cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12797059
title: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)

description: Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.

 

This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.

 

Baylor Scott and White (BSW) cohort: 10x.visium.tar.gz, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital. 

Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available. 

 

For Georgia validation cohort, 400 genes used for validation of ESG signatures (associated with BA-Community 1 and WA-Community-1) were obtained and provided by Ritu Aneja's lab. These 400 genes' spot-based expression data across Black and White TNBC patients are provided. See file georgia.validation.visium.tar.gz. Expression was normalized by total counts per spot, followed by log-normalization by Giotto.

 

As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. GSM_giotto_processed.tar.gz refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.
DOI: 10.5281/zenodo.12797060
title: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC

description: Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.

 

This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.

Ritu: ritu.tar.gz file, containing 12 patients with TNBC from University of Alabama hospital. MB1-6 are AA patients (African American). MB7-12 are EA patients (European American).

Baylor: 10x.visium.tar.gz, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital. 

Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available.
DOI: 10.5281/zenodo.15247064
title: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)

description: Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.

 

This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.

 

Baylor Scott and White (BSW) cohort: 10x.visium.tar.gz, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital. 

Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available. 

For Georgia cohort used in the paper, the data was generated by our collaborator Ritu Aneja. Please request from her the permission to download and use the data.

 

As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. GSM_giotto_processed.tar.gz refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.
DOI: 10.5281/zenodo.15252874
title: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)

description: Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.

 

This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.

 

Baylor Scott and White (BSW) cohort: 10x.visium.tar.gz, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital. 

Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available. 

 

For Georgia validation cohort, 400 genes used for validation of ESG signatures (associated with BA-Community 1 and WA-Community-1) were obtained and provided by Ritu Aneja's lab. These 400 genes' spot-based expression data across Black and White TNBC patients are provided. See file georgia.validation.visium.tar.gz. Expression was normalized by total counts per spot, followed by log-normalization by Giotto.

 

As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. GSM_giotto_processed.tar.gz refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.
DOI: 10.48580/d42dg.v82
title: Resurrection of Crypturgus subcribrosus Eggers 1933 stat. n., and its close phylogenetic relationship to Nearctic Crypturgus (Coleoptera, Scolytinae)
DOI: 10.48580/d42dk.v83
title: Description of a new species of Paraxenylla (Collembola, Hypogastruridae) from Brazil, with comments on the genus
DOI: 10.48580/d42dl.v79
title: Descriptions of larvae of the tribe Hyperini (Coleoptera: Curculionidae): III. Mature larvae of the genus Donus Jekel, 1865
DOI: 10.48580/d42df.v82
title: The tribe Lepturini in South America (Coleoptera: Cerambycidae: Lepturinae)
DOI: 10.48580/d42dh.v86
title: Redescription of four Polish Endonura Cassagnau, 1979 (Collembola, Neanuridae, Neanurinae), with a nomenclature of the ventral chaetae of antennae
DOI: 10.48580/d42d4.v79
title: The southernmost South American record of the genus Halicyclops Norman, 1903 (Cyclopoida: Cyclopidae) with the description of a new species
DOI: 10.48580/d42d6.v85
title: Montealtosuchus arrudacamposi, a new peirosaurid crocodile (Mesoeucrocodylia) from the Late Cretaceous Adamantina Formation of Brazil
DOI: 10.48580/d42db.v86
title: A systematic study of the genus Matsumuraeses Issiki from China (Lepidoptera: Tortricidae: Olethreutinae)
DOI: 10.48580/d42d3.v81
title: A review of the genus Forficuloecus Conci (Phthiraptera: Philopteridae) from parrots (Psittaciformes: Psittacidae), with descriptions of four new species
DOI: 10.48580/d42dd.v77
title: A new species of Xestocoris Van Duzee, with comments on the genus (Hemiptera: Heteroptera: Rhyparochromidae: Rhyparochrominae)
DOI: 10.48580/d42cv.v80
title: New Venezuelan genus of Hubardiidae (Arachnida: Schizomida)
DOI: 10.48580/d42cw.v82
title: A redescription of Leptodactylus jolyi Sazima and Bokermann (Anura, Leptodactylidae) and the recognition of a new closely related species
DOI: 10.48580/d42cz.v81
title: Edwardsiid sea anemones of California (Cnidaria: Actiniaria: Edwardsiidae), with descriptions of eight new species
DOI: 10.48580/d42cp.v80
title: Heteromolpadia joyceae, a new species of sea cucumber from New Zealand, with a key to New Zealand Molpadiidae (Echinodermata: Holothuroidea: Molpadiida)
DOI: 10.48580/d42ct.v81
title: Review of Cermatobius Haase, 1885 (Chilopoda: Henicopidae) of China and Neotype Designation for Cermatobius longicornis (Takakuwa, 1939)
DOI: 10.48580/d42cl.v86
title: A new species of Leptodactylus Fitzinger (Anura, Leptodactylidae) from Serra do Brigadeiro, State of Minas Gerais, Southeastern Brazil
DOI: 10.48580/d42cm.v80
title: Botia udomritthiruji, a new species of botiid loach from southern Myanmar (Teleostei: Botiidae)
DOI: 10.48580/d42cn.v77
title: Two new spider species of the genera Aysenia and Aysenoides from southern Chile and Argentina: description and phylogenetic relationships (Araneae: Anyphaenidae, Amaurobioidinae)
DOI: 10.48580/d42c8.v79
title: Taxonomic notes and new records of the genus Sphingonaepiopsis Wallengren, 1858 (Lepidoptera: Sphingidae) in Iran
DOI: 10.48580/d42c9.v79
title: Melvicalathis, a new brachiopod genus (Terebratulida: Chlidonophoridae) from deep sea volcanic substrates, and the biogeographic significance of the mid­ocean ridge system *
DOI: 10.48580/d42ch.v84
title: A new Satsuma species (Pulmonata: Camaenidae) endemic to Taiwan
DOI: 10.48580/d42cj.v79
title: On the validity of Stegoloxodon Kretzoi, 1950 (Mammalia: Proboscidea)
DOI: 10.48580/d42ck.v81
title: Akysis pulvinatus, a new species of catfish (Siluriformes: Akysidae) from southern Thailand
DOI: 10.48580/d42c4.v80
title: A new species of deep-water spider crab of the genus Rochinia A. Milne-Edwards, 1875, from Guam (Crustacea: Brachyura: Majidae)
DOI: 10.48580/d42c5.v83
title: New Acanthomeniidae (Solenogastres, Cavibelonia) from the abyssal Angola Basin *
DOI: 10.48580/d42c6.v85
title: A new species of Hemigrammus Gill, 1858 (Characiformes: Characidae) from Río Caura, Venezuela
DOI: 10.48580/d42bx.v82
title: Catalog of the types of Staphylinidae (Insecta, Coleoptera) deposited at Museo de La Plata (Argentina)
DOI: 10.48580/d42c2.v79
title: Sulabanus gen. nov., a new genus of Lycidae (Coleoptera) from Sulawesi
DOI: 10.48580/d42bw.v79
title: Argestes angolaensis sp. nov. (Copepoda: Harpacticoida: Argestidae) from the Angola Basin (Southeast Atlantic), and the phylogenetic characterization of the taxon Argestes Sars, including the redescription of A. mollis Sars, 1910, and A. reductus (Itô, 1983) *
DOI: 10.48580/d42by.v81
title: First discovery of a new species of Newmanella Ross, 1969 (Balanomorpha: Tetraclitidae) in the western Pacific, with a note on the new status of Neonrosella Jones, 2010
DOI: 10.48580/d42bz.v81
title: A summary of reports of abyssal and hadal Monoplacophora and Polyplacophora (Mollusca) *
DOI: 10.5281/zenodo.18668042
title: MultiPhysio-HRC: Multimodal Physiological Signals Dataset for industrial Human-Robot Collaboration

description: MultiPhysio-HRC is a multimodal dataset collected to study mental state perception in industrial Human–Robot Collaboration (HRC) scenarios. The dataset includes synchronized physiological, audio, and facial data acquired during controlled cognitive tasks, immersive virtual reality experiences, and real-world industrial disassembly tasks performed both manually and in collaboration with a robot. Recorded modalities include EEG, ECG, electrodermal activity (EDA), respiration (RESP), electromyography (EMG), together with voice recordings and facial action units. Ground-truth annotations were obtained using validated self-assessment questionnaires, including STAI-Y1, NASA-TLX, SAM, and NARS, enabling the study of stress, cognitive load, and affective states. MultiPhysio-HRC is designed to support research in affective computing, multimodal learning, and human-aware robotics, and to foster the development of adaptive robotic systems aligned with the human-centric vision of Industry 5.0.The dataset documentation, structure, and feature descriptions are provided in the accompanying README.
DOI: 10.5281/zenodo.18668043
title: MultiPhysio-HRC: Multimodal Physiological Signals Dataset for industrial Human-Robot Collaboration

description: MultiPhysio-HRC is a multimodal dataset collected to study mental state perception in industrial Human–Robot Collaboration (HRC) scenarios. The dataset includes synchronized physiological, audio, and facial data acquired during controlled cognitive tasks, immersive virtual reality experiences, and real-world industrial disassembly tasks performed both manually and in collaboration with a robot. Recorded modalities include EEG, ECG, electrodermal activity (EDA), respiration (RESP), electromyography (EMG), together with voice recordings and facial action units. Ground-truth annotations were obtained using validated self-assessment questionnaires, including STAI-Y1, NASA-TLX, SAM, and NARS, enabling the study of stress, cognitive load, and affective states. MultiPhysio-HRC is designed to support research in affective computing, multimodal learning, and human-aware robotics, and to foster the development of adaptive robotic systems aligned with the human-centric vision of Industry 5.0.The dataset documentation, structure, and feature descriptions are provided in the accompanying README.
DOI: 10.48580/d42bn.v81
title: A new species of deep­sea Tegastidae (Crustacea: Copepoda: Harpacticoida) from 9 ° 50´N on the East Pacific Rise, with remarks on its ecology *
DOI: 10.48580/d42bs.v79
title: Description of Luciola aquatilis sp. nov., a new aquatic firefly (Coleoptera: Lampyridae: Luciolinae) from Thailand
DOI: 10.48580/d42bt.v79
title: A new species of Ischnomesidae (Crustacea: Isopoda) from the Southern Ocean, Stylomesus weddellensis sp. nov.
DOI: 10.48580/d42bv.v78
title: A new species and first stage associations in Crinitella (Ephemeroptera: Ephemerellidae: Ephemerellinae)
DOI: 10.48580/d42bg.v81
title: A new species of S cinax (Anura, Hylidae) of the S. ruber clade from Minas Gerais, Brazil
DOI: 10.48580/d42bh.v81
title: First record of the genus Pseudomesochra T. Scott (Harpacticoida: Pseudotachidiidae) in the South Atlantic with description of a deep­sea species: Pseudomesochra longiseta sp. nov. *
DOI: 10.48580/d42bj.v77
title: Shallow-water reef ophiuroids (Echinodermata: Ophiuroidea) of Réunion (Mascarene Islands), with biogeographic considerations
DOI: 10.48580/d42bb.v79
title: Genetic and morphological differentiation of Mosor rock lizards, Dinarolacerta mosorensis (Kolombatović, 1886), with the description of a new species from the Prokletije Mountain Massif (Montenegro) (Squamata: Lacertidae)
DOI: 10.48580/d42bc.v81
title: Breaking molds: Oswaldella laertesi, sp. nov., a unique Antarctic species of Oswaldella Stechow, 1919 (Cnidaria: Hydrozoa: Kirchenpaueriidae)
DOI: 10.48580/d42b6.v90
title: Euconnus octosetosus Franz transferred to Plaumanniola Costa Lima: implications for the systematics of Scydmaeninae (Coleoptera: Staphylinidae)
DOI: 10.48580/d42b7.v79
title: Taxonomic status and ecology of Oriental Pheretima darnleiensis (Fletcher, 1886) and other earthworms (Oligochaeta: Megascolecidae) from Mt Kinabalu, Borneo
DOI: 10.48580/d42b9.v88
title: New species of Bairdioidea (Crustacea, Ostracoda) from the Southern Ocean and discussions on Bairdoppilata simplex (Brady, 1880),? Bairdoppilata labiata (Müller, 1908) and Bythopussella aculeata (Müller, 1908) *
DOI: 10.15468/dl.3tcvmr
title: Occurrence Download

description: A dataset containing 545 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Actinocladum McClure ex Soderstr."
 ]
}

 The dataset includes 545 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007745-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pm4ta7
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "InstitutionCode is one of (magnt, nhmuk, fmnh, sama, csiro, am, nmv)",
 "TaxonKey is Chaenocephalus aceratus (Lönnberg, 1906)"
 ]
}

 The dataset's 1 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001403-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7yhqsw
title: Occurrence Download

description: A dataset containing 353 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Anthoscopus parvulus",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 353 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061838-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2zxv8
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adesmia araucana Phil."
 ]
}

 The dataset includes 12 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001426-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s8ghd8
title: Occurrence Download

description: A dataset containing 3493 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Human Observation, Observation)",
 "Country is one of (China, Hong Kong, Macao)",
 "TaxonKey is Platalea leucorodia Linnaeus, 1758"
 ]
}

 The dataset includes 3493 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002794-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2p27cw
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alcea longipedicellata Rilke"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007747-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97zvq6
title: Occurrence Download

description: A dataset containing 32257 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Anthracoceros albirostris",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 32257 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061843-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f94ubs
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alcea mozaffarianii Ghahr., Pakravan & Assadi"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007754-230224095556074/datasets/export for details.
DOI: 10.15468/dl.9dxxnu
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aeschynanthus obovatus C.B.Clarke"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002837-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hg254k
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adesmia candida Hook.f."
 ]
}

 The dataset includes 58 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001457-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.