cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15138768
title: Table 2 in A reassessment of the genus Oligoneuriopsis Crass, 1947 (Ephemeroptera, Oligoneuriidae, Oligoneuriellini)

description: Table 2. Available data and knowledge gaps for the species of Oligoneuriopsis.
SpeciesImago describedNymph describedCOI sequencedO. dobbsi+++O. elisabethae+O. jessicae+O. lawrencei+++O. orontensis+++O. skhounate+++O. villosus++O. sp. (Iran)+
description: Published as part of Barber-James, Helen M., Zrelli, Sonia, Yanai, Zohar & Sartori, Michel, 2020, A reassessment of the genus Oligoneuriopsis Crass, 1947 (Ephemeroptera, Oligoneuriidae, Oligoneuriellini), pp. 15 in ZooKeys 985 on page 15, DOI: 10.3897/zookeys.985.56649
DOI: 10.5281/zenodo.15138769
title: Table 2 in A reassessment of the genus Oligoneuriopsis Crass, 1947 (Ephemeroptera, Oligoneuriidae, Oligoneuriellini)

description: Table 2. Available data and knowledge gaps for the species of Oligoneuriopsis.
SpeciesImago describedNymph describedCOI sequencedO. dobbsi+++O. elisabethae+O. jessicae+O. lawrencei+++O. orontensis+++O. skhounate+++O. villosus++O. sp. (Iran)+
description: Published as part of Barber-James, Helen M., Zrelli, Sonia, Yanai, Zohar & Sartori, Michel, 2020, A reassessment of the genus Oligoneuriopsis Crass, 1947 (Ephemeroptera, Oligoneuriidae, Oligoneuriellini), pp. 15 in ZooKeys 985 on page 15, DOI: 10.3897/zookeys.985.56649
DOI: 10.15468/dl.7f4nub
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cedrela saltensis M.A.Zapater & del Castillo"
 ]
}

 The dataset includes 38 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028649-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.krezb3
title: Occurrence Download

description: A dataset containing 292 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polytaenia nuttallii DC.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 292 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0162312-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k3e98q
title: Occurrence Download

description: A dataset containing 117098 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Bunchosia polystachya (Andrews) DC., Bunias erucago L., Bunias orientalis L., Bunium bulbocastanum L., Bupleurum americanum J.M.Coult. & Rose, Bupleurum lancifolium Hornem., Bupleurum odontites L., Bupleurum rotundifolium L., Burmannia biflora L., Burmannia capitata (Walter ex J.F.Gmel.) Mart.)"
 ]
}

 The dataset includes 117098 records from 1006 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007463-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bha9ri
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Herpestes naso de Winton, 1901"
 ]
}

 The dataset includes 108 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028652-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sqyyn5
title: Occurrence Download

description: A dataset containing 72252 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Anchusa capensis Thunb., Anchusa officinalis L., Ancistrachne uncinulata (R.Br.) S.T.Blake, Sclerocactus brevihamatus (Engelm.) D.R.Hunt, Sclerocactus scheerii (Salm-Dyck) N.P.Taylor, Ancistrocarphus filagineus A.Gray, Andira inermis (W.Wright) DC., Gaultheria rupestris (G.Forst.) R.Br., Andryala rothia Pers., Azorella nivalis Phil.)"
 ]
}

 The dataset includes 72252 records from 777 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007474-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57756/58udvj
title: Dataset to: Reier S., Trontelj P., Kruckenhauser L., Kapun M., Wanka, A., Palandačić A. (2025) "Factors beyond karstification have shaped the population structure of a surface-dwelling minnow (Phoxinus lumaireul) able to disperse underground"

description: The Dinaric Karst, a biodiversity hotspot,
features complex surface and subterranean hydrological networks that influence
aquatic species distribution. This study investigates how karst hydrology
shapes the genetic structure of the surface-dwelling minnow <i>Phoxinus lumaireul</i>,
examining both large-scale and fine-scale population patterns. Using mitochondrial
DNA (mtDNA) and genome-wide single nucleotide polymorphism (SNP) data of 827
specimens of <i>P. lumaireul</i>, three hypotheses were tested: (1) karst underground
water connections facilitate genetic connectivity within and across river
systems, whereas non-karst rivers exhibit genetic connectivity mostly within
the same system; (2) historical and occasional hydrological connections have
shaped present-day population structure, leaving genetic signatures of
relatedness where no contemporary hydrological links exist; and (3) genomic
approaches provide additional insights into biologically relevant connections
that may not be captured by classical tracing tests. The large-scale analyses
confirmed three main genetic groups (1a–c), whose structure was likely shaped
by Pleistocene glaciations and associated microrefugia rather than by karst
hydrology. Fine-scale structure analyses revealed that while karst hydrology
facilitated gene flow within specific areas, connectivity was uneven and
influenced by local hydrological dynamics and historical admixture events.
Furthermore, some underground pathways identified by classical tracing tests
lacked evidence of genetic connectivity, underscoring the limitations of
traditional methods and the added value of genomic data in indirectly detecting
biologically relevant hydrological connections. These findings highlight the
influence of both historical processes and contemporary karst hydrology on <i>P.
lumaireul</i> populations, emphasizing their vulnerability to karst ecosystems and
the need for targeted conservation efforts.
DOI: 10.6084/m9.figshare.c.3636584_d1.v1
title: Additional file 9: of Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

description: DLBCL sample subtype classification. Data showing the classification of the 104 primary DLBCL subtypes as ABC or GCB. (XLSX 37 kb)
DOI: 10.15468/dl.yp8s9t
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Inimicus japonicus (Cuvier, 1829)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 147 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035626-241126133413365/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.3636332_d1.v1
title: Additional file 2: Figure S2. of Epigenetic associations of type 2 diabetes and BMI in an Arab population

description: Manhattan plots for epigenome-wide association of CpG methylation sites with (A) BMI (B) T2D. Coordinates are in hg19. The red line indicates a conservative Bonferroni significance threshold of p value = 1.07 × 10−7. 277 KB
DOI: 10.6084/m9.figshare.c.3636332_d2.v1
title: Additional file 4: of Epigenetic associations of type 2 diabetes and BMI in an Arab population

description: Whole list of BMI associations with CpG methylation sites from the EWAS in the Qatari family sample (provided in csv-separated format). Coordinates are in hg19. 31.5 MB
DOI: 10.6084/m9.figshare.c.3636317_d1.v1
title: Additional file 1: Table S1. of A single dose of the Îł-secretase inhibitor semagacestat alters the cerebrospinal fluid peptidome in humans

description: Identified peptides. Peptides identified and quantified in at least four participants in each of the three treatment groups. Quantitative data are presented as percent change relative to CSF sampled at the time point when the drug was administered. The values are normalized to the average relative peptide abundance in the placebo group for each time point. (XLSX 86Â kb)
DOI: 10.15468/dl.esks4v
title: Occurrence Download

description: A dataset containing 11364 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is IND.29.17.11_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 11364 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035627-241126133413365/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.3636032_d1.v1
title: Additional file 1: Table S1. of Discovering gene expression signatures responding to tyrosine kinase inhibitor treatment in chronic myeloid leukemia

description: Lists of differentially expressed genes of each dataset (GSE1467, GSE2535, and GSE33224). (XLS 115Â kb)
DOI: 10.6084/m9.figshare.c.3636032_d2.v1
title: Additional file 2: Table S2. of Discovering gene expression signatures responding to tyrosine kinase inhibitor treatment in chronic myeloid leukemia

description: Lists of functional annotation terms of differentially expressed genes of each dataset (GSE14671, GSE2535, and GSE33224). (XLS 143Â kb)
DOI: 10.6084/m9.figshare.c.3636023_d10.v1
title: Additional file 7: of Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation

description: Differentially expressed O. unilateralis s.l. genes. Tables displaying all O. unilateralis s.l. genes, including their expression levels and annotation, that were found to be differentially expressed during manipulated biting behavior in comparison to baseline gene expression in fungal cultures (sheets 2 and 3), after manipulated biting behavior in comparison to baseline gene expression (sheets 4 and 5), and during manipulated biting behavior versus death after manipulated biting behavior (sheets 6 and 7). (XLSX 891Â kb)
DOI: 10.6084/m9.figshare.c.3636023_d7.v1
title: Additional file 8: of Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation

description: O. unilateralis s.l. genes uniquely up- or down regulated during manipulated biting behavior. Tables displaying all O. unilateralis s.l. genes, including their expression levels and annotation that were found to be up-regulated during manipulated biting behavior followed by being down-regulated again after the biting event had taken place (sheet 2), and that were found to be down-regulated during manipulated biting behavior followed by being up-regulated again after the biting event had taken place (sheet 3). (XLSX 232Â kb)
DOI: 10.6084/m9.figshare.c.3636023_d5.v1
title: Additional file 10: of Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation

description: Differentially expressed C. castaneus genes. Tables displaying all C. castaneus genes, including their expression levels and annotation, that were found to be differentially expressed in healthy ant heads at 2 different time points during the day; 10:00 h and 14:00 h (sheets 2 and 3), during manipulated biting behavior in comparison to healthy ant heads at 10:00 h (sheets 4 and 5), after manipulated biting behavior in comparison to healthy ant heads at 14:00 h (sheets 6 and 7), and during manipulated biting behavior versus death after manipulated biting behavior (sheets 8 and 9). (XLSX 339 kb)
DOI: 10.6084/m9.figshare.c.3636008_d5.v1
title: Additional file 2: Table S5. of Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis

description: Discrete Bayes Factors from SPREAD. Locations are denoted with two letter codes (Additional file 5: Table S3). The upper half of the matrix shows the mean (standard deviation) for the discrete Bayes Factor calculated for the 12 discrete trait models. The lower half of the matrix shows how many times a linkage had a Bayes Factor greater than 3.0. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3636008_d4.v1
title: Additional file 5: Table S3. of Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis

description: List of location codes used for phylogeographic analysis. A. List of two letter location codes. B. List of countries conflated into the WH, PC and AF location codes. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3636008_d2.v1
title: Additional file 3: Table S1. of Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis

description: List of primers used in amplification and sequencing. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3636008_d3.v1
title: Additional file 1: Table S4. of Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis

description: Location probabilities for the Pakistan clade. The top four location probabilities for each of the 12 discrete trait runs are listed by the two letter location code with the highest probability on the left. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3636008_d1.v1
title: Additional file 4: Table S2. of Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis

description: List of complete sequences used in the analysis. List of sequences downloaded from GenBank/EMBL/DDBJ. Sequences are by their accession numbers, country of origin, location code and year of collection. Full length sequences used in phylogeography analysis are written in bold. (XLSX 15 kb)
DOI: 10.15468/dl.qusc7z
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pelor japonicum Cuvier, 1829",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035628-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3635765_d1.v1
title: Additional file 1: of Patient-Reported Outcomes Measurement Information System (PROMIS) instruments among individuals with symptomatic knee osteoarthritis: a cross-sectional study of floor/ceiling effects and construct validity

description: The additional file contains a supplemental table entitled â  Matrix of Spearman correlation coefficients between PROMIS short-form instruments and legacy measures.â   The file also includes the raw data used for the figures and the appropriate references. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3635693_d14.v1
title: Additional file 9: Table S9. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Association of each pair between a pathway and a clinic index (for Normal samples) on diabetes datasets. (XLS 56 kb)
DOI: 10.6084/m9.figshare.c.3635693_d13.v1
title: Additional file 14: Table A4. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Pathways ranking for colorectal cancer. (XLS 97 kb)
DOI: 10.6084/m9.figshare.c.3635693_d11.v1
title: Additional file 10: Table S10. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Association of each pair between a pathway and a clinic index (for Diabetes samples) on diabetes datasets. (XLS 60 kb)
DOI: 10.6084/m9.figshare.c.3635693_d10.v1
title: Additional file 6: Table S6. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Overlaps between pathway genes and disease associated genes on diabetes datasets. (XLS 39 kb)
DOI: 10.6084/m9.figshare.c.3635693_d9.v1
title: Additional file 15: Table A5. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Pathway-pair as a crosstalk (colorectal cancer). (XLS 133 kb)
DOI: 10.6084/m9.figshare.c.3635693_d7.v1
title: Additional file 12: Table S12. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Association of each pair between a DEVG and a clinic index (for Diabetes samples) on diabetes datasets. (XLS 119 kb)
DOI: 10.6084/m9.figshare.c.3635693_d8.v1
title: Additional file 8: Table S8. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Pathway-pair as a crosstalk identified on diabetes datasets. (XLS 107 kb)
DOI: 10.6084/m9.figshare.c.3635693_d6.v1
title: Additional file 11: Table S11. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Association of each pair between a DEVG and a clinic index (for Normal samples) on diabetes datasets. (XLS 96 kb)
DOI: 10.6084/m9.figshare.c.3635693_d5.v1
title: Additional file 7: Table S7. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

description: Pathway ranking by different methods on diabetes datasets. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3635678_d4.v1
title: Additional file 5: Table S1. of Up-regulation of A20/ABIN1 contributes to inefficient M1 macrophage polarization during Hepatitis C virus infection

description: Characteristics of the study subjects. (XLS 18 kb)
DOI: 10.6084/m9.figshare.c.3635378_d12.v1
title: Additional file 5: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

description: Chain files, GFF mapping and transcript status of OGS2 on Nvit_2.1 genome assembly. (XLS 17233Â kb)
DOI: 10.6084/m9.figshare.c.3635378_d13.v1
title: Additional file 2: Table S1. of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

description: Consensus in the location of the OGS2 gene set on the genome assemblies of sibling species Nasonia longicornis and N. giraulti, including recent, high identity paralogs. Almost all OGS2 genes are located on 2 sibling species draft assemblies [4], using GMAP [36] transcript mapping. Paralog locus consensus patterns are tabulated for inparalogs (sharing orthology to other species) and uniquepar (lacking strong homology to other species). Of the total paralog families, each with several genes, most paralogs are on different scaffolds for all species. The counts of tandem paralogs with different separations are indicated. Table S2. A set of 62 orthology groups found in Nasonia transcript assemblies that are poorly mapped onto the current genome, but should be considered as part of a complete Nasonia gene set. Table S3. A total of 75 orthology groups missing from Nasonia but found in 9 other insect genomes. Table S4. Histone genes present in OGS2.0 annotated with presence or absence of lineage-specific expansions. NA entries were not assigned to orthologous groups at the level of Hymenoptera. (ZIP 33Â kb)
DOI: 10.6084/m9.figshare.c.3635378_d11.v1
title: Additional file 4: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

description: OrthoDB6 BUSCO (Benchmarking Universal Single Copy Orthologs) genes present in multiple copies in OGS2. (XLS 51Â kb)
DOI: 10.6084/m9.figshare.c.3635378_d10.v1
title: Additional file 9: of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

description: Protein alignment of the OG EOG6R4ZDK (hymenopteran histone H3). Clipped to include only residues shared between all genes. (TXT 13Â kb)
DOI: 10.6084/m9.figshare.c.3635378_d9.v1
title: Additional file 1: Figure S1. of OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis

description: Expression values relative to gene structures for RNA-Seq (Reads) and genome tiling path microarrays (Tile) for species Nasonia (purple, this project), Drosophila (red, blue, [74]) and Daphnia (green, [107]). Annotated gene near-exon spans are scored per base for average expression scores from the data sets, and relative expression plotted with respect to gene transcript start (first exon), stop (last exon), and inner exon start, stop positions. Both methods (genome tiling and RNA-Seq) have abrupt expression strength changes at exon boundaries, on average, indicating their value in modeling gene structure positions. Expression scores are read-coverage for RNA-Seq, and log-normalized intensity for tiling array, as described in the Methods section. Figure S2. Gene modeling example with tile expression data, including gene evidence (upper tracks with tiling, introns, proteins), tiling TAR-exon to Exonerate models (middle), and gene predictions from tile TAR hints (lower), on genome map. The lower tracks have excessive false UTR spans attached to gene models, primarily due to tiling expression that lacks gene start/stop and intron splice joining signals. These false UTR spans are supported by expression evidence, but as a combination of alternate exons, separate gene loci, and non-coding expression. Intermediate tracks (Exonerate models) often match gene structures from other methods, but have a high proportion of unsupported exon extensions as for lower track. Figure S3. Gene join error example. A mistaken gene model from honey bee (tan, lower, LOC552483) is transferred to Nasonia in NCBI RefSeq models (dark orange, middle), merging a ribosomal protein (right) and Ankyrin repeat protein (left). EvidentialGene models (yellow, top) did not contain this mistake, due to the combination of RNA-Seq assemblies (purple, bottom) that are un-joined (but could be parts of one gene), the lack of intron joining evidence, and the orthology assessment metrics that distinguish gene joins from true complete genes. NCBI Refseq models for both Apis (new LOC102654426 and mRpL52 in NCBI Apis rel. 102) and Nasonia have been updated to correct this join error. Figure S4. Log counts of methylated and unmethylated genes in different classes of expression support. Grey bars indicate genes with no known methylation status. (ZIP 938Â kb)