cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3634949_d2
title: Additional file 7: Table S5. of Immunosenescence of the CD8+ T cell compartment is associated with HIV-infection, but only weakly reflects age-related processes of adipose tissue, metabolism, and muscle in antiretroviral therapy-treated HIV-infected patients and controls

description: Unadjusted and adjusted associations between PD-1+CD8+ T cell subsets and ageing parameters in HIV+. Adjusted analyses are in grey. Age was adjusted for HIV-duration, ART-duration, and current ART; IL-6, suPAR, HOMA-IR, metabolic syndrome, VAT, and lLMI were adjusted for age, HIV-duration, ART-duration, and current ART. †Parameters were transformed using log2(x). Estimates and confidence intervals are back transformed using (2β-1) × 100, and shown as percent change in the outcome per unit increase of the covariate. Abbreviations: HOMA-IR: homeostatic model assessment of insulin resistance, IL-6: interleukin-6, PD-1: programmed death-1, lLMI: leg lean mass index, suPAR: soluble urokinase plasminogen activator receptor, TCM: central memory T cell, TED: early differentiated T cell, TEM: effector memory T cell, TEMRA: effector memory T cell re-expressing CD45RA, TID: intermediate differentiated T cell, TLD: late differentiated T cell, TN: naïve T cell, VAT: visceral adipose tissue. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3634949_d3
title: Additional file 5: Table S3. of Immunosenescence of the CD8+ T cell compartment is associated with HIV-infection, but only weakly reflects age-related processes of adipose tissue, metabolism, and muscle in antiretroviral therapy-treated HIV-infected patients and controls

description: Unadjusted and adjusted associations between KLRG1+CD8+ T cell subsets and ageing parameters in HIV+. Adjusted analyses are in grey. Age was adjusted for HIV-duration, ART-duration, and current ART; IL-6, suPAR, HOMA-IR, metabolic syndrome, VAT, and lLMI were adjusted for age, HIV-duration, ART-duration, and current ART. †Parameters were transformed using log2(x). Estimates and confidence intervals are back transformed using (2β-1) × 100, and shown as percent change in the outcome per unit increase of the covariate. The bold values are statistically significant at *P
DOI: 10.6084/m9.figshare.c.3634949_d5
title: Additional file 3: Table S1. of Immunosenescence of the CD8+ T cell compartment is associated with HIV-infection, but only weakly reflects age-related processes of adipose tissue, metabolism, and muscle in antiretroviral therapy-treated HIV-infected patients and controls

description: Linear regression analyses for the effect of HIV-infection on CD8+ T cell maturation and differentiation. †Parameter was transformed using log2(x). Estimates and confidence intervals are back transformed using (2β-1) × 100, and shown as percent change in the outcome per unit increase of the covariate. The bold values are statistically significant at *P
DOI: 10.6084/m9.figshare.c.3634949_d7
title: Additional file 4: Table S2. of Immunosenescence of the CD8+ T cell compartment is associated with HIV-infection, but only weakly reflects age-related processes of adipose tissue, metabolism, and muscle in antiretroviral therapy-treated HIV-infected patients and controls

description: Unadjusted and adjusted associations between CD8+ T cell subset sizes and ageing parameters in HIV+. Adjusted analyses are in grey. Age was adjusted for HIV-duration, ART-duration, and current ART; IL-6, suPAR, HOMA-IR, metabolic syndrome, VAT, and lLMI were adjusted for age, HIV-duration, ART-duration, and current ART. †Parameters were transformed using log2(x). Estimates and confidence intervals are back transformed using (2β-1) × 100, and shown as percent change in the outcome per unit increase of the covariate. The bold values are statistically significant at *P
DOI: 10.6084/m9.figshare.c.3634961_d2
title: Additional file 4 of STON: exploring biological pathways using the SBGN standard and graph databases

description: SBGN files in a COMBINE Archive. This COMBINE Archive contains the five SBGN-ML files used to generate the benchmark table present in the Additional file 1. (OMEX 181 kb)
DOI: 10.6084/m9.figshare.c.3634961_d4
title: Additional file 3 of STON: exploring biological pathways using the SBGN standard and graph databases

description: The queries. This text file contains the queries for Figs. 2 and 3 in the â  Resultsâ   Section. (TXT 1.95 kb)
DOI: 10.6084/m9.figshare.c.3635009_d1
title: Additional file 1: of Comparison of Kompetitive Allele Specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize

description: Summary of the 200 KASP SNPs used for genotyping. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3635033_d2
title: Additional file 2. of lobChIP: from cells to sequencing ready ChIP libraries in a single day

description: Excel file with list of samples, read statistics and overlap between the datasets.
DOI: 10.15468/dl.xjun84
title: Occurrence Download

description: A dataset containing 142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "Geometry POLYGON ((-97.85 17.08333, -97.83333 17.08333, -97.83333 17.2, -97.85 17.2, -97.85 17.08333))",
 "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 142 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033839-241126133413365/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.3635060_d1
title: Additional file 13: Table S10. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

description: KEGG pathways differing in the functional metagenomic profiles of GI communities from healthy children and adults. Between-group differences were evaluated with Whiteâ  s non-parametric t-tests and Storeyâ  s false discovery rate corrections. (TIF 15.5 kb)
DOI: 10.6084/m9.figshare.c.3635060_d4
title: Additional file 3: Table S3. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

description: Subject and SRA sequence identifiers for the shotgun metagenomic sequence data used in this study. (XLSX 14.5 kb)
DOI: 10.6084/m9.figshare.c.3635060_d5
title: Additional file 4: Table S4. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

description: Sequence and assembly metrics for the shotgun metagenomic sequence libraries used in this study. (XLSX 23.0 kb)
DOI: 10.6084/m9.figshare.c.3635060_d6
title: Additional file 11: Table S8. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

description: Species abundances which differed in the WGS-based profiles of healthy child and adult GI communities. Between-group differences were evaluated with two-tailed Whiteâ  s non-parametric t-tests with Storeyâ  s FDR corrections. (XLSX 11.1 kb)
DOI: 10.6084/m9.figshare.c.3635060_d9
title: Additional file 12: Table S9. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

description: KEGG ortholog groups (KO) differing in the GI communities of healthy children and adults. Between-group differences were evaluated with two-tailed Whiteâ  s non-parametric t-tests with Storeyâ  s FDR corrections. N/A indicates KO without Enzyme Commission (EC) numbers. (TIF 155 kb)
DOI: 10.6084/m9.figshare.c.3635060_d13
title: Additional file 2: Table S2. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

description: Subject and SRA sequence identifiers for the 16S rRNA gene data (V3-V5 region) used in this study. (XLSX 18.5 kb)
DOI: 10.6084/m9.figshare.c.3635060_d14
title: Additional file 9: Table S7. of Structure and function of the healthy pre-adolescent pediatric gut microbiome

description: Genera differing in the 16S profiles of healthy child and adult GI communities. Between-group differences were evaluated with two-tailed Whiteâ  s non-parametric t-tests with Storeyâ  s FDR corrections. (XLSX 14.6 kb)
DOI: 10.6084/m9.figshare.c.3635075_d3
title: Additional file 4: of Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization

description: Details on the genes sets prioritized by the respective approaches. (TXT 23 kb)
DOI: 10.6084/m9.figshare.c.3635075_d2
title: Additional file 3: of Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization

description: Details of the reduced gene set by using the mRMR software. (TXT 54 kb)
DOI: 10.6084/m9.figshare.c.3635075_d4
title: Additional file 2: of Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization

description: Normalized expression values of the 8477 common genes for each of the 102 samples, sample and study identifiers, disease factor (PD or HC), as well as the distribution of training and test samples. (TXT 10084 kb)
DOI: 10.6084/m9.figshare.c.3635075_d5
title: Additional file 5: of Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization

description: 1) Results of the Limma prioritization for the top 1016 genes with uncorrected p-values
DOI: 10.6084/m9.figshare.c.3635096_d1
title: Additional file 8: of Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

description: SM6-UnigeneAllGenomes[91cds].fasta. Alignment file for all legume Albumin I coding sequences (corresponding to phylogenetic tree showed in Fig.Â 4). (FASTA 50 kb)
DOI: 10.6084/m9.figshare.c.3635096_d2
title: Additional file 3: Table S3. of Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

description: Diversity of the cysteine motif in Medicaco truncatula PA1b types. The consensus motif of each PA1b type was deduced from the analysis of the mature sequences of the 53 Medicago truncatula PA1b presented in Additional file 1: Table S1. Medtr3g438140.1 and Medtr3g438170.1 are very short sequences and were excluded from the survey. Similarly, Medtr8g056800 was excluded from this table because it lacks the A1b sequence. A cysteine residue is missing in AJ574790.1 and Medtr3g467750.1. Medtr3g067830.1 and Medtr6g082060.1 subfamily members harbor an extra cysteine residue. Medtr3g067445.1 and Medtr3g067430.1 subfamily members harbor two extra cysteine residues. Medtr6g082060.1 displays no CXC motif. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3635096_d3
title: Additional file 7: of Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

description: SM5-UnigeneAllGenomes[91pep].fasta. Alignment file for all legume Albumin I peptides (corresponding to species from tree in Fig.Â 4). (FASTA 20 kb)
DOI: 10.6084/m9.figshare.c.3635180_d4
title: Additional file 7: Table S3. of The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource

description: Sequencing, assembly and gene content analyses for strains sequenced for this study. (XLSX 146 kb)
DOI: 10.6084/m9.figshare.c.3635180_d7
title: Additional file 6: Supplementary Material. of The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource

description: Table S4. Selected references for each genus and species. Figure S5. Number of plasmids detected in Collection strains by laboratory and in silico approaches. Marker size is scaled by the number of strains and the trendline represents the overall correlation. (ZIP 175 kb)
DOI: 10.6084/m9.figshare.c.3635231_d2
title: Additional file 2 of A multiple kernel learning algorithm for drug-target interaction prediction

description: Spreadsheet. p-values under pairwise Wilcoxon Rank Sum statistical tests of all competing methods in pair, drug and target prediction tasks. (XLS 24 kb)
DOI: 10.15468/dl.7subp6
title: Occurrence Download

description: A dataset containing 302 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Insecta",
 "Geometry POLYGON ((-96.91861 17.62639, -96.91389 17.62639, -96.91389 17.64778, -96.91861 17.64778, -96.91861 17.62639))",
 "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 302 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033841-241126133413365/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.28027826
title: Triteleia sp. raw GC-MS files

description: Metabolite extraction from Triteleia sp.
DOI: 10.6084/m9.figshare.28027826.v1
title: Triteleia sp. raw GC-MS files

description: Metabolite extraction from Triteleia sp.
DOI: 10.6084/m9.figshare.c.3635324_d2
title: Additional file 5: of FoCo: a simple and robust quantification algorithm of nuclear foci

description: Test image set. The test image set contains RGB and grayscale microscopy images of MRC-5 cells 1 hour after 2.5 Gy and 3 hours after 10 Gy irradiation and of non-irradiated MRC-5 cells. The included image of MRC-5 cells after 10 Gy irradiation (‘10Gy.tif’) was used for creating documentation for using FoCo. The user may use this image to verify if he/she is using the program correctly. (ZIP 1961 kb)
DOI: 10.6084/m9.figshare.c.3635324_d3
title: Additional file 4: of FoCo: a simple and robust quantification algorithm of nuclear foci

description: CellProfiler pipeline for analyzing microscopy images. (CP 9 kb)
DOI: 10.6084/m9.figshare.c.3635324_d4
title: Additional file 8: of FoCo: a simple and robust quantification algorithm of nuclear foci

description: Simulated foci images. We included simulated foci images from Fig. 4câ  d used as representative images for demonstrating automatic foci quantifications. (ZIP 23 kb)
DOI: 10.6084/m9.figshare.c.3635324_d5
title: Additional file 7: of FoCo: a simple and robust quantification algorithm of nuclear foci

description: CellProfiler pipeline for analyzing simulated images. (CP 5 kb)
DOI: 10.6084/m9.figshare.c.3635324_d7
title: Additional file 2: of FoCo: a simple and robust quantification algorithm of nuclear foci

description: GUI FoCo with source code. (ZIP 69 kb)
DOI: 10.6084/m9.figshare.c.3635324_d6
title: Additional file 6: of FoCo: a simple and robust quantification algorithm of nuclear foci

description: Source code for simulating foci images and analyzing with FoCo algorithm. The source code is written in Matlab. For simulating a foci image run the M-file ‘CreateAnalyzeArtificialImages.m’. (ZIP 5 kb)
DOI: 10.6084/m9.figshare.c.3635330_d1
title: Additional file 2: of Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean

description: Description of population genetic statistics of 1205 SNP markers in 421 soybean accessions. (XLSX 130 kb)
DOI: 10.6084/m9.figshare.c.3635327_d6
title: Additional file 6: of Smokeless tobacco and oral potentially malignant disorders in South Asia: a protocol for a systematic review

description: Data extraction spreadsheet. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3635330_d2
title: Additional file 1: of Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean

description: Information for the 421 worldwide soybean accessions analyzed. (XLS 106 kb)
DOI: 10.6084/m9.figshare.c.3635342_d1
title: Additional file 1: of Association of SNPs in LCP1 and CTIF with hearing in 11Â year old children: Findings from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort and the G-EAR consortium

description: Results for all the SNPs included in the analyses of data from ALSPAC or G-EAR.
DOI: 10.6084/m9.figshare.c.3635399_d1
title: MOESM1 of Using multivariate cross correlations, Granger causality and graphical models to quantify spatiotemporal synchronization and causality between pest populations

description: Additional file 1. Actual ecological time series registered during successive growth seasons of the years 2003–2011 (3-day time intervals). W1: temperature (°C), W2: relative humidity (%), X1–X8: A. orana, Y1–Y3: A. lineatella and Z1–Z2: G. molesta moth populations (individuals).
DOI: 10.6084/m9.figshare.c.3635402_d2
title: Additional file 1 of Comparative transcriptomics reveals similarities and differences between astrocytoma grades

description: Contains supporting Tables S1â  S7. Table S1: Summary of considered astrocytoma samples. Table S2: Summary of t-test results for PA I, AS II, AS III and GBM IV. Table S3: Signature genes distinguishing PA I from AS II, AS III and GBM IV. Table S4: Regulatory network associated with expression differences of signature genes. Table S5: Summary of integrated gene annotations. Table S6: Verhaak classification results for PA I, AS II, AS III and GBM IV. Table S7: Correlation statistics for macrophage marker genes included in the Verhaak-classifier. (ZIP 3287 kb)
DOI: 10.6084/m9.figshare.c.3635426_d1
title: Additional file 13: Table S8. of svclassify: a method to establish benchmark structural variant calls

description: Manual inspection characteristics of all 10 of the randomly selected Personalis sites with 0.9
DOI: 10.6084/m9.figshare.c.3635426_d4
title: Additional file 17: Table S12. of svclassify: a method to establish benchmark structural variant calls

description: Manual inspection characteristics of the 8 randomly selected 1000 Genomes sites with 0.7
DOI: 10.6084/m9.figshare.c.3635426_d5
title: Additional file 2: Table S2. of svclassify: a method to establish benchmark structural variant calls

description: Annotations for each of the SV calls as well as likely non-SV regions from the Illumina HiSeq (read lengthâ  =â  250Â bps) aligned sequence dataset for NA12878 using svclassify. (CSV 4 kb)
DOI: 10.6084/m9.figshare.c.3635426_d8
title: Additional file 1: Table S1. of svclassify: a method to establish benchmark structural variant calls

description: Annotations for each of the SV calls as well as likely non-SV regions from the Platinum Genomes 2x100bps HiSeq aligned sequence dataset for NA12878 using svclassify. (CSV 4 kb)
DOI: 10.6084/m9.figshare.c.3635426_d9
title: Additional file 3: Table S3. of svclassify: a method to establish benchmark structural variant calls

description: Annotations for each of the SV calls as well as likely non-SV regions from the Moleculo aligned sequence dataset for NA12878 using svclassify. (CSV 3.02 kb)
DOI: 10.6084/m9.figshare.c.3635426_d12
title: Additional file 12: Table S7. of svclassify: a method to establish benchmark structural variant calls

description: Manual inspection characteristics of the 20 randomly selected Personalis sites with Ď â  &gt;â  0.99 of one-class results. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3635426_d13
title: Additional file 14: Table S9. of svclassify: a method to establish benchmark structural variant calls

description: Manual inspection characteristics of all 8 of the randomly selected Personalis sites with Ď â
DOI: 10.6084/m9.figshare.c.3635426_d14
title: Additional file 19: Table S14. of svclassify: a method to establish benchmark structural variant calls

description: Manual inspection characteristics of the insertions from Spiral Genetics using svviz. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.c.3635426_d16
title: Additional file 16: Table S11. of svclassify: a method to establish benchmark structural variant calls

description: Manual inspection characteristics of the 9 randomly selected 1000 Genomes sites with 0.9
DOI: 10.6084/m9.figshare.c.3635426_d17
title: Additional file 18: Table S13. of svclassify: a method to establish benchmark structural variant calls

description: Manual inspection characteristics of the 7 randomly selected 1000 Genomes sites with Ď â
DOI: 10.6084/m9.figshare.c.3635471_d4
title: Additional file 9: of Male-specific association between MT-ND4 11719 A/G polymorphism and ulcerative colitis: a mitochondria-wide genetic association study

description: Data in aggregate form. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3635477_d1
title: Additional file 2: of Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans

description: Details of enrichment tests for the selected footprint SNPs in cis-regulatory regions of different cell types (Fig.Â 1b; Additional file 1: Figure S5). (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3635477_d2
title: Additional file 4: of Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans

description: Enrichment of the selected SNPs for TF binding QTLs. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3635477_d3
title: Additional file 3: of Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans

description: GO categories enriched in genes associated with the selected SNPs. (XLSX 18 kb)
DOI: 10.15468/dl.jf8crb
title: Occurrence Download

description: A dataset containing 5965 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mammalia",
 "Geometry POLYGON ((-97.81194 17.54, -96.99 17.54, -96.99 18.88194, -97.81194 18.88194, -97.81194 17.54))",
 "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 5965 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033842-241126133413365/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.3635525_d7
title: MOESM5 of Metabolomic, enzymatic, and histochemical analyzes of cassava roots during postharvest physiological deterioration

description: Additional file 5. An html report of all statistical analyses conducted in the manuscript and produced in R Software (version 3.2.2).
DOI: 10.6084/m9.figshare.c.3635525_d8
title: MOESM3 of Metabolomic, enzymatic, and histochemical analyzes of cassava roots during postharvest physiological deterioration

description: Additional file 3. Raw data (in csv format) of enzymes used for decision tree model of Fig. 3b.
DOI: 10.6084/m9.figshare.c.3635525_d9
title: MOESM8 of Metabolomic, enzymatic, and histochemical analyzes of cassava roots during postharvest physiological deterioration

description: Additional file 8. Raw data (csv format) of sugars and organic acids used for decision tree model of Fig. 3e.
DOI: 10.6084/m9.figshare.c.3635528_d2
title: Additional file 4: Table S3. of A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions

description: Relative expression amount of the 1510 proteins among the treatment and repliactions. (XLS 510 kb)
DOI: 10.6084/m9.figshare.c.3635528_d3
title: Additional file 6: Table S4. of A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions

description: Differntailly expressed protein in Tong88-7. (XLS 63 kb)
DOI: 10.6084/m9.figshare.c.3635528_d4
title: Additional file 1: Table S1. of A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions

description: List of total 2626 identified non-redundant proteins and their spectral counts in each sample. (XLS 530 kb)
DOI: 10.6084/m9.figshare.c.3635528_d5
title: Additional file 7: Table S5. of A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions

description: Enriched GO terms of the differentially expressed proteins in the resistant response of Tong887 and the susceptible response of Milyang23. (XLSX 70025 kb)