cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3628559_d8
title: Additional file 3: of Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

description: Fom genes up or down-regulated in A17 plants versus in vitro. (XLSX 167 kb)
DOI: 10.15468/dl.j7vv6c
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Sonidos de la Ecoreserva Campo Rubiales (Puerto Gaitán, Meta) - Proyecto FIBRAS"
 ]
}

 The dataset includes 99 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033940-241126133413365/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.3628631_d15
title: MOESM10 of Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid

description: Additional file 10. Orthologous genes used for genome-based phylogenetic analysis.
DOI: 10.6084/m9.figshare.c.3628700_d3
title: Additional file 1: Data S1. of De novo transcriptome sequencing of black pepper (Piper nigrum L.) and an analysis of genes involved in phenylpropanoid metabolism in response to Phytophthora capsici

description: The differentially expressed transcripts between P. nigrum and P. flaviflorum. (XLS 2838Â kb)
DOI: 10.6084/m9.figshare.c.3628709_d1
title: MOESM2 of Upstream AUGs and upstream ORFs can regulate the downstream ORF in Plasmodium falciparum

description: Additional file 2: Table S2. Numbers of uATGs associated with each annotated CDS in the parasite genome.
DOI: 10.6084/m9.figshare.c.3628709_d2
title: MOESM4 of Upstream AUGs and upstream ORFs can regulate the downstream ORF in Plasmodium falciparum

description: Additional file 4: Table S3. Frequency of different Kozak sequences in annotated CDS in the parasite genome.
DOI: 10.6084/m9.figshare.c.3628631_d18
title: MOESM11 of Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid

description: Additional file 11. Gene symbols, annotations and expression abundance data for S. fibuligera genes involved in carbon and sulfur metabolism.
DOI: 10.6084/m9.figshare.c.3628700_d5
title: Additional file 4: Data S2. of De novo transcriptome sequencing of black pepper (Piper nigrum L.) and an analysis of genes involved in phenylpropanoid metabolism in response to Phytophthora capsici

description: The differentially expressed transcripts enriched in phenylpropanoid metabolic pathways. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3628724_d1
title: MOESM5 of Classifying publications from the clinical and translational science award program along the translational research spectrum: a machine learning approach

description: Additional file 5. Threshold validation: For 50 articles randomly chosen from each decile of the scores returned by the T0 classifier this file lists the PMID, the classifier score, and a manual classification of either “T0” or “not T0”.
DOI: 10.6084/m9.figshare.c.3628730_d1
title: Additional file 1: of Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae

description: Figure S1. Efficient bisulfite conversion of non-methylated cytosine residues. Figure S2. Characterization of Arabidopsis thaliana T-DNA mutants. Figure S3. Specificity of tRNA and rRNA MTases. Figure S4. Multiple sequence alignment of methyltransferase motifs from Arabidopsis thaliana RMTases. The amino acid sequences of two subfamilies of RMTases in Arabidopsis; (A) TRM4A and TRM4B; (B) NOP2A/OLI2, NOP2B and NOP2C were aligned using Clustal Omega [72]. Table S1. Unique tRNA isodecoder consensus sequences used for tRNA expression and methylation analysis. Table S2. Annotation table of tRNA isodecoder sequences detected in diverse plant species. Table S3. Ribosomal RNA sequences used for methylation analysis in diverse plant species and number of m5C sites. Table S4. Methylation % of tRNAs from A. thaliana, B. rapa, T. durum, C. taxifolia, N. occulata and G. biloba. Table S5. Methylation % of rRNAs from A. thaliana, B. rapa, T. durum, C. taxifolia, N. occulata and G. biloba. Table S6. Primer sequences used in this study [73]. Table S7. Read coverage of libraries sequenced. (ZIP 5681 kb)
DOI: 10.6084/m9.figshare.c.3628724_d2
title: MOESM1 of Classifying publications from the clinical and translational science award program along the translational research spectrum: a machine learning approach

description: Additional file 1. Filter terms: Search terms used to filter randomly selected articles indexed to CTSA grants in order to increase the incidence of T1 and T2 articles in the training set.
DOI: 10.6084/m9.figshare.c.3628724_d3
title: MOESM3 of Classifying publications from the clinical and translational science award program along the translational research spectrum: a machine learning approach

description: Additional file 3. External validation: For each of 300 PMIDs (top 100 scored from each classifier), the file lists the classifier for which it received a top score, the classification given by the two coders, and, when applicable, the decision of the third coder.
DOI: 10.6084/m9.figshare.c.3628868_d4
title: Additional file 2: Table S1. of Silencing of GATA3 defines a novel stem cell-like subgroup of ETP-ALL

description: List of DEG comparing patients with low and high GATA3 mRNA expression. Microarray analyses of diagnostic bone marrow samples of 83 adult patients with T-ALL were used to generate a list of DEG comparing GATA3low and GATA3high. Only probe sets with at least 1.5-fold up- or downregulation with respect to GATA3 expression and a FDR &lt;0.05 were included. (XLSX 102 kb)
DOI: 10.6084/m9.figshare.c.3628883_d1
title: MOESM2 of Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

description: Additional file 2: Analysis of Gene Ontology categories associated with differential expression during HIV 89.6 infection of primary CD4 + T cells. Counts of differentially expressed genes for each Gene Ontology category are stored in a csv file with columns categoryÂ name, the numbers of genes differentially up- and downregulated or not significantly changed and odds ratios and p-values from Fisherâ  s exact tests.
DOI: 10.6084/m9.figshare.c.3628883_d3
title: MOESM4 of Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

description: Additional file 4: Genes called as up- or downregulated by studies of expression during HIV infection. Genes called as differentially expressed in the five studies analyzed in the meta-analysis of differential expression with HIV infection are stored in a csv file with columns study, the gene name(s) and whether the differential expression was up or down.
DOI: 10.6084/m9.figshare.c.3628991_d2
title: Additional file 8 of Profound impact of sample processing delay on gene expression of multiple myeloma plasma cells

description: Table S4 - Genes of PAM predictor. Table listing the 17 genes that make up the PAM predictor. (XLSX 9.86 KB)
DOI: 10.6084/m9.figshare.c.3628991_d3
title: Additional file 5 of Profound impact of sample processing delay on gene expression of multiple myeloma plasma cells

description: Table S5 - Genes differentially expressed in risk predictors. Subset of genes from IFM15, GEP70 & EMC-92 that show differential expression between shipped and in-house samples. (XLSX 16.3 KB)
DOI: 10.6084/m9.figshare.c.3628991_d5
title: Additional file 1 of Profound impact of sample processing delay on gene expression of multiple myeloma plasma cells

description: Participating_centers.xls. Names of the participating centers and the ethics committees that granted approval to this study. (XLS 35.5 KB)
DOI: 10.6084/m9.figshare.c.3629027_d1
title: Additional file 3: of Tryptophan metabolism, its relation to inflammation and stress markers and association with psychological and cognitive functioning: Tasmanian Chronic Kidney Disease pilot study

description: Table S2. Spearman rank correlation coefficients for associations of psychological and cognitive functioning, with clinical parameters and serum metabolites. (XLS 36Â kb)
DOI: 10.6084/m9.figshare.c.3629129_d2
title: Additional file 2: of Scrapie incidence and PRNP polymorphisms: rare small ruminant breeds of Sicily with TSE protecting genetic reservoirs

description: Total number of analysed animals for each Sicilian goat breed with single polymorphism frequency and percentage. (XLS 56Â kb)
DOI: 10.6084/m9.figshare.c.3629099_d10
title: Additional file 2: of A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle

description: Functional effects of 52 variants in LD with BH2. The functional consequences of the non-reference alleles were predicted using the Variant Effect Predictor tool from Ensembl. (TXT 16Â kb)
DOI: 10.6084/m9.figshare.c.3629147_d1
title: Additional file 2: of cFinder: definition and quantification of multiple haplotypes in a mixed sample

description: Archive containing test data. Include annotations and exemplary alignment files from AVA and CLC for sample 5, as well as simulated test reads for overlapping amplicons.
DOI: 10.6084/m9.figshare.c.3629150_d1
title: Additional file 4 of Functional networks inference from rule-based machine learning models

description: Enriched terms. Complete list of enriched terms for each dataset and network. (XZ 3041 kb)
DOI: 10.6084/m9.figshare.c.3629147_d2
title: Additional file 1: of cFinder: definition and quantification of multiple haplotypes in a mixed sample

description: Archive containing the cFinder software. Includes executable, library and settings files.
DOI: 10.6084/m9.figshare.c.3629153_d1
title: Additional file 4 of FlexFlux: combining metabolic flux and regulatory network analyses

description: Comparison between rFBA and RSA on 125 conditions and 110 gene knock-outs of E. coli regulatory and metabolic networks. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3629150_d3
title: Additional file 2 of Functional networks inference from rule-based machine learning models

description: Networks. All networks used in the analysis given as a list of edges. (XZ 11980 kb)
DOI: 10.6084/m9.figshare.c.3629153_d2
title: Additional file 5 of FlexFlux: combining metabolic flux and regulatory network analyses

description: Constraint file used to run FlexFlux simulations of the lactose and maltose operon. (TXT 939 bytes)
DOI: 10.6084/m9.figshare.c.3629255_d3
title: Additional file 3: Dataset S2. of The intracellular bacterium Anaplasma phagocytophilum selectively manipulates the levels of vertebrate host proteins in the tick vector Ixodes scapularis

description: Proteomics results for sheep host proteins in tick tissues. (XLSX 208 kb)
DOI: 10.6084/m9.figshare.c.3629246_d3
title: Additional file 3: Table S2. of Transposable element detection from whole genome sequence data

description: Sample-level examination of intersections between TE detection methods. (XLSX 6 kb)
DOI: 10.6084/m9.figshare.c.3629267_d4
title: Additional file 4: Table S1. of Using genome-wide associations to identify metabolic pathways involved in maize aflatoxin accumulation resistance

description: Association effect and p values for tagSNPs and genes in the 17 pathways with FDRâ
DOI: 10.6084/m9.figshare.c.3629258_d4
title: Additional file 3: Table S8. of Eligibility of real-life patients with COPD for inclusion in trials of inhaled long-acting bronchodilator therapy

description: Overview of inclusion and exclusion criteria of RCTs testing tiotropium. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3629258_d5
title: Additional file 4: Table S9. of Eligibility of real-life patients with COPD for inclusion in trials of inhaled long-acting bronchodilator therapy

description: Overview of inclusion and exclusion criteria of RCTs testing for RCTs testing other single treatments. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3629378_d2
title: Additional file 4: of Difference in C3â  C4 metabolism underlies tradeoff between growth rate and biomass yield in Methylobacterium extorquens AM1

description: Detailed table for simulated flux with absolute values for all four conditions with 3 replicates each. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.c.3629372_d3
title: Additional file 5: Table S5. of Variation in life history traits and transcriptome associated with adaptation to diet shifts in the ladybird Cryptolaemus montrouzieri

description: Annotation of differentially expressed genes (DEGs) in comparison of fourth instar larvae feeding on mealybugs and aphids (LM vs LA). (XLS 353 kb)
DOI: 10.6084/m9.figshare.c.3629378_d4
title: Additional file 2: of Difference in C3â  C4 metabolism underlies tradeoff between growth rate and biomass yield in Methylobacterium extorquens AM1

description: Central carbon metabolism model for M. extorquens AM1 and list of metabolites with full name. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.c.3629375_d5
title: Additional file 1: of Independent mitochondrial and nuclear exchanges arising in Rhizophagus irregularis crossed-isolates support the presence of a mitochondrial segregation mechanism

description: Table showing qPCR data (ct values) of mitochondrial genotyping. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3629372_d4
title: Additional file 6: Table S6. of Variation in life history traits and transcriptome associated with adaptation to diet shifts in the ladybird Cryptolaemus montrouzieri

description: Annotation of differentially expressed genes (DEGs) in comparison of female adults feeding on mealybugs and aphids (AM vs AA). (XLS 149 kb)
DOI: 10.6084/m9.figshare.c.3629378_d5
title: Additional file 3: of Difference in C3â  C4 metabolism underlies tradeoff between growth rate and biomass yield in Methylobacterium extorquens AM1

description: Three replicates of isotopomer labeling pattern of metabolites used in the simulation. (XLSX 77Â kb)
DOI: 10.6084/m9.figshare.c.3629387_d1
title: MOESM1 of Early hyperreactive malarial splenomegaly and risk factors for evolution into the full-blown syndrome: a single-centre, retrospective, longitudinal study

description: Additional file 1. Study database.
DOI: 10.6084/m9.figshare.c.3629372_d6
title: Additional file 7: Table S7. of Variation in life history traits and transcriptome associated with adaptation to diet shifts in the ladybird Cryptolaemus montrouzieri

description: Candidate differentially expressed genes (DEGs) in comparison of fourth instar larvae feeding on mealybugs and aphids (LM vs LA). (XLS 126 kb)
DOI: 10.6084/m9.figshare.c.3629522_d1
title: Additional file 1: of Plumage quality mediates a life-history trade-off in a migratory bird

description: Raw data for feather measurements, moult status, and migratory traits of the first-year common snipe. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3629528_d1
title: Additional file 2: of Dynamics of Rex3 in the genomes of endangered Iberian Leuciscinae (Teleostei, Cyprinidae) and their natural hybrids

description: BLASTn megablast results (limit set: 1000 hits). Minimum, maximum (green) and calculated average (grey) percentage of similarity for each pair of species as well as the overall average (yellow) are shown. Fish systematics followed. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3629528_d2
title: Additional file 1: of Dynamics of Rex3 in the genomes of endangered Iberian Leuciscinae (Teleostei, Cyprinidae) and their natural hybrids

description: Estimates of evolutionary divergence between selected Rex3 partial sequences (Neighbour-Joining method, 1000 replicates) [ 37, 38 ]. Species are referred to by a three-letter code followed by GenBank accession numbers (alphabetical order). For more details refer to the text and Fig. 2. (XLS 42 kb)
DOI: 10.6084/m9.figshare.c.3629546_d1
title: Additional file 1: of Poor awareness of syphilis prevention and treatment knowledge among six different populations in south China

description: Dataset of the syphilis awareness survey among six different populations in Shenzhen, China. (XLS 934Â kb)
DOI: 10.6084/m9.figshare.c.3629630_d5
title: Additional file 4: of A systematic review of reported reassortant viral lineages of influenza A

description: Database S1. (XLSX 127 kb)
DOI: 10.6084/m9.figshare.c.3629600_d9
title: Additional file 11: Table S2. of IMPACT is a GCN2 inhibitor that limits lifespan in Caenorhabditis elegans

description: qPCR data of Additional file 2: Figure S2. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3629654_d1
title: Additional file 2: of Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs

description: List of GO terms enriched for amongst differentially expressed genes. The full list of GO terms that are enriched for amongst the differentially expressed genes in (1) PPvNN and (2) PPvPT. Direction indicates whether genes enriching for a given GO term are overexpressed (up) or underexpressed (down). (XLS 336 kb)
DOI: 10.6084/m9.figshare.c.3629654_d3
title: Additional file 5: of Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs

description: Hub genes of the blue module. List of the hub genes in the PPvNN blue module (GS â Ľ 10, MM â Ľ 0.8). (TXT 747 bytes)
DOI: 10.6084/m9.figshare.c.3629720_d5
title: Additional file 6: of Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design

description: Counts and analysis for eight â  no-drugâ   replicates. (XLSX 211 kb)
DOI: 10.6084/m9.figshare.c.3629747_d2
title: MOESM11 of Identification of QTL markers contributing to plant growth, oil yield and fatty acid composition in the oilseed crop Jatropha curcas L.

description: Additional file 11: Phenotype and genotype date from mapping population G33Â Ă Â G43
DOI: 10.6084/m9.figshare.c.3629729_d9
title: Additional file 2: Table S2. of Multiple regulatory variants located in cell type-specific enhancers within the PKP2 locus form major risk and protective haplotypes for canine atopic dermatitis in German shepherd dogs

description: Genotypes for 104 SNPs and haplotypes in all breeds. (TXT 161 kb)
DOI: 10.6084/m9.figshare.c.3629720_d6
title: Additional file 11: of Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design

description: Drug-specific effects (D) for all drugs tested for each gRNA. (XLSX 416 kb)
DOI: 10.6084/m9.figshare.c.3629729_d10
title: Additional file 9: Table S9. of Multiple regulatory variants located in cell type-specific enhancers within the PKP2 locus form major risk and protective haplotypes for canine atopic dermatitis in German shepherd dogs

description: Genotypes for candidate SNP 27:19,093,355 from the Taqman assay. (TXT 27 kb)
DOI: 10.6084/m9.figshare.c.3629720_d7
title: Additional file 9: of Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design

description: Sequence read information and raw counts from MiSeq data. (XLSX 3070 kb)
DOI: 10.6084/m9.figshare.c.3629747_d5
title: MOESM3 of Identification of QTL markers contributing to plant growth, oil yield and fatty acid composition in the oilseed crop Jatropha curcas L.

description: Additional file 3: Table S14. Mapping of genes involved in seed oil biosynthesis onto the Jatropha curcas linkage map
DOI: 10.15468/dl.s9pkc3
title: Occurrence Download

description: A dataset containing 934153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is France",
 "Year 1978-2023"
 ]
}

 The dataset includes 934153 records from 1339 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033941-241126133413365/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.3629858_d1
title: Additional file 1: of Human leukocyte antigen class 1 genotype distribution and analysis in persons with active tuberculosis and household contacts from Central Uganda

description: Table S1. Distributional differences in baseline characteristics between active TB patients and household contacts in the study. Table comparing the baseline characteristics of active TB patients and household contacts in the study. (XLS 26 kb)
DOI: 10.6084/m9.figshare.c.3629858_d2
title: Additional file 2: of Human leukocyte antigen class 1 genotype distribution and analysis in persons with active tuberculosis and household contacts from Central Uganda

description: Table S2. Total allelic frequencies of the study subjects from Kawempe, Kampala. Table of the total allele frequencies for HLA-A, HLA-B and HLA-C alleles of both active TB patients and household contacts in the study. (XLS 28 kb)
DOI: 10.6084/m9.figshare.c.3629861_d2
title: Additional file 2: Table S1. of Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

description: Expected product size obtained from Gramene and observed product size for the SSR markers used in this study. (XLS 170 kb)
DOI: 10.6084/m9.figshare.c.3629861_d3
title: Additional file 3: Table S2. of Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

description: Allele matrix of 192 accessions x 61 SSRs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3629858_d3
title: Additional file 3: of Human leukocyte antigen class 1 genotype distribution and analysis in persons with active tuberculosis and household contacts from Central Uganda

description: Table S3. Comparison of allelic frequencies between active TB patients and household contacts in the study. Table comparing the allele frequencies for HLA-A, HLA-B and HLA-C alleles between active TB patients and household contacts in the study. (XLS 49 kb)
DOI: 10.6084/m9.figshare.c.3629918_d13
title: Additional file 13: of Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes

description: Folder containing pymol session files showing APBS maps of the homology models. Colour coding is same as in Additional file 8. (ZIP 35165 kb)
DOI: 10.6084/m9.figshare.c.3630134_d1
title: Additional file 1: of Metformin use and its effect on survival in diabetic patients with advanced non-small cell lung cancer

description: Dataset supporting the conclusion of this article. (XLSX 115 kb)
DOI: 10.6084/m9.figshare.c.3630263_d1
title: Additional file 1: of The origin of Î˛-strand bending in globular proteins

description: List of PDB codes. The file contains a list of all the PDB codes and protein names used in our study. (TXT 139 kb)
DOI: 10.6084/m9.figshare.c.3630278_d1
title: Additional file 12: of Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress

description: KEGG enrichment analysis of co-expression gene clusters. (XLS 50Â kb)
DOI: 10.6084/m9.figshare.c.3630278_d2
title: Additional file 6: of Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress

description: List of drought responsive PbWRKY TFs that located in co-expression clusters. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.c.3630281_d1
title: Additional file 1: of Epidemiology of burns in pediatric patients of Beijing City

description: Raw data of epidemiology in pediatric burned patients of Beijing City. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3630278_d3
title: Additional file 10: of Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress

description: GO enrichment analysis of co-expression gene clusters. (XLS 39Â kb)