cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3640085_d2.v1
title: Additional file 2 of Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

description: List of differentially expressed genes. Dataset of differentially expressed genes, as originally published by [24]. Here, those genes are listed that are differentially expressed in at least one of the 4 time points and in either the more (FDR &lt; 0.05) or less (FDR &lt; 0.1) stringent dataset. This file also depicts the overlap of genes at the different time points. (XLSX 514 KB)
DOI: 10.15468/dl.gr4hcf
title: Occurrence Download

description: A dataset containing 574 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 574 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037980-241126133413365/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.3640121_d2.v1
title: Additional file 2: of Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis

description: Supplementary data files. Pathways.zip full set model predictions for all metabolites during transcription factor induction based on genome-wise expression. Pathways_specific.zip full set model predictions for all metabolites during transcription factor induction based on TF regulon specific expression. Model.xml: Genome scale MTB metabolic model used. Table S1 the binding network used for the transcription factor overexpression analyses and median-scaled metabolite abundance values for normoxic and hypoxic conditions. (ZIP 2706Â kb)
DOI: 10.6084/m9.figshare.c.3640133_d1.v1
title: Additional file 3: of Behavioural responses to heat in desert birds: implications for predicting vulnerability to climate warming

description: Raw data as presented in Table S1 and Table S2. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3640133_d2.v1
title: Additional file 2: of Behavioural responses to heat in desert birds: implications for predicting vulnerability to climate warming

description: Behavioural observation data of birds collected during the austral summers (November-March) of 2009/2010 and 2010/2011. (XLSX 1.09 mb)
DOI: 10.6084/m9.figshare.c.3640136_d2.v1
title: Additional file 19: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Candidate CRNs of Pl. halstedii, predictions based on ORFs generated from the un-masked genome. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d5.v1
title: Additional file 16: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Kazal-like domain features among the different genomes. (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d6.v1
title: Additional file 18: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Candidate CRNs of Pl. halstedii, predictions based on gene models. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d9.v1
title: Additional file 13: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: 19 candidate NLPs of Pl. halstedii. (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.c.3640139_d10.v1
title: Additional file 27: of Ascertainment bias from imputation methods evaluation in wheat

description: Best linear unbiased predictors (BLUPs) for each genotype for days to heading. (txt 8 kb)
DOI: 10.6084/m9.figshare.c.3640139_d11.v1
title: Additional file 19: of Ascertainment bias from imputation methods evaluation in wheat

description: Barley SNP marker map. Markers, chromosome and position (cM) are presented as columns. (txt 18 kb)
DOI: 10.6084/m9.figshare.c.3640139_d13.v1
title: Additional file 24: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS dataset with 35 % missing information. Genotypes are presented as rows and SNPs as columns. (txt 16.3 Mb)
DOI: 10.6084/m9.figshare.c.3640139_d14.v1
title: Additional file 18: of Ascertainment bias from imputation methods evaluation in wheat

description: Barley SNP marker score array. Genotypes are presented as rows and SNPs as columns. (txt 278 kb)
DOI: 10.6084/m9.figshare.c.3640139_d16.v1
title: Additional file 25: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS bin map for 35 % coverage. Markers, chromosome and position (bins) are presented as columns. (txt 287 kb)
DOI: 10.6084/m9.figshare.c.3640139_d20.v1
title: Additional file 28: of Ascertainment bias from imputation methods evaluation in wheat

description: Best linear unbiased predictors (BLUPs) for each genotype for thousands kernel weight. (txt 9 kb)
DOI: 10.6084/m9.figshare.c.3640139_d23.v1
title: Additional file 20: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS dataset with 50 % missing information. Genotypes are presented as rows and SNPs as columns. (txt 16.3 Mb)
DOI: 10.6084/m9.figshare.c.3640139_d25.v1
title: Additional file 22: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS dataset with 25 % missing information. Genotypes are presented as rows and SNPs as columns. (txt 16.3 Mb)
DOI: 10.6084/m9.figshare.c.3640139_d24.v1
title: Additional file 21: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS bin map for 50 % coverage. Markers, chromosome and position (bins) are presented as columns. (txt 287 kb)
DOI: 10.6084/m9.figshare.c.3640139_d29.v1
title: Additional file 23: of Ascertainment bias from imputation methods evaluation in wheat

description: Wheat GBS bin map for 25 % coverage. Markers, chromosome and position (bins) are presented as columns. (txt 287 kb)
DOI: 10.5519/qd.npym2rza
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (132 records)
DOI: 10.6084/m9.figshare.c.3640142_d3.v1
title: Additional file 1: of Ex vivo immunosuppressive effects of mesenchymal stem cells on Crohn’s disease mucosal T cells are largely dependent on indoleamine 2,3-dioxygenase activity and cell-cell contact

description: Mesenchymal stem cells with T cells from inflamed Crohn’s mucosa. Representative time-lapse imaging of a co-culture with bone marrow-derived mesenchymal stem cells of a healthy donor and T cells isolated from inflamed mucosa of a patient with Crohn’s disease. A dynamic and intense interaction is clearly evident mostly during the first 6 h, when the binding between these two cell populations is non-fixed but instead appears as a continuous attachment and detachment, after which a growing number of cells with morphological features of apoptosis (those with nuclear fragmentation and cellular swelling) and apoptotic bodies become evident. The images were serially recorded every 30 min for 12 h. Magnification: 100×. (ZIP 6780 kb)
DOI: 10.15468/dl.ta9d9h
title: Occurrence Download

description: A dataset listing the 8587 species recorded in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "GadmGid is USA.47_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year 2014-2024"
 ]
}

 The dataset's 8587 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037976-241126133413365/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.3640142_d1.v1
title: Additional file 2: of Ex vivo immunosuppressive effects of mesenchymal stem cells on Crohn’s disease mucosal T cells are largely dependent on indoleamine 2,3-dioxygenase activity and cell-cell contact

description: Mesenchymal stem cells with T cells from non-inflamed Crohn’s mucosa. Representative time-lapse imaging of a co-culture with bone marrow-derived mesenchymal stem cells of a healthy donor and T cells isolated from non-inflamed mucosa of a patient with Crohn’s disease. A slow and continuous interaction is evident, and a few cells with morphological features of apoptosis (those with nuclear fragmentation and cellular swelling) and apoptotic bodies become evident at the end of the period of registration. The images were serially recorded every 30 min for 12 h. Magnification: 100×. (ZIP 6800 kb)
DOI: 10.6084/m9.figshare.c.3640142_d2.v1
title: Additional file 3: of Ex vivo immunosuppressive effects of mesenchymal stem cells on Crohnâ  s disease mucosal T cells are largely dependent on indoleamine 2,3-dioxygenase activity and cell-cell contact

description: Mesenchymal stem cells with T cells from healthy mucosa. Representative time-lapse imaging of a co-culture with bone marrow-derived mesenchymal stem cells of a healthy donor and T cells isolated from healthy mucosa of a control subject. The absence of any active interaction during the entire period of registration is clearly evident. The images were serially recorded every 30Â min for 12Â h. Magnification: 100Ă . (ZIP 9020 kb)
DOI: 10.6084/m9.figshare.c.3640178_d1.v1
title: Additional file 1: of Countrywide serological evaluation of canine prevalence for Anaplasma spp., Borrelia burgdorferi (sensu lato), Dirofilaria immitis and Ehrlichia canis in Mexico

description: Dataset supporting the conclusions of this article. (XLSX 227 kb)
DOI: 10.6084/m9.figshare.c.3640181_d1.v1
title: Additional file 1: of GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

description: R script used to generate figures, tables and numbers used in the described analysis of Hi-C data. (RMD 7 kb)
DOI: 10.6084/m9.figshare.c.3640181_d2.v1
title: Additional file 2: of GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

description: R script used to generate figures, tables and numbers used in the described analysis of ChIA-PET data. (RMD 14 kb)
DOI: 10.6084/m9.figshare.c.3640184_d2.v1
title: Additional file 2: Table S2. of Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes

description: Table S2, derived from MaxQuant output table Peptides, contains all identified peptide sequences belonging to the proteins of Table S1 in alphabetic order starting with the first amino acid: It also contains other relevant data such as scores, charge states, and mass accuracy. (XLSX 2472Â kb)
DOI: 10.6084/m9.figshare.c.3640184_d4.v1
title: Additional file 5: Table S4. of Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes

description: Curated version of the MaxQuant output file Phospho (STY) sites with phosphopeptide sequences, localization probabilities, scores, mass errors and other relevant data. Also included are phosphopeptides with site probabilities lower than 0.75, which were not included into TableÂ 2. (XLS 99Â kb)
DOI: 10.6084/m9.figshare.c.3640256_d2.v1
title: Additional file 3: of Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia

description: Results of estimates of Hardy-Weinberg equilibrium tests conducted for each locus in the NT and East Coast populations (Pâ
DOI: 10.6084/m9.figshare.c.3640256_d3.v1
title: Additional file 1: of Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia

description: R script used to perform filtering of the isolated SNPs. This file has to be read with R. (R 14Â kb)
DOI: 10.6084/m9.figshare.c.3640256_d4.v1
title: Additional file 4: of Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia

description: BayeScan results for analysis for SNPs under natural selection. The first column is the tag of the selected reads. For each SNP, â  probâ   represents the posterior probability of departure from neutrality; PO (posterior odds) is the ratio of posterior probabilities and is indicative of how more likely the model with selection is compared to the neutral model. The q value estimates the statistical significance of the deviation. The three lowest values are highlighted in yellow. The q value was used for ordering of the rows in the table. (XLSX 150Â kb)
DOI: 10.15468/dl.mwexbv
title: Occurrence Download

description: A dataset containing 263 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is one of (Xeno-canto - Bird sounds from around the world, Macaulay Library Audio and Video Collection, Borror Lab of Bioacoustics (BLB), Ohio State University, NHMO Bird collection, NEON breeding landbird point counts, Mohonk Preserve Historical Observational Biodiversity Data, CM Birds Collection, Mohonk Preserve Phenology Observations)",
 "Month is one of (May, June, July)",
 "TaxonKey is Setophaga cerulea (A.Wilson, 1810)",
 "Year 1976-2024"
 ]
}

 The dataset includes 263 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037981-241126133413365/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.3640283_d1.v1
title: Additional file 3: of RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues

description: Pathways found in the annotated portion of the transcriptomes. (ZIP 4950 kb)
DOI: 10.6084/m9.figshare.c.3640283_d2.v1
title: Additional file 1: of RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues

description: Table listing Mytilus galloprovincialis transcripts, including the sequence, length, RPKM, description, accession number of the description (Hit ACC) and e-value obtained in each database used for annotation and the GO terms ascribed to each sequence. (XLSX 38412 kb)
DOI: 10.6084/m9.figshare.c.3640283_d3.v1
title: Additional file 5: of RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues

description: Mytilus galloprovincialis transcriptome in FASTA format. (ZIP 25884 kb)
DOI: 10.6084/m9.figshare.c.3640283_d4.v1
title: Additional file 2: of RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues

description: Figure representing the number of transcripts obtained after the assembly of increasing number of mapped reads. (XLSX 743 kb)
DOI: 10.6084/m9.figshare.c.3640283_d5.v1
title: Additional file 4: of RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues

description: Tables and figures showing the non-shared C1q variants found in the hemocytes, mantle, muscle and gills. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3640331_d1.v1
title: Additional file 3: Table S2. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the annotated information of the 1,807 experiment 2 only senDMPs. (CSV 539 kb)
DOI: 10.6084/m9.figshare.c.3640331_d2.v1
title: Additional file 8: Table S6. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Panther DB pathway analysis of the 1,807 experiment 2 only senDMPs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3640331_d3.v1
title: Additional file 2: Table S1. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the annotated information of the 969 experiment 1 only senDMPs. (CSV 290 kb)
DOI: 10.6084/m9.figshare.c.3640331_d5.v1
title: Additional file 4: Table S3. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the annotated information of the 725 agree senDMPs. (CSV 244 kb)
DOI: 10.6084/m9.figshare.c.3640331_d6.v1
title: Additional file 7: Table S5. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Panther DB pathway analysis of the 969 experiment 1 only senDMPs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3640331_d7.v1
title: Additional file 6: Table S7. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Panther DB pathway analysis of the 725 agree senDMPs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3640331_d8.v1
title: Additional file 5: Table S8. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the P values for the difference in methylation between the EP cells and each of the FACs sorted populations as well as the FACs sorted populations against each other. (CSV 89758 kb)
DOI: 10.6084/m9.figshare.c.3640331_d9.v1
title: Additional file 9: Table S4. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the annotated information of the senescence associated probes reaching 0.01 FDR and beta value difference &gt;0.3 in both experiment 1 and experiment 2 which are located on chrX. (CSV 1 kb)
DOI: 10.6084/m9.figshare.c.3640367_d3.v1
title: Additional file 6: Figure S4. of CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation

description: Relationship between the p value threshold for SNP inclusion and trait clustering. a Similar clusters for obesity (I), autoimmunity (II), and atherosclerosis (III) are observed with the different p value thresholds. Therefore, the detection of informative clusters is robust to varying the number of SNPs in the analysis, although traits are lost as the p value threshold is made more stringent. In all cases, the number of clusters (k) in the analysis was set to 20. The locations of the three clusters were also marked in the entire dendrogram and heat map of pairwise human traits for the p value threshold of 10â  5 (b), 10â  7 (c) and 10â  10 (d). (ZIP 3188 kb)
DOI: 10.6084/m9.figshare.c.3640367_d8.v1
title: Additional file 3: Table S2. of CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation

description: CPAG results based on NHGRI GWAS Catalog (last visit on 4 September 2013). Listed are associated diseaseâ  trait pairs and counts of overlap based on the SNP, SNP_LD, and gene-based methods. Based on these counts, a series of statistical tests were done to test the significance of the similarity, including Fisherâ  s exact test, an empirical permutations test (10,000 permutations), hypergeometric test and binomial test. The last three columns list the overlapping genes, SNPs and SNPs in LD. (XLSX 1076 kb)
DOI: 10.15468/dl.t8t9ru
title: Occurrence Download

description: A dataset containing 4496 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Siproeta epaphus (Latreille, 1813)"
 ]
}

 The dataset includes 4496 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037982-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34943/a3e5e2d7-0222-4014-8ac2-824115d7a335
title: ODP 1027C Hydrophone Deployed 2020-10-01

description: The Ocean Sonics icListen HF Hydrophone 6017 was deployed on 2020-10-01 at ODP 1027C. ODP 1027C is a borehole site used to pinpoint an area within Cascadia Basin. This device is a Hydrophone. Hydrophones are devices containing transducers that convert underwater sound waves into electrical signals. They are acoustic instruments that can process data while they are being collected to produce calibrated waveform data. Hydrophones are typically used to study vocalizations of marine mammals, ship traffic and ambient noise. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.6084/m9.figshare.c.3640409_d7.v1
title: Additional file 4: Table S3. of Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers

description: Raw poly(A)+ mRNA transcriptome data and calculations based on reads per million (RPM). Sheet 1: Alignment statistics and correlations between the different datasets, calculated from RPM using the unique gene set only. cBS: cultured Lister 427 bloodstream forms expressing the tet repressor from pHD1313. BT1-3: Tbr729; LW - new isolates; PC - cultured Lister 427 procyclic forms. Sheet 2: Read counts for all genes. Sheet 3: Data for unique gene list [39] with reads per million (RPM). Column R shows the regulation pattern according to a custom script. Samples giving significantly peak RPMs (relative to other samples) are indicated by “max” and troughs are indicated by “min”. The threshold was set at 2-fold. Sheet 4: Sheet 3 results, filtered to remove genes for which the maximum RPM value was less than 10. Column T shows correlation coefficients of the RPM results with PIP39 (Tb927.9.6090). Colour code for ratios: Blue is less than 0.25×, green is less than 0.5×, orange is greater than 2× and red is greater than 4×. Comparisons with other datasets are indicated as follows: ST/SL Kabani; stumpy/slender ratio from [6]; ST/SL BS Jensen - stumpy/slender ratio from [7]; SLvST mRNA Capewell and ST polysomes/mRNA Capewell - data from [13]; SG/cBS: salivary gland trypanosomes relative to cultured bloodstream forms from [30]; SG/PC: salivary gland trypanosomes [30] relative to our results for cultured Lister 427 procyclic forms. Sheet 5: calculated RPMs for selected recognised stumpy-form markers. Reads for the ESAG9s and the PAD genes are not unique and precise allocation to a particular variant was not attempted. Sheet 6: Genes showing increased RPM values in both LW032 and LW042 and metacyclic (salivary gland, SG) forms. Sheet 7: Genes showing reduced RPM values in both LW032 and LW042 and metacyclic (salivary gland, SG) forms. (XLSX 3928 kb)
DOI: 10.6084/m9.figshare.c.3640412_d2.v1
title: Additional file 1: of Significance of soluble triggering receptor expressed on myeloid cells-1 elevation in patients admitted to the intensive care unit with sepsis

description: Whole data set used for statistical analysis evaluating prognostic value of biomarkers and severity scores. (XLSX 129Â kb)
DOI: 10.6084/m9.figshare.c.3640424_d2.v1
title: MOESM2 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 2. Feature set SVM RFE.
DOI: 10.6084/m9.figshare.c.3640424_d1.v1
title: MOESM1 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 1. Feature set VARSEL RF.
DOI: 10.6084/m9.figshare.c.3640424_d3.v1
title: MOESM5 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 5. Feature set SVM.
DOI: 10.6084/m9.figshare.c.3640424_d5.v1
title: MOESM6 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 6. Feature set LASSO.