cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3641837_d1
title: Additional file 4 of GenAp: a distributed SQL interface for genomic data

description: The SAM equivalent of the Additional File 3. (SAM 3 kb)
DOI: 10.6084/m9.figshare.c.3641837_d2
title: Additional file 6 of GenAp: a distributed SQL interface for genomic data

description: This is sample code that uses Spark SQL to perform an interval based join to the contents of sampleReads.adam with the contents of Additional File 5. (SCALA 1 kb)
DOI: 10.6084/m9.figshare.c.3641837_d4
title: Additional file 1 of GenAp: a distributed SQL interface for genomic data

description: This file contains instructions on how to clone and build our modification of Apache spark and run it in local mode on a userâ  s computer. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3641837_d5
title: Additional file 3 of GenAp: a distributed SQL interface for genomic data

description: This tarball contains a sample file of aligned reads in ADAM format. Note that this is a binary format and we provide a user the oportunity to explore this file by attaching the equivalent SAM file of the same alignments. (TAR 21 kb)
DOI: 10.6084/m9.figshare.c.3641837_d6
title: Additional file 5 of GenAp: a distributed SQL interface for genomic data

description: This is a sample vcf file similar to the one we used in the results section. (VCF 9 kb)
DOI: 10.6084/m9.figshare.c.3641837_d7
title: Additional file 7 of GenAp: a distributed SQL interface for genomic data

description: This tarball contains the custom C++ software that we wrote to implement the last query of the results section. For reference, it also contains the respective Spark SQL implementation. (TAR 9 kb)
DOI: 10.15468/dl.vp4up6
title: Occurrence Download

description: A dataset containing 1439 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles claviger (Meigen, 1804)"
 ]
}

 The dataset includes 1439 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033977-241126133413365/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.3641879_d9
title: Additional file 9: Table S3. of Phenotypic convergence in bacterial adaptive evolution to ethanol stress

description: (CSV 11Â kb)Identified mutations in the tolerant strain A.
DOI: 10.6084/m9.figshare.c.3641879_d14
title: Additional file 4: Table S2. of Phenotypic convergence in bacterial adaptive evolution to ethanol stress

description: (CSV 7Â kb)Intracellular metabolite concentrations in the parent and tolerant strains.
DOI: 10.6084/m9.figshare.c.3641900_d1
title: MOESM3 of Whole-genome sequencing and comparative genomic analysis of Escherichia coli O91 strains isolated from symptomatic and asymptomatic human carriers

description: Additional file 3. Phage-associated regions in NCCP15736 and NCCP15737.
DOI: 10.6084/m9.figshare.c.3641900_d2
title: MOESM2 of Whole-genome sequencing and comparative genomic analysis of Escherichia coli O91 strains isolated from symptomatic and asymptomatic human carriers

description: Additional file 2. Virulence genes of NCCP15736 and NCCP15737.
DOI: 10.6084/m9.figshare.c.3641900_d3
title: MOESM1 of Whole-genome sequencing and comparative genomic analysis of Escherichia coli O91 strains isolated from symptomatic and asymptomatic human carriers

description: Additional file 1. Annotated genes of NCCP15736 and NCCP15737 using the RAST server.
DOI: 10.6084/m9.figshare.c.3641942_d7
title: Additional file 8: Table S5. of MAPK signaling is necessary for neurogenesis in Nematostella vectensis

description: Selection of 100 genes downregulated after U0126 treatments. Selected genes that were significantly (Pâ
DOI: 10.6084/m9.figshare.c.3641942_d8
title: Additional file 6: Table S3. of MAPK signaling is necessary for neurogenesis in Nematostella vectensis

description: Genes with at least a 2-fold change after U0126 treatments based on our array analysis. (XLSX 3983 kb)
DOI: 10.6084/m9.figshare.c.3641942_d9
title: Additional file 14: Table S6. of MAPK signaling is necessary for neurogenesis in Nematostella vectensis

description: Primer pairs used in this study for qPCR analysis. (XLS 53 kb)
DOI: 10.6084/m9.figshare.c.3641942_d10
title: Additional file 1: Table S1. of MAPK signaling is necessary for neurogenesis in Nematostella vectensis

description: Dose-dependent effects of U0126 on Nvsprouty, Nvbrachyury, and Nv-fgfA1 expression. Dose-dependent effects of U0126 analyzed by in situ hybridization. Analyzed U0126 concentration as indicated in Row 1 and number of embryos with phenotype scored based on expansion/reduction of the domain of expression as indicated in the column on the right. (XLS 33 kb)
DOI: 10.6084/m9.figshare.c.3641942_d12
title: Additional file 7: Table S4. of MAPK signaling is necessary for neurogenesis in Nematostella vectensis

description: Selection of 22 genes upregulated after U0126 treatment. Selected genes that were significantly (Pâ
DOI: 10.6084/m9.figshare.c.3641945_d1
title: Additional file 1: of Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network

description: Table detailing the accession numbers of isolates used within the study. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3641966_d1
title: Additional file 2: Table S7. of Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function

description: Full list of transcription factors, with properties and their classification. (XLS 945 kb)
DOI: 10.6084/m9.figshare.c.3641966_d3
title: Additional file 3: Table S8. of Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function

description: Functional Annotation Clustering output from DAVID enrichment analysis. (XLS 1695 kb)
DOI: 10.15468/dl.qghdya
title: Occurrence Download

description: A dataset containing 318 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles coustani Laveran, 1900"
 ]
}

 The dataset includes 318 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033978-241126133413365/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.3642017_d5
title: Additional file 3: Table S2. of Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types

description: Relative enrichment of driver TFs domains for somatic mutations across approximately 7,000 tumors. (XLS 79 kb)
DOI: 10.6084/m9.figshare.c.3642017_d6
title: Additional file 6: Table S8.  of Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types

description: Driver circuits involving a TF and a partner driver tested across 15 tumor types. (XLS 49 kb)
DOI: 10.6084/m9.figshare.c.3642017_d7
title: Additional file 4: Table S6. of Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types

description: List of significant targets detected across 15 TCGA cohorts (XLS 466 kb)
DOI: 10.6084/m9.figshare.c.3642020_d2
title: Additional file 3: of Crowdsourced direct-to-consumer genomic analysis of a family quartet

description: Table summary of ingenuity analysis results. (XLS 96 kb)
DOI: 10.6084/m9.figshare.c.3642020_d1
title: Additional file 2: of Crowdsourced direct-to-consumer genomic analysis of a family quartet

description: Genome Trax table with homozygous deleterious SNPs and their associated disease. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3642038_d2
title: Additional file 13: Dataset S3. of Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster

description: Gene set enrichment analysis (GSEA) of GO terms comparing diapause and response to restricted diet in D. melanogaster. We compare our study of three weeks diapause (3wD) to that of an analysis of effects of restricted diet (RF) [145]. (A) GSEA for upregulated transcripts identified mostly terms connected to cell cycle and gene expression. (B) Transcripts mostly from carbohydrate metabolism are regulated in opposite way in 3wD and RF. (C) For downregulated transcripts no significant enriched GO terms (ns) were identified. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3642038_d3
title: Additional file 3: Dataset S1. of Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster

description: Gene list of significantly regulated probes and reciprocal comparison. Transcripts that are significantly altered more than two-fold (|log2FC| ≥ 1, q ≤ 0.05) are shown. 3wDvs1wN represent transcripts regulated upon 3 weeks of diapause compared to 1 week control flies, 3wDvs3wN represent genes regulated in diapause samples with comparison to 3 week old sibling controls, 3wNvs1wN represent genes influenced by aging in 3 week old control flies compared to 1 week old control flies. Significantly inhibited transcripts are highlighted in blue, significantly activated in orange. Links to Flybase, Wikigene, Genecard, NCBI, ENSEMBL and ExPASy databases are included. (XLSX 2131 kb)
DOI: 10.6084/m9.figshare.c.3642038_d6
title: Additional file 12: Dataset S2. of Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster

description: List of genes shared between diapause and response to restricted diet in D. melanogaster. We compared our study of three weeks diapause (3wD) to that of an analysis of effects of restricted diet (RF) [145]. Significantly inhibited transcripts are highlighted in blue, significantly activated in orange (for the RF study, genes with q ≤ 0.05 were considered significantly regulated, as was used in original study). Links to Flybase and Genecard databases are included. The Venn diagram summarizes the numbers of significantly regulated genes and how they overlap. (XLSX 173 kb)
DOI: 10.6084/m9.figshare.c.3642038_d7
title: Additional file 9: Table S4. of Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster

description: Genes affected by 3 weeks diapause compared to ones implicated in aging and increased longevity. Microarray study of aging response genes [136], longevity mapping study [33], transcriptome changes in mated and non-mated aging females [7] and candidate study for lifespan genes [135]. Significantly inhibited transcripts are highlighted in blue, significantly activated in orange. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.c.3642038_d12
title: Additional file 14: Dataset S4. of Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster

description: Comparisons of diapause response genes from our study of D. melanogaster with other transcription studies on reproductive diapause. We compared our study to a D. montana candidate gene microarray study [149] and Culex pipiens diapause response genes [152]. Significantly inhibited transcripts are highlighted in blue, significantly activated in orange. Links to Flybase are included at genes shared with D. melanogaster. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3642080_d2
title: Additional file 1: Sheet 1. of A multi-factorial analysis of response to warfarin in a UK prospective cohort

description: Interaction coefficients of drugs known to be interacting with warfarin. Drugs known to interact with warfarin were classified according to their effect on warfarin dosing, with a plus sign for potentiating drugs, and minus for the opposite effect, the absolute value representing the scale of the effect. When several of these drugs were used concomitantly the sum of these coefficients was used. Sheet 2. List of all concomitant drugs taken by patients. Sheet 3. Top signals from linear regressions on SMWD. P values marked with an asterisk were obtained from the regression only adjusting for non-genetic factors, while other P values where obtained from a multiple regression after conditioning on rs9923231, rs1799853 and rs1057910. Sheet 4. Top signals from logistic regressions on INR &gt;4 during first week of treatment. P values marked with an asterisk were obtained from the regression only adjusting for non-genetic factors, while other P values where obtained from a multiple regression after conditioning on rs2288004 and rs1072753. P values for rs9923231, CYP2C9 *2 and *3 are reported, albeit they were not the most statistically significant signals in their respective region. 95 % confidence intervals for odds ratios are indicated in parentheses. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3642098_d2
title: Additional file 2: of Epidemiology, impact and control of bovine cysticercosis in Europe: a systematic review

description: List of references for the records included in the review. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3642200_d1
title: MOESM2 of Effect of topically applied Saccharomyces boulardii on the healing of acute porcine wounds: a preliminary study

description: Additional file 2. Wound microbiology.
DOI: 10.6084/m9.figshare.c.3642200_d2
title: MOESM1 of Effect of topically applied Saccharomyces boulardii on the healing of acute porcine wounds: a preliminary study

description: Additional file 1. Wound measurements.
DOI: 10.6084/m9.figshare.c.3642218_d5
title: Additional file 7: of SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer

description: KEGG pathways associated with genes in TableÂ 1. Pathway image files downloaded from KEGG and the html file is linked to these images. (ZIP 963 kb)
DOI: 10.15468/dl.f94ew6
title: Occurrence Download

description: A dataset containing 64153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles crucians Wiedemann, 1828"
 ]
}

 The dataset includes 64153 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033980-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tdd5ar
title: Occurrence Download

description: A dataset containing 50477 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Mammalia",
 "Year 2023-2023"
 ]
}

 The dataset includes 50477 records from 121 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033981-241126133413365/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.3642263_d1
title: Additional file 7: of Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.)

description: Marker-assisted selection-suitable markers identified by SDvEP method. The file contains several tabs. Each tab is dedicated to one of the MAS-suitable markers. Each tab contains two images. The image on the left shows how a putative GLS resistance allele discriminated by a MAS-suitable marker is well-conserved in DAS-001 (GLS resistant parent of DH population) and absent in 109 GLS susceptible lines. The image on the right shows that a putative GLS resistance allele conserved in DAS-001 was also found in several other GLS resistance lines with a genetic background different from DAS-001. (XLSX 114 kb)
DOI: 10.6084/m9.figshare.c.3642260_d5
title: Additional file 5: of Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris

description: Table S1. Primers used in this study and detailed plasmid construction. Primers used for creating the S. pombe and P. pastoris plasmids are separated. Also primers for construction of the plasmids are separated from primers for sequencing and insertion of GOIs. In addition separate spreadsheets are providing information on the exact construction of the plasmids by listing the PCR products and restriction enzymes used for assembly.
DOI: 10.6084/m9.figshare.c.3642260_d4
title: Additional file 3: of Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris

description: Plasmid sequences of the constructs used in this study in Genbank format.
DOI: 10.6084/m9.figshare.c.3642263_d3
title: Additional file 1: of Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.)

description: Maize inbred lines representing Association Panel used for genome wide association study with their reaction to Cercospora represented by the average value of the Area Under Disease Progress Curve (AUDPC) in all four environments. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3642266_d2
title: Additional file 11: Table S2. of A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration

description: The distribution of genes between the COMPACT groups and the WGCNA dynamic modules prior to merging in WGCNA. The column labels correspond to the module colors assigned by WGCNA. The row labels indicate the COMPACT group size, carbohydrate pattern and ethanol pattern. For example, the row label 0589-c0-10-e0-10 corresponds to a COMPACT group that contains 589 genes showing a downregulation only at 6Â h time point in both the dietary groups. (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.c.3642263_d7
title: Additional file 2: of Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.)

description: Days to silking data collected from the representatives of the Association panel planted in Sidney (IL) in 2012. Independent field trial was conducted in Sidney (IL) in 2012, where flowering time data were collected from 254 representatives of the Association Panel. Flowering time data were represented by days to silking (DTS) and measured as days from planting to silk emergence in 50Â % of plants in row. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3642266_d4
title: Additional file 1: Table S1. of A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration

description: Normalized gene expression data for the statistically significant genes from the LLM samples, corresponding to the ethanol-adapted state. (XLSX 320Â kb)
DOI: 10.6084/m9.figshare.c.3642266_d11
title: Additional file 13: Table S4. of A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration

description: List of real-time PCR primers. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3642266_d12
title: Additional file 12: Table S3. of A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration

description: The distribution of genes between the COMPACT groups and the WGCNA merging modules. The column labels correspond to the module colors assigned by WGCNA. The row labels indicate the COMPACT group size, carbohydrate pattern and ethanol pattern. For example, the row label 0589-c0-10-e0-10 corresponds to a COMPACT group that contains 589 genes showing a downregulation only at 6Â h time point in both the dietary groups. (XLSX 47Â kb)
DOI: 10.15468/dl.h4rzt3
title: Occurrence Download

description: A dataset containing 218121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is one of (Aponogeton distachyos L.f., Arthurdendyus triangulatus (Dendy, 1895), Cabomba caroliniana A.Gray, Callosciurus finlaysonii (Horsfield, 1823), Cherax destructor Clark, 1936, Corvus splendens Vieillot, 1817, Crassula helmsii (Kirk) Cockayne, Elodea densa (Planch.) Casp., Eriocheir sinensis H.Milne Edwards, 1853, Erythranthe guttata (DC.) G.L.Nesom, Faxonius immunis (Hagen, 1870), Faxonius juvenilis (Hagen, 1870), Faxonius rusticus (Girard, 1852), Faxonius virilis (Hagen, 1870), Gambusia affinis (Baird & Girard, 1853), Heracleum mantegazzianum Sommier & Levier, Heracleum persicum Desf. ex Fisch., C.A.Mey. & Avé-Lall., Heracleum pubescens (Hoffm.) M.Bieb., Houttuynia cordata Thunb., Hydrocotyle ranunculoides L.f., Impatiens glandulifera Royle, Koenigia polystachya (Wall. ex Meisn.) T.M.Schust. & Reveal, Lagarosiphon major (Ridl.) Moss, Lepomis gibbosus (Linnaeus, 1758), Limnoperna fortunei (Dunker, 1857), Ludwigia grandiflora (Michx.) Greuter & Burdet, Ludwigia peploides (Kunth) P.H.Raven, Lysichiton americanus Hultén & H.St.John, Morone americana (Gmelin, 1789), Muntiacus reevesi (Ogilby, 1839), Myriophyllum aquaticum (Vell.) Verdc., Myriophyllum heterophyllum Michx., Pacifastacus leniusculus (Dana, 1852), Petasites japonicus (Siebold & Zucc.) Maxim., Pontederia cordata L., Procambarus acutus (Girard, 1852), Procambarus clarkii (Girard, 1852), Procambarus virginalis Lyko, 2017, Pseudorasbora parva (Temminck & Schlegel, 1846), Pycnonotus cafer (Linnaeus, 1766), Saururus cernuus L., Sciurus carolinensis Gmelin, 1788, Sciurus niger Linnaeus, 1758, Solenopsis invicta Buren, 1972, Solenopsis richteri Forel, 1909, Threskiornis aethiopicus (Latham, 1790), Vespa velutina Lepeletier, 1836, Zizania latifolia (Griseb.) Hance ex F.Muell.)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 218121 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033955-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.52ataj
title: Occurrence Download

description: A dataset containing 596310169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Animalia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is United States of America",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2020"
 ]
}

 The dataset includes 596310169 records from 800 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033964-241126133413365/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.3642302_d1
title: Additional file 3: Table S3. of eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants

description: Dataset 1 results at p-value significance of 0.01. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3642302_d3
title: Additional file 2: Table S2. of eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants

description: Annotation of 20 variants (excluding 5 proof of principle variants) from different prediction tools. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.c.3642302_d2
title: Additional file 1: Table S1. of eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants

description: Distribution of samples across the two datasets. (XLSX 44 kb)