cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3603362_d12
title: Additional file 13: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: This Additional File is an Excel File containing 2 spreadsheets (Additional Tables 18 and 19) indicating the genes identified as having their peak expression at the middle segment and demonstrating the gene ontology analysis of those genes. Table S18. Genes with expression peaking at the M segment. Table S19. Enriched KEGG pathways for genes with expression peaking at the M segment. In grey are highlighted the significant KEGG pathways. (XLSX 92 kb)
DOI: 10.6084/m9.figshare.c.3603392_d4
title: Additional file 5: of Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance

description: Overrepresented GO Categories of all significantly changing transcripts with the Genotype x Treatment x Time interaction. (XLSX 130Â kb)
DOI: 10.6084/m9.figshare.c.3603395_d4
title: Additional file 9: of High throughput techniques to reveal the molecular physiology and evolution of digestion in spiders

description: Astacin multiple alignments used for phylogenetic reconstruction. (FAS 83 kb)
DOI: 10.6084/m9.figshare.c.3603362_d13
title: Additional file 14: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: List of sugarcane genes and primers used for qRT-PCR. Table S20. qRT-PCR Primers. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3603392_d5
title: Additional file 6: of Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance

description: Updated annotation of genes involved in ABA metabolism and signaling, ethylene metabolism and signaling, and transcription factors including those in Figs.Â 1, 2, 3 and 4. (XLS 285Â kb)
DOI: 10.6084/m9.figshare.c.3603395_d5
title: Additional file 3: of High throughput techniques to reveal the molecular physiology and evolution of digestion in spiders

description: Translated and annotated contig database used for proteome identification. (FAS 8034 kb)
DOI: 10.6084/m9.figshare.c.3603362_d14
title: Additional file 8: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: Input data (read count per gene per condition) and R code, to reproduce the differential gene expression analysis for the sugarcane leaf development segments. (BZ2 15159 kb)
DOI: 10.6084/m9.figshare.c.3603392_d6
title: Additional file 8: of Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance

description: Summary table of WGCNA modules including top hub genes and gene ontologies. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.c.3603338_d15
title: Additional file 18: of Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods

description: All figures in high resolution. (ZIP 127 MB)
DOI: 10.6084/m9.figshare.c.3603395_d6
title: Additional file 7: of High throughput techniques to reveal the molecular physiology and evolution of digestion in spiders

description: Quantitative transcriptome data. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.c.3603392_d8
title: Additional file 4: of Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance

description: Overrepresented GO categories of all significantly changing transcripts in response to Genotype x Treatment interaction. (XLSX 192Â kb)
DOI: 10.6084/m9.figshare.c.3603428_d4
title: Additional file 3: of Invaders, natives and their enemies: distribution patterns of amphipods and their microsporidian parasites in the Ruhr Metropolis, Germany

description: Haplotypes of amphipod species and accession numbers. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3603458_d1
title: MOESM2 of Composition and genomic organization of arthropod Hox clusters

description: Additional file 2: Table S4. Â  Positive BLAST hits and genomic locations of conserved Hox gene-associated miRNAs in Mesobuthus, Metaseiulus, Tetranychus, and Strigamia.
DOI: 10.15468/dl.383kta
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aedes aegypti (Linnaeus, 1762)",
 "Country is Guatemala",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032490-241126133413365/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.3603458_d2
title: MOESM7 of Composition and genomic organization of arthropod Hox clusters

description: Additional file 7. Global alignment of Tetranychus fushi tarazu and Antennnapedia nucleotide and protein sequences.
DOI: 10.6084/m9.figshare.c.3603461_d2
title: Additional file 2: Table S2. of Identification of stromal ColXÎą1 and tumor-infiltrating lymphocytes as putative predictive markers of neoadjuvant therapy in estrogen receptor-positive/HER2-positive breast cancer

description: List of 30 genes significantly differentially expressed between good and poor responders. Rows in blue highlight the collagens. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3603461_d3
title: Additional file 5: Table S4. of Identification of stromal ColXÎą1 and tumor-infiltrating lymphocytes as putative predictive markers of neoadjuvant therapy in estrogen receptor-positive/HER2-positive breast cancer

description: Cancer hallmarks gene sets enriched in positively or negatively correlated Col10A1 expression. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3603467_d1
title: Additional file 1: of Diagnosis of TIA (DOT) score â   design and validation of a new clinical diagnostic tool for transient ischaemic attack

description: Online supplement DOTS Calculator. (html 20.5 kb)
DOI: 10.6084/m9.figshare.c.3603458_d4
title: MOESM1 of Composition and genomic organization of arthropod Hox clusters

description: Additional file 1: Table S1. Â Gene accession numbers or genomic locations of Hox genes used in this analysis.
DOI: 10.6084/m9.figshare.c.3603473_d1
title: Additional file 4: Table S4. of Identification of expression patterns in the progression of disease stages by integration of transcriptomic data

description: Functional Enrichment Analyses of lists of genes included in the expression patterns found along the progressive stages of 3 diseases: MDS, AD, CRC. (A) Functional enrichment on terms from Gene Ontology Biological Process (GO-BP) for the 24 genes included in MDS pattern 1. (B) Functional enrichment on GO-BP terms for the 39 genes included in AD pattern 4; (C) Functional enrichment on GO-BP terms for the 168 genes included in CRC patterns 2, 3 and 4. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3603461_d5
title: Additional file 4: Table S3. of Identification of stromal ColXÎą1 and tumor-infiltrating lymphocytes as putative predictive markers of neoadjuvant therapy in estrogen receptor-positive/HER2-positive breast cancer

description: Gene Ontology (GO) gene sets enriched in either good or poor respondingÂ  tumors. The gene sets further examined in this study are highlighted in blue. (XLSX 70 kb)
DOI: 10.15468/dl.e3kmre
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Insecta",
 "Geometry POLYGON ((-96.49764 17.17117, -96.40241 17.17117, -96.40241 17.26216, -96.49764 17.26216, -96.49764 17.17117))",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material citation)"
 ]
 }
 }
 ]
}

 The dataset includes 197 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032494-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.up44nm
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pandalus japonicus (Balss, 1914)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032492-241126133413365/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.3603494_d2
title: Additional file 2: Table S2. of High prevalence of multidrug resistant Enterobacteriaceae isolated from outpatient urine samples but not the hospital environment in Bo, Sierra Leone

description: Full results of isolate identification. The full results of identification of isolates included in this study, including full results of phenotypic and molecular identification assays. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.c.3603494_d3
title: Additional file 3: Table S3. of High prevalence of multidrug resistant Enterobacteriaceae isolated from outpatient urine samples but not the hospital environment in Bo, Sierra Leone

description: Sensitivity testing results of non-Enterobacteriaceae environmental isolates. Results of sensitivity testing of environmental isolates other than Enterobacteriaceae using disk diffusion method. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3603509_d1
title: MOESM2 of Liver cirrhosis mortality, alcohol consumption and tobacco consumption over a 62Â year period in a high alcohol consumption country: a trend analysis

description: Additional file 2. Data file 2 (substance use disorder treatments).
DOI: 10.6084/m9.figshare.c.3603515_d1
title: Additional file 1: of The epigenetic signature of subcutaneous fat cells is linked to altered expression of genes implicated in lipid metabolism in obese women

description: Additional tables with data on DMS and differentially expressed genes between obese cases versus never-obese controls Table S1. Differentially methylated DNA sites linked to genes between obese and never-obese women. Table S2. Differentially expressed genes between obese and never-obese women. Table S3. Differentially DNA methylated sites accompanied by differential expression. Table S4. Differentially expressed genes with DMS in Adipogenesis, Insulin Signaling, and Fatty Acid Biosynthesis pathways. Table S5. Differentially expressed genes with DMS in candidate genes for BMI according to GWAS. Table S6. Differentially expressed genes with DMS in candidate genes for fat distribution according to GWAS. Table S7. DMS in WAT in relation to obesity. Table S8. DMS in WAT in relation to weight loss (Benton MC et al., Genome Biology 2015). Table S9. DMS in WAT in relation to BMI (Rönn T et al., Human Molecular Genetics 2015). Table S10. DMS in WAT in relation to T2D (Nilsson E et al., Diabetes 2014). (XLSX 5076 kb)
DOI: 10.6084/m9.figshare.c.3603509_d2
title: MOESM1 of Liver cirrhosis mortality, alcohol consumption and tobacco consumption over a 62Â year period in a high alcohol consumption country: a trend analysis

description: Additional file 1. Data file 1 (alcohol liters, cigarette equivalents, liver cirrhosis death cases).
DOI: 10.6084/m9.figshare.c.3603527_d1
title: Additional file 1: of Do schistosome vaccine trials in mice have an intrinsic flaw that generates spurious protection data?

description: Spreadsheet calculations documenting the predicted migration profile of schistosomula when the probablility of getting stuck in the lungs on each circuit of the vascular system is modified. a Cercarial challenge, maturation in the naive mouse = 32 %. b Intravenous injection of day 7 schistosomula to the pulmonary vasculature, maturation = 50 %. c Cercarial challenge of an antigen-vaccinated mouse, 40 % protection. d Ditto, 70 % protection. (XLSX 31.2Â kb)
DOI: 10.6084/m9.figshare.c.3603509_d3
title: MOESM3 of Liver cirrhosis mortality, alcohol consumption and tobacco consumption over a 62Â year period in a high alcohol consumption country: a trend analysis

description: Additional file 3. Data file 3 (hospital treatment cases).
DOI: 10.15468/dl.gsjd98
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plecturocebus miltoni (Dalponte, Silva & Silva-Júnior, 2014)"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032496-241126133413365/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.3603536_d1
title: Additional file 9: Table S9. of Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine

description: Differentially expressed genes between matched tumor tissue and VHLmut cultures. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3603545_d1
title: Additional file 4: Table S4: of QTL underlying some agronomic traits in barley detected by SNP markers

description: List of 221 QTLs detected for 10 agronomic traits, their position, likelihood of odd (LOD), additive effect, explained variance and 2-LOD confidence interval. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.28020965
title: How to Improve Usability in Open-Source Software Projects? An Analysis of Evaluation Techniques through a Multiple Case Study

description: Implementation materials (forms, invitations, results, etc) associated with the titled research: "How to Improve Usability in Open-Source Software Projects? An Analysis of Evaluation Techniques through a Multiple Case Study".
DOI: 10.15468/dl.8yj3ch
title: Occurrence Download

description: A dataset containing 323 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Octopus conispadiceus (Sasaki, 1917)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 323 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032497-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hrtp4d
title: Occurrence Download

description: A dataset containing 95756 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PhylumKey is one of (Bryophyta, Marchantiophyta, Anthocerotophyta)",
 "StateProvince is one of (Québec, Quebec, Qc, QC, PQ, Qubec, Nunavik, Québec-Nunavik, Québec - Nunavik, Quebec (Prov.), Québec (Prov.), Quebec Province, Nouveau-Quebec)"
 ]
}

 The dataset includes 95756 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032493-241126133413365/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.3603674_d1
title: Additional file 1: Table S1. of Diversity of susceptible hosts in canine distemper virus infection: a systematic review and data synthesis

description: Full database of CDV infection in non-dog hosts. (XLSX 31Â kb)
DOI: 10.15468/dl.8a4vce
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Insecta",
 "Geometry POLYGON ((-92.40296 14.60903, -92.30984 14.60903, -92.30984 14.70009, -92.40296 14.70009, -92.40296 14.60903))",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material citation)"
 ]
 }
 }
 ]
}

 The dataset includes 60 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032499-241126133413365/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.3603713_d5
title: Additional file 7 of Common disease signatures from gene expression analysis in Huntingtonâ  s disease human blood and brain

description: Immune response signature. In this file we include detailed information about the immune response signature, including the annotations and gene identifiers of each module that participates in this signature. (XLS 15 kb)
DOI: 10.6084/m9.figshare.c.3603743_d1
title: Additional file 1: Table S1. of Gene expression profiling in non-human primate jejunum, ileum and colon after total-body irradiation: a comparative study of segment-specific molecular and cellular responses

description: An excel file containing 18 lists of genes altered ≥ 2.0-Fold from jejunum, ileum and colon at days 4, 7 and 12 after 6.7-Gy and 7.4-Gy TBI including fold-change and P-values. (XLS 3319 kb)
DOI: 10.6084/m9.figshare.c.3603713_d6
title: Additional file 4 of Common disease signatures from gene expression analysis in Huntingtonâ  s disease human blood and brain

description: Annotations of blood modules associated with HD. In this file we include detailed information about the annotations per semantic type of each module in blood that is associated with HD. (XLS 37 kb)
DOI: 10.15468/dl.vz7jue
title: Occurrence Download

description: A dataset containing 16894 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-81.64288 3.96584,-81.56648 3.96609,-81.56711 4.03934,-81.64374 4.03929,-81.64288 3.96584))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 16894 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032498-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vhfeqf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Enteroctopus conispadiceus (Sasaki, 1917)",
 "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/0032500-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.27931557
title: HG38_PD_PHannotations.xlsx

description: This submission contain gene annotations for an Illumina microarray (HorvathMammalMethylChip40) for the human genome (HG38) and the genomes of two species of bats, Phyllostomus discolor (HLphyDis3) and P. hastatus (TTU_PhHast_1.1). The array design is available from the Gene Expression Omnibus (GEO) at NCBI as platform GPL28271.The alignment was done using the QUASR package (Gaidatzis et al., 2015) with the assumption for bisulfite conversion treatment of the genomic DNA. For each species’ genome sequence, QUASR creates an in-silico-bisulfite-treated version of the genome. The set of nucleotide sequences of the designed probes, which includes degenerate base positions due to the bisulfite conversion, was expanded into a larger set of nucleotide sequences representing every possible combination of degenerate bases. We then ran QUASR (a wrapper for Bowtie2) with parameters -k 2 --strata --best -v 3 and bisulfite = "undir” to align the enlarged set of probe sequences to each prepared genome. From these files, we collected only alignments where the entire length of the probe perfectly matched to the genome sequence (i.e. the CIGAR string 50M and flag XM=0).Following the alignment, the CpGs were annotated based on the distance to the closest transcriptional start site using the Chipseeker package (Yu et al., 2015). A gff file with these was created using these positions, sorted by scaffold and position, and compared to the location of each probe in BAM format. We report probes whose variants only mapped to one unique locus in a particular genome. Genomic location of each CpG is categorized as intergenic, 3’ UTR, 5’ UTR, promoter region (minus 10 kb to plus 1000 bp from the nearest TSS), exon, or intron.The file includes the location of androgen sensitive sites as described by Sugrue et al. (2021).Gaidatzis, D., Lerch, A., Hahne, F., and Stadler, M.B. (2015). QuasR: quantification and annotation of short reads in R. Bioinformatics 31, 1130-1132.Sugrue, V. J., Zoller, J. A., Narayan, P., Lu, A. T., Ortega-Recalde, O. J., Grant, M. J., . . . Horvath, S. (2021). Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci. Elife, 10. doi:10.7554/eLife.64932Yu, G., Wang, L.G., and He, Q.Y. (2015). ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382-2383.
DOI: 10.6084/m9.figshare.c.3603788_d2
title: Additional file 1: Table S1. of Development of foraging skills in two orangutan populations: needing to learn or needing to grow?

description: Overview of the data used for the different analyses. Study site, focal individual, sex and date of birth of the focal individual, mother of the focal individual, as well as the years in which the different types of data (diet data, feeding rates, ramble ratios and laser measurements) were taken. Table S2. GLMM with absolute feeding rate of the adult females as dependent variable. To see if the if there is a difference between feeding rates obtained by video coding as opposed to direct observation this was included as as a binary variable (“Video”). Shown are effects, estimates, standard errors and p-values as well as number of levels for the categorical variables. The number in parentheses represents the total number of individual feeding rates included in the analyses: Only rates of fruits on which we had data from the same individual obtained via video coding as well as via direct observation were included. Table S3. GLMM with feeding rate in percentage of the mothers feeding rates as a dependent variable. To see if the presence absence of a simultaneous feeding rate taken on the mother has an effect it was included as a binary variable (“Simultaneous mother sample”). Effects, estimates, standard errors and p-values as well as number of number of levels for the categorical variables and AIC values of the models. The number in parentheses represents the total number of individual - age - species combinations.  Table S4. GLMM with feeding rate of the Tuanan immatures in percentage of the mothers feeding rates as a dependent variable without (a) and with fruit toughness and size included as a fixed effect (b). Effects, estimates, standard errors and p-values as well as number of levels for the categorical variables and AIC values of the model. (ZIP 23 kb)
DOI: 10.6084/m9.figshare.c.3603782_d4
title: Additional file 1: Table S1. of Emergence and evolution of yeast prion and prion-like proteins

description: List of fungal proteomes and their sources (weblinks). (XLS 37 kb)