cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63zb6
title: Intestinal macrophages modulate synucleinopathy along the gut-brain axis

description: We generated a digital spatial profiling (DSP) dataset from duodenal
 myenteric plexus of 3-month-old 3KL and WT mice, analyzing 2–3 ROIs per
 slide across 2 animals per genotype. The dataset comprises expression
 values for 25 proteins, including PD-associated targets, lysosomal and
 autophagy markers, internal housekeeping and background controls.
 Normalized digital counts were obtained per ROI, enabling comparative
 analysis of protein signatures between genotypes at an early stage of
 pathology
description: # Intestinal macrophages modulate synucleinopathy along the gut-brain axis
 Dataset DOI: [10.5061/dryad.12jm63zb6](10.5061/dryad.12jm63zb6) ##
 Description of the data and file structure The dataset was generated using
 digital spatial profiling of duodenal myenteric plexus from 3-month-old
 3KL and WT mice to capture early molecular changes in enteric
 synucleinopathy. These data were collected to assess how early α-synuclein
 pathology correlates with lysosomal stress in the ENS. 5 μm thick FFPE
 sections of the myenteric plexus were deparaffinized and incubated with
 antibodies against bIII-tubulin to select myenteric ganglia as segmented
 ROI, according to the manufacturer’s instructions. Cell nuclei were
 stained with DAPI. Each ROI was manually drawn around myenteric ganglia in
 the myenteric plexus (geometric segments), encompassing both neurons and
 glial cells, resulting in a total of 2-3 analysed ROIs per slide. Each
 slide was incubated with an antibody panel containing antibodies
 conjugated to a unique UV-photocleavable oligonucleotide tag. Selected
 ROIs were individually illuminated with UV light using NanoString's
 GeoMx™ Digital Spatial Profiler System (NanoString Technologies). ###
 Files and variables #### File: GI_HKNorm_Data_Final.xlsx **Description:** 
 ##### Variables * **Genotype**: 3KL vs. WT mice * ME 3KL=
 3KL_55A_24_GI_3mo_scan1_001 3KL_55A_24_GI_3mo_scan1_002
 3KL_55A_24_GI_3mo_scan1_003 3KL56_GI_PD_001 3KL56_GI_PD_002
 3KL56_GI_PD_003 ME WT= WT_292A_32_GI_3mo_scan1_001
 WT_292A_32_GI_3mo_scan1_002 WT_293A_38_GI_3mo_001 WT_293A_38_GI_3mo_002
 WT_293A_38_GI_3mo_003 LP 3KL= 3KL_55A_24_GI_3mo_scan1_004
 3KL_55A_24_GI_3mo_scan1_005 3KL56_GI_PD_004 3KL56_GI_PD_005 LP WT=
 WT_292A_32_GI_3mo_scan1_003 WT_292A_32_GI_3mo_scan1_004
 WT_293A_38_GI_3mo_004 WT_293A_38_GI_3mo_005 * **Protein expression
 values**: normalized digital counts per ROI
DOI: 10.15468/dl.ggeer6
title: Occurrence Download

description: A dataset containing 7357 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sturnira lilium",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 }
 ]
}

 The dataset includes 7357 records from 187 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003904-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3wdzgh
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Anthanassa argentea"
 ]
}

 The dataset includes 44 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003905-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txj6n3
title: Occurrence Download

description: A dataset containing 3063 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sturnira ludovici",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 }
 ]
}

 The dataset includes 3063 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003908-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1jwstqk8h
title: Supplementary data from: Early vertebrate biomineralisation and eye structure determined by synchrotron X-ray analyses of Silurian jawless fish

description: Understanding the origin and early diversification of vertebrates has
 always been a challenge because of the ambiguous and conflicting
 interpretations of the soft-bodied, pre-biomineralisation fossil record.
 Here, we apply synchrotron radiation techniques to Jamoytius and Lasanius,
 two soft-bodied Silurian vertebrates, key taxa for discerning vertebrate
 bone evolution due to highly localised, but debated, biomineralisation. We
 map soft-tissue structures and quantify details of biochemical residue
 impossible to resolve with traditional methods. We present the first
 unequivocal evidence for biomineralised apatitic scales in Jamoytius by
 combining Synchrotron Rapid Scanning X-ray Fluorescence (SRS-XRF) and
 Fourier Transform Infra-Red (FTIR) spectroscopy (elevated Ca 37% and P
 21%). This approach also recovers robust evidence for apatitic
 biomineralisation in Lasanius. Chemical mapping of the optical anatomy of
 Jamoytius recovers a close correlation with Zn and Cu distribution,
 providing evidence for a retinal pigmented epithelium and complex eyes. In
 both taxa, chemical maps reveal original anatomical details not apparent
 in visible light, including potential evidence of other sensory anatomy in
 Jamoytius. Our work resolves long-standing fundamental anatomical debates,
 indicating stem-group origins for bone and complex eyes in vertebrates. We
 highlight the potential of using a powerful combination of analytical
 techniques to unlock otherwise inaccessible data in problematic fossils.
description: # Supplementary data from: Early vertebrate biomineralisation and eye
 structure determined by synchrotron X-ray analyses of Silurian jawless
 fish Dataset DOI:
 [10.5061/dryad.1jwstqk8h](https://doi.org/10.5061/dryad.1jwstqk8h) ##
 Description of the data and file structure This contains additional
 supporting text, images and data. ### Files and variables #### File:
 Reeves_et_al_2025_Supplementary_Information_.pdf
 **Description:** Supplementary Text and Data
DOI: 10.6084/m9.figshare.30655661
title: <b>Global impacts of transportation infrastructure on forest degradation and loss: Datasets</b>

description: The full global input datasets support calculating the Comprehensive Environmental Index (CEI) and quantifying transportation infrastructure impacts on forest degradation and loss—consistent with the analyses in the published Nature Communications paper "Global Impacts of Transportation Infrastructure on Forest Degradation and Loss" (DOI: https://doi.org/10.1038/s41467-026-69150-4). The global study extent is divided into 13,804 grid cells (1 km spatial resolution, World Sinusoidal projection, CRS: ESRI 54008), each processable independently to reproduce key results (e.g., absolute/relative road impacts on forest cover, height, patch density, and NPP). The corresponding Python code (implementing PCA for CEI and GEM-BR method for impact quantification) is publicly accessible on GitHub: https://github.com/DechengZHOU/RoadImpactsForests.git.
DOI: 10.6084/m9.figshare.30655661.v2
title: <b>Global impacts of transportation infrastructure on forest degradation and loss: Datasets</b>

description: The full global input datasets support calculating the Comprehensive Environmental Index (CEI) and quantifying transportation infrastructure impacts on forest degradation and loss—consistent with the analyses in the published Nature Communications paper "Global Impacts of Transportation Infrastructure on Forest Degradation and Loss" (DOI: https://doi.org/10.1038/s41467-026-69150-4). The global study extent is divided into 13,804 grid cells (1 km spatial resolution, World Sinusoidal projection, CRS: ESRI 54008), each processable independently to reproduce key results (e.g., absolute/relative road impacts on forest cover, height, patch density, and NPP). The corresponding Python code (implementing PCA for CEI and GEM-BR method for impact quantification) is publicly accessible on GitHub: https://github.com/DechengZHOU/RoadImpactsForests.git.
DOI: 10.6084/m9.figshare.30655661.v1
title: <b>Global Transportation Infrastructure Impacts on Forest Degradation and Loss: Datasets (Submitted to Nature Communications)</b>

description: The full global input datasets required for calculating the Comprehensive Environmental Index (CEI) and quantifying road impacts on forests. The global study extent is divided into 13,804 grid cells, each of which can be processed independently to reproduce the analyses presented in this publication. The code for implementing these calculations (consistent with the global-scale analyses in the manuscript) is publicly accessible on GitHub: https://github.com/DechengZHOU/RoadImpactsForests.git.
DOI: 10.15468/dl.jreaqj
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Anthanassa frisia"
 ]
}

 The dataset includes 95 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003909-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bcmazf
title: Occurrence Download

description: A dataset containing 4369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Anthanassa texana"
 ]
}

 The dataset includes 4369 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003912-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnzfp5
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Artemisia ordosica"
 ]
}

 The dataset includes 123 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003913-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ga9v3g
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sturnira mordax",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 }
 ]
}

 The dataset includes 145 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003914-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6wfzju
title: Occurrence Download

description: A dataset containing 229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Anthocharis cethura"
 ]
}

 The dataset includes 229 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003917-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/14692602
title: SOLANA Price Data Binance API (2020–Now)
DOI: 10.15468/dl.mejdt8
title: Occurrence Download

description: A dataset containing 594 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sturnira oporaphilum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 }
 ]
}

 The dataset includes 594 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003918-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m7vpzw
title: Occurrence Download

description: A dataset containing 256586 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carcinus maenas"
 ]
}

 The dataset includes 256586 records from 489 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003881-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cxz26g
title: Occurrence Download

description: A dataset containing 13973917 records in GBIF matching the query:
SELECT 
 "gbifid", "taxonkey", "phylum", "class", "order", "eventdate", "datasetkey", "countrycode", "stateprovince", "decimallongitude", "decimallatitude" 
FROM occurrence 
WHERE 
 ("hasgeospatialissues" = 'false') AND 
 ("hascoordinate" = 'true') AND 
 ("occurrencestatus" = 'PRESENT') AND 
 NOT("basisofrecord" IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')) AND 
 ("decimallatitude" &gt;= -90) AND 
 ("decimallatitude" &lt; 27) AND 
 ("decimallongitude" &gt;= -81) AND 
 ("decimallongitude" &lt; -80) AND 
 ("year" &lt;= 2025)

 The dataset's 13973917 records were derived from 1372 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003898-260129131611470/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.27203073.v1
title: Large protein databases reveal structural complementarity and functional locality

description: Recent breakthroughs in protein structure prediction have led to an unprecedented surge in high-quality 3D models, highlighting the need for efficient computational solutions to manage and analyze this wealth of structural data. In our work, we comprehensively examine the structural clusters obtained from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We create a single cohesive low-dimensional representation of the resulting protein space. Our results show that, while each database occupies distinct regions within the protein structure space, they collectively exhibit significant overlap in their functional profiles. High-level biological functions tend to cluster in particular regions, revealing a shared functional landscape despite the diverse sources of data. To facilitate exploration and improve access to our data, we developed an open-access web server. Our findings lay the groundwork for more in-depth studies concerning protein sequence-structure-function relationships, where various biological questions can be asked about taxonomic assignments, environmental factors, or functional specificity.
DOI: 10.6084/m9.figshare.27766323.v1
title: Norman et al. 2019 Perturb-seq

description: Preprocessed CRISPRa Perturb-seq data from Norman et al., 2019 (https://www.science.org/doi/10.1126/science.aax4438) as used in as used in "Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+" (Weinberger et al., 2024).
DOI: 10.6084/m9.figshare.c.3643244_d1.v1
title: Additional file 1 of The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

description: Annotation of Floras 1. The file contains the manual annotation of Salacia erecta, Cucumeropsis mannii, Oxalis, and Basella alba. The file includes identified phenotypes and the mapping to FLOPO. It also highlights missing classes in PATO or PO. (XLSX 24 kb)
DOI: 10.1594/pangaea.116068
title: Total carbon dioxide and total alkalinity at station TT043_20-1
DOI: 10.1594/pangaea.121271
title: Total carbon dioxide and alkalinity at station TT008_5-CTD38
DOI: 10.17632/s99c7tmmmg
title: The inflammatory proteome of hidradenitis suppurativa skin is more expansive than that of psoriasis vulgaris

description: Supplementary material for publication "The inflammatory proteome of hidradenitis suppurativa skin is more expansive than that of psoriasis vulgaris ".
DOI: 10.17632/y56c75gbp5
title: Data for: Data on the agricultural household's dietary diversity and health in the South West geopolitical zone of Nigeria

description: Data was collected through multi stage sampling technique
DOI: 10.6084/m9.figshare.20126543.v2
title: Data, Code, and Results for the Mediation Analysis with Measurement Error Manuscript

description: Data and code used for the Mediation Analysis with Measurement Error Manuscript. Data includes liver tissue gene expression, protein abundance, and genotypes from 192 Diversity Outbred (DO) mice and 116 Collaborative Cross mice; kidney tissue gene expression and genotypes from 188 DO mice; and gene expression and chromatin accessibility from 63 human Lymphoblastoid Cell Lines. Code for simulatng and processing data, running analyses, and producing figures are included.
DOI: 10.6084/m9.figshare.21623802.v1
title: D4 - Coassemblies

description: The samples were clustered by &gt;99% 18S rDNA identity, leading to three clusters that corresponded to the 18S groups 1, 2a and 2b. The reads belonging to each cluster were co-assembled with Spades to form COSAG 1, COSAG 2a and COSAG 2b. The contigs fasta files are included here. <br> Prodigal was used to predict the ORFs and amino acid sequence. The protein fasta and gff3 files are included.
DOI: 10.6084/m9.figshare.24589536.v1
title: GWPD

description: Global Water Pathogen <b>Database</b>
DOI: 10.6084/m9.figshare.25998718.v1
title: Long-Read Sequencing with Oxford Nanopore Technologies of different samples using an improved method for nucleic acid isolation method.

description: <b>The proposed method yields high-purity HMW DNA from complex plant and soil samples. </b>Nucleic acid preparation extracted with SDS/Proteinase K from <i>Zingeria trichopoda</i> and <i>Artemisia vulgaris</i> leaves, which served as an input for HMW DNA purification using the proposed method. <br>barcodes: 71-77:F1 (Artemisia) 71 RB71F2 (Artemisia) 72 RB72P1 (Artemisia) 73 RB73P2 (Artemisia) 74 RB74S1 (soil) 75 RB75Z1 (Zingeria) 76 RB76Z2 (Zingeria) 77 RB77<br>
DOI: 10.1594/pangaea.121254
title: Total carbon dioxide and alkalinity at station TT008_5-CTD21
DOI: 10.1594/pangaea.144820
title: Underway physical oceanography and carbon dioxide measurements during KNORR cruise WOCE_A15-AR15

description: Detailed metadata description of each cruise doi:10.1594/PANGAEA.769638
DOI: 10.17632/8gsjdwtxbx
title: Economic Inequality and Social Capital

description: Raw dataset used in the study of economic inequality and social capital.
DOI: 10.6084/m9.figshare.25375873.v1
title: Data_JBZhang_Nature Geoscience_2024

description: Supplementary Tables 1 to 3
DOI: 10.6084/m9.figshare.29093894.v1
title: Efficient Genome Indexing for Large-Scale Linked Interval Data

description: Efficiently querying specific genomic regions is fundamental in bioinformatics, which allows to extract relevant feature information from large genomic datasets. While existing tools provide query capabilities, they are limited to interval manipulation and do not natively support linked interval data or complex relationship between genomic features. We introduce genogrove, a hybrid graph data structure designed to facilitate scalable interval queries. We demonstrate how it serves as an efficient interval search structure for large-scale datasets and lays the foundation for more advanced genomic analyses, supporting a wide range of applications in bioinformatics.
DOI: 10.1594/pangaea.121317
title: Total carbon dioxide and alkalinity at station TT012_5-CTD23
DOI: 10.1594/pangaea.121326
title: Total carbon dioxide and alkalinity at station TT012_5-CTD38
DOI: 10.6084/m9.figshare.11695653.v1
title: British_India_crudebirthrate.dat from Emergence of oscillations in a simple epidemic model with demographic data

description: A simple susceptible–infectious–removed epidemic model for smallpox, with birth and death rates based on historical data, produces oscillatory dynamics with remarkably accurate periodicity. Stochastic population data cause oscillations to be sustained rather than damped, and data analysis regarding the oscillations provides insights into the same set of population data. Notably, oscillations arise naturally from the model, instead of from a periodic forcing term or other exogenous mechanism that guarantees oscillation: the model has no such mechanism. These emergent natural oscillations display appropriate periodicity for smallpox, even when the model is applied to different locations and populations. The model and datasets, in turn, offer new observations about disease dynamics and solution trajectories. These results call for renewed attention to relatively simple models, in combination with datasets from real outbreaks.
DOI: 10.6084/m9.figshare.12652100.v9
title: Global surface ocean pCO2 from CSIR-ML6 (v2021)

description: An update to the original CSIR-ML6 method. The following changes have been made: <b>- SOCATv2020:</b> ERA5 wind data and MSLP are used (instead of ERA interim).<b>- SOCATv2021:</b> all same data sources, extended to the end of 2020. <br><b>NETCDF FILE</b>sfco2 = surface fugacity of CO2 for the ensemble averagefgco2 = air-sea CO2 fluxes ocean_area = the area per pixel - doubles as mask for the data<br><b>XLS FILES</b>- fluxes annually resampled fluxes (PgC/yr) for global, &gt;30N, 30N - 30S, &lt;30S- areas (km2) for the regions mentioned above<br><b>CITATION</b>Please cite the dataset (doi:10.6084/m9.figshare.12652100) as well as the original publication (doi:10.5194/gmd-12-5113-2019).
DOI: 10.6084/m9.figshare.19297700.v1
title: OvineSNP50 BeadChip of 75 purebred Charollais sheep in China

description: 75 CHA-C individuals, sampled from the Chaomu Breeding Farm, were genotyped using Illumina OvineSNP50 BeadChip
DOI: 10.6084/m9.figshare.20069900.v1
title: Global watershed data

description: We searched within the Web of Science and the Chinese Science Citation Database using the keyword combinations “forest hydrology” AND “runoff OR evapotranspiration OR water yield”. Nearly 3000 papers were found and filtered. In total, we identified 496 watersheds scattered across 36 countries globally.
DOI: 10.6084/m9.figshare.28840514.v2
title: A geospatial dataset of PFOS and PFOA occurrence records in China’s multi-media environments (2021–2024)

description: We provide a comprehensive dataset on the occurrence and distribution of PFOS and PFOA, comprising 2,653 records from 287 publications spanning the period from 2021 to 2024. This dataset offers detailed metadata including ecological categories, detected concentrations, collection methodologies, and geographic coordinates across various administrative levels.
DOI: 10.1594/pangaea.121302
title: Total carbon dioxide and alkalinity at station TT008_7-CTD66
DOI: 10.17632/dxcdgrpnh6
title: Articles on Income Inequality

description: The dataset includes bibliographic information of 7,505 articles of the topic of Income Inequality in the Scopus database