cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/g2uzwr
title: Terrestrial Mollusca of Cuc Phuong National Park, Vietnam – Results from the 2019 VIETBIO inventory work. Collection data

description: Collection data of terrestrial Mollusca from the 2019 VIETBIO inventory work in Cuc Phuong National Park, Vietnam.
DOI: 10.5281/zenodo.16779450
title: Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis (MERFISH dataset)

description: Endothelial cells (ECs) are critical regulators of vascular function and exhibit specialized, organ-specific roles across tissues. During aging, these cells become dysfunctional, resulting in increased susceptibility to cardiovascular disease and its associated mortality. While single-cell transcriptomics studies have revealed extensive endothelial heterogeneity across tissues and conditions, a comprehensive atlas of human EC transcriptomes over the course of the adult human lifespan is still lacking. Here, we present the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 ECs from 12 human tissues throughout adulthood. Using HAECA, we identified age-associated transcriptional shifts, including a decline in angiogenic gene expression in venous ECs and widespread alterations in extracellular matrix (ECM)- and mechanotransduction-associated pathways. We validated these findings in aging human skin and further uncovered a p21-linked transcriptional program in ECs, confirmed in both in vitro and in vivo models and linked to cellular senescence. Together, our study provides a high-resolution transcriptome reference across spatial as well as temporal axes of the human endothelium.
DOI: 10.5281/zenodo.16920965
title: Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis (MERFISH dataset)

description: Endothelial cells (ECs) are critical regulators of vascular function and exhibit specialized, organ-specific roles across tissues. During aging, these cells become dysfunctional, resulting in increased susceptibility to cardiovascular disease and its associated mortality. While single-cell transcriptomics studies have revealed extensive endothelial heterogeneity across tissues and conditions, a comprehensive atlas of human EC transcriptomes over the course of the adult human lifespan is still lacking. Here, we present the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 ECs from 12 human tissues throughout adulthood. Using HAECA, we identified age-associated transcriptional shifts, including a decline in angiogenic gene expression in venous ECs and widespread alterations in extracellular matrix (ECM)- and mechanotransduction-associated pathways. We validated these findings in aging human skin and further uncovered a p21-linked transcriptional program in ECs, confirmed in both in vitro and in vivo models and linked to cellular senescence. Together, our study provides a high-resolution transcriptome reference across spatial as well as temporal axes of the human endothelium.
DOI: 10.15468/dl.rw4kv3
title: Occurrence Download

description: A dataset containing 29312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Gaudinia fragilis"
 ]
}

 The dataset includes 29312 records from 778 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028778-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nzjt2n
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Entada abyssinica"
 ]
}

 The dataset includes 64 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028780-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9938r
title: Occurrence Download

description: A dataset containing 8127 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is InboVeg - NICHE-Vlaanderen groundwater related vegetation relevés for Flanders, Belgium"
 ]
}

 The dataset includes 8127 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028782-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtm6pp
title: Occurrence Download

description: A dataset containing 136916 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is INBO collaborator Occurrences of vertebrates recorded in waarnemingen.be in Flanders, Belgium"
 ]
}

 The dataset includes 136916 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028769-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hbxnbt
title: Occurrence Download

description: A dataset containing 1553 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is InboVeg - Amphibious vegetation of shallow lakes at Turnhout"
 ]
}

 The dataset includes 1553 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028781-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16920975
title: Dataset related to article: Spiking Patterns in the Globus Pallidus Highlight Convergent Neural Dynamics across Diverse Genetic Dystonia Syndromes

description: Demographic and clinical data of dystonia scales at different timepoints (before and after DBS implant).
DOI: 10.5281/zenodo.16920974
title: Dataset related to article: Spiking Patterns in the Globus Pallidus Highlight Convergent Neural Dynamics across Diverse Genetic Dystonia Syndromes

description: Demographic and clinical data of dystonia scales at different timepoints (before and after DBS implant).
DOI: 10.7910/dvn/gghnax
title: Metabolomics Dataset

description: Metabolomics and Lipidomics datasets for Inactivating Lipotoxic Ceramides to Treat Cardiomyopathy in Long-Chain Fatty Acid Oxidation Disorders
DOI: 10.5281/zenodo.14620918
title: The European Commission's Understanding of the Term 'Ecosystem': Lessons for Future Enforcement under the Revised Notice on the Definition of the Relevant Market – Atlas.ti reports

description: Dataset is a collection of the uses of the word 'ecosystem' in the Commission's decisions that we analyse in the article The European Commission’s Understanding of the Term ‘Ecosystem’: Lessons for Future Enforcement under the Revised Notice on the Definition of the Relevant Market.

Funding: Joanna Mazur is supported by the research grant of the National Science Centre, Poland (grant number 2024/53/B/HS5/00169).
DOI: 10.5281/zenodo.14620919
title: The European Commission's Understanding of the Term 'Ecosystem': Lessons for Future Enforcement under the Revised Notice on the Definition of the Relevant Market – Atlas.ti reports

description: Dataset is a collection of the uses of the word 'ecosystem' in the Commission's decisions that we analyse in the article The European Commission’s Understanding of the Term ‘Ecosystem’: Lessons for Future Enforcement under the Revised Notice on the Definition of the Relevant Market.

Funding: Joanna Mazur is supported by the research grant of the National Science Centre, Poland (grant number 2024/53/B/HS5/00169).
DOI: 10.17028/rd.lboro.24319237
title: Supplementary information files for: carbon viability of retrofitting office buildings to residential use

description: Supplementary files for article: "Carbon viability of retrofitting office buildings to residential use"<br>The paper evaluates the carbon viability of office-to-residential retrofits. It aims to determine at what point in time a retrofit becomes more carbon-intensive than a theoretical newbuild scenario (with a similar design in the same location), primarily due to enhanced operational performance of the latter. Comparative Life cycle Assessments (LCAs) showed that despite the high embodied carbon savings of the retrofit, the newbuild scenario has a lesser carbon impact overall when considering a typical lifespan of 60–100 years. This was due to the newbuild outperforming the retrofit with regards to lower operational carbon emissions, annulling the initial embodied carbon advantage after 22 years. Considering that LCA is typically conducted for 60–80 years, and that on average a buildings’ lifespan in the UK is 60–100 years, it can be concluded that the retrofit would present a significantly higher carbon footprint over the entire life cycle, when compared to demolition and reconstruction. To address this, the paper also presents recommendations for minimal energy standards for retrofits, which aims to result in significant carbon savings.<br>© The Authors, CC BY-4.0<br>
DOI: 10.17028/rd.lboro.24319237.v1
title: Supplementary information files for: carbon viability of retrofitting office buildings to residential use

description: Supplementary files for article: "Carbon viability of retrofitting office buildings to residential use"<br>The paper evaluates the carbon viability of office-to-residential retrofits. It aims to determine at what point in time a retrofit becomes more carbon-intensive than a theoretical newbuild scenario (with a similar design in the same location), primarily due to enhanced operational performance of the latter. Comparative Life cycle Assessments (LCAs) showed that despite the high embodied carbon savings of the retrofit, the newbuild scenario has a lesser carbon impact overall when considering a typical lifespan of 60–100 years. This was due to the newbuild outperforming the retrofit with regards to lower operational carbon emissions, annulling the initial embodied carbon advantage after 22 years. Considering that LCA is typically conducted for 60–80 years, and that on average a buildings’ lifespan in the UK is 60–100 years, it can be concluded that the retrofit would present a significantly higher carbon footprint over the entire life cycle, when compared to demolition and reconstruction. To address this, the paper also presents recommendations for minimal energy standards for retrofits, which aims to result in significant carbon savings.<br>© The Authors, CC BY-4.0<br>
DOI: 10.15468/dl.4df57r
title: Occurrence Download

description: A dataset containing 185 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvelinus fontinalis",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 185 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028783-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4737m4
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salvelinus fontinalis",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028784-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8z6xbs
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028787-250811113504898/datasets/export for details.
DOI: 10.15468/dl.axd2bk
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028785-250811113504898/datasets/export for details.
DOI: 10.15468/dl.7z8yg9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tephrosia candida",
 "Country is Saint Vincent and the Grenadines",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028786-250811113504898/datasets/export for details.
DOI: 10.15468/dl.sdpeyx
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Invasive plants in Luronium natans habitats in Flanders, Belgium"
 ]
}

 The dataset includes 71 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028788-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13026/637d-3e59
title: Organ Retrieval and Collection of Health Information for Donation (ORCHID)

description: There are well-documented inefficiencies and inequities in the current system
of deceased donor organ transplantation. While much prior research has focused
on designing better allocation systems to distribute donated organs, more can
be done to study organ procurement, the process by which organs are recovered
from deceased donors. Improvements to organ procurement can greatly increase
the supply of a scarce public resource, improving health outcomes for the more
than 100,000 patients currently waiting for an organ transplant. Such changes
will also impact health equity, as a disproportionate number of waitlisted
patients come from marginalized communities. So far, research into organ
procurement has been hamstrung by a lack of transparent data. To address this
pressing issue, we have collected the first ever multi-center dataset on organ
procurement, covering ten years of clinical, financial, and administrative
information from six organ procurement organizations (OPOs). This novel
dataset can be used to identify opportunities to improve current practice,
build tools to help OPOs make better decisions, and recommend policy changes
to increase procurement.
DOI: 10.15468/dl.fn5hqt
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Material citation, Living Specimen, Occurrence evidence)",
 "Geometry POLYGON((-99.1835 19.49643,-98.99835 19.49643,-98.99835 19.64305,-99.1835 19.64305,-99.1835 19.49643))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tillandsia recurvata",
 "Year 2025-2025"
 ]
}

 The dataset includes 42 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028789-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16919347
title: Systematic Enhancer Mapping and Functional Analysis in Zebrafish with Optimized CRISPR Interference

description: Optimization and Application of CRISPRi for Cis-Regulatory Element Analysis in Zebrafish Embryos

 

ATAC-seq

Publicly available ATAC-seq data for wild-type zebrafish embryos at 48 hpf were obtained from the NCBI Sequence Read Archive (SRA) under the following accessions:





SRA run: SRR12435907 (corresponding to SRX8931602)


SRA run: SRR12435908 (corresponding to SRX8931603)


The initial raw data were retrieved using the following command:

SRR12435907_1="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/007/SRR12435907/SRR12435907_1.fastq.gz"SRR12435907_2="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/007/SRR12435907/SRR12435907_2.fastq.gz"

SRR12435908_1="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/008/SRR12435908/SRR12435908_1.fastq.gz"SRR12435908_2="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/008/SRR12435908/SRR12435908_2.fastq.gz"

ATAC-seq data analysis was conducted using the workflow described in the document available at the following link:



ATAC Workflow


 

CUT&Tag

The data processing workflow for CUT&Tag can be found in this file:

./CUT_Tag.sh

 

Hi-C

In this study, we employed the following files as part of the Hi-C data analysis pipeline:

./up_demo_hic_code.sh

 

Other Datasets

The bw, BED, and BEDPE files used in this study have also been uploaded.

 

Contact



Jiulin Chan ( jlchan@shou.edu.cn )

Peng Hu ( penghu@upenn.edu )

Xiaolong Li ( lixllil@163.com )
DOI: 10.15468/dl.yfc9by
title: Occurrence Download

description: A dataset containing 38853 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Invasive species - American bullfrog (Lithobates catesbeianus) in Flanders, Belgium (post 2018)"
 ]
}

 The dataset includes 38853 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028791-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u94f47
title: Occurrence Download

description: A dataset containing 11637 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Invasive species - American bullfrog (Lithobates catesbeianus) in Flanders, Belgium"
 ]
}

 The dataset includes 11637 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028790-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t3sv5d
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028792-250811113504898/datasets/export for details.
DOI: 10.6084/m9.figshare.29925356
title: <b>Novel Gammacoronavirus Species Identified in Poultry from Southern China: A Genomic Characterization</b>

description: Gammacoronaviruses (γ-CoVs) are widespread in avian populations. This study reports the identification and genomic characterization of a novel γ-CoV species, designated DCoV-JX621, from a live poultry market in southern China. The complete genome of DCoV-JX621 is 29,437 nucleotides long with 40.2% GC content and exhibits significant divergence from known coronaviruses, particularly in the spike (S) protein and untranslated regions (UTRs). The 5’ UTR displays low sequence similarity (61.32%) to other DCoVs, while the 3’ UTR contains a conserved octanucleotide motif. Notably, DCoV-JX621 encodes six accessory proteins and harbors an 819-nt region downstream of the N protein with no detectable homology to known γ-CoV proteins. It lacks a functional NSP1 but possesses 14 NSPs similar to Goose coronavirus. Phylogenetic analysis revealed a distinct evolutionary lineage for DCoV-JX621, suggesting its recent emergence through recombination or other evolutionary mechanisms. The discovery of this novel γ-CoV species underscores the ongoing evolution and diversification of gammacoronaviruses in avian species.
DOI: 10.6084/m9.figshare.29925356.v1
title: <b>Novel Gammacoronavirus Species Identified in Poultry from Southern China: A Genomic Characterization</b>

description: Gammacoronaviruses (γ-CoVs) are widespread in avian populations. This study reports the identification and genomic characterization of a novel γ-CoV species, designated DCoV-JX621, from a live poultry market in southern China. The complete genome of DCoV-JX621 is 29,437 nucleotides long with 40.2% GC content and exhibits significant divergence from known coronaviruses, particularly in the spike (S) protein and untranslated regions (UTRs). The 5’ UTR displays low sequence similarity (61.32%) to other DCoVs, while the 3’ UTR contains a conserved octanucleotide motif. Notably, DCoV-JX621 encodes six accessory proteins and harbors an 819-nt region downstream of the N protein with no detectable homology to known γ-CoV proteins. It lacks a functional NSP1 but possesses 14 NSPs similar to Goose coronavirus. Phylogenetic analysis revealed a distinct evolutionary lineage for DCoV-JX621, suggesting its recent emergence through recombination or other evolutionary mechanisms. The discovery of this novel γ-CoV species underscores the ongoing evolution and diversification of gammacoronaviruses in avian species.
DOI: 10.15468/dl.ttejb8
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028793-250811113504898/datasets/export for details.
DOI: 10.15468/dl.txjmap
title: Occurrence Download

description: A dataset containing 216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "TaxonKey is Lysiloma divaricatum"
 ]
}

 The dataset includes 216 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028794-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16921057
title: Recolonisation strategies of early animals in the Avalon (Ediacaran 574 – 560 Ma)

description: Supplementary material and data for "Recolonisation strategies of early animals in the Avalon (Ediacaran 574 – 560 Ma)".
DOI: 10.5281/zenodo.16921058
title: Recolonisation strategies of early animals in the Avalon (Ediacaran 574 – 560 Ma)

description: Supplementary material and data for "Recolonisation strategies of early animals in the Avalon (Ediacaran 574 – 560 Ma)".
DOI: 10.15468/dl.4tzahy
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Material citation, Living Specimen, Occurrence evidence)",
 "Geometry POLYGON((-99.1835 19.49643,-98.99835 19.49643,-98.99835 19.64305,-99.1835 19.64305,-99.1835 19.49643))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tillandsia recurvata",
 "Year 2025-2025"
 ]
}

 The dataset includes 42 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028795-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z8by53
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.654 5.563,-75.578 5.563,-75.578 5.64,-75.654 5.64,-75.654 5.563))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 159 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028796-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.