cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3634556_d1
title: MOESM6 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production

description: Additional file 6: Table S5. Results for General Linear Model (GLM) analyses of effect of rs110675140 genotype on DBP, ALB, 25(OH)D2, 25(OH)D3 and total 25(OH)D; free 25(OH)D2, 25(OH)D3 and total 25(OH)D; bioavailable (i.e., free and ALB-bound) 25(OH)D2, 25(OH)D3 and total 25(OH)D; DBP-bound total 25(OH)D; and ALB-bound total 25(OH)D serum concentrations. Detailed results of GLM analyses of genotype effect on several serum protein levels in 50 NR cows.
DOI: 10.6084/m9.figshare.c.3634556_d2
title: MOESM4 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production

description: Additional file 4: Table S3. Results for single marker association analyses of seven mastitis traits and five milk traits on BTA6 markers from the Illumina BovineHD BeadChip. rs numbers, positions in basepairs, â  log10(p value), SNP effects and alleles for all markers on BTA6 on the Illumina BovineHD BeadChip. The file contains twelve sheets, one for each trait.
DOI: 10.6084/m9.figshare.c.3634556_d4
title: MOESM5 of Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production

description: Additional file 5: Table S4. Results for single marker association analyses of CM1, CM4, CM6, kg milk, kg protein and kg fat on imputed full sequence data. Positions in basepairs, rs numbers, â  log10(p value), minor allele frequency, SNP effects, alleles, putative consequences of the variants on the protein sequence and nearest gene for the imputed full sequence SNPs. The file contains six sheets, one for each tested trait.
DOI: 10.6084/m9.figshare.c.3634592_d1
title: Additional file 2: of Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome

description: Novel Miniopterus natalensis transpsoable elements were identified using de novo methods and manual curation. Sequences are in FastA format. (FAS 39 kb)
DOI: 10.6084/m9.figshare.c.3634592_d2
title: Additional file 1: of Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome

description: The average Kimura 2-parameter, genetic distance was calculated among all insertions for each element. Highly mutable CpG sites were excluded from distance calculations. Distances were only calculated if the element was occupied more than 10 kilobases in a species. For species where elements were absent or occupied less than 10 kilobases of their genome, values are given as "NA"s. Calculations for all meeting these critera are shown here. TableÂ 2 in the manuscript is reduced fascimilie of this table containing only elements specifically discussed in the text. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3634598_d2
title: MOESM2 of Seasonal rainfall at long-term migratory staging sites is associated with altered carry-over effects in a Palearctic-African migratory bird

description: Additional file 2. The raw data collected from great reed warblers at the Zambian study site. Information includes year, sex, age (1 = juvenile, 2 = adult) time at capture (time.count = minutes since 0600 h), winter CORTf (feathercort.C), staging CORTf (feathercort.F), BUTY, TRIG, scaled mass index, δ13C, δ15N, δ 2H, and the estimated isotope cluster.
DOI: 10.6084/m9.figshare.c.3634601_d2
title: Additional file 2: of Closely related fungi employ diverse enzymatic strategies to degrade plant biomass

description: Combines Additional file Tables S2–S4 (excel format). Table S2A. Numbers of putative genes per CAZy family for the 10 genomes addressed in this study. Table S2B. Numbers of putative genes per Plant Polysaccharide Degradation-related CAZy family for the 10 genomes addressed in this study. Table S3A. Orthology clusters of feruloyl esterase (SF), glycoside hydrolase (GH), carbohydrate esterase and polysaccharide lyase (PL) families. Table S3B. Orthology clusters of auxiliary activities (AA). Table S4A. Detection of proteins in cultures grown on wheat bran sorted by CAZy family. Table S4B. Detection of proteins in cultures grown on sugar beet pulp sorted by CAZy family. Table S4C. Detected proteins in cultures grown on wheat bran sorted by number of species that contain an orthologue. Table S4D. Detected proteins in cultures grown on sugar beet pulp sorted by number of species that contain an orthologue.
DOI: 10.6084/m9.figshare.c.3634613_d4
title: Additional file 7: of EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions

description: Expression analyses based on microarray data of genes presented with FUS, EWS, FUS and EWS, and Ac-H3K9 ChIP-seq peaks. (XLS 70 kb)
DOI: 10.6084/m9.figshare.c.3634613_d5
title: Additional file 8: of EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions

description: Microarray data gene probe sets for actively transcribed genes also presented with FUS and Ac-H3K9 (n = 35), EWS and Ac-H3K9 (n = 135), or FUS and EWS and Ac-H3K9 (n = 58) ChIP-seq peaks. The probe sets were used in GO analysis. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3634613_d8
title: Additional file 9: of EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions

description: List of FUS and EWS ChIP-seq peaks assigned with a position downstream the poly(A)-signal of a target gene. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3634628_d1
title: Additional file 3: Table S3. of Systematics and historical biogeography of the old world butterfly subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrinae)

description: The estimated mean values and Effective Sample Sizes of parameters used in the BEAST time of divergence analyses. The figures are combined values of three independent BEAST Monte Carlo Markov Chain analyses, each ran for 50 Million generations. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3634628_d2
title: Additional file 1: Table S1. of Systematics and historical biogeography of the old world butterfly subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrinae)

description: List of exemplar mycalesines taxa included in the study and the gene regions amplified and sequenced per taxon. “x” denotes a case where a gene region was successfully amplified and sequenced for the taxon. Gene regions (COI, Ef1a, MDH, CAD) more than 800 base pairs long were amplified in two parts. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3634628_d5
title: Additional file 5: Table S4. of Systematics and historical biogeography of the old world butterfly subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrinae)

description: BEAST priors sensitivity test. Comparison of time of divergence at 40 nodes selected across different parts of the Mycalesina tree, using different tree-shape (birth-death, yule, calibrated-yule) and clock (normal and uniform) priors. (XLSX 29Â kb)
DOI: 10.6084/m9.figshare.c.3634634_d1
title: Additional file 1: of Ultrathin bronchoscopy for solitary pulmonary lesions in a region endemic for tuberculosis: a randomised pilot trial

description: The supplemental file. (XLS 16 kb)
DOI: 10.6084/m9.figshare.c.3634643_d1
title: Additional file 1: of Comparison of the frequency of bacterial and viral infections among children with community-acquired pneumonia hospitalized across distinct severity categories: a prospective cross-sectional study

description: Dataset of children hospitalized with community-acquired pneumonia in distinct severity categories with aetiology results. Demographic, clinical, and aetiology data on children hospitalized with community-acquired pneumonia. (XLS 219Â kb)
DOI: 10.6084/m9.figshare.c.3634652_d1
title: Additional file 2: of Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

description: List of core genome sites included in our analysis. Site numbers are relative to the published ST59 genome used as a reference for mapping short reads (GenBank accession CP003166). (TXT 20378 kb)
DOI: 10.6084/m9.figshare.c.3634652_d3
title: Additional file 4: of Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

description: Genes associated with either USA or East Asia clade. Genes whose presence differed significantly between the USA and East Asia clades are listed. We also report the proportion of isolates within the USA and East Asia clades for which each gene was present and note those that share the same pattern of presence or absence across the isolates (identified by having the same â  column patternâ  ). Results for genes whose presence differed significantly between the USA and Taiwan isolates (as opposed to the USA and East Asia clades) are presented in a separate worksheet. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3634652_d2
title: Additional file 3: of Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

description: Output from in silico antibiotic resistance testing. Genes associated with antibiotic resistance were detected using SRST2. Gene presence is denoted by the name of the gene (asterisks indicates at least one mismatched SNP or indel and a question mark indicates some low-depth bases, as described on the SRST2 website: https://github.com/katholt/srst2 ). Gene absence is denoted by a hyphen. The amino acid residue (IUPAC single letter code) is given for gyrA, grlA and grlB sites associated with fluoroquinolone resistance. Presence or absence of PVL based on mapping of short reads to lukF-PV and lukS-PV reference sequences is also reported. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3634661_d1
title: Additional file 8: Table S7. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: lncRNAs directly induced/repressed by TGF-Î˛ signaling pathway. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3634661_d2
title: Additional file 15: Table S14. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: The expression levels in FPKM of lncRNAs in TGF-Î˛ starvation and TGF-Î˛ treatment adult HSCs. (XLSX 250 kb)
DOI: 10.6084/m9.figshare.c.3634661_d3
title: Additional file 14: Table S13. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: The mean expression levels in FPKM of lncRNAs in adult HSCs, PSCs, dermal fibroblasts, and livers. (XLSX 328 kb)
DOI: 10.6084/m9.figshare.c.3634661_d4
title: Additional file 1: Table S1. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: GTEx samples used in expression analyses. (XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3634661_d5
title: Additional file 16: Table S15. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: H3K4me1:H3K4me3 ratio of the 851 lncRNAs in hiF cells. (XLS 78 kb)
DOI: 10.6084/m9.figshare.c.3634661_d6
title: Additional file 2: Table S2. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: GTEx ID and pathology reads of eight normal livers, two cirrhosis livers, and two bridging-fibrosis livers. (XLS 22 kb)
DOI: 10.6084/m9.figshare.c.3634661_d7
title: Additional file 11: Table S10. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: Co-expression pairs and gene lists of major functional modules in clusters I, II and IV. (XLS 988 kb)
DOI: 10.6084/m9.figshare.c.3634661_d8
title: Additional file 9: Table S8. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: Expression profiles of HSC-specific lncRNAs across HSC myofibroblasts, TGF-Î˛ HSCs, and 43 human tissues or cell types. (XLS 389 kb)
DOI: 10.6084/m9.figshare.c.3634661_d9
title: Additional file 5: Table S4. of Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

description: The genomic locations of super-enhancers. (XLS 60 kb)
DOI: 10.6084/m9.figshare.c.3634793_d1
title: Additional file 1: Table S1. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

description: Differentially regulated host proteins in control and infected leaf tissues of Navel orange (p-valueâ
DOI: 10.6084/m9.figshare.c.3634793_d3
title: Additional file 2: Table S2. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

description: Differentially regulated host proteins in control and infected leaf tissues of Volkameriana (p-valueâ
DOI: 10.6084/m9.figshare.c.3634820_d2
title: Additional file 5: of Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option

description: Gene models in fasta format. (TGZ 545 kb)
DOI: 10.6084/m9.figshare.c.3634820_d3
title: Additional file 1: of Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option

description: Genome assembly information for the species studied, includes: BioProjectID, assembly N50, CEGMA results, PubMedID of publication. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3634820_d4
title: Additional file 4: of Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option

description: Gene models in gff format. (TGZ 240 kb)
DOI: 10.6084/m9.figshare.c.3634820_d5
title: Additional file 6: of Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option

description: Newick tree format for Figure 4. (TXT 3 kb)
DOI: 10.6084/m9.figshare.c.3634820_d6
title: Additional file 2: of Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option

description: Gene match results for transcriptomes from Haemonchus contortus, Strongyloides ratti and Trichuris suis. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.27180369
title: Dataset and scripts related to dietary or pharmacological inhibition of insulin-like growth factor-1 protects from renal ischemia-reperfusion injury, published in iScience.

description: Dataset and scripts related to dietary or pharmacological inhibition of insulin-like growth factor-1 protects from renal ischemia-reperfusion injury, published in iScience.One-week protein restriction (PR) limits ischemia-reperfusion (IR) damages and improves metabolic fitness. Similarly, longer-term calory restriction results in increased lifespan, partly via reduced Insulin-Like Growth Factor (IGF)-1. However, the influence of short-term PR on IGF-1 and its impact on IR are unknown. PR was achieved in mice via one-week carbohydrate loading and/or through a low-protein diet. PR decreased IGF-1 circulating levels as well as renal and hepatic expression. Upon renal IR, serum IGF-1 positively correlated with renal dysfunction and tissular damages, independently of sex and age. Exogenous IGF-1 administration abrogated PR benefits during IR, while IGF-1 receptor inhibition with linsitinib was protective. IGF-1 was associated with a reduction in forkhead box O (FoxO), and AMP-activated protein kinase (AMPK) signaling pathways previously demonstrated to improve IR resilience in various organs. These data support dietary or pharmacological reduction of IGF1 signaling to mitigate IR injury prior to solid organ transplantation and beyond.
DOI: 10.6084/m9.figshare.27180369.v1
title: Data set and scripts related to Dietary or Pharmacological inhibition of Insulin-Like Growth Factor-1 Protects from Renal Ischemia-Reperfusion Injury. published in iScience

description: Data and script from Dietary or Pharmacological inhibition of Insulin-Like Growth Factor-1 Protects from Renal Ischemia-Reperfusion Injury. Submitted to iScience. Ischemia-Reperfusion Injury.One-week protein restriction (PR) limits ischemia-reperfusion (IR) damages and improves metabolic fitness. Similarly, longer-term calory restriction results in increased lifespan, partly via reduced Insulin-Like Growth Factor (IGF)-1. However, the influence of short-term PR on IGF-1 and its impact on IR are unknown. PR was achieved in mice via one-week carbohydrate loading and/or through a low-protein diet. PR decreased IGF-1 circulating levels as well as renal and hepatic expression. Upon renal IR, serum IGF-1 positively correlated with renal dysfunction and tissular damages, independently of sex and age. Exogenous IGF-1 administration abrogated PR benefits during IR, while IGF-1 receptor inhibition with linsitinib was protective. IGF-1 was associated with a reduction in forkhead box O (FoxO), and AMP-activated protein kinase (AMPK) signaling pathways previously demonstrated to improve IR resilience in various organs. These data support dietary or pharmacological reduction of IGF1 signaling to mitigate IR injury prior to solid organ transplantation and beyond.
DOI: 10.15468/dl.yj5hgq
title: Occurrence Download

description: A dataset containing 53179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "Geometry POLYGON ((-90.46806 17.81083, -89.15111 17.81083, -89.15111 19.2, -90.46806 19.2, -90.46806 17.81083))",
 "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 53179 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033838-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mq4asc
title: Occurrence Download

description: A dataset listing the 145 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.07462 4.76578,-74.07421 4.76694,-74.07881 4.77462,-74.08388 4.78398,-74.08707 4.79066,-74.09029 4.79721,-74.09163 4.79872,-74.09457 4.80108,-74.09875 4.79961,-74.10019 4.7958,-74.09786 4.78909,-74.08947 4.77633,-74.07798 4.76009,-74.07462 4.76578))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 145 records were derived from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033832-241126133413365/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.3634859_d2
title: Additional file 3: of Differential effect of mild and severe pulmonary embolism on the rat lung transcriptome

description: ANOVAs of 2-hour and 18-hour PE treatments. (XLS 1660 kb)
DOI: 10.6084/m9.figshare.c.3634859_d1
title: Additional file 1: of Differential effect of mild and severe pulmonary embolism on the rat lung transcriptome

description: Rat lung 6-group 2-way ANOVA. (XLS 3757 kb)
DOI: 10.6084/m9.figshare.c.3634859_d3
title: Additional file 2: of Differential effect of mild and severe pulmonary embolism on the rat lung transcriptome

description: Pairwise t-test of PE treatments. (XLS 2775 kb)
DOI: 10.6084/m9.figshare.c.3634883_d11
title: Additional file 14: Table S11. of A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes

description: bHLH genes in soybean. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3634883_d13
title: Additional file 9: Table S6. of A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes

description: Significant GO terms leaf 2Â h. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3634883_d14
title: Additional file 10: Table S7. of A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes

description: Significant GO terms leaf 5Â h. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3634883_d15
title: Additional file 8: Table S5. of A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes

description: Significant GO terms root 5Â h. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3634883_d17
title: Additional file 13: Table S10. of A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes

description: Differentially expressed calcium signaling-associated genes from MapMan (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3634892_d1
title: Additional file 2: of Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia

description: Tables S1 to S21. (ZIP 10219 kb)
DOI: 10.6084/m9.figshare.c.3634892_d3
title: Additional file 3: of Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia

description: iDOS R package and associated R scripts used in this study. (ZIP (379183 kb)
DOI: 10.6084/m9.figshare.c.3634895_d3
title: Additional file 3: of The challenge of mothers learning about secondhand smoke (MLASS): a quasi-experimental, mixed methods feasibility study

description: Interventions A, B, C and D. (ZIP 1154 kb)
DOI: 10.6084/m9.figshare.28027823
title: Yucca filamentosa raw GC-MS files

description: Metabolite extraction from Yucca filamentosa
DOI: 10.6084/m9.figshare.28027823.v1
title: Yucca filamentosa raw GC-MS files

description: Metabolite extraction from Yucca filamentosa
DOI: 10.6084/m9.figshare.c.3634913_d1
title: Additional file 1: of Biofilm-associated proteins: news from Acinetobacter

description: A. baumannii strains analyzed. (XLS 84Â kb)
DOI: 10.6084/m9.figshare.c.3634913_d2
title: Additional file 9: of Biofilm-associated proteins: news from Acinetobacter

description: Distribution of surface proteins in strains expressing different BAP types. (XLS 49Â kb)
DOI: 10.6084/m9.figshare.c.3634949_d1
title: Additional file 6: Table S4. 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 groups 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 15 kb)