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chore(xml-jats): separate authors and affiliations

Browse Source 
In XML PubMed (JATS) backend, convert authors and affiliations as they
are typically rendered on PDFs.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
This commit is contained in:
Cesar Berrospi Ramis 2025-02-05 17:46:46 +01:00
parent ffbde1d1b0
commit 21a99fc27d
10 changed files with 1343 additions and 1273 deletions
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46
docling/backend/xml/pubmed_backend.py
View File

@ -142,9 +142,13 @@ class PubMedDocumentBackend(DeclarativeDocumentBackend):
# Get mapping between affiliation ids and names
affiliation_names = []
for affiliation_node in self.tree.xpath(".//aff[@id]"):
affiliation_names.append(
": ".join([t for t in affiliation_node.itertext() if t != "\n"])
)
aff = ", ".join([t for t in affiliation_node.itertext() if t.strip()])
aff = aff.replace("\n", " ")
label = affiliation_node.xpath("label")
if label:
# TODO: once superscript is supported, add label with formatting
aff = aff.removeprefix(f"{label[0].text}, ")
affiliation_names.append(aff)
affiliation_ids_names = {
id: name
for id, name in zip(self.tree.xpath(".//aff[@id]/@id"), affiliation_names)
@ -170,9 +174,9 @@ class PubMedDocumentBackend(DeclarativeDocumentBackend):
# Name
author["name"] = (
author_node.xpath("name/surname")[0].text
author_node.xpath("name/given-names")[0].text
+ " "
+ author_node.xpath("name/given-names")[0].text
+ author_node.xpath("name/surname")[0].text
)
authors.append(author)
@ -415,17 +419,29 @@ class PubMedDocumentBackend(DeclarativeDocumentBackend):
return
def _add_authors(self, doc: DoclingDocument, xml_components: XMLComponents) -> None:
authors_affiliations: list = []
for author in xml_components["authors"]:
authors_affiliations.append(author["name"])
authors_affiliations.append(", ".join(author["affiliation_names"]))
authors_affiliations_str = "; ".join(authors_affiliations)
# TODO: once docling supports text formatting, add affiliation reference to
# author names through superscripts
authors: list = [item["name"] for item in xml_components["authors"]]
authors_str = ", ".join(authors)
affiliations: list = [
item
for author in xml_components["authors"]
for item in author["affiliation_names"]
]
affiliations_str = "; ".join(list(dict.fromkeys(affiliations)))
if authors_str:
doc.add_text(
parent=self.parents["Title"],
text=authors_str,
label=DocItemLabel.PARAGRAPH,
)
if affiliations_str:
doc.add_text(
parent=self.parents["Title"],
text=affiliations_str,
label=DocItemLabel.PARAGRAPH,
)
doc.add_text(
parent=self.parents["Title"],
text=authors_affiliations_str,
label=DocItemLabel.PARAGRAPH,
)
return
def _add_abstract(

295
tests/data/groundtruth/docling_v2/elife-56337.xml.itxt
View File

@ -1,165 +1,166 @@
item-0 at level 0: unspecified: group _root_
item-1 at level 1: title: KRAB-zinc finger protein gene ex ... retrotransposons in the murine lineage
item-2 at level 2: paragraph: Wolf Gernot; 1: The Eunice Kenne ... tes of Health: Bethesda: United States
item-3 at level 2: section_header: Abstract
item-4 at level 3: text: The Krüppel-associated box zinc ... edundant role restricting TE activity.
item-5 at level 2: section_header: Introduction
item-6 at level 3: text: Nearly half of the human and mou ... s are active beyond early development.
item-7 at level 3: text: TEs, especially long terminal re ... f evolutionarily young KRAB-ZFP genes.
item-8 at level 2: section_header: Results
item-9 at level 3: section_header: Mouse KRAB-ZFPs target retrotransposons
item-10 at level 4: text: We analyzed the RNA expression p ... duplications (Kauzlaric et al., 2017).
item-11 at level 4: text: To determine the binding sites o ... ctive in the early embryo (Figure 1A).
item-12 at level 4: text: We generally observed that KRAB- ... responsible for this silencing effect.
item-13 at level 4: text: To further test the hypothesis t ... t easily evade repression by mutation.
item-14 at level 4: text: Our KRAB-ZFP ChIP-seq dataset al ... ntirely shift the mode of DNA binding.
item-15 at level 3: section_header: Genetic deletion of KRAB-ZFP gen ... leads to retrotransposon reactivation
item-16 at level 4: text: The majority of KRAB-ZFP genes a ... ung et al., 2014; Deniz et al., 2018).
item-17 at level 3: section_header: KRAB-ZFP cluster deletions license TE-borne enhancers
item-18 at level 4: text: We next used our RNA-seq dataset ... vating effects of TEs on nearby genes.
item-19 at level 4: text: While we generally observed that ... he internal region and not on the LTR.
item-20 at level 3: section_header: ETn retrotransposition in Chr4-cl KO and WT mice
item-21 at level 4: text: IAP, ETn/ETnERV and MuLV/RLTR4 r ... s may contribute to reduced viability.
item-22 at level 4: text: We reasoned that retrotransposon ... Tn insertions at a high recovery rate.
item-23 at level 4: text: Using this dataset, we first con ... nsertions in our pedigree (Figure 4A).
item-24 at level 4: text: To validate some of the novel ET ... ess might have truncated this element.
item-25 at level 4: text: Besides novel ETn insertions tha ... tions (Figure 4—figure supplement 3D).
item-26 at level 4: text: Finally, we asked whether there ... s clearly also play an important role.
item-27 at level 2: section_header: Discussion
item-28 at level 3: text: C2H2 zinc finger proteins, about ... ) depending upon their insertion site.
item-29 at level 3: text: Despite a lack of widespread ETn ... ion of the majority of KRAB-ZFP genes.
item-30 at level 2: section_header: Materials and methods
item-31 at level 3: section_header: Cell lines and transgenic mice
item-32 at level 4: text: Mouse ES cells and F9 EC cells w ... KO/KO and KO/WT (B6/129 F2) offspring.
item-33 at level 3: section_header: Generation of KRAB-ZFP expressing cell lines
item-34 at level 4: text: KRAB-ZFP ORFs were PCR-amplified ... led and further expanded for ChIP-seq.
item-35 at level 3: section_header: CRISPR/Cas9 mediated deletion of KRAB-ZFP clusters and an MMETn insertion
item-36 at level 4: text: All gRNAs were expressed from th ... PCR genotyping (Supplementary file 3).
item-37 at level 3: section_header: ChIP-seq analysis
item-38 at level 4: text: For ChIP-seq analysis of KRAB-ZF ... 010 or Khil et al., 2012 respectively.
item-39 at level 4: text: ChIP-seq libraries were construc ... were re-mapped using Bowtie (--best).
item-40 at level 3: section_header: Luciferase reporter assays
item-41 at level 4: text: For KRAB-ZFP repression assays, ... after transfection as described above.
item-42 at level 3: section_header: RNA-seq analysis
item-43 at level 4: text: Whole RNA was purified using RNe ... lemented in the R function p.adjust().
item-44 at level 3: section_header: Reduced representation bisulfite sequencing (RRBS-seq)
item-45 at level 4: text: For RRBS-seq analysis, Chr4-cl W ... h sample were considered for analysis.
item-46 at level 3: section_header: Retrotransposition assay
item-47 at level 4: text: The retrotransposition vectors p ... were stained with Amido Black (Sigma).
item-48 at level 3: section_header: Capture-seq screen
item-49 at level 4: text: To identify novel retrotransposo ... assembly using the Unicycler software.
item-50 at level 2: section_header: Tables
item-51 at level 3: table with [9x5]
item-51 at level 4: caption: Table 1.: * 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-52 at level 3: table with [31x5]
item-52 at level 4: caption: Key resources table:
item-53 at level 2: section_header: Figures
item-54 at level 3: picture
item-54 at level 4: caption: Figure 1.: Genome-wide binding patterns of mouse KRAB-ZFPs.
item-2 at level 2: paragraph: Gernot Wolf, Alberto de Iaco, Mi ... Ralls, Didier Trono, Todd S Macfarlan
item-3 at level 2: paragraph: The Eunice Kennedy Shriver Natio ... Lausanne (EPFL), Lausanne, Switzerland
item-4 at level 2: section_header: Abstract
item-5 at level 3: text: The Krüppel-associated box zinc ... edundant role restricting TE activity.
item-6 at level 2: section_header: Introduction
item-7 at level 3: text: Nearly half of the human and mou ... s are active beyond early development.
item-8 at level 3: text: TEs, especially long terminal re ... f evolutionarily young KRAB-ZFP genes.
item-9 at level 2: section_header: Results
item-10 at level 3: section_header: Mouse KRAB-ZFPs target retrotransposons
item-11 at level 4: text: We analyzed the RNA expression p ... duplications (Kauzlaric et al., 2017).
item-12 at level 4: text: To determine the binding sites o ... ctive in the early embryo (Figure 1A).
item-13 at level 4: text: We generally observed that KRAB- ... responsible for this silencing effect.
item-14 at level 4: text: To further test the hypothesis t ... t easily evade repression by mutation.
item-15 at level 4: text: Our KRAB-ZFP ChIP-seq dataset al ... ntirely shift the mode of DNA binding.
item-16 at level 3: section_header: Genetic deletion of KRAB-ZFP gen ... leads to retrotransposon reactivation
item-17 at level 4: text: The majority of KRAB-ZFP genes a ... ung et al., 2014; Deniz et al., 2018).
item-18 at level 3: section_header: KRAB-ZFP cluster deletions license TE-borne enhancers
item-19 at level 4: text: We next used our RNA-seq dataset ... vating effects of TEs on nearby genes.
item-20 at level 4: text: While we generally observed that ... he internal region and not on the LTR.
item-21 at level 3: section_header: ETn retrotransposition in Chr4-cl KO and WT mice
item-22 at level 4: text: IAP, ETn/ETnERV and MuLV/RLTR4 r ... s may contribute to reduced viability.
item-23 at level 4: text: We reasoned that retrotransposon ... Tn insertions at a high recovery rate.
item-24 at level 4: text: Using this dataset, we first con ... nsertions in our pedigree (Figure 4A).
item-25 at level 4: text: To validate some of the novel ET ... ess might have truncated this element.
item-26 at level 4: text: Besides novel ETn insertions tha ... tions (Figure 4—figure supplement 3D).
item-27 at level 4: text: Finally, we asked whether there ... s clearly also play an important role.
item-28 at level 2: section_header: Discussion
item-29 at level 3: text: C2H2 zinc finger proteins, about ... ) depending upon their insertion site.
item-30 at level 3: text: Despite a lack of widespread ETn ... ion of the majority of KRAB-ZFP genes.
item-31 at level 2: section_header: Materials and methods
item-32 at level 3: section_header: Cell lines and transgenic mice
item-33 at level 4: text: Mouse ES cells and F9 EC cells w ... KO/KO and KO/WT (B6/129 F2) offspring.
item-34 at level 3: section_header: Generation of KRAB-ZFP expressing cell lines
item-35 at level 4: text: KRAB-ZFP ORFs were PCR-amplified ... led and further expanded for ChIP-seq.
item-36 at level 3: section_header: CRISPR/Cas9 mediated deletion of KRAB-ZFP clusters and an MMETn insertion
item-37 at level 4: text: All gRNAs were expressed from th ... PCR genotyping (Supplementary file 3).
item-38 at level 3: section_header: ChIP-seq analysis
item-39 at level 4: text: For ChIP-seq analysis of KRAB-ZF ... 010 or Khil et al., 2012 respectively.
item-40 at level 4: text: ChIP-seq libraries were construc ... were re-mapped using Bowtie (--best).
item-41 at level 3: section_header: Luciferase reporter assays
item-42 at level 4: text: For KRAB-ZFP repression assays, ... after transfection as described above.
item-43 at level 3: section_header: RNA-seq analysis
item-44 at level 4: text: Whole RNA was purified using RNe ... lemented in the R function p.adjust().
item-45 at level 3: section_header: Reduced representation bisulfite sequencing (RRBS-seq)
item-46 at level 4: text: For RRBS-seq analysis, Chr4-cl W ... h sample were considered for analysis.
item-47 at level 3: section_header: Retrotransposition assay
item-48 at level 4: text: The retrotransposition vectors p ... were stained with Amido Black (Sigma).
item-49 at level 3: section_header: Capture-seq screen
item-50 at level 4: text: To identify novel retrotransposo ... assembly using the Unicycler software.
item-51 at level 2: section_header: Tables
item-52 at level 3: table with [9x5]
item-52 at level 4: caption: Table 1.: * 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-53 at level 3: table with [31x5]
item-53 at level 4: caption: Key resources table:
item-54 at level 2: section_header: Figures
item-55 at level 3: picture
item-55 at level 4: 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.
Figure 1—source data 1.KRAB-ZFP expression in 40 mouse tissues and cell lines (ENCODE).Mean values of replicates are shown as log2 transcripts per million.
Figure 1—source data 2.Probability heatmap of KRAB-ZFP binding to TEs.Values corresponds to -log10 (adjusted p-value) enrichment of ChIP-seq peak overlap with TE groups (Fisher’s exact test).
item-55 at level 3: picture
item-55 at level 4: caption: Figure 1—figure supplement 1.: ES cell-specific expression of KRAB-ZFP gene clusters.
(A) Heatmap showing expression patterns of mouse KRAB-ZFPs in 40 mouse tissues and cell lines (ENCODE). Heatmap colors indicate gene expression levels in log2 transcripts per million (TPM). The asterisk indicates a group of 30 KRAB-ZFPs that are exclusively expressed in ES cells. (B) Physical location of the genes encoding for the 30 KRAB-ZFPs that are exclusively expressed in ES cells. (C) Phylogenetic (Maximum likelihood) tree of the KRAB domains of mouse KRAB-ZFPs. KRAB-ZFPs encoded on the gene clusters on chromosome 2 and 4 are highlighted. The scale bar at the bottom indicates amino acid substitutions per site.
item-56 at level 3: picture
item-56 at level 4: caption: Figure 1—figure supplement 2.: KRAB-ZFP binding motifs and their repression activity.
(A) Comparison of computationally predicted (bottom) and experimentally determined (top) KRAB-ZFP binding motifs. Only significant pairs are shown (FDR < 0.1). (B) Luciferase reporter assays to confirm KRAB-ZFP repression of the identified target sites. Bars show the luciferase activity (normalized to Renilla luciferase) of reporter plasmids containing the indicated target sites cloned upstream of the SV40 promoter. Reporter plasmids were co-transfected into 293 T cells with a Renilla luciferase plasmid for normalization and plasmids expressing the targeting KRAB-ZFP. Normalized mean luciferase activity (from three replicates) is shown relative to luciferase activity of the reporter plasmid co-transfected with an empty pcDNA3.1 vector.
item-56 at level 4: caption: Figure 1—figure supplement 1.: ES cell-specific expression of KRAB-ZFP gene clusters.
(A) Heatmap showing expression patterns of mouse KRAB-ZFPs in 40 mouse tissues and cell lines (ENCODE). Heatmap colors indicate gene expression levels in log2 transcripts per million (TPM). The asterisk indicates a group of 30 KRAB-ZFPs that are exclusively expressed in ES cells. (B) Physical location of the genes encoding for the 30 KRAB-ZFPs that are exclusively expressed in ES cells. (C) Phylogenetic (Maximum likelihood) tree of the KRAB domains of mouse KRAB-ZFPs. KRAB-ZFPs encoded on the gene clusters on chromosome 2 and 4 are highlighted. The scale bar at the bottom indicates amino acid substitutions per site.
item-57 at level 3: picture
item-57 at level 4: caption: Figure 1—figure supplement 3.: KRAB-ZFP binding to ETn retrotransposons.
(A) Comparison of the PBSLys1,2 sequence with Zfp961 binding motifs in nonrepetitive peaks (Nonrep) and peaks at ETn elements. (B) Retrotransposition assays of original (ETnI1-neoTNF and MusD2-neoTNF Ribet et al., 2004) and modified reporter vectors where the Rex2 or Gm13051 binding motifs where removed. Schematic of reporter vectors are displayed at the top. HeLa cells were transfected as described in the Materials and Methods section and neo-resistant colonies, indicating retrotransposition events, were selected and stained. (C) Stem-loop structure of the ETn RNA export signal, the Gm13051 motif on the corresponding DNA is marked with red circles, the part of the motif that was deleted is indicated with grey crosses (adapted from Legiewicz et al., 2010).
item-57 at level 4: caption: Figure 1—figure supplement 2.: KRAB-ZFP binding motifs and their repression activity.
(A) Comparison of computationally predicted (bottom) and experimentally determined (top) KRAB-ZFP binding motifs. Only significant pairs are shown (FDR < 0.1). (B) Luciferase reporter assays to confirm KRAB-ZFP repression of the identified target sites. Bars show the luciferase activity (normalized to Renilla luciferase) of reporter plasmids containing the indicated target sites cloned upstream of the SV40 promoter. Reporter plasmids were co-transfected into 293 T cells with a Renilla luciferase plasmid for normalization and plasmids expressing the targeting KRAB-ZFP. Normalized mean luciferase activity (from three replicates) is shown relative to luciferase activity of the reporter plasmid co-transfected with an empty pcDNA3.1 vector.
item-58 at level 3: picture
item-58 at level 4: caption: Figure 2.: Retrotransposon reactivation in KRAB-ZFP cluster KO ES cells.
item-58 at level 4: caption: Figure 1—figure supplement 3.: KRAB-ZFP binding to ETn retrotransposons.
(A) Comparison of the PBSLys1,2 sequence with Zfp961 binding motifs in nonrepetitive peaks (Nonrep) and peaks at ETn elements. (B) Retrotransposition assays of original (ETnI1-neoTNF and MusD2-neoTNF Ribet et al., 2004) and modified reporter vectors where the Rex2 or Gm13051 binding motifs where removed. Schematic of reporter vectors are displayed at the top. HeLa cells were transfected as described in the Materials and Methods section and neo-resistant colonies, indicating retrotransposition events, were selected and stained. (C) Stem-loop structure of the ETn RNA export signal, the Gm13051 motif on the corresponding DNA is marked with red circles, the part of the motif that was deleted is indicated with grey crosses (adapted from Legiewicz et al., 2010).
item-59 at level 3: picture
item-59 at level 4: 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.
Figure 2—source data 1.Differential H3K9me3 and KAP1 distribution in WT and KRAB-ZFP cluster KO ES cells at TE families and KRAB-ZFP bound TE insertions.Differential read counts and statistical testing were determined by DESeq2.
item-59 at level 3: picture
item-59 at level 4: caption: Figure 2—figure supplement 1.: Epigenetic changes at TEs and TE-borne enhancers in KRAB-ZFP cluster KO ES cells.
(A) Differential analysis of summative (all individual insertions combined) H3K9me3 enrichment at TE groups in Chr10-cl, Chr13.1-cl and Chr13.2-cl KO ES cells. TE groups targeted by one or several KRAB-ZFPs encoded within the deleted clusters are highlighted in orange (differential enrichment over the entire TE sequences) and red (differential enrichment at TE regions that overlap with KRAB-ZFP ChIP-seq peaks). (B) Top: Schematic view of the Cd59a/Cd59b locus with a 5’ truncated ETn insertion. 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). Bottom: Transcriptional activity of a 5 kb fragment with or without fragments of the ETn insertion was tested by luciferase reporter assay in Chr4-cl WT and KO ES cells.
item-60 at level 3: picture
item-60 at level 4: 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-60 at level 4: caption: Figure 2—figure supplement 1.: Epigenetic changes at TEs and TE-borne enhancers in KRAB-ZFP cluster KO ES cells.
(A) Differential analysis of summative (all individual insertions combined) H3K9me3 enrichment at TE groups in Chr10-cl, Chr13.1-cl and Chr13.2-cl KO ES cells. TE groups targeted by one or several KRAB-ZFPs encoded within the deleted clusters are highlighted in orange (differential enrichment over the entire TE sequences) and red (differential enrichment at TE regions that overlap with KRAB-ZFP ChIP-seq peaks). (B) Top: Schematic view of the Cd59a/Cd59b locus with a 5’ truncated ETn insertion. 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). Bottom: Transcriptional activity of a 5 kb fragment with or without fragments of the ETn insertion was tested by luciferase reporter assay in Chr4-cl WT and KO ES cells.
item-61 at level 3: picture
item-61 at level 4: caption: Figure 4.: ETn retrotransposition in Chr4-cl KO mice.
item-61 at level 4: 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-62 at level 3: picture
item-62 at level 4: 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.
Figure 4—source data 1.Coordinates of identified novel ETn insertions and supporting capture-seq read counts.Genomic regions indicate cluster of supporting reads.
Figure 4—source data 2.Sequences of capture-seq probes used to enrich genomic DNA for ETn and MuLV (RLTR4) insertions.
item-62 at level 3: picture
item-62 at level 4: caption: Figure 4—figure supplement 1.: Birth statistics of KRAB-ZFP cluster KO mice and TE reactivation in adult tissues.
(A) Birth statistics of Chr4- and Chr2-cl mice derived from KO/WT x KO/WT matings in different strain backgrounds. (B) RNA-seq analysis of TE expression in Chr2- (left) and Chr4-cl (right) KO tissues. TE groups with the highest reactivation phenotype in ES cells are shown separately. Significantly up- and downregulated elements (adjusted p-value<0.05) are highlighted in red and green, respectively. Experiments were performed in at least two biological replicates.
item-63 at level 3: picture
item-63 at level 4: caption: Figure 4—figure supplement 2.: Identification of polymorphic ETn and MuLV retrotransposon insertions in Chr4-cl KO and WT mice.
Heatmaps show normalized capture-seq read counts in RPM (Read Per Million) for identified polymorphic ETn (A) and MuLV (B) loci in different mouse strains. Only loci with strong support for germ line ETn or MuLV insertions (at least 100 or 3000 ETn or MuLV RPM, respectively) in at least two animals are shown. Non-polymorphic insertion loci with high read counts in all screened mice were excluded for better visibility. The sample information (sample name and cell type/tissue) is annotated at the bottom, with the strain information indicated by color at the top. The color gradient indicates log10(RPM+1).
item-63 at level 4: caption: Figure 4—figure supplement 1.: Birth statistics of KRAB-ZFP cluster KO mice and TE reactivation in adult tissues.
(A) Birth statistics of Chr4- and Chr2-cl mice derived from KO/WT x KO/WT matings in different strain backgrounds. (B) RNA-seq analysis of TE expression in Chr2- (left) and Chr4-cl (right) KO tissues. TE groups with the highest reactivation phenotype in ES cells are shown separately. Significantly up- and downregulated elements (adjusted p-value<0.05) are highlighted in red and green, respectively. Experiments were performed in at least two biological replicates.
item-64 at level 3: picture
item-64 at level 4: caption: Figure 4—figure supplement 3.: Confirmation of novel ETn insertions identified by capture-seq.
item-64 at level 4: caption: Figure 4—figure supplement 2.: Identification of polymorphic ETn and MuLV retrotransposon insertions in Chr4-cl KO and WT mice.
Heatmaps show normalized capture-seq read counts in RPM (Read Per Million) for identified polymorphic ETn (A) and MuLV (B) loci in different mouse strains. Only loci with strong support for germ line ETn or MuLV insertions (at least 100 or 3000 ETn or MuLV RPM, respectively) in at least two animals are shown. Non-polymorphic insertion loci with high read counts in all screened mice were excluded for better visibility. The sample information (sample name and cell type/tissue) is annotated at the bottom, with the strain information indicated by color at the top. The color gradient indicates log10(RPM+1).
item-65 at level 3: picture
item-65 at level 4: caption: Figure 4—figure supplement 3.: Confirmation of novel ETn insertions identified by capture-seq.
(A) PCR validation of novel ETn insertions in genomic DNA of three littermates (IDs: T09673, T09674 and T00436) and their parents (T3913 and T3921). Primer sequences are shown in Supplementary file 3. (B) ETn capture-seq read counts (RPM) at putative novel somatic (loci identified exclusively in one single animal), novel germ line (loci identified in several littermates) insertions, and at B6 reference ETn elements. (C) Heatmap shows capture-seq read counts (RPM) of a Chr4-cl KO mouse (ID: C6733) as determined in different tissues. Each row represents a novel ETn locus that was identified in at least one tissue. The color gradient indicates log10(RPM+1). (D) Heatmap shows the capture-seq RPM in technical replicates using the same Chr4-cl KO DNA sample (rep1/rep2) or replicates with DNA samples prepared from different sections of the tail from the same mouse at different ages (tail1/tail2). Each row represents a novel ETn locus that was identified in at least one of the displayed samples. The color gradient indicates log10(RPM+1).
item-65 at level 2: section_header: References
item-66 at level 3: list: group list
item-67 at level 4: list_item: TL Bailey; M Boden; FA Buske; M ... arching. Nucleic Acids Research (2009)
item-68 at level 4: list_item: C Baust; L Gagnier; GJ Baillie; ... the mouse. Journal of Virology (2003)
item-69 at level 4: list_item: K Blaschke; KT Ebata; MM Karimi; ... -like state in ES cells. Nature (2013)
item-70 at level 4: list_item: A Brodziak; E Ziółko; M Muc-Wier ... erimental and Clinical Research (2012)
item-71 at level 4: list_item: N Castro-Diaz; G Ecco; A Colucci ... stem cells. Genes & Development (2014)
item-72 at level 4: list_item: EB Chuong; NC Elde; C Feschotte. ... ndogenous retroviruses. Science (2016)
item-73 at level 4: list_item: J Dan; Y Liu; N Liu; M Chiourea; ... n silencing. Developmental Cell (2014)
item-74 at level 4: list_item: A De Iaco; E Planet; A Coluccio; ... cental mammals. Nature Genetics (2017)
item-75 at level 4: list_item: Ö Deniz; L de la Rica; KCL Cheng ... onic stem cells. Genome Biology (2018)
item-76 at level 4: list_item: M Dewannieux; T Heidmann. Endoge ... rs. Current Opinion in Virology (2013)
item-77 at level 4: list_item: G Ecco; M Cassano; A Kauzlaric; ... ult tissues. Developmental Cell (2016)
item-78 at level 4: list_item: G Ecco; M Imbeault; D Trono. KRAB zinc finger proteins. Development (2017)
item-79 at level 4: list_item: JA Frank; C Feschotte. Co-option ... on. Current Opinion in Virology (2017)
item-80 at level 4: list_item: L Gagnier; VP Belancio; DL Mager ... ansposon insertions. Mobile DNA (2019)
item-81 at level 4: list_item: AC Groner; S Meylan; A Ciuffi; N ... omatin spreading. PLOS Genetics (2010)
item-82 at level 4: list_item: DC Hancks; HH Kazazian. Roles fo ... ns in human disease. Mobile DNA (2016)
item-83 at level 4: list_item: M Imbeault; PY Helleboid; D Tron ... ene regulatory networks. Nature (2017)
item-84 at level 4: list_item: FM Jacobs; D Greenberg; N Nguyen ... SVA/L1 retrotransposons. Nature (2014)
item-85 at level 4: list_item: H Kano; H Kurahashi; T Toda. Gen ... e dactylaplasia phenotype. PNAS (2007)
item-86 at level 4: list_item: MM Karimi; P Goyal; IA Maksakova ... cripts in mESCs. Cell Stem Cell (2011)
item-87 at level 4: list_item: A Kauzlaric; G Ecco; M Cassano; ... related genetic units. PLOS ONE (2017)
item-88 at level 4: list_item: PP Khil; F Smagulova; KM Brick; ... ction of ssDNA. Genome Research (2012)
item-89 at level 4: list_item: F Krueger; SR Andrews. Bismark: ... eq applications. Bioinformatics (2011)
item-90 at level 4: list_item: B Langmead; SL Salzberg. Fast ga ... t with bowtie 2. Nature Methods (2012)
item-91 at level 4: list_item: M Legiewicz; AS Zolotukhin; GR P ... Journal of Biological Chemistry (2010)
item-92 at level 4: list_item: JA Lehoczky; PE Thomas; KM Patri ... n Polypodia mice. PLOS Genetics (2013)
item-93 at level 4: list_item: D Leung; T Du; U Wagner; W Xie; ... methyltransferase Setdb1. PNAS (2014)
item-94 at level 4: list_item: J Lilue; AG Doran; IT Fiddes; M ... unctional loci. Nature Genetics (2018)
item-95 at level 4: list_item: S Liu; J Brind'Amour; MM Karimi; ... germ cells. Genes & Development (2014)
item-96 at level 4: list_item: MI Love; W Huber; S Anders. Mode ... ata with DESeq2. Genome Biology (2014)
item-97 at level 4: list_item: F Lugani; R Arora; N Papeta; A P ... short tail mouse. PLOS Genetics (2013)
item-98 at level 4: list_item: TS Macfarlan; WD Gifford; S Dris ... ous retrovirus activity. Nature (2012)
item-99 at level 4: list_item: IA Maksakova; MT Romanish; L Gag ... mouse germ line. PLOS Genetics (2006)
item-100 at level 4: list_item: T Matsui; D Leung; H Miyashita; ... methyltransferase ESET. Nature (2010)
item-101 at level 4: list_item: HS Najafabadi; S Mnaimneh; FW Sc ... y lexicon. Nature Biotechnology (2015)
item-102 at level 4: list_item: C Nellåker; TM Keane; B Yalcin; ... 8 mouse strains. Genome Biology (2012)
item-103 at level 4: list_item: H O'Geen; S Frietze; PJ Farnham. ... s. Methods in Molecular Biology (2010)
item-104 at level 4: list_item: A Patel; P Yang; M Tinkham; M Pr ... ndem zinc finger proteins. Cell (2018)
item-105 at level 4: list_item: D Ribet; M Dewannieux; T Heidman ... s-mobilization. Genome Research (2004)
item-106 at level 4: list_item: SR Richardson; P Gerdes; DJ Gerh ... d early embryo. Genome Research (2017)
item-107 at level 4: list_item: HM Rowe; J Jakobsson; D Mesnard; ... in embryonic stem cells. Nature (2010)
item-108 at level 4: list_item: HM Rowe; A Kapopoulou; A Corsino ... nic stem cells. Genome Research (2013)
item-109 at level 4: list_item: SN Schauer; PE Carreira; R Shukl ... carcinogenesis. Genome Research (2018)
item-110 at level 4: list_item: DC Schultz; K Ayyanathan; D Nego ... r proteins. Genes & Development (2002)
item-111 at level 4: list_item: K Semba; K Araki; K Matsumoto; H ... short tail mice. PLOS Genetics (2013)
item-112 at level 4: list_item: SP Sripathy; J Stevens; DC Schul ... Molecular and Cellular Biology (2006)
item-113 at level 4: list_item: JH Thomas; S Schneider. Coevolut ... c finger genes. Genome Research (2011)
item-114 at level 4: list_item: PJ Thompson; TS Macfarlan; MC Lo ... tory repertoire. Molecular Cell (2016)
item-115 at level 4: list_item: RS Treger; SD Pope; Y Kong; M To ... irus expression SNERV. Immunity (2019)
item-116 at level 4: list_item: CN Vlangos; AN Siuniak; D Robins ... Ptf1a expression. PLOS Genetics (2013)
item-117 at level 4: list_item: J Wang; G Xie; M Singh; AT Ghanb ... s naive-like stem cells. Nature (2014)
item-118 at level 4: list_item: D Wolf; K Hug; SP Goff. TRIM28 m ... iruses in embryonic cells. PNAS (2008)
item-119 at level 4: list_item: G Wolf; D Greenberg; TS Macfarla ... ger protein family. Mobile DNA (2015a)
item-120 at level 4: list_item: G Wolf; P Yang; AC Füchtbauer; E ... roviruses. Genes & Development (2015b)
item-121 at level 4: list_item: M Yamauchi; B Freitag; C Khan; B ... silencers. Journal of Virology (1995)
item-122 at level 4: list_item: Y Zhang; T Liu; CA Meyer; J Eeck ... ChIP-Seq (MACS). Genome Biology (2008)
item-123 at level 1: caption: Table 1.: * Number of protein-co ... ChIP-seq was performed in this study.
item-124 at level 1: caption: Key resources table:
item-125 at level 1: caption: Figure 1.: Genome-wide binding p ... with TE groups (Fisher’s exact test).
item-126 at level 1: caption: Figure 1—figure supplement 1.: E ... tes amino acid substitutions per site.
item-127 at level 1: caption: Figure 1—figure supplement 2.: K ... sfected with an empty pcDNA3.1 vector.
item-128 at level 1: caption: Figure 1—figure supplement 3.: K ... (adapted from Legiewicz et al., 2010).
item-129 at level 1: caption: Figure 2.: Retrotransposon react ... cal testing were determined by DESeq2.
item-130 at level 1: caption: Figure 2—figure supplement 1.: E ... r assay in Chr4-cl WT and KO ES cells.
item-131 at level 1: caption: Figure 3.: TE-dependent gene act ... Gm13051 are indicated by dashed lines.
item-132 at level 1: caption: Figure 4.: ETn retrotranspositio ... A for ETn and MuLV (RLTR4) insertions.
item-133 at level 1: caption: Figure 4—figure supplement 1.: B ... in at least two biological replicates.
item-134 at level 1: caption: Figure 4—figure supplement 2.: I ... color gradient indicates log10(RPM+1).
item-135 at level 1: caption: Figure 4—figure supplement 3.: C ... color gradient indicates log10(RPM+1).
item-66 at level 2: section_header: References
item-67 at level 3: list: group list
item-68 at level 4: list_item: TL Bailey; M Boden; FA Buske; M ... arching. Nucleic Acids Research (2009)
item-69 at level 4: list_item: C Baust; L Gagnier; GJ Baillie; ... the mouse. Journal of Virology (2003)
item-70 at level 4: list_item: K Blaschke; KT Ebata; MM Karimi; ... -like state in ES cells. Nature (2013)
item-71 at level 4: list_item: A Brodziak; E Ziółko; M Muc-Wier ... erimental and Clinical Research (2012)
item-72 at level 4: list_item: N Castro-Diaz; G Ecco; A Colucci ... stem cells. Genes & Development (2014)
item-73 at level 4: list_item: EB Chuong; NC Elde; C Feschotte. ... ndogenous retroviruses. Science (2016)
item-74 at level 4: list_item: J Dan; Y Liu; N Liu; M Chiourea; ... n silencing. Developmental Cell (2014)
item-75 at level 4: list_item: A De Iaco; E Planet; A Coluccio; ... cental mammals. Nature Genetics (2017)
item-76 at level 4: list_item: Ö Deniz; L de la Rica; KCL Cheng ... onic stem cells. Genome Biology (2018)
item-77 at level 4: list_item: M Dewannieux; T Heidmann. Endoge ... rs. Current Opinion in Virology (2013)
item-78 at level 4: list_item: G Ecco; M Cassano; A Kauzlaric; ... ult tissues. Developmental Cell (2016)
item-79 at level 4: list_item: G Ecco; M Imbeault; D Trono. KRAB zinc finger proteins. Development (2017)
item-80 at level 4: list_item: JA Frank; C Feschotte. Co-option ... on. Current Opinion in Virology (2017)
item-81 at level 4: list_item: L Gagnier; VP Belancio; DL Mager ... ansposon insertions. Mobile DNA (2019)
item-82 at level 4: list_item: AC Groner; S Meylan; A Ciuffi; N ... omatin spreading. PLOS Genetics (2010)
item-83 at level 4: list_item: DC Hancks; HH Kazazian. Roles fo ... ns in human disease. Mobile DNA (2016)
item-84 at level 4: list_item: M Imbeault; PY Helleboid; D Tron ... ene regulatory networks. Nature (2017)
item-85 at level 4: list_item: FM Jacobs; D Greenberg; N Nguyen ... SVA/L1 retrotransposons. Nature (2014)
item-86 at level 4: list_item: H Kano; H Kurahashi; T Toda. Gen ... e dactylaplasia phenotype. PNAS (2007)
item-87 at level 4: list_item: MM Karimi; P Goyal; IA Maksakova ... cripts in mESCs. Cell Stem Cell (2011)
item-88 at level 4: list_item: A Kauzlaric; G Ecco; M Cassano; ... related genetic units. PLOS ONE (2017)
item-89 at level 4: list_item: PP Khil; F Smagulova; KM Brick; ... ction of ssDNA. Genome Research (2012)
item-90 at level 4: list_item: F Krueger; SR Andrews. Bismark: ... eq applications. Bioinformatics (2011)
item-91 at level 4: list_item: B Langmead; SL Salzberg. Fast ga ... t with bowtie 2. Nature Methods (2012)
item-92 at level 4: list_item: M Legiewicz; AS Zolotukhin; GR P ... Journal of Biological Chemistry (2010)
item-93 at level 4: list_item: JA Lehoczky; PE Thomas; KM Patri ... n Polypodia mice. PLOS Genetics (2013)
item-94 at level 4: list_item: D Leung; T Du; U Wagner; W Xie; ... methyltransferase Setdb1. PNAS (2014)
item-95 at level 4: list_item: J Lilue; AG Doran; IT Fiddes; M ... unctional loci. Nature Genetics (2018)
item-96 at level 4: list_item: S Liu; J Brind'Amour; MM Karimi; ... germ cells. Genes & Development (2014)
item-97 at level 4: list_item: MI Love; W Huber; S Anders. Mode ... ata with DESeq2. Genome Biology (2014)
item-98 at level 4: list_item: F Lugani; R Arora; N Papeta; A P ... short tail mouse. PLOS Genetics (2013)
item-99 at level 4: list_item: TS Macfarlan; WD Gifford; S Dris ... ous retrovirus activity. Nature (2012)
item-100 at level 4: list_item: IA Maksakova; MT Romanish; L Gag ... mouse germ line. PLOS Genetics (2006)
item-101 at level 4: list_item: T Matsui; D Leung; H Miyashita; ... methyltransferase ESET. Nature (2010)
item-102 at level 4: list_item: HS Najafabadi; S Mnaimneh; FW Sc ... y lexicon. Nature Biotechnology (2015)
item-103 at level 4: list_item: C Nellåker; TM Keane; B Yalcin; ... 8 mouse strains. Genome Biology (2012)
item-104 at level 4: list_item: H O'Geen; S Frietze; PJ Farnham. ... s. Methods in Molecular Biology (2010)
item-105 at level 4: list_item: A Patel; P Yang; M Tinkham; M Pr ... ndem zinc finger proteins. Cell (2018)
item-106 at level 4: list_item: D Ribet; M Dewannieux; T Heidman ... s-mobilization. Genome Research (2004)
item-107 at level 4: list_item: SR Richardson; P Gerdes; DJ Gerh ... d early embryo. Genome Research (2017)
item-108 at level 4: list_item: HM Rowe; J Jakobsson; D Mesnard; ... in embryonic stem cells. Nature (2010)
item-109 at level 4: list_item: HM Rowe; A Kapopoulou; A Corsino ... nic stem cells. Genome Research (2013)
item-110 at level 4: list_item: SN Schauer; PE Carreira; R Shukl ... carcinogenesis. Genome Research (2018)
item-111 at level 4: list_item: DC Schultz; K Ayyanathan; D Nego ... r proteins. Genes & Development (2002)
item-112 at level 4: list_item: K Semba; K Araki; K Matsumoto; H ... short tail mice. PLOS Genetics (2013)
item-113 at level 4: list_item: SP Sripathy; J Stevens; DC Schul ... Molecular and Cellular Biology (2006)
item-114 at level 4: list_item: JH Thomas; S Schneider. Coevolut ... c finger genes. Genome Research (2011)
item-115 at level 4: list_item: PJ Thompson; TS Macfarlan; MC Lo ... tory repertoire. Molecular Cell (2016)
item-116 at level 4: list_item: RS Treger; SD Pope; Y Kong; M To ... irus expression SNERV. Immunity (2019)
item-117 at level 4: list_item: CN Vlangos; AN Siuniak; D Robins ... Ptf1a expression. PLOS Genetics (2013)
item-118 at level 4: list_item: J Wang; G Xie; M Singh; AT Ghanb ... s naive-like stem cells. Nature (2014)
item-119 at level 4: list_item: D Wolf; K Hug; SP Goff. TRIM28 m ... iruses in embryonic cells. PNAS (2008)
item-120 at level 4: list_item: G Wolf; D Greenberg; TS Macfarla ... ger protein family. Mobile DNA (2015a)
item-121 at level 4: list_item: G Wolf; P Yang; AC Füchtbauer; E ... roviruses. Genes & Development (2015b)
item-122 at level 4: list_item: M Yamauchi; B Freitag; C Khan; B ... silencers. Journal of Virology (1995)
item-123 at level 4: list_item: Y Zhang; T Liu; CA Meyer; J Eeck ... ChIP-Seq (MACS). Genome Biology (2008)
item-124 at level 1: caption: Table 1.: * Number of protein-co ... ChIP-seq was performed in this study.
item-125 at level 1: caption: Key resources table:
item-126 at level 1: caption: Figure 1.: Genome-wide binding p ... with TE groups (Fisher’s exact test).
item-127 at level 1: caption: Figure 1—figure supplement 1.: E ... tes amino acid substitutions per site.
item-128 at level 1: caption: Figure 1—figure supplement 2.: K ... sfected with an empty pcDNA3.1 vector.
item-129 at level 1: caption: Figure 1—figure supplement 3.: K ... (adapted from Legiewicz et al., 2010).
item-130 at level 1: caption: Figure 2.: Retrotransposon react ... cal testing were determined by DESeq2.
item-131 at level 1: caption: Figure 2—figure supplement 1.: E ... r assay in Chr4-cl WT and KO ES cells.
item-132 at level 1: caption: Figure 3.: TE-dependent gene act ... Gm13051 are indicated by dashed lines.
item-133 at level 1: caption: Figure 4.: ETn retrotranspositio ... A for ETn and MuLV (RLTR4) insertions.
item-134 at level 1: caption: Figure 4—figure supplement 1.: B ... in at least two biological replicates.
item-135 at level 1: caption: Figure 4—figure supplement 2.: I ... color gradient indicates log10(RPM+1).
item-136 at level 1: caption: Figure 4—figure supplement 3.: C ... color gradient indicates log10(RPM+1).

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# KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage
Wolf Gernot; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States; de Iaco Alberto; 2: School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL): Lausanne: Switzerland; Sun Ming-An; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States; Bruno Melania; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States; Tinkham Matthew; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States; Hoang Don; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States; Mitra Apratim; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States; Ralls Sherry; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States; Trono Didier; 2: School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL): Lausanne: Switzerland; Macfarlan Todd S; 1: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health: Bethesda: United States
Gernot Wolf, Alberto de Iaco, Ming-An Sun, Melania Bruno, Matthew Tinkham, Don Hoang, Apratim Mitra, Sherry Ralls, Didier Trono, Todd S Macfarlan
The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, United States; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
## Abstract

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item-0 at level 0: unspecified: group _root_
item-1 at level 1: title: Risk factors associated with fai ... s: Results of a multi-country analysis
item-2 at level 2: paragraph: Burgert-Brucker Clara R.; 1: Glo ... shington, DC, United States of America
item-3 at level 2: section_header: Abstract
item-4 at level 3: text: Achieving elimination of lymphat ... ine prevalence and/or lower elevation.
item-5 at level 2: section_header: Introduction
item-6 at level 3: text: Lymphatic filariasis (LF), a dis ... 8 countries remain endemic for LF [3].
item-7 at level 3: text: The road to elimination as a pub ... t elimination be officially validated.
item-8 at level 3: text: Pre-TAS include at least one sen ... me of day that blood can be taken [5].
item-9 at level 3: text: When a country fails to meet the ... o ensure rounds of MDA are not missed.
item-10 at level 3: text: This study aims to understand wh ... e of limited LF elimination resources.
item-11 at level 2: section_header: Methods
item-12 at level 3: text: This is a secondary data analysi ... rch; no ethical approval was required.
item-13 at level 3: text: Building on previous work, we de ... available global geospatial data sets.
item-14 at level 3: section_header: Data sources
item-15 at level 4: text: Information on baseline prevalen ... publicly available sources (Table 1).
item-16 at level 3: section_header: Outcome and covariate variables
item-17 at level 4: text: The outcome of interest for this ... r than or equal to 1% Mf or 2% Ag [4].
item-18 at level 4: text: Potential covariates were derive ... is and the final categorizations used.
item-19 at level 4: section_header: Baseline prevalence
item-20 at level 5: text: Baseline prevalence can be assum ... (2) using the cut-off of <10% or ≥10%.
item-21 at level 4: section_header: Agent
item-22 at level 5: text: In terms of differences in trans ... dazole (DEC-ALB)] from the MDA domain.
item-23 at level 4: section_header: Environment
item-24 at level 5: text: LF transmission intensity is inf ... dicates a higher level of “greenness.”
item-25 at level 5: text: We included the socio-economic v ... proxy for socio-economic status [33].
item-26 at level 5: text: Finally, all or parts of distric ... s were co-endemic with onchocerciasis.
item-27 at level 4: section_header: MDA
item-28 at level 5: text: Treatment effectiveness depends ... esent a threat to elimination [41,42].
item-29 at level 5: text: We considered three approaches w ... unds ever documented in that district.
item-30 at level 4: section_header: Pre-TAS implementation
item-31 at level 5: text: Pre-TAS results can be influence ... d throughout the time period of study.
item-32 at level 3: section_header: Data inclusion criteria
item-33 at level 4: text: The dataset, summarized at the d ... al analysis dataset had 554 districts.
item-34 at level 3: section_header: Statistical analysis and modeling
item-35 at level 4: text: Statistical analysis and modelin ... d the number of variables accordingly.
item-36 at level 4: text: Sensitivity analysis was perform ... ot have been truly LF-endemic [43,44].
item-37 at level 2: section_header: Results
item-38 at level 3: text: The overall pre-TAS pass rate fo ... ts had baseline prevalences below 20%.
item-39 at level 3: text: Fig 3 shows the unadjusted analy ... overage, and sufficient rounds of MDA.
item-40 at level 3: text: The final log-binomial model inc ... igh baseline and diagnostic test used.
item-41 at level 3: text: Fig 4 shows the risk ratio resul ... of failing pre-TAS (95% CI 1.95–4.83).
item-42 at level 3: text: Sensitivity analyses were conduc ... gnified by large confidence intervals.
item-43 at level 3: text: Overall 74 districts in the data ... or 51% of all the failures (38 of 74).
item-44 at level 2: section_header: Discussion
item-45 at level 3: text: This paper reports for the first ... ctors associated with TAS failure [7].
item-46 at level 3: text: Though diagnostic test used was ... FTS was more sensitive than ICT [45].
item-47 at level 3: text: Elevation was the only environme ... ich impact vector chances of survival.
item-48 at level 3: text: The small number of failures ove ... search has shown the opposite [15,16].
item-49 at level 3: text: All other variables included in ... are not necessary to lower prevalence.
item-50 at level 3: text: Limitations to this study includ ... reducing LF prevalence [41,48,51–53].
item-51 at level 3: text: Fourteen districts were excluded ... ta to extreme outliners in a district.
item-52 at level 3: text: As this analysis used data acros ... of individuals included in the survey.
item-53 at level 3: text: This paper provides evidence fro ... th high baseline and/or low elevation.
item-54 at level 2: section_header: Tables
item-55 at level 3: table with [18x8]
item-55 at level 4: caption: Table 1: Categorization of potential factors influencing pre-TAS results.
item-56 at level 3: table with [11x6]
item-56 at level 4: caption: Table 2: Adjusted risk ratios for pre-TAS failure from log-binomial model sensitivity analysis.
item-57 at level 2: section_header: Figures
item-58 at level 3: picture
item-58 at level 4: caption: Fig 1: Number of pre-TAS by country.
item-2 at level 2: paragraph: Clara R. Burgert-Brucker, Kathry ... garet Baker, John Kraemer, Molly Brady
item-3 at level 2: paragraph: Global Health Division, RTI Inte ... shington, DC, United States of America
item-4 at level 2: section_header: Abstract
item-5 at level 3: text: Achieving elimination of lymphat ... ine prevalence and/or lower elevation.
item-6 at level 2: section_header: Introduction
item-7 at level 3: text: Lymphatic filariasis (LF), a dis ... 8 countries remain endemic for LF [3].
item-8 at level 3: text: The road to elimination as a pub ... t elimination be officially validated.
item-9 at level 3: text: Pre-TAS include at least one sen ... me of day that blood can be taken [5].
item-10 at level 3: text: When a country fails to meet the ... o ensure rounds of MDA are not missed.
item-11 at level 3: text: This study aims to understand wh ... e of limited LF elimination resources.
item-12 at level 2: section_header: Methods
item-13 at level 3: text: This is a secondary data analysi ... rch; no ethical approval was required.
item-14 at level 3: text: Building on previous work, we de ... available global geospatial data sets.
item-15 at level 3: section_header: Data sources
item-16 at level 4: text: Information on baseline prevalen ... publicly available sources (Table 1).
item-17 at level 3: section_header: Outcome and covariate variables
item-18 at level 4: text: The outcome of interest for this ... r than or equal to 1% Mf or 2% Ag [4].
item-19 at level 4: text: Potential covariates were derive ... is and the final categorizations used.
item-20 at level 4: section_header: Baseline prevalence
item-21 at level 5: text: Baseline prevalence can be assum ... (2) using the cut-off of <10% or ≥10%.
item-22 at level 4: section_header: Agent
item-23 at level 5: text: In terms of differences in trans ... dazole (DEC-ALB)] from the MDA domain.
item-24 at level 4: section_header: Environment
item-25 at level 5: text: LF transmission intensity is inf ... dicates a higher level of “greenness.”
item-26 at level 5: text: We included the socio-economic v ... proxy for socio-economic status [33].
item-27 at level 5: text: Finally, all or parts of distric ... s were co-endemic with onchocerciasis.
item-28 at level 4: section_header: MDA
item-29 at level 5: text: Treatment effectiveness depends ... esent a threat to elimination [41,42].
item-30 at level 5: text: We considered three approaches w ... unds ever documented in that district.
item-31 at level 4: section_header: Pre-TAS implementation
item-32 at level 5: text: Pre-TAS results can be influence ... d throughout the time period of study.
item-33 at level 3: section_header: Data inclusion criteria
item-34 at level 4: text: The dataset, summarized at the d ... al analysis dataset had 554 districts.
item-35 at level 3: section_header: Statistical analysis and modeling
item-36 at level 4: text: Statistical analysis and modelin ... d the number of variables accordingly.
item-37 at level 4: text: Sensitivity analysis was perform ... ot have been truly LF-endemic [43,44].
item-38 at level 2: section_header: Results
item-39 at level 3: text: The overall pre-TAS pass rate fo ... ts had baseline prevalences below 20%.
item-40 at level 3: text: Fig 3 shows the unadjusted analy ... overage, and sufficient rounds of MDA.
item-41 at level 3: text: The final log-binomial model inc ... igh baseline and diagnostic test used.
item-42 at level 3: text: Fig 4 shows the risk ratio resul ... of failing pre-TAS (95% CI 1.95–4.83).
item-43 at level 3: text: Sensitivity analyses were conduc ... gnified by large confidence intervals.
item-44 at level 3: text: Overall 74 districts in the data ... or 51% of all the failures (38 of 74).
item-45 at level 2: section_header: Discussion
item-46 at level 3: text: This paper reports for the first ... ctors associated with TAS failure [7].
item-47 at level 3: text: Though diagnostic test used was ... FTS was more sensitive than ICT [45].
item-48 at level 3: text: Elevation was the only environme ... ich impact vector chances of survival.
item-49 at level 3: text: The small number of failures ove ... search has shown the opposite [15,16].
item-50 at level 3: text: All other variables included in ... are not necessary to lower prevalence.
item-51 at level 3: text: Limitations to this study includ ... reducing LF prevalence [41,48,51–53].
item-52 at level 3: text: Fourteen districts were excluded ... ta to extreme outliners in a district.
item-53 at level 3: text: As this analysis used data acros ... of individuals included in the survey.
item-54 at level 3: text: This paper provides evidence fro ... th high baseline and/or low elevation.
item-55 at level 2: section_header: Tables
item-56 at level 3: table with [18x8]
item-56 at level 4: caption: Table 1: Categorization of potential factors influencing pre-TAS results.
item-57 at level 3: table with [11x6]
item-57 at level 4: caption: Table 2: Adjusted risk ratios for pre-TAS failure from log-binomial model sensitivity analysis.
item-58 at level 2: section_header: Figures
item-59 at level 3: picture
item-59 at level 4: caption: Fig 2: District-level baseline prevalence by country.
item-59 at level 4: caption: Fig 1: Number of pre-TAS by country.
item-60 at level 3: picture
item-60 at level 4: caption: Fig 3: Percent pre-TAS failure by each characteristic (unadjusted).
item-60 at level 4: caption: Fig 2: District-level baseline prevalence by country.
item-61 at level 3: picture
item-61 at level 4: caption: Fig 4: Adjusted risk ratios for pre-TAS failure with 95% Confidence Interval from log-binomial model.
item-61 at level 4: caption: Fig 3: Percent pre-TAS failure by each characteristic (unadjusted).
item-62 at level 3: picture
item-62 at level 4: caption: Fig 5: Analysis of failures by model combinations.
item-63 at level 2: section_header: References
item-64 at level 3: list: group list
item-65 at level 4: list_item: World Health Organization. Lymph ... rategic plan 2010–2020. Geneva; 2010.
item-66 at level 4: list_item: World Health Organization. Valid ... public health problem. Geneva; 2017.
item-67 at level 4: list_item: Global programme to eliminate ly ... eport, 2018. Wkly Epidemiol Rec (2019)
item-68 at level 4: list_item: World Health Organization. Globa ... ss drug administration. Geneva; 2011.
item-69 at level 4: list_item: World Health Organization. Stren ... isease-specific Indicators. 2016; 42.
item-70 at level 4: list_item: Kyelem D; Biswas G; Bockarie MJ; ... search needs. Am J Trop Med Hyg (2008)
item-71 at level 4: list_item: Goldberg EM; King JD; Mupfasoni ... c filariasis. Am J Trop Med Hyg (2019)
item-72 at level 4: list_item: Cano J; Rebollo MP; Golding N; P ... present. Parasites and Vectors (2014)
item-73 at level 4: list_item: CGIAR-CSI. CGIAR-CSI SRTM 90m DEM Digital Elevation Database. In: .
item-74 at level 4: list_item: USGS NASA. Vegetation indices 16 ... et]. [cited 1 May 2018]. Available: .
item-75 at level 4: list_item: Funk C; Peterson P; Landsfeld M; ... r monitoring extremes. Sci Data (2015)
item-76 at level 4: list_item: Lloyd CT; Sorichetta A; Tatem AJ ... in population studies. Sci Data (2017)
item-77 at level 4: list_item: Elvidge CD; Baugh KE; Zhizhin M; ... hts. Proc Asia-Pacific Adv Netw (2013)
item-78 at level 4: list_item: Jambulingam P; Subramanian S; De ... dicators. Parasites and Vectors (2016)
item-79 at level 4: list_item: Michael E; Malecela-Lazaro MN; S ... c filariasis. Lancet Infect Dis (2004)
item-80 at level 4: list_item: Stolk WA; Swaminathan S; van Oor ... simulation study. J Infect Dis (2003)
item-81 at level 4: list_item: Grady CA; De Rochars MB; Direny ... asis programs. Emerg Infect Dis (2007)
item-82 at level 4: list_item: Evans D; McFarland D; Adamani W; ... Nigeria. Ann Trop Med Parasitol (2011)
item-83 at level 4: list_item: Richards FO; Eigege A; Miri ES; ... in Nigeria. PLoS Negl Trop Dis (2011)
item-84 at level 4: list_item: Biritwum NK; Yikpotey P; Marfo B ... Ghana. Trans R Soc Trop Med Hyg (2016)
item-85 at level 4: list_item: Moraga P; Cano J; Baggaley RF; G ... odelling. Parasites and Vectors (2015)
item-86 at level 4: list_item: Irvine MA; Njenga SM; Gunawarden ... ction. Trans R Soc Trop Med Hyg (2016)
item-87 at level 4: list_item: Ottesen EA. Efficacy of diethylc ... ariae in humans. Rev Infect Dis (1985)
item-88 at level 4: list_item: Gambhir M; Bockarie M; Tisch D; ... lymphatic filariasis. BMC Biol (2010)
item-89 at level 4: list_item: World Health Organization. Globa ... al entomology handbook. Geneva; 2013.
item-90 at level 4: list_item: Slater H; Michael E. Predicting ... gical niche modelling. PLoS One (2012)
item-91 at level 4: list_item: Slater H; Michael E. Mapping, Ba ... prevalence in Africa. PLoS One (2013)
item-92 at level 4: list_item: Sabesan S; Raju KHK; Subramanian ... odel. Vector-Borne Zoonotic Dis (2013)
item-93 at level 4: list_item: Stanton MC; Molyneux DH; Kyelem ... in Burkina Faso. Geospat Health (2013)
item-94 at level 4: list_item: Manhenje I; Teresa Galán-Puchade ... hern Mozambique. Geospat Health (2013)
item-95 at level 4: list_item: Ngwira BM; Tambala P; Perez a M; ... infection in Malawi. Filaria J (2007)
item-96 at level 4: list_item: Simonsen PE; Mwakitalu ME. Urban ... hatic filariasis. Parasitol Res (2013)
item-97 at level 4: list_item: Proville J; Zavala-Araiza D; Wag ... socio-economic trends. PLoS One (2017)
item-98 at level 4: list_item: Endeshaw T; Taye A; Tadesse Z; K ... st Ethiopia. Pathog Glob Health (2015)
item-99 at level 4: list_item: Richards FO; Eigege A; Pam D; Ka ... eas of co-endemicity. Filaria J (2005)
item-100 at level 4: list_item: Kyelem D; Sanou S; Boatin B a; M ... cations. Ann Trop Med Parasitol (2003)
item-101 at level 4: list_item: Weil GJ; Lammie PJ; Richards FO; ... ne and ivermectin. J Infect Dis (1991)
item-102 at level 4: list_item: Kumar A; Sachan P. Measuring imp ... rug administration. Trop Biomed (2014)
item-103 at level 4: list_item: Njenga SM; Mwandawiro CS; Wamae ... control. Parasites and Vectors (2011)
item-104 at level 4: list_item: Boyd A; Won KY; McClintock SK; D ... gane, Haiti. PLoS Negl Trop Dis (2010)
item-105 at level 4: list_item: Irvine MA; Reimer LJ; Njenga SM; ... mination. Parasites and Vectors (2015)
item-106 at level 4: list_item: Irvine MA; Stolk WA; Smith ME; S ... elling study. Lancet Infect Dis (2017)
item-107 at level 4: list_item: Pion SD; Montavon C; Chesnais CB ... crofilaremia. Am J Trop Med Hyg (2016)
item-108 at level 4: list_item: Wanji S; Esum ME; Njouendou AJ; ... in Cameroon. PLoS Negl Trop Dis (2018)
item-109 at level 4: list_item: Chesnais CB; Awaca-Uvon NP; Bola ... a in Africa. PLoS Negl Trop Dis (2017)
item-110 at level 4: list_item: Silumbwe A; Zulu JM; Halwindi H; ... haran Africa. BMC Public Health (2017)
item-111 at level 4: list_item: Adams AM; Vuckovic M; Birch E; B ... nistration. Trop Med Infect Dis (2018)
item-112 at level 4: list_item: Rao RU; Samarasekera SD; Nagodav ... n Sri Lanka. PLoS Negl Trop Dis (2017)
item-113 at level 4: list_item: Xu Z; Graves PM; Lau CL; Clement ... is in American Samoa. Epidemics (2018)
item-114 at level 4: list_item: Id CM; Tettevi EJ; Mechan F; Idu ... rural Ghana. PLoS Negl Trop Dis (2019)
item-115 at level 4: list_item: Eigege A; Kal A; Miri E; Sallau ... in Nigeria. PLoS Negl Trop Dis (2013)
item-116 at level 4: list_item: Van den Berg H; Kelly-Hope LA; L ... r management. Lancet Infect Dis (2013)
item-117 at level 4: list_item: Webber R.. Eradication of Wucher ... ntrol. Trans R Soc Trop Med Hyg (1979)
item-118 at level 1: caption: Table 1: Categorization of potential factors influencing pre-TAS results.
item-119 at level 1: caption: Table 2: Adjusted risk ratios fo ... g-binomial model sensitivity analysis.
item-120 at level 1: caption: Fig 1: Number of pre-TAS by country.
item-121 at level 1: caption: Fig 2: District-level baseline prevalence by country.
item-122 at level 1: caption: Fig 3: Percent pre-TAS failure by each characteristic (unadjusted).
item-123 at level 1: caption: Fig 4: Adjusted risk ratios for ... ence Interval from log-binomial model.
item-124 at level 1: caption: Fig 5: Analysis of failures by model combinations.
item-62 at level 4: caption: Fig 4: Adjusted risk ratios for pre-TAS failure with 95% Confidence Interval from log-binomial model.
item-63 at level 3: picture
item-63 at level 4: caption: Fig 5: Analysis of failures by model combinations.
item-64 at level 2: section_header: References
item-65 at level 3: list: group list
item-66 at level 4: list_item: World Health Organization. Lymph ... rategic plan 2010–2020. Geneva; 2010.
item-67 at level 4: list_item: World Health Organization. Valid ... public health problem. Geneva; 2017.
item-68 at level 4: list_item: Global programme to eliminate ly ... eport, 2018. Wkly Epidemiol Rec (2019)
item-69 at level 4: list_item: World Health Organization. Globa ... ss drug administration. Geneva; 2011.
item-70 at level 4: list_item: World Health Organization. Stren ... isease-specific Indicators. 2016; 42.
item-71 at level 4: list_item: Kyelem D; Biswas G; Bockarie MJ; ... search needs. Am J Trop Med Hyg (2008)
item-72 at level 4: list_item: Goldberg EM; King JD; Mupfasoni ... c filariasis. Am J Trop Med Hyg (2019)
item-73 at level 4: list_item: Cano J; Rebollo MP; Golding N; P ... present. Parasites and Vectors (2014)
item-74 at level 4: list_item: CGIAR-CSI. CGIAR-CSI SRTM 90m DEM Digital Elevation Database. In: .
item-75 at level 4: list_item: USGS NASA. Vegetation indices 16 ... et]. [cited 1 May 2018]. Available: .
item-76 at level 4: list_item: Funk C; Peterson P; Landsfeld M; ... r monitoring extremes. Sci Data (2015)
item-77 at level 4: list_item: Lloyd CT; Sorichetta A; Tatem AJ ... in population studies. Sci Data (2017)
item-78 at level 4: list_item: Elvidge CD; Baugh KE; Zhizhin M; ... hts. Proc Asia-Pacific Adv Netw (2013)
item-79 at level 4: list_item: Jambulingam P; Subramanian S; De ... dicators. Parasites and Vectors (2016)
item-80 at level 4: list_item: Michael E; Malecela-Lazaro MN; S ... c filariasis. Lancet Infect Dis (2004)
item-81 at level 4: list_item: Stolk WA; Swaminathan S; van Oor ... simulation study. J Infect Dis (2003)
item-82 at level 4: list_item: Grady CA; De Rochars MB; Direny ... asis programs. Emerg Infect Dis (2007)
item-83 at level 4: list_item: Evans D; McFarland D; Adamani W; ... Nigeria. Ann Trop Med Parasitol (2011)
item-84 at level 4: list_item: Richards FO; Eigege A; Miri ES; ... in Nigeria. PLoS Negl Trop Dis (2011)
item-85 at level 4: list_item: Biritwum NK; Yikpotey P; Marfo B ... Ghana. Trans R Soc Trop Med Hyg (2016)
item-86 at level 4: list_item: Moraga P; Cano J; Baggaley RF; G ... odelling. Parasites and Vectors (2015)
item-87 at level 4: list_item: Irvine MA; Njenga SM; Gunawarden ... ction. Trans R Soc Trop Med Hyg (2016)
item-88 at level 4: list_item: Ottesen EA. Efficacy of diethylc ... ariae in humans. Rev Infect Dis (1985)
item-89 at level 4: list_item: Gambhir M; Bockarie M; Tisch D; ... lymphatic filariasis. BMC Biol (2010)
item-90 at level 4: list_item: World Health Organization. Globa ... al entomology handbook. Geneva; 2013.
item-91 at level 4: list_item: Slater H; Michael E. Predicting ... gical niche modelling. PLoS One (2012)
item-92 at level 4: list_item: Slater H; Michael E. Mapping, Ba ... prevalence in Africa. PLoS One (2013)
item-93 at level 4: list_item: Sabesan S; Raju KHK; Subramanian ... odel. Vector-Borne Zoonotic Dis (2013)
item-94 at level 4: list_item: Stanton MC; Molyneux DH; Kyelem ... in Burkina Faso. Geospat Health (2013)
item-95 at level 4: list_item: Manhenje I; Teresa Galán-Puchade ... hern Mozambique. Geospat Health (2013)
item-96 at level 4: list_item: Ngwira BM; Tambala P; Perez a M; ... infection in Malawi. Filaria J (2007)
item-97 at level 4: list_item: Simonsen PE; Mwakitalu ME. Urban ... hatic filariasis. Parasitol Res (2013)
item-98 at level 4: list_item: Proville J; Zavala-Araiza D; Wag ... socio-economic trends. PLoS One (2017)
item-99 at level 4: list_item: Endeshaw T; Taye A; Tadesse Z; K ... st Ethiopia. Pathog Glob Health (2015)
item-100 at level 4: list_item: Richards FO; Eigege A; Pam D; Ka ... eas of co-endemicity. Filaria J (2005)
item-101 at level 4: list_item: Kyelem D; Sanou S; Boatin B a; M ... cations. Ann Trop Med Parasitol (2003)
item-102 at level 4: list_item: Weil GJ; Lammie PJ; Richards FO; ... ne and ivermectin. J Infect Dis (1991)
item-103 at level 4: list_item: Kumar A; Sachan P. Measuring imp ... rug administration. Trop Biomed (2014)
item-104 at level 4: list_item: Njenga SM; Mwandawiro CS; Wamae ... control. Parasites and Vectors (2011)
item-105 at level 4: list_item: Boyd A; Won KY; McClintock SK; D ... gane, Haiti. PLoS Negl Trop Dis (2010)
item-106 at level 4: list_item: Irvine MA; Reimer LJ; Njenga SM; ... mination. Parasites and Vectors (2015)
item-107 at level 4: list_item: Irvine MA; Stolk WA; Smith ME; S ... elling study. Lancet Infect Dis (2017)
item-108 at level 4: list_item: Pion SD; Montavon C; Chesnais CB ... crofilaremia. Am J Trop Med Hyg (2016)
item-109 at level 4: list_item: Wanji S; Esum ME; Njouendou AJ; ... in Cameroon. PLoS Negl Trop Dis (2018)
item-110 at level 4: list_item: Chesnais CB; Awaca-Uvon NP; Bola ... a in Africa. PLoS Negl Trop Dis (2017)
item-111 at level 4: list_item: Silumbwe A; Zulu JM; Halwindi H; ... haran Africa. BMC Public Health (2017)
item-112 at level 4: list_item: Adams AM; Vuckovic M; Birch E; B ... nistration. Trop Med Infect Dis (2018)
item-113 at level 4: list_item: Rao RU; Samarasekera SD; Nagodav ... n Sri Lanka. PLoS Negl Trop Dis (2017)
item-114 at level 4: list_item: Xu Z; Graves PM; Lau CL; Clement ... is in American Samoa. Epidemics (2018)
item-115 at level 4: list_item: Id CM; Tettevi EJ; Mechan F; Idu ... rural Ghana. PLoS Negl Trop Dis (2019)
item-116 at level 4: list_item: Eigege A; Kal A; Miri E; Sallau ... in Nigeria. PLoS Negl Trop Dis (2013)
item-117 at level 4: list_item: Van den Berg H; Kelly-Hope LA; L ... r management. Lancet Infect Dis (2013)
item-118 at level 4: list_item: Webber R.. Eradication of Wucher ... ntrol. Trans R Soc Trop Med Hyg (1979)
item-119 at level 1: caption: Table 1: Categorization of potential factors influencing pre-TAS results.
item-120 at level 1: caption: Table 2: Adjusted risk ratios fo ... g-binomial model sensitivity analysis.
item-121 at level 1: caption: Fig 1: Number of pre-TAS by country.
item-122 at level 1: caption: Fig 2: District-level baseline prevalence by country.
item-123 at level 1: caption: Fig 3: Percent pre-TAS failure by each characteristic (unadjusted).
item-124 at level 1: caption: Fig 4: Adjusted risk ratios for ... ence Interval from log-binomial model.
item-125 at level 1: caption: Fig 5: Analysis of failures by model combinations.

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# Risk factors associated with failing pre-transmission assessment surveys (pre-TAS) in lymphatic filariasis elimination programs: Results of a multi-country analysis
Burgert-Brucker Clara R.; 1: Global Health Division, RTI International, Washington, DC, United States of America; Zoerhoff Kathryn L.; 1: Global Health Division, RTI International, Washington, DC, United States of America; Headland Maureen; 1: Global Health Division, RTI International, Washington, DC, United States of America, 2: Global Health, Population, and Nutrition, FHI 360, Washington, DC, United States of America; Shoemaker Erica A.; 1: Global Health Division, RTI International, Washington, DC, United States of America; Stelmach Rachel; 1: Global Health Division, RTI International, Washington, DC, United States of America; Karim Mohammad Jahirul; 3: Department of Disease Control, Ministry of Health and Family Welfare, Dhaka, Bangladesh; Batcho Wilfrid; 4: National Control Program of Communicable Diseases, Ministry of Health, Cotonou, Benin; Bougouma Clarisse; 5: Lymphatic Filariasis Elimination Program, Ministère de la Santé, Ouagadougou, Burkina Faso; Bougma Roland; 5: Lymphatic Filariasis Elimination Program, Ministère de la Santé, Ouagadougou, Burkina Faso; Benjamin Didier Biholong; 6: National Onchocerciasis and Lymphatic Filariasis Control Program, Ministry of Health, Yaounde, Cameroon; Georges Nko'Ayissi; 6: National Onchocerciasis and Lymphatic Filariasis Control Program, Ministry of Health, Yaounde, Cameroon; Marfo Benjamin; 7: Neglected Tropical Diseases Programme, Ghana Health Service, Accra, Ghana; Lemoine Jean Frantz; 8: Ministry of Health, Port-au-Prince, Haiti; Pangaribuan Helena Ullyartha; 9: National Institute Health Research &amp; Development, Ministry of Health, Jakarta, Indonesia; Wijayanti Eksi; 9: National Institute Health Research &amp; Development, Ministry of Health, Jakarta, Indonesia; Coulibaly Yaya Ibrahim; 10: Filariasis Unit, International Center of Excellence in Research, Faculty of Medicine and Odontostomatology, Bamako, Mali; Doumbia Salif Seriba; 10: Filariasis Unit, International Center of Excellence in Research, Faculty of Medicine and Odontostomatology, Bamako, Mali; Rimal Pradip; 11: Epidemiology and Disease Control Division, Department of Health Service, Kathmandu, Nepal; Salissou Adamou Bacthiri; 12: Programme Onchocercose et Filariose Lymphatique, Ministère de la Santé, Niamey, Niger; Bah Yukaba; 13: National Neglected Tropical Disease Program, Ministry of Health and Sanitation, Freetown, Sierra Leone; Mwingira Upendo; 14: Neglected Tropical Disease Control Programme, National Institute for Medical Research, Dar es Salaam, Tanzania; Nshala Andreas; 15: IMA World Health/Tanzania NTD Control Programme, Uppsala University, &amp; TIBA Fellow, Dar es Salaam, Tanzania; Muheki Edridah; 16: Programme to Eliminate Lymphatic Filariasis, Ministry of Health, Kampala, Uganda; Shott Joseph; 17: Division of Neglected Tropical Diseases, Office of Infectious Diseases, Bureau for Global Health, USAID, Washington, DC, United States of America; Yevstigneyeva Violetta; 17: Division of Neglected Tropical Diseases, Office of Infectious Diseases, Bureau for Global Health, USAID, Washington, DC, United States of America; Ndayishimye Egide; 2: Global Health, Population, and Nutrition, FHI 360, Washington, DC, United States of America; Baker Margaret; 1: Global Health Division, RTI International, Washington, DC, United States of America; Kraemer John; 1: Global Health Division, RTI International, Washington, DC, United States of America, 18: Georgetown University, Washington, DC, United States of America; Brady Molly; 1: Global Health Division, RTI International, Washington, DC, United States of America
Clara R. Burgert-Brucker, Kathryn L. Zoerhoff, Maureen Headland, Erica A. Shoemaker, Rachel Stelmach, Mohammad Jahirul Karim, Wilfrid Batcho, Clarisse Bougouma, Roland Bougma, Biholong Benjamin Didier, Nko'Ayissi Georges, Benjamin Marfo, Jean Frantz Lemoine, Helena Ullyartha Pangaribuan, Eksi Wijayanti, Yaya Ibrahim Coulibaly, Salif Seriba Doumbia, Pradip Rimal, Adamou Bacthiri Salissou, Yukaba Bah, Upendo Mwingira, Andreas Nshala, Edridah Muheki, Joseph Shott, Violetta Yevstigneyeva, Egide Ndayishimye, Margaret Baker, John Kraemer, Molly Brady
Global Health Division, RTI International, Washington, DC, United States of America; Global Health, Population, and Nutrition, FHI 360, Washington, DC, United States of America; Department of Disease Control, Ministry of Health and Family Welfare, Dhaka, Bangladesh; National Control Program of Communicable Diseases, Ministry of Health, Cotonou, Benin; Lymphatic Filariasis Elimination Program, Ministère de la Santé, Ouagadougou, Burkina Faso; National Onchocerciasis and Lymphatic Filariasis Control Program, Ministry of Health, Yaounde, Cameroon; Neglected Tropical Diseases Programme, Ghana Health Service, Accra, Ghana; Ministry of Health, Port-au-Prince, Haiti; National Institute Health Research &amp; Development, Ministry of Health, Jakarta, Indonesia; Filariasis Unit, International Center of Excellence in Research, Faculty of Medicine and Odontostomatology, Bamako, Mali; Epidemiology and Disease Control Division, Department of Health Service, Kathmandu, Nepal; Programme Onchocercose et Filariose Lymphatique, Ministère de la Santé, Niamey, Niger; National Neglected Tropical Disease Program, Ministry of Health and Sanitation, Freetown, Sierra Leone; Neglected Tropical Disease Control Programme, National Institute for Medical Research, Dar es Salaam, Tanzania; IMA World Health/Tanzania NTD Control Programme, Uppsala University, &amp; TIBA Fellow, Dar es Salaam, Tanzania; Programme to Eliminate Lymphatic Filariasis, Ministry of Health, Kampala, Uganda; Division of Neglected Tropical Diseases, Office of Infectious Diseases, Bureau for Global Health, USAID, Washington, DC, United States of America; Georgetown University, Washington, DC, United States of America
## Abstract

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item-0 at level 0: unspecified: group _root_
item-1 at level 1: title: Potential to reduce greenhouse g ... cattle systems in subtropical regions
item-2 at level 2: paragraph: Ribeiro-Filho Henrique M. N.; 1: ... , California, United States of America
item-3 at level 2: section_header: Abstract
item-4 at level 3: text: Carbon (C) footprint of dairy pr ... uce the C footprint to a small extent.
item-5 at level 2: section_header: Introduction
item-6 at level 3: text: Greenhouse gas (GHG) emissions f ... suitable for food crop production [4].
item-7 at level 3: text: Considering the key role of live ... anagement to mitigate the C footprint.
item-8 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]).
item-9 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake.
item-10 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated.
item-11 at level 2: section_header: Materials and methods
item-12 at level 3: text: An LCA was developed according t ... 90816 - https://www.udesc.br/cav/ceua.
item-13 at level 3: section_header: System boundary
item-14 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary.
item-15 at level 3: section_header: Functional unit
item-16 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows:
item-17 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1.
item-18 at level 3: section_header: Data sources and livestock system description
item-19 at level 4: text: The individual feed requirements ... ed to the ad libitum TMR intake group.
item-20 at level 4: text: Using experimental data, three s ... med during an entire lactation period.
item-21 at level 3: section_header: Impact assessment
item-22 at level 4: text: The CO2e emissions were calculat ... 65 for CO2, CH4 and N2O, respectively.
item-23 at level 3: section_header: Feed production
item-24 at level 4: section_header: Diets composition
item-25 at level 5: text: The DM intake of each ingredient ... collected throughout the experiments.
item-26 at level 4: section_header: GHG emissions from crop and pasture production
item-27 at level 5: text: GHG emission factors used for of ... onsume 70% of pastures during grazing.
item-28 at level 5: text: Emissions from on-farm feed prod ... factors described by Rotz et al. [42].
item-29 at level 3: section_header: Animal husbandry
item-30 at level 4: text: The CH4 emissions from enteric f ... 1) = 13.8 + 0.185 × NDF (% DM intake).
item-31 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals
item-32 at level 4: text: The CH4 emission from manure (kg ... for dietary GE per kg of DM (MJ kg-1).
item-33 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively.
item-34 at level 4: text: The N2O-N emissions from urine a ... using the IPCC [38] emission factors.
item-35 at level 3: section_header: Farm management
item-36 at level 4: text: Emissions due to farm management ... crop and pasture production’ section.
item-37 at level 4: text: The amount of fuel use for manur ... me that animals stayed on confinement.
item-38 at level 4: text: The emissions from fuel were est ... × kg CO2e (kg machinery mass)-1 [42].
item-39 at level 4: text: Emissions from electricity for m ... ws in naturally ventilated barns [47].
item-40 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint.
item-41 at level 4: text: Emissions from farm management d ... gas and hard coal, respectively [46].
item-42 at level 3: section_header: Co-product allocation
item-43 at level 4: text: The C footprint for milk produce ... directly assigned to milk production.
item-44 at level 3: section_header: Sensitivity analysis
item-45 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint.
item-46 at level 2: section_header: Results and discussion
item-47 at level 3: text: The study has assessed the impac ... , feed production and electricity use.
item-48 at level 3: section_header: Greenhouse gas emissions
item-49 at level 4: text: Depending on emission factors us ... more than 5% of overall GHG emissions.
item-50 at level 4: text: Considering IPCC emission factor ... the C footprint of the dairy systems.
item-51 at level 4: text: The similarity of C footprint be ... of TMR was replaced by pasture access.
item-52 at level 4: text: The lower C footprint in scenari ... r, averaging 0.004 kg N2O-N kg-1 [37].
item-53 at level 3: section_header: Methane emissions
item-54 at level 4: text: The enteric CH4 intensity was si ... ], which did not happen in this study.
item-55 at level 4: text: The lack of difference in enteri ... same scenarios as in this study [26].
item-56 at level 3: section_header: Emissions from excreta and feed production
item-57 at level 4: text: Using IPCC emission factors for ... may not be captured by microbes [65].
item-58 at level 4: text: Using local emission factors for ... be revised for the subtropical region.
item-59 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9].
item-60 at level 3: section_header: Assumptions and limitations
item-61 at level 4: text: The milk production and composit ... ions as a function of soil management.
item-62 at level 3: section_header: Further considerations
item-63 at level 4: text: The potential for using pasture ... g ECM)-1 in case of foot lesions [72].
item-64 at level 4: text: Grazing lands may also improve b ... hange of CO2 would be negligible [76].
item-65 at level 2: section_header: Conclusions
item-66 at level 3: text: This study assessed the C footpr ... on with or without access to pastures.
item-67 at level 2: section_header: Tables
item-68 at level 3: table with [13x3]
item-68 at level 4: caption: Table 1: Descriptive characteristics of the herd.
item-69 at level 3: table with [21x11]
item-69 at level 4: caption: Table 2: Dairy cows’ diets in different scenariosa.
item-70 at level 3: table with [9x5]
item-70 at level 4: caption: Table 3: GHG emission factors for Off- and On-farm feed production.
item-71 at level 3: table with [28x5]
item-71 at level 4: caption: Table 4: GHG emissions from On-farm feed production.
item-72 at level 3: table with [12x4]
item-72 at level 4: caption: Table 5: Factors for major resource inputs in farm management.
item-73 at level 2: section_header: Figures
item-74 at level 3: picture
item-74 at level 4: caption: Fig 1: Overview of the milk production system boundary considered in the study.
item-2 at level 2: paragraph: Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab
item-3 at level 2: paragraph: Department of Animal Science, Un ... atarina, Lages, Santa Catarina, Brazil
item-4 at level 2: section_header: Abstract
item-5 at level 3: text: Carbon (C) footprint of dairy pr ... uce the C footprint to a small extent.
item-6 at level 2: section_header: Introduction
item-7 at level 3: text: Greenhouse gas (GHG) emissions f ... suitable for food crop production [4].
item-8 at level 3: text: Considering the key role of live ... anagement to mitigate the C footprint.
item-9 at level 3: text: In subtropical climate zones, co ... t in tropical pastures (e.g. [17–19]).
item-10 at level 3: text: It has been shown that dairy cow ... sions from crop and reduced DM intake.
item-11 at level 3: text: The aim of this work was to quan ... uring lactation periods was evaluated.
item-12 at level 2: section_header: Materials and methods
item-13 at level 3: text: An LCA was developed according t ... 90816 - https://www.udesc.br/cav/ceua.
item-14 at level 3: section_header: System boundary
item-15 at level 4: text: The goal of the study was to ass ... n were outside of the system boundary.
item-16 at level 3: section_header: Functional unit
item-17 at level 4: text: The functional unit was one kilo ... tein according to NRC [20] as follows:
item-18 at level 4: text: ECM = Milk production × (0.0929 ... characteristics described in Table 1.
item-19 at level 3: section_header: Data sources and livestock system description
item-20 at level 4: text: The individual feed requirements ... ed to the ad libitum TMR intake group.
item-21 at level 4: text: Using experimental data, three s ... med during an entire lactation period.
item-22 at level 3: section_header: Impact assessment
item-23 at level 4: text: The CO2e emissions were calculat ... 65 for CO2, CH4 and N2O, respectively.
item-24 at level 3: section_header: Feed production
item-25 at level 4: section_header: Diets composition
item-26 at level 5: text: The DM intake of each ingredient ... collected throughout the experiments.
item-27 at level 4: section_header: GHG emissions from crop and pasture production
item-28 at level 5: text: GHG emission factors used for of ... onsume 70% of pastures during grazing.
item-29 at level 5: text: Emissions from on-farm feed prod ... factors described by Rotz et al. [42].
item-30 at level 3: section_header: Animal husbandry
item-31 at level 4: text: The CH4 emissions from enteric f ... 1) = 13.8 + 0.185 × NDF (% DM intake).
item-32 at level 3: section_header: Manure from confined cows and urine and dung from grazing animals
item-33 at level 4: text: The CH4 emission from manure (kg ... for dietary GE per kg of DM (MJ kg-1).
item-34 at level 4: text: The OM digestibility was estimat ... h were 31%, 26% and 46%, respectively.
item-35 at level 4: text: The N2O-N emissions from urine a ... using the IPCC [38] emission factors.
item-36 at level 3: section_header: Farm management
item-37 at level 4: text: Emissions due to farm management ... crop and pasture production’ section.
item-38 at level 4: text: The amount of fuel use for manur ... me that animals stayed on confinement.
item-39 at level 4: text: The emissions from fuel were est ... × kg CO2e (kg machinery mass)-1 [42].
item-40 at level 4: text: Emissions from electricity for m ... ws in naturally ventilated barns [47].
item-41 at level 4: text: The lower impact of emissions fr ... greater than 5% of total C footprint.
item-42 at level 4: text: Emissions from farm management d ... gas and hard coal, respectively [46].
item-43 at level 3: section_header: Co-product allocation
item-44 at level 4: text: The C footprint for milk produce ... directly assigned to milk production.
item-45 at level 3: section_header: Sensitivity analysis
item-46 at level 4: text: A sensitivity index was calculat ... ses a similar change in the footprint.
item-47 at level 2: section_header: Results and discussion
item-48 at level 3: text: The study has assessed the impac ... , feed production and electricity use.
item-49 at level 3: section_header: Greenhouse gas emissions
item-50 at level 4: text: Depending on emission factors us ... more than 5% of overall GHG emissions.
item-51 at level 4: text: Considering IPCC emission factor ... the C footprint of the dairy systems.
item-52 at level 4: text: The similarity of C footprint be ... of TMR was replaced by pasture access.
item-53 at level 4: text: The lower C footprint in scenari ... r, averaging 0.004 kg N2O-N kg-1 [37].
item-54 at level 3: section_header: Methane emissions
item-55 at level 4: text: The enteric CH4 intensity was si ... ], which did not happen in this study.
item-56 at level 4: text: The lack of difference in enteri ... same scenarios as in this study [26].
item-57 at level 3: section_header: Emissions from excreta and feed production
item-58 at level 4: text: Using IPCC emission factors for ... may not be captured by microbes [65].
item-59 at level 4: text: Using local emission factors for ... be revised for the subtropical region.
item-60 at level 4: text: Emissions for feed production de ... act, particularly in confinements [9].
item-61 at level 3: section_header: Assumptions and limitations
item-62 at level 4: text: The milk production and composit ... ions as a function of soil management.
item-63 at level 3: section_header: Further considerations
item-64 at level 4: text: The potential for using pasture ... g ECM)-1 in case of foot lesions [72].
item-65 at level 4: text: Grazing lands may also improve b ... hange of CO2 would be negligible [76].
item-66 at level 2: section_header: Conclusions
item-67 at level 3: text: This study assessed the C footpr ... on with or without access to pastures.
item-68 at level 2: section_header: Tables
item-69 at level 3: table with [13x3]
item-69 at level 4: caption: Table 1: Descriptive characteristics of the herd.
item-70 at level 3: table with [21x11]
item-70 at level 4: caption: Table 2: Dairy cows’ diets in different scenariosa.
item-71 at level 3: table with [9x5]
item-71 at level 4: caption: Table 3: GHG emission factors for Off- and On-farm feed production.
item-72 at level 3: table with [28x5]
item-72 at level 4: caption: Table 4: GHG emissions from On-farm feed production.
item-73 at level 3: table with [12x4]
item-73 at level 4: caption: Table 5: Factors for major resource inputs in farm management.
item-74 at level 2: section_header: Figures
item-75 at level 3: picture
item-75 at level 4: 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-75 at level 4: caption: Fig 1: Overview of the milk production system boundary considered in the study.
item-76 at level 3: picture
item-76 at level 4: 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-76 at level 4: 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-77 at level 3: picture
item-77 at level 4: caption: Fig 4: Greenhouse gas emissions (GHG) from manure and feed production in dairy cattle systems.
item-77 at level 4: 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-78 at level 3: picture
item-78 at level 4: 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.
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item-156 at level 1: caption: Table 1: Descriptive characteristics of the herd.
item-157 at level 1: caption: Table 2: Dairy cows’ diets in different scenariosa.
item-158 at level 1: caption: Table 3: GHG emission factors for Off- and On-farm feed production.
item-159 at level 1: caption: Table 4: GHG emissions from On-farm feed production.
item-160 at level 1: caption: Table 5: Factors for major resource inputs in farm management.
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item-79 at level 2: section_header: References
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item-157 at level 1: caption: Table 1: Descriptive characteristics of the herd.
item-158 at level 1: caption: Table 2: Dairy cows’ diets in different scenariosa.
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item-165 at level 1: caption: Fig 4: Greenhouse gas emissions ... uestered CO2-C from perennial pasture.

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# Potential to reduce greenhouse gas emissions through different dairy cattle systems in subtropical regions
Ribeiro-Filho Henrique M. N.; 1: Department of Animal Science, University of California, Davis, California, United States of America, 2: Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil; Civiero Maurício; 2: Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil; Kebreab Ermias; 1: Department of Animal Science, University of California, Davis, California, United States of America
Henrique M. N. Ribeiro-Filho, Maurício Civiero, Ermias Kebreab
Department of Animal Science, University of California, Davis, California, United States of America; Programa de Pós-graduação em Ciência Animal, Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brazil
## Abstract