cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15429455
title: Global Compilation of Lowermost Mantle Anisotropy Observations - Database of Study regions

description: This database presents digitized geographical regions where lowermost mantle anisotropy has been observed. It compiles and organizes all previously reported observations up to the date of publication, providing a comprehensive and accessible reference for researchers.
DOI: 10.15468/dl.uutk2v
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.0251 -31.3959,30.5701 -30.7329,30.5701 -28.5786,25.5395 -28.5786,25.5395 -32.9007,28.2048 -32.9007,28.5753 -32.6569,29.4902 -31.7517,30.0251 -31.3959))"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050142-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15392699
title: Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma - Processed datasets and notebook

description: This entry accompanies the manuscript "Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma" (preprint).

Contents:

1. Processed CODEX MIF Data (CODEX-MIF.zip)

CODEX data from 48 fields of view (identified by region_id) are provided in the following files:



{region_id}.cell_data.csv: A table with three columns—CELL_ID, X, and Y—containing the centroid coordinates of all segmented cells in the corresponding field of view.

{region_id}.cell_types.csv: A table with two columns—CELL_ID and CELL_TYPE—containing cell type annotations for all cells in the region.

{region_id}.cell_features.csv: A table with multiple columns—CELL_ID, SIZE, ORIENTATION, etc.—containing morphological features of all cells in the corresponding field of view.

{region_id}.expression.csv: A table with multiple columns—CELL_ID, DAPI, CD45, etc.—providing normalized protein biomarker expression levels for all cells in the region.


2. Processed Visium ST Data (Visium-ST.zip)

Visium spatial transcriptomics (ST) data from 22 samples are provided in the following files:



visium_all.h5ad: An AnnData object containing raw gene expression counts for all spatial transcriptomics spots across the 22 samples.

{region_label}_tissue_positions_list.csv: A table with multiple columns—barcode, transformed coords x, transformed coords y, etc.—providing ST spot coordinates co-registered with the corresponding CODEX MIF data. The transformed coordinates align with the cell centroid coordinates specified in the CODEX datasets.


3. Metadata (metadata.csv)

A metadata file in CSV format that maps region_id to key attributes, including:



Region label

Patient ID

Pre-/Post-treatment status

Response to immunotherapy

Treatment type


4. Data Analysis Notebook (notebook_and_resources.zip)

A zip file containing:



A Jupyter Notebook to reproduce the analytical workflows for generating the main figure panels in the manuscript.

Intermediate data files related to plotting and visualization.


Citation:

When using this dataset, please cite the original manuscript (DOI: 10.1101/2025.06.11.656869) and this Zenodo entry (DOI:  10.5281/zenodo.15392699).
DOI: 10.5281/zenodo.15392698
title: Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma - Processed datasets and notebook

description: This entry accompanies the manuscript "Spatial multi-omics and deep learning reveal fingerprints of immunotherapy response and resistance in hepatocellular carcinoma" (preprint).

Contents:

1. Processed CODEX MIF Data (CODEX-MIF.zip)

CODEX data from 48 fields of view (identified by region_id) are provided in the following files:



{region_id}.cell_data.csv: A table with three columns—CELL_ID, X, and Y—containing the centroid coordinates of all segmented cells in the corresponding field of view.

{region_id}.cell_types.csv: A table with two columns—CELL_ID and CELL_TYPE—containing cell type annotations for all cells in the region.

{region_id}.cell_features.csv: A table with multiple columns—CELL_ID, SIZE, ORIENTATION, etc.—containing morphological features of all cells in the corresponding field of view.

{region_id}.expression.csv: A table with multiple columns—CELL_ID, DAPI, CD45, etc.—providing normalized protein biomarker expression levels for all cells in the region.


2. Processed Visium ST Data (Visium-ST.zip)

Visium spatial transcriptomics (ST) data from 22 samples are provided in the following files:



visium_all.h5ad: An AnnData object containing raw gene expression counts for all spatial transcriptomics spots across the 22 samples.

{region_label}_tissue_positions_list.csv: A table with multiple columns—barcode, transformed coords x, transformed coords y, etc.—providing ST spot coordinates co-registered with the corresponding CODEX MIF data. The transformed coordinates align with the cell centroid coordinates specified in the CODEX datasets.


3. Metadata (metadata.csv)

A metadata file in CSV format that maps region_id to key attributes, including:



Region label

Patient ID

Pre-/Post-treatment status

Response to immunotherapy

Treatment type


4. Data Analysis Notebook (notebook_and_resources.zip)

A zip file containing:



A Jupyter Notebook to reproduce the analytical workflows for generating the main figure panels in the manuscript.

Intermediate data files related to plotting and visualization.


Citation:

When using this dataset, please cite the original manuscript (DOI: 10.1101/2025.06.11.656869) and this Zenodo entry (DOI:  10.5281/zenodo.15392699).
DOI: 10.15468/dl.wa5uwj
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.5701 -24.0715,25.5395 -24.0715,25.5395 -28.5786,30.5701 -28.5786,30.5701 -24.0715))"
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050143-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15674388
title: Data from: Temperature-modulated ocean CO2 uptake in response to CO2 increase and decrease
DOI: 10.5281/zenodo.15674389
title: Data from: Temperature-modulated ocean CO2 uptake in response to CO2 increase and decrease
DOI: 10.15468/dl.jsv2w4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1332 -20.158,25.5395 -23.2724,25.5395 -24.0715,30.5701 -24.0715,30.5701 -20.3186,29.6496 -19.6123,28.947 -19.4003,28.1821 -19.4609,27.6072 -19.7214,27.1332 -20.158))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050144-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kykfdv
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "TaxonKey is Elephas maximus Linnaeus, 1758"
 ]
}

 The dataset includes 106 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050145-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m2ajw2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.0214 -34.0501,25.5395 -34.1098,25.5395 -32.9007,20.509 -32.9007,20.509 -34.5676,20.524 -34.555,20.8859 -34.5419,20.9606 -34.4398,21.2995 -34.5131,21.5296 -34.4338,21.8696 -34.4439,22.0323 -34.2835,22.221 -34.2428,22.2566 -34.1304,22.5993 -34.0741,22.9652 -34.1674,23.4069 -34.1858,23.4955 -34.0792,23.6056 -34.0563,24.8471 -34.2877,24.9447 -34.2397,25.0214 -34.0501))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050146-250525065834625/datasets/export for details.
DOI: 10.15468/dl.cd74ws
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((32.064 -28.9416,32.4847 -28.5786,30.5701 -28.5786,30.5701 -30.7329,30.6252 -30.6659,31.4179 -29.4257,31.8178 -29.0299,32.064 -28.9416))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050147-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15679162
title: Dataset for "Electrical Switching of Altermagnetism"

description: This dataset provides raw data for the spin accumulation of bilayer MnTe used in the research paper "Electrical Switching of Altermagnetism" by Yiyuan Chen, Xiaoxiong Liu, Hai-Zhou Lu, and X. C. Xie.
DOI: 10.15468/dl.p6e9dq
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.5808 -24.13,35.5909 -24.0715,30.5701 -24.0715,30.5701 -28.5786,32.4847 -28.5786,32.55 -28.5222,33.0346 -26.8668,32.9741 -26.7838,33.0415 -26.059,32.9304 -26.0011,32.7994 -26.1281,32.6834 -26.0015,32.813 -25.8728,32.8513 -25.7166,33.3048 -25.3731,35.1489 -24.6699,35.5808 -24.13))"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050148-250525065834625/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/12190352
title: Layline Shareholder activism dataset
DOI: 10.15468/dl.4r3q42
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((31.8862 -21.3285,30.5701 -20.3186,30.5701 -24.0715,35.5909 -24.0715,35.6007 -24.0157,35.6007 -23.8125,35.4969 -23.7035,35.6007 -23.165,35.6007 -22.9702,35.227 -22.2482,34.6862 -21.6944,34.013 -21.3095,33.5 -21.1593,32.9675 -21.1092,32.4352 -21.1612,31.8862 -21.3285))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050150-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n2s79b
title: Occurrence Download

description: A dataset containing 5238 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is Specimen",
 "SpeciesKey is Agkistrodon contortrix (Linnaeus, 1766)"
 ]
}

 The dataset includes 5238 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050151-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t9q6wm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1586 -33.5889,28.2048 -32.9007,25.5395 -32.9007,25.5395 -34.1098,25.6468 -34.1222,25.7787 -34.0734,25.7098 -33.9109,25.8639 -33.797,26.4806 -33.8473,27.1586 -33.5889))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050152-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.29334158
title: Additional file 4 of Quercetagetin alleviates liver fibrosis in non-alcoholic fatty liver disease by promoting ferroptosis of hepatic stellate cells through GPX4 ubiquitination

description: Supplementary Materials 4.
DOI: 10.6084/m9.figshare.29334158.v1
title: Additional file 4 of Quercetagetin alleviates liver fibrosis in non-alcoholic fatty liver disease by promoting ferroptosis of hepatic stellate cells through GPX4 ubiquitination

description: Supplementary Materials 4.
DOI: 10.6084/m9.figshare.29334160.v1
title: Additional file 8 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 8: Suppl file S1. The ingredients and chemical composition of diet for the experiment dairy cows
DOI: 10.6084/m9.figshare.29334163
title: Additional file 9 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 9: Suppl file S2. The circadian rhythm information of ruminal microbial taxa
DOI: 10.6084/m9.figshare.29334160
title: Additional file 8 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 8: Suppl file S1. The ingredients and chemical composition of diet for the experiment dairy cows
DOI: 10.6084/m9.figshare.29334163.v1
title: Additional file 9 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 9: Suppl file S2. The circadian rhythm information of ruminal microbial taxa
DOI: 10.6084/m9.figshare.29334166
title: Additional file 10 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 10: Suppl file S3. The circadian rhythm information of functional pathways in ruminal microbiota
DOI: 10.6084/m9.figshare.29334166.v1
title: Additional file 10 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 10: Suppl file S3. The circadian rhythm information of functional pathways in ruminal microbiota
DOI: 10.6084/m9.figshare.29334169
title: Additional file 11 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 11: Suppl file S4. The information of the top 20 bins that contribute to HoS and DL process, respectively. HoS. homogeneous selection, DL: dispersal limitation
DOI: 10.6084/m9.figshare.29334169.v1
title: Additional file 11 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 11: Suppl file S4. The information of the top 20 bins that contribute to HoS and DL process, respectively. HoS. homogeneous selection, DL: dispersal limitation
DOI: 10.6084/m9.figshare.29334172
title: Additional file 12 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 12: Suppl file S5. The circadian rhythm information of feed intake, rumination time, and rumen fermentation parameters
DOI: 10.6084/m9.figshare.29334172.v1
title: Additional file 12 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 12: Suppl file S5. The circadian rhythm information of feed intake, rumination time, and rumen fermentation parameters
DOI: 10.6084/m9.figshare.29334175
title: Additional file 13 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 13: Suppl file S6. The cross-lagged correlation between microbial taxa and feed intake, as well as rumination, and ruminal fermentation parameters
DOI: 10.6084/m9.figshare.29334175.v1
title: Additional file 13 of Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome

description: Supplementary Material 13: Suppl file S6. The cross-lagged correlation between microbial taxa and feed intake, as well as rumination, and ruminal fermentation parameters
DOI: 10.15468/dl.84pxst
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dierama medium N.E.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((18.2339 -32.5266,18.1411 -32.657,18.1007 -32.7021,18.0224 -32.6366,17.8923 -32.6419,17.754 -32.8255,17.7723 -32.9007,20.509 -32.9007,20.509 -28.5786,16.2782 -28.5786,16.4358 -28.7202,16.726 -29.1235,17.1957 -30.3752,17.6655 -31.1743,18.1322 -31.7679,18.2495 -32.2638,18.2339 -32.5266))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050153-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.29334238
title: Additional file 6 of The impact of early-life exposures on growth and adult gut microbiome composition is dependent on genetic strain and parent- of- origin

description: Additional file 6: Supplemental Tables 1 through 13.
DOI: 10.6084/m9.figshare.29334238.v1
title: Additional file 6 of The impact of early-life exposures on growth and adult gut microbiome composition is dependent on genetic strain and parent- of- origin

description: Additional file 6: Supplemental Tables 1 through 13.
DOI: 10.6084/m9.figshare.29334247
title: Additional file 2 of Diversity and horizontal gene transfer of mycoviruses in Exserohilum turcicum population from northern corn leaf blight of maize

description: Additional file 2: Table S1. Summary of NGS data mapped to each virus, including the number of reads, sequencing depth, and genome coverage. Table S2. The primers used in this study. Table S3. Information on the isolated strains in this study.
DOI: 10.6084/m9.figshare.29334247.v1
title: Additional file 2 of Diversity and horizontal gene transfer of mycoviruses in Exserohilum turcicum population from northern corn leaf blight of maize

description: Additional file 2: Table S1. Summary of NGS data mapped to each virus, including the number of reads, sequencing depth, and genome coverage. Table S2. The primers used in this study. Table S3. Information on the isolated strains in this study.
DOI: 10.6084/m9.figshare.29334257.v1
title: Additional file 10 of Interrogating the plasma proteome of repetitive head impact exposure and chronic traumatic encephalopathy

description: Additional file 10: Supplementary Figure 9. Bar chart displaying the percentage of semi-quantitative composite medial temporal lobeburden scores accounted by specific MTL subregions in all autopsy casesand within CTE+ cases.
DOI: 10.6084/m9.figshare.29334257
title: Additional file 10 of Interrogating the plasma proteome of repetitive head impact exposure and chronic traumatic encephalopathy

description: Additional file 10: Supplementary Figure 9. Bar chart displaying the percentage of semi-quantitative composite medial temporal lobeburden scores accounted by specific MTL subregions in all autopsy casesand within CTE+ cases.
DOI: 10.6084/m9.figshare.29334125
title: Understanding Risks involved for PPP projects in Uttarakhand (Responses) (1).xlsx

description: <b>Risk Evaluation in PPP Infrastructure Projects in Fragile Urban Topographies: A Methodological Study Based in India</b>
DOI: 10.6084/m9.figshare.29334125.v1
title: Understanding Risks involved for PPP projects in Uttarakhand (Responses) (1).xlsx

description: <b>Risk Evaluation in PPP Infrastructure Projects in Fragile Urban Topographies: A Methodological Study Based in India</b>
DOI: 10.6084/m9.figshare.29334278
title: Additional file 1 of Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.29334278.v1
title: Additional file 1 of Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.29334284
title: Additional file 3 of Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.29334284.v1
title: Additional file 3 of Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.29334287
title: Additional file 4 of Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways

description: Supplementary Material 4