diff --git a/docling/backend/asciidoc_backend.py b/docling/backend/asciidoc_backend.py
index 63c984b44b..e699b00e9d 100644
--- a/docling/backend/asciidoc_backend.py
+++ b/docling/backend/asciidoc_backend.py
@@ -627,10 +627,11 @@ def _add_picture_item(
         parents: dict[int, GroupItem | None],
     ) -> tuple[list[str], bool, ListItem | None]:
         """Add a picture with its pending caption, if any."""
+        parent = last_list_item if in_list else self._get_current_parent(parents)
         caption: Optional[TextItem] = None
         if len(caption_data) > 0:
             caption = doc.add_text(
-                text=" ".join(caption_data), label=DocItemLabel.CAPTION
+                text=" ".join(caption_data), label=DocItemLabel.CAPTION, parent=parent
             )
 
         caption_data = []
@@ -645,11 +646,7 @@ def _add_picture_item(
                 else None
             )
             image = self._image_loader.load_image_ref(item["uri"], base_path)
-        doc.add_picture(
-            image=image,
-            caption=caption,
-            parent=last_list_item if in_list else self._get_current_parent(parents),
-        )
+        doc.add_picture(image=image, caption=caption, parent=parent)
         return caption_data, in_list, last_list_item
 
     def _add_block(
@@ -740,11 +737,13 @@ def _add_literal_block(
             text_data=text_data,
             parent=self._get_current_parent(parents),
         )
+        parent = last_list_item if in_list else self._get_current_parent(parents)
         caption: Optional[TextItem] = None
         if caption_data:
             caption = doc.add_text(
                 text=" ".join(caption_data),
                 label=DocItemLabel.CAPTION,
+                parent=parent,
             )
             caption_data = []
         code_language = (
@@ -756,7 +755,7 @@ def _add_literal_block(
             text=block.text,
             code_language=code_language,
             caption=caption,
-            parent=(last_list_item if in_list else self._get_current_parent(parents)),
+            parent=parent,
         )
         return text_data, caption_data, in_list, last_list_item, False
 
@@ -1020,7 +1019,7 @@ def _add_table_if_nonempty(
         caption = None
         if caption_data:
             caption = doc.add_text(
-                text=" ".join(caption_data), label=DocItemLabel.CAPTION
+                text=" ".join(caption_data), label=DocItemLabel.CAPTION, parent=parent
             )
 
         data = AsciiDocBackend._populate_table_as_grid(table_data)
diff --git a/docling/backend/xml/jats_backend.py b/docling/backend/xml/jats_backend.py
index e1474a1def..143cec93e7 100644
--- a/docling/backend/xml/jats_backend.py
+++ b/docling/backend/xml/jats_backend.py
@@ -947,7 +947,7 @@ def _add_figure_captions(
         # TODO: format label vs caption once styling is supported
         fig_text: str = f"{label}{' ' if label and caption else ''}{caption}"
         fig_caption: TextItem | None = (
-            doc.add_text(label=DocItemLabel.CAPTION, text=fig_text)
+            doc.add_text(label=DocItemLabel.CAPTION, text=fig_text, parent=parent)
             if fig_text
             else None
         )
@@ -1167,7 +1167,7 @@ def _add_table(
         caption = table_xml_component["caption"]
         table_text: str = f"{label}{' ' if label and caption else ''}{caption}"
         table_caption: TextItem | None = (
-            doc.add_text(label=DocItemLabel.CAPTION, text=table_text)
+            doc.add_text(label=DocItemLabel.CAPTION, text=table_text, parent=parent)
             if table_text
             else None
         )
diff --git a/tests/data/jats/groundtruth/elife-56337.nxml.itxt b/tests/data/jats/groundtruth/elife-56337.nxml.itxt
index 7a401a7e90..c2c735bfd8 100644
--- a/tests/data/jats/groundtruth/elife-56337.nxml.itxt
+++ b/tests/data/jats/groundtruth/elife-56337.nxml.itxt
@@ -17,287 +17,287 @@ item-0 at level 0: unspecified: group _root_
           item-16 at level 5: text: To determine the binding sites o ... overlapped at least one TE subfamily (
           item-17 at level 5: text: adjusted p-value
           item-18 at level 5: text: <1e-5). Altogether, 81 LTR retro ... ctive in the early embryo (Figure 1A).
-        item-19 at level 4: picture
-          item-19 at level 5: caption: Figure 1. Genome-wide binding patterns of mouse KRAB-ZFPs. (A) Probability heatmap of KRAB-ZFP binding to TEs. Blue color intensity (main field) corresponds to -log10 (adjusted p-value) enrichment of ChIP-seq peak overlap with TE groups (Fisher’s exact test). The green/red color intensity (top panel) represents mean KAP1 (GEO accession: GSM1406445) and H3K9me3 (GEO accession: GSM1327148) enrichment (respectively) at peaks overlapping significantly targeted TEs (adjusted p-value<1e-5) in WT ES cells. (B) Summarized ChIP-seq signal for indicated KRAB-ZFPs and previously published KAP1 and H3K9me3 in WT ES cells across 127 intact ETn elements. (C) Heatmaps of KRAB-ZFP ChIP-seq signal at ChIP-seq peaks. For better comparison, peaks for all three KRAB-ZFPs were called with the same parameters (p<1e-10, peak enrichment >20). The top panel shows a schematic of the arrangement of the contact amino acid composition of each zinc finger. Zinc fingers are grouped and colored according to similarity, with amino acid differences relative to the five consensus fingers highlighted in white.
-        item-20 at level 4: table with [9x5]
-          item-20 at level 5: caption: Table 1. KRAB-ZFP genes clusters in the mouse genome that were investigated in this study. * Number of protein-coding KRAB-ZFP genes identified in a previously published screen (Imbeault et al., 2017) and the ChIP-seq data column indicates the number of KRAB-ZFPs for which ChIP-seq was performed in this study.
-        item-21 at level 4: inline: group group
-          item-22 at level 5: text: We generally observed that KRAB- ... ZFP961 motif closely resembles the PBS
-          item-23 at level 5: text: Lys1,2
-          item-24 at level 5: text: (Figure 1—figure supplement 3A), ... f et al., 2008). Repression of the PBS
+        item-19 at level 4: caption: Figure 1. Genome-wide binding pa ... onsensus fingers highlighted in white.
+        item-20 at level 4: picture
+          item-20 at level 5: caption: Figure 1. Genome-wide binding patterns of mouse KRAB-ZFPs. (A) Probability heatmap of KRAB-ZFP binding to TEs. Blue color intensity (main field) corresponds to -log10 (adjusted p-value) enrichment of ChIP-seq peak overlap with TE groups (Fisher’s exact test). The green/red color intensity (top panel) represents mean KAP1 (GEO accession: GSM1406445) and H3K9me3 (GEO accession: GSM1327148) enrichment (respectively) at peaks overlapping significantly targeted TEs (adjusted p-value<1e-5) in WT ES cells. (B) Summarized ChIP-seq signal for indicated KRAB-ZFPs and previously published KAP1 and H3K9me3 in WT ES cells across 127 intact ETn elements. (C) Heatmaps of KRAB-ZFP ChIP-seq signal at ChIP-seq peaks. For better comparison, peaks for all three KRAB-ZFPs were called with the same parameters (p<1e-10, peak enrichment >20). The top panel shows a schematic of the arrangement of the contact amino acid composition of each zinc finger. Zinc fingers are grouped and colored according to similarity, with amino acid differences relative to the five consensus fingers highlighted in white.
+        item-21 at level 4: caption: Table 1. KRAB-ZFP genes clusters ...  ChIP-seq was performed in this study.
+        item-22 at level 4: table with [9x5]
+          item-22 at level 5: caption: Table 1. KRAB-ZFP genes clusters in the mouse genome that were investigated in this study. * Number of protein-coding KRAB-ZFP genes identified in a previously published screen (Imbeault et al., 2017) and the ChIP-seq data column indicates the number of KRAB-ZFPs for which ChIP-seq was performed in this study.
+        item-23 at level 4: inline: group group
+          item-24 at level 5: text: We generally observed that KRAB- ... ZFP961 motif closely resembles the PBS
           item-25 at level 5: text: Lys1,2
-          item-26 at level 5: text: by ZFP961 was also confirmed in  ... responsible for this silencing effect.
-        item-27 at level 4: text: To further test the hypothesis t ... t easily evade repression by mutation.
-        item-28 at level 4: text: Our KRAB-ZFP ChIP-seq dataset al ... ntirely shift the mode of DNA binding.
-      item-29 at level 3: section_header: Genetic deletion of KRAB-ZFP gen ...  leads to retrotransposon reactivation
-        item-30 at level 4: text: The majority of KRAB-ZFP genes a ... ung et al., 2014; Deniz et al., 2018).
-        item-31 at level 4: picture
-          item-31 at level 5: caption: Figure 2. Retrotransposon reactivation in KRAB-ZFP cluster KO ES cells. (A) RNA-seq analysis of TE expression in five KRAB-ZFP cluster KO ES cells. Green and grey squares on top of the panel represent KRAB-ZFPs with or without ChIP-seq data, respectively, within each deleted gene cluster. Reactivated TEs that are bound by one or several KRAB-ZFPs are indicated by green squares in the panel. Significantly up- and downregulated elements (adjusted p-value<0.05) are highlighted in red and green, respectively. (B) Differential KAP1 binding and H3K9me3 enrichment at TE groups (summarized across all insertions) in Chr2-cl and Chr4-cl KO ES cells. TE groups targeted by one or several KRAB-ZFPs encoded within the deleted clusters are highlighted in blue (differential enrichment over the entire TE sequences) and red (differential enrichment at TE regions that overlap with KRAB-ZFP ChIP-seq peaks). (C) DNA methylation status of CpG sites at indicated TE groups in WT and Chr4-cl KO ES cells grown in serum containing media or in hypomethylation-inducing media (2i + Vitamin C). P-values were calculated using paired t-test.
-      item-32 at level 3: section_header: KRAB-ZFP cluster deletions license TE-borne enhancers
-        item-33 at level 4: text: We next used our RNA-seq dataset ... vating effects of TEs on nearby genes.
+          item-26 at level 5: text: (Figure 1—figure supplement 3A), ... f et al., 2008). Repression of the PBS
+          item-27 at level 5: text: Lys1,2
+          item-28 at level 5: text: by ZFP961 was also confirmed in  ... responsible for this silencing effect.
+        item-29 at level 4: text: To further test the hypothesis t ... t easily evade repression by mutation.
+        item-30 at level 4: text: Our KRAB-ZFP ChIP-seq dataset al ... ntirely shift the mode of DNA binding.
+      item-31 at level 3: section_header: Genetic deletion of KRAB-ZFP gen ...  leads to retrotransposon reactivation
+        item-32 at level 4: text: The majority of KRAB-ZFP genes a ... ung et al., 2014; Deniz et al., 2018).
+        item-33 at level 4: caption: Figure 2. Retrotransposon reacti ... s were calculated using paired t-test.
         item-34 at level 4: picture
-          item-34 at level 5: caption: Figure 3. TE-dependent gene activation in KRAB-ZFP cluster KO ES cells. (A) Differential gene expression in Chr2-cl and Chr4-cl KO ES cells. Significantly up- and downregulated genes (adjusted p-value<0.05) are highlighted in red and green, respectively, KRAB-ZFP genes within the deleted clusters are shown in blue. (B) Correlation of TEs and gene deregulation. Plots show enrichment of TE groups within 100 kb of up- and downregulated genes relative to all genes. Significantly overrepresented LTR and LINE groups (adjusted p-value<0.1) are highlighted in blue and red, respectively. (C) Schematic view of the downstream region of Chst1 where a 5’ truncated ETn insertion is located. ChIP-seq (Input subtracted from ChIP) data for overexpressed epitope-tagged Gm13051 (a Chr4-cl KRAB-ZFP) in F9 EC cells, and re-mapped KAP1 (GEO accession: GSM1406445) and H3K9me3 (GEO accession: GSM1327148) in WT ES cells are shown together with RNA-seq data from Chr4-cl WT and KO ES cells (mapped using Bowtie (-a -m 1 --strata -v 2) to exclude reads that cannot be uniquely mapped). (D) RT-qPCR analysis of Chst1 mRNA expression in Chr4-cl WT and KO ES cells with or without the CRISPR/Cas9 deleted ETn insertion near Chst1. Values represent mean expression (normalized to Gapdh) from three biological replicates per sample (each performed in three technical replicates) in arbitrary units. Error bars represent standard deviation and asterisks indicate significance (p<0.01, Student’s t-test). n.s.: not significant. (E) Mean coverage of ChIP-seq data (Input subtracted from ChIP) in Chr4-cl WT and KO ES cells over 127 full-length ETn insertions. The binding sites of the Chr4-cl KRAB-ZFPs Rex2 and Gm13051 are indicated by dashed lines.
-        item-35 at level 4: inline: group group
-          item-36 at level 5: text: While we generally observed that ... ETn insertion to the first exon of the
-          item-37 at level 5: text: Cd59a
-          item-38 at level 5: text: gene, which is strongly activate ... is located about 60 kb from the TSS of
-          item-39 at level 5: text: Chst1
-          item-40 at level 5: text: , one of the top-upregulated gen ... C). RT-qPCR analysis revealed that the
-          item-41 at level 5: text: Chst1
-          item-42 at level 5: text: upregulation phenotype in Chr4-c ... ontrolled ETn-borne enhancer regulates
+          item-34 at level 5: caption: Figure 2. Retrotransposon reactivation in KRAB-ZFP cluster KO ES cells. (A) RNA-seq analysis of TE expression in five KRAB-ZFP cluster KO ES cells. Green and grey squares on top of the panel represent KRAB-ZFPs with or without ChIP-seq data, respectively, within each deleted gene cluster. Reactivated TEs that are bound by one or several KRAB-ZFPs are indicated by green squares in the panel. Significantly up- and downregulated elements (adjusted p-value<0.05) are highlighted in red and green, respectively. (B) Differential KAP1 binding and H3K9me3 enrichment at TE groups (summarized across all insertions) in Chr2-cl and Chr4-cl KO ES cells. TE groups targeted by one or several KRAB-ZFPs encoded within the deleted clusters are highlighted in blue (differential enrichment over the entire TE sequences) and red (differential enrichment at TE regions that overlap with KRAB-ZFP ChIP-seq peaks). (C) DNA methylation status of CpG sites at indicated TE groups in WT and Chr4-cl KO ES cells grown in serum containing media or in hypomethylation-inducing media (2i + Vitamin C). P-values were calculated using paired t-test.
+      item-35 at level 3: section_header: KRAB-ZFP cluster deletions license TE-borne enhancers
+        item-36 at level 4: text: We next used our RNA-seq dataset ... vating effects of TEs on nearby genes.
+        item-37 at level 4: caption: Figure 3. TE-dependent gene acti ... Gm13051 are indicated by dashed lines.
+        item-38 at level 4: picture
+          item-38 at level 5: caption: Figure 3. TE-dependent gene activation in KRAB-ZFP cluster KO ES cells. (A) Differential gene expression in Chr2-cl and Chr4-cl KO ES cells. Significantly up- and downregulated genes (adjusted p-value<0.05) are highlighted in red and green, respectively, KRAB-ZFP genes within the deleted clusters are shown in blue. (B) Correlation of TEs and gene deregulation. Plots show enrichment of TE groups within 100 kb of up- and downregulated genes relative to all genes. Significantly overrepresented LTR and LINE groups (adjusted p-value<0.1) are highlighted in blue and red, respectively. (C) Schematic view of the downstream region of Chst1 where a 5’ truncated ETn insertion is located. ChIP-seq (Input subtracted from ChIP) data for overexpressed epitope-tagged Gm13051 (a Chr4-cl KRAB-ZFP) in F9 EC cells, and re-mapped KAP1 (GEO accession: GSM1406445) and H3K9me3 (GEO accession: GSM1327148) in WT ES cells are shown together with RNA-seq data from Chr4-cl WT and KO ES cells (mapped using Bowtie (-a -m 1 --strata -v 2) to exclude reads that cannot be uniquely mapped). (D) RT-qPCR analysis of Chst1 mRNA expression in Chr4-cl WT and KO ES cells with or without the CRISPR/Cas9 deleted ETn insertion near Chst1. Values represent mean expression (normalized to Gapdh) from three biological replicates per sample (each performed in three technical replicates) in arbitrary units. Error bars represent standard deviation and asterisks indicate significance (p<0.01, Student’s t-test). n.s.: not significant. (E) Mean coverage of ChIP-seq data (Input subtracted from ChIP) in Chr4-cl WT and KO ES cells over 127 full-length ETn insertions. The binding sites of the Chr4-cl KRAB-ZFPs Rex2 and Gm13051 are indicated by dashed lines.
+        item-39 at level 4: inline: group group
+          item-40 at level 5: text: While we generally observed that ... ETn insertion to the first exon of the
+          item-41 at level 5: text: Cd59a
+          item-42 at level 5: text: gene, which is strongly activate ... is located about 60 kb from the TSS of
           item-43 at level 5: text: Chst1
-          item-44 at level 5: text: expression (Figure 3D). Furtherm ... he internal region and not on the LTR.
-      item-45 at level 3: section_header: ETn retrotransposition in Chr4-cl KO and WT mice
-        item-46 at level 4: text: IAP, ETn/ETnERV and MuLV/RLTR4 r ... s may contribute to reduced viability.
-        item-47 at level 4: text: We reasoned that retrotransposon ... Tn insertions at a high recovery rate.
-        item-48 at level 4: text: Using this dataset, we first con ... nsertions in our pedigree (Figure 4A).
-        item-49 at level 4: picture
-          item-49 at level 5: caption: Figure 4. ETn retrotransposition in Chr4-cl KO mice. (A) Pedigree of mice used for transposon insertion screening by capture-seq in mice of different strain backgrounds. The number of novel ETn insertions (only present in one animal) are indicated. For animals whose direct ancestors have not been screened, the ETn insertions are shown in parentheses since parental inheritance cannot be excluded in that case. Germ line insertions are indicated by asterisks. All DNA samples were prepared from tail tissues unless noted (-S: spleen, -E: ear, -B:Blood) (B) Statistical analysis of ETn insertion frequency in tail tissue from 30 Chr4-cl KO, KO/WT and WT mice that were derived from one Chr4-c KO x KO/WT and two Chr4-cl KO/WT x KO/WT matings. Only DNA samples that were collected from juvenile tails were considered for this analysis. P-values were calculated using one-sided Wilcoxon Rank Sum Test. In the last panel, KO, WT and KO/WT mice derived from all matings were combined for the statistical analysis.
-        item-50 at level 4: text: To validate some of the novel ET ... ess might have truncated this element.
-        item-51 at level 4: text: Besides novel ETn insertions tha ... tions (Figure 4—figure supplement 3D).
-        item-52 at level 4: text: Finally, we asked whether there  ... s clearly also play an important role.
-    item-53 at level 2: section_header: Discussion
-      item-54 at level 3: text: C2H2 zinc finger proteins, about ... ) depending upon their insertion site.
-      item-55 at level 3: text: Despite a lack of widespread ETn ... ion of the majority of KRAB-ZFP genes.
-    item-56 at level 2: section_header: Materials and methods
-      item-57 at level 3: table with [31x5]
-        item-57 at level 4: caption: Key resources table
-      item-58 at level 3: section_header: Cell lines and transgenic mice
-        item-59 at level 4: inline: group group
-          item-60 at level 5: text: Mouse ES cells and F9 EC cells w ... nes originate from JM8A3.N1 C57BL/6N-A
-          item-61 at level 5: text: tm1Brd
-          item-62 at level 5: text: ES cells (KOMP Repository). Chr2 ... KO/KO and KO/WT (B6/129 F2) offspring.
-      item-63 at level 3: section_header: Generation of KRAB-ZFP expressing cell lines
-        item-64 at level 4: inline: group group
-          item-65 at level 5: text: KRAB-ZFP ORFs were PCR-amplified ... r 3XHA tags in F9 EC or ES cells using
-          item-66 at level 5: text: Sleeping beauty
-          item-67 at level 5: text: transposon-based (Wolf et al., 2 ... led and further expanded for ChIP-seq.
-      item-68 at level 3: section_header: CRISPR/Cas9 mediated deletion of KRAB-ZFP clusters and an MMETn insertion
-        item-69 at level 4: inline: group group
-          item-70 at level 5: text: All gRNAs were expressed from th ... -Chimeric_BB-CBh-hSpCas9 vector (RRID:
-          item-71 at level 5: text: Addgene_42230
-          item-72 at level 5: text: ) and nucleofected into 10
-          item-73 at level 5: text: 6
-          item-74 at level 5: text: ES cells using Amaxa nucleofecti ... PCR genotyping (Supplementary file 3).
-      item-75 at level 3: section_header: ChIP-seq analysis
-        item-76 at level 4: inline: group group
-          item-77 at level 5: text: For ChIP-seq analysis of KRAB-ZFP expressing cells, 5–10 × 10
-          item-78 at level 5: text: 7
-          item-79 at level 5: text: cells were crosslinked and immun ... -FLAG (Sigma-Aldrich Cat# F1804, RRID:
-          item-80 at level 5: text: AB_262044
-          item-81 at level 5: text: ) or anti-HA (Abcam Cat# ab9110, RRID:
-          item-82 at level 5: text: AB_307019
-          item-83 at level 5: text: or Covance Cat# MMS-101P-200, RRID:
-          item-84 at level 5: text: AB_10064068
-          item-85 at level 5: text: ) antibody using one of two prev ...  serum (Active Motif Cat# 39161, RRID:
-          item-86 at level 5: text: AB_2532132
-          item-87 at level 5: text: ) as described previously (Karim ...  Fisher Scientific Cat# A-11122, RRID:
-          item-88 at level 5: text: AB_221569
-          item-89 at level 5: text: ) using a previously described p ... inst H3K4me3 (Abcam Cat# ab8580, RRID:
-          item-90 at level 5: text: AB_306649
-          item-91 at level 5: text: ), H3K4me1 (Abcam Cat# ab8895, RRID:
-          item-92 at level 5: text: AB_306847
-          item-93 at level 5: text: ) and H3K27ac (Abcam Cat# ab4729, RRID:
-          item-94 at level 5: text: AB_2118291
-          item-95 at level 5: text: ) following the protocol develop ... 010 or Khil et al., 2012 respectively.
-        item-96 at level 4: inline: group group
-          item-97 at level 5: text: ChIP-seq libraries were construc ...  to the mm9 genome using Bowtie (RRID:
-          item-98 at level 5: text: SCR_005476
-          item-99 at level 5: text: ; settings: --best) or Bowtie2 ( ...  Peaks were called using MACS14 (RRID:
-          item-100 at level 5: text: SCR_013291
-          item-101 at level 5: text: ) under high stringency settings ...  element in UCSC Genome Browser (RRID:
-          item-102 at level 5: text: SCR_005780
-          item-103 at level 5: text: ) were calculated by using the b ... ettings: -f 0.25) from BEDTools (RRID:
-          item-104 at level 5: text: SCR_006646
-          item-105 at level 5: text: ). The right-tailed p-values bet ...  were re-mapped using Bowtie (--best).
-      item-106 at level 3: section_header: Luciferase reporter assays
-        item-107 at level 4: inline: group group
-          item-108 at level 5: text: For KRAB-ZFP repression assays,  ... y of the MMETn element upstream of the
-          item-109 at level 5: text: Cd59a
-          item-110 at level 5: text: gene, fragments of varying sizes ... after transfection as described above.
-      item-111 at level 3: section_header: RNA-seq analysis
-        item-112 at level 4: inline: group group
-          item-113 at level 5: text: Whole RNA was purified using RNe ...  reads on an Illumina HiSeq2500 (RRID:
-          item-114 at level 5: text: SCR_016383
-          item-115 at level 5: text: ) or HiSeq3000 (RRID:
-          item-116 at level 5: text: SCR_016386
-          item-117 at level 5: text: ) machine (Supplementary file 4) ... mouse genome (mm9) using Tophat (RRID:
-          item-118 at level 5: text: SCR_013035
-          item-119 at level 5: text: ; settings: --I 200000 g 1) unle ... h TEs annotated in Repeatmasker (RRID:
-          item-120 at level 5: text: SCR_012954
-          item-121 at level 5: text: ) were counted using BEDTools Mu ... expression analysis with DESeq2 (RRID:
-          item-122 at level 5: text: SCR_015687
-          item-123 at level 5: text: ). For differential gene express ... function of BED tools. The probability
-          item-124 at level 5: text: p
-          item-125 at level 5: text: in the binomial distribution was ... apped with KRAB-ZFP peaks. Then, given
-          item-126 at level 5: text: n
-          item-127 at level 5: text: which is the number of specific groups of genes, and
-          item-128 at level 5: text: x
-          item-129 at level 5: text: which is the number of this grou ... lemented in the R function p.adjust().
-      item-130 at level 3: section_header: Reduced representation bisulfite sequencing (RRBS-seq)
-        item-131 at level 4: text: For RRBS-seq analysis, Chr4-cl W ... h sample were considered for analysis.
-      item-132 at level 3: section_header: Retrotransposition assay
-        item-133 at level 4: inline: group group
-          item-134 at level 5: text: The retrotransposition vectors p ... MusD retrotransposition assays, 5 × 10
-          item-135 at level 5: text: 4
-          item-136 at level 5: text: HeLa cells (ATCC CCL-2) were tra ... were stained with Amido Black (Sigma).
-      item-137 at level 3: section_header: Capture-seq screen
-        item-138 at level 4: inline: group group
-          item-139 at level 5: text: To identify novel retrotransposo ... target enrichment using the SureSelect
-          item-140 at level 5: text: QXT
-          item-141 at level 5: text: Target Enrichment kit (Agilent). ... assembly using the Unicycler software.
-    item-142 at level 2: section_header: Funding Information
-      item-143 at level 3: text: This paper was supported by the following grants:
-      item-144 at level 3: list: group list
-        item-145 at level 4: list_item: http://dx.doi.org/10.13039/10000 ... ment 1ZIAHD008933 to Todd S Macfarlan.
-        item-146 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... ndation 310030_152879 to Didier Trono.
-        item-147 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... dation 310030B_173337 to Didier Trono.
-        item-148 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... ch Council No. 268721 to Didier Trono.
-        item-149 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... rch Council No 694658 to Didier Trono.
-    item-150 at level 2: section_header: Acknowledgements
-      item-151 at level 3: text: We thank Alex Grinberg, Jeanne Y ...  268721; Transpos-X, No. 694658) (DT).
-    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: 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-44 at level 5: text: , one of the top-upregulated gen ... C). RT-qPCR analysis revealed that the
+          item-45 at level 5: text: Chst1
+          item-46 at level 5: text: upregulation phenotype in Chr4-c ... ontrolled ETn-borne enhancer regulates
+          item-47 at level 5: text: Chst1
+          item-48 at level 5: text: expression (Figure 3D). Furtherm ... he internal region and not on the LTR.
+      item-49 at level 3: section_header: ETn retrotransposition in Chr4-cl KO and WT mice
+        item-50 at level 4: text: IAP, ETn/ETnERV and MuLV/RLTR4 r ... s may contribute to reduced viability.
+        item-51 at level 4: text: We reasoned that retrotransposon ... Tn insertions at a high recovery rate.
+        item-52 at level 4: text: Using this dataset, we first con ... nsertions in our pedigree (Figure 4A).
+        item-53 at level 4: caption: Figure 4. ETn retrotransposition ... combined for the statistical analysis.
+        item-54 at level 4: picture
+          item-54 at level 5: caption: Figure 4. ETn retrotransposition in Chr4-cl KO mice. (A) Pedigree of mice used for transposon insertion screening by capture-seq in mice of different strain backgrounds. The number of novel ETn insertions (only present in one animal) are indicated. For animals whose direct ancestors have not been screened, the ETn insertions are shown in parentheses since parental inheritance cannot be excluded in that case. Germ line insertions are indicated by asterisks. All DNA samples were prepared from tail tissues unless noted (-S: spleen, -E: ear, -B:Blood) (B) Statistical analysis of ETn insertion frequency in tail tissue from 30 Chr4-cl KO, KO/WT and WT mice that were derived from one Chr4-c KO x KO/WT and two Chr4-cl KO/WT x KO/WT matings. Only DNA samples that were collected from juvenile tails were considered for this analysis. P-values were calculated using one-sided Wilcoxon Rank Sum Test. In the last panel, KO, WT and KO/WT mice derived from all matings were combined for the statistical analysis.
+        item-55 at level 4: text: To validate some of the novel ET ... ess might have truncated this element.
+        item-56 at level 4: text: Besides novel ETn insertions tha ... tions (Figure 4—figure supplement 3D).
+        item-57 at level 4: text: Finally, we asked whether there  ... s clearly also play an important role.
+    item-58 at level 2: section_header: Discussion
+      item-59 at level 3: text: C2H2 zinc finger proteins, about ... ) depending upon their insertion site.
+      item-60 at level 3: text: Despite a lack of widespread ETn ... ion of the majority of KRAB-ZFP genes.
+    item-61 at level 2: section_header: Materials and methods
+      item-62 at level 3: caption: Key resources table
+      item-63 at level 3: table with [31x5]
+        item-63 at level 4: caption: Key resources table
+      item-64 at level 3: section_header: Cell lines and transgenic mice
+        item-65 at level 4: inline: group group
+          item-66 at level 5: text: Mouse ES cells and F9 EC cells w ... nes originate from JM8A3.N1 C57BL/6N-A
+          item-67 at level 5: text: tm1Brd
+          item-68 at level 5: text: ES cells (KOMP Repository). Chr2 ... KO/KO and KO/WT (B6/129 F2) offspring.
+      item-69 at level 3: section_header: Generation of KRAB-ZFP expressing cell lines
+        item-70 at level 4: inline: group group
+          item-71 at level 5: text: KRAB-ZFP ORFs were PCR-amplified ... r 3XHA tags in F9 EC or ES cells using
+          item-72 at level 5: text: Sleeping beauty
+          item-73 at level 5: text: transposon-based (Wolf et al., 2 ... led and further expanded for ChIP-seq.
+      item-74 at level 3: section_header: CRISPR/Cas9 mediated deletion of KRAB-ZFP clusters and an MMETn insertion
+        item-75 at level 4: inline: group group
+          item-76 at level 5: text: All gRNAs were expressed from th ... -Chimeric_BB-CBh-hSpCas9 vector (RRID:
+          item-77 at level 5: text: Addgene_42230
+          item-78 at level 5: text: ) and nucleofected into 10
+          item-79 at level 5: text: 6
+          item-80 at level 5: text: ES cells using Amaxa nucleofecti ... PCR genotyping (Supplementary file 3).
+      item-81 at level 3: section_header: ChIP-seq analysis
+        item-82 at level 4: inline: group group
+          item-83 at level 5: text: For ChIP-seq analysis of KRAB-ZFP expressing cells, 5–10 × 10
+          item-84 at level 5: text: 7
+          item-85 at level 5: text: cells were crosslinked and immun ... -FLAG (Sigma-Aldrich Cat# F1804, RRID:
+          item-86 at level 5: text: AB_262044
+          item-87 at level 5: text: ) or anti-HA (Abcam Cat# ab9110, RRID:
+          item-88 at level 5: text: AB_307019
+          item-89 at level 5: text: or Covance Cat# MMS-101P-200, RRID:
+          item-90 at level 5: text: AB_10064068
+          item-91 at level 5: text: ) antibody using one of two prev ...  serum (Active Motif Cat# 39161, RRID:
+          item-92 at level 5: text: AB_2532132
+          item-93 at level 5: text: ) as described previously (Karim ...  Fisher Scientific Cat# A-11122, RRID:
+          item-94 at level 5: text: AB_221569
+          item-95 at level 5: text: ) using a previously described p ... inst H3K4me3 (Abcam Cat# ab8580, RRID:
+          item-96 at level 5: text: AB_306649
+          item-97 at level 5: text: ), H3K4me1 (Abcam Cat# ab8895, RRID:
+          item-98 at level 5: text: AB_306847
+          item-99 at level 5: text: ) and H3K27ac (Abcam Cat# ab4729, RRID:
+          item-100 at level 5: text: AB_2118291
+          item-101 at level 5: text: ) following the protocol develop ... 010 or Khil et al., 2012 respectively.
+        item-102 at level 4: inline: group group
+          item-103 at level 5: text: ChIP-seq libraries were construc ...  to the mm9 genome using Bowtie (RRID:
+          item-104 at level 5: text: SCR_005476
+          item-105 at level 5: text: ; settings: --best) or Bowtie2 ( ...  Peaks were called using MACS14 (RRID:
+          item-106 at level 5: text: SCR_013291
+          item-107 at level 5: text: ) under high stringency settings ...  element in UCSC Genome Browser (RRID:
+          item-108 at level 5: text: SCR_005780
+          item-109 at level 5: text: ) were calculated by using the b ... ettings: -f 0.25) from BEDTools (RRID:
+          item-110 at level 5: text: SCR_006646
+          item-111 at level 5: text: ). The right-tailed p-values bet ...  were re-mapped using Bowtie (--best).
+      item-112 at level 3: section_header: Luciferase reporter assays
+        item-113 at level 4: inline: group group
+          item-114 at level 5: text: For KRAB-ZFP repression assays,  ... y of the MMETn element upstream of the
+          item-115 at level 5: text: Cd59a
+          item-116 at level 5: text: gene, fragments of varying sizes ... after transfection as described above.
+      item-117 at level 3: section_header: RNA-seq analysis
+        item-118 at level 4: inline: group group
+          item-119 at level 5: text: Whole RNA was purified using RNe ...  reads on an Illumina HiSeq2500 (RRID:
+          item-120 at level 5: text: SCR_016383
+          item-121 at level 5: text: ) or HiSeq3000 (RRID:
+          item-122 at level 5: text: SCR_016386
+          item-123 at level 5: text: ) machine (Supplementary file 4) ... mouse genome (mm9) using Tophat (RRID:
+          item-124 at level 5: text: SCR_013035
+          item-125 at level 5: text: ; settings: --I 200000 g 1) unle ... h TEs annotated in Repeatmasker (RRID:
+          item-126 at level 5: text: SCR_012954
+          item-127 at level 5: text: ) were counted using BEDTools Mu ... expression analysis with DESeq2 (RRID:
+          item-128 at level 5: text: SCR_015687
+          item-129 at level 5: text: ). For differential gene express ... function of BED tools. The probability
+          item-130 at level 5: text: p
+          item-131 at level 5: text: in the binomial distribution was ... apped with KRAB-ZFP peaks. Then, given
+          item-132 at level 5: text: n
+          item-133 at level 5: text: which is the number of specific groups of genes, and
+          item-134 at level 5: text: x
+          item-135 at level 5: text: which is the number of this grou ... lemented in the R function p.adjust().
+      item-136 at level 3: section_header: Reduced representation bisulfite sequencing (RRBS-seq)
+        item-137 at level 4: text: For RRBS-seq analysis, Chr4-cl W ... h sample were considered for analysis.
+      item-138 at level 3: section_header: Retrotransposition assay
+        item-139 at level 4: inline: group group
+          item-140 at level 5: text: The retrotransposition vectors p ... MusD retrotransposition assays, 5 × 10
+          item-141 at level 5: text: 4
+          item-142 at level 5: text: HeLa cells (ATCC CCL-2) were tra ... were stained with Amido Black (Sigma).
+      item-143 at level 3: section_header: Capture-seq screen
+        item-144 at level 4: inline: group group
+          item-145 at level 5: text: To identify novel retrotransposo ... target enrichment using the SureSelect
+          item-146 at level 5: text: QXT
+          item-147 at level 5: text: Target Enrichment kit (Agilent). ... assembly using the Unicycler software.
+    item-148 at level 2: section_header: Funding Information
+      item-149 at level 3: text: This paper was supported by the following grants:
+      item-150 at level 3: list: group list
+        item-151 at level 4: list_item: http://dx.doi.org/10.13039/10000 ... ment 1ZIAHD008933 to Todd S Macfarlan.
+        item-152 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... ndation 310030_152879 to Didier Trono.
+        item-153 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... dation 310030B_173337 to Didier Trono.
+        item-154 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... ch Council No. 268721 to Didier Trono.
+        item-155 at level 4: list_item: http://dx.doi.org/10.13039/50110 ... rch Council No 694658 to Didier Trono.
+    item-156 at level 2: section_header: Acknowledgements
+      item-157 at level 3: text: We thank Alex Grinberg, Jeanne Y ...  268721; Transpos-X, No. 694658) (DT).
+    item-158 at level 2: section_header: Additional information
+      item-159 at level 3: section_header: Competing interests
+        item-160 at level 4: list: group footnotes
           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-162 at level 6: footnote: No competing interests declared.
+      item-163 at level 3: section_header: Author contributions
+        item-164 at level 4: list: group footnotes
           item-165 at level 5: list_item: 
-            item-166 at level 6: footnote: Conceptualization, Formal analys ... igation, Writing - review and editing.
+            item-166 at level 6: footnote: Conceptualization, Data curation ... Methodology, Writing - original draft.
           item-167 at level 5: list_item: 
-            item-168 at level 6: footnote: Investigation.
+            item-168 at level 6: footnote: Conceptualization, Data curation ... l draft, Writing - review and editing.
           item-169 at level 5: list_item: 
-            item-170 at level 6: footnote: Investigation.
+            item-170 at level 6: footnote: Conceptualization, Data curation ... odology, Writing - review and editing.
           item-171 at level 5: list_item: 
-            item-172 at level 6: footnote: Data curation, Software, Formal analysis, Visualization.
+            item-172 at level 6: footnote: Conceptualization, Formal analys ... igation, Writing - review and editing.
           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-176 at level 6: footnote: Investigation.
           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-178 at level 6: footnote: Data curation, Software, Formal analysis, Visualization.
+          item-179 at level 5: list_item: 
+            item-180 at level 6: footnote: Investigation.
           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 ... OI: 10.1093/nar/gkp335, PMID: 19458158
-        item-197 at level 4: list_item: Baust C, Gagnier L, Baillie GJ,  ... 77.21.11448-11458.2003, PMID: 14557630
-        item-198 at level 4: list_item: Blaschke K, Ebata KT, Karimi MM, ... I: 10.1038/nature12362, PMID: 23812591
-        item-199 at level 4: list_item: Brodziak A, Ziółko E, Muc-Wierzg ... I: 10.12659/msm.882892, PMID: 22648263
-        item-200 at level 4: list_item: Castro-Diaz N, Ecco G, Coluccio  ... 10.1101/gad.241661.114, PMID: 24939876
-        item-201 at level 4: list_item: Chuong EB, Elde NC, Feschotte C. ... 0.1126/science.aad5497, PMID: 26941318
-        item-202 at level 4: list_item: Dan J, Liu Y, Liu N, Chiourea M, ... 6/j.devcel.2014.03.004, PMID: 24735877
-        item-203 at level 4: list_item: De Iaco A, Planet E, Coluccio A, ... . DOI: 10.1038/ng.3858, PMID: 28459456
-        item-204 at level 4: list_item: Deniz Ö, de la Rica L, Cheng KCL ... 1186/s13059-017-1376-y, PMID: 29351814
-        item-205 at level 4: list_item: Dewannieux M, Heidmann T. 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 2: section_header: Decision letter
-      item-253 at level 3: text: In the interests of transparency ... and the accompanying author responses.
-      item-254 at level 3: text: Acceptance summary:
-      item-255 at level 3: text: This is the first study that add ... ontrol ever adapting retrotransposons.
-      item-256 at level 3: text: Decision letter after peer review:
-      item-257 at level 3: inline: group group
-        item-258 at level 4: text: Thank you for submitting your ar ... e murine lineage" for consideration by
-        item-259 at level 4: text: eLife
-        item-260 at level 4: text: . Your article has been reviewed ... ir identity: Joan Barau (Reviewer #3).
-      item-261 at level 3: text: The reviewers have discussed the ... help you prepare a revised submission.
-      item-262 at level 3: text: Summary:
-      item-263 at level 3: text: Restriction of transposable elem ... rganization in large genomic clusters.
-      item-264 at level 3: text: In this study, the authors probe ... omes, but this was not addressed here.
-      item-265 at level 3: text: This is the first study of this  ... effects of cluster deletions – if any.
-      item-266 at level 3: text: Essential revisions:
-      item-267 at level 3: text: 1) Related to the identification ... ted in Figure 4—figure supplement 3A).
-      item-268 at level 3: text: 2) It is not very clear as to wh ... vated (according to the RNA-seq data).
-      item-269 at level 3: text: 3) As most of the manuscript is  ... e (C57bl6/J) genome and also in 129Sv.
-      item-270 at level 3: text: 4) Figure 2C: Was CpG methylatio ... ns repression. Changes may be greater.
-      item-271 at level 3: text: 5) The data graphed in Figure 4B ... igree in 4A to produce the boxplot 4B.
-    item-272 at level 2: section_header: Author response
-      item-273 at level 3: text: Essential revisions:
-      item-274 at level 3: text: 1) Related to the identification ... ted in Figure 4—figure supplement 3A).
-      item-275 at level 3: text: We compiled a list of largely in ... t 3B and refer to it in the main text.
-      item-276 at level 3: text: As for the PCR validation, the f ... ipeline has a low false positive rate.
-      item-277 at level 3: text: We compiled a list of all novel  ... nd added it as Figure 4—source data 1.
-      item-278 at level 3: text: 2) It is not very clear as to wh ... vated (according to the RNA-seq data).
-      item-279 at level 3: text: We screened the two KO/WT ES cel ... us ETn elements in WT and KO ES cells.
-      item-280 at level 3: text: We attempted repeatedly to perfo ... relative to other cultured cell lines.
-      item-281 at level 3: text: As for Chr2-cl KO ES cells, such ... uses on IAP and L1 retrotransposition.
-      item-282 at level 3: text: 3) As most of the manuscript is  ... e (C57bl6/J) genome and also in 129Sv.
-      item-283 at level 3: text: We have added the following to the manuscript:
-      item-284 at level 3: text: “including the closely related M ... mouse strains Gagnier et al., 2019().”
-      item-285 at level 3: text: 4) Figure 2C: Was CpG methylatio ... ns repression. Changes may be greater.
-      item-286 at level 3: text: We determined CpG methylation se ...  internal ETn region and not the LTRs.
-      item-287 at level 3: text: As for IAP, we saw a substantial ... Gm21082, lose methylation in Chr4 KOs.
-      item-288 at level 3: text: 5) The data graphed in Figure 4B ... igree in 4A to produce the boxplot 4B.
-      item-289 at level 3: text: The data in Figure 4B indeed com ... ssues (Figure 4—figure supplement 3C).
-      item-290 at level 3: text: We now show the data separated b ... aragraph in the main text accordingly.
-  item-291 at level 1: caption: Figure 1. Genome-wide binding pa ... onsensus fingers highlighted in white.
-  item-292 at level 1: caption: Table 1. KRAB-ZFP genes clusters ...  ChIP-seq was performed in this study.
-  item-293 at level 1: caption: Figure 2. Retrotransposon reacti ... s were calculated using paired t-test.
-  item-294 at level 1: caption: Figure 3. TE-dependent gene acti ... Gm13051 are indicated by dashed lines.
-  item-295 at level 1: caption: Figure 4. ETn retrotransposition ... combined for the statistical analysis.
-  item-296 at level 1: caption: Key resources table
\ No newline at end of file
+            item-182 at level 6: footnote: Conceptualization, Resources, Su ... igation, Writing - review and editing.
+          item-183 at level 5: list_item: 
+            item-184 at level 6: footnote: Conceptualization, Resources, Su ... tration, Writing - review and editing.
+      item-185 at level 3: section_header: Ethics
+        item-186 at level 4: list: group footnotes
+          item-187 at level 5: list_item: 
+            item-188 at level 6: footnote: Animal experimentation: All stud ... er IACUC animal protocol (ASP )18-026.
+    item-189 at level 2: section_header: Additional files
+    item-190 at level 2: section_header: Data availability
+      item-191 at level 3: text: All NGS data has been deposited  ... GenBank database (MH449667- MH449669).
+      item-192 at level 3: text: The following datasets were generated:
+      item-193 at level 3: text: Wolf G. Retrotransposon reactiva ... ession Omnibus (2019). NCBI: GSE115291
+      item-194 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449667
+      item-195 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449668
+      item-196 at level 3: text: Wolf G. Mus musculus musculus st ... e. NCBI GenBank (2019). NCBI: MH449669
+      item-197 at level 3: text: The following previously published datasets were used:
+      item-198 at level 3: text: Castro-Diaz N, Ecco G, Coluccio  ... ssion Omnibus (2014). NCBI: GSM1406445
+      item-199 at level 3: text: Andrew ZX. H3K9me3_ChIPSeq (Ctrl ... ssion Omnibus (2014). NCBI: GSM1327148
+    item-200 at level 2: section_header: References
+      item-201 at level 3: list: group list
+        item-202 at level 4: list_item: Bailey TL, Boden M, Buske FA, Fr ... OI: 10.1093/nar/gkp335, PMID: 19458158
+        item-203 at level 4: list_item: Baust C, Gagnier L, Baillie GJ,  ... 77.21.11448-11458.2003, PMID: 14557630
+        item-204 at level 4: list_item: Blaschke K, Ebata KT, Karimi MM, ... I: 10.1038/nature12362, PMID: 23812591
+        item-205 at level 4: list_item: Brodziak A, Ziółko E, Muc-Wierzg ... I: 10.12659/msm.882892, PMID: 22648263
+        item-206 at level 4: list_item: Castro-Diaz N, Ecco G, Coluccio  ... 10.1101/gad.241661.114, PMID: 24939876
+        item-207 at level 4: list_item: Chuong EB, Elde NC, Feschotte C. ... 0.1126/science.aad5497, PMID: 26941318
+        item-208 at level 4: list_item: Dan J, Liu Y, Liu N, Chiourea M, ... 6/j.devcel.2014.03.004, PMID: 24735877
+        item-209 at level 4: list_item: De Iaco A, Planet E, Coluccio A, ... . DOI: 10.1038/ng.3858, PMID: 28459456
+        item-210 at level 4: list_item: Deniz Ö, de la Rica L, Cheng KCL ... 1186/s13059-017-1376-y, PMID: 29351814
+        item-211 at level 4: list_item: Dewannieux M, Heidmann T. Endoge ... 6/j.coviro.2013.08.005, PMID: 24004725
+        item-212 at level 4: list_item: Ecco G, Cassano M, Kauzlaric A,  ... 6/j.devcel.2016.02.024, PMID: 27003935
+        item-213 at level 4: list_item: Ecco G, Imbeault M, Trono D. KRA ... OI: 10.1242/dev.132605, PMID: 28765213
+        item-214 at level 4: list_item: Frank JA, Feschotte C. Co-option ... 6/j.coviro.2017.07.021, PMID: 28818736
+        item-215 at level 4: list_item: Gagnier L, Belancio VP, Mager DL ... 1186/s13100-019-0157-4, PMID: 31011371
+        item-216 at level 4: list_item: Groner AC, Meylan S, Ciuffi A, Z ... 1/journal.pgen.1000869, PMID: 20221260
+        item-217 at level 4: list_item: Hancks DC, Kazazian HH. Roles fo ... 1186/s13100-016-0065-9, PMID: 27158268
+        item-218 at level 4: list_item: Imbeault M, Helleboid PY, Trono  ... I: 10.1038/nature21683, PMID: 28273063
+        item-219 at level 4: list_item: Jacobs FM, Greenberg D, Nguyen N ... I: 10.1038/nature13760, PMID: 25274305
+        item-220 at level 4: list_item: Kano H, Kurahashi H, Toda T. Gen ... 0.1073/pnas.0705483104, PMID: 17984064
+        item-221 at level 4: list_item: Karimi MM, Goyal P, Maksakova IA ... 016/j.stem.2011.04.004, PMID: 21624812
+        item-222 at level 4: list_item: Kauzlaric A, Ecco G, Cassano M,  ... 1/journal.pone.0173746, PMID: 28334004
+        item-223 at level 4: list_item: Khil PP, Smagulova F, Brick KM,  ...  10.1101/gr.130583.111, PMID: 22367190
+        item-224 at level 4: list_item: Krueger F, Andrews SR. Bismark:  ... /bioinformatics/btr167, PMID: 21493656
+        item-225 at level 4: list_item: Langmead B, Salzberg SL. Fast ga ... OI: 10.1038/nmeth.1923, PMID: 22388286
+        item-226 at level 4: list_item: Legiewicz M, Zolotukhin AS, Pilk ... 0.1074/jbc.M110.182840, PMID: 20978285
+        item-227 at level 4: list_item: Lehoczky JA, Thomas PE, Patrie K ... 1/journal.pgen.1003967, PMID: 24339789
+        item-228 at level 4: list_item: Leung D, Du T, Wagner U, Xie W,  ... 0.1073/pnas.1322273111, PMID: 24757056
+        item-229 at level 4: list_item: Lilue J, Doran AG, Fiddes IT, Ab ... 1038/s41588-018-0223-8, PMID: 30275530
+        item-230 at level 4: list_item: Liu S, Brind'Amour J, Karimi MM, ... 10.1101/gad.244848.114, PMID: 25228647
+        item-231 at level 4: list_item: Love MI, Huber W, Anders S. Mode ... 1186/s13059-014-0550-8, PMID: 25516281
+        item-232 at level 4: list_item: Lugani F, Arora R, Papeta N, Pat ... 1/journal.pgen.1003206, PMID: 23437001
+        item-233 at level 4: list_item: Macfarlan TS, Gifford WD, Drisco ... I: 10.1038/nature11244, PMID: 22722858
+        item-234 at level 4: list_item: Maksakova IA, Romanish MT, Gagni ... 1/journal.pgen.0020002, PMID: 16440055
+        item-235 at level 4: list_item: Matsui T, Leung D, Miyashita H,  ... I: 10.1038/nature08858, PMID: 20164836
+        item-236 at level 4: list_item: Najafabadi HS, Mnaimneh S, Schmi ...  DOI: 10.1038/nbt.3128, PMID: 25690854
+        item-237 at level 4: list_item: Nellåker C, Keane TM, Yalcin B,  ... .1186/gb-2012-13-6-r45, PMID: 22703977
+        item-238 at level 4: list_item: O'Geen H, Frietze S, Farnham PJ. ... 7/978-1-60761-753-2_27, PMID: 20680851
+        item-239 at level 4: list_item: Patel A, Yang P, Tinkham M, Prad ... 016/j.cell.2018.02.058, PMID: 29551271
+        item-240 at level 4: list_item: Ribet D, Dewannieux M, Heidmann  ... OI: 10.1101/gr.2924904, PMID: 15479948
+        item-241 at level 4: list_item: Richardson SR, Gerdes P, Gerhard ...  10.1101/gr.219022.116, PMID: 28483779
+        item-242 at level 4: list_item: Rowe HM, Jakobsson J, Mesnard D, ... I: 10.1038/nature08674, PMID: 20075919
+        item-243 at level 4: list_item: Rowe HM, Kapopoulou A, Corsinott ...  10.1101/gr.147678.112, PMID: 23233547
+        item-244 at level 4: list_item: Schauer SN, Carreira PE, Shukla  ...  10.1101/gr.226993.117, PMID: 29643204
+        item-245 at level 4: list_item: Schultz DC, Ayyanathan K, Negore ... OI: 10.1101/gad.973302, PMID: 11959841
+        item-246 at level 4: list_item: Semba K, Araki K, Matsumoto K, S ... 1/journal.pgen.1003204, PMID: 23436999
+        item-247 at level 4: list_item: Sripathy SP, Stevens J, Schultz  ... : 10.1128/MCB.00487-06, PMID: 16954381
+        item-248 at level 4: list_item: Thomas JH, Schneider S. Coevolut ...  10.1101/gr.121749.111, PMID: 21784874
+        item-249 at level 4: list_item: Thompson PJ, Macfarlan TS, Lorin ... 6/j.molcel.2016.03.029, PMID: 27259207
+        item-250 at level 4: list_item: Treger RS, Pope SD, Kong Y, Toku ... 6/j.immuni.2018.12.022, PMID: 30709743
+        item-251 at level 4: list_item: Vlangos CN, Siuniak AN, Robinson ... 1/journal.pgen.1003205, PMID: 23437000
+        item-252 at level 4: list_item: Wang J, Xie G, Singh M, Ghanbari ... I: 10.1038/nature13804, PMID: 25317556
+        item-253 at level 4: list_item: Wolf D, Hug K, Goff SP. TRIM28 m ... 0.1073/pnas.0805540105, PMID: 18713861
+        item-254 at level 4: list_item: Wolf G, Greenberg D, Macfarlan T ... 1186/s13100-015-0050-8, PMID: 26435754
+        item-255 at level 4: list_item: Wolf G, Yang P, Füchtbauer AC, F ... 10.1101/gad.252767.114, PMID: 25737282
+        item-256 at level 4: list_item: Yamauchi M, Freitag B, Khan C, B ... JVI.69.2.1142-1149.1995, PMID: 7529329
+        item-257 at level 4: list_item: Zhang Y, Liu T, Meyer CA, Eeckho ... .1186/gb-2008-9-9-r137, PMID: 18798982
+    item-258 at level 2: section_header: Decision letter
+      item-259 at level 3: text: In the interests of transparency ... and the accompanying author responses.
+      item-260 at level 3: text: Acceptance summary:
+      item-261 at level 3: text: This is the first study that add ... ontrol ever adapting retrotransposons.
+      item-262 at level 3: text: Decision letter after peer review:
+      item-263 at level 3: inline: group group
+        item-264 at level 4: text: Thank you for submitting your ar ... e murine lineage" for consideration by
+        item-265 at level 4: text: eLife
+        item-266 at level 4: text: . Your article has been reviewed ... ir identity: Joan Barau (Reviewer #3).
+      item-267 at level 3: text: The reviewers have discussed the ... help you prepare a revised submission.
+      item-268 at level 3: text: Summary:
+      item-269 at level 3: text: Restriction of transposable elem ... rganization in large genomic clusters.
+      item-270 at level 3: text: In this study, the authors probe ... omes, but this was not addressed here.
+      item-271 at level 3: text: This is the first study of this  ... effects of cluster deletions – if any.
+      item-272 at level 3: text: Essential revisions:
+      item-273 at level 3: text: 1) Related to the identification ... ted in Figure 4—figure supplement 3A).
+      item-274 at level 3: text: 2) It is not very clear as to wh ... vated (according to the RNA-seq data).
+      item-275 at level 3: text: 3) As most of the manuscript is  ... e (C57bl6/J) genome and also in 129Sv.
+      item-276 at level 3: text: 4) Figure 2C: Was CpG methylatio ... ns repression. Changes may be greater.
+      item-277 at level 3: text: 5) The data graphed in Figure 4B ... igree in 4A to produce the boxplot 4B.
+    item-278 at level 2: section_header: Author response
+      item-279 at level 3: text: Essential revisions:
+      item-280 at level 3: text: 1) Related to the identification ... ted in Figure 4—figure supplement 3A).
+      item-281 at level 3: text: We compiled a list of largely in ... t 3B and refer to it in the main text.
+      item-282 at level 3: text: As for the PCR validation, the f ... ipeline has a low false positive rate.
+      item-283 at level 3: text: We compiled a list of all novel  ... nd added it as Figure 4—source data 1.
+      item-284 at level 3: text: 2) It is not very clear as to wh ... vated (according to the RNA-seq data).
+      item-285 at level 3: text: We screened the two KO/WT ES cel ... us ETn elements in WT and KO ES cells.
+      item-286 at level 3: text: We attempted repeatedly to perfo ... relative to other cultured cell lines.
+      item-287 at level 3: text: As for Chr2-cl KO ES cells, such ... uses on IAP and L1 retrotransposition.
+      item-288 at level 3: text: 3) As most of the manuscript is  ... e (C57bl6/J) genome and also in 129Sv.
+      item-289 at level 3: text: We have added the following to the manuscript:
+      item-290 at level 3: text: “including the closely related M ... mouse strains Gagnier et al., 2019().”
+      item-291 at level 3: text: 4) Figure 2C: Was CpG methylatio ... ns repression. Changes may be greater.
+      item-292 at level 3: text: We determined CpG methylation se ...  internal ETn region and not the LTRs.
+      item-293 at level 3: text: As for IAP, we saw a substantial ... Gm21082, lose methylation in Chr4 KOs.
+      item-294 at level 3: text: 5) The data graphed in Figure 4B ... igree in 4A to produce the boxplot 4B.
+      item-295 at level 3: text: The data in Figure 4B indeed com ... ssues (Figure 4—figure supplement 3C).
+      item-296 at level 3: text: We now show the data separated b ... aragraph in the main text accordingly.
\ 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 30b44f3eab..90d0a89e15 100644
--- a/tests/data/jats/groundtruth/elife-56337.nxml.json
+++ b/tests/data/jats/groundtruth/elife-56337.nxml.json
@@ -19,24 +19,6 @@
     "children": [
       {
         "$ref": "#/texts/0"
-      },
-      {
-        "$ref": "#/texts/16"
-      },
-      {
-        "$ref": "#/texts/17"
-      },
-      {
-        "$ref": "#/texts/27"
-      },
-      {
-        "$ref": "#/texts/30"
-      },
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-        "$ref": "#/texts/44"
-      },
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-        "$ref": "#/texts/52"
       }
     ],
     "content_layer": "body",
@@ -962,9 +944,15 @@
         {
           "$ref": "#/groups/1"
         },
+        {
+          "$ref": "#/texts/16"
+        },
         {
           "$ref": "#/pictures/0"
         },
+        {
+          "$ref": "#/texts/17"
+        },
         {
           "$ref": "#/tables/0"
         },
@@ -1043,7 +1031,7 @@
     {
       "self_ref": "#/texts/16",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/11"
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       "content_layer": "body",
@@ -1055,7 +1043,7 @@
     {
       "self_ref": "#/texts/17",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/11"
       },
       "children": [],
       "content_layer": "body",
@@ -1171,6 +1159,9 @@
         {
           "$ref": "#/texts/26"
         },
+        {
+          "$ref": "#/texts/27"
+        },
         {
           "$ref": "#/pictures/1"
         }
@@ -1197,7 +1188,7 @@
     {
       "self_ref": "#/texts/27",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/25"
       },
       "children": [],
       "content_layer": "body",
@@ -1215,6 +1206,9 @@
         {
           "$ref": "#/texts/29"
         },
+        {
+          "$ref": "#/texts/30"
+        },
         {
           "$ref": "#/pictures/2"
         },
@@ -1244,7 +1238,7 @@
     {
       "self_ref": "#/texts/30",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/28"
       },
       "children": [],
       "content_layer": "body",
@@ -1404,6 +1398,9 @@
         {
           "$ref": "#/texts/43"
         },
+        {
+          "$ref": "#/texts/44"
+        },
         {
           "$ref": "#/pictures/3"
         },
@@ -1463,7 +1460,7 @@
     {
       "self_ref": "#/texts/44",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/40"
       },
       "children": [],
       "content_layer": "body",
@@ -1558,6 +1555,9 @@
         "$ref": "#/texts/0"
       },
       "children": [
+        {
+          "$ref": "#/texts/52"
+        },
         {
           "$ref": "#/tables/1"
         },
@@ -1599,7 +1599,7 @@
     {
       "self_ref": "#/texts/52",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/51"
       },
       "children": [],
       "content_layer": "body",
diff --git a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt
index c02654ddaa..fba23c6e26 100644
--- a/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt
+++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.itxt
@@ -21,197 +21,197 @@ item-0 at level 0: unspecified: group _root_
     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: ) 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 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: , and (4) only districts with
-        item-103 at level 4: text: Anopheles
-        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: . 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. Geneva; 2017.
-        item-152 at level 4: list_item: World Health Organization. Globa ...  Wkly Epidemiol Rec. 2019;94: 457–472.
-        item-153 at level 4: list_item: World Health Organization. Globa ... ass drug administration. Geneva; 2011.
-        item-154 at level 4: list_item: World Health Organization. Stren ... Disease-specific Indicators. 2016; 42.
-        item-155 at level 4: list_item: KyelemD, BiswasG, BockarieMJ, Br ... Trop Med Hyg. 2008;79: 480–4. 18840733
-        item-156 at level 4: list_item: GoldbergEM, KingJD, MupfasoniD,  ... . 2019; 10.4269/ajtmh.18-0721 31115301
-        item-157 at level 4: list_item: CanoJ, RebolloMP, GoldingN, Pull ... : 1–19. 10.1186/1756-3305-7-1 24411014
-        item-158 at level 4: list_item: CGIAR-CSI. CGIAR-CSI SRTM 90m DE ...  Available: http://srtm.csi.cgiar.org/
-        item-159 at level 4: list_item: USGS NASA. Vegetation indices 16 ... /lpdaac.usgs.gov/products/myd13a1v006/
-        item-160 at level 4: list_item: FunkC, PetersonP, LandsfeldM, Pe ...  2015;2 10.1038/sdata.2015.66 26646728
-        item-161 at level 4: list_item: LloydCT, SorichettaA, TatemAJ. H ... : 170001 10.1038/sdata.2017.1 28140386
-        item-162 at level 4: list_item: ElvidgeCD, BaughKE, ZhizhinM, Hs ... Network; 2013;35: 62 10.7125/apan.35.7
-        item-163 at level 4: list_item: JambulingamP, SubramanianS, De V ... 18. 10.1186/s13071-015-1291-6 26728523
-        item-164 at level 4: list_item: MichaelE, Malecela-LazaroMN, Sim ... 10.1016/S1473-3099(04)00973-9 15050941
-        item-165 at level 4: list_item: StolkWA, SwaminathanS, van Oortm ... ;188: 1371–81. 10.1086/378354 14593597
-        item-166 at level 4: list_item: GradyCA, De RocharsMB, DirenyAN, ... 8–610. 10.3201/eid1304.061063 17553278
-        item-167 at level 4: list_item: EvansD, McFarlandD, AdamaniW, Ei ... 0.1179/2047773211Y.0000000010 22325813
-        item-168 at level 4: list_item: RichardsFO, EigegeA, MiriES, Kal ...  10.1371/journal.pntd.0001346 22022627
-        item-169 at level 4: list_item: BiritwumNK, YikpoteyP, MarfoBK,  ... 90–695. 10.1093/trstmh/trx007 28938053
-        item-170 at level 4: list_item: MoragaP, CanoJ, BaggaleyRF, Gyap ... 16. 10.1186/s13071-014-0608-1 25561160
-        item-171 at level 4: list_item: IrvineMA, NjengaSM, GunawardenaS ... 18–124. 10.1093/trstmh/trv096 26822604
-        item-172 at level 4: list_item: OttesenEA. Efficacy of diethylca ... iae in humans. Rev Infect Dis. 1985;7.
-        item-173 at level 4: list_item: GambhirM, BockarieM, TischD, Kaz ... 2010;8 10.1186/1741-7007-8-22 20236528
-        item-174 at level 4: list_item: World Health Organization. Globa ... cal entomology handbook. Geneva; 2013.
-        item-175 at level 4: list_item: SlaterH, MichaelE. Predicting th ...  10.1371/journal.pone.0032202 22359670
-        item-176 at level 4: list_item: SlaterH, MichaelE. Mapping, Baye ...  10.1371/journal.pone.0071574 23951194
-        item-177 at level 4: list_item: SabesanS, RajuKHK, SubramanianS, ... 57–665. 10.1089/vbz.2012.1238 23808973
-        item-178 at level 4: list_item: StantonMC, MolyneuxDH, KyelemD,  ... : 159–173. 10.4081/gh.2013.63 24258892
-        item-179 at level 4: list_item: ManhenjeI, Teresa Galán-Puchades ... : 391–398. 10.4081/gh.2013.96 23733300
-        item-180 at level 4: list_item: NgwiraBM, TambalaP, Perez aM, Bo ... ;6: 12 10.1186/1475-2883-6-12 18047646
-        item-181 at level 4: list_item: SimonsenPE, MwakitaluME. Urban l ... 44. 10.1007/s00436-012-3226-x 23239094
-        item-182 at level 4: list_item: ProvilleJ, Zavala-AraizaD, Wagne ...  10.1371/journal.pone.0174610 28346500
-        item-183 at level 4: list_item: EndeshawT, TayeA, TadesseZ, Kata ... 10.1080/20477724.2015.1103501 26878935
-        item-184 at level 4: list_item: RichardsFO, EigegeA, PamD, KalA, ... 4: 3–5. 10.1186/1475-2883-4-3 15916708
-        item-185 at level 4: list_item: KyelemD, SanouS, BoatinB a., Med ... 8. 10.1179/000349803225002462 14754495
-        item-186 at level 4: list_item: WeilGJ, LammiePJ, RichardsFO, Eb ... –816. 10.1093/infdis/164.4.814 1894943
-        item-187 at level 4: list_item: KumarA, SachanP. Measuring impac ... rop Biomed. 2014;31: 225–229. 25134891
-        item-188 at level 4: list_item: NjengaSM, MwandawiroCS, WamaeCN, ... 4: 1–9. 10.1186/1756-3305-4-1 21205315
-        item-189 at level 4: list_item: BoydA, WonKY, McClintockSK, Dono ...  10.1371/journal.pntd.0000640 20351776
-        item-190 at level 4: list_item: IrvineMA, ReimerLJ, NjengaSM, Gu ... 19. 10.1186/s13071-014-0608-1 25561160
-        item-191 at level 4: list_item: IrvineMA, StolkWA, SmithME, Subr ... 10.1016/S1473-3099(16)30467-4 28012943
-        item-192 at level 4: list_item: PionSD, MontavonC, ChesnaisCB, K ... 7–1423. 10.4269/ajtmh.16-0547 27729568
-        item-193 at level 4: list_item: WanjiS, EsumME, NjouendouAJ, Mbe ...  10.1371/journal.pntd.0007192 30849120
-        item-194 at level 4: list_item: ChesnaisCB, Awaca-UvonNP, BolayF ...  10.1371/journal.pntd.0005703 28892473
-        item-195 at level 4: list_item: SilumbweA, ZuluJM, HalwindiH, Ja ... 15. 10.1186/s12889-017-4414-5 28532397
-        item-196 at level 4: list_item: AdamsAM, VuckovicM, BirchE, Bran ... ;3 10.3390/tropicalmed3040122 30469342
-        item-197 at level 4: list_item: RaoRU, SamarasekeraSD, Nagodavit ...  10.1371/journal.pntd.0006066 29084213
-        item-198 at level 4: list_item: XuZ, GravesPM, LauCL, ClementsA, ...  10.1016/j.epidem.2018.12.003 30611745
-        item-199 at level 4: list_item: IdCM, TetteviEJ, MechanF, IdunB, ... 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
+      item-23 at level 3: caption: Table 1 Categorization of potential factors influencing pre-TAS results.
+      item-24 at level 3: table with [18x8]
+        item-24 at level 4: caption: Table 1 Categorization of potential factors influencing pre-TAS results.
+      item-25 at level 3: section_header: Data sources
+        item-26 at level 4: text: Information on baseline prevalen ...  publicly available sources (Table 1).
+      item-27 at level 3: section_header: Outcome and covariate variables
+        item-28 at level 4: text: The outcome of interest for this ... r than or equal to 1% Mf or 2% Ag [4].
+        item-29 at level 4: inline: group group
+          item-30 at level 5: text: Potential covariates were derive ... ous variables were derived from either
+          item-31 at level 5: text: a priori
+          item-32 at level 5: text: knowledge or through exploratory ... is and the final categorizations used.
+        item-33 at level 4: section_header: Baseline prevalence
+          item-34 at level 5: text: Baseline prevalence can be assum ... (2) using the cut-off of <10% or ≥10%.
+        item-35 at level 4: section_header: Agent
+          item-36 at level 5: inline: group group
+            item-37 at level 6: text: In terms of differences in trans ... mics by agent, research has shown that
+            item-38 at level 6: text: Brugia
+            item-39 at level 6: text: spp. are more susceptible to the anti-filarial drug regimens than
+            item-40 at level 6: text: Wuchereria bancrofti
+            item-41 at level 6: text: parasites [23]. Thus, we combined districts reporting
+            item-42 at level 6: text: B
+            item-43 at level 6: text: .
+            item-44 at level 6: text: malayi
+            item-45 at level 6: text: and
+            item-46 at level 6: text: B
+            item-47 at level 6: text: .
+            item-48 at level 6: text: timori
+            item-49 at level 6: text: and compared them to areas with
+            item-50 at level 6: text: W
+            item-51 at level 6: text: .
+            item-52 at level 6: text: bancrofti
+            item-53 at level 6: text: or mixed parasites. Two variable ... e were variables delineating vectors (
+            item-54 at level 6: text: Anopheles
+            item-55 at level 6: text: or
+            item-56 at level 6: text: Mansonia
+            item-57 at level 6: text: compared to
+            item-58 at level 6: text: Culex
+            item-59 at level 6: text: ) from the environmental domain  ... dazole (DEC-ALB)] from the MDA domain.
+        item-60 at level 4: section_header: Environment
+          item-61 at level 5: text: LF transmission intensity is inf ... dicates a higher level of “greenness.”
+          item-62 at level 5: inline: group group
+            item-63 at level 6: text: We included the socio-economic v ...  countries LF is mostly transmitted by
+            item-64 at level 6: text: Culex
+            item-65 at level 6: text: in urban areas and by
+            item-66 at level 6: text: Anopheles
+            item-67 at level 6: text: in rural areas [32]. Additionall ...  proxy for socio-economic status [33].
+          item-68 at level 5: text: Finally, all or parts of distric ... s were co-endemic with onchocerciasis.
+        item-69 at level 4: section_header: MDA
+          item-70 at level 5: text: Treatment effectiveness depends  ... esent a threat to elimination [41,42].
+          item-71 at level 5: text: We considered three approaches w ... unds ever documented in that district.
+        item-72 at level 4: section_header: Pre-TAS implementation
+          item-73 at level 5: text: Pre-TAS results can be influence ... d throughout the time period of study.
+      item-74 at level 3: section_header: Data inclusion criteria
+        item-75 at level 4: text: The dataset, summarized at the d ... al analysis dataset had 554 districts.
+      item-76 at level 3: section_header: Statistical analysis and modeling
+        item-77 at level 4: text: Statistical analysis and modelin ... d the number of variables accordingly.
+        item-78 at level 4: inline: group group
+          item-79 at level 5: text: Sensitivity analysis was perform ... ica, (3) including only districts with
+          item-80 at level 5: text: W
+          item-81 at level 5: text: .
+          item-82 at level 5: text: bancrofti
+          item-83 at level 5: text: parasite, and (4) including only districts with
+          item-84 at level 5: text: Anopheles
+          item-85 at level 5: text: as the primary vector. The sensi ... ot have been truly LF-endemic [43,44].
+    item-86 at level 2: section_header: Results
+      item-87 at level 3: text: The overall pre-TAS pass rate fo ... ts had baseline prevalences below 20%.
+      item-88 at level 3: caption: Fig 1 Number of pre-TAS by country.
+      item-89 at level 3: picture
+        item-89 at level 4: caption: Fig 1 Number of pre-TAS by country.
+      item-90 at level 3: caption: Fig 2 District-level baseline prevalence by country.
+      item-91 at level 3: picture
+        item-91 at level 4: caption: Fig 2 District-level baseline prevalence by country.
+      item-92 at level 3: inline: group group
+        item-93 at level 4: text: Fig 3 shows the unadjusted analy ... FTS diagnostic test, primary vector of
+        item-94 at level 4: text: Culex
+        item-95 at level 4: text: , treatment with DEC-ALB, higher ... overage, and sufficient rounds of MDA.
+      item-96 at level 3: caption: Fig 3 Percent pre-TAS failure by each characteristic (unadjusted).
+      item-97 at level 3: picture
+        item-97 at level 4: caption: Fig 3 Percent pre-TAS failure by each characteristic (unadjusted).
+      item-98 at level 3: text: The final log-binomial model inc ... igh baseline and diagnostic test used.
+      item-99 at level 3: text: Fig 4 shows the risk ratio resul ... of failing pre-TAS (95% CI 1.95–4.83).
+      item-100 at level 3: caption: Fig 4 Adjusted risk ratios for p ... ence Interval from log-binomial model.
+      item-101 at level 3: picture
+        item-101 at level 4: caption: Fig 4 Adjusted risk ratios for pre-TAS failure with 95% Confidence Interval from log-binomial model.
+      item-102 at level 3: inline: group group
+        item-103 at level 4: text: Sensitivity analyses were conduc ... cts in Africa, (3) only districts with
+        item-104 at level 4: text: W
+        item-105 at level 4: text: .
+        item-106 at level 4: text: bancrofti
+        item-107 at level 4: text: , and (4) only districts with
+        item-108 at level 4: text: Anopheles
+        item-109 at level 4: text: as primary vector. The results o ... hough the estimate was unstable in the
+        item-110 at level 4: text: W
+        item-111 at level 4: text: .
+        item-112 at level 4: text: bancrofti
+        item-113 at level 4: text: -only and
+        item-114 at level 4: text: Anopheles
+        item-115 at level 4: text: -only models (models 3 and 4 res ... gnified by large confidence intervals.
+      item-116 at level 3: caption: Table 2 Adjusted risk ratios for ... g-binomial model sensitivity analysis.
+      item-117 at level 3: table with [11x6]
+        item-117 at level 4: caption: Table 2 Adjusted risk ratios for pre-TAS failure from log-binomial model sensitivity analysis.
+      item-118 at level 3: text: Overall 74 districts in the data ... or 51% of all the failures (38 of 74).
+      item-119 at level 3: caption: Fig 5 Analysis of failures by model combinations.
+      item-120 at level 3: picture
+        item-120 at level 4: caption: Fig 5 Analysis of failures by model combinations.
+    item-121 at level 2: section_header: Discussion
+      item-122 at level 3: inline: group group
+        item-123 at level 4: text: This paper reports for the first ...  similar to what was found in Goldberg
+        item-124 at level 4: text: et al
+        item-125 at level 4: text: ., which explored ecological and ... ctors associated with TAS failure [7].
+      item-126 at level 3: text: Though diagnostic test used was  ...  FTS was more sensitive than ICT [45].
+      item-127 at level 3: inline: group group
+        item-128 at level 4: text: Elevation was the only environme ... ous studies [8,31], including Goldberg
+        item-129 at level 4: text: et al
+        item-130 at level 4: text: . [7], who used a cutoff of 200  ... ich impact vector chances of survival.
+      item-131 at level 3: inline: group group
+        item-132 at level 4: text: The small number of failures ove ... ied in the bivariate analyses, such as
+        item-133 at level 4: text: Culex
+        item-134 at level 4: text: vector, higher population densit ... ecisions. Other models have shown that
+        item-135 at level 4: text: Culex
+        item-136 at level 4: text: as the predominant vector in a district, compared to
+        item-137 at level 4: text: Anopheles
+        item-138 at level 4: text: , results in more intense interv ... search has shown the opposite [15,16].
+      item-139 at level 3: inline: group group
+        item-140 at level 4: text: All other variables included in  ... -TAS failure in our analysis. Goldberg
+        item-141 at level 4: text: et al
+        item-142 at level 4: text: . found
+        item-143 at level 4: text: Brugia
+        item-144 at level 4: text: spp. to be significantly associa ...  to the small number of districts with
+        item-145 at level 4: text: Brugia
+        item-146 at level 4: text: spp. in our dataset (6%) compared to 46% in the Goldberg
+        item-147 at level 4: text: et al
+        item-148 at level 4: text: . article [7]. MDA coverage leve ... are not necessary to lower prevalence.
+      item-149 at level 3: text: Limitations to this study includ ...  reducing LF prevalence [41,48,51–53].
+      item-150 at level 3: text: Fourteen districts were excluded ... ta to extreme outliners in a district.
+      item-151 at level 3: text: As this analysis used data acros ... of individuals included in the survey.
+      item-152 at level 3: text: This paper provides evidence fro ... th high baseline and/or low elevation.
+    item-153 at level 2: section_header: Acknowledgments
+      item-154 at level 3: text: The authors would like to thank  ... e surveys financially and technically.
+    item-155 at level 2: section_header: References
+      item-156 at level 3: list: group list
+        item-157 at level 4: list_item: World Health Organization. Lymph ... trategic plan 2010–2020. Geneva; 2010.
+        item-158 at level 4: list_item: World Health Organization. Valid ... a public health problem. Geneva; 2017.
+        item-159 at level 4: list_item: World Health Organization. Globa ...  Wkly Epidemiol Rec. 2019;94: 457–472.
+        item-160 at level 4: list_item: World Health Organization. Globa ... ass drug administration. Geneva; 2011.
+        item-161 at level 4: list_item: World Health Organization. Stren ... Disease-specific Indicators. 2016; 42.
+        item-162 at level 4: list_item: KyelemD, BiswasG, BockarieMJ, Br ... Trop Med Hyg. 2008;79: 480–4. 18840733
+        item-163 at level 4: list_item: GoldbergEM, KingJD, MupfasoniD,  ... . 2019; 10.4269/ajtmh.18-0721 31115301
+        item-164 at level 4: list_item: CanoJ, RebolloMP, GoldingN, Pull ... : 1–19. 10.1186/1756-3305-7-1 24411014
+        item-165 at level 4: list_item: CGIAR-CSI. CGIAR-CSI SRTM 90m DE ...  Available: http://srtm.csi.cgiar.org/
+        item-166 at level 4: list_item: USGS NASA. Vegetation indices 16 ... /lpdaac.usgs.gov/products/myd13a1v006/
+        item-167 at level 4: list_item: FunkC, PetersonP, LandsfeldM, Pe ...  2015;2 10.1038/sdata.2015.66 26646728
+        item-168 at level 4: list_item: LloydCT, SorichettaA, TatemAJ. H ... : 170001 10.1038/sdata.2017.1 28140386
+        item-169 at level 4: list_item: ElvidgeCD, BaughKE, ZhizhinM, Hs ... Network; 2013;35: 62 10.7125/apan.35.7
+        item-170 at level 4: list_item: JambulingamP, SubramanianS, De V ... 18. 10.1186/s13071-015-1291-6 26728523
+        item-171 at level 4: list_item: MichaelE, Malecela-LazaroMN, Sim ... 10.1016/S1473-3099(04)00973-9 15050941
+        item-172 at level 4: list_item: StolkWA, SwaminathanS, van Oortm ... ;188: 1371–81. 10.1086/378354 14593597
+        item-173 at level 4: list_item: GradyCA, De RocharsMB, DirenyAN, ... 8–610. 10.3201/eid1304.061063 17553278
+        item-174 at level 4: list_item: EvansD, McFarlandD, AdamaniW, Ei ... 0.1179/2047773211Y.0000000010 22325813
+        item-175 at level 4: list_item: RichardsFO, EigegeA, MiriES, Kal ...  10.1371/journal.pntd.0001346 22022627
+        item-176 at level 4: list_item: BiritwumNK, YikpoteyP, MarfoBK,  ... 90–695. 10.1093/trstmh/trx007 28938053
+        item-177 at level 4: list_item: MoragaP, CanoJ, BaggaleyRF, Gyap ... 16. 10.1186/s13071-014-0608-1 25561160
+        item-178 at level 4: list_item: IrvineMA, NjengaSM, GunawardenaS ... 18–124. 10.1093/trstmh/trv096 26822604
+        item-179 at level 4: list_item: OttesenEA. Efficacy of diethylca ... iae in humans. Rev Infect Dis. 1985;7.
+        item-180 at level 4: list_item: GambhirM, BockarieM, TischD, Kaz ... 2010;8 10.1186/1741-7007-8-22 20236528
+        item-181 at level 4: list_item: World Health Organization. Globa ... cal entomology handbook. Geneva; 2013.
+        item-182 at level 4: list_item: SlaterH, MichaelE. Predicting th ...  10.1371/journal.pone.0032202 22359670
+        item-183 at level 4: list_item: SlaterH, MichaelE. Mapping, Baye ...  10.1371/journal.pone.0071574 23951194
+        item-184 at level 4: list_item: SabesanS, RajuKHK, SubramanianS, ... 57–665. 10.1089/vbz.2012.1238 23808973
+        item-185 at level 4: list_item: StantonMC, MolyneuxDH, KyelemD,  ... : 159–173. 10.4081/gh.2013.63 24258892
+        item-186 at level 4: list_item: ManhenjeI, Teresa Galán-Puchades ... : 391–398. 10.4081/gh.2013.96 23733300
+        item-187 at level 4: list_item: NgwiraBM, TambalaP, Perez aM, Bo ... ;6: 12 10.1186/1475-2883-6-12 18047646
+        item-188 at level 4: list_item: SimonsenPE, MwakitaluME. Urban l ... 44. 10.1007/s00436-012-3226-x 23239094
+        item-189 at level 4: list_item: ProvilleJ, Zavala-AraizaD, Wagne ...  10.1371/journal.pone.0174610 28346500
+        item-190 at level 4: list_item: EndeshawT, TayeA, TadesseZ, Kata ... 10.1080/20477724.2015.1103501 26878935
+        item-191 at level 4: list_item: RichardsFO, EigegeA, PamD, KalA, ... 4: 3–5. 10.1186/1475-2883-4-3 15916708
+        item-192 at level 4: list_item: KyelemD, SanouS, BoatinB a., Med ... 8. 10.1179/000349803225002462 14754495
+        item-193 at level 4: list_item: WeilGJ, LammiePJ, RichardsFO, Eb ... –816. 10.1093/infdis/164.4.814 1894943
+        item-194 at level 4: list_item: KumarA, SachanP. Measuring impac ... rop Biomed. 2014;31: 225–229. 25134891
+        item-195 at level 4: list_item: NjengaSM, MwandawiroCS, WamaeCN, ... 4: 1–9. 10.1186/1756-3305-4-1 21205315
+        item-196 at level 4: list_item: BoydA, WonKY, McClintockSK, Dono ...  10.1371/journal.pntd.0000640 20351776
+        item-197 at level 4: list_item: IrvineMA, ReimerLJ, NjengaSM, Gu ... 19. 10.1186/s13071-014-0608-1 25561160
+        item-198 at level 4: list_item: IrvineMA, StolkWA, SmithME, Subr ... 10.1016/S1473-3099(16)30467-4 28012943
+        item-199 at level 4: list_item: PionSD, MontavonC, ChesnaisCB, K ... 7–1423. 10.4269/ajtmh.16-0547 27729568
+        item-200 at level 4: list_item: WanjiS, EsumME, NjouendouAJ, Mbe ...  10.1371/journal.pntd.0007192 30849120
+        item-201 at level 4: list_item: ChesnaisCB, Awaca-UvonNP, BolayF ...  10.1371/journal.pntd.0005703 28892473
+        item-202 at level 4: list_item: SilumbweA, ZuluJM, HalwindiH, Ja ... 15. 10.1186/s12889-017-4414-5 28532397
+        item-203 at level 4: list_item: AdamsAM, VuckovicM, BirchE, Bran ... ;3 10.3390/tropicalmed3040122 30469342
+        item-204 at level 4: list_item: RaoRU, SamarasekeraSD, Nagodavit ...  10.1371/journal.pntd.0006066 29084213
+        item-205 at level 4: list_item: XuZ, GravesPM, LauCL, ClementsA, ...  10.1016/j.epidem.2018.12.003 30611745
+        item-206 at level 4: list_item: IdCM, TetteviEJ, MechanF, IdunB, ... Ghana. PLoS Negl Trop Dis. 2019; 1–17.
+        item-207 at level 4: list_item: EigegeA, KalA, MiriE, SallauA, U ...  10.1371/journal.pntd.0002508 24205421
+        item-208 at level 4: list_item: Van den BergH, Kelly-HopeLA, Lin ... 10.1016/S1473-3099(12)70148-2 23084831
+        item-209 at level 4: list_item: WebberR. Eradication of Wucherer ... ol. Trans R Soc Trop Med Hyg. 1979;73.
\ 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 0221913779..15062fa235 100644
--- a/tests/data/jats/groundtruth/pntd.0008301.nxml.json
+++ b/tests/data/jats/groundtruth/pntd.0008301.nxml.json
@@ -19,27 +19,6 @@
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         "$ref": "#/texts/0"
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-        "$ref": "#/texts/81"
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-        "$ref": "#/texts/104"
       }
     ],
     "content_layer": "body",
@@ -885,6 +864,9 @@
         {
           "$ref": "#/texts/19"
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+        {
+          "$ref": "#/texts/20"
+        },
         {
           "$ref": "#/tables/0"
         },
@@ -935,7 +917,7 @@
     {
       "self_ref": "#/texts/20",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/17"
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       "children": [],
       "content_layer": "body",
@@ -1831,15 +1813,24 @@
         {
           "$ref": "#/texts/79"
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+        {
+          "$ref": "#/texts/80"
+        },
         {
           "$ref": "#/pictures/0"
         },
+        {
+          "$ref": "#/texts/81"
+        },
         {
           "$ref": "#/pictures/1"
         },
         {
           "$ref": "#/groups/6"
         },
+        {
+          "$ref": "#/texts/85"
+        },
         {
           "$ref": "#/pictures/2"
         },
@@ -1849,18 +1840,27 @@
         {
           "$ref": "#/texts/87"
         },
+        {
+          "$ref": "#/texts/88"
+        },
         {
           "$ref": "#/pictures/3"
         },
         {
           "$ref": "#/groups/7"
         },
+        {
+          "$ref": "#/texts/102"
+        },
         {
           "$ref": "#/tables/1"
         },
         {
           "$ref": "#/texts/103"
         },
+        {
+          "$ref": "#/texts/104"
+        },
         {
           "$ref": "#/pictures/4"
         }
@@ -1887,7 +1887,7 @@
     {
       "self_ref": "#/texts/80",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/78"
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       "content_layer": "body",
@@ -1899,7 +1899,7 @@
     {
       "self_ref": "#/texts/81",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/78"
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       "children": [],
       "content_layer": "body",
@@ -1954,7 +1954,7 @@
     {
       "self_ref": "#/texts/85",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/78"
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       "content_layer": "body",
@@ -1990,7 +1990,7 @@
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       "self_ref": "#/texts/88",
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+        "$ref": "#/texts/78"
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       "content_layer": "body",
@@ -2200,7 +2200,7 @@
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       "self_ref": "#/texts/102",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/78"
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       "content_layer": "body",
@@ -2224,7 +2224,7 @@
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       "self_ref": "#/texts/104",
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-        "$ref": "#/body"
+        "$ref": "#/texts/78"
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diff --git a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt
index 05490bad52..a2c1bed2c1 100644
--- a/tests/data/jats/groundtruth/pone.0234687.nxml.itxt
+++ b/tests/data/jats/groundtruth/pone.0234687.nxml.itxt
@@ -52,547 +52,547 @@ item-0 at level 0: unspecified: group _root_
         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-54 at level 4: caption: Fig 1 Overview of the milk produ ... stem boundary considered in the study.
+        item-55 at level 4: picture
+          item-55 at level 5: caption: Fig 1 Overview of the milk production system boundary considered in the study.
+      item-56 at level 3: section_header: Functional unit
+        item-57 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows:
+        item-58 at level 4: text: ECM = Milk production × (0.0929  ...  characteristics described in Table 1.
+        item-59 at level 4: caption: Table 1 Descriptive characteristics of the herd.
+        item-60 at level 4: table with [13x3]
+          item-60 at level 5: caption: Table 1 Descriptive characteristics of the herd.
+      item-61 at level 3: section_header: Data sources and livestock system description
+        item-62 at level 4: inline: group group
+          item-63 at level 5: text: The individual feed requirements ...  cows that received both 75 and 50% of
+          item-64 at level 5: text: ad libitum
+          item-65 at level 5: text: TMR intake with access to grazing a tropical pasture (pearl-millet,
+          item-66 at level 5: text: Pennisetum glaucum
+          item-67 at level 5: text: ‘Campeiro’) compared to cows receiving
+          item-68 at level 5: text: ad libitum
+          item-69 at level 5: text: TMR intake. Cows grazing on a temperate pasture (ryegrass,
+          item-70 at level 5: text: Lolium multiflorum
+          item-71 at level 5: text: ‘Maximus’) did not need changes to ECM production compared to the
+          item-72 at level 5: text: ad libitum
+          item-73 at level 5: text: TMR intake group.
+        item-74 at level 4: inline: group group
+          item-75 at level 5: text: Using experimental data, three s ... evaluated during the lactation period:
           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-77 at level 5: text: TMR intake, and 75, and 50% of
+          item-78 at level 5: text: ad libitum
+          item-79 at level 5: text: TMR intake with access to grazin ... nction of month ([26], Civiero et al.,
+          item-80 at level 5: text: in press
+          item-81 at level 5: text: ). From April to October (210 da ... med during an entire lactation period.
+      item-82 at level 3: section_header: Impact assessment
+        item-83 at level 4: inline: group group
+          item-84 at level 5: text: The 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-86 at level 5: text: e emissions were calculated by multiplying the emissions of CO
+          item-87 at level 5: text: 2
+          item-88 at level 5: text: , CH
+          item-89 at level 5: text: 4
+          item-90 at level 5: text: and N
+          item-91 at level 5: text: 2
+          item-92 at level 5: text: O by their 100-year global warming potential (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: , 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-94 at level 5: text: ), based on IPCC assessment report 5 (AR5; [27]). The values of GWP
+          item-95 at level 5: text: 100
+          item-96 at level 5: text: are 1, 28 and 265 for CO
+          item-97 at level 5: text: 2
+          item-98 at level 5: text: , CH
+          item-99 at level 5: text: 4
+          item-100 at level 5: text: and N
+          item-101 at level 5: text: 2
+          item-102 at level 5: text: O, respectively.
+      item-103 at level 3: section_header: Feed production
+        item-104 at level 4: section_header: Diets composition
+          item-105 at level 5: inline: group group
+            item-106 at level 6: text: The DM intake of each ingredient ... ennial tropical pasture (kikuyu grass,
+            item-107 at level 6: text: Pennisetum clandestinum
+            item-108 at level 6: text: ). The DM intake of calves, heif ...  meet the net energy for lactation (NE
+            item-109 at level 6: text: L
+            item-110 at level 6: text: ) and metabolizable protein (MP) ... grated in the software INRAtion 4.07 (
+            item-111 at level 6: text: https://www.inration.educagri.fr/fr/forum.php
+            item-112 at level 6: text: ). The nutrient intake was calcu ...  collected throughout the experiments.
+          item-113 at level 5: caption: Table 2 Dairy cows’ diets in different scenariosa.
+          item-114 at level 5: table with [21x11]
+            item-114 at level 6: caption: Table 2 Dairy cows’ diets in different scenariosa.
+        item-115 at level 4: section_header: GHG emissions from crop and pasture production
+          item-116 at level 5: inline: group group
+            item-117 at level 6: text: GHG emission factors used for of ... s productions were 3300 and 1500 kg CO
+            item-118 at level 6: text: 2
+            item-119 at level 6: text: e ha
+            item-120 at level 6: text: -1
+            item-121 at level 6: text: , respectively [32]. The DM production (kg ha
+            item-122 at level 6: text: -1
+            item-123 at level 6: text: ) of corn silage and pastures we ... onsume 70% of pastures during grazing.
+          item-124 at level 5: caption: Table 3 GHG emission factors for Off- and On-farm feed production.
+          item-125 at level 5: table with [9x5]
+            item-125 at level 6: caption: Table 3 GHG emission factors for Off- and On-farm feed production.
+          item-126 at level 5: inline: group group
+            item-127 at level 6: text: Emissions from on-farm feed prod ... ary sources were direct and indirect 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-129 at level 6: text: O-N emissions from organic and s ... tilizers and crop/pasture residues, CO
+            item-130 at level 6: text: 2
+            item-131 at level 6: text: -C emissions from lime and urea  ...  well as fuel combustion. The direct 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-133 at level 6: text: O-N emission factor (kg (kg N input)
+            item-134 at level 6: text: -1
+            item-135 at level 6: text: ) is based on a local study performed previously [37]. For indirect N
+            item-136 at level 6: text: 2
+            item-137 at level 6: text: O-N emissions (kg N
+            item-138 at level 6: text: 2
+            item-139 at level 6: text: O-N (kg NH
+            item-140 at level 6: text: 3
+            item-141 at level 6: text: -N + NO
+            item-142 at level 6: text: x
+            item-143 at level 6: text: )
             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: yield (g (kg DM intake)
-          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-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-145 at level 6: text: ), as well as CO
+            item-146 at level 6: text: 2
+            item-147 at level 6: text: -C emissions from lime + urea, d ... stures, a C sequestration of 0.57 t ha
+            item-148 at level 6: text: -1
+            item-149 at level 6: text: was used based on a 9-year study ... red was 8.9 (no-tillage) and 14.3 L ha
+            item-150 at level 6: text: -1
+            item-151 at level 6: text: (disking) for annual tropical an ... te pastures, respectively [40]. The CO
+            item-152 at level 6: text: 2
+            item-153 at level 6: text: from fuel combustion was 2.7 kg CO
+            item-154 at level 6: text: 2
+            item-155 at level 6: text: L
+            item-156 at level 6: text: -1
+            item-157 at level 6: text: [41]. Secondary sources of emiss ... factors described by Rotz et al. [42].
+          item-158 at level 5: caption: Table 4 GHG emissions from On-farm feed production.
+          item-159 at level 5: table with [28x5]
+            item-159 at level 6: caption: Table 4 GHG emissions from On-farm feed production.
+      item-160 at level 3: section_header: Animal husbandry
+        item-161 at level 4: inline: group group
+          item-162 at level 5: text: The CH
+          item-163 at level 5: text: 4
+          item-164 at level 5: text: emissions from enteric fermentation intensity (g (kg ECM)
+          item-165 at level 5: text: -1
+          item-166 at level 5: text: ) was a function of estimated CH
+          item-167 at level 5: text: 4
+          item-168 at level 5: text: yield (g (kg DM intake)
+          item-169 at level 5: text: -1
+          item-170 at level 5: text: ), actual DM intake and ECM. The enteric CH
+          item-171 at level 5: text: 4
+          item-172 at level 5: text: yield was estimated as a functio ... proposed by Niu et al. [43], where: CH
+          item-173 at level 5: text: 4
+          item-174 at level 5: text: yield (g (kg DM intake)
+          item-175 at level 5: text: -1
+          item-176 at level 5: text: ) = 13.8 + 0.185 × NDF (% DM intake).
+      item-177 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals
+        item-178 at level 4: inline: group group
+          item-179 at level 5: text: The CH
+          item-180 at level 5: text: 4
+          item-181 at level 5: text: emission from manure (kg (kg ECM)
+          item-182 at level 5: text: -1
+          item-183 at level 5: text: ) was a function of daily CH
+          item-184 at level 5: text: 4
+          item-185 at level 5: text: emission from manure (kg cow
+          item-186 at level 5: text: -1
+          item-187 at level 5: text: ) and daily ECM (kg cow
+          item-188 at level 5: text: -1
+          item-189 at level 5: text: ). The daily CH
+          item-190 at level 5: text: 4
+          item-191 at level 5: text: emission from manure was estimat ... olatile solid (VS) excreted (kg DM cow
+          item-192 at level 5: text: -1
+          item-193 at level 5: text: ) in manure. The daily VS was es ... n an organic matter (OM) basis (kg day
+          item-194 at level 5: text: -1
+          item-195 at level 5: text: ), NDOMI = non-digestible OM intake (kg day
+          item-196 at level 5: text: -1
+          item-197 at level 5: text: ): (1- OM digestibility) × OM in ... .04), GE = gross energy intake (MJ day
+          item-198 at level 5: text: -1
+          item-199 at level 5: text: ), OM = organic matter (g), 18.4 ... tor for dietary GE per kg of DM (MJ kg
+          item-200 at level 5: text: -1
+          item-201 at level 5: text: ).
+        item-202 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively.
+        item-203 at level 4: inline: group group
+          item-204 at level 5: text: The N
+          item-205 at level 5: text: 2
+          item-206 at level 5: text: O-N emissions from urine and fec ... ations 10 and 12, respectively). The N
+          item-207 at level 5: text: 2
+          item-208 at level 5: text: O emissions from stored manure a ... alculated based on the conversion of N
+          item-209 at level 5: text: 2
+          item-210 at level 5: text: O-N emissions to N
+          item-211 at level 5: text: 2
+          item-212 at level 5: text: O emissions, where N
+          item-213 at level 5: text: 2
+          item-214 at level 5: text: O emissions = N
+          item-215 at level 5: text: 2
+          item-216 at level 5: text: O-N emissions × 44/28. The emission factors were 0.002 kg N
+          item-217 at level 5: text: 2
+          item-218 at level 5: text: O-N (kg N)
+          item-219 at level 5: text: -1
+          item-220 at level 5: text: stored in a pit below animal confinements, and 0.02 kg N
+          item-221 at level 5: text: 2
+          item-222 at level 5: text: O-N (kg of urine and dung)
+          item-223 at level 5: text: -1
+          item-224 at level 5: text: deposited on pasture [38]. The indirect N
+          item-225 at level 5: text: 2
+          item-226 at level 5: text: O emissions from storage manure  ...  using the IPCC [38] emission factors.
+      item-227 at level 3: section_header: Farm management
+        item-228 at level 4: text: Emissions due to farm management ...  crop and pasture production’ section.
+        item-229 at level 4: caption: Table 5 Factors for major resource inputs in farm management.
+        item-230 at level 4: table with [12x4]
+          item-230 at level 5: caption: Table 5 Factors for major resource inputs in farm management.
         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-232 at level 5: text: The amount of fuel use for manur ... quired for manure handling (L diesel t
+          item-233 at level 5: text: -1
+          item-234 at level 5: text: ) [42]. The amount of manure was estimated from OM excretions (kg cow
           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-236 at level 5: text: ), assuming that the manure has  ... me that animals stayed on confinement.
+        item-237 at level 4: inline: group group
+          item-238 at level 5: text: The emissions from fuel were est ... uired for manure handling (L) × (kg CO
+          item-239 at level 5: text: 2
+          item-240 at level 5: text: e L
           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-242 at level 5: text: ) [41]. The secondary emissions  ... roduction and transport of fuel (kg CO
+          item-243 at level 5: text: 2
+          item-244 at level 5: text: e L
+          item-245 at level 5: text: -1
+          item-246 at level 5: text: ) [41]. Emissions from manufactu ... w (t) × (kg machinery mass (kg manure)
           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-248 at level 5: text: × 10
+          item-249 at level 5: text: −3
+          item-250 at level 5: text: ) [42] × kg CO
           item-251 at level 5: text: 2
-          item-252 at level 5: text: kWh
+          item-252 at level 5: text: e (kg machinery mass)
           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-254 at level 5: text: [42].
+        item-255 at level 4: inline: group group
+          item-256 at level 5: text: Emissions from electricity for m ... ated using two emission factors (kg CO
+          item-257 at level 5: text: 2
+          item-258 at level 5: text: kWh
+          item-259 at level 5: text: -1
+          item-260 at level 5: text: ). The first one is based on Uni ... ivities is 0.06 kWh (kg milk produced)
+          item-261 at level 5: text: -1
+          item-262 at level 5: text: [47]. The annual electricity use for lighting was 75 kWh cow
+          item-263 at level 5: text: -1
+          item-264 at level 5: text: , which is the value considered  ... ws in naturally ventilated barns [47].
+      item-265 at level 3: section_header: Co-product allocation
+        item-266 at level 4: inline: group group
+          item-267 at level 5: text: The C footprint for milk produce ... ibed by Thoma et al. [48]. Briefly, 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-269 at level 5: text: = 1–6.04 × BMR, where
+          item-270 at level 5: text: :
+          item-271 at level 5: text: AR
+          item-272 at level 5: text: milk
+          item-273 at level 5: text: is the allocation ratio for milk ...  during cow`s entire life (kg). The AR
+          item-274 at level 5: text: milk
+          item-275 at level 5: text: were 0.854 and 0.849 for TMR and ... asture scenarios, respectively. The AR
+          item-276 at level 5: text: milk
+          item-277 at level 5: text: was applied to the whole emissio ...  directly assigned to milk production.
+      item-278 at level 3: section_header: Sensitivity analysis
+        item-279 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint.
+    item-280 at level 2: section_header: Results and discussion
+      item-281 at level 3: text: The study has assessed the impac ... , feed production and electricity use.
+      item-282 at level 3: section_header: Greenhouse gas emissions
+        item-283 at level 4: inline: group group
+          item-284 at level 5: text: Depending on emission factors us ...  2A and 2B) or decreased by 0.04 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: 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: 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: 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-288 at level 5: text: (Fig 2C and 2D) in scenarios that included pastures compared to
+          item-289 at level 5: text: ad libitum
+          item-290 at level 5: text: TMR intake. Due to differences i ...  values ranged from 0.92 to 1.04 kg CO
+          item-291 at level 5: text: 2
+          item-292 at level 5: text: e (kg ECM)
+          item-293 at level 5: text: -1
+          item-294 at level 5: text: for dairy cows receiving TMR exclusively, and from 0.88 to 1.04 kg CO
+          item-295 at level 5: text: 2
+          item-296 at level 5: text: e (kg ECM)
+          item-297 at level 5: text: -1
+          item-298 at level 5: text: for cows with access to pasture. ... ocal emission factors for estimating N
+          item-299 at level 5: text: 2
+          item-300 at level 5: text: O-N emissions [37], manure emiss ... more than 5% of overall GHG emissions.
+        item-301 at level 4: caption: Fig 2 Overall greenhouse gas emi ... lectricity = 0.205 kg CO2e kWh-1 [46].
+        item-302 at level 4: picture
+          item-302 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-303 at level 4: inline: group group
+          item-304 at level 5: text: Considering IPCC emission factors for N
+          item-305 at level 5: text: 2
+          item-306 at level 5: text: O emissions from urine and dung  ... otprint ranged from 0.99 to 1.04 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: , and was close to those reporte ... , which ranged from 0.98 to 1.16 kg CO
+          item-311 at level 5: text: 2
+          item-312 at level 5: text: e (kg ECM)
+          item-313 at level 5: text: -1
+          item-314 at level 5: text: . When local emission factors for N
+          item-315 at level 5: text: 2
+          item-316 at level 5: text: O emissions from urine and dung  ...  without accounting for sequestered CO
+          item-317 at level 5: text: 2
+          item-318 at level 5: text: -C from perennial pasture—0.91 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: —was lower than the range of val ... , which ranged from 0.52 to 0.89 kg CO
+          item-323 at level 5: text: 2
+          item-324 at level 5: text: e (kg ECM)
+          item-325 at level 5: text: -1
+          item-326 at level 5: text: . Regardless of which emission f ... nt, which ranged from 1.4 to 2.3 kg CO
+          item-327 at level 5: text: 2
+          item-328 at level 5: text: e (kg ECM)
+          item-329 at level 5: text: -1
+          item-330 at level 5: text: [8,55]. Thus, even though differ ... e emissions estimation, sequestered CO
+          item-331 at level 5: text: 2
+          item-332 at level 5: text: -C, etc.), herd productivity and ...  the C footprint of the dairy systems.
+        item-333 at level 4: inline: group group
+          item-334 at level 5: text: The similarity of C footprint be ... served that an increase of 1000 kg cow
+          item-335 at level 5: text: -1
+          item-336 at level 5: text: (5000 to 6000 kg ECM) reduced the C footprint by 0.12 kg CO
+          item-337 at level 5: text: 2
+          item-338 at level 5: text: e (kg ECM)
+          item-339 at level 5: text: -1
+          item-340 at level 5: text: , which may explain an apparent  ...  milk production of around 7000 kg cow
+          item-341 at level 5: text: -1
+          item-342 at level 5: text: . Experimental data showed a red ... of TMR was replaced by pasture access.
+        item-343 at level 4: inline: group group
+          item-344 at level 5: text: The lower C footprint in scenari ...  emission factors [37] were used for N
+          item-345 at level 5: text: 2
+          item-346 at level 5: text: O emissions from urine and dung  ... enarios including pastures compared to
+          item-347 at level 5: text: ad libitum
+          item-348 at level 5: text: TMR intake. Whereas the IPCC [38] considers an emission of 0.02 kg N
+          item-349 at level 5: text: 2
+          item-350 at level 5: text: O-N (kg N)
+          item-351 at level 5: text: -1
+          item-352 at level 5: text: for urine and dung from grazing  ... five times lower, averaging 0.004 kg N
+          item-353 at level 5: text: 2
+          item-354 at level 5: text: O-N kg
+          item-355 at level 5: text: -1
+          item-356 at level 5: text: [37].
+      item-357 at level 3: section_header: Methane emissions
+        item-358 at level 4: inline: group group
+          item-359 at level 5: text: The enteric CH
+          item-360 at level 5: text: 4
+          item-361 at level 5: text: intensity was similar between di ... Fig 3). The large effect of enteric CH
+          item-362 at level 5: text: 4
+          item-363 at level 5: text: emissions on the whole C footpri ... cted, because the impact of enteric CH
+          item-364 at level 5: text: 4
+          item-365 at level 5: text: on GHG emissions of milk product ... o range from 44 to 60% of the total CO
+          item-366 at level 5: text: 2
+          item-367 at level 5: text: e [50,52,57,58]. However, emissi ... trate feeds are greater than 0.7 kg CO
+          item-368 at level 5: text: 2
+          item-369 at level 5: text: e kg
           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 may decrease with incl ... ybean meal [60] or increase enteric CH
+          item-371 at level 5: text: [59], which did not happen in this study.
+        item-372 at level 4: caption: Fig 3 Sensitivity of the C footp ... lectricity = 0.205 kg CO2e kWh-1 [46].
+        item-373 at level 4: picture
+          item-373 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-374 at level 4: inline: group group
+          item-375 at level 5: text: The lack of difference in 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-377 at level 5: text: emissions in different systems c ... nual temperate pastures (495 g (kg DM)
+          item-378 at level 5: text: -1
+          item-379 at level 5: text: ) compared to corn silage (550 g (kg DM)
+          item-380 at level 5: text: -1
+          item-381 at level 5: text: ). Hence, an expected, increase  ...  have shown that the actual enteric CH
+          item-382 at level 5: text: 4
+          item-383 at level 5: text: emissions may decrease with incl ... ybean meal [60] or increase enteric CH
+          item-384 at level 5: text: 4
+          item-385 at level 5: text: emissions when dairy cows grazin ...  silage [61]. Additionally, enteric CH
+          item-386 at level 5: text: 4
+          item-387 at level 5: text: emissions did not differ between ...  same scenarios as in this study [26].
+      item-388 at level 3: section_header: Emissions from excreta and feed production
+        item-389 at level 4: inline: group group
+          item-390 at level 5: text: Using IPCC emission factors for 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-392 at level 5: text: O emissions from urine and dung [38] and those from Table 3, CH
+          item-393 at level 5: text: 4
+          item-394 at level 5: text: emissions from manure decreased 0.07 kg CO
+          item-395 at level 5: text: 2
+          item-396 at level 5: text: e (kg ECM)
+          item-397 at level 5: text: -1
+          item-398 at level 5: text: , but N
           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-400 at level 5: text: O emissions from manure increased 0.09 kg CO
+          item-401 at level 5: text: 2
+          item-402 at level 5: text: e (kg ECM)
+          item-403 at level 5: text: -1
+          item-404 at level 5: text: , as TMR intake was restricted to 50%
+          item-405 at level 5: text: ad libitum
+          item-406 at level 5: text: (Fig 4A). Emissions for pastures increased by 0.06 kg CO
           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-408 at level 5: text: e (kg ECM)
+          item-409 at level 5: text: -1
+          item-410 at level 5: text: , whereas emissions for producin ... nd corn silage decreased by 0.09 kg CO
+          item-411 at level 5: text: 2
+          item-412 at level 5: text: e (kg ECM)
           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-414 at level 5: text: , as TMR intake decreased (Fig 4 ... ctating dairy cow diets. The greater N
+          item-415 at level 5: text: 2
+          item-416 at level 5: text: O-N emissions from manure with pasture was a consequence of higher N
+          item-417 at level 5: text: 2
+          item-418 at level 5: text: O-N emissions due to greater CP  ... g CP content from 185 to 152 g (kg DM)
+          item-419 at level 5: text: -1
+          item-420 at level 5: text: , N intake decreased by 20% and  ... g dairy cows ranged from 150 g (kg DM)
+          item-421 at level 5: text: -1
+          item-422 at level 5: text: on TMR system to 198 g (kg DM)
+          item-423 at level 5: text: -1
+          item-424 at level 5: text: on 50% TMR with pasture. Additio ...  may not be captured by microbes [65].
+        item-425 at level 4: caption: Fig 4 Greenhouse gas emissions ( ... uestered CO2-C from perennial pasture.
+        item-426 at level 4: picture
+          item-426 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-427 at level 4: inline: group group
+          item-428 at level 5: text: Using local emission factors for N
+          item-429 at level 5: text: 2
+          item-430 at level 5: text: O emissions from urine and dung  ... d those from Table 4, reductions in CH
+          item-431 at level 5: text: 4
+          item-432 at level 5: text: emissions from stocked manure, w ... iets, did not offset by increases in N
           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-434 at level 5: text: O emissions from excreta (Fig 4C ... much lower emission factors used for N
+          item-435 at level 5: text: 2
+          item-436 at level 5: text: O emissions from urine and dung. ... be revised for the subtropical region.
+        item-437 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9].
+      item-438 at level 3: section_header: Farm management
+        item-439 at level 4: text: The lower impact of emissions fr ...  greater than 5% of total C footprint.
+        item-440 at level 4: inline: group group
+          item-441 at level 5: text: Emissions from farm management d ... or electricity generation (0.205 kg CO
+          item-442 at level 5: text: 2
+          item-443 at level 5: text: e kWh
+          item-444 at level 5: text: -1
+          item-445 at level 5: text: [46]) is much lower than that in a LCA study conducted in US (0.73 kg CO
+          item-446 at level 5: text: 2
+          item-447 at level 5: text: e kWh
+          item-448 at level 5: text: -1
+          item-449 at level 5: text: [42]). This apparent discrepancy ...  has an emission factor of 0.074 kg CO
+          item-450 at level 5: text: 2
+          item-451 at level 5: text: e kWh
+          item-452 at level 5: text: -1
+          item-453 at level 5: text: against 0.382 and 0.926 kg 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-455 at level 5: text: e kWh
+          item-456 at level 5: text: -1
+          item-457 at level 5: text: produced by natural gas and hard coal, respectively [46].
+      item-458 at level 3: section_header: Assumptions and limitations
+        item-459 at level 4: inline: group group
+          item-460 at level 5: text: The milk production and composit ... sion factors for direct and indirect N
+          item-461 at level 5: text: 2
+          item-462 at level 5: text: O emissions from urine and dung  ... sary to reduce the uncertainty. The 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. Chapter 5: Food Security. 2019.
-        item-505 at level 4: list_item: HerreroM, HendersonB, HavlíkP, T ...  2016;6: 452–461. 10.1038/nclimate2925
-        item-506 at level 4: list_item: Rivera-FerreMG, López-i-GelatsF, ... hang. 2016;7: 869–892. 10.1002/wcc.421
-        item-507 at level 4: list_item: van ZantenHHE, MollenhorstH, Klo ... 21: 747–758. 10.1007/s11367-015-0944-1
-        item-508 at level 4: list_item: HristovAN, OhJ, FirkinsL, Dijkst ... 5–5069. 10.2527/jas.2013-6583 24045497
-        item-509 at level 4: list_item: HristovAN, OttT, TricaricoJ, Rot ... 5–5113. 10.2527/jas.2013-6585 24045470
-        item-510 at level 4: list_item: MontesF, MeinenR, DellC, RotzA,  ... 0–5094. 10.2527/jas.2013-6584 24045493
-        item-511 at level 4: list_item: LedgardSF, WeiS, WangX, Falconer ... : 155–163. 10.1016/j.agwat.2018.10.009
-        item-512 at level 4: list_item: O’BrienD, ShallooL, PattonJ, Buc ... 107: 33–46. 10.1016/j.agsy.2011.11.004
-        item-513 at level 4: list_item: SalouT, Le MouëlC, van der WerfH ... od. 2017 10.1016/j.jclepro.2016.05.019
-        item-514 at level 4: list_item: LizarraldeC, PicassoV, RotzCA, C ... gric Res. 2014;3: 1 10.5539/sar.v3n2p1
-        item-515 at level 4: list_item: ClarkCEF, KaurR, MillapanLO, Gol ... –5465. 10.3168/jds.2017-13388 29550132
-        item-516 at level 4: list_item: Food and Agriculture Organization. FAOSTAT. 2017.
-        item-517 at level 4: list_item: VogelerI, MackayA, VibartR, Rend ... .1016/j.scitotenv.2016.05.006 27203517
-        item-518 at level 4: list_item: WilkinsonJM, LeeMRF, RiveroMJ, C ... 0;75: 1–17. 10.1111/gfs.12458 32109974
-        item-519 at level 4: list_item: WalesWJ, MarettLC, GreenwoodJS,  ... i. 2013;53: 1167–1178. 10.1071/AN13207
-        item-520 at level 4: list_item: BargoF, MullerLD, DelahoyJE, Cas ... 168/jds.S0022-0302(02)74381-6 12487461
-        item-521 at level 4: list_item: VibartRE, FellnerV, BurnsJC, Hun ... 80. 10.1017/S0022029908003361 18701000
-        item-522 at level 4: list_item: MendozaA, CajarvilleC, RepettoJL ... –1944. 10.3168/jds.2015-10257 26778319
-        item-523 at level 4: list_item: NRC. Nutrient Requirements of Da ... gton DC: National Academy Press; 2001.
-        item-524 at level 4: list_item: INRA. INRA Feeding System for Ru ... shiers; 2018 10.3920/978-90-8686-872-8
-        item-525 at level 4: list_item: LorenzH, ReinschT, HessS, TaubeF ... 161–170. 10.1016/j.jclepro.2018.11.113
-        item-526 at level 4: list_item: ISO 14044. INTERNATIONAL STANDAR ... rements and guidelines. 2006;2006: 46.
-        item-527 at level 4: list_item: ISO 14040. The International Sta ... ;2006: 1–28. 10.1136/bmj.332.7550.1107
-        item-528 at level 4: list_item: FAO. Environmental Performance o ... nerships/leap/resources/guidelines/en/
-        item-529 at level 4: list_item: CivieroM, Ribeiro-FilhoHMN, Scha ... nce,. Foz do Iguaçu; 2019 pp. 141–141.
-        item-530 at level 4: list_item: IPCC—Intergovernmental Panel on  ... /2018/05/SYR_AR5_FINAL_full_wcover.pdf
-        item-531 at level 4: list_item: INRA. Alimentation des bovins, o ... Inra 2007. 4th ed. INRA, editor. 2007.
-        item-532 at level 4: list_item: DelagardeR, FaverdinP, BaratteC, ... 5–60. 10.1111/j.1365-2494.2010.00770.x
-        item-533 at level 4: list_item: MaBL, LiangBC, BiswasDK, Morriso ... 2;94: 15–31. 10.1007/s10705-012-9522-0
-        item-534 at level 4: list_item: RauccciGS, MoreiraCS, AlvesPS, M ... State. J Clean Prod. 2015;96: 418–425.
-        item-535 at level 4: list_item: CamargoGGT, RyanMR, RichardTL. E ... 3;63: 263–273. 10.1525/bio.2013.63.4.6
-        item-536 at level 4: list_item: da SilvaMSJ, JobimCC, PoppiEC, T ... 3–313. 10.1590/S1806-92902015000900001
-        item-537 at level 4: list_item: Duchini PGPGGuzatti GCGC, Ribeir ... Sci. 2016;67: 574–581. 10.1071/CP15170
-        item-538 at level 4: list_item: ScaravelliLFB, PereiraLET, Olivo ... teiras. Cienc Rural. 2007;37: 841–846.
-        item-539 at level 4: list_item: SbrissiaAF, DuchiniPG, ZaniniGD, ... : 945–954. 10.2135/cropsci2017.07.0447
-        item-540 at level 4: list_item: AlmeidaJGR, Dall-OrsolettaAC, Oz ... 12. 10.1017/S1751731119003057 31907089
-        item-541 at level 4: list_item: Intergovernamental Panel on Clim ... Global Environmental Strategies; 2006.
-        item-542 at level 4: list_item: RamalhoB, DieckowJ, BarthG, Simo ... il Sci. 2020; 1–14. 10.1111/ejss.12933
-        item-543 at level 4: list_item: FernandesHC, da SilveiraJCM, Rin ... –1587. 10.1590/s1413-70542008000500034
-        item-544 at level 4: list_item: Wang M Q. GREET 1.8a Spreadsheet ... transportation.anl.gov/software/GREET/
-        item-545 at level 4: list_item: RotzCAA, MontesF, ChianeseDS, Ch ... 6–1282. 10.3168/jds.2009-2162 20172247
-        item-546 at level 4: list_item: NiuM, KebreabE, HristovAN, OhJ,  ...  3368–3389. 10.1111/gcb.14094 29450980
-        item-547 at level 4: list_item: EugèneM, SauvantD, NozièreP, Via ... 10.1016/j.jenvman.2018.10.086 30602259
-        item-548 at level 4: list_item: ReedKF, MoraesLE, CasperDP, Kebr ... 5–3035. 10.3168/jds.2014-8397 25747829
-        item-549 at level 4: list_item: BarrosMV, PiekarskiCM, De Franci ... . Energies. 2018;11 10.3390/en11061412
-        item-550 at level 4: list_item: LudingtonD, JohnsonE. Dairy Farm ...  York State Energy Res Dev Auth. 2003.
-        item-551 at level 4: list_item: ThomaG, JollietO, WangY. A bioph ...  2013;31 10.1016/j.idairyj.2012.08.012
-        item-552 at level 4: list_item: NaranjoA, JohnsonA, RossowH. 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-464 at level 5: text: emitted from lime and urea appli ... ions as a function of soil management.
+      item-465 at level 3: section_header: Further considerations
+        item-466 at level 4: inline: group group
+          item-467 at level 5: text: The potential for using pasture  ...  reduced the C footprint by 0.12 kg CO
+          item-468 at level 5: text: 2
+          item-469 at level 5: text: e (kg ECM)
+          item-470 at level 5: text: -1
+          item-471 at level 5: text: , whereas an increase from 10,00 ... ced the C footprint by only 0.06 kg CO
+          item-472 at level 5: text: 2
+          item-473 at level 5: text: e (kg ECM)
+          item-474 at level 5: text: -1
+          item-475 at level 5: text: . Hence, the impact of increasin ... C footprint may increase by 0.03 kg CO
+          item-476 at level 5: text: 2
+          item-477 at level 5: text: e (kg ECM)
+          item-478 at level 5: text: -1
+          item-479 at level 5: text: in subclinical ketosis [71] and by 0.02 kg CO
+          item-480 at level 5: text: 2
+          item-481 at level 5: text: e (kg ECM)
+          item-482 at level 5: text: -1
+          item-483 at level 5: text: in case of foot lesions [72].
+        item-484 at level 4: inline: group group
+          item-485 at level 5: text: Grazing lands may also improve b ... n subtropical areas by 0.5 to 1.5 t ha
+          item-486 at level 5: text: -1
+          item-487 at level 5: text: [75]. If 50% of tilled areas were under perennial grasslands, 1.0 t C ha
+          item-488 at level 5: text: -1
+          item-489 at level 5: text: would be sequestered, further re ... e C footprint by 0.015 and 0.025 kg CO
+          item-490 at level 5: text: 2
+          item-491 at level 5: text: e (kg ECM)
+          item-492 at level 5: text: -1
+          item-493 at level 5: text: for the scenarios using 75 and 5 ... emissions would be 0.03 and 0.05 kg CO
+          item-494 at level 5: text: 2
+          item-495 at level 5: text: e (kg ECM)
+          item-496 at level 5: text: -1
+          item-497 at level 5: text: for 75 and 50% TMR, respectively ...  C storage, so that net exchange of CO
+          item-498 at level 5: text: 2
+          item-499 at level 5: text: would be negligible [76].
+    item-500 at level 2: section_header: Conclusions
+      item-501 at level 3: inline: group group
+        item-502 at level 4: text: This study assessed the C footpr ...  attributable to the evidence of low N
+        item-503 at level 4: text: 2
+        item-504 at level 4: text: O emissions from urine and dung  ... ical areas. Even though the enteric CH
+        item-505 at level 4: text: 4
+        item-506 at level 4: text: intensity was the largest source of CO
+        item-507 at level 4: text: 2
+        item-508 at level 4: text: e emissions, it did not change b ... on with or without access to pastures.
+    item-509 at level 2: section_header: Acknowledgments
+      item-510 at level 3: text: Thanks to Anna Naranjo for helpf ...  of the herd considered in this study.
+    item-511 at level 2: section_header: References
+      item-512 at level 3: list: group list
+        item-513 at level 4: list_item: IPCC. Climate Change and Land. Chapter 5: Food Security. 2019.
+        item-514 at level 4: list_item: HerreroM, HendersonB, HavlíkP, T ...  2016;6: 452–461. 10.1038/nclimate2925
+        item-515 at level 4: list_item: Rivera-FerreMG, López-i-GelatsF, ... hang. 2016;7: 869–892. 10.1002/wcc.421
+        item-516 at level 4: list_item: van ZantenHHE, MollenhorstH, Klo ... 21: 747–758. 10.1007/s11367-015-0944-1
+        item-517 at level 4: list_item: HristovAN, OhJ, FirkinsL, Dijkst ... 5–5069. 10.2527/jas.2013-6583 24045497
+        item-518 at level 4: list_item: HristovAN, OttT, TricaricoJ, Rot ... 5–5113. 10.2527/jas.2013-6585 24045470
+        item-519 at level 4: list_item: MontesF, MeinenR, DellC, RotzA,  ... 0–5094. 10.2527/jas.2013-6584 24045493
+        item-520 at level 4: list_item: LedgardSF, WeiS, WangX, Falconer ... : 155–163. 10.1016/j.agwat.2018.10.009
+        item-521 at level 4: list_item: O’BrienD, ShallooL, PattonJ, Buc ... 107: 33–46. 10.1016/j.agsy.2011.11.004
+        item-522 at level 4: list_item: SalouT, Le MouëlC, van der WerfH ... od. 2017 10.1016/j.jclepro.2016.05.019
+        item-523 at level 4: list_item: LizarraldeC, PicassoV, RotzCA, C ... gric Res. 2014;3: 1 10.5539/sar.v3n2p1
+        item-524 at level 4: list_item: ClarkCEF, KaurR, MillapanLO, Gol ... –5465. 10.3168/jds.2017-13388 29550132
+        item-525 at level 4: list_item: Food and Agriculture Organization. FAOSTAT. 2017.
+        item-526 at level 4: list_item: VogelerI, MackayA, VibartR, Rend ... .1016/j.scitotenv.2016.05.006 27203517
+        item-527 at level 4: list_item: WilkinsonJM, LeeMRF, RiveroMJ, C ... 0;75: 1–17. 10.1111/gfs.12458 32109974
+        item-528 at level 4: list_item: WalesWJ, MarettLC, GreenwoodJS,  ... i. 2013;53: 1167–1178. 10.1071/AN13207
+        item-529 at level 4: list_item: BargoF, MullerLD, DelahoyJE, Cas ... 168/jds.S0022-0302(02)74381-6 12487461
+        item-530 at level 4: list_item: VibartRE, FellnerV, BurnsJC, Hun ... 80. 10.1017/S0022029908003361 18701000
+        item-531 at level 4: list_item: MendozaA, CajarvilleC, RepettoJL ... –1944. 10.3168/jds.2015-10257 26778319
+        item-532 at level 4: list_item: NRC. Nutrient Requirements of Da ... gton DC: National Academy Press; 2001.
+        item-533 at level 4: list_item: INRA. INRA Feeding System for Ru ... shiers; 2018 10.3920/978-90-8686-872-8
+        item-534 at level 4: list_item: LorenzH, ReinschT, HessS, TaubeF ... 161–170. 10.1016/j.jclepro.2018.11.113
+        item-535 at level 4: list_item: ISO 14044. INTERNATIONAL STANDAR ... rements and guidelines. 2006;2006: 46.
+        item-536 at level 4: list_item: ISO 14040. The International Sta ... ;2006: 1–28. 10.1136/bmj.332.7550.1107
+        item-537 at level 4: list_item: FAO. Environmental Performance o ... nerships/leap/resources/guidelines/en/
+        item-538 at level 4: list_item: CivieroM, Ribeiro-FilhoHMN, Scha ... nce,. Foz do Iguaçu; 2019 pp. 141–141.
+        item-539 at level 4: list_item: IPCC—Intergovernmental Panel on  ... /2018/05/SYR_AR5_FINAL_full_wcover.pdf
+        item-540 at level 4: list_item: INRA. Alimentation des bovins, o ... Inra 2007. 4th ed. INRA, editor. 2007.
+        item-541 at level 4: list_item: DelagardeR, FaverdinP, BaratteC, ... 5–60. 10.1111/j.1365-2494.2010.00770.x
+        item-542 at level 4: list_item: MaBL, LiangBC, BiswasDK, Morriso ... 2;94: 15–31. 10.1007/s10705-012-9522-0
+        item-543 at level 4: list_item: RauccciGS, MoreiraCS, AlvesPS, M ... State. J Clean Prod. 2015;96: 418–425.
+        item-544 at level 4: list_item: CamargoGGT, RyanMR, RichardTL. E ... 3;63: 263–273. 10.1525/bio.2013.63.4.6
+        item-545 at level 4: list_item: da SilvaMSJ, JobimCC, PoppiEC, T ... 3–313. 10.1590/S1806-92902015000900001
+        item-546 at level 4: list_item: Duchini PGPGGuzatti GCGC, Ribeir ... Sci. 2016;67: 574–581. 10.1071/CP15170
+        item-547 at level 4: list_item: ScaravelliLFB, PereiraLET, Olivo ... teiras. Cienc Rural. 2007;37: 841–846.
+        item-548 at level 4: list_item: SbrissiaAF, DuchiniPG, ZaniniGD, ... : 945–954. 10.2135/cropsci2017.07.0447
+        item-549 at level 4: list_item: AlmeidaJGR, Dall-OrsolettaAC, Oz ... 12. 10.1017/S1751731119003057 31907089
+        item-550 at level 4: list_item: Intergovernamental Panel on Clim ... Global Environmental Strategies; 2006.
+        item-551 at level 4: list_item: RamalhoB, DieckowJ, BarthG, Simo ... il Sci. 2020; 1–14. 10.1111/ejss.12933
+        item-552 at level 4: list_item: FernandesHC, da SilveiraJCM, Rin ... –1587. 10.1590/s1413-70542008000500034
+        item-553 at level 4: list_item: Wang M Q. GREET 1.8a Spreadsheet ... transportation.anl.gov/software/GREET/
+        item-554 at level 4: list_item: RotzCAA, MontesF, ChianeseDS, Ch ... 6–1282. 10.3168/jds.2009-2162 20172247
+        item-555 at level 4: list_item: NiuM, KebreabE, HristovAN, OhJ,  ...  3368–3389. 10.1111/gcb.14094 29450980
+        item-556 at level 4: list_item: EugèneM, SauvantD, NozièreP, Via ... 10.1016/j.jenvman.2018.10.086 30602259
+        item-557 at level 4: list_item: ReedKF, MoraesLE, CasperDP, Kebr ... 5–3035. 10.3168/jds.2014-8397 25747829
+        item-558 at level 4: list_item: BarrosMV, PiekarskiCM, De Franci ... . Energies. 2018;11 10.3390/en11061412
+        item-559 at level 4: list_item: LudingtonD, JohnsonE. Dairy Farm ...  York State Energy Res Dev Auth. 2003.
+        item-560 at level 4: list_item: ThomaG, JollietO, WangY. A bioph ...  2013;31 10.1016/j.idairyj.2012.08.012
+        item-561 at level 4: list_item: NaranjoA, JohnsonA, RossowH. Gre ... . 2020 10.3168/jds.2019-16576 32037166
+        item-562 at level 4: list_item: JayasundaraS, WordenD, WeersinkA ... 18–1028. 10.1016/j.jclepro.2019.04.013
+        item-563 at level 4: list_item: WilliamsSRO, FisherPD, Berrisfor ... 4;19: 69–78. 10.1007/s11367-013-0619-8
+        item-564 at level 4: list_item: GollnowS, LundieS, MooreAD, McLa ... : 31–38. 10.1016/j.idairyj.2014.02.005
+        item-565 at level 4: list_item: O’BrienD, CapperJL, GarnsworthyP ... i. 2014 10.3168/jds.2013-7174 24440256
+        item-566 at level 4: list_item: ChobtangJ, McLarenSJ, LedgardSF, ... 2017;21: 1139–1152. 10.1111/jiec.12484
+        item-567 at level 4: list_item: GargMR, PhondbaBT, SherasiaPL, M ... Sci. 2016;56: 423–436. 10.1071/AN15464
+        item-568 at level 4: list_item: de LéisCM, CherubiniE, RuviaroCF ... 5;20: 46–60. 10.1007/s11367-014-0813-3
+        item-569 at level 4: list_item: O’BrienD, GeogheganA, McNamaraK, ... Sci. 2016;56: 495–500. 10.1071/AN15490
+        item-570 at level 4: list_item: O’BrienD, BrennanP, HumphreysJ,  ... : 1469–1481. 10.1007/s11367-014-0755-9
+        item-571 at level 4: list_item: BaekCY, LeeKM, ParkKH. Quantific ... : 50–60. 10.1016/j.jclepro.2014.02.010
+        item-572 at level 4: list_item: Dall-OrsolettaAC, AlmeidaJGR, Ca ... –4383. 10.3168/jds.2015-10396 27016830
+        item-573 at level 4: list_item: Dall-OrsolettaAC, OziemblowskiMM ... 5–73. 10.1016/j.anifeedsci.2019.05.009
+        item-574 at level 4: list_item: NiuM, AppuhamyJADRN, LeytemAB, D ... Sci. 2016;56: 312–321. 10.1071/AN15498
+        item-575 at level 4: list_item: WaghornGC, LawN, BryantM, Pachec ... i. 2019;59: 1261–1270. 10.1071/AN18018
+        item-576 at level 4: list_item: DickhoeferU, GlowackiS, GómezCA, ...  109–118. 10.1016/j.livsci.2018.08.004
+        item-577 at level 4: list_item: SchwabCG, BroderickGA. A 100-Yea ... 10112. 10.3168/jds.2017-13320 29153157
+        item-578 at level 4: list_item: SordiA, DieckowJ, BayerC, Alburq ... 90: 94–103. 10.1016/j.agee.2013.09.004
+        item-579 at level 4: list_item: SimonPL, DieckowJ, de KleinCAM,  ... 267: 74–82. 10.1016/j.agee.2018.08.013
+        item-580 at level 4: list_item: WangX, LedgardS, LuoJ, GuoY, Zha ... .1016/j.scitotenv.2017.12.259 29291563
+        item-581 at level 4: list_item: PirloG, LolliS. Environmental im ... 962–971. 10.1016/j.jclepro.2018.11.070
+        item-582 at level 4: list_item: HerzogA, WincklerC, ZollitschW.  ... 7: 174–187. 10.1016/j.agee.2018.07.029
+        item-583 at level 4: list_item: MostertPF, van MiddelaarCE, Bokk ... od. 2018 10.1016/j.jclepro.2017.10.019
+        item-584 at level 4: list_item: MostertPF, van MiddelaarCE, de B ... 7: 206–212. 10.1016/j.agsy.2018.09.006
+        item-585 at level 4: list_item: FoleyJA, RamankuttyN, BraumanKA, ...  337–342. 10.1038/nature10452 21993620
+        item-586 at level 4: list_item: LalR. Soil Carbon Sequestration  ... 1627. 10.1126/science.1097396 15192216
+        item-587 at level 4: list_item: BoddeyRM, JantaliaCP, ConceiçaoP ... –795. 10.1111/j.1365-2486.2009.02020.x
+        item-588 at level 4: list_item: McConkeyB, AngersD, BenthamM, Bo ...  the LULUCF sector for NIR 2014. 2014.
\ 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..d5f147f7eb 100644
--- a/tests/data/jats/groundtruth/pone.0234687.nxml.json
+++ b/tests/data/jats/groundtruth/pone.0234687.nxml.json
@@ -19,33 +19,6 @@
     "children": [
       {
         "$ref": "#/texts/0"
-      },
-      {
-        "$ref": "#/texts/49"
-      },
-      {
-        "$ref": "#/texts/53"
-      },
-      {
-        "$ref": "#/texts/102"
-      },
-      {
-        "$ref": "#/texts/111"
-      },
-      {
-        "$ref": "#/texts/143"
-      },
-      {
-        "$ref": "#/texts/210"
-      },
-      {
-        "$ref": "#/texts/276"
-      },
-      {
-        "$ref": "#/texts/342"
-      },
-      {
-        "$ref": "#/texts/392"
       }
     ],
     "content_layer": "body",
@@ -2661,6 +2634,9 @@
         {
           "$ref": "#/texts/48"
         },
+        {
+          "$ref": "#/texts/49"
+        },
         {
           "$ref": "#/pictures/0"
         }
@@ -2687,7 +2663,7 @@
     {
       "self_ref": "#/texts/49",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/47"
       },
       "children": [],
       "content_layer": "body",
@@ -2708,6 +2684,9 @@
         {
           "$ref": "#/texts/52"
         },
+        {
+          "$ref": "#/texts/53"
+        },
         {
           "$ref": "#/tables/0"
         }
@@ -2746,7 +2725,7 @@
     {
       "self_ref": "#/texts/53",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/50"
       },
       "children": [],
       "content_layer": "body",
@@ -3384,6 +3363,9 @@
         {
           "$ref": "#/groups/7"
         },
+        {
+          "$ref": "#/texts/102"
+        },
         {
           "$ref": "#/tables/1"
         }
@@ -3497,7 +3479,7 @@
     {
       "self_ref": "#/texts/102",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/94"
       },
       "children": [],
       "content_layer": "body",
@@ -3515,12 +3497,18 @@
         {
           "$ref": "#/groups/8"
         },
+        {
+          "$ref": "#/texts/111"
+        },
         {
           "$ref": "#/tables/2"
         },
         {
           "$ref": "#/groups/9"
         },
+        {
+          "$ref": "#/texts/143"
+        },
         {
           "$ref": "#/tables/3"
         }
@@ -3640,7 +3628,7 @@
     {
       "self_ref": "#/texts/111",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/103"
       },
       "children": [],
       "content_layer": "body",
@@ -4129,7 +4117,7 @@
     {
       "self_ref": "#/texts/143",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/103"
       },
       "children": [],
       "content_layer": "body",
@@ -5134,6 +5122,9 @@
         {
           "$ref": "#/texts/209"
         },
+        {
+          "$ref": "#/texts/210"
+        },
         {
           "$ref": "#/tables/4"
         },
@@ -5169,7 +5160,7 @@
     {
       "self_ref": "#/texts/210",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/208"
       },
       "children": [],
       "content_layer": "body",
@@ -5917,6 +5908,9 @@
         {
           "$ref": "#/groups/17"
         },
+        {
+          "$ref": "#/texts/276"
+        },
         {
           "$ref": "#/pictures/1"
         },
@@ -6200,7 +6194,7 @@
     {
       "self_ref": "#/texts/276",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/258"
       },
       "children": [],
       "content_layer": "body",
@@ -6998,6 +6992,9 @@
         {
           "$ref": "#/groups/21"
         },
+        {
+          "$ref": "#/texts/342"
+        },
         {
           "$ref": "#/pictures/2"
         },
@@ -7213,7 +7210,7 @@
     {
       "self_ref": "#/texts/342",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/328"
       },
       "children": [],
       "content_layer": "body",
@@ -7429,6 +7426,9 @@
         {
           "$ref": "#/groups/23"
         },
+        {
+          "$ref": "#/texts/392"
+        },
         {
           "$ref": "#/pictures/3"
         },
@@ -7988,7 +7988,7 @@
     {
       "self_ref": "#/texts/392",
       "parent": {
-        "$ref": "#/body"
+        "$ref": "#/texts/356"
       },
       "children": [],
       "content_layer": "body",
diff --git a/tests/test_backend_asciidoc.py b/tests/test_backend_asciidoc.py
index 3b227cf375..2934f2c04a 100644
--- a/tests/test_backend_asciidoc.py
+++ b/tests/test_backend_asciidoc.py
@@ -646,6 +646,33 @@ def test_literal_block_attaches_caption_to_code_item() -> None:
     assert code_items[0].captions[0].resolve(doc).text == "Literal example"
 
 
+@pytest.mark.parametrize(
+    ("block", "label"),
+    [
+        ("image::x.png[]", DocItemLabel.PICTURE),
+        ("|===\n| a | b\n|===", DocItemLabel.TABLE),
+        ("----\nx = 1\n----", DocItemLabel.CODE),
+    ],
+    ids=["picture", "table", "code"],
+)
+def test_block_title_caption_stays_in_the_section_of_its_block(
+    block: str, label: DocItemLabel
+) -> None:
+    # The caption must be a sibling of its block, not a child of the body
+    # collected after the last section.
+    src = f"= Title\n\n== One\n\n.Block title\n{block}\n\n== Two\n\nText.\n"
+    doc = _convert_adoc(src.encode())
+
+    item = next(item for item, _ in doc.iterate_items() if item.label == label)
+    caption = item.captions[0].resolve(doc)
+    assert caption.text == "Block title"
+    assert caption.parent == item.parent
+
+    section = item.parent.resolve(doc)
+    assert section.text == "One"
+    assert [ref.cref for ref in section.children] == [caption.self_ref, item.self_ref]
+
+
 def test_block_title_before_list_renders_as_bold_paragraph() -> None:
     # A block title preceding a list (GroupItem) has no caption slot; it must
     # be emitted as a bold PARAGRAPH immediately before the list.
diff --git a/tests/test_backend_jats_captions.py b/tests/test_backend_jats_captions.py
new file mode 100644
index 0000000000..9c936b8d15
--- /dev/null
+++ b/tests/test_backend_jats_captions.py
@@ -0,0 +1,42 @@
+# SPDX-FileCopyrightText: The Docling Contributors
+# SPDX-License-Identifier: MIT
+
+"""Tests for the placement of figure and table captions in the JATS backend."""
+
+from docling_core.types.doc import DocItemLabel, TextItem
+
+from .test_backend_jats import convert_jats_body
+
+
+def test_jats_captions_stay_in_the_section_of_their_figure_and_table():
+    doc = convert_jats_body(
+        """
+    <sec><title>One</title>
+      <fig id="f1"><label>Figure 1.</label><caption><p>A figure.</p></caption></fig>
+      <table-wrap id="t1"><label>Table 1.</label><caption><p>A table.</p></caption>
+        <table><tbody><tr><td>a</td><td>b</td></tr></tbody></table>
+      </table-wrap>
+    </sec>
+    <sec><title>Two</title><p>Para two.</p></sec>
+"""
+    )
+
+    picture, table = doc.pictures[0], doc.tables[0]
+    section = picture.parent.resolve(doc)
+    assert isinstance(section, TextItem)
+    assert section.text == "One"
+    assert table.parent == picture.parent
+
+    fig_caption = picture.captions[0].resolve(doc)
+    table_caption = table.captions[0].resolve(doc)
+    assert fig_caption.text == "Figure 1. A figure."
+    assert table_caption.text == "Table 1. A table."
+    assert [ref.cref for ref in section.children] == [
+        fig_caption.self_ref,
+        picture.self_ref,
+        table_caption.self_ref,
+        table.self_ref,
+    ]
+    assert all(
+        ref.resolve(doc).label != DocItemLabel.CAPTION for ref in doc.body.children
+    )