cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3737764_d2
title: Additional file 2: Figure S1. of Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar

description: Results from differential expression analysis of female and male brain tissue. A) MA plot for each transcript comparing the log2 fold-change versus the average transcript expression. Each dot represents a transcript and the significantly differentially expressed (false discovery rate (FDR)
DOI: 10.6084/m9.figshare.c.3737710_d10.v1
title: Additional file 7: Table S3. of Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals

description: The percentages of promoter regions overlapping with CpG islands. (XLS 36Â kb)
DOI: 10.6084/m9.figshare.c.3737782_d2.v1
title: Additional file 2: of Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

description: S1 is an Excel spread sheet containing the MC58 genome annotation data together with the results of the pairwise genome comparison with Îą522 and the microarray data. (XLSX 418 kb)
DOI: 10.6084/m9.figshare.c.3737782_d2
title: Additional file 2: of Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

description: S1 is an Excel spread sheet containing the MC58 genome annotation data together with the results of the pairwise genome comparison with Îą522 and the microarray data. (XLSX 418 kb)
DOI: 10.6084/m9.figshare.c.3737782_d3.v1
title: Additional file 3: of Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

description: S2 is an Excel spread sheet containing the results of the elementary mode analyses in human blood based on MC58 metabolic network model. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3737785_d2.v1
title: MOESM2 of Bacterial flora of combat wounds from eastern Ukraine and time-specified changes of bacterial recovery during treatment in Ukrainian military hospital

description: Additional file 2: Table S2. Antibiotic susceptibility profiles of Gram-positive bacteria isolated from wounds.
DOI: 10.6084/m9.figshare.c.3737755_d8.v1
title: Additional file 8: of 
                     Eobowenia gen. nov. from the Early Cretaceous of Patagonia: indication for an early divergence of Bowenia?

description: Zip file containing matrices and trees. (ZIP 1603Â kb)
DOI: 10.6084/m9.figshare.c.3737782_d3
title: Additional file 3: of Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

description: S2 is an Excel spread sheet containing the results of the elementary mode analyses in human blood based on MC58 metabolic network model. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3737785_d2
title: MOESM2 of Bacterial flora of combat wounds from eastern Ukraine and time-specified changes of bacterial recovery during treatment in Ukrainian military hospital

description: Additional file 2: Table S2. Antibiotic susceptibility profiles of Gram-positive bacteria isolated from wounds.
DOI: 10.5281/zenodo.14341918
title: Evaluating approaches for integrating species distributions in spatial conservation planning

description: This zip file contains data and code to reproduce the analyses in the article 'Evaluating approaches for integrating species distributions in spatial conservation planning' published in Conservation Science and Practice. Raw data (i.e., WWHCS DST shapefile and raster inputs) are stored in the 'data' folder, and output files are stored in the 'outputs' folder. R scripts should be run in order to prepare the shapefiles, download eBird Status and Trends relative abundance rasters, prepare these rasters as conservation capital and opportunity inputs, run the expert opinion and eBird versions of the DST, compare expert habitat suitability and eBird relative abundance layers, estimate correlations between mean habitat suitability and relative abundance, calculate agreement between top-ranked watersheds for the two versions of the DST, and create manuscript figures.We note that downloading and prepping eBird relative abundance products has changed since our analysis was completed (i.e., the ebirdst package transitioned from 'raster' package to 'terra' package rasters and products have been updated). Therefore R scripts 01 and 02 will need to be modified, or users can skip script 01.Please contact jwiniarski@wisc.edu if you have any questions.
DOI: 10.5281/zenodo.14341919
title: Evaluating approaches for integrating species distributions in spatial conservation planning

description: This zip file contains data and code to reproduce the analyses in the article 'Evaluating approaches for integrating species distributions in spatial conservation planning' published in Conservation Science and Practice. Raw data (i.e., WWHCS DST shapefile and raster inputs) are stored in the 'data' folder, and output files are stored in the 'outputs' folder. R scripts should be run in order to prepare the shapefiles, download eBird Status and Trends relative abundance rasters, prepare these rasters as conservation capital and opportunity inputs, run the expert opinion and eBird versions of the DST, compare expert habitat suitability and eBird relative abundance layers, estimate correlations between mean habitat suitability and relative abundance, calculate agreement between top-ranked watersheds for the two versions of the DST, and create manuscript figures.We note that downloading and prepping eBird relative abundance products has changed since our analysis was completed (i.e., the ebirdst package transitioned from 'raster' package to 'terra' package rasters and products have been updated). Therefore R scripts 01 and 02 will need to be modified, or users can skip script 01.Please contact jwiniarski@wisc.edu if you have any questions.
DOI: 10.6084/m9.figshare.c.3737755_d8
title: Additional file 8: of 
                     Eobowenia gen. nov. from the Early Cretaceous of Patagonia: indication for an early divergence of Bowenia?

description: Zip file containing matrices and trees. (ZIP 1603Â kb)
DOI: 10.5281/zenodo.14504546
title: Protocol for oral fecal gavage to reshape the gut microbiota in mice

description: The oral Fecal microbiota transplantation (FMT) is preferred in experimental mice. The upper gastrointestinal tract influences microbe selection, though its role is unclear. Our study shows oral fecal gavage (OFG) reduces liver failure severity in mice. We present protocols for preparing the fresh feces for OFG and OPG, revealing OFG recipient gut microbiota evolved rapidly, resembling that of donors by day seven. The colonization of commensal microbes after OFG, with Lactobacillaceae, Akkermansiaceae, and Lachnospiraceae becoming enriched over time.
DOI: 10.5281/zenodo.14504547
title: Protocol for oral fecal gavage to reshape the gut microbiota in mice

description: The oral Fecal microbiota transplantation (FMT) is preferred in experimental mice. The upper gastrointestinal tract influences microbe selection, though its role is unclear. Our study shows oral fecal gavage (OFG) reduces liver failure severity in mice. We present protocols for preparing the fresh feces for OFG and OPG, revealing OFG recipient gut microbiota evolved rapidly, resembling that of donors by day seven. The colonization of commensal microbes after OFG, with Lactobacillaceae, Akkermansiaceae, and Lachnospiraceae becoming enriched over time.
DOI: 10.15468/dl.g3zke6
title: Occurrence Download

description: A dataset containing 1876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chauliodus sloani Bloch & Schneider, 1801",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 1876 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038434-241126133413365/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.3737806_d2.v1
title: Additional file 11 of Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

description: Dataset: classified OTU table. Tab-separated text file that compiles the complete OTU table with all samples, read counts, representative FASTA sequences, and classifications. (CSV 1920 kb)
DOI: 10.6084/m9.figshare.c.3737800_d3
title: Additional file 2: Dataset S2. of Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin

description: Spread sheet containing the full analysis of the RNAseq data including all 23,623 identified genes (all analysis), genes significantly differentially expressed due to treatment (diff_res_to_treat) and species specific genes with significant differential expression (spp_diff_res_to_treat). (XLSX 13892 kb)
DOI: 10.6084/m9.figshare.c.3737806_d2
title: Additional file 11 of Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

description: Dataset: classified OTU table. Tab-separated text file that compiles the complete OTU table with all samples, read counts, representative FASTA sequences, and classifications. (CSV 1920 kb)
DOI: 10.6084/m9.figshare.c.3737806_d3.v1
title: Additional file 12 of Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

description: Dataset: environmental parameters. Tab-separated text file that compiles all environmental parameters. (CSV 1570 kb)
DOI: 10.6084/m9.figshare.c.3737806_d3
title: Additional file 12 of Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

description: Dataset: environmental parameters. Tab-separated text file that compiles all environmental parameters. (CSV 1570 kb)
DOI: 10.6084/m9.figshare.c.3737848_d1.v1
title: Additional file 1: of SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

description: Abstract files of SNPPhenA corpus. (ZIP 651 kb)
DOI: 10.6084/m9.figshare.c.3737848_d1
title: Additional file 1: of SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

description: Abstract files of SNPPhenA corpus. (ZIP 651 kb)
DOI: 10.6084/m9.figshare.c.3737800_d7.v1
title: Additional file 6: Dataset S4. of Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin

description: The full cyctoscape file to allow for more detailed examination of genes/pathways and how they have responded to the water deficit treatment (SS) and well watered control (WW). To view file, please download the Cytoscape V3.3.0 program free from the following website: http://www.cytoscape.org/ . Interpretation instructions can be found in Additional file 7. Please note the node pie colours are not available in this file and readers should refer to Fig.Â 3 and Additional file 5: Figure S2. (CYS 639 kb)
DOI: 10.6084/m9.figshare.c.3737800_d7
title: Additional file 6: Dataset S4. of Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin

description: The full cyctoscape file to allow for more detailed examination of genes/pathways and how they have responded to the water deficit treatment (SS) and well watered control (WW). To view file, please download the Cytoscape V3.3.0 program free from the following website: http://www.cytoscape.org/ . Interpretation instructions can be found in Additional file 7. Please note the node pie colours are not available in this file and readers should refer to Fig.Â 3 and Additional file 5: Figure S2. (CYS 639 kb)
DOI: 10.6084/m9.figshare.c.3737954_d1.v1
title: Additional file 1: Table S1. of GRMD cardiac and skeletal muscle metabolism gene profiles are distinct

description: Statistically significant gene list. Column A = Affymetrix unique probe set ID, Column B = Gene ID, Column C = gene symbol, Column D = RefSeq ID, Column E = gene assignment, Column F = gene title, Column G = gene symbol, Column H = ANOVA-generated p values for all groups, Column I = ANOVA-generated p values for comparison of left ventricular (LV) tissues from 6 month-old (6 m) Golden Retriever Muscular Dystrophy (GRMD) dogs versus LV from 6 m normal controls, Column J = Fold difference for [LV 6 m GRMD/LV 6 m normal], Column K = ANOVA-generated p values for comparison of LV 12 m GRMD versus LV 12 m normal, Column L = Fold difference for [LV 12 m GRMD/LV 12 m normal], Column M = ANOVA-generated p values for comparison of medial head of the gastrocnemius (MG) from 6 m GRMD versus MG 6 m normal, Column N = Fold difference for [MG 6 m GRMD/MG 6 m normal], Column O = ANOVA-generated p values for comparison of MG 12 m GRMD versus MG 12 m normal, Column P = Fold difference for [MG 12 m GRMD/MG 12 m normal]. Gene annotations were obtained within Partek (Columns B-C) and using Affymetrix NetAffx database information (Columns D-G). (XLSX 995 kb)
DOI: 10.6084/m9.figshare.c.3737954_d1
title: Additional file 1: Table S1. of GRMD cardiac and skeletal muscle metabolism gene profiles are distinct

description: Statistically significant gene list. Column A = Affymetrix unique probe set ID, Column B = Gene ID, Column C = gene symbol, Column D = RefSeq ID, Column E = gene assignment, Column F = gene title, Column G = gene symbol, Column H = ANOVA-generated p values for all groups, Column I = ANOVA-generated p values for comparison of left ventricular (LV) tissues from 6 month-old (6 m) Golden Retriever Muscular Dystrophy (GRMD) dogs versus LV from 6 m normal controls, Column J = Fold difference for [LV 6 m GRMD/LV 6 m normal], Column K = ANOVA-generated p values for comparison of LV 12 m GRMD versus LV 12 m normal, Column L = Fold difference for [LV 12 m GRMD/LV 12 m normal], Column M = ANOVA-generated p values for comparison of medial head of the gastrocnemius (MG) from 6 m GRMD versus MG 6 m normal, Column N = Fold difference for [MG 6 m GRMD/MG 6 m normal], Column O = ANOVA-generated p values for comparison of MG 12 m GRMD versus MG 12 m normal, Column P = Fold difference for [MG 12 m GRMD/MG 12 m normal]. Gene annotations were obtained within Partek (Columns B-C) and using Affymetrix NetAffx database information (Columns D-G). (XLSX 995 kb)
DOI: 10.15468/dl.qfk3hh
title: Occurrence Download

description: A dataset containing 334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chaunax pictus Lowe, 1846",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 334 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038435-241126133413365/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.3737987_d1.v1
title: Additional file 1: Table S1. of Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates

description: 500 lncRNA genes with the most variable expression in 426 HNSCC samples from TCGA. Table S2. lncRNA-based HNSCC TCGA sample clusters. Table S3. Surrogate lncRNA genes per sample cluster. Table S4. Common lncRNAs between surrogate c5 and overexpressed in TP53 WT-infected samples from Nohata et al. (ref [20]). Table S5. Common lncRNAs between surrogate c5 and overexpressed in HPV-infected samples from Nohata et al. (ref [20]). Table S6. Common lncRNAs between surrogate c1 to c5 samples and suborgan-specific from Nohata et al. (ref [20]). Table S7. Protein-coding genes correlated with surrogate lncRNAs per sample cluster. (XLSX 125 kb)
DOI: 10.6084/m9.figshare.c.3737987_d1
title: Additional file 1: Table S1. of Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates

description: 500 lncRNA genes with the most variable expression in 426 HNSCC samples from TCGA. Table S2. lncRNA-based HNSCC TCGA sample clusters. Table S3. Surrogate lncRNA genes per sample cluster. Table S4. Common lncRNAs between surrogate c5 and overexpressed in TP53 WT-infected samples from Nohata et al. (ref [20]). Table S5. Common lncRNAs between surrogate c5 and overexpressed in HPV-infected samples from Nohata et al. (ref [20]). Table S6. Common lncRNAs between surrogate c1 to c5 samples and suborgan-specific from Nohata et al. (ref [20]). Table S7. Protein-coding genes correlated with surrogate lncRNAs per sample cluster. (XLSX 125 kb)
DOI: 10.6084/m9.figshare.c.3737978_d4.v1
title: Additional file 4: Table S2. of A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray

description: List of the 1559 genes used for the PEHM hybridization model evaluation. For each gene, abbreviated name, full name, alias and accession number are provided. As indicated in the paper, each of these genes is targeted by three probesets, two derived from Affymetrix arrays U133 (GeneChip Human Genome U133 Plus 2.0 Array), HTA (GeneChip Human Transcriptome Array 2.0) and one designed using our probes and probesets selection procedure. (XLS 119 kb)
DOI: 10.6084/m9.figshare.c.3737978_d4
title: Additional file 4: Table S2. of A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray

description: List of the 1559 genes used for the PEHM hybridization model evaluation. For each gene, abbreviated name, full name, alias and accession number are provided. As indicated in the paper, each of these genes is targeted by three probesets, two derived from Affymetrix arrays U133 (GeneChip Human Genome U133 Plus 2.0 Array), HTA (GeneChip Human Transcriptome Array 2.0) and one designed using our probes and probesets selection procedure. (XLS 119 kb)
DOI: 10.15468/dl.dxhyw8
title: Occurrence Download

description: A dataset containing 444514 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scutellaria L."
 ]
}

 The dataset includes 444514 records from 2113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038430-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.1.5040.3285
title: 40+ ecology papers, links to free articles (RG), environmental science, toxicology, water quality, with explanation of novelty, usefulness; https://www.researchgate.net/publication/283490595
DOI: 10.15468/dl.vtvmag
title: Occurrence Download

description: A dataset containing 6986 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Accipitriformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-120 -30,-90 -30,-90 0,-120 0,-120 -30))"
 ]
}

 The dataset includes 6986 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061215-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cdbwn4
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Jacquemontia rufa (Choisy) Hallier fil."
 ]
}

 The dataset includes 80 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256271-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hyxce6
title: Occurrence Download

description: A dataset containing 830 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Toxomerus floralis (Fabricius, 1798)"
 ]
}

 The dataset includes 830 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005455-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k6u7t9
title: Occurrence Download

description: A dataset containing 169034 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-110.16625 36.63634,-100.07102 36.63634,-100.07102 42.41506,-110.09358 42.4083,-110.16625 36.63634))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Haliaeetus leucocephalus (Linnaeus, 1766)"
 ]
}

 The dataset includes 169034 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069921-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x9uqbf
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ipomoea concolor (Matuda) D.Austin"
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0253962-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4qcatw
title: Occurrence Download

description: A dataset containing 107474 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ara severus (Linnaeus, 1758))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 107474 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069913-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.emn29y
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mutisia splendens Renjifo"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044546-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nfc6me
title: Occurrence Download

description: A dataset containing 1768 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leymus chinensis (Trin.) Tzvelev"
 ]
}

 The dataset includes 1768 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256274-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.