cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3610364_d1.v1
title: Additional file 2: of Quantification of the natural history of visceral leishmaniasis and consequences for control

description: Matlab file for numerically solving the system of ordinary differential equations (ODEs) that can be used to represent the 5-state model for a given set of parameter values. (M 1Â kb)
DOI: 10.6084/m9.figshare.c.3610367_d1.v1
title: Additional file 1: of Childhood diarrhea in high and low hotspot districts of Amhara Region, northwest Ethiopia: a multilevel modeling

description: Additional file on results of high and low hotspot districts in the study area. (XLS 31 kb)
DOI: 10.6084/m9.figshare.c.3610412_d1.v1
title: Additional file 2: of RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt

description: Correlation degrees between RNA-Seq and qRT-PCR experiments. qRT-PCR and RNA-seq fold-change values of 20 selected genes were represented in a graphic to obtain the correlation degrees in both conditions. Genes and primer sequences are shown (XLS 38 kb)
DOI: 10.6084/m9.figshare.c.3610412_d3.v1
title: Additional file 5: of RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt

description: Whole genome differential expression in R. tropici CIAT 899 cultures supplemented with salt. Python and R were used to study differential expression among sample groups. Algorism proposed by DESeq2 was used for gene differential expression, taking as a dispersion model a negative binomial distribution. Differentially expressed genes were established in those genes with a fold change lower or higher than−4 or 4, respectively (See the Material and Methods section). Fold change values are represented by bars. Each bar corresponds to one gene and they are ordered according to their relative position in each replicon. Blue bars: genes not differentially expressed. Yellow bars: differentially expressed genes. The arrows indicate names of some differentially expressed genes. Ch: chromosome, pC: pRtrCIAT899c, pB: pRtrCIAT899b, pA: pRtrCIAT899a (XLSX 654 kb)
DOI: 10.6084/m9.figshare.c.3610412_d4.v1
title: Additional file 3: of RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt

description: Functions (Gene Onthology, GO) associated to R. tropici CIAT 899 responses to apigenin and salt. A hypergeometric test performed in the platform R (See the Material and Methods section) was carried out to assign the statistical over-represented functional categories in presence of both nod gene inducing molecules (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3610412_d5.v1
title: Additional file 4: of RNA-seq analysis of the Rhizobium tropici CIAT 899 transcriptome shows similarities in the activation patterns of symbiotic genes in the presence of apigenin and salt

description: Whole genome differential expression in R. tropici CIAT 899 cultures supplemented with apigenin. Python and R were used to study differential expression among sample groups. Algorism proposed by DESeq2 was used for gene differential expression, taking as a dispersion model a negative binomial distribution. Differentially expressed genes were established in those genes with a fold change lower or higher than−4 or 4, respectively (See the Material and Methods section). Fold-change values are represented by bars. Each bar corresponds to one gene and they are ordered according to their relative position in each replicon. Blue bars: genes not differentially expressed. Yellow bars: differentially expressed genes. The arrows indicate names of some differentially expressed genes. Ch: chromosome, pC: pRtrCIAT899c, pB: pRtrCIAT899b, pA: pRtrCIAT899a (XLSX 750 kb)
DOI: 10.6084/m9.figshare.c.3610427_d1.v1
title: Additional file 5: Table S3. of Integrated ordination of miRNA and mRNA expression profiles

description: MiRNAs with the same seed sequence, found among the 109 miRNAs differentially expressed in patients with HBV-associated acute liver failure (ALF). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3610427_d2.v1
title: Additional file 2: Movie 1. of Integrated ordination of miRNA and mRNA expression profiles

description: 360Â° rotation of 3D MDS dispersion ellipses of mRNA functional clusters of ALF livers. Labels are shown in the two last frames (38â  39) at the end of the rotation cycle. If the media player runs continuously, it should be stopped manually to visualize the labels. The original frame size is 731x712. The player window should be properly resized to optimize the image quality. (SWF 1150 kb)
DOI: 10.6084/m9.figshare.c.3610484_d1.v1
title: Additional file 5: of Vitamin D interacts with Esr1 and Igf1 to regulate molecular pathways relevant to Alzheimer’s disease

description: List of DEGs known to be related to vitamin D action in the corertx and hippocampus of Wt and Tg mice. Genes containing a VDRE sequence are highlighted in grey. Table S13. Vitamin D related DEGs in Tg Cont, Tg VitD and Wt VitD mice. Table S14. Common vitamin D related DEGS between Tg Cont and TgVitD or between Tg Cont and Wt VitD. Table S15. Common vitamin D related DEGs between Tg Cont, Tg VitD and Wt VitD mice. (XLSX 95 kb)
DOI: 10.15468/dl.gby7hn
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((45 30,90 30,90 50,45 50,45 30))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Varanus griseus (Daudin, 1803)"
 ]
}

 The dataset includes 102 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0261321-220831081235567/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.3610463_d5.v1
title: Additional file 5: Table S5. of Establishment of a patient-derived intrahepatic cholangiocarcinoma xenograft model with KRAS mutation

description: Deregulated microRNA in PDX compared to primary tumor (PR). (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3610484_d2.v1
title: Additional file 4: of Vitamin D interacts with Esr1 and Igf1 to regulate molecular pathways relevant to Alzheimer’s disease

description: List of canonical pathways modified by a vitamin D3-enriched diet in Wt and Tg animals. Table S10. Common canonical pathways between Wt and Tg mice supplemented with vitamin D3 and associated DEGs. Table S11. Canonical pathways specifically modified in Wt VitD animals. Table S12. Canonical pathways specifically modified in Tg VitD animals. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3610472_d4.v1
title: Additional file 3: of Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes

description: Sectm1 expression across human tissues (EST profile). (XLS 106 kb)
DOI: 10.6084/m9.figshare.c.3610472_d5.v1
title: Additional file 2: of Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes

description: Tex19 and Sectm1 homolog detection across the 4 super-orders of eutherians. (XLS 85 kb)
DOI: 10.6084/m9.figshare.c.3610484_d4.v1
title: Additional file 3: of Vitamin D interacts with Esr1 and Igf1 to regulate molecular pathways relevant to Alzheimer’s disease

description: Table S9. Common DEGs in at least 3 out 4 conditions (cortex; hippocampus; WtVitD; TgVitD). (XLSX 61 kb)
DOI: 10.6084/m9.figshare.c.3610484_d6.v1
title: Additional file 2: of Vitamin D interacts with Esr1 and Igf1 to regulate molecular pathways relevant to Alzheimer’s disease

description: Comparative analysis of DEGs between different conditions. Table S2. Common DEGs between cortex and hippocampus in Wt mice supplemented with vitamin D3. Table S3. Specific DEGs in cortex of Wt mice supplemented with vitamin D3. Table S4. Specific DEGs in hippocampus of Wt mice supplemented with vitamin D3. Table S5. Common DEGs between cortex and hippocampus in Tg mice supplemented with vitamin D3. Table S6. Specific DEGs in cortex of Tg mice supplemented with vitamin D3. Table S7. Specific DEGs in hippocampus of Tg mice supplemented with vitamin D3. Table S8. Common DEGs between cortex and hippocampus of both Wt and Tg mice supplemented with vitamin D3. (XLSX 214 kb)
DOI: 10.6084/m9.figshare.c.3610529_d1.v1
title: Additional file 3: of Transcriptional reprogramming of metabolic pathways in critically ill patients

description: Correlation between neutrophils counts and glycolytic genes.
DOI: 10.6084/m9.figshare.c.3610604_d1.v1
title: Additional file 1: of Longitudinal changes in physical activity and sedentary time in adults around retirement age: what is the moderating role of retirement status, gender and educational level?

description: Data file used for statistical analyses reported in this paper. (CSV 769Â kb)
DOI: 10.6084/m9.figshare.c.3610607_d1.v1
title: Additional file 8: of Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel

description: List of DEGs identified from FW MRCs and FW PVCs, and SW MRCs and SW PVCs. (XLSX 173 kb)
DOI: 10.6084/m9.figshare.c.3610583_d4.v1
title: Additional file 6: of Structural and functional annotation of the MADS-box transcription factor family in grapevine

description: Original expression data (RMA normalized) from the expression experiments described in Additional file 4. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.c.3610583_d5.v1
title: Additional file 2: of Structural and functional annotation of the MADS-box transcription factor family in grapevine

description: Complete annotation of grapevine MADS-box genes. These data were also been deposited at the Grapevine annotation platform. http://bioinformatics.psb.ugent.be/orcae/ (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3610592_d4.v1
title: Additional file 4: Tables S1-S4. of EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data

description: Are Excel spreadsheets containing the EPIG-Seq clustered genes from the TCGA data samples 1 â   4 respectively. (XLSX 665 kb)
DOI: 10.6084/m9.figshare.c.3610607_d2.v1
title: Additional file 7: of Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel

description: Gene ontology of DEGs identified from FW MRCs and SW MRCs. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3610607_d3.v1
title: Additional file 6: of Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel

description: List of the 400 DEGs identified from FW PVCs and SW PVCs. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.c.3610607_d4.v1
title: Additional file 3: of Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel

description: Comparison of the present cell-type specific transcriptome data to our previous whole-gill tissue transcriptome. (XLSX 1505 kb)
DOI: 10.6084/m9.figshare.c.3610607_d5.v1
title: Additional file 4: of Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel

description: List of the 970 DEGs identified from FW PVCs and SW PVCs. (XLSX 117 kb)
DOI: 10.5281/zenodo.14505714
title: Datasets and scripts used in Gonzalo/Jacquiod et al. for rhizosphere microbiota network analysis

description: This submission contains all the datasets and intermediate files generated in the study by Gonzalo/Jacquiod et al. on the rhizosphere microbiota network analysis.

The zip file contains the following items:



The OTU tables (16S and ITS)

The design file

The plant data file

The R script used for network buidling using Poisson Log Normal method with the StARS approach (STStability Approach to Regularization Selection)

The Python script used ofr searching for cycle basis in the networks

The nine networks generated at 97% stability 

All intermediates files that were generated
DOI: 10.6084/m9.figshare.c.3610667_d1.v1
title: Additional file 2: of Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery

description: Expression datasets used in this study. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3610667_d2.v1
title: Additional file 7: of Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery

description: Overlap between M30 and significantly upregulated genes after 6Â h of treatment. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3610682_d2.v1
title: Additional file 2: of Fibromyalgia-related costs and loss of productivity: a substantial societal burden

description: Dataset. (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.c.3610697_d5.v1
title: MOESM3 of HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

description: Additional file 3: Table S2. Cuffdiff output for differentially expressed (RNA-seq) genes following 72-hour NaBut or SAHA treatment of K562 cells.
DOI: 10.6084/m9.figshare.c.3610703_d3.v1
title: Additional file 3: Table S2. of Transcriptome profiling reveals differential gene expression of detoxification enzymes in a hemimetabolous tobacco pest after feeding on jasmonate-silenced Nicotiana attenuata plants

description: Differentially expressed isotigs identified using RSEM estimated abundances. (XLS 40 kb)
DOI: 10.6084/m9.figshare.c.3610730_d1.v1
title: Additional file 2: Table S2. of The major horse satellite DNA family is associated with centromere competence

description: un-normalized read counts from ChIP-seq experiment and input control. (XLS 27Â kb)
DOI: 10.6084/m9.figshare.c.3610730_d2.v1
title: Additional file 1: Table S1. of The major horse satellite DNA family is associated with centromere competence

description: Enriched regions found on the unplaced contigs. The columns represent: the accession number of the contigs, the start and end position of the enriched region within the contig, the length of the region, and the statistical parameters calculated by the peak caller [pile-up, fold enrichment, -log10(p-value), -log10(q-value)]. Regions are listed according to their contig number. (XLS 211Â kb)
DOI: 10.6084/m9.figshare.c.3610736_d1.v1
title: Additional file 3: of Weevil endosymbiont dynamics is associated with a clamping of immunity

description: Detailed statistical analysis of RT-qPCR results. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3610736_d2.v1
title: Additional file 1: of Weevil endosymbiont dynamics is associated with a clamping of immunity

description: Primers used in RT-qPCR experiments. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3610697_d8.v1
title: MOESM1 of HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

description: Additional file 1: Table S1. DESeq2 output for differential accessibility (DNase-seq) following 72-h NaBut or SAHA treatment of K562 cells.
DOI: 10.6084/m9.figshare.c.3610742_d1.v1
title: Additional file 2: Table S2. of Exposure to various abscission-promoting treatments suggests substantial ERF subfamily transcription factors involvement in the regulation of cassava leaf abscission

description: Putative AP2/ERF genes expressed during ethylene- and water-deficit stress-induced leaf abscission. (XLS 1472 kb)
DOI: 10.6084/m9.figshare.c.3610742_d2.v1
title: Additional file 3: Table S3. of Exposure to various abscission-promoting treatments suggests substantial ERF subfamily transcription factors involvement in the regulation of cassava leaf abscission

description: SOTA clustering and annotation of AP2/ERF genes expressed in response to water-deficit stress treatment. (XLS 62 kb)
DOI: 10.6084/m9.figshare.c.3610736_d4.v1
title: Additional file 2: of Weevil endosymbiont dynamics is associated with a clamping of immunity

description: Characteristics of sequences used in RT-qPCR experiments. (XLS 38 kb)
DOI: 10.6084/m9.figshare.c.3610742_d3.v1
title: Additional file 4: Table S4. of Exposure to various abscission-promoting treatments suggests substantial ERF subfamily transcription factors involvement in the regulation of cassava leaf abscission

description: SOTA clustering and annotation of AP2/ERF genes expressed in response to ethylene treatment. (XLS 67 kb)
DOI: 10.6084/m9.figshare.c.3610799_d1.v1
title: Additional file 1: of Assessment of aortic valve in regard to its anatomical variants morphology in 2053 patients using 64-slice CT retrospective coronary angiography

description: Matedial data. (XLS 22 kb)
DOI: 10.6084/m9.figshare.c.3610805_d1.v1
title: Additional file 1: of Arterial stiffness in patients with coronary artery disease: relation with in-stent restenosis following percutaneous coronary intervention

description: The study data. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3610778_d5.v1
title: Additional file 7: Table S4. of Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles

description: Relationship between total number of DEGs and connectivity score among treatment conditions within FHM 15K. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.c.3610778_d6.v1
title: Additional file 2: Table S2. of Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles

description: A complete list of query signatures constructed in the current study. Signatures were named after fish sample treatment conditions by the order of chemical, dose, gender, tissue, and exposure duration. Some conditions may each have multiple signatures generated because of either repeated experiments or different parameters in analysis. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3610778_d7.v1
title: Additional file 1: Table S1. of Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles

description: A complete list of microarray data used in the current study. (XLSX 111Â kb)
DOI: 10.6084/m9.figshare.c.3610817_d1.v1
title: Additional file 2: of Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation

description: Genes with hypermethylated sites (25Â % &gt; methylation difference) in Fertilized embryos. Genes with hypermethylated sites (25Â % &gt; methylation difference) in Thelytokous embryos. Genes with a combination of hypermethylated sites (25Â % &gt; methylation difference) from both Fertilized and Thelytokous embryos. (XLSX 60 kb)
DOI: 10.15468/dl.vbytmv
title: Occurrence Download

description: A dataset containing 674823 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Amphibia",
 "Year 2022-2022"
 ]
}

 The dataset includes 674823 records from 1184 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037543-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.svsdka
title: Occurrence Download

description: A dataset containing 186014 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-175 -60,-60 -60,-60 75,-175 75,-175 -60))",
 "TaxonKey is Cephalopoda"
 ]
}

 The dataset includes 186014 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028439-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5dnwu
title: Occurrence Download

description: A dataset containing 286 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Triosteum aurantiacum E.P.Bicknell",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 286 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163106-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3abyu6
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gigantochloa hasskarliana (Kurz) Backer"
 ]
}

 The dataset includes 24 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012543-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xpoli3
title: Occurrence Download

description: A dataset containing 162533 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "Country is Türkiye",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 162533 records from 150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028440-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ahgun3
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mononeuria caroliniana (Walter) Dillenb. & Rabeler",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 46 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163126-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jbm85k
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium expressiusculum Omang"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020806-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yaxmtw
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Pinus rzedowskii Madrigal & M.Caball.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 408 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028440-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gjtfs1
title: Occurrence Download

description: A dataset containing 433754 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Observation",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Year 1970-2020"
 ]
}

 The dataset includes 433754 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013105-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.