cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.vqrh8r
title: Occurrence Download

description: A dataset containing 2065 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is one of (Togo, Niger, Mauritania, Cabo Verde, Senegal, Mali, Nigeria, Guinea, Gambia, Guinea-Bissau, Côte d’Ivoire, Sierra Leone, Liberia, Ghana, Burkina Faso, Benin)",
 "TaxonKey is Boscia senegalensis Lam."
 ]
}

 The dataset includes 2065 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034390-241126133413365/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.3639074_d1
title: Additional file 5: of Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

description: Kruskal-Wallis test statistic for combined expression profiles of target genes based on microarray and qPCR data. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3639074_d3
title: Additional file 2: of Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

description: Mapping of T. thynnus transcripts to T. orientalis genome. (TXT 5528 kb)
DOI: 10.6084/m9.figshare.c.3639074_d2
title: Additional file 3: of Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

description: Results of network analyses and clustering using Markov algorithm for T. thynnus transcripts. Log2 normalised averaged signals are provided for each probe. (XLSX 904 kb)
DOI: 10.6084/m9.figshare.c.3639074_d4
title: Additional file 4: of Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

description: RT-qPCR related data. Table sheets containing primer sequences for genes included in qPCR analyses, BestKeeper stability for reference genes and Log2 transformed data for all targets. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3639074_d5
title: Additional file 1: of Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

description: Mapping of T. thynnus transcripts to O. niloticus genome. (TXT 2853 kb)
DOI: 10.6084/m9.figshare.c.3639074_d6
title: Additional file 6: of Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

description: KEGG pathway analyses of T. thynnus tissue expression profiles. The analyses were performed by choosing each tissue as experimental state and all other as reference. The same was repeated by denoting combinations of two tissues together as a test sample. Data are given only for statistically significant pathways (q
DOI: 10.6084/m9.figshare.c.3639086_d4
title: Additional file 1: of Ribosome reinitiation at leader peptides increases translation of bacterial proteins

description: Lists of used genomes and taxonomic groups of bacteria. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.c.3639116_d2
title: Additional file 2: of New tools to convert bacterial artificial chromosomes to a self-excising design and their application to a herpes simplex virus type 1 infectious clone

description: Raw Data. Raw data used for the production of Figs.Â 1, 2 and 3. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3641105_d1
title: Additional file 9: Table S4. of High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants

description: Differentially expressed (DE) miRNAs identified in response to MAB-R and MAB-S infection. miRNAs were regarded as DE if they had an absolute Log2 Fold Change of at least 1, and an adjusted P-value (FDR) of less than 0.05. (XLSX 7 kb)
DOI: 10.6084/m9.figshare.c.3641105_d3
title: Additional file 5: Table S2. of High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants

description: Differentially expressed (DE) mRNAs identified in response to MAB-R and MAB-S infection. Genes were regarded as DE if they had an absolute Log2 Fold Change of at least 1, and an adjusted P-value (FDR) of less than 0.05. (XLSX 336 kb)
DOI: 10.6084/m9.figshare.c.3641105_d2
title: Additional file 3: Table S1. of High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants

description: Read mapping statistics for RNA-seq and small RNA-seq (sRNA-seq) libraries. For RNA-seq libraries, the numbers of reads mapping uniquely to the human reference genome are indicated. For sRNA-seq libraries, the numbers of reads mapping to mature miRNAs from miRBase are given. (XLSX 7 kb)
DOI: 10.6084/m9.figshare.c.3641105_d9
title: Additional file 6: Table S3. of High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants

description: Overlap of the core responses to MAB and MTB. 73 genes were identified in both datasets. “Induced” indicates that the gene shows an increase in abundance upon infection; “Repressed” indicates that the gene shows a decrease in abundance upon infection. (XLSX 8 kb)
DOI: 10.5281/zenodo.14474906
title: Datasets for "Topological Deep Learning for Enhanced Diagnosis of Blood Disorders"
DOI: 10.5281/zenodo.14474907
title: Datasets for "Topological Deep Learning for Enhanced Diagnosis of Blood Disorders"
DOI: 10.15468/dl.7ku256
title: Occurrence Download

description: A dataset containing 2534 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei, Hong Kong, Macao)",
 "Geometry POLYGON((105.23348 18.30064,126.27610 18.30064,126.27610 26.71408,105.23348 26.71408,105.23348 18.30064))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oreochromis niloticus (Linnaeus, 1758)",
 "Year 2015-2024"
 ]
}

 The dataset includes 2534 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034391-241126133413365/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.3642389_d2
title: Additional file 6: of Modular reorganization of the global network of gene regulatory interactions during perinatal human brain development

description: Transcription factor binding site enrichment analysis per module obtained using Webgestalt [27]. Statistically significant overrepresentation of transcription factor binding motifs terms was assessed based on the toolâ  s standard hypergeometric test. Separate tabs are included in this file for each separate module. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.c.3642389_d4
title: Additional file 4: of Modular reorganization of the global network of gene regulatory interactions during perinatal human brain development

description: Gene ontology enrichment analysis per module. Only gene ontology terms annotated to at least 150 genes are included. Statistically significant overrepresentation of GO terms was assessed based on a Z-score test. Mean and standard deviation for the expected number of genes annotated to each GO term per module were estimated based on 10,000 equally-sized random samples drawn from the background gene population. P values, where adjusted for multiple testing using Benjamini-Hochberg correction. Separate tabs are included in this file for each separate module. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3642389_d3
title: Additional file 5: of Modular reorganization of the global network of gene regulatory interactions during perinatal human brain development

description: Gene ontology enrichment analysis per module obtained using Webgestalt [27]. Statistically significant overrepresentation of GO terms was assessed based on the toolâ  s standard hypergeometric test. Only biological process terms were considered. Separate tabs are included in this file for each separate module. (XLSX 235 kb)
DOI: 10.6084/m9.figshare.c.3642398_d1
title: MOESM1 of Integrating text mining, data mining, and network analysis for identifying genetic breast cancer trends

description: Additional file 1. Additional Tables.
DOI: 10.6084/m9.figshare.c.3642404_d4
title: Additional file 2: of Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria

description: W. intricata UH strain HT-29-1 and H. welwitschii UH strain IC-52-3 102 housekeeping genes, COGs. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.c.3643415_d4
title: Additional file 11: Table S5. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Predictive accuracy of SupportMix by cross-validation. Averaged across 50 runs of the genome-wide proportion of ancestry in subsets of wild barley analyzed as testing samples, using the remaining wild individuals as the validation dataset.
DOI: 10.6084/m9.figshare.c.3643415_d5
title: Additional file 16: Table S8. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Summary of number of private alleles from wild barley populations present in the landraces. Average allele frequency of alleles private to wild populations in the landraces (in parenthesis). The number of private alleles in each wild population is shown in brackets.
DOI: 10.6084/m9.figshare.c.3643415_d10
title: Additional file 4: Table S2. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Median and maximum focal F ST values from comparisons of each landrace population to all other landraces.
DOI: 10.6084/m9.figshare.c.3643415_d9
title: Additional file 1: Table S1. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: 803 landrace accessions used in this study with latitude and longitude information.
DOI: 10.6084/m9.figshare.c.3643415_d15
title: Additional file 21: Table S10. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: 1,896 SNPs shared between wild barley and landrace populations.
DOI: 10.6084/m9.figshare.c.3643415_d18
title: Additional file 19: Table S9. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Proportion of individuals involved in IBS segments (30 SNP each) between each landrace population and the 277 wild barley lines.
DOI: 10.6084/m9.figshare.c.3643415_d20
title: Additional file 7: Table S3. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Chromosome painting. Individual landrace ancestry inferred at each genomic region. The cells are colored according to their inferred ancestry from the wild populations. Two haplotypes (rows) per landrace accession are depicted.
DOI: 10.6084/m9.figshare.c.3643415_d19
title: Additional file 15: Table S7. of Barley landraces are characterized by geographically heterogeneous genomic origins

description: Frequency of alleles private to the wild present in each of the landrace populations. Private SNPs in wild barley that are present in the landraces, including linkage group and their frequency in each landrace population.
DOI: 10.6084/m9.figshare.c.3643421_d1
title: Additional file 7: Table S3. of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Alignment and Analysis of TcTS Architectures. (a) Of the 3209 TcTS sequences in this study, 3176 contained at least 1 motif with an e-value of 1e-01 as determined by the described MEME analysis. The architectures, the in-order sequence of motifs, of each TcTS sequence were extracted and aligned as described. (b) Confidence heat map. Top row contains the motif numbers of the “model” TcTS architecture, where the model is determined by choosing the motif that is most frequent over all TcTS at each position. The cells are colored red if the model motif at that position is found in &gt;1000 sequences, black for motifs preceding the signal peptide sequence or in the hyper-variable region containing SAPA repeats, and blue otherwise. The 2nd row displays a bar-graph of the minimum smoothed entropy for the motif region. The remainder of the table is color-coded according to the “confidence score” of the motif-to-architecture for each cell. The confidence score is calculated as: (-1 * loge(MEME e-value))1.5 and the colors range from white (low) to blue (mid) to red (high). Note that the score reflects the assigned motif at each position regardless of whether it matches the model. (XLSX 1439 kb)
DOI: 10.6084/m9.figshare.c.3643421_d2
title: Additional file 15: of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Generation of control recombination positive dataset. Two types of recombination events were introduced to simulated sequences: gene conversion and homologous recombination (reciprocal exchange). For gene conversion recombination, a subsequence from a randomly chosen donor gene is extracted, and used to replace the homologous subsequence in a randomly chosen recipient gene. For homologous recombination (reciprocal exchange), homologous subsequences from two randomly chosen genes are extracted and exchanged. Normal distribution is used to model the length of the recombination region. Exponential distribution is used to model the number of recombination events per gene. Exponential distribution with probability density function y = 0.52622e − 0.52622x is a good approximation of the distribution of frequency of number of recombination events per gene observed in our preliminary analysis. A custom perl program script was used to introduce multiple recombination events in a single dataset. The perl script takes 4 parameters, percentage of Gene conversion recombination“g%”, total recombination gene number “n”, recombination region mean length, “l” and standard deviation of recombination region length, “std”. The program randomly chose g% of the genes to introduce recombination into. For each recombinant gene, the program sampled the exponential distribution described above to determine the number of recombination events to introduce into the gene. For each recombination event, g% probability to introduce gene conversion event, and 1-g% probability to introduce homologous recombination events (reciprocal exchange), the length of recombination event was sampled from the normal distribution (l, std2). (ZIP 23 kb)
DOI: 10.6084/m9.figshare.c.3643421_d3
title: Additional file 11: Table S5. of Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

description: Recombination events. a) Detailed information of 2087 recombination events detected in TcTS gene family. b) Summary of number and percentage of newly annotated TcTS and previously annotated TcTS participating in recombination events as recombinant product, major donor or minor donor. (XLSX 549 kb)
DOI: 10.15468/dl.e25ak5
title: Occurrence Download

description: A dataset containing 9506 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cervus nippon Temminck, 1838"
 ]
}

 The dataset includes 9506 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034392-241126133413365/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.3644255_d13
title: Additional file 12: Table S7. of An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimerâ  s disease

description: IPA of diseases and functions annotation of genes preferentially expressed in cerebrovascular endothelial cells. Table S7 notes the diseases and functions that are upregulated in Alzheimerâ  s disease and downregulated by candesartan and are preferentially expressed in cerebrovascular endothelial cells. (XLS 126 kb)
DOI: 10.6084/m9.figshare.c.3644282_d3
title: Additional file 1: of Visualizing sound: counting wolves by using a spectral view of the chorus howling

description: R Script for wolf choruses analysis with Seewave package in R environment. (R 1 kb)
DOI: 10.6084/m9.figshare.c.3644285_d3
title: Additional file 3: of LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer

description: It contains detailed results of our analyses in Table S1-S4. (XLS 265 kb)
DOI: 10.6084/m9.figshare.c.3644285_d1
title: Additional file 2: of LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer

description: It contains detailed results of our analyses in Table S5 and S6. (XLSX 232 kb)
DOI: 10.15468/dl.rkm8pe
title: Occurrence Download

description: A dataset containing 470358 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Branta canadensis (Linnaeus, 1758)",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 470358 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034389-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9h9zxe
title: Occurrence Download

description: A dataset containing 135950 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vermivora chrysoptera (Linnaeus, 1766)",
 "HasCoordinate is True",
 "Country is United States of America",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2024",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False"
 ]
}

 The dataset includes 135950 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034384-241126133413365/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.3645185_d4
title: Additional file 6: of Could the erythrocyte indices or serum ferritin predict the therapeutic response to a trial with oral iron during pregnancy? Results from the Accuracy study for Maternal Anaemia diagnosis (AMA)

description: Data set of AMA study (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3645221_d1
title: Additional file 7: Table S7. of RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states

description: Differential usage of exons in AD vs CF comparison. (XLSX 103Â kb)
DOI: 10.6084/m9.figshare.c.3645221_d2
title: Additional file 6: Table S6. of RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states

description: Differential usage of exons in AD vs CRM comparison. (XLSX 25Â kb)
DOI: 10.6084/m9.figshare.c.3646118_d3
title: Additional file 1: of A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes

description: The data collection forms. This excel document allows users to easily edit and print the data collection forms. The master dictionary is also included with the data collection forms. (XLSX 143Â kb)
DOI: 10.6084/m9.figshare.c.3646139_d1
title: Additional file 2: Table S2. of Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

description: Medium composition and biomass formulation. The biomass equations are given with the metabolites abbreviations IDs as found in the models (sheet 2). In the sheet three, the 1st column contains the medium composition used to constrain Recon 1 using the metabolites abbreviation as used in the model. In the second column are displayed the medium composition for Recon 2. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3646139_d3
title: Additional file 6: Table S8. of Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

description: List of cofactor combinations that were not considered in the reaction equations for the determination of the entry points in Fig.Â 6. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3646139_d4
title: Additional file 5: Table S5. of Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

description: Lists of the significantly up- (sheet 1) and down-regulated genes (sheet 2) (FDR 1)) during monocyte to macrophage differentiation. Columns represent probe IDs, Gene symbol, log2 ratio between day 2 and day 11 of differentiation, fold change between the same time points, the p-value obtained after performing Empirical bayesian statistique (limma) and the FDR. (XLSX 186 kb)
DOI: 10.6084/m9.figshare.c.3646139_d5
title: Additional file 4: of Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

description: Reconstructed models in SBML format. The zipped file with 3 subfolders (cancer, monocyte and macrophage models, 156 primary cells models) contains 2 cancer models (cancer 1, cancer 2), 4 macrophage models (day 2, day 4, day 7, day 11), and 156 primary cells models, respectively. (7z 25 mb)
DOI: 10.6084/m9.figshare.c.3646139_d6
title: Additional file 3: Table S4. of Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

description: List of selected 156 arrays ordered in function the Jaccard similarity index used for Fig. 1 and of the remaining 745 arrays that compose the primary cell atlas dataset. The first column contains the Gene Omnibus ID of the arrays. The second and third column contains a description of the arrays and the array names and the last column the order of the arrays in the cluster plot (Fig. 1a) from left to right. Arrays stated as not selected were not depicted for the Fig. 1 but were used to produce together with 156 arrays to produce Figs. 5 and 7. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3653936_d1
title: Additional file 3: Table S3. of Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequencesâ   mobility

description: Localization of specific genome elements in BCG Russia genome. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.c.3653942_d1
title: Additional file 1: Table S1. of Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer

description: Differential expression profiles of genes and transcripts in colon adenocarcinomas compared to matched normal tissues (TCGA data analyzed by CrossHub). (XLSX 43 MB)
DOI: 10.6084/m9.figshare.c.3653933_d2
title: Additional file 3: of Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

description: Bordor.325.Cent40.tgz. Phylogenomic alignment files and single gene trees for each gene included in the phylogeomic supermatrix. (TGZ 8396 kb)
DOI: 10.6084/m9.figshare.c.3653936_d2
title: Additional file 1: Table S1. of Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequencesâ   mobility

description: Primers used for BCG Russia 368 genome gaps closure by PCR and Sanger sequencing. (XLSX 14Â kb)