cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.r8agw2
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-88.19875 30.1154,-87.95743 30.1154,-87.95743 30.24707,-88.19875 30.24707,-88.19875 30.1154))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lutjanus campechanus (Poey, 1860)"
 ]
}

 The dataset includes 49 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021079-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygz73w
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lontra provocax (Thomas, 1908)"
 ]
}

 The dataset includes 106 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021081-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ckuzf4
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Leopardus guigna guigna"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021082-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zuvbsb
title: Occurrence Download

description: A dataset containing 43572 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prunus persica (L.) Stokes"
 ]
}

 The dataset includes 43572 records from 747 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021078-240626123714530/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.26240402
title: Effect sizes calculated using MD and MC

description: This dataset of effect sizes was calculated using mean difference with burnt-unburnt designs and mean change for before-after designs.
DOI: 10.6084/m9.figshare.26240402.v2
title: Effect sizes calculated using MD and MC

description: This dataset of effect sizes was calculated using mean difference with burnt-unburnt designs and mean change for before-after designs.
DOI: 10.6084/m9.figshare.26240402.v1
title: Effect sizes calculated using MD

description: This dataset of effect sizes was calculated using mean difference with burnt-unburnt designs.
DOI: 10.15468/dd.zwsc6b
title: Dnipro river basin Animals

description: Number of records was cropped only for Dnipro river basin
DOI: 10.15468/dl.2xfwpn
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GenusKey is Tapirus Brisson, 1762",
 "Country is Brazil",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 28 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021086-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zy6ps6
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GenusKey is Tapirus Brisson, 1762",
 "Country is Colombia",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 27 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021085-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vkr74j
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GenusKey is Tapirus Brisson, 1762",
 "Country is Peru",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 19 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021087-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vmzq3v
title: Occurrence Download

description: A dataset containing 1512422296 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is e2e717bf-551a-4917-bdc9-4fa0f342c530",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 1512422296 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021014-240626123714530/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.26240411
title: Effect sizes calculated using SMD and SMCC

description: A dataset of effect sizes calculated using SMD for burnt-unburnt designs and SMCC for before-after designs. This can be used for the main analysis presented in Driscoll et al 2024, and for the analysis using standardised differences that include before-after designs.
DOI: 10.6084/m9.figshare.26240411.v1
title: Effect sizes calculated using SMD

description: A dataset of effect sizes calculated using SMD with burnt-unburnt designs. This can be used for the main analysis presented in Driscoll et al 2024.
DOI: 10.6084/m9.figshare.26240411.v2
title: Effect sizes calculated using SMD and SMCC

description: A dataset of effect sizes calculated using SMD for burnt-unburnt designs and SMCC for before-after designs. This can be used for the main analysis presented in Driscoll et al 2024, and for the analysis using standardised differences that include before-after designs.
DOI: 10.15468/dl.ccywca
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plukenetia carabiasiae J.Jiménez Ram."
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021088-240626123714530/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.26264318
title: <b>Bone marrow macrophage-exosomes with HuR deficiency limits ANG-II induced cardiac fibrosis and LV dysfunction in mice</b>

description: <b>Injection of diabetic (db/db) bone marrow macrophage-exosomes with HuR deficiency preserves LV function in ANG-II treated mice</b>. Clodronate liposome or control liposome (150 μL; FormuMax Scientific, Sunnyvale, CA, USA) was intraperitoneally injected into 8-weeks old C57BL/6J mice and macrophage depletion was confirmed using FACS analysis (BD LSR II Analyzer). After 48 hours, vehicle (saline) or ANG II (1000 ng.kg−1.min−1; EMD Millipore) was continuously administered using osmotic mini-pumps (ALZET DURECT, Cupertino, CA). Exosomes from Control or HuR shRNA- treated BMMØ derived from diabetic (db/db) mice (Exo-db/dbHuR KD vs Exo-db/dbWT) were injected intravenous through tail vein on day 2 and day 4 after pump implantation. Heart function was evaluated by echocardiography (Vevo 2100; VisualSonics, Toronto, Canada). Mice were euthanized on day 28; heart was collected for further analysis. Transthoracic two-dimensional B-Mode and M-Mode echocardiogram was obtained using Vevo 2100 (VisualSonics, Toronto, Canada) equipped with 30 MHz transducer. Echocardiographic studies were performed after ANG II mini- osmotic pump implantation on mice anesthetized with a mixture of 1.5% isoflurane and oxygen (1 L/min). B-Mode and M-Mode tracings were used to measure left ventricle (LV) percent fractional shortening (%FS) and percent ejection fraction (�) respectively. Observation: Echocardiography analysis showing improvements in heart function as shown by higher % ejection fraction and % fractional shortening in mice receiving Exo- db/dbHuR KD. The full dataset is uploaded as an excel spreadsheet file.Masson’s Trichrome staining and analysis showing lower interstitial fibrosis in hearts of mice receiving diabetic (db/db) BMMØ-exosomes with HuR deficiency (Exo-db/dbHuR KD), as compared to db/db-Exo injected mice at 28 days post-administration. The full dataset is attached as a spreadsheet.
DOI: 10.6084/m9.figshare.26264318.v1
title: <b>Bone marrow macrophage-exosomes with HuR deficiency limits ANG-II induced cardiac fibrosis and LV dysfunction in mice</b>

description: <b>Injection of diabetic (db/db) bone marrow macrophage-exosomes with HuR deficiency preserves LV function in ANG-II treated mice</b>. Clodronate liposome or control liposome (150 μL; FormuMax Scientific, Sunnyvale, CA, USA) was intraperitoneally injected into 8-weeks old C57BL/6J mice and macrophage depletion was confirmed using FACS analysis (BD LSR II Analyzer). After 48 hours, vehicle (saline) or ANG II (1000 ng.kg−1.min−1; EMD Millipore) was continuously administered using osmotic mini-pumps (ALZET DURECT, Cupertino, CA). Exosomes from Control or HuR shRNA- treated BMMØ derived from diabetic (db/db) mice (Exo-db/dbHuR KD vs Exo-db/dbWT) were injected intravenous through tail vein on day 2 and day 4 after pump implantation. Heart function was evaluated by echocardiography (Vevo 2100; VisualSonics, Toronto, Canada). Mice were euthanized on day 28; heart was collected for further analysis. Transthoracic two-dimensional B-Mode and M-Mode echocardiogram was obtained using Vevo 2100 (VisualSonics, Toronto, Canada) equipped with 30 MHz transducer. Echocardiographic studies were performed after ANG II mini- osmotic pump implantation on mice anesthetized with a mixture of 1.5% isoflurane and oxygen (1 L/min). B-Mode and M-Mode tracings were used to measure left ventricle (LV) percent fractional shortening (%FS) and percent ejection fraction (�) respectively. Observation: Echocardiography analysis showing improvements in heart function as shown by higher % ejection fraction and % fractional shortening in mice receiving Exo- db/dbHuR KD. The full dataset is uploaded as an excel spreadsheet file.Masson’s Trichrome staining and analysis showing lower interstitial fibrosis in hearts of mice receiving diabetic (db/db) BMMØ-exosomes with HuR deficiency (Exo-db/dbHuR KD), as compared to db/db-Exo injected mice at 28 days post-administration. The full dataset is attached as a spreadsheet.
DOI: 10.6084/m9.figshare.26240360
title: Effect sizes calculated using MD and MC, excluding outliers

description: Effect sizes calculated using mean difference for burnt-unburnt study designs and mean change for before-after desings. Outliers, as defined in the methods section of the paper, were excluded prior to calculating effect sizes.
DOI: 10.6084/m9.figshare.26240360.v2
title: Effect sizes calculated using MD and MC, excluding outliers

description: Effect sizes calculated using mean difference for burnt-unburnt study designs and mean change for before-after desings. Outliers, as defined in the methods section of the paper, were excluded prior to calculating effect sizes.
DOI: 10.6084/m9.figshare.26240360.v1
title: Effect sizes calculated using MD, excluding outliers

description: Effect sizes calculated using mean difference, for burnt-unburnt study designs. Outliers, as defined in the methods section of the paper, were excluded prior to calculating effect sizes.
DOI: 10.5281/zenodo.12725972
title: Data and Codes for Publication: "Sexually Dimorphic Computational Histopathological Signatures Prognostic of Overall Survival in High-Grade Gliomas via Deep Learning"

description: Data

The patches and the associated tumor segmentation labels (expert-vetted) from our analysis are available in Patches.pytable file.CodesThe codes for training tumor segmentation models and conducting survival analysis are available in the following files



ResNet-train: Code to train Resnet18 model for Tumor Segmentation

Tumor_Segmentation: Code to segment tumor regions from WSI using ResNet18 model

ResNet_Cox_train: Code to train ResNet-Cox model in 5 folds cross-validation setting

Evaluate_ResNetCox: Code to evaluate ResNet-Cox model
description: High-grade glioma (HGG) is an aggressive brain tumor. Sex is an important factor that differentially impacts survival outcomes in HGG. We employed an end-to-end deep-learning approach on Hematoxylin and eosin (H&E) scans to (1) identify explainable, sex-specific histopathological attributes of the tumor microenvironment (TME) that may be associated with patient-outcomes, and (2) create sex-specific risk profiles to prognosticate overall survival. Surgically resected H&E-stained tissue slides were analyzed in a two-stage approach using ResNet18 deep-learning models, first, to segment the viable tumor regions, and second, to build sex-specific prognostic models for prediction of overall survival. Our mResNet-Cox model yielded C-index (0.696, 0.736, 0.731, 0.729) for the female cohort and C-index (0.729, 0.738, 0.724, 0.696) for the male cohort across training and three independent validation cohorts, respectively. End-to-end deep-learning approaches using routine H&E-stained slides, trained separately on male and female HGG patients, may allow for identifying sex-specific histopathological attributes of the TME associated with survival and, ultimately, build patient-centric prognostic risk-assessment models.
DOI: 10.5281/zenodo.12725973
title: Data and Codes for Publication: "Sexually Dimorphic Computational Histopathological Signatures Prognostic of Overall Survival in High-Grade Gliomas via Deep Learning"

description: Data

The patches and the associated tumor segmentation labels (expert-vetted) from our analysis are available in Patches.pytable file.CodesThe codes for training tumor segmentation models and conducting survival analysis are available in the following files



ResNet-train: Code to train Resnet18 model for Tumor Segmentation

Tumor_Segmentation: Code to segment tumor regions from WSI using ResNet18 model

ResNet_Cox_train: Code to train ResNet-Cox model in 5 folds cross-validation setting

Evaluate_ResNetCox: Code to evaluate ResNet-Cox model
description: High-grade glioma (HGG) is an aggressive brain tumor. Sex is an important factor that differentially impacts survival outcomes in HGG. We employed an end-to-end deep-learning approach on Hematoxylin and eosin (H&E) scans to (1) identify explainable, sex-specific histopathological attributes of the tumor microenvironment (TME) that may be associated with patient-outcomes, and (2) create sex-specific risk profiles to prognosticate overall survival. Surgically resected H&E-stained tissue slides were analyzed in a two-stage approach using ResNet18 deep-learning models, first, to segment the viable tumor regions, and second, to build sex-specific prognostic models for prediction of overall survival. Our mResNet-Cox model yielded C-index (0.696, 0.736, 0.731, 0.729) for the female cohort and C-index (0.729, 0.738, 0.724, 0.696) for the male cohort across training and three independent validation cohorts, respectively. End-to-end deep-learning approaches using routine H&E-stained slides, trained separately on male and female HGG patients, may allow for identifying sex-specific histopathological attributes of the TME associated with survival and, ultimately, build patient-centric prognostic risk-assessment models.
DOI: 10.15468/dl.duf749
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.42262 -37.07718,-72.42951 -37.10315,-72.41264 -37.10239,-72.40789 -37.12816,-72.36726 -37.12797,-72.36678 -37.0878,-72.42262 -37.07718))",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 4 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021083-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rv7ykt
title: Occurrence Download

description: A dataset containing 246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Chile",
 "DatasetKey is Registros Eulidia yarrellii (estimaciones poblacionales) 2003-2021",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Eulidia yarrellii (Bourcier, 1847)"
 ]
}

 The dataset includes 246 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021089-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12722918
title: Datasets annd Resources for the ReNeuIR 2024 Shared Task at SIGIR 2024

description: This record contains the datasets and resources for shared task at the third ReNeuIR Workshop that was co-located with ACM SIGIR in Washington D.C., USA, in July 2024.
DOI: 10.5281/zenodo.12722917
title: Datasets annd Resources for the ReNeuIR 2024 Shared Task at SIGIR 2024

description: This record contains the datasets and resources for shared task at the third ReNeuIR Workshop that was co-located with ACM SIGIR in Washington D.C., USA, in July 2024.
DOI: 10.5281/zenodo.12728703
title: Datasets annd Resources for the ReNeuIR 2024 Shared Task at SIGIR 2024

description: This record contains the datasets and resources for shared task at the third ReNeuIR Workshop that was co-located with ACM SIGIR in Washington D.C., USA, in July 2024.
DOI: 10.7295/w9cil55787
title: CIL:55787, Homo sapiens, Pediatric inflammatory bowel disease (IBD)
DOI: 10.7295/w9cil55781
title: CIL:55781, Homo sapiens, Pediatric inflammatory bowel disease (IBD)
DOI: 10.7295/w9cil39108
title: CIL_39108, epithelial cell of lung
DOI: 10.6084/m9.figshare.26263217
title: HuR knockdown in bone marrow macrophages

description: Western blot and Densitometry analysis showing HuR knockdown in mouse bone marrow derived macrophage cells using lentiviral HuR-specific <i>sh</i>RNA (KD; BMMØHuR KD), 48h after infection. BMMØWT (WT), macrophages transduced with control non-specific shRNA. Data normalized to GAPDH.
DOI: 10.6084/m9.figshare.26263217.v1
title: HuR knockdown in bone marrow macrophages

description: Western blot and Densitometry analysis showing HuR knockdown in mouse bone marrow derived macrophage cells using lentiviral HuR-specific <i>sh</i>RNA (KD; BMMØHuR KD), 48h after infection. BMMØWT (WT), macrophages transduced with control non-specific shRNA. Data normalized to GAPDH.
DOI: 10.15468/dl.huzteq
title: Occurrence Download

description: A dataset containing 3533 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Canada, Peru, Venezuela (Bolivarian Republic of), Argentina, Brazil, Ecuador, Chile, Colombia, Bolivia (Plurinational State of))",
 "TaxonKey is Brachythecium Schimp."
 ]
}

 The dataset includes 3533 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021090-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7k2qym
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.42262 -37.07718,-72.42951 -37.10315,-72.41264 -37.10239,-72.40789 -37.12816,-72.36726 -37.12797,-72.36678 -37.0878,-72.42262 -37.07718))",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021091-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.35yf49
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Brongniartia stipitata Hemsl."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021092-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.94fvzx
title: Occurrence Download

description: A dataset containing 5581 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-82.54322 -18.03090,-57.91514 -18.03090,-57.91514 -8.18992,-82.54322 -8.18992,-82.54322 -18.03090))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Vultur gryphus Linnaeus, 1758"
 ]
}

 The dataset includes 5581 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021093-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jf6d74
title: Occurrence Download

description: A dataset containing 209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Brachythecium occidentale (Hampe) A.Jaeger"
 ]
}

 The dataset includes 209 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021094-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wrw282
title: Occurrence Download

description: A dataset containing 731 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diaphorina citri Kuwayama, 1908",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 731 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021095-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-1792200986
title: The Netherlands BAG

description: The Netherlands BAG includes structural biology and enzymology groups situated at six Dutch universities (Utrecht, Groningen, Wageningen, Leiden, Eindhoven and Maastricht) and at the Netherlands Cancer Institute in Amsterdam, with a total of fourteen PIs. While the structural biology research projects carried out in these groups are highly diverse, they can be largely classified into two major themes: (i) research on proteins and systems with a strong biomedical relevance and (ii) research concerning the design of new biocatalysts for green chemistry and new-to-nature reactions. Projects deal with prokaryotic and eukaryotic proteins, membrane and soluble proteins, cell surface receptors, and protein-protein, protein-ribonucleotide, protein-drug and enzyme-ligand complexes.