038/nature08858, PMID: 20164836 + item-230 at level 4: list_item: Najafabadi HS, Mnaimneh S, Schmi ... DOI: 10.1038/nbt.3128, PMID: 25690854 + item-231 at level 4: list_item: Nellåker C, Keane TM, Yalcin B, ... .1186/gb-2012-13-6-r45, PMID: 22703977 + item-232 at level 4: list_item: O'Geen H, Frietze S, Farnham PJ. ... 7/978-1-60761-753-2_27, PMID: 20680851 + item-233 at level 4: list_item: Patel A, Yang P, Tinkham M, Prad ... 016/j.cell.2018.02.058, PMID: 29551271 + item-234 at level 4: list_item: Ribet D, Dewannieux M, Heidmann ... OI: 10.1101/gr.2924904, PMID: 15479948 + item-235 at level 4: list_item: Richardson SR, Gerdes P, Gerhard ... 10.1101/gr.219022.116, PMID: 28483779 + item-236 at level 4: list_item: Rowe HM, Jakobsson J, Mesnard D, ... I: 10.1038/nature08674, PMID: 20075919 + item-237 at level 4: list_item: Rowe HM, Kapopoulou A, Corsinott ... 10.1101/gr.147678.112, PMID: 23233547 + item-238 at level 4: list_item: Schauer SN, Carreira PE, Shukla ... 10.1101/gr.226993.117, PMID: 29643204 + item-239 at level 4: list_item: Schultz DC, Ayyanathan K, Negore ... OI: 10.1101/gad.973302, PMID: 11959841 + item-240 at level 4: list_item: Semba K, Araki K, Matsumoto K, S ... 1/journal.pgen.1003204, PMID: 23436999 + item-241 at level 4: list_item: Sripathy SP, Stevens J, Schultz ... : 10.1128/MCB.00487-06, PMID: 16954381 + item-242 at level 4: list_item: Thomas JH, Schneider S. Coevolut ... 10.1101/gr.121749.111, PMID: 21784874 + item-243 at level 4: list_item: Thompson PJ, Macfarlan TS, Lorin ... 6/j.molcel.2016.03.029, PMID: 27259207 + item-244 at level 4: list_item: Treger RS, Pope SD, Kong Y, Toku ... 6/j.immuni.2018.12.022, PMID: 30709743 + item-245 at level 4: list_item: Vlangos CN, Siuniak AN, Robinson ... 1/journal.pgen.1003205, PMID: 23437000 + item-246 at level 4: list_item: Wang J, Xie G, Singh M, Ghanbari ... I: 10.1038/nature13804, PMID: 25317556 + item-247 at level 4: list_item: Wolf D, Hug K, Goff SP. TRIM28 m ... 0.1073/pnas.0805540105, PMID: 18713861 + item-248 at level 4: list_item: Wolf G, Greenberg D, Macfarlan T ... 1186/s13100-015-0050-8, PMID: 26435754 + item-249 at level 4: list_item: Wolf G, Yang P, Füchtbauer AC, F ... 10.1101/gad.252767.114, PMID: 25737282 + item-250 at level 4: list_item: Yamauchi M, Freitag B, Khan C, B ... JVI.69.2.1142-1149.1995, PMID: 7529329 + item-251 at level 4: list_item: Zhang Y, Liu T, Meyer CA, Eeckho ... .1186/gb-2008-9-9-r137, PMID: 18798982 + item-252 at level 1: caption: Figure 1. Genome-wide binding pa ... onsensus fingers highlighted in white. + item-253 at level 1: caption: Table 1. KRAB-ZFP genes clusters ... ChIP-seq was performed in this study. + item-254 at level 1: caption: Figure 2. Retrotransposon reacti ... s were calculated using paired t-test. + item-255 at level 1: caption: Figure 3. TE-dependent gene acti ... Gm13051 are indicated by dashed lines. + item-256 at level 1: caption: Figure 4. ETn retrotransposition ... combined for the statistical analysis. + item-257 at level 1: caption: Key resources table \ No newline at end of file diff --git a/tests/data/jats/groundtruth/elife-56337.nxml.json b/tests/data/jats/groundtruth/elife-56337.nxml.json index 5b90a4d1e0..cd7949980c 100644 --- a/tests/data/jats/groundtruth/elife-56337.nxml.json +++ b/tests/data/jats/groundtruth/elife-56337.nxml.json @@ -485,38 +485,38 @@ { "self_ref": "#/groups/15", "parent": { - "$ref": "#/texts/140" + "$ref": "#/texts/141" }, "children": [ { - "$ref": "#/texts/141" + "$ref": "#/texts/142" }, { - "$ref": "#/texts/142" + "$ref": "#/texts/144" }, { - "$ref": "#/texts/143" + "$ref": "#/texts/146" }, { - "$ref": "#/texts/144" + "$ref": "#/texts/148" }, { - "$ref": "#/texts/145" + "$ref": "#/texts/150" }, { - "$ref": "#/texts/146" + "$ref": "#/texts/152" }, { - "$ref": "#/texts/147" + "$ref": "#/texts/154" }, { - "$ref": "#/texts/148" + "$ref": "#/texts/156" }, { - "$ref": "#/texts/149" + "$ref": "#/texts/158" }, { - 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"children": [], + "children": [ + { + "$ref": "#/texts/164" + } + ], "content_layer": "body", "label": "list_item", "prov": [], - "orig": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026.", - "text": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026.", + "orig": "", + "text": "", "enumerated": false, "marker": "" }, { - "self_ref": "#/texts/153", + "self_ref": "#/texts/164", + "parent": { + "$ref": "#/texts/163" + }, + "children": [], + "content_layer": "body", + "label": "footnote", + "prov": [], + "orig": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026.", + "text": "Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026." + }, + { + "self_ref": "#/texts/165", "parent": { "$ref": "#/texts/0" }, @@ -3005,37 +3197,37 @@ "level": 1 }, { - "self_ref": "#/texts/154", + "self_ref": "#/texts/166", "parent": { "$ref": "#/texts/0" }, "children": [ { - "$ref": "#/texts/155" + "$ref": "#/texts/167" }, { - "$ref": "#/texts/156" + "$ref": "#/texts/168" }, { - "$ref": "#/texts/157" + "$ref": "#/texts/169" }, { - "$ref": "#/texts/158" + "$ref": "#/texts/170" }, { - "$ref": "#/texts/159" + "$ref": "#/texts/171" }, { - "$ref": "#/texts/160" + "$ref": "#/texts/172" }, { - "$ref": "#/texts/161" + "$ref": "#/texts/173" }, { - "$ref": "#/texts/162" + "$ref": "#/texts/174" }, { - "$ref": "#/texts/163" + "$ref": "#/texts/175" } ], "content_layer": "body", @@ -3046,9 +3238,9 @@ "level": 1 }, { - "self_ref": "#/texts/155", + "self_ref": "#/texts/167", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3058,9 +3250,9 @@ "text": "All NGS data has been deposited in GEO (GSE115291). Sequences of full-length de novo ETn insertions have been deposited in the GenBank database (MH449667- MH449669)." }, { - "self_ref": "#/texts/156", + "self_ref": "#/texts/168", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3070,9 +3262,9 @@ "text": "The following datasets were generated:" }, { - "self_ref": "#/texts/157", + "self_ref": "#/texts/169", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3082,9 +3274,9 @@ "text": "Wolf G. Retrotransposon reactivation and mobilization upon deletions of megabase scale KRAB zinc finger gene clusters in mice. NCBI Gene Expression Omnibus (2019). NCBI: GSE115291" }, { - "self_ref": "#/texts/158", + "self_ref": "#/texts/170", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3094,9 +3286,9 @@ "text": "Wolf G. Mus musculus musculus strain C57BL/6x129X1/SvJ retrotransposon MMETn-int, complete sequence. NCBI GenBank (2019). NCBI: MH449667" }, { - "self_ref": "#/texts/159", + "self_ref": "#/texts/171", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3106,9 +3298,9 @@ "text": "Wolf G. Mus musculus musculus strain C57BL/6x129X1/SvJ retrotransposon MMETn-int, complete sequence. NCBI GenBank (2019). NCBI: MH449668" }, { - "self_ref": "#/texts/160", + "self_ref": "#/texts/172", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3118,9 +3310,9 @@ "text": "Wolf G. Mus musculus musculus strain C57BL/6x129X1/SvJ retrotransposon MMETn-int, complete sequence. NCBI GenBank (2019). NCBI: MH449669" }, { - "self_ref": "#/texts/161", + "self_ref": "#/texts/173", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3130,9 +3322,9 @@ "text": "The following previously published datasets were used:" }, { - "self_ref": "#/texts/162", + "self_ref": "#/texts/174", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3142,9 +3334,9 @@ "text": "Castro-Diaz N, Ecco G, Coluccio A, Kapopoulou A, Duc J, Trono D. Evollutionally dynamic L1 regulation in embryonic stem cells. NCBI Gene Expression Omnibus (2014). NCBI: GSM1406445" }, { - "self_ref": "#/texts/163", + "self_ref": "#/texts/175", "parent": { - "$ref": "#/texts/154" + "$ref": "#/texts/166" }, "children": [], "content_layer": "body", @@ -3154,7 +3346,7 @@ "text": "Andrew ZX. H3K9me3_ChIPSeq (Ctrl). NCBI Gene Expression Omnibus (2014). NCBI: GSM1327148" }, { - "self_ref": "#/texts/164", + "self_ref": "#/texts/176", "parent": { "$ref": "#/texts/0" }, @@ -3171,7 +3363,7 @@ "level": 1 }, { - "self_ref": "#/texts/165", + "self_ref": "#/texts/177", "parent": { "$ref": "#/groups/17" }, @@ -3185,7 +3377,7 @@ "marker": "" }, { - "self_ref": "#/texts/166", + "self_ref": "#/texts/178", "parent": { "$ref": "#/groups/17" }, @@ -3199,7 +3391,7 @@ "marker": "" }, { - "self_ref": "#/texts/167", + "self_ref": "#/texts/179", "parent": { "$ref": "#/groups/17" }, @@ -3213,7 +3405,7 @@ "marker": "" }, { - "self_ref": "#/texts/168", + "self_ref": "#/texts/180", "parent": { "$ref": "#/groups/17" }, @@ -3227,7 +3419,7 @@ "marker": "" }, { - "self_ref": "#/texts/169", + "self_ref": "#/texts/181", "parent": { "$ref": "#/groups/17" }, @@ -3241,7 +3433,7 @@ "marker": "" }, { - "self_ref": "#/texts/170", + "self_ref": "#/texts/182", "parent": { "$ref": "#/groups/17" }, @@ -3255,7 +3447,7 @@ "marker": "" }, { - "self_ref": "#/texts/171", + "self_ref": "#/texts/183", "parent": { "$ref": "#/groups/17" }, @@ -3269,7 +3461,7 @@ "marker": "" }, { - "self_ref": "#/texts/172", + "self_ref": "#/texts/184", "parent": { "$ref": "#/groups/17" }, @@ -3283,7 +3475,7 @@ "marker": "" }, { - "self_ref": "#/texts/173", + "self_ref": "#/texts/185", "parent": { "$ref": "#/groups/17" }, @@ -3297,7 +3489,7 @@ "marker": "" }, { - "self_ref": "#/texts/174", + "self_ref": "#/texts/186", "parent": { "$ref": "#/groups/17" }, @@ -3311,7 +3503,7 @@ "marker": "" }, { - "self_ref": "#/texts/175", + "self_ref": "#/texts/187", "parent": { "$ref": "#/groups/17" }, @@ -3325,7 +3517,7 @@ "marker": "" }, { - "self_ref": "#/texts/176", + "self_ref": "#/texts/188", "parent": { "$ref": "#/groups/17" }, @@ -3339,7 +3531,7 @@ "marker": "" }, { - "self_ref": "#/texts/177", + "self_ref": "#/texts/189", "parent": { "$ref": "#/groups/17" }, @@ -3353,7 +3545,7 @@ "marker": "" }, { - "self_ref": "#/texts/178", + "self_ref": "#/texts/190", "parent": { "$ref": "#/groups/17" }, @@ -3367,7 +3559,7 @@ "marker": "" }, { - "self_ref": "#/texts/179", + "self_ref": "#/texts/191", "parent": { "$ref": "#/groups/17" }, @@ -3381,7 +3573,7 @@ "marker": "" }, { - "self_ref": "#/texts/180", + "self_ref": "#/texts/192", "parent": { "$ref": "#/groups/17" }, @@ -3395,7 +3587,7 @@ "marker": "" }, { - "self_ref": "#/texts/181", + "self_ref": "#/texts/193", "parent": { "$ref": "#/groups/17" }, @@ -3409,7 +3601,7 @@ "marker": "" }, { - "self_ref": "#/texts/182", + "self_ref": "#/texts/194", "parent": { "$ref": "#/groups/17" }, @@ -3423,7 +3615,7 @@ "marker": "" }, { - "self_ref": "#/texts/183", + "self_ref": "#/texts/195", "parent": { "$ref": "#/groups/17" }, @@ -3437,7 +3629,7 @@ "marker": "" }, { - "self_ref": "#/texts/184", + "self_ref": "#/texts/196", "parent": { "$ref": "#/groups/17" }, @@ -3451,7 +3643,7 @@ "marker": "" }, { - "self_ref": "#/texts/185", + "self_ref": "#/texts/197", "parent": { "$ref": "#/groups/17" }, @@ -3465,7 +3657,7 @@ "marker": "" }, { - "self_ref": "#/texts/186", + "self_ref": "#/texts/198", "parent": { "$ref": "#/groups/17" }, @@ -3479,7 +3671,7 @@ "marker": "" }, { - "self_ref": "#/texts/187", + "self_ref": "#/texts/199", "parent": { "$ref": "#/groups/17" }, @@ -3493,7 +3685,7 @@ "marker": "" }, { - "self_ref": "#/texts/188", + "self_ref": "#/texts/200", "parent": { "$ref": "#/groups/17" }, @@ -3507,7 +3699,7 @@ "marker": "" }, { - "self_ref": "#/texts/189", + "self_ref": "#/texts/201", "parent": { "$ref": "#/groups/17" }, @@ -3521,7 +3713,7 @@ "marker": "" }, { - "self_ref": "#/texts/190", + "self_ref": "#/texts/202", "parent": { "$ref": "#/groups/17" }, @@ -3535,7 +3727,7 @@ "marker": "" }, { - "self_ref": "#/texts/191", + "self_ref": "#/texts/203", "parent": { "$ref": "#/groups/17" }, @@ -3549,7 +3741,7 @@ "marker": "" }, { - "self_ref": "#/texts/192", + "self_ref": "#/texts/204", "parent": { "$ref": "#/groups/17" }, @@ -3563,7 +3755,7 @@ "marker": "" }, { - "self_ref": "#/texts/193", + "self_ref": "#/texts/205", "parent": { "$ref": "#/groups/17" }, @@ -3577,7 +3769,7 @@ "marker": "" }, { - "self_ref": "#/texts/194", + "self_ref": "#/texts/206", "parent": { "$ref": "#/groups/17" }, @@ -3591,7 +3783,7 @@ "marker": "" }, { - "self_ref": "#/texts/195", + "self_ref": "#/texts/207", "parent": { "$ref": "#/groups/17" }, @@ -3605,7 +3797,7 @@ "marker": "" }, { - "self_ref": "#/texts/196", + "self_ref": "#/texts/208", "parent": { "$ref": "#/groups/17" }, @@ -3619,7 +3811,7 @@ "marker": "" }, { - "self_ref": "#/texts/197", + "self_ref": "#/texts/209", "parent": { "$ref": "#/groups/17" }, @@ -3633,7 +3825,7 @@ "marker": "" }, { - "self_ref": "#/texts/198", + "self_ref": "#/texts/210", "parent": { "$ref": "#/groups/17" }, @@ -3647,7 +3839,7 @@ "marker": "" }, { - "self_ref": "#/texts/199", + "self_ref": "#/texts/211", "parent": { "$ref": "#/groups/17" }, @@ -3661,7 +3853,7 @@ "marker": "" }, { - "self_ref": "#/texts/200", + "self_ref": "#/texts/212", "parent": { "$ref": "#/groups/17" }, @@ -3675,7 +3867,7 @@ "marker": "" }, { - "self_ref": "#/texts/201", + "self_ref": "#/texts/213", "parent": { "$ref": "#/groups/17" }, @@ -3689,7 +3881,7 @@ "marker": "" }, { - "self_ref": "#/texts/202", + "self_ref": "#/texts/214", "parent": { "$ref": "#/groups/17" }, @@ -3703,7 +3895,7 @@ "marker": "" }, { - "self_ref": "#/texts/203", + "self_ref": "#/texts/215", "parent": { "$ref": "#/groups/17" }, @@ -3717,7 +3909,7 @@ "marker": "" }, { - "self_ref": "#/texts/204", + "self_ref": "#/texts/216", "parent": { "$ref": "#/groups/17" }, @@ -3731,7 +3923,7 @@ "marker": "" }, { - "self_ref": "#/texts/205", + "self_ref": "#/texts/217", "parent": { "$ref": "#/groups/17" }, @@ -3745,7 +3937,7 @@ "marker": "" }, { - "self_ref": "#/texts/206", + "self_ref": "#/texts/218", "parent": { "$ref": "#/groups/17" }, @@ -3759,7 +3951,7 @@ "marker": "" }, { - "self_ref": "#/texts/207", + "self_ref": "#/texts/219", "parent": { "$ref": "#/groups/17" }, @@ -3773,7 +3965,7 @@ "marker": "" }, { - "self_ref": "#/texts/208", + "self_ref": "#/texts/220", "parent": { "$ref": "#/groups/17" }, @@ -3787,7 +3979,7 @@ "marker": "" }, { - "self_ref": "#/texts/209", + "self_ref": "#/texts/221", "parent": { "$ref": "#/groups/17" }, @@ -3801,7 +3993,7 @@ "marker": "" }, { - "self_ref": "#/texts/210", + "self_ref": "#/texts/222", "parent": { "$ref": "#/groups/17" }, @@ -3815,7 +4007,7 @@ "marker": "" }, { - "self_ref": "#/texts/211", + "self_ref": "#/texts/223", "parent": { "$ref": "#/groups/17" }, @@ -3829,7 +4021,7 @@ "marker": "" }, { - "self_ref": "#/texts/212", + "self_ref": "#/texts/224", "parent": { "$ref": "#/groups/17" }, @@ -3843,7 +4035,7 @@ "marker": "" }, { - "self_ref": "#/texts/213", + "self_ref": "#/texts/225", "parent": { "$ref": "#/groups/17" }, @@ -3857,7 +4049,7 @@ "marker": "" }, { - "self_ref": "#/texts/214", + "self_ref": "#/texts/226", "parent": { "$ref": "#/groups/17" }, @@ -3871,7 +4063,7 @@ "marker": "" }, { - "self_ref": "#/texts/215", + "self_ref": "#/texts/227", "parent": { "$ref": "#/groups/17" }, @@ -3885,7 +4077,7 @@ "marker": "" }, { - "self_ref": "#/texts/216", + "self_ref": "#/texts/228", "parent": { "$ref": "#/groups/17" }, @@ -3899,7 +4091,7 @@ "marker": "" }, { - "self_ref": "#/texts/217", + "self_ref": "#/texts/229", "parent": { "$ref": "#/groups/17" }, @@ -3913,7 +4105,7 @@ "marker": "" }, { - "self_ref": "#/texts/218", + "self_ref": "#/texts/230", "parent": { "$ref": "#/groups/17" }, @@ -3927,7 +4119,7 @@ "marker": "" }, { - "self_ref": "#/texts/219", + "self_ref": "#/texts/231", "parent": { "$ref": "#/groups/17" }, @@ -3941,7 +4133,7 @@ "marker": "" }, { - "self_ref": "#/texts/220", + "self_ref": "#/texts/232", "parent": { "$ref": "#/groups/17" }, diff --git a/tests/data/jats/groundtruth/elife-56337.nxml.md b/tests/data/jats/groundtruth/elife-56337.nxml.md index e167e08611..0eb9c186a9 100644 --- a/tests/data/jats/groundtruth/elife-56337.nxml.md +++ b/tests/data/jats/groundtruth/elife-56337.nxml.md @@ -180,24 +180,36 @@ We thank Alex Grinberg, Jeanne Yimdjo and Victoria Carter for generating and mai ### Competing interests -- No competing interests declared. +- +No competing interests declared. ### Author contributions -- Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing - original draft. -- Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing - original draft, Writing - review and editing. -- Conceptualization, Data curation, Software, Formal analysis, Investigation, Visualization, Methodology, Writing - review and editing. -- Conceptualization, Formal analysis, Investigation, Writing - review and editing. -- Investigation. -- Investigation. -- Data curation, Software, Formal analysis, Visualization. -- Investigation. -- Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Writing - review and editing. -- Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing - original draft, Project administration, Writing - review and editing. +- +Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing - original draft. +- +Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing - original draft, Writing - review and editing. +- +Conceptualization, Data curation, Software, Formal analysis, Investigation, Visualization, Methodology, Writing - review and editing. +- +Conceptualization, Formal analysis, Investigation, Writing - review and editing. +- +Investigation. +- +Investigation. +- +Data curation, Software, Formal analysis, Visualization. +- +Investigation. +- +Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Writing - review and editing. +- +Conceptualization, Resources, Supervision, Funding acquisition, Investigation, Methodology, Writing - original draft, Project administration, Writing - review and editing. ### Ethics -- Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026. +- +Animal experimentation: All studies using mice were performed in accordance to the Guide for the Care and Use of Laboratory Animals of the NIH, under IACUC animal protocol (ASP )18-026. ## Additional files diff --git a/tests/test_backend_jats.py b/tests/test_backend_jats.py index 11c8c24c7f..a4b6923b0f 100644 --- a/tests/test_backend_jats.py +++ b/tests/test_backend_jats.py @@ -484,9 +484,8 @@ def test_jats_plain_footnote_without_styling_stays_a_single_text_item(): ) assert _inline_group_items(doc) == [] - list_items = [t.text for t in doc.texts if t.label == DocItemLabel.LIST_ITEM] - assert list_items == ["Plain footnote."] - assert "- Plain footnote." in doc.export_to_markdown() + footnotes = [t.text for t in doc.texts if t.label == DocItemLabel.FOOTNOTE] + assert footnotes == ["Plain footnote."] def test_jats_footnote_styling_is_preserved():