cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.f6zbgm
title: Occurrence Download

description: A dataset containing 152077 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen)",
 "DatasetKey is one of (EOD – eBird Observation Dataset, Atlas de las Aves de México: Fase II, Bell Museum birds, iNaturalist Research-grade Observations, Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (vertebrados), Delaware Museum of Nature & Science — Birds, CUMV Bird Collection, UAM Bird Collection (Arctos), MLZ Bird Collection (Arctos), Sistematización de las colecciones científicas del Instituto de Historia Natural y Ecología, (IHNE) Chiapas)",
 "Geometry POLYGON((-95.20577 18.67792,-95.26176 18.47401,-95.05254 18.44047,-95.00245 18.39014,-94.86689 18.25027,-94.71366 18.35379,-94.82859 18.51034,-94.98771 18.54946,-95.0938 18.62487,-95.20577 18.67792))",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EX, EW, CR, EN, VU, NT, LC, DD, NE)",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (e2e717bf-551a-4917-bdc9-4fa0f342c530, ff90b050-c256-11db-b71b-b8a03c50a862, 927f1e70-cf74-11d8-bf68-b8a03c50a862, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, a42867f0-813a-11dc-82e0-b8a03c50a862, cf9ceb80-9f3d-11da-b791-b8a03c50a862, d9699a79-4736-45c2-925c-f4033ac67d52, 247b85e0-4e6b-46d1-b1c8-47b00bb8ced7)",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 152077 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019798-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3838951_d1
title: Additional file 1: of Shoaling promotes place over response learning but does not facilitate individual learning of that strategy in zebrafish (Danio rerio)

description: File format: xlsx. Raw data file. This file contains the raw data that was used in the analysis of this paper. (XLSX 219Â kb)
DOI: 10.6084/m9.figshare.5258410.v2
title: Additional file 1 of Shoaling promotes place over response learning but does not facilitate individual learning of that strategy in zebrafish (Danio rerio)

description: File format: xlsx. Raw data file. This file contains the raw data that was used in the analysis of this paper. (XLSX 219 kb)
DOI: 10.6084/m9.figshare.c.3838951_d1.v1
title: Additional file 1: of Shoaling promotes place over response learning but does not facilitate individual learning of that strategy in zebrafish (Danio rerio)

description: File format: xlsx. Raw data file. This file contains the raw data that was used in the analysis of this paper. (XLSX 219Â kb)
DOI: 10.6084/m9.figshare.4689571.v2
title: Additional file 2 of Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

description: Details of software, versions and parameters used in analysis. (TSV 5 kb)
DOI: 10.6084/m9.figshare.c.3701998_d1
title: Additional file 2: of 
                     Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

description: Details of software, versions and parameters used in analysis. (TSV 5 kb)
DOI: 10.6084/m9.figshare.c.3701998_d1.v1
title: Additional file 2: of 
                     Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

description: Details of software, versions and parameters used in analysis. (TSV 5 kb)
DOI: 10.6084/m9.figshare.c.3701998_d3
title: Additional file 3: of 
                     Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

description: Accessions and links to genome-derived protein sequence data used in phylogenetic analysis. (TSV 4 kb)
DOI: 10.6084/m9.figshare.4689607.v2
title: Additional file 3 of Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

description: Accessions and links to genome-derived protein sequence data used in phylogenetic analysis. (TSV 4 kb)
DOI: 10.6084/m9.figshare.28637021
title: Additional file 2 of Analyzing the use of specialized palliative care in intensive care unit patients in Germany: a cross-sectional study

description: Supplementary Material 2: Supplemental Table 2. Hospital. The table presents a breakdown of the number of case treatments categorized by the ownership and bed capacity of the treating hospitals.
DOI: 10.6084/m9.figshare.28637021.v1
title: Additional file 2 of Analyzing the use of specialized palliative care in intensive care unit patients in Germany: a cross-sectional study

description: Supplementary Material 2: Supplemental Table 2. Hospital. The table presents a breakdown of the number of case treatments categorized by the ownership and bed capacity of the treating hospitals.
DOI: 10.6084/m9.figshare.c.3701998_d3.v1
title: Additional file 3: of 
                     Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

description: Accessions and links to genome-derived protein sequence data used in phylogenetic analysis. (TSV 4 kb)
DOI: 10.6084/m9.figshare.5327143.v2
title: Additional file 1 of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: Title of data: Cytochrome b GenBank information. Taxa names and accession numbers for cytochrome b genes downloaded from GenBank in Additional file 3: Figure S1. (XLS 28 kb)
DOI: 10.6084/m9.figshare.5327173.v2
title: Additional file 2 of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: Whole mitochondrial exomes. Description: Alignment of the protein coding genes of each assembled mitogenome along with Akodon montensis, downloaded from GenBank. (TXT 257 kb)
DOI: 10.6084/m9.figshare.c.3857911_d1
title: Additional file 1: Table S1. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: Title of data: Cytochrome b GenBank information. Taxa names and accession numbers for cytochrome b genes downloaded from GenBank in Additional file 3: Figure S1. (XLS 28 kb)
DOI: 10.6084/m9.figshare.c.3857911_d1.v1
title: Additional file 1: Table S1. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: Title of data: Cytochrome b GenBank information. Taxa names and accession numbers for cytochrome b genes downloaded from GenBank in Additional file 3: Figure S1. (XLS 28 kb)
DOI: 10.6084/m9.figshare.c.3857911_d2
title: Additional file 2: of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: Whole mitochondrial exomes. Description: Alignment of the protein coding genes of each assembled mitogenome along with Akodon montensis, downloaded from GenBank. (TXT 257 kb)
DOI: 10.6084/m9.figshare.c.3857911_d2.v1
title: Additional file 2: of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: Whole mitochondrial exomes. Description: Alignment of the protein coding genes of each assembled mitogenome along with Akodon montensis, downloaded from GenBank. (TXT 257 kb)
DOI: 10.6084/m9.figshare.c.3857911_d4
title: Additional file 4: Table S2. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: v2. Cytochrome b blast validation. Best hits to GenBank entries for cytochrome b genes from assembled mitochondrial genomes. For N. mexicana, the best hit was to a closely related species, with the second best hit to N. mexicana. (XLS 38 kb)
DOI: 10.6084/m9.figshare.5327203.v2
title: Additional file 4 of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: v2. Cytochrome b blast validation. Best hits to GenBank entries for cytochrome b genes from assembled mitochondrial genomes. For N. mexicana, the best hit was to a closely related species, with the second best hit to N. mexicana. (XLS 38 kb)
DOI: 10.6084/m9.figshare.c.3857911_d4.v1
title: Additional file 4: Table S2. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice

description: v2. Cytochrome b blast validation. Best hits to GenBank entries for cytochrome b genes from assembled mitochondrial genomes. For N. mexicana, the best hit was to a closely related species, with the second best hit to N. mexicana. (XLS 38 kb)
DOI: 10.6084/m9.figshare.28637036
title: Additional file 2 of A reciprocal relationship between markers of genomic DNA damage and alpha-synuclein pathology in dementia with Lewy bodies

description: Supplementary Material 2. Supplementary table 2. Proteomic detection list and abundance analysis. Proteins identified as per the UniProt database and subsequently confirmed to be present with &gt;2 unique peptides as well as being detected in &gt;70% of samples are listed. For each protein, Entrez gene ID, gene name, individual Z-scores within batches (B1-3) for each sample are provided as well as pooled difference (DLB-Con), -Log(p-value) and significance (FDR&lt;0.1). + = significant. Supplementary table 3. DAVID UniProt Keywords. Significantly enriched clusters from DAVID uniport keywords analysis. Enrichment database category, Keyword number, Keyword term, number of proteins present in upregulated list (count), % coverage of enrichment term, p value, associated genes and protein names are provided. Additionally detected term associated proteins within the background reference list (List Total), total proteins associated with the term (Pop Total), the fold enrichment, FDR adjustment and-Log10FDR values are provided. Supplementary table 4. DAVID GO Terms. Significantly enriched clusters from David GO terms analysis. Enrichment database category, Go number, term name, number of proteins present in upregulated list (count), % coverage of enrichment term, p value, associated genes and protein names are provided. Additionally detected term associated proteins within the background reference list (List Total), total proteins associated with the term (Pop Total), the fold enrichment, FDR adjustment and -Log10FDR values are provided. Supplementary table 5. STRING database GO term analysis of Cellular response to DNA damaging stimulus. All GO terms mapped to those proteins significantly upregulated which are associated with cellular response to DNA damaging stimulus. term ID, description, those upregulated proteins associated with the term (observed gene count), those present in the background list (Background gene count), strength of enrichment, FDR and matching protein ID and names are provided. Supplementary table 6. STRING database identified proteins and their associated DNA damage repair function. Identified proteins are listed with Gene symbol, Entrez gene ID, Gene names, an indication of their involvement in DNA damage repair pathways, a suggested DDR function and supportive citations. For DDR pathways, base-excision repair (BER), Double strand break repair (DSB), Non-homologous end joining (NHEJ) and homologous recombination (HR) as well as general role in repair is provided.
DOI: 10.6084/m9.figshare.28637036.v1
title: Additional file 2 of A reciprocal relationship between markers of genomic DNA damage and alpha-synuclein pathology in dementia with Lewy bodies

description: Supplementary Material 2. Supplementary table 2. Proteomic detection list and abundance analysis. Proteins identified as per the UniProt database and subsequently confirmed to be present with &gt;2 unique peptides as well as being detected in &gt;70% of samples are listed. For each protein, Entrez gene ID, gene name, individual Z-scores within batches (B1-3) for each sample are provided as well as pooled difference (DLB-Con), -Log(p-value) and significance (FDR&lt;0.1). + = significant. Supplementary table 3. DAVID UniProt Keywords. Significantly enriched clusters from DAVID uniport keywords analysis. Enrichment database category, Keyword number, Keyword term, number of proteins present in upregulated list (count), % coverage of enrichment term, p value, associated genes and protein names are provided. Additionally detected term associated proteins within the background reference list (List Total), total proteins associated with the term (Pop Total), the fold enrichment, FDR adjustment and-Log10FDR values are provided. Supplementary table 4. DAVID GO Terms. Significantly enriched clusters from David GO terms analysis. Enrichment database category, Go number, term name, number of proteins present in upregulated list (count), % coverage of enrichment term, p value, associated genes and protein names are provided. Additionally detected term associated proteins within the background reference list (List Total), total proteins associated with the term (Pop Total), the fold enrichment, FDR adjustment and -Log10FDR values are provided. Supplementary table 5. STRING database GO term analysis of Cellular response to DNA damaging stimulus. All GO terms mapped to those proteins significantly upregulated which are associated with cellular response to DNA damaging stimulus. term ID, description, those upregulated proteins associated with the term (observed gene count), those present in the background list (Background gene count), strength of enrichment, FDR and matching protein ID and names are provided. Supplementary table 6. STRING database identified proteins and their associated DNA damage repair function. Identified proteins are listed with Gene symbol, Entrez gene ID, Gene names, an indication of their involvement in DNA damage repair pathways, a suggested DDR function and supportive citations. For DDR pathways, base-excision repair (BER), Double strand break repair (DSB), Non-homologous end joining (NHEJ) and homologous recombination (HR) as well as general role in repair is provided.
DOI: 10.6084/m9.figshare.c.3887428_d1
title: Additional file 1: of Effects of agrochemicals on disease severity of Acanthostomum burminis infections (Digenea: Trematoda) in the Asian common toad, Duttaphrynus melanostictus

description: Raw data and R statistics. Brief description of the data- This Excel file provides survival, growth and malformation data of tadpoles belonging to four different clutches (four trials), used in the study. Stat section provides R statistics of the analyses; General linear model, post-hoc analysis, and goodness of fit analyses. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.5435434.v2
title: Additional file 1 of Effects of agrochemicals on disease severity of Acanthostomum burminis infections (Digenea: Trematoda) in the Asian common toad, Duttaphrynus melanostictus

description: Raw data and R statistics. Brief description of the data- This Excel file provides survival, growth and malformation data of tadpoles belonging to four different clutches (four trials), used in the study. Stat section provides R statistics of the analyses; General linear model, post-hoc analysis, and goodness of fit analyses. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.c.3887428_d1.v1
title: Additional file 1: of Effects of agrochemicals on disease severity of Acanthostomum burminis infections (Digenea: Trematoda) in the Asian common toad, Duttaphrynus melanostictus

description: Raw data and R statistics. Brief description of the data- This Excel file provides survival, growth and malformation data of tadpoles belonging to four different clutches (four trials), used in the study. Stat section provides R statistics of the analyses; General linear model, post-hoc analysis, and goodness of fit analyses. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.28637099
title: Additional file 2 of Which carbon footprint for my ICU? Benchmark, hot spots and perspectives

description: Supplementary material 2.
DOI: 10.6084/m9.figshare.28637099.v1
title: Additional file 2 of Which carbon footprint for my ICU? Benchmark, hot spots and perspectives

description: Supplementary material 2.
DOI: 10.6084/m9.figshare.28637114
title: Additional file 1 of CTCF-anchored chromatin loop dynamics during human meiosis

description: Additional file 1: Table S1 Confidence of loop predictions using ChIA-PET as a control. Table S2 GO enrichments in eight germline cell types. Table S3 Functional GO enrichments at ssDNA sites that do not progress as recombination hotspots (ssDNA + /rec_HS − compared to ssDNA + /rec_HS +).
DOI: 10.6084/m9.figshare.28637114.v1
title: Additional file 1 of CTCF-anchored chromatin loop dynamics during human meiosis

description: Additional file 1: Table S1 Confidence of loop predictions using ChIA-PET as a control. Table S2 GO enrichments in eight germline cell types. Table S3 Functional GO enrichments at ssDNA sites that do not progress as recombination hotspots (ssDNA + /rec_HS − compared to ssDNA + /rec_HS +).
DOI: 10.6084/m9.figshare.28637120
title: Additional file 3 of CTCF-anchored chromatin loop dynamics during human meiosis

description: Additional file 3: Genomic coordinates (hg19) of predicted chromatin loops in the eight germline cell types.
DOI: 10.6084/m9.figshare.28637120.v1
title: Additional file 3 of CTCF-anchored chromatin loop dynamics during human meiosis

description: Additional file 3: Genomic coordinates (hg19) of predicted chromatin loops in the eight germline cell types.
DOI: 10.6084/m9.figshare.28637123
title: Additional file 4 of CTCF-anchored chromatin loop dynamics during human meiosis

description: Additional file 4: Table S4 Datasets used in this study.
DOI: 10.6084/m9.figshare.28637123.v1
title: Additional file 4 of CTCF-anchored chromatin loop dynamics during human meiosis

description: Additional file 4: Table S4 Datasets used in this study.
DOI: 10.6084/m9.figshare.28637145
title: Additional file 3 of Rediscovering a forgotten canid species

description: Metric data. Contains all the morphometric measurements taken for the study. (XLS 127 kb)
DOI: 10.6084/m9.figshare.28637145.v1
title: Additional file 3 of Rediscovering a forgotten canid species

description: Metric data. Contains all the morphometric measurements taken for the study. (XLS 127 kb)
DOI: 10.6084/m9.figshare.28637180
title: Additional file 1 of Genome-wide analysis of CHYR gene family and BnA03.CHYR.1 functional verification under salt stress in Brassica napus L.

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.28637180.v1
title: Additional file 1 of Genome-wide analysis of CHYR gene family and BnA03.CHYR.1 functional verification under salt stress in Brassica napus L.

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.28637211
title: Additional file 1 of Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

description: Supplementary Material 1. Figure S1. Similarities between the genomes of Tunturi 1-5 viruses and UViGs retrieved from the IMG/VR database. UViGs IDs are labeled skipping the “IMGVR_UViG_” prefix, for more information about UViGs, see Table S4. Ribbons are colored by % identity (see the key). Minimum and maximum % identities: (A) 64.71 and 100.00, (B) 64.96 and 100.00, (C) 65.11 and 95.83, (D) 64.79 and 90.32, (E) 64.69 and 79.45. Orientation is clockwise for all sequences. Figure S2. Distribution of the Tunturi 1-5 isolates across the 22 Kilpisjärvi meadow and fen metagenomes shown as (A) the percentage of reads mapped to their CDSs and (B) the percentage of detected CDSs per virus. Figure S3. Relative abundance of different taxonomic groups assigned to Kilpisjärvi vOTUs. Figure S4. PCoA of (A) Kilpisjärvi vOTUs (n=1881) and (B) Acidobacteriota-associated vOTUs (n=125) in 22 Kilpisjärvi meadow and fen metagenomes. Convex hulls show actual spread of points. The minimum 50% horizontal coverage was applied. The R2 and p-values were obtained separately for each variable. Figure S5. High-quality (96-100% complete) vOTUs assigned to Acidobacteriota. (A) Genomes with ORFs shown as arrows and colored according to the functional categories (see the color key). (B) Distribution of ORFs according to the functional categories, same color key as in (A). Figure S6. Putative acidobacterial proviruses identified in this study and related vOTUs reported in Emerson et al. 2018 (PMID: 30013236), Candidatus Koribacter versatilis provirus reported in Eichorst et al. 2018 (PMID: 29327410), and NCBI references. ORFs are shown as arrows and similarities between genomes (BLASTn) are in shades of gray (direct) or purple (invert). RC, reverse complement. Figure S7. VConTACT2 viral cluster comprising the isolate Tunturi 3, o12215_NODE_6138 (this study) and three vOTUs reported in Emerson et al. 2018 (PMID: 30013236). Similarities between the genomes (BLASTn) are shown with the shades of gray (direct) or purple (invert). Table S1. Soil samples used in this study. Table S2. Acidobacteriota strains used in this study. Table S3. Tunturi 1-5 genome annotations. Table S4. UViGs (scaffolds) retrieved from the IMG/VR database for Tunturi 1-5 viruses. Table S5. Metagenome quality statistics. Table S6. vOTUs detected in Kilpisjärvi fen and meadow metagenomes. Table S7. Genome annotations for high-quality vOTUs linked to Acidobacteriota. Table S8. AMGs found in Kilpisjärvi vOTUs using DRAM-v. Table S9. Virus clusters identified by the VConTACT2 analysis.
DOI: 10.6084/m9.figshare.28637211.v1
title: Additional file 1 of Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

description: Supplementary Material 1. Figure S1. Similarities between the genomes of Tunturi 1-5 viruses and UViGs retrieved from the IMG/VR database. UViGs IDs are labeled skipping the “IMGVR_UViG_” prefix, for more information about UViGs, see Table S4. Ribbons are colored by % identity (see the key). Minimum and maximum % identities: (A) 64.71 and 100.00, (B) 64.96 and 100.00, (C) 65.11 and 95.83, (D) 64.79 and 90.32, (E) 64.69 and 79.45. Orientation is clockwise for all sequences. Figure S2. Distribution of the Tunturi 1-5 isolates across the 22 Kilpisjärvi meadow and fen metagenomes shown as (A) the percentage of reads mapped to their CDSs and (B) the percentage of detected CDSs per virus. Figure S3. Relative abundance of different taxonomic groups assigned to Kilpisjärvi vOTUs. Figure S4. PCoA of (A) Kilpisjärvi vOTUs (n=1881) and (B) Acidobacteriota-associated vOTUs (n=125) in 22 Kilpisjärvi meadow and fen metagenomes. Convex hulls show actual spread of points. The minimum 50% horizontal coverage was applied. The R2 and p-values were obtained separately for each variable. Figure S5. High-quality (96-100% complete) vOTUs assigned to Acidobacteriota. (A) Genomes with ORFs shown as arrows and colored according to the functional categories (see the color key). (B) Distribution of ORFs according to the functional categories, same color key as in (A). Figure S6. Putative acidobacterial proviruses identified in this study and related vOTUs reported in Emerson et al. 2018 (PMID: 30013236), Candidatus Koribacter versatilis provirus reported in Eichorst et al. 2018 (PMID: 29327410), and NCBI references. ORFs are shown as arrows and similarities between genomes (BLASTn) are in shades of gray (direct) or purple (invert). RC, reverse complement. Figure S7. VConTACT2 viral cluster comprising the isolate Tunturi 3, o12215_NODE_6138 (this study) and three vOTUs reported in Emerson et al. 2018 (PMID: 30013236). Similarities between the genomes (BLASTn) are shown with the shades of gray (direct) or purple (invert). Table S1. Soil samples used in this study. Table S2. Acidobacteriota strains used in this study. Table S3. Tunturi 1-5 genome annotations. Table S4. UViGs (scaffolds) retrieved from the IMG/VR database for Tunturi 1-5 viruses. Table S5. Metagenome quality statistics. Table S6. vOTUs detected in Kilpisjärvi fen and meadow metagenomes. Table S7. Genome annotations for high-quality vOTUs linked to Acidobacteriota. Table S8. AMGs found in Kilpisjärvi vOTUs using DRAM-v. Table S9. Virus clusters identified by the VConTACT2 analysis.