cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.974788
title: Molecular DOM composition (relative peak intensities) derived from ultra-high resolution mass spectrometry (FT-ICR-MS)

description: We studied dissolved organic matter (DOM) dynamics in a mangrove-fringed estuary in North Brazil, linking DOM composition to redox conditions at its formation sites. By combining molecular analyses with nutrient and trace metal data, we highlight the outwelling of recalcitrant DOM as a significant contributor to coastal carbon storage and present a novel molecular index (ISuP) for distinguishing DOM sources in complex coastal ecosystems. This dataset contains dissolved organic matter (DOM) molecular data from ultrahigh-resolution mass spectrometry (Fourier-transform ion cyclotron resonance mass spectrometer, FT-ICR-MS), molecular indices calculated from the FT-ICR-MS data (ISuP and ITerr) and environmental data, including dissolved organic carbon (DOC), nutrient (NOx and phosphate), and trace metal (Fe,Mn, Ba) data. Water samples were collected along a mangrove-fringed estuary near Bragança in Pará State (Brazil). Furthermore, it contains porewater samples from eight locations in the mangrove forest and tidal water samples from a mangrove creek, as described in Knoke et al. (2024).
description: Samples were analysed with Electrospray ionisation Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS, solariX XR, Bruker Daltonik GmbH, Bremen, Germany) connected to a 15 Tesla superconducting magnet (Bruker Biospin, Wissembourg, France) and with ICBM-OCEAN (https://rhea.icbm.uni-oldenburg.de/geomol/).
DOI: 10.1594/pangaea.51352
title: Calcium carbonate content of sediment core V29-219
DOI: 10.34740/kaggle/dsv/11882913
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.34740/kaggle/dsv/13711975
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.u9zhks
title: Occurrence Download

description: A dataset containing 468 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taxus floridana"
 ]
}

 The dataset includes 468 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029708-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v7vtj8
title: Occurrence Download

description: A dataset containing 450 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Canada",
 "Country is Canada"
 ]
 },
 {
 "and" : [
 "PublishingCountry is one of (Canada)",
 "TaxonKey is one of (Eucephalus [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 450 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029709-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y3vmd5
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taxus florinii"
 ]
}

 The dataset includes 60 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029710-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57830/2314569
title: Field data for the Vegetation Mapping Inventory Project of Great Smoky Mountains National Park - Open Format Data Package (1997-2002)

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Great Smoky Mountains National Park.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314570
title: Field data for the Vegetation Mapping Inventory Project of Great Smoky Mountains National Park - Open Format Data Package (2016-2019)

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Great Smoky Mountains National Park.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.5281/zenodo.17594928
title: Data in Hirauchi et al., 2025, submitted to J. Geophys. Res. Solid Earth

description: This is an archive of structural measurement data in Hirauchi et al., 2025, submitted to Journal of Geophysical Research: Solid Earth.
DOI: 10.5281/zenodo.17594929
title: Data in Hirauchi et al., 2025, submitted to J. Geophys. Res. Solid Earth

description: This is an archive of structural measurement data in Hirauchi et al., 2025, submitted to Journal of Geophysical Research: Solid Earth.
DOI: 10.15468/dl.zq82ch
title: Occurrence Download

description: A dataset containing 52979 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "TaxonKey is Chromista"
 ]
}

 The dataset includes 52979 records from 133 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029693-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57830/2314572
title: Field data for the Vegetation Mapping Inventory Project of Guilford Courthouse National Military Park - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Guilford Courthouse National Military Park.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314573
title: Field data for the Vegetation Mapping Inventory Project of Gulf Islands National Seashore - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Gulf Islands National Seashore.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.15468/dl.dsq3bn
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera filicifolia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 156 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029711-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17594957
title: A Conceptual Framework for an Innovative Hybrid Ocean Energy Harvesting Technology: Harnessing Waves, Tides, Thermal Gradients, and Salinity for Sustainable, Stable, and Cost-Effective Electricity Generation

description: This paper presents a rigorous conceptual framework for a hybrid ocean energy harvesting system (HOEHS) that integrates wave, tidal, closed-cycle ocean thermal energy conversion (OTEC), and salinity gradient (blue) energy technologies, integrated with reverse osmosis (RO) desalination for salinity sourcing. Leveraging bio-inspired nanomaterials for corrosion and biofouling mitigation in hypersaline environments, AI-driven reinforcement learning (RL) control with a multi-objective function optimizes net power output, minimizes structural stress, and ensures grid stability. Multi-physics modeling incorporates advanced derivations for coupled energy flux, stochastic wave spectra, net OTEC accounting for 35% parasitic losses, and hybrid efficiency η_HOEHS > 30%. A reproducible Python simulation, verified via numerical integration against ECMWF reanalysis data, projects mean power of 5.1 kW and capacity factor (CF) of 25.4% under Red Sea conditions (H_s ~ 0.5-1.5 m, ΔT=12°C, ΔS=70 psu), incorporating dynamic variations in tidal cycles, seasonal thermal gradients, and wave statistics with FSI corrections. Supported by Monte Carlo sensitivity analysis (σ_P / μ_P = 12%), Gaussian process-based Bayesian inference for parameter posterior estimation (MAP H_s=0.9 m, 95% CI: 0.7--1.1 m), epistemic uncertainty quantification via KL divergence (0.12 nats), and model form uncertainty assessment via ensemble CFD-BEM comparisons (bias <5%). Popperian falsifiability criteria (reject if CF <20% at p<0.05). Red Sea-specific environmental mitigations include deep OTEC discharge and nanomaterial coatings. Grid integration via unified power converters and hydraulic storage ensures IEEE 1547 compliance. A phased roadmap projects LCOE <$0.10/kWh by 2035, driven by 30% OPEX reductions from predictive AI maintenance and durable composites. This framework advances sustainable ocean energy, addressing intermittency with unprecedented depth and precision, extendable to Gulf of Aden applications, with potential to unlock 2--4 TW global ocean renewables for decarbonization.
DOI: 10.57830/2314574
title: Field data for the Vegetation Mapping Inventory Project of Guadalupe Mountains National Park - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Guadalupe Mountains National Park.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314575
title: Field data for the Vegetation Mapping Inventory Project of George Washington Carver National Monument - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of George Washington Carver National Monument.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314576
title: Field data for the Vegetation Mapping Inventory Project of Hagerman Fossil Beds National Monument - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Hagerman Fossil Beds National Monument.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314580
title: Field data for the Vegetation Mapping Inventory Project of Haleakala National Park - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Haleakala National Park.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314581
title: Field data for the Vegetation Mapping Inventory Project of Hawaii Volcanoes National Park - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Hawaii Volcanoes National Park.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314582
title: Field data for the Vegetation Mapping Inventory Project of Herbert Hoover National Historic Site - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Herbert Hoover National Historic Site.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.57830/2314583
title: Field data for the Vegetation Mapping Inventory Project of Horseshoe Bend National Military Park - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Horseshoe Bend National Military Park.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.15468/dl.478epc
title: Occurrence Download

description: A dataset containing 286142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Apis mellifera"
 ]
}

 The dataset includes 286142 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029700-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vygh26
title: Occurrence Download

description: A dataset containing 1055 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hypostomus plecostomus"
 ]
}

 The dataset includes 1055 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029713-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17594747
title: inferring cellular communication through mapping cells in space using Tangram 2 | Reproducibility Dataset

description: This record provides the data artifacts that support Huang et al., 2025, “Inferring cellular communication through mapping cells in space using Tangram 2” (preprint: https://doi.org/10.1101/2025.09.28.679077). It includes real and simulated single-cell and spatial transcriptomics resources used to reproduce the figures and results in the paper.

Contents





Curated inputs from publicly available single-cell and spatial datasets (referenced by their original repository DOIs/accessions).




Tangram 2 analysis outputs required to regenerate the main and extended figures (e.g., preprocessed matrices, mappings, interaction/communication scores, and figure-level source data tables).




Simulation configurations, seeds, and generated synthetic datasets used for benchmarks and ablations.



Data sources (public inputs)No new primary human-subject data were collected. Public datasets used in this study include:





Slide-tags tonsil snRNA-seq (Broad SCP2169): https://singlecell.broadinstitute.org/single_cell/study/SCP2169/slide-tags-snrna-seq-on-human-tonsil




Cell cultures (GEO GSE135382): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135382




Colon collection (CELLxGENE): https://cellxgene.cziscience.com/collections/4fa07e63-f712-4d8c-b885-2c515b5e2743




Lymph node (10x Visium): https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Human_Lymph_Node




Lymphoid scRNA-seq (cell2location): https://cell2location.cog.sanger.ac.uk/paper/integrated_lymphoid_organ_scrna/RegressionNBV4Torch_57covariates_73260cells_10237genes/sc.h5ad




Cutaneous squamous cell carcinoma (GEO GSE144240): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144240




Breast cancer atlas (Zenodo 4739739): https://zenodo.org/records/4739739




TCGA Lung Squamous Cell Carcinoma (cBioPortal): https://www.cbioportal.org/study/summary?id=lusc_tcga_pan_can_atlas_2018




TCGA Head & Neck Squamous Cell Carcinoma (cBioPortal): https://www.cbioportal.org/study/summary?id=hnsc_tcga_pan_can_atlas_2018




TCGA Skin Cutaneous Melanoma (cBioPortal): https://www.cbioportal.org/study/summary?id=skcm_tcga_pan_can_atlas_2018




Breast dataset (CELLxGENE): https://cellxgene.cziscience.com/e/9fddb063-056d-4202-8b8a-4b0ee531d3ce.cxg/



Reproducibility





The analysis code and exact workflow to regenerate all results are available at: https://github.com/Genentech/tangram2. Environment files and step-by-step instructions are provided there.
DOI: 10.5281/zenodo.17594748
title: inferring cellular communication through mapping cells in space using Tangram 2 | Reproducibility Dataset

description: This record provides the data artifacts that support Huang et al., 2025, “Inferring cellular communication through mapping cells in space using Tangram 2” (preprint: https://doi.org/10.1101/2025.09.28.679077). It includes real and simulated single-cell and spatial transcriptomics resources used to reproduce the figures and results in the paper.

Contents





Curated inputs from publicly available single-cell and spatial datasets (referenced by their original repository DOIs/accessions).




Tangram 2 analysis outputs required to regenerate the main and extended figures (e.g., preprocessed matrices, mappings, interaction/communication scores, and figure-level source data tables).




Simulation configurations, seeds, and generated synthetic datasets used for benchmarks and ablations.



Data sources (public inputs)No new primary human-subject data were collected. Public datasets used in this study include:





Slide-tags tonsil snRNA-seq (Broad SCP2169): https://singlecell.broadinstitute.org/single_cell/study/SCP2169/slide-tags-snrna-seq-on-human-tonsil




Cell cultures (GEO GSE135382): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135382




Colon collection (CELLxGENE): https://cellxgene.cziscience.com/collections/4fa07e63-f712-4d8c-b885-2c515b5e2743




Lymph node (10x Visium): https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Human_Lymph_Node




Lymphoid scRNA-seq (cell2location): https://cell2location.cog.sanger.ac.uk/paper/integrated_lymphoid_organ_scrna/RegressionNBV4Torch_57covariates_73260cells_10237genes/sc.h5ad




Cutaneous squamous cell carcinoma (GEO GSE144240): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144240




Breast cancer atlas (Zenodo 4739739): https://zenodo.org/records/4739739




TCGA Lung Squamous Cell Carcinoma (cBioPortal): https://www.cbioportal.org/study/summary?id=lusc_tcga_pan_can_atlas_2018




TCGA Head & Neck Squamous Cell Carcinoma (cBioPortal): https://www.cbioportal.org/study/summary?id=hnsc_tcga_pan_can_atlas_2018




TCGA Skin Cutaneous Melanoma (cBioPortal): https://www.cbioportal.org/study/summary?id=skcm_tcga_pan_can_atlas_2018




Breast dataset (CELLxGENE): https://cellxgene.cziscience.com/e/9fddb063-056d-4202-8b8a-4b0ee531d3ce.cxg/



Reproducibility





The analysis code and exact workflow to regenerate all results are available at: https://github.com/Genentech/tangram2. Environment files and step-by-step instructions are provided there.
DOI: 10.15468/dl.anb75q
title: Occurrence Download

description: A dataset containing 244863 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((639.53444 43.4577,639.76068 43.33165,640.00357 43.4577,640.00357 43.77976,639.76217 43.78492,639.53444 43.77976,639.53444 43.4577))",
 "Year 2024-2025"
 ]
}

 The dataset includes 244863 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029705-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/ocgrca
title: Replication Data for: Market Design in Regulated Health Insurance Markets: Risk Adjustment vs. Subsidies

description: This is the replication package for "Market Design in Regulated Health Insurance Markets: Risk Adjustment vs. Subsidies," accepted in 2025 by the Journal of Political Economy Microeconomics.
DOI: 10.15468/dl.q4z5uf
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursera fragilis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 54 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029714-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57830/2314584
title: Field data for the Vegetation Mapping Inventory Project of Grand Portage National Monument - Open Format Data Package

description: These data were converted from the originally delivered Microsoft Access PLOTs database from the Vegetation Mapping Inventory Project of Grand Portage National Monument.  These comma-delimited data tables contain(s) vegetation mapping plot classification and accuracy assessment data, as well as summary information about the data itself. If a table is empty, then it was empty in the original database.
DOI: 10.15468/dl.nfshgy
title: Occurrence Download

description: A dataset containing 487327 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "GadmGid is one of (COL.30.22_2)"
 ]
}

 The dataset includes 487327 records from 189 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029702-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3a249z
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is October",
 "TaxonKey is Dismorphia amphione",
 "Year 2025-2025"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029715-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yradby
title: Occurrence Download

description: A dataset containing 41795878 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 41795878 records from 5084 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029699-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.