cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9m5ng9
title: Occurrence Download

description: A dataset containing 1382 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyperus pilosus Vahl"
 ]
}

 The dataset includes 1382 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011622-240906103802322/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.26985076.v1
title: Additional file 2 of The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

description: Additional file 2: Oral microbiome bacteria, bacteria response in association with smoking, oral sampling site location and citations from reviewed studies.
DOI: 10.6084/m9.figshare.26985082
title: Additional file 4 of The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

description: Additional file 4: Shared and unique responses to cigarette smoking, e-cigarette smoking and cardiovascular risk/disease stratified by increased and decreased bacterial relative abundance associations.
DOI: 10.6084/m9.figshare.26985082.v1
title: Additional file 4 of The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

description: Additional file 4: Shared and unique responses to cigarette smoking, e-cigarette smoking and cardiovascular risk/disease stratified by increased and decreased bacterial relative abundance associations.
DOI: 10.15468/dl.n83dp2
title: Occurrence Download

description: A dataset containing 317 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "TaxonKey is Cryptosepalum exfoliatum De Wild.",
 "Continent is Africa"
 ]
}

 The dataset includes 317 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011623-240906103802322/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.26985130
title: Additional file 2 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 2: Table S2.1. Aggregation-inducing exoproteome CDS differentially expressed between males and females. Table S2.2. Significantly upregulated secreted CDS in male tissues/organs. Table S2.3. 68 secreted CDS that are upregulated in males and highly expressed in the testes.
DOI: 10.6084/m9.figshare.26985154
title: Additional file 10 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 10: Phylip tree file of Fig. 4D.
DOI: 10.6084/m9.figshare.26985127
title: Additional file 1 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 1: Table S1.1. Transcriptome statistics (read counts and mapping). Table S1.2. Significantly upregulated CDS in oral tissues/organs. Table S1.3. GO terms significantly enriched in oral tissues/organs. Table S1.4. Significantly upregulated CDS in aboral tissues/organs. Table S1.5: GO terms significantly enriched in aboral tissues/organs. Table S1.6. Significantly upregulated CDS in the coelomocytes. Table S1.7. GO terms significantly enriched in the coelomocytes. Table S1.8. Significantly upregulated CDS in the gonads. Table S1.9. GO terms significantly enriched in the gonads. Table S1.10. Significantly differentially expressed genes between males and females. Table S1.11. GO terms significantly enriched in the testes. Table S1.12. GO terms significantly enriched in the ovaries.
DOI: 10.6084/m9.figshare.26985133
title: Additional file 3 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 3: Table S3.1. Expressed neuropeptides. Table S3.2. Significantly differentially expressed neuropeptides between males and females. Table S3.3. Significantly differentially expressed CDS between male and female sensory tentacles. Table S3.4. DeSeq2 results of 15,777 expressed CDS in male and female sensory tentacles.
DOI: 10.6084/m9.figshare.26985079
title: Additional file 3 of The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

description: Additional file 3: Oral microbiome bacteria, bacteria response in association with cardiovascular-associated risk measure or disease, oral sampling site location and citations from reviewed studies.
DOI: 10.6084/m9.figshare.26985079.v1
title: Additional file 3 of The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

description: Additional file 3: Oral microbiome bacteria, bacteria response in association with cardiovascular-associated risk measure or disease, oral sampling site location and citations from reviewed studies.
DOI: 10.6084/m9.figshare.26985133.v1
title: Additional file 3 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 3: Table S3.1. Expressed neuropeptides. Table S3.2. Significantly differentially expressed neuropeptides between males and females. Table S3.3. Significantly differentially expressed CDS between male and female sensory tentacles. Table S3.4. DeSeq2 results of 15,777 expressed CDS in male and female sensory tentacles.
DOI: 10.6084/m9.figshare.26985181.v1
title: Additional file 4 of Association between friendship quality and subjective wellbeing among adolescents: a systematic review

description: Additional file 4. Methodological quality assessment.
DOI: 10.6084/m9.figshare.26985127.v1
title: Additional file 1 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 1: Table S1.1. Transcriptome statistics (read counts and mapping). Table S1.2. Significantly upregulated CDS in oral tissues/organs. Table S1.3. GO terms significantly enriched in oral tissues/organs. Table S1.4. Significantly upregulated CDS in aboral tissues/organs. Table S1.5: GO terms significantly enriched in aboral tissues/organs. Table S1.6. Significantly upregulated CDS in the coelomocytes. Table S1.7. GO terms significantly enriched in the coelomocytes. Table S1.8. Significantly upregulated CDS in the gonads. Table S1.9. GO terms significantly enriched in the gonads. Table S1.10. Significantly differentially expressed genes between males and females. Table S1.11. GO terms significantly enriched in the testes. Table S1.12. GO terms significantly enriched in the ovaries.
DOI: 10.6084/m9.figshare.26985139
title: Additional file 5 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 5: Table S5.1. Expressed GPCRs. Table S5.2. Expressed GPCRs in the sensory tentacles. Table S5.3. Uniquely expressed GPCRs in the sensory tentacles.
DOI: 10.6084/m9.figshare.26985181
title: Additional file 4 of Association between friendship quality and subjective wellbeing among adolescents: a systematic review

description: Additional file 4. Methodological quality assessment.
DOI: 10.6084/m9.figshare.26985202
title: Additional file 6 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 6: Supplementary Table 3. Predicted virus-host connections for vOTUs. The highest confidence host for each vOTU is highlighted.
DOI: 10.6084/m9.figshare.26985139.v1
title: Additional file 5 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 5: Table S5.1. Expressed GPCRs. Table S5.2. Expressed GPCRs in the sensory tentacles. Table S5.3. Uniquely expressed GPCRs in the sensory tentacles.
DOI: 10.6084/m9.figshare.26985154.v1
title: Additional file 10 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 10: Phylip tree file of Fig. 4D.
DOI: 10.6084/m9.figshare.26985157
title: Additional file 1 of Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy

description: Additional file 1: Table S1. List of the primers used in the study. Table S2. Photoreceptor specific gene dataset. Table S3. Housekeeping gene dataset. Table S4. CRX direct gene targets. Table S5. NRL direct gene targets. Table S6. Genes downregulated in SCA7 (FC &lt; 0.7, p &lt; 0.05). Table S7. 71 genes coding for proteins located in cilium and OS structures and downregulated in SCA7. Table S8. Genes upregulated in SCA7 (FC &gt; 1.3, p &lt; 0.05). Table S9. Occurrence of TF binding motifs in genomic loci associated with cluster 10. Table S10. Genomic coordinates of 268 super-enhancers predicted by ROSE. Table S11. Genic properties of lncRNAs identified in the retina.
DOI: 10.6084/m9.figshare.26985187.v1
title: Additional file 1 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 1: Supplementary Table 1. Metagenome datasets used for analysis in this study.
DOI: 10.6084/m9.figshare.26985208
title: Additional file 8 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 8: Supplementary Table 4. Annotation of putative auxiliary metabolic genes.
DOI: 10.15468/dl.7mkcht
title: Occurrence Download

description: A dataset containing 712 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 },
 "TaxonKey is Cryptosepalum maraviense Oliv.",
 "Continent is Africa"
 ]
}

 The dataset includes 712 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011624-240906103802322/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.26985208.v1
title: Additional file 8 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 8: Supplementary Table 4. Annotation of putative auxiliary metabolic genes.
DOI: 10.6084/m9.figshare.26985076
title: Additional file 2 of The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

description: Additional file 2: Oral microbiome bacteria, bacteria response in association with smoking, oral sampling site location and citations from reviewed studies.
DOI: 10.6084/m9.figshare.26985202.v1
title: Additional file 6 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 6: Supplementary Table 3. Predicted virus-host connections for vOTUs. The highest confidence host for each vOTU is highlighted.
DOI: 10.6084/m9.figshare.26985187
title: Additional file 1 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 1: Supplementary Table 1. Metagenome datasets used for analysis in this study.
DOI: 10.6084/m9.figshare.26985193
title: Additional file 3 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 3: Supplementary Table 2. Characteristics of vOTUs recovered from hydrothermal vent metagenomes. The taxonomic affiliation of vOTUs was inferred using the last common ancestor algorithm in CAT v5.0.3. The completeness of the viral genomes and viral lifestyles were determined using the CheckV pipeline.
DOI: 10.6084/m9.figshare.26985151
title: Additional file 9 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 9: Fasta file of sequences used to infer RGP receptor phylogeny.
DOI: 10.6084/m9.figshare.26985151.v1
title: Additional file 9 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 9: Fasta file of sequences used to infer RGP receptor phylogeny.
DOI: 10.6084/m9.figshare.26985130.v1
title: Additional file 2 of Sex-specific expression of pheromones and other signals in gravid starfish

description: Additional file 2: Table S2.1. Aggregation-inducing exoproteome CDS differentially expressed between males and females. Table S2.2. Significantly upregulated secreted CDS in male tissues/organs. Table S2.3. 68 secreted CDS that are upregulated in males and highly expressed in the testes.
DOI: 10.6084/m9.figshare.26985229
title: Additional file 2 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 2: Table S1. Sample metadata including location, year, research vessel, number of metagenome reads and accession numbers. Table S2. MAG genome properties, accession numbers and taxonomic classifications. Taxonomy was assigned using GTDB-Tk, and mis-classified MAGs were taxonomically re-assigned at the phylum level (Bacteria) and class level (Archaea) using curated archaeal and bacterial phylogenetic trees. Genome quality statistics are based on completion and contamination (high quality, &gt;90% completion, &lt;5% contamination; medium quality, ≥50% completion, ≤10% contamination). Average contamination was 4.02%. Table S3. Average amino acid identity (AAI) matrices for the (A) Bacteria and (B) Archaea. Matrices are grouped by GTDB taxonomy and include MAGs that could not be assigned to a known genus by GTDB-Tk. Details are provided which recently identified MAGs were from Brothers volcano hydrothermal deposits. Table S4. Relative abundance of GTDB taxa by site, based on read coverage of MAGs normalized to 100M reads per sample. MAG coverage for each site was summed and expressed as a percent. Table S5. METABOLIC-G results for JALSQH01 (3 MAGs) and JALWCF01 (13 MAGs). In the summary rows for JALSQH01 and JALWCF01, functions and modules are listed as “present” if identified in ≥50% of all MAGs, “partially present” if found in &lt;50% of the MAGs, and “absent” if undetected in the MAGs. Table S6. Selected functional genes found in Patescibacteria MAGs, based on annotation with GhostKOALA. KEGG module numbers are shown in parentheses. Table S7. Functional genes identified in selected &gt; 80%-completeness MAGs from the Chloroflexota. (A) Genes are marked as present (1; green highlight) or not detected (0) in individual MAGs. (B) The proportion of &gt; 80%-completeness MAGs in six GTDB orders that encode functional genes is also shown, with proportions ≥50% highlighted in green. Table S8. Identification and distribution of functional genes in this study. (A) The HMMs, MEROPS peptidases, and CAZymes used to identify functional genes. Gene call numbers were calculated using the component (C) or accumulative (A) methods described in the methods. Genes requiring manual validation (M) are indicated. (B) Functional gene abundance, calculated as described in the methods. Table S9. Percentage of MAGs in phylogenetic clusters that encode core metabolic genes. Unless otherwise indicated, Archaea are shown at the class level, and Bacteria are shown at the phylum level. Genes were detected using METABOLIC, with additional validation steps for oxidative and reductive Dsr, Sdo, PmoA and McrA. Table S10. Comparative (A) relative abundance and (B) functional gene abundance for the Gammaproteobacteria and Campylobacteria, used to generate Fig. 10.
DOI: 10.6084/m9.figshare.26985232.v1
title: Additional file 3 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 3: Data S1. Newick format archaeal concatenated protein phylogenetic tree, including both MAGs and GTDB reference genomes.
DOI: 10.6084/m9.figshare.26985157.v1
title: Additional file 1 of Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy

description: Additional file 1: Table S1. List of the primers used in the study. Table S2. Photoreceptor specific gene dataset. Table S3. Housekeeping gene dataset. Table S4. CRX direct gene targets. Table S5. NRL direct gene targets. Table S6. Genes downregulated in SCA7 (FC &lt; 0.7, p &lt; 0.05). Table S7. 71 genes coding for proteins located in cilium and OS structures and downregulated in SCA7. Table S8. Genes upregulated in SCA7 (FC &gt; 1.3, p &lt; 0.05). Table S9. Occurrence of TF binding motifs in genomic loci associated with cluster 10. Table S10. Genomic coordinates of 268 super-enhancers predicted by ROSE. Table S11. Genic properties of lncRNAs identified in the retina.
DOI: 10.6084/m9.figshare.26985232
title: Additional file 3 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 3: Data S1. Newick format archaeal concatenated protein phylogenetic tree, including both MAGs and GTDB reference genomes.
DOI: 10.6084/m9.figshare.26985241
title: Additional file 6 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 6:Data S4. MAG-only bacterialconcatenated phylogenetic protein tree in Newick format.
DOI: 10.6084/m9.figshare.26985229.v1
title: Additional file 2 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 2: Table S1. Sample metadata including location, year, research vessel, number of metagenome reads and accession numbers. Table S2. MAG genome properties, accession numbers and taxonomic classifications. Taxonomy was assigned using GTDB-Tk, and mis-classified MAGs were taxonomically re-assigned at the phylum level (Bacteria) and class level (Archaea) using curated archaeal and bacterial phylogenetic trees. Genome quality statistics are based on completion and contamination (high quality, &gt;90% completion, &lt;5% contamination; medium quality, ≥50% completion, ≤10% contamination). Average contamination was 4.02%. Table S3. Average amino acid identity (AAI) matrices for the (A) Bacteria and (B) Archaea. Matrices are grouped by GTDB taxonomy and include MAGs that could not be assigned to a known genus by GTDB-Tk. Details are provided which recently identified MAGs were from Brothers volcano hydrothermal deposits. Table S4. Relative abundance of GTDB taxa by site, based on read coverage of MAGs normalized to 100M reads per sample. MAG coverage for each site was summed and expressed as a percent. Table S5. METABOLIC-G results for JALSQH01 (3 MAGs) and JALWCF01 (13 MAGs). In the summary rows for JALSQH01 and JALWCF01, functions and modules are listed as “present” if identified in ≥50% of all MAGs, “partially present” if found in &lt;50% of the MAGs, and “absent” if undetected in the MAGs. Table S6. Selected functional genes found in Patescibacteria MAGs, based on annotation with GhostKOALA. KEGG module numbers are shown in parentheses. Table S7. Functional genes identified in selected &gt; 80%-completeness MAGs from the Chloroflexota. (A) Genes are marked as present (1; green highlight) or not detected (0) in individual MAGs. (B) The proportion of &gt; 80%-completeness MAGs in six GTDB orders that encode functional genes is also shown, with proportions ≥50% highlighted in green. Table S8. Identification and distribution of functional genes in this study. (A) The HMMs, MEROPS peptidases, and CAZymes used to identify functional genes. Gene call numbers were calculated using the component (C) or accumulative (A) methods described in the methods. Genes requiring manual validation (M) are indicated. (B) Functional gene abundance, calculated as described in the methods. Table S9. Percentage of MAGs in phylogenetic clusters that encode core metabolic genes. Unless otherwise indicated, Archaea are shown at the class level, and Bacteria are shown at the phylum level. Genes were detected using METABOLIC, with additional validation steps for oxidative and reductive Dsr, Sdo, PmoA and McrA. Table S10. Comparative (A) relative abundance and (B) functional gene abundance for the Gammaproteobacteria and Campylobacteria, used to generate Fig. 10.
DOI: 10.6084/m9.figshare.26985235
title: Additional file 4 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 4: DataS2. Newick file ofbacterial concatenated protein phylogenetic tree including MAGs and GTDBreference genomes, generated using IQ-TREE.
DOI: 10.6084/m9.figshare.26985235.v1
title: Additional file 4 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 4: DataS2. Newick file ofbacterial concatenated protein phylogenetic tree including MAGs and GTDBreference genomes, generated using IQ-TREE.
DOI: 10.6084/m9.figshare.26985238
title: Additional file 5 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 5: Data S3. Concatenated protein phylogenetic tree of bacterial MAGs and GTDB reference genomes, generated with FastTree (Newick format).
DOI: 10.6084/m9.figshare.26985241.v1
title: Additional file 6 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 6:Data S4. MAG-only bacterialconcatenated phylogenetic protein tree in Newick format.
DOI: 10.6084/m9.figshare.26985244
title: Additional file 7 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 7: Data S5. Concatenated protein phylogeny of archaeal MAGs in Newick format.
DOI: 10.6084/m9.figshare.26985244.v1
title: Additional file 7 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 7: Data S5. Concatenated protein phylogeny of archaeal MAGs in Newick format.
DOI: 10.6084/m9.figshare.26985238.v1
title: Additional file 5 of Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

description: Additional file 5: Data S3. Concatenated protein phylogenetic tree of bacterial MAGs and GTDB reference genomes, generated with FastTree (Newick format).
DOI: 10.6084/m9.figshare.26985193.v1
title: Additional file 3 of Virus diversity and interactions with hosts in deep-sea hydrothermal vents

description: Additional file 3: Supplementary Table 2. Characteristics of vOTUs recovered from hydrothermal vent metagenomes. The taxonomic affiliation of vOTUs was inferred using the last common ancestor algorithm in CAT v5.0.3. The completeness of the viral genomes and viral lifestyles were determined using the CheckV pipeline.
DOI: 10.6084/m9.figshare.26985286
title: Additional file 13 of Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals

description: Additional file 13: Table S6. LpNIZO2877-mutated genes persisting over the course of the experimental evolution in the mouse intestine. The targets were chosen by selecting mutated genes that persisted in at least seven Host-evolved Lp populations. Predicted functional categories have been determined according to their COG group with EggNOG v.5.1.