cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3601574_d12
title: Additional file 11: of The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

description: 1: Nucleotide-level variants calling filters, list and features in VCF format– Part 1. A zip compressed file with the first part of a list of all the variants identified in the pepino transcripts, including their positions and the nucleotide changes. 2: Nucleotide-level variants calling filters, list and features in VCF format– Part 2. A zip compressed file with the second part of a list of all the variants identified in the pepino transcripts, including their positions and the nucleotide changes. (ZIP 51450 kb)
DOI: 10.6084/m9.figshare.c.3601691_d2
title: Additional file 3: of Filling gaps in notification data: a model-based approach applied to travel related campylobacteriosis cases in New Zealand

description: Number of campylobacteriosis notifications and overseas travels in New Zealand District Health Boards (DHBs) (2000-2010). (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3601775_d6
title: Additional file 5 of Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

description: Half-Lives. A table of half-lives measured for genes in M. acetivorans. Only genes with positive half-life and coefficients of variation in the fit &lt;0.5 are included. (XLSX 756 KB)
DOI: 10.6084/m9.figshare.c.3601775_d7
title: Additional file 6 of Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

description: Code. Code used to compute differentially expressed genes. (ZIP 3 KB)
DOI: 10.15468/dl.67nqav
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus mongholicus var. nakaianus (Y.N.Lee) I.S.Choi & B.H.Choi"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032659-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.swcubd
title: Occurrence Download

description: A dataset containing 711 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus schelichowii Turcz."
 ]
}

 The dataset includes 711 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032660-241126133413365/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.3601997_d1
title: Additional file 12: of Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on Îą-cellulose, xylan, cellobiose and xylose

description: Proteomic expression values and Znet scores of previously run iTRAQ on 2Â g/L each of Îą-cellulose and cellobiose (XLSX 208 kb)
DOI: 10.6084/m9.figshare.c.3601997_d4
title: Additional file 7: of Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose

description: Znet scores of LacI transcriptional regulators and Histidine containing proteins in C. termitidis. Normalized proteomic Z-scores Pnet are represented as: (i) P0: xylose grown cells – cellobiose grown cells; (ii) P1: α-cellulose grown cells – cellobiose grown cells; and (iii) P2: xylan grown cells – cellobiose grown cells. Normalized transcriptomic Z-scores Rnet are represented as: (i) R0: xylose grown cells – cellobiose grown cells; (ii) R1: α-cellulose grown cells – cellobiose grown cells; and (iii) R2: xylan grown cells – cellobiose grown cells. Highlighted cells represent Znet-value threshold for up and down regulation of ± 1.65 (representing the outermost 10 % of the data set). (XLSX 11 kb)
DOI: 10.15468/dl.nkm4zs
title: Occurrence Download

description: A dataset containing 5155 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hedysarum alpinum L."
 ]
}

 The dataset includes 5155 records from 171 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032661-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pyxpje
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hedysarum vicioides var. japonicum (B.Fedtsch.) B.H.Choi & H.Ohashi"
 ]
}

 The dataset includes 96 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032662-241126133413365/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.3602105_d1
title: Additional file 7: of The incidence of tuberculosis among hiv-positive individuals with high CD4 counts: implications for policy

description: Enrolment and follow up database. (XLS 2101Â kb)
DOI: 10.6084/m9.figshare.c.3602105_d5
title: Additional file 8: of The incidence of tuberculosis among hiv-positive individuals with high CD4 counts: implications for policy

description: TB cases database. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.c.3602123_d1
title: Additional file 3: of Extent of pre-translational regulation for the control of nucleocytoplasmic protein localization

description: Classification of all NES motifs considered in this study, including their sequence, regulation modes, number of encoding transcripts and number of encoding exons. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3602240_d1
title: Additional file 1: Table S1. of The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials

description: Cytogenetic data used for the reconstructions of ancestral diploid numbers and presence of interstitial telomeric signals (ITS). Multi states codes used in BayesTraits were A: 2n = 14, B: 2n = 18, C: 2n = 22, D: 2n = 10, E: 2n = 12, F: 2n = 16, G: 2n = 18, H: 2n = 20, I: 2n = 24, J: 2n = 32; K: presence of ITS, L: absence of ITS. Missing data code (−) was used for diploid numbers and/or ITS of species without these cytogenetic data. (XLS 44 kb)
DOI: 10.6084/m9.figshare.c.3602213_d5
title: Additional file 5: Table S2. of Quantitative proteomics of the tobacco pollen tube secretome identifies novel pollen tube guidance proteins important for fertilization

description: Tobacco semi-in vivo pollen tube secreted proteins of ≤ 20 kDa. (XLSX 306 kb)
DOI: 10.6084/m9.figshare.c.3602213_d9
title: Additional file 6: Table S3. of Quantitative proteomics of the tobacco pollen tube secretome identifies novel pollen tube guidance proteins important for fertilization

description: Identified protein families and domains of semi-in vivo pollen tube-secreted proteins. (XLSX 515 kb)
DOI: 10.6084/m9.figshare.c.3602213_d11
title: Additional file 21: Table S8. of Quantitative proteomics of the tobacco pollen tube secretome identifies novel pollen tube guidance proteins important for fertilization

description: List of primers used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3602273_d1
title: Additional file 1 of Identification of in vitro and in vivo disconnects using transcriptomic data

description: Genes of top 10 biclusters in vitro . List of disconnected genes that appeared in the top 10 biclusters in vitro.
DOI: 10.6084/m9.figshare.c.3602318_d8
title: Additional file 8: Table S5. of Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model

description: Gene set enrichment analysis of ribosome profiling data (related to Fig.Â 3d). (XLSX 11.1 kb)
DOI: 10.6084/m9.figshare.c.3602342_d7
title: MOESM3 of Molecular phylogeny, morphology and life-history comparisons within Circus cyaneus reveal the presence of two distinct evolutionary lineages

description: Additional file 3: S5. Pairwise genetic distance matrix for Cytochrome b.
DOI: 10.6084/m9.figshare.c.3602318_d9
title: Additional file 5: Table S3. of Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model

description: Gene ontology term enrichments for RNA-Seq data from differentiated TSC2 deletion cell lines and microarray data of patient cortical tubers (related to Fig.Â 2e). (XLSX 19.8 kb)
DOI: 10.6084/m9.figshare.c.3602345_d7
title: Additional file 1: Table S1. of Ridaforolimus (MK-8669) synergizes with Dalotuzumab (MK-0646) in hormone-sensitive breast cancer

description: Statistical analysis of IGF1R expression for samples depicted in Fig.Â 1. (XLSX 44Â kb)
DOI: 10.6084/m9.figshare.c.3602345_d8
title: Additional file 6: Table S6. of Ridaforolimus (MK-8669) synergizes with Dalotuzumab (MK-0646) in hormone-sensitive breast cancer

description: Ingenuity Pathway Analysis. (XLSX 115Â kb)
DOI: 10.6084/m9.figshare.c.3602318_d10
title: Additional file 10: Table S7. of Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model

description: RNA-Seq and ribosome profiling data of differentiated TSC2 wild-type and homozygous deletion cell lines treated with mTOR inhibitors (related to Fig.Â 4). (XLSB 7.52 mb)
DOI: 10.6084/m9.figshare.c.3602318_d11
title: Additional file 9: Table S6. of Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model

description: Gene ontology term enrichments for ribosome profiling data (related to Fig.Â 3f). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3602375_d1
title: Additional file 1: Table S1. of A cultured approach to canine urothelial carcinoma: molecular characterization of five cell lines

description: Comparisons analysis of primary tumors and cell lines. oaCGH data from primary tumors and cell lines were simultaneously analyzed and compared using the Comparisons algorithm (Nexus Copy Number, Biodiscovery). Few aberrant regions were evident in only the primary tumors or the cell lines without being present in the other. (XLSX 9Â kb)
DOI: 10.15468/dl.f6rk94
title: Occurrence Download

description: A dataset containing 98 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhamnus taquetii (H.Lév. & Vaniot) H.Lév."
 ]
}

 The dataset includes 98 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032663-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c267sa
title: Occurrence Download

description: A dataset containing 1136 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Geranium dahuricum DC."
 ]
}

 The dataset includes 1136 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032664-241126133413365/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.3602441_d9
title: Additional file 15: File S8. of Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response

description: List of genes with functional annotation, LFC values and predicted protein sequence that were used to construct the model of L. theobromae response to HS (shown in Fig. 5). (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3602474_d3
title: Additional file 1: Table S1. of Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats

description: Number of reads/sequences retained at each stage of the assembly process. Table S2. Transcript length and read depth in relation to the number of species in which transcripts were identified. Transcripts from each Rotaria species in turn were used as queries in a BLASTN search of the other three Rotaria transcriptomes (e-value ≤1e-10). Mean transcript length and FPKM is presented in relation to the number of species transcripts were identified in. Table S3. Percentage of transcripts with h u ≥30 with varying HGT detection thresholds. Left: percentage of transcripts with h u ≥30, for decreasing e-value thresholds for accepting transcripts for analysis. Right: percentage of transcripts with h u ≥30, for increasing minimum transcript length for analysis. Red, R. magnacalcarata; blue, R. socialis; green, R. sordida; and black, R. tardigrada. Table S4. The number of orthologs that are unique to different subclades based on presence/absence in transcriptomes for different methods of identifying orthologs and different criteria for assigning orthologs as foreign or not. Table S5. BLASTN matches in the R. magnacalcarata genome of genes inferred to be unique to particular species based on transcriptome presences/absences. Table S6. Best BLASTN matches of scaffolds that contain a foreign gene but no non-foreign gene in R. magnacalcarata in GenBank. Table S7. Reconstruction of numbers and rates of gains and losses of foreign genes on different branches or sets of branches on the Rotaria tree. Results based on two methods of assigning orthologs are shown: 1) reciprocal BLAST and 2) Markov clusters; and excluding or including correction based on R. magnacalcarata genome matches. Table S8. Results of topGO enrichment analysis for GO annotation categories that are over-represented in particular species or sets of species relative to numbers across the whole foreign ortholog dataset. Fisher’s exact tests with P &lt;0.01 are shown in bold. The “Weight01” option was used to correct for significance of nested annotation terms. Only terms with more than five orthologs present in the whole dataset are shown. Table S9. List of foreign transcripts (h U &gt;30), results of the HGT analysis, GO annotation and matches to the R. magnacalcarata draft genome. Table S10. List of nuclear genes used in phylogenetic reconstruction. (XLSX 3668 kb)
DOI: 10.6084/m9.figshare.c.3602441_d10
title: Additional file 12: File S6. of Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response

description: List of genes with functional annotation separated by clusters of co-regulated genes. (XLSX 216 kb)
DOI: 10.6084/m9.figshare.c.3602444_d10
title: Additional file 10: of Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

description: Enrichment of identified trans-genes in GO terms based on 20Â k permutations. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.c.3602486_d1
title: Additional file 1: of Age and HPV type as risk factors for HPV persistence after loop excision in patients with high grade cervical lesions: an observational study

description: Datasets. (XLS 106 kb)
DOI: 10.6084/m9.figshare.c.3602498_d1
title: MOESM1 of Impact of degradable nanowires on long-term brain tissue responses

description: Additional file 1. Excel-file with raw data.
DOI: 10.15468/dl.yyd92k
title: Occurrence Download

description: A dataset containing 545 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bupleurum euphorbioides Nakai"
 ]
}

 The dataset includes 545 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032665-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7vbqte
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tantilla calamarina Cope, 1866"
 ]
}

 The dataset includes 105 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032666-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mjvgu6
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gentiana chosenica Okuyama"
 ]
}

 The dataset includes 60 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032667-241126133413365/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.3602591_d6
title: Additional file 2 of Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

description: Table S1. Genome coverage of the different repeat families. For each repeat family, a coverage calculation has been performed and the percentage of coverage of each family was calculated.by relating the cover of every family with respect to the overall repeat coverage of the genome. Table S2. Compartmentalization of the tomato genome in three major regions. Coordinates in gff3 format of the three regions of the genome based on the repeats and genes coverage calculation into 500Â kb windows with overlap of 50Â kb.Table S3. Names of identified TE-genes. List of ID and name of each gene identified as a TE-gene. Table S4. Statistical results of the analysis of transposable elements consensus by the method of Makarevitch and al. Table S5. Functional annotation of differentially expressed genes candidate as RIN targets. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.c.3602627_d2
title: Additional file 2: Table S1. of Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation

description: Divergence times estimates from BEAST, MCMCTREE and Reltime, including minimum and maximum 95 % CI. Node numbers refer to Additional file 1: Figure S1. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3602633_d1
title: Additional file 1: Table 5. of Impact of 3T multiparametric MRI and FDG-PET-CT in the evaluation of occult primary cancer with cervical node metastasis

description: Data collection. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3602756_d1
title: Additional file 2: of Development and application of an automated algorithm to identify a window of consecutive days of accelerometer wear for large-scale studies

description: R code for execution of OPACH algorithm.
DOI: 10.6084/m9.figshare.c.3602762_d2
title: Additional file 2 of Accurate chromosome segregation by probabilistic self-organisation

description: Mathematica codes. The Mathematica codes used in this study. To read the file, Wolfram CDF player (available free from https://www.wolfram.com/cdf-player/ ) or Mathematica (Wolfram Research) is required. (ZIP 62 kb)
DOI: 10.6084/m9.figshare.c.3602765_d2
title: MOESM6 of Effect of secretory pathway gene overexpression on secretion of a fluorescent reporter protein in Aspergillus nidulans

description: Additional file 6: Table 2.  Plasmids used in this study.
DOI: 10.6084/m9.figshare.c.3602768_d1
title: Additional file 8: of MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

description: KEGG pathway analysis of dre-mir-29b and genes involved in the regulation of RNA metabolic process. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3602768_d2
title: Additional file 3: of MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

description: Heat maps of cold-related miRNAs and genes. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.c.3602768_d3
title: Additional file 1: of MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

description: Lists of primers. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3602774_d2
title: Additional file 1: Table S1. of Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster

description: CCRT under varying environmental conditions (XLS 26Â kb)
DOI: 10.6084/m9.figshare.c.3602768_d4
title: Additional file 6: of MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

description: List of cold-related genes and GO term analysis. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.c.3602774_d3
title: Additional file 4: Table S3. of Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster

description: Downregulated genes CS vs. RT (FDR
DOI: 10.6084/m9.figshare.c.3602768_d5
title: Additional file 4: of MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

description: Lists of cold-related miRNAs and target genes. (XLSX 530 kb)
DOI: 10.6084/m9.figshare.c.3602765_d6
title: MOESM5 of Effect of secretory pathway gene overexpression on secretion of a fluorescent reporter protein in Aspergillus nidulans

description: Additional file 5: Table 1.  Primers used in this study.
DOI: 10.6084/m9.figshare.c.3602768_d6
title: Additional file 7: of MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

description: Expression profiles of miRNAs and their target mRNAs. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.c.3602774_d5
title: Additional file 5: Table S4. of Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster

description: Upregulated genes rec15 vs. RT (FDR
DOI: 10.6084/m9.figshare.c.3602825_d11
title: Additional file 3: of In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians

description: A ranked list of the top 1000 highly variable transcripts with means, coefficients of variation, and the hierarchical clustering group in which the average expression was highest. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.c.3602825_d13
title: Additional file 11: of In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians

description: A table of raw read counts obtained for all 168 single cell samples aligned to the SmedASXL planarian transcriptome assembly. (TXT 23858 kb)
DOI: 10.6084/m9.figshare.c.3602897_d1
title: MOESM1 of Long-term effect of sitagliptin on endothelial function in type 2 diabetes: a sub-analysis of the PROLOGUE study

description: Additional file 1. All dataset supporting the conclusions of this article.
DOI: 10.15468/dl.vb55gx
title: Occurrence Download

description: A dataset containing 480 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gentiana jamesii Hemsl."
 ]
}

 The dataset includes 480 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032668-241126133413365/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.3602903_d1
title: Additional file 1: of Genetic signals of high-altitude adaptation in amphibians: a comparative transcriptome analysis

description: List of putative positively selected genes (PSGs) in high-altitude Asiatic toads (Bufo gargarizons) and the plateau brown frog (Rana kukunoris), as well as the Gene Ontology categories over-represented (Pâ
DOI: 10.6084/m9.figshare.c.3602825_d14
title: Additional file 13: of In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians

description: An annotation file for use with the vignette. (TAB 999 bytes)
DOI: 10.6084/m9.figshare.c.3602903_d2
title: Additional file 2: of Genetic signals of high-altitude adaptation in amphibians: a comparative transcriptome analysis

description: List of the 89 nutrient metabolism associated genes and their tag SNPs. These candidate genes are identified according to GO and KEGG annotation and are subjected to FST outlier analysis. (XLSX 13Â kb)