cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3612509_d13
title: Additional file 3: Figure S2. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: A. False positive rate distributions for datasets A1–A3. Violin plot of distributions of false positive rate (FPR) in 150 iterations for each case proportion in datasets A1–A3 (vertical panels), analyzed with all differential relative abundance methods (horizontal panels). FPR is defined as the fraction of OTUs with p
DOI: 10.6084/m9.figshare.c.3612509_d14
title: Additional file 8: Figure S7. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: A. Area under the curve distributions for multiplicative spike-ins in dataset A4. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of multiplicative spike-in magnitude and case proportion (vertical panels) in dataset A4, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. B. Area under the curve distributions for additive spike-ins in dataset A4. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of additive spike-in magnitude and case proportion (vertical panels) in dataset A4, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. C. Area under the curve distributions for mixed multiplicative spike-ins in dataset A4. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each case proportion (vertical panels) in dataset A4, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. (ZIP 1831 kb)
DOI: 10.6084/m9.figshare.c.3612566_d1
title: Additional file 2: Table S2. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

description: CTR-NT Differentially regulated genes. Breakdown of genes differentially up and downregulated with â Ľ1.5 fold change in CTR-NT blastocyst compared to in vitro fertilized embryos. Red and green colors represent up and downregulation, respectively. (XLS 261Â kb)
DOI: 10.6084/m9.figshare.c.3612575_d2
title: Additional file 6: Table S2. of Deciphering the transcriptional regulation and spatiotemporal distribution of immunity response in barley to Pyrenophora graminea fungal invasion

description: Primers used in this work (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3612566_d3
title: Additional file 4: Table S4. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

description: Unique gene expression in CTR-NT and TSA-NT. A breakdown of genes predominantly or commonly expressed in CTR-NT- and TSA-NT-derived blastocysts. (XLS 416Â kb)
DOI: 10.6084/m9.figshare.c.3612575_d3
title: Additional file 9: of Deciphering the transcriptional regulation and spatiotemporal distribution of immunity response in barley to Pyrenophora graminea fungal invasion

description: Supporting data. Go analysis. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.c.3612617_d1
title: Additional file 6: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The interspecific Tajimaâ  s D values of TFBS, coding sequences (CDS) and introns. (XLS 1229 kb)
DOI: 10.6084/m9.figshare.c.3612617_d2
title: Additional file 3: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The predicted transcription factor binding sites (TFBSs) in the promoters of genes in the pathways of photoperiod, vernalization and pathway integration in Arabidopsis, Brachypodium, wheat and barley. (XLSX 406 kb)
DOI: 10.6084/m9.figshare.c.3612617_d3
title: Additional file 5: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The intraspecific Tajimaâ  s D values of TFBSs in Arabidopsis, Brachypodium, wheat and barley. (XLS 110 kb)
DOI: 10.6084/m9.figshare.c.3612617_d4
title: Additional file 4: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The overlapping transcription factor binding sites (TFBSs) for each gene that is concurrent in Arabidopsis, Brachypodium, wheat and barley. (XLSX 197 kb)
DOI: 10.6084/m9.figshare.c.3612617_d5
title: Additional file 2: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The ortholog groups and genes in the flowering pathways in Arabidopsis, Brachypodium, wheat and barley. (XLS 62 kb)
DOI: 10.6084/m9.figshare.c.3612629_d2
title: Additional file 1: of Supplementation of transport and freezing media with anti-apoptotic drugs improves ovarian cortex survival

description: Statistical analyses between the different conditions and treatments. Table S1 and Table S2. Primordial follicular density. Table S3 and Table S4. Density of morphologically normal primordial follicules. Table S5. Density of proliferative granulosa cells between treatments. Table S6. Density of global proliferative cells between treatments. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3612671_d3
title: Additional file 3. of Cleansing effect of acidic L-arginine on human oral biofilm

description: Summary of percent abundance of salivary microbiota from healthy volunteers. (XLS 48 kb)
DOI: 10.60656/947f9bc51b554dc5
title: Custom collection of MWR brightness temperature data from Munich between 1 Jan 2017 and 13 Dec 2024
DOI: 10.6084/m9.figshare.c.3612743_d1
title: Additional file 1: of The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

description: Supplementary tables. (XLSX 148 kb)
DOI: 10.6084/m9.figshare.c.3612761_d2
title: Additional file 4: of Level of nutrition knowledge and its association with fat consumption among college students

description: Copy of Regression and Correlation Analysis (CSV 996 bytes)
DOI: 10.6084/m9.figshare.c.3612761_d3
title: Additional file 3: of Level of nutrition knowledge and its association with fat consumption among college students

description: A copy of the raw data file. (CSV 157Â kb)
DOI: 10.6084/m9.figshare.c.3612776_d1
title: Additional file 2 of CNARA: reliability assessment for genomic copy number profiles

description: Supplementary Table S1. A complete list of the 1522 copy number profiles, including GEO accession number and reliability label. (TSV 58 kb)
DOI: 10.6084/m9.figshare.c.3612773_d1
title: Additional file 1: Table S1. of Assessing the reproducibility of exome copy number variations predictions

description: Lists all the IDs used in this study. Table S2 gives details of independent dataset analysis. Tables S3 and S4 give details of size and capture analyses. Table S5 lists ClinSeqÂŽ CNVs identified from SNP chips used in this study. Table S6 lists the summary of CNV sizes for 300 ClinSeq run at base pair and exon resolution. Table S7 lists SNP array CNV calls used for 300 ClinSeq samples. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3612761_d4
title: Additional file 2: of Level of nutrition knowledge and its association with fat consumption among college students

description: A copy of the studyâ  s questionnaire. (XML 412Â kb)
DOI: 10.6084/m9.figshare.c.3612761_d5
title: Additional file 1: of Level of nutrition knowledge and its association with fat consumption among college students

description: Consent Form. A sample of the consent form that was given to participants in this study. (TXT 5Â kb)
DOI: 10.6084/m9.figshare.c.3612815_d6
title: Additional file 10: Table S9. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Summary of publicly available data used for L1 ASP analysis. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3612833_d1
title: Additional file 2: of A phase I clinical study of immunotherapy for advanced colorectal cancers using carcinoembryonic antigen-pulsed dendritic cells mixed with tetanus toxoid and subsequent IL-2 treatment

description: The results of T cell proliferation assay. (XLS 93Â kb)
DOI: 10.6084/m9.figshare.c.3612815_d7
title: Additional file 3: Table S2. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Gene ontology analysis for 988 genes that we identified with associated L1 ASP transcripts using Panther online database. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3612839_d1
title: Additional file 7: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the SCL-90-R in the Ukrainian general population: correlations between latent factors. Results of confirmatory factor analysis. Correlations between the latent variables measured by SCL-90-R items in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3612815_d9
title: Additional file 11: Table S10. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Primers used for empirical validation of L1 ASP transcripts. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3612839_d2
title: Additional file 8: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the BSI-53 in the Ukrainian general population: correlations between latent factors. Results of confirmatory factor analysis. Correlations between the latent variables measured by BSI-53 items in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612839_d3
title: Additional file 11: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the SCL-14 in the Ukrainian general population: correlations between latent factors. Results of confirmatory factor analysis. Correlations between the latent variables measured by SCL-14 items in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3612839_d10
title: Additional file 9: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the SCL-27 in the Ukrainian general population: correlations between latent factors. Results of confirmatory factor analysis. Correlations between the latent variables measured by SCL-27 items in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3612839_d11
title: Additional file 10: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the BSI-18 in the Ukrainian general population: correlations between latent factors. Results of confirmatory factor analysis. Correlations between the latent variables measured by BSI-18 items in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3612875_d2
title: Additional file 5: of Composition and dynamics of the respiratory tract microbiome in intubated patients

description: R markdown analysis outline. The code used to read study data, aggregate OTUs for heatmap analysis, determine OTU proportional abundance, evaluate alpha and beta diversity, and perform generalized estimating equations (GEE) modeling of longitudinal data is demonstrated. (RMD 8.30 KB)
DOI: 10.6084/m9.figshare.c.3612875_d3
title: Additional file 4: of Composition and dynamics of the respiratory tract microbiome in intubated patients

description: De novo OTU table. Taxonomic assignments of de novo OTUs. Sequence data was analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics pipeline, version 1.8.0. Sequence alignment was performed via PyNAST, with de novo operational taxonomic unit (OTU) formation via uclust as per QIIME default settings. Taxonomic assignment of de novo OTUs was based on BLAST of representative sequences against the Living Tree Project database (SSU release 119), with the highest bit-score chosen. De novo OTUs were used in comparison to clinical culture data. (ZIP 404 KB)
DOI: 10.6084/m9.figshare.c.3612890_d1
title: Additional file 1: Table S1. of Molecular epidemiology of carbapenem resistant Enterobacteriaceae in Valle dâ  Aosta region, Italy, shows the emergence of KPC-2 producing Klebsiella pneumoniae clonal complex 101 (ST101 and ST1789)

description: Phenotypic and genotypic features of Enterobacteriaceae included in the study. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3612875_d4
title: Additional file 2: Figure S2. of Composition and dynamics of the respiratory tract microbiome in intubated patients

description: Comparison of Illumina MiSeq and Roche/454 sequencing applied to identical samples. (A) Subjects 1–5 had upper and lower respiratory tract samples 16S rRNA gene sequencing performed on both the Illumina MiSeq and Roche/454 platforms. A heatmap displays family-level taxonomic assignment (as in Fig. 2). Vertical black lines separate each sample pair, allowing direct comparison of results obtained across the two sequencing platforms. (B) Procrustes analysis comparing weighted, normalized UniFrac distances calculated from the closed-reference OTUs formed from each sequencing platform. Balls indicate samples, colored by subject (red—subject 001, blue—subject 002, orange—subject 003, green—subject 004, purple—subject 005); edges connect the results of sequencing on Roche/454 and Illumina MiSeq platforms. Procrustes m2 was 0.13 (p
DOI: 10.6084/m9.figshare.c.3612893_d1
title: Additional file 1: Table S1. of 
                     Panx3 links body mass index and tumorigenesis in a genetically heterogeneous mouse model of carcinogen-induced cancer

description: Genotype marker locations and associated rsIDs. An Excel file (.xlsx) containing information about the genotyping markers used in this analysis. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.c.3612875_d5
title: Additional file 3: of Composition and dynamics of the respiratory tract microbiome in intubated patients

description: Closed-reference OTU table. Closed-reference OTU taxonomic assignments. Sequence data was analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics pipeline, version 1.8.0. Sequence alignment was performed via PyNAST, closed-reference operational taxonomic unit (OTU) formation, and taxonomic assignment was based on the Greengenes (13.8) taxonomy. Closed-reference OTUs were used in all comparisons between intubated subjects and healthy controls. (ZIP 90.8 KB)
DOI: 10.6084/m9.figshare.c.3612941_d1
title: Additional file 1: of Heterosexual transmission of HIV in the Dominican Republic: gendered indicators are associated with disparities in condom use

description: Tables for nested logistic models. The additional file 1 is an Excel document which contains three separate sheets, each one with a different table that displays the results of the nested analyses for condom use: Table S5 displays the nested logistic models for condom use among all Dominicans age 15 to 45Â years in the sample. Table S6 displays the disaggregated nested logistic models for condom use by men. Table S5 displays the disaggregated nested logistic models for condom use by women. (XLSX 37Â kb)
DOI: 10.15468/dl.6x9m7w
title: Occurrence Download

description: A dataset containing 1062017 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 {
 "or" : [
 "StateProvince ~Ibagué",
 "StateProvince ~Tolima"
 ]
 },
 "Year 2010-2024"
 ]
 }
 ]
}

 The dataset includes 1062017 records from 214 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032749-241126133413365/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.3612959_d4
title: Additional file 9: of Changes in the composition of the RNA virome mark evolutionary transitions in green plants

description: Maximum-likelihood tree (Newick format) of RdRPs from viruses in order Tymovirales. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3612983_d3
title: Additional file 1: Table S1. of Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza)

description: Oryza samples used in analyses. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3612959_d6
title: Additional file 12: of Changes in the composition of the RNA virome mark evolutionary transitions in green plants

description: Maximum-likelihood phylogenetic tree (Newick format) of XRN nucleases from Selaginella moellendorffii and its relatives. (TXT 3 kb)
DOI: 10.6084/m9.figshare.c.3612983_d4
title: Additional file 5: Table S2. of Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated and weedy rice (Oryza)

description: PSTOL1 primers used in PCR genotyping and sequencing. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3612989_d1
title: Additional file 5: of PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

description: Stoichiometric matrix and experimental data for Escherichia coli. A Microsoft Excel spreadsheet file with i) the stoichiometric matrix of E. coli and ii) the experimental datasets taken from the literature. This includes measurements of biomass, glycerol, OUR, CPR and pyruvate. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3612959_d7
title: Additional file 8: of Changes in the composition of the RNA virome mark evolutionary transitions in green plants

description: Alignment (Phylip format) of RdRP from viruses in order Tymovirales. (TXT 11 kb)
DOI: 10.6084/m9.figshare.c.3612992_d7
title: Additional file 15: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Summary of line specific variations leading to stop sites. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612992_d9
title: Additional file 10: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Gene deletion detected in 35 chickpea genotypes used in this study. (XLSX 67Â kb)
DOI: 10.6084/m9.figshare.c.3613013_d1
title: Additional file 1: of Common data elements for secondary use of electronic health record data for clinical trial execution and serious adverse event reporting

description: Title of data: CTE & SAE Data Inventory. Description of data: List of common data elements in clinical trials with domain, availability/completeness, occurrence in trials, semantic codes and definition. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3612992_d11
title: Additional file 17: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Summary of all variant effects predicted by SNPEff. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3613016_d2
title: Additional file 2: Table S1. of PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing

description: The list of restriction enzymes being used by PhytoCRISP-Ex. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3612992_d12
title: Additional file 23: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Summary of variations identified in the â   QTL-hotspot â   region reported by Varshney et al. [6, 8]. (XLSX 91Â kb)
DOI: 10.6084/m9.figshare.c.3612992_d15
title: Additional file 8: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Summary of Indel ratio among 35 chickpea genotypes re-sequenced. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3613040_d1
title: Additional file 1: of The using of a piglets as a model for evaluating the dipyrone hematological effects

description: Numerical raw data. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3612992_d16
title: Additional file 9: of Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

description: Gene duplications observed in 35 chickpea genotypes. (XLSX 2979Â kb)
DOI: 10.6084/m9.figshare.c.3613076_d4
title: Additional file 1: of Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

description: Detected regions of recombination in all strains. Information regarding the 21 detected regions of recombination across all examinied X. citri pv. citri strains, including information about the strains in which the event is detected, the genes contained within the recombination zone and functional information about the genes where available. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3613091_d1
title: Additional file 1: of Biomechanical and biochemical properties of the thoracic aorta in warmblood horses, Friesian horses, and Friesians with aortic rupture

description: Summary of the biomechanical and biochemical properties of the equine thoracic aorta in the 3 groups of horses. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3613076_d5
title: Additional file 2: of Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

description: Pathotype-specific regions of recombination and number of introduced variant residues in genes. Information about the pathotype-specific recombination regions, including which genes are involved in each event, and the number of pathotype-specific variant residues found in each gene. “-” denotes cases where the number of pathotype-specific residues could not be calculated. (XLSX 10 kb)