cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.99rak4
title: Occurrence Download

description: A dataset containing 810470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tachycineta thalassina (Swainson, 1827)",
 "Year 1000-2020"
 ]
}

 The dataset includes 810470 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032109-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111295882
title: Bulla, Belonging to Berekyahu, son of Neriyahu, the scribe, Avigad & Sass 417

description: [Text Description:] Bulla, Belonging to Berekyahu, son of Neriyahu, the scribe ❧ [Text or Publication Number Note:] Avigad & Sass 417 ❧ [Excavation Description:] unprovenanced ❧ [Medium:] Clay ❧ [Script Note:] Hebrew ❧ [Physical Object Description:] Seal impression, 1.3x1.1 cm, bezel groove; single-line border, double-line field dividers; fiber grooves on back ❧ [Physical Object Note:] 3 inscribed registers ❧
DOI: 10.15468/dl.7qreqy
title: Occurrence Download

description: A dataset containing 108949 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Orchis mascula (L.) L."
 ]
}

 The dataset includes 108949 records from 412 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031071-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ca5ed3
title: Occurrence Download

description: A dataset containing 9381 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mantisalca salmantica (L.) Briq. & Cavill."
 ]
}

 The dataset includes 9381 records from 186 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019141-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zfbthq
title: Occurrence Download

description: A dataset containing 737 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Grindelia inuloides Willd."
 ]
}

 The dataset includes 737 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233579-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfsxgy
title: Occurrence Download

description: A dataset containing 102464 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Elodea canadensis Michx."
 ]
}

 The dataset includes 102464 records from 782 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234473-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.48j58p
title: Occurrence Download

description: A dataset containing 2460 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chlorophytum comosum (Thunb.) Jacques"
 ]
}

 The dataset includes 2460 records from 146 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030121-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9wet49
title: Occurrence Download

description: A dataset containing 4719 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rodentia",
 "Country is Zimbabwe"
 ]
}

 The dataset includes 4719 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019131-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qqyzn9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is ×Gymplatanthera borelii L.C.Lamb."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234479-230224095556074/datasets/export for details.
DOI: 10.15468/dl.ckuu5s
title: Occurrence Download

description: A dataset containing 3533 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arthropoda, Nematoda, Tardigrada, Rotifera, Annelida, Mollusca, Platyhelminthes)",
 "Geometry POLYGON ((-87.965062 32.675895, -87.962171 32.405302, -87.643178 32.407334, -87.64511 32.677948, -87.965062 32.675895))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 1900",
 {
 "not" : {
 "CoordinateUncertaintyInMeters" : [
 "is one of (301, 3036, 999, 9999)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 3533 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233570-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c457ha
title: Occurrence Download

description: A dataset containing 8044111 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Ecuador"
 ]
}

 The dataset includes 8044111 records from 2030 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233549-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zqjgnw
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aconitum firmum Rchb."
 ]
}

 The dataset includes 111 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181799-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.84tfda
title: Occurrence Download

description: A dataset containing 8985 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Phenology and biological traits of migrating river lamprey (Lampetra fluviatilis) sampled by trapping in the Bresle river (France)."
 ]
}

 The dataset includes 8985 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000318-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gm4tjl
title: Occurrence Download

description: A dataset containing 357 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bunchosia argentea (Jacq.) DC."
 ]
}

 The dataset includes 357 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030325-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rqpros
title: Occurrence Download

description: A dataset containing 32613440 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Mexico"
 ]
}

 The dataset includes 32613440 records from 2266 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002029-180920211646547/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vb4t36
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Praravinia multinervia"
 ]
}

 The dataset includes 11 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059918-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g3ka7r
title: Occurrence Download

description: A dataset containing 677 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lindera rubronervia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 677 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059919-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17290934
title: Bathymetry and slide thickness data off Shikoku in the Nankai subduction zone

description: This dataset comprises bathymetry and slide thickness data used in the following paper.

Title: Two-dimensional non-hydrostatic two-layer model for the generation and propagation of submarine landslide tsunamis, 

Submitted to the special collection entitled Advances in Computer Modelling of Water-Related Disasters in Engineering Applications of Computational Fluid Dynamics on October 8, 2025.
DOI: 10.5281/zenodo.17290933
title: Bathymetry and slide thickness data off Shikoku in the Nankai subduction zone

description: This dataset comprises bathymetry and slide thickness data used in the following paper.

Title: Two-dimensional non-hydrostatic two-layer model for the generation and propagation of submarine landslide tsunamis, 

Submitted to the special collection entitled Advances in Computer Modelling of Water-Related Disasters in Engineering Applications of Computational Fluid Dynamics on October 8, 2025.
DOI: 10.15468/dl.uwjh2n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pelargonium radens",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059922-250920141307145/datasets/export for details.
DOI: 10.15468/dl.fdzn2h
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pelargonium radens",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059925-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.62zqex
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((125.96358551621947 34.767050135844116,129.96358551621947 34.767050135844116,129.96358551621947 38.767050135844116,125.96358551621947 38.767050135844116,125.96358551621947 34.767050135844116))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lamprocapnos spectabilis",
 "Year 2000-2024"
 ]
}

 The dataset includes 307 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059923-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nd2nzn
title: Occurrence Download

description: A dataset containing 41956 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Antheraea polyphemus",
 "Year 1970-2025"
 ]
}

 The dataset includes 41956 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059920-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ed9s7r
title: Occurrence Download

description: A dataset containing 2675 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Gobiidae [GBIF Backbone Taxonomy])",
 "Country is one of (Colombia)"
 ]
 }
 ]
}

 The dataset includes 2675 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059924-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fyjtvj
title: Occurrence Download

description: A dataset containing 2675 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Gobiidae [GBIF Backbone Taxonomy])",
 "Country is one of (Colombia)"
 ]
 }
 ]
}

 The dataset includes 2675 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059926-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.99kd8y
title: Occurrence Download

description: A dataset containing 88786 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Columbiformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((90 30,120 30,120 60,90 60,90 30))"
 ]
}

 The dataset includes 88786 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059865-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17232578
title: Single-cell transcriptomic analysis reveals distinct cancer-associated fibroblast signatures in treatment-refractory esophageal squamous cell carcinoma

description: Esophageal squamous cell carcinoma (ESCC) remains a leading cause of cancer-related mortality. Despite neoadjuvant concurrent chemoradiotherapy (nCCRT), approximately half of patients exhibit incomplete pathological response with persistent lymph node (LN) infiltration. We performed single-cell RNA sequencing on tumor and adjacent normal tissues from 10 ESCC patients post-nCCRT, stratified by LN infiltration status (n=5 each group).
DOI: 10.5281/zenodo.17232579
title: Single-cell transcriptomic analysis reveals distinct cancer-associated fibroblast signatures in treatment-refractory esophageal squamous cell carcinoma

description: Esophageal squamous cell carcinoma (ESCC) remains a leading cause of cancer-related mortality. Despite neoadjuvant concurrent chemoradiotherapy (nCCRT), approximately half of patients exhibit incomplete pathological response with persistent lymph node (LN) infiltration. We performed single-cell RNA sequencing on tumor and adjacent normal tissues from 10 ESCC patients post-nCCRT, stratified by LN infiltration status (n=5 each group).
DOI: 10.5517/ccdc.csd.cc2jyqlt
title: CCDC 2352267: Experimental Crystal Structure Determination

description: Related Article: A. Pantousas, A. Pakhomova, G. Aprilis. L. Dubrovinsky|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.jtv3sd
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Bahrain",
 "Year is 2016",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059928-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9xbg7
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Praravinia negrosensis"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059930-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.faemgd
title: Occurrence Download

description: A dataset containing 221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Liquidambar acalycina)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 221 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059931-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zuu3bc
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acanthus montanus",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059932-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpv4hm
title: Occurrence Download

description: A dataset containing 757 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Australoheros facetus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 757 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059927-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bduxv6
title: Occurrence Download

description: A dataset containing 787218 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Lauraceae"
 ]
}

 The dataset includes 787218 records from 1113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059890-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3dxdgz
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Nocardioides islandensis Dastager et al., 2009"
 ]
}

 The dataset includes 22 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012745-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/6cddmnmwh9
title: The immunometabolic topography of cellular organization and bacterial control in tuberculosis granulomas

description: Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. We previously discovered that human TB granulomas are enriched for immunosuppressive factors typically associated with tumor-immune evasion, raising the intriguing possibility that they promote tolerance to infection. In this study, our goal was to identify candidate drivers for establishing this tolerogenic niche and to determine if the magnitude of this response correlates with bacterial persistence. To do this, we conducted a multimodal spatial analysis of 52 granulomas from 16 non-human primates (NHP) infected with low dose Mtb for 9-12 weeks. Notably, each granuloma’s bacterial burden was individually quantified, allowing us to directly ask how granuloma spatial structure and function relate to infection control. With this imaging resource, we found that a universal feature of TB granulomas was partitioning of the myeloid core into two distinct metabolic environments, one of which is hypoxic. This hypoxic environment associated with pathologic immune cell states, dysfunctional cellular organization of the granuloma, and a near-complete blockade of lymphocyte infiltration that would be required for a successful host response. The extent of these hypoxia-associated features correlated with worsened bacterial burden. We conclude that hypoxia correlates with immune cell state and organization within granulomas and is possibly a potent driver of subverted immunity during TB.

This repository comprises the: 

1. Single cell data generated from the multiplexed imaging data
2. All masks utilized in image analysis 
3. The spatial transcriptomics dataset

The MIBI-TOF imaging data and histology images for all regions imaged can be access at: 10.6019/S-BIAD2359.
DOI: 10.17632/6cddmnmwh9.1
title: The immunometabolic topography of cellular organization and bacterial control in tuberculosis granulomas

description: Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. We previously discovered that human TB granulomas are enriched for immunosuppressive factors typically associated with tumor-immune evasion, raising the intriguing possibility that they promote tolerance to infection. In this study, our goal was to identify candidate drivers for establishing this tolerogenic niche and to determine if the magnitude of this response correlates with bacterial persistence. To do this, we conducted a multimodal spatial analysis of 52 granulomas from 16 non-human primates (NHP) infected with low dose Mtb for 9-12 weeks. Notably, each granuloma’s bacterial burden was individually quantified, allowing us to directly ask how granuloma spatial structure and function relate to infection control. With this imaging resource, we found that a universal feature of TB granulomas was partitioning of the myeloid core into two distinct metabolic environments, one of which is hypoxic. This hypoxic environment associated with pathologic immune cell states, dysfunctional cellular organization of the granuloma, and a near-complete blockade of lymphocyte infiltration that would be required for a successful host response. The extent of these hypoxia-associated features correlated with worsened bacterial burden. We conclude that hypoxia correlates with immune cell state and organization within granulomas and is possibly a potent driver of subverted immunity during TB.

This repository comprises the: 

1. Single cell data generated from the multiplexed imaging data
2. All masks utilized in image analysis 
3. The spatial transcriptomics dataset

The MIBI-TOF imaging data and histology images for all regions imaged can be access at: 10.6019/S-BIAD2359.