cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27978381
title: Additional file 2 of The host genotype actively shapes its microbiome across generations in laboratory mice

description: Additional file 2. Analysis repository. We performed all the presented analysis and graph generation through a single jupyter notebook. It lists necessary dependencies for full reproducibility. We have outsourced some of the functions into a public 16s rRNA gene analysis code repository: https://github.com/sjanssen2/ggmap. By default, external system calls are submitted to a Slurm cluster. You can instead run on your local machine by providing the optional argument use_grid=False. Additional conda environments can be conveniently created via "cd recipes && make all-env" after cloning the above repository and changing into its working directory. All files necessary for our analysis, the jupyter notebook and a static HTML version of the jupyter notebook for ease of readability are packaged as one zip compressed file
DOI: 10.6084/m9.figshare.27978381.v1
title: Additional file 2 of The host genotype actively shapes its microbiome across generations in laboratory mice

description: Additional file 2. Analysis repository. We performed all the presented analysis and graph generation through a single jupyter notebook. It lists necessary dependencies for full reproducibility. We have outsourced some of the functions into a public 16s rRNA gene analysis code repository: https://github.com/sjanssen2/ggmap. By default, external system calls are submitted to a Slurm cluster. You can instead run on your local machine by providing the optional argument use_grid=False. Additional conda environments can be conveniently created via "cd recipes && make all-env" after cloning the above repository and changing into its working directory. All files necessary for our analysis, the jupyter notebook and a static HTML version of the jupyter notebook for ease of readability are packaged as one zip compressed file
DOI: 10.6084/m9.figshare.27978397
title: Additional file 1 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.27978397.v1
title: Additional file 1 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.27978400
title: Additional file 2 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.27978400.v1
title: Additional file 2 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.27978403
title: Additional file 3 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.27978403.v1
title: Additional file 3 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.27978406
title: Additional file 4 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.27978406.v1
title: Additional file 4 of Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.27978408
title: Additional file 2 of Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment

description: Additional File 2. Tables S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17: Table S1. Number of Cells That Passed Quality Control on Primary Tumor FOV. Abbreviation: FOV, fields of view; Table S2. Differentially Expressed Genes Identified From Subclustering InSituType-Assigned T Cells and Mononucleic Phagocytes; Table S3. Differential Gene Expression Using FindMarkers Between Malignant Proximal Tubule and Normal Proximal Tubule Cells. These cells were used for LASSO regression and genes selected by LASSO for final model. Abbreviation: LASSO, least absolute shrinkage and selection operator; Table S4. Abundance Differences for Cell Phenotypes in the Tumor and Stromal FOV of the Cohorts. Positive estimate indicates lower abundance in IO-naïve nonsarcomatoid. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S5. Association of Ripley’s K Between Cohorts in Tumor and Stromal FOV Tissue at a Radius of 150 px (27 µm). Negative-estimate values indicate lower clustering in IO-naïve nonsarcomatoid samples. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S6. Differential Gene Expression of Primary ccRCC Tumor and Stroma Samples Between Cohorts. Abbreviation: ccRCC, clear-cell renal-cell carcinoma; Table S7. Differential Gene Expression for Each Cell Phenotype in Primary-Tumor FOV Between Pre- and Post-IO. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S8. Differential Gene Expression for Each Phenotype on Primary Tumor FOV Before Undergoing IO With and Without Sarcomatoid Features. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S9. Differential Gene Expression in Stromal FOV, Between Pre- and Post-IO Primary Samples. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S10. Differential Gene Expression for Each Phenotype on Primary Stromal FOV Before Undergoing IO With and Without Sarcomatoid Features. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S2. Results of the Spatial Enrichment of Hallmark Gene Sets in All Samples; Table S12. T-Test Results Comparing Bivariate Moran’s I of Ligand/Receptor Pairs From EMT Gene Set in Tumor and Stromal FOV. Abbreviations: EMT, epithelial-mesenchymal transition; FOV, fields of view; Table S13. T-Test Results Comparing Bivariate Moran’s I of Ligand/Receptor Pairs From IL6/JAK/STAT3 Signaling Gene-Set Tumor and Stromal FOV. Abbreviation: FOV, fields of view; Table S14. Comparisons Between ITGAV and COL4A1 Abundance in the Tumor and Stromal Compartments; Table S15. Results of Beta-Binomial Modeling of Phenotypes Between Cohorts of the Validation mIF. Abbreviation: mIF, multiplex immunofluorescence; Table S16. Nanostrisng CosMx SMI Probe Targets; Table S17. Kidney Cell Atlas Phenotype Names Before (InsituType_Manual) and After (Final) Collapsing Similar Cell Types.
DOI: 10.6084/m9.figshare.27978408.v1
title: Additional file 2 of Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment

description: Additional File 2. Tables S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16, S17: Table S1. Number of Cells That Passed Quality Control on Primary Tumor FOV. Abbreviation: FOV, fields of view; Table S2. Differentially Expressed Genes Identified From Subclustering InSituType-Assigned T Cells and Mononucleic Phagocytes; Table S3. Differential Gene Expression Using FindMarkers Between Malignant Proximal Tubule and Normal Proximal Tubule Cells. These cells were used for LASSO regression and genes selected by LASSO for final model. Abbreviation: LASSO, least absolute shrinkage and selection operator; Table S4. Abundance Differences for Cell Phenotypes in the Tumor and Stromal FOV of the Cohorts. Positive estimate indicates lower abundance in IO-naïve nonsarcomatoid. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S5. Association of Ripley’s K Between Cohorts in Tumor and Stromal FOV Tissue at a Radius of 150 px (27 µm). Negative-estimate values indicate lower clustering in IO-naïve nonsarcomatoid samples. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S6. Differential Gene Expression of Primary ccRCC Tumor and Stroma Samples Between Cohorts. Abbreviation: ccRCC, clear-cell renal-cell carcinoma; Table S7. Differential Gene Expression for Each Cell Phenotype in Primary-Tumor FOV Between Pre- and Post-IO. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S8. Differential Gene Expression for Each Phenotype on Primary Tumor FOV Before Undergoing IO With and Without Sarcomatoid Features. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S9. Differential Gene Expression in Stromal FOV, Between Pre- and Post-IO Primary Samples. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S10. Differential Gene Expression for Each Phenotype on Primary Stromal FOV Before Undergoing IO With and Without Sarcomatoid Features. Abbreviations: FOV, fields of view; IO, immunotherapy; Table S2. Results of the Spatial Enrichment of Hallmark Gene Sets in All Samples; Table S12. T-Test Results Comparing Bivariate Moran’s I of Ligand/Receptor Pairs From EMT Gene Set in Tumor and Stromal FOV. Abbreviations: EMT, epithelial-mesenchymal transition; FOV, fields of view; Table S13. T-Test Results Comparing Bivariate Moran’s I of Ligand/Receptor Pairs From IL6/JAK/STAT3 Signaling Gene-Set Tumor and Stromal FOV. Abbreviation: FOV, fields of view; Table S14. Comparisons Between ITGAV and COL4A1 Abundance in the Tumor and Stromal Compartments; Table S15. Results of Beta-Binomial Modeling of Phenotypes Between Cohorts of the Validation mIF. Abbreviation: mIF, multiplex immunofluorescence; Table S16. Nanostrisng CosMx SMI Probe Targets; Table S17. Kidney Cell Atlas Phenotype Names Before (InsituType_Manual) and After (Final) Collapsing Similar Cell Types.
DOI: 10.6084/m9.figshare.27978411
title: Additional file 3 of Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment

description: Additional File 3. Information related to antibodies and stains used for multiplex immunofluorescence, reagents and equipment used for the imaging and Nanostring Spatial Molecular Imager platform, location of deposited data and code, and R packages/versions used for analysis.
DOI: 10.6084/m9.figshare.27978411.v1
title: Additional file 3 of Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment

description: Additional File 3. Information related to antibodies and stains used for multiplex immunofluorescence, reagents and equipment used for the imaging and Nanostring Spatial Molecular Imager platform, location of deposited data and code, and R packages/versions used for analysis.
DOI: 10.6084/m9.figshare.27978427
title: Additional file 1 of Revisiting microgenderome: detecting and cataloguing sexually unique and enriched species in human microbiomes

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.27978427.v1
title: Additional file 1 of Revisiting microgenderome: detecting and cataloguing sexually unique and enriched species in human microbiomes

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.27978432
title: Additional file 2 of Cross cultural adaptation and validation of the Hindi version of foot function index

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.27978432.v1
title: Additional file 2 of Cross cultural adaptation and validation of the Hindi version of foot function index

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.27978439
title: Additional file 1 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.27978439.v1
title: Additional file 1 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.27978442
title: Additional file 2 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.27978442.v1
title: Additional file 2 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.27978445
title: Additional file 3 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.27978445.v1
title: Additional file 3 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.27978448
title: Additional file 4 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.27978448.v1
title: Additional file 4 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.27978451
title: Additional file 5 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.27978454
title: Additional file 6 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.27978451.v1
title: Additional file 5 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.27978454.v1
title: Additional file 6 of Triolein alleviates ischemic stroke brain injury by regulating autophagy and inflammation through the AKT/mTOR signaling pathway

description: Supplementary Material 6
DOI: 10.15468/dl.ynk8bg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthopagrus sheim Iwatsuki, 2013",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021797-241126133413365/datasets/export for details.
DOI: 10.15468/dl.fwxh7r
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthopagrus morrisoni Iwatsuki, 2013",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021798-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2e2g8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthopagrus longispinnis (Valenciennes, 1830)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021799-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.673w9k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthopagrus arabicus Iwatsuki, 2013",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021800-241126133413365/datasets/export for details.
DOI: 10.15468/dl.hy2tk8
title: Occurrence Download

description: A dataset containing 192074 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2024-11-10",
 "EventDate is less than or equal to 2024-12-10",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 192074 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021789-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10115799
title: Layline Shareholder activism dataset
DOI: 10.15468/dl.8wty6a
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sparus latus Houttuyn, 1782",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021801-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6b5bm
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sebastes vulpes Döderlein, 1884",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 60 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021802-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.32y2gv
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thunnus albacares (Bonnaterre, 1788)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 43 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021803-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r29tsp
title: Occurrence Download

description: A dataset containing 401 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spratelloides gracilis (Temminck & Schlegel, 1846)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 401 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021805-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hy9qyn
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is KUBI Mammalogy Collection",
 "GadmGid is DOM",
 "TaxonKey is Chiroptera",
 "Year 1967-1972"
 ]
}

 The dataset includes 85 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021806-241126133413365/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.27978003
title: 脯氨酸的原始数据提示血清杀伤 KP.xlsx

description: 这项研究表明，脯氨酸是一种有效的代谢物，通过通量进入丙酮酸/TCA 循环，在体外和体内逆转肺炎克雷伯菌血清耐药性，丙酮酸/TCA 循环上调补体结合蛋白和 PMF 的表达，允许形成 MAC，最终导致细胞死亡。
DOI: 10.15468/dl.t3bs4f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clupea gracilis Temminck & Schlegel, 1846",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021807-241126133413365/datasets/export for details.
DOI: 10.5281/zenodo.14280024
title: LGHAP v2: Global monthly mean 1-km gap-free PM2.5 grids (2000-2021)

description: A Long-term Gap-free High-resolution Air Pollutants concentration dataset (abbreviated as LGHAP) is of great significance for environmental management and earth system science analysis. In the current release of LGHAP dataset (LGHAP v2), we provide 22-year-long gap free aerosol optical depth (AOD) and near-surface PM2.5 concentrations with daily 1-km resolution covering the global land area from 2000 to 2021. Leveraging an improved big earth data analytic framework with attention-reinforced tensor construction and adaptive background information updating schemes, gap-free AOD grids were firstly derived via an integration of multimodal AODs and air quality measurements acquired from diverse satellites, ground monitors, and numerical models. For better predicting PM2.5 concentration across the globe, a scene-aware ensemble learning graph attention network (SCAGAT) was then developed to account for large modeling bias over regions with limited or even none in situ air quality measurements. These datasets were archived in the NetCDF (nc) format, while data in every year were archived as an individual submission. Python, MATLAB, R, and IDL codes were also provided to help users read and visualize the LGHAP v2 data.
DOI: 10.5281/zenodo.14280025
title: LGHAP v2: Global monthly mean 1-km gap-free PM2.5 grids (2000-2021)

description: A Long-term Gap-free High-resolution Air Pollutants concentration dataset (abbreviated as LGHAP) is of great significance for environmental management and earth system science analysis. In the current release of LGHAP dataset (LGHAP v2), we provide 22-year-long gap free aerosol optical depth (AOD) and near-surface PM2.5 concentrations with daily 1-km resolution covering the global land area from 2000 to 2021. Leveraging an improved big earth data analytic framework with attention-reinforced tensor construction and adaptive background information updating schemes, gap-free AOD grids were firstly derived via an integration of multimodal AODs and air quality measurements acquired from diverse satellites, ground monitors, and numerical models. For better predicting PM2.5 concentration across the globe, a scene-aware ensemble learning graph attention network (SCAGAT) was then developed to account for large modeling bias over regions with limited or even none in situ air quality measurements. These datasets were archived in the NetCDF (nc) format, while data in every year were archived as an individual submission. Python, MATLAB, R, and IDL codes were also provided to help users read and visualize the LGHAP v2 data.