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

description: A dataset containing 11684 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Mucoromycota, Blastocladiomycota, Chytridiomycota, Zoopagomycota, Glomeromycota, Entomophthoromycota, Zygomycota, Neocallimastigomycota)"
 ]
}

 The dataset includes 11684 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008415-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13983462
title: Association of copy number alterations with the immune transcriptomic landscape in cancer

description: This repository contains supplementary materials and data for the paper "Association of copy number alterations with the immune transcriptomic landscape in cancer". The materials are organized in the following folders:



00_code: code to reproduce the analysis

01_ica_datasets: transcriptional components, sample mixing matrix activities, and gene set enrichment analysis results of the GPL570, ARCHS4, and TCGA datasets

02_ica_cna_tc: identified CNA-TCs and their captured CNA regions, genomic plots of CNA-TCs

03_ica_immune_tc: identified immune-TCs, list of immune gene sets

04_ica_tc_dataset_overlap: reproducibility results of CNA-TCs and immune-TCs across datasets

05_immune_gene_occurences: frequency of genes with high gene weight in immune-TCs, list potential novel immune involved ORFs

06_projection_immune_tc_datasets: GPL570 and TCGA cancer samples corrected mixing matrix activitiy for CNA-TCs and immune-TCs of the other dataset

07_inferred_cna_profiles: TACNA profiles and CNA burden per cancer sample

08_cna_burden_immune_tc_association: cancer sample associations of CNA burden, individual CNAs, and single gene CNAs with immune-TCs

09_projection_single_cell: cell type activity of immune-TCs in a single-cell tumor immune atlas for precision oncology  

10_projection_spatial_transcriptomics: activity of immune-TCs and CNA-TCs for each spot in spatial transcriptomic datasets from 10x Genomics

11_immunotherapy_response: gene expression data, sample annotation, and mixing matrix of projected GPL570 immune- TCs and CNA-TCs for 13 immunotherapy response datasets with predictive performance
DOI: 10.5281/zenodo.17715512
title: Association of copy number alterations with the immune transcriptomic landscape in cancer

description: This repository contains supplementary materials and data for the paper "Association of copy number alterations with the immune transcriptomic landscape in cancer". The materials are organized in the following folders:



00_code: code to reproduce the analysis

01_ica_datasets: transcriptional components, sample mixing matrix activities, and gene set enrichment analysis results of the GPL570, ARCHS4, and TCGA datasets

02_ica_cna_tc: identified CNA-TCs and their captured CNA regions, genomic plots of CNA-TCs

03_ica_immune_tc: identified immune-TCs, list of immune gene sets

04_ica_tc_dataset_overlap: reproducibility results of CNA-TCs and immune-TCs across datasets

05_immune_gene_occurences: frequency of genes with high gene weight in immune-TCs, list potential novel immune involved ORFs

06_projection_immune_tc_datasets: GPL570 and TCGA cancer samples corrected mixing matrix activitiy for CNA-TCs and immune-TCs of the other dataset

07_inferred_cna_profiles: TACNA profiles and CNA burden per cancer sample

08_cna_burden_immune_tc_association: cancer sample associations of CNA burden, individual CNAs, and single gene CNAs with immune-TCs

09_projection_single_cell: cell type activity of immune-TCs in a single-cell tumor immune atlas for precision oncology  

10_projection_spatial_transcriptomics: activity of immune-TCs and CNA-TCs for each spot in spatial transcriptomic datasets from 10x Genomics

11_immunotherapy_response: gene expression data, sample annotation, and mixing matrix of projected GPL570 immune- TCs and CNA-TCs for 13 immunotherapy response datasets with predictive performance
DOI: 10.15468/dl.uekx78
title: Occurrence Download

description: A dataset containing 31823 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Juniperus",
 "GadmGid is one of (USA.6_1, USA.17_1, USA.27_1, USA.28_1, USA.32_1, USA.35_1, USA.37_1, USA.42_1, USA.44_1, USA.51_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Machine Observation)"
 ]
}

 The dataset includes 31823 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008417-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17715799
title: Pitfall Trap and Ant Morphological Trait Datasets

description: The datasets provided assess invertebrates collected from pitfall traps in Kingston, Jamaica in July 2024 and the morphological features of the ants collected.
DOI: 10.5281/zenodo.17715798
title: Pitfall Trap and Ant Morphological Trait Datasets

description: The datasets provided assess invertebrates collected from pitfall traps in Kingston, Jamaica in July 2024 and the morphological features of the ants collected.
DOI: 10.15468/dl.gwpdcw
title: Occurrence Download

description: A dataset containing 9462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Juniperus virginiana",
 "GadmGid is one of (USA.6_1, USA.17_1, USA.27_1, USA.28_1, USA.32_1, USA.35_1, USA.37_1, USA.42_1, USA.44_1, USA.51_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Machine Observation)"
 ]
}

 The dataset includes 9462 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008419-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dd.uk9xds
title: Dataset generated from Esri tool

description: Derived dataset generated by Esri geoprocessing tool using GBIF API
DOI: 10.15468/dl.2hn3xr
title: Occurrence Download

description: A dataset containing 27954 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is GBR.1_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Numenius arquata",
 "Year 2000-2015"
 ]
}

 The dataset includes 27954 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008420-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57783/1kj5-ns64
title: Massachusetts HCUP
DOI: 10.15468/dl.tq6aaz
title: Occurrence Download

description: A dataset containing 2134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "GadmGid is USA.48_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Taricha granulosa"
 ]
}

 The dataset includes 2134 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008422-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98tw74
title: Occurrence Download

description: A dataset containing 299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lantana camara",
 "GadmGid is one of (USA.6_1, USA.17_1, USA.27_1, USA.28_1, USA.32_1, USA.35_1, USA.37_1, USA.42_1, USA.44_1, USA.51_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Machine Observation)"
 ]
}

 The dataset includes 299 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008424-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ykav9t
title: Occurrence Download

description: A dataset containing 5277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-110.34139 24.25836,-110.3426 24.24878,-110.34166 24.24027,-110.33658 24.22385,-110.31941 24.21711,-110.30275 24.21073,-110.28963 24.21309,-110.27368 24.21628,-110.26552 24.22018,-110.26363 24.2255,-110.26079 24.23082,-110.26115 24.2359,-110.25997 24.24075,-110.25548 24.24347,-110.25548 24.24784,-110.25784 24.25623,-110.26836 24.25977,-110.28017 24.27065,-110.29235 24.27715,-110.30369 24.27443,-110.31551 24.2736,-110.34139 24.25836))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 1999-2025"
 ]
}

 The dataset includes 5277 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008423-251120083545085/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.30258464
title: Tsunami heights on the Korean east coast from submarine active faults along the eastern margin of the Sea of Japan

description: Large earthquakes along the eastern margin of the Sea of Japan, such as the 1983 Central Japan Sea Earthquake (M 7.7) or the 1993 Southwest Off Hokkaido Earthquake (M 7.8) generated tsunamis that reached and caused damage on the east coast of Korea, whereas tsunamis from the recent 2024 Noto Peninsula Earthquake (M 7.6) were much smaller. In this study, we computed tsunamis on the Korean east coast from 60 fault models proposed by a Japanese committee in 2014 (MLIT model). The maximum tsunami height at many locations is produced by the F24 fault (Mw 7.9, corresponding to the 1983 earthquake) and the F17 fault (Mw 7.8, a model of the 1993 earthquake). In addition, the F20 (Mw 7.8), F28 (Mw 7.7), and F30 (Mw 7.8) faults, located off Aomori, Akita, and Yamagata Prefectures, also produce large tsunamis on the Korean coast, because of their fault strike and propagation effects through Yamato Rise. The tsunami heights from fault models of the 1940 Off Shakotan Peninsula Earthquake (F07), the 1964 Niigata Earthquake (F34), and the 2024 Noto Peninsula Earthquake (F43) are smaller, as they are located further to the north or on the continental shelf with shallower water depth.
DOI: 10.6084/m9.figshare.30258464.v1
title: Tsunami heights on the Korean east coast from submarine active faults along the eastern margin of the Sea of Japan

description: Large earthquakes along the eastern margin of the Sea of Japan, such as the 1983 Central Japan Sea Earthquake (M 7.7) or the 1993 Southwest Off Hokkaido Earthquake (M 7.8) generated tsunamis that reached and caused damage on the east coast of Korea, whereas tsunamis from the recent 2024 Noto Peninsula Earthquake (M 7.6) were much smaller. In this study, we computed tsunamis on the Korean east coast from 60 fault models proposed by a Japanese committee in 2014 (MLIT model). The maximum tsunami height at many locations is produced by the F24 fault (Mw 7.9, corresponding to the 1983 earthquake) and the F17 fault (Mw 7.8, a model of the 1993 earthquake). In addition, the F20 (Mw 7.8), F28 (Mw 7.7), and F30 (Mw 7.8) faults, located off Aomori, Akita, and Yamagata Prefectures, also produce large tsunamis on the Korean coast, because of their fault strike and propagation effects through Yamato Rise. The tsunami heights from fault models of the 1940 Off Shakotan Peninsula Earthquake (F07), the 1964 Niigata Earthquake (F34), and the 2024 Noto Peninsula Earthquake (F43) are smaller, as they are located further to the north or on the continental shelf with shallower water depth.
DOI: 10.6084/m9.figshare.30384692.v1
title: Constraining a high-slip offshore fault area during the 2024 Noto Peninsula earthquake using tsunami inundation data and numerical simulations

description: The 2024 Noto Peninsula earthquake (Mw 7.5) caused significant tsunami inundation along the northeastern coast of the Noto Peninsula in Ishikawa Prefecture, Japan. To investigate the offshore slip distribution, we conducted field surveys and constructed a dataset of tsunami inundation depths. Using this dataset, we evaluated the performance of six previously proposed source fault models – developed based on crustal deformation and tsunami waveform data – in reproducing observed onshore tsunami inundation. Most of the models underestimated the tsunami inundation depth, likely due to insufficient constraints on the offshore slip amount resulting from limited geophysical observations. To address this issue, we introduced high-slip areas into offshore fault segments and tested multiple scenarios. This approach led to substantial improvements in model performance, with an appropriate scenario achieving a geometric mean (<i>K</i>) of 1.32 and a geometric standard deviation (<i>κ</i>) of 1.95. The substantial improvements in model performance demonstrate that tsunami inundation depth data provide a valuable complementary constraint for modeling offshore slip. This constraint is particularly important in areas where direct geophysical observations are scarce and key features of the slip distribution may otherwise go undetected.
DOI: 10.6084/m9.figshare.30384692
title: Constraining a high-slip offshore fault area during the 2024 Noto Peninsula earthquake using tsunami inundation data and numerical simulations

description: The 2024 Noto Peninsula earthquake (Mw 7.5) caused significant tsunami inundation along the northeastern coast of the Noto Peninsula in Ishikawa Prefecture, Japan. To investigate the offshore slip distribution, we conducted field surveys and constructed a dataset of tsunami inundation depths. Using this dataset, we evaluated the performance of six previously proposed source fault models – developed based on crustal deformation and tsunami waveform data – in reproducing observed onshore tsunami inundation. Most of the models underestimated the tsunami inundation depth, likely due to insufficient constraints on the offshore slip amount resulting from limited geophysical observations. To address this issue, we introduced high-slip areas into offshore fault segments and tested multiple scenarios. This approach led to substantial improvements in model performance, with an appropriate scenario achieving a geometric mean (<i>K</i>) of 1.32 and a geometric standard deviation (<i>κ</i>) of 1.95. The substantial improvements in model performance demonstrate that tsunami inundation depth data provide a valuable complementary constraint for modeling offshore slip. This constraint is particularly important in areas where direct geophysical observations are scarce and key features of the slip distribution may otherwise go undetected.
DOI: 10.15468/dl.jcqzd2
title: Occurrence Download

description: A dataset containing 96749 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-73.13829 10.8259,-73.01838 10.62968,-72.5878 11.03574,-72.46789 11.12839,-72.49514 11.2047,-72.68863 11.23877,-73.13829 10.8259))",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 96749 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008394-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/b8fa53
title: James Cook University - Dugong Aerial Survey

description: The Dugong Aerial Survey Database comprises multi-decade dugong aerial survey studies conducted by James Cook University (JCU) across nine broad regions along the Australian coast since 1984. Each survey may cover part of a region, a whole region, or several regions.
Regions include:
 - Shark Bay (WA)
- Exmouth (includes Ningaloo) (WA)
- Pilbara (WA); the Gulf of Carpentaria (NT and QLD)
- Torres Strait (QLD); northern Great Barrier Reef (QLD)
- Southern Great Barrier Reef (QLD)
- Hervey Bay (QLD), and Moreton Bay (QLD) 

It was co-funded by JCU, the Australian Marine Mammal Centre, the Australian Antarctic Division of the Department of Climate Change, Energy, the Environment and Water (formerly Department of the Environment).
JCU and the Memorandum of Understanding on the Conservation and Management of Dugongs (Dugong dugon) and their Habitats throughout their Range (UNEP/CMS) have supported the maintenance and updating of the database in 2022-2024. 

The database project is led by Helene Marsh (TropWATER, JCU), was designed by Steven van der Valk (formerly eResearch Centre, JCU), maintained by Susan Sobtzick (formerly TropWATER, JCU) until 2022 and by Mélanie Hamel (TropWATER, JCU) since 2022.
DOI: 10.5281/zenodo.7995532
title: Data for: "The metatranscriptomic response of the wheat rhizosphere to drought varies with growth stages."

description: Microbes can help plant sustain abiotic stresses, such as drought. Plant-microbe interactions are, however, dynamic and the timing of the stress will affect both partners, directly and indirectly. Here, we wanted to know how the wheat rhizosphere microbiome would respond to drought stress applied at key growth stages. We grew wheat in pots and stopped watering them at stem elongation, booting, or flowering. We then sampled the rhizosphere soil and sequenced its metatranscriptome. The timing of the drought strongly affected the transcriptional response of the microbes, but few transcripts were differentially abundant at all stages. Some common patterns were, however, observed at higher taxonomical or functional levels. Drought also affected the normal succession across wheat growth stages. Many of the transcripts, taxa and functions that varied from one growth stage to the next in the control were not seen under drought. Our results suggest that the timing of the drought event is paramount to the microbial rhizosphere communities, and that it will be difficult to discern any common response to such events.
DOI: 10.15468/dl.jmuvat
title: Occurrence Download

description: A dataset containing 611 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Observation)",
 "Continent is Europe",
 "Country is France",
 "DatasetKey is one of (16 - Inventaire général de la flore et de la fonge - CBNA - inventaire général de la flore et de la fonge réalisé sur le terrain, Données de l'inventaire forestier national de l'IGN-Relevés floristiques du protocole de l'Inventaire National Forestier de l'IGN, Anciennes données CBNBP-Anciennes données Flora CBNBP, Protocole d'inventaire de la flore vasculaire à l'échelle communale-Inventaire de la flore vasculaire par commune, Pl@ntNet automatically identified occurrences, Données issues du portail Sigogne - Bourgogne-Franche-Comté - TAXA - Flore et habitats naturels de Franche-Comté, DIGITALE - Observations flore et habitat centralisées par le CBN de Bailleul-Données d'occurrence taxon (Plantes vasculaires, Bryophytes et Algues) de la région des Hauts-de-France mises au format standard OccTax v3.1 par le CBN de Bailleul en mai 2023 (Données issues de Digitale2 : digitale.cbnbl.org), Observations du Conservatoire botanique national du Bassin parisien., Données acquises par le Conservatoire botanique national du Bassin parisien et son réseau (bénévoles, associations, autres structures professionnelles) - Flore du Bassin parisien (CBNBP), INPN - Données flore des CBN agrégées par la FCBN)",
 "GadmGid is one of (FRA.12.5_1, FRA.10.5_1, FRA.10.1_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Alnus glutinosa",
 "Year 2000-2025"
 ]
}

 The dataset includes 611 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008425-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7tdycs
title: Occurrence Download

description: A dataset containing 861054 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Pakistan",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 861054 records from 599 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008402-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2phtfg
title: CCDC 2487856: Experimental Crystal Structure Determination

description: Related Article: Baldeep Sidhu, Amelia Kacperkiewicz, Jason Braun, David Herbert|2025|Dalton Trans.|54|17211|doi:10.1039/D5DT02202A
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: 10.5517/ccdc.csd.cc2phtgh
title: CCDC 2487857: Experimental Crystal Structure Determination

description: Related Article: Baldeep Sidhu, Amelia Kacperkiewicz, Jason Braun, David Herbert|2025|Dalton Trans.|54|17211|doi:10.1039/D5DT02202A
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: 10.7910/dvn/mzzpuc
title: Replication Data for "The Diagnostic Performance of the Visitect Advanced Disease Point-Of-Care CD4 Platform: A Pragmatic, Mixed-Methods, Multisite Validation, Costing, and Qualitative Analysis"

description: The Visitect CD4 Advanced Disease test (AccuBio, Alva, United Kingdom) is a rapid, semiquantitative assay that estimates CD4 results above or below 200 cells per microliter. We evaluated the performance of the Visitect CD4 assay in semiurban laboratories in Uganda.

We performed a pragmatic laboratory validation of the Visitect CD4 platform in 4 routine HIV clinics in Uganda, nested within a cluster randomized trial evaluating an enhanced package of screening and treatment for persons with advanced HIV disease (NCT05085171). As part of the clinical trial, samples processed on the Visitect CD4 platform were confirmed using another CD4 testing method. We compared the diagnostic performance of the Visitect CD4 platform against the confirmatory method by evaluating the sensitivity, specificity, and positive and negative predictive values.

Of 1495 venous blood samples that were processed both by the Visitect CD4 test and another confirmatory CD4 platform at clinics in Kampala, Uganda, specificity was 81% [95% confidence interval (CI): 79% to 84%] and the positive predictive value was 69% (95% CI: 66% to 73%). There were no samples for which the Visitect test was &gt;200 cells per microliter and the confirmatory test was ≤200 cells per microliter, resulting in a sensitivity of 100%. Among Visitect CD4 tests that were read as ≤200 cells per microliter with confirmatory results &gt;200 cells per microliter, the median confirmatory CD4 result was 397 (IQR, 281-590) cells per microliter. Specificity varied by clinic ranging from 63% to 99%.