cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18685612
title: Reproducible scRNA-seq PBMC Workflow: Reference, Toy Demonstration Data, and Analysis Outputs

description: Description

This record provides a reproducible, containerized single-cell RNA-seq (scRNA-seq) workflow for peripheral blood mononuclear cell (PBMC) data analysis.

The workflow implements an end-to-end pipeline:





FASTQ quality control (FastQC, MultiQC)




Optional read trimming (Cutadapt)




STARsolo alignment and gene–cell count matrix generation




Seurat-based quality control, normalization, feature selection, clustering, and annotation




Pseudobulk differential expression analysis using DESeq2




Two one-sided tests (TOST) for equivalence testing




Gene set enrichment analysis (GSEA / ORA)




Cell-type–specific co-expression network construction and module enrichment



Execution is managed via Snakemake and Docker to ensure reproducibility and environment consistency. The repository associated with this record contains the complete workflow definition and container configuration.

Contents of Version 2.0.0

This version provides a lightweight demonstration bundle designed to validate workflow execution:





A chromosome 1 (chr1) GRCh38 mini-reference




A pre-built STAR index for chr1




A reduced FASTQ subset (~100,000 reads)




Representative pipeline outputs from a full PBMC run



The toy dataset is intended for rapid testing and reproducibility verification. It runs in approximately 5–10 minutes on a standard workstation after container setup and demonstrates upstream processing through Seurat object creation.

Reproducibility Notes

The full GRCh38 reference genome and annotation files are not included in this archive due to size. Exact reference sources, versions, and configuration details required to reproduce the full analysis are documented in the associated GitHub repository.

The complete workflow, including configuration, container definition, and execution instructions, is available at:

https://github.com/Inkasimo/scRNAseq-pbmc-workflow

This version reflects a stable snapshot of the demonstration data and representative analysis outputs aligned with the corresponding tagged software release.
DOI: 10.48580/dgwpn.v1
title: Description of two new species of the genus Parathyas Lundblad, 1926 (Acari: Hydryphantoidea: Hydryphantidae: Euthyadinae) from China
DOI: 10.48580/dgwpl.v2
title: Cave-dwelling species of Brasineura Silva-Neto & García Aldrete, 2015 (Psocodea: Ptiloneuridae) from southwestern Brazil: new species, wing variation, and new geographic and troglophile status records
DOI: 10.15468/dl.8zdkca
title: Occurrence Download

description: A dataset containing 44167 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lutjanus lutjanus"
 ]
}

 The dataset includes 44167 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028042-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.anrhnx
title: Occurrence Download

description: A dataset containing 46659 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lutjanus apodus"
 ]
}

 The dataset includes 46659 records from 175 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028041-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mh2k4e
title: Occurrence Download

description: A dataset containing 63637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Mormo maura"
 ]
}

 The dataset includes 63637 records from 397 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028011-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hbtvt4
title: Occurrence Download

description: A dataset containing 78508 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ursus arctos"
 ]
}

 The dataset includes 78508 records from 350 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028009-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fppmuc
title: Occurrence Download

description: A dataset containing 2087 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 "Year is 1847"
 ]
}

 The dataset includes 2087 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028043-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17844788
title: SinoBF-1: satellite mapping of every building's function in 109 major cities in China reveals deep built environment disparities

description: The vector files (.shp) of the SinoBF-1 product represent a national-scale, building-level functional map covering 109 major cities in China, created using the Paraformer mapping framework (Paper link), which is available at Paraformer. We processed over 69 TB of satellite data, including 1-meter Google Earth optical imagery, 10-meter nighttime lights (SGDSAT-1), and building height data (CNBH-10m).

The data, method, and analysis have been published by Nature Communications: https://www.nature.com/articles/s41467-026-69589-5

We strongly recommend that users consult the associated paper before downloading or using the SinoBF-1 dataset.

NOTE: Additional related work can be found on the author’s homepage: https://lizhuohong.github.io/lzh/. If you have any questions or technical issues, contact us at zhuohong.li@duke.edu (Zhuohong Li).

User guide:

This version of the dataset includes building-level functional maps of 109 Chinese cities, organized in the ESRI Shapefile format. The .shp file for each city is stored in a “.zip” archive. Each city file is named G_P_C.zip, where:





G indicates the geographical region (South, Central, East, North, Northeast, Northwest, Southwest)




P indicates the provincial administrative region




C indicates the city name



For example, the building functional map for Wuhan City, Hubei Province, is named Central_Hubei_Wuhan.zip.

Furthermore, each shapefile contains building functional types stored in the attribute "Function", with the corresponding building functions listed below:

Value in "Function":



Residential building

Commercial building

Industrial building

Healthcare building

Sport and art building

Educational building

Public service building

Administrative building


Note: Due to Zenodo’s limit of 100 files, the cities in Hubei Province and Hainan Province were grouped into single compressed packages (i.e., Central_Hubei.zip and South_Hainan.zip).
DOI: 10.5281/zenodo.17844789
title: SinoBF-1: satellite mapping of every building's function in 109 major cities in China reveals deep built environment disparities

description: The vector files (.shp) of the SinoBF-1 product represent a national-scale, building-level functional map covering 109 major cities in China, created using the Paraformer mapping framework (Paper link), which is available at Paraformer. We processed over 69 TB of satellite data, including 1-meter Google Earth optical imagery, 10-meter nighttime lights (SGDSAT-1), and building height data (CNBH-10m).

The data, method, and analysis have been published by Nature Communications: https://www.nature.com/articles/s41467-026-69589-5

We strongly recommend that users consult the associated paper before downloading or using the SinoBF-1 dataset.

NOTE: Additional related work can be found on the author’s homepage: https://lizhuohong.github.io/lzh/. If you have any questions or technical issues, contact us at zhuohong.li@duke.edu (Zhuohong Li).

User guide:

This version of the dataset includes building-level functional maps of 109 Chinese cities, organized in the ESRI Shapefile format. The .shp file for each city is stored in a “.zip” archive. Each city file is named G_P_C.zip, where:





G indicates the geographical region (South, Central, East, North, Northeast, Northwest, Southwest)




P indicates the provincial administrative region




C indicates the city name



For example, the building functional map for Wuhan City, Hubei Province, is named Central_Hubei_Wuhan.zip.

Furthermore, each shapefile contains building functional types stored in the attribute "Function", with the corresponding building functions listed below:

Value in "Function":



Residential building

Commercial building

Industrial building

Healthcare building

Sport and art building

Educational building

Public service building

Administrative building


Note: Due to Zenodo’s limit of 100 files, the cities in Hubei Province and Hainan Province were grouped into single compressed packages (i.e., Central_Hubei.zip and South_Hainan.zip).
DOI: 10.5281/zenodo.18685614
title: Table 1 in Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads

description: Table 1. Sequences used in the phylogenetic tree of Cyathodium Kunze ex Lehm., including taxa, vouchers, locations, and GenBank accession numbers. ‘–’ missing data.
TaxonVoucher informationLocalitiesGenBank accessionpsb A- trn Hrbc Lrps4Corsinia coriandrina ISchill 9 (E)PortugalDQ265750DQ286006DQ220680C. coriandrina IILong 35445 (E)ItalyKT793462KT793560KT793710Cronisia fimbriata IPeralta 10276 (E)BrazilKT793463KT793561–C. fimbriata IIPeralta 10272 (E)BrazilKT793464KT793562–C. weddelliiPeralta 10213 (E)BrazilKT793465KT793563–Exormotheca pustulosaSchill 8 (E)PortugalDQ265754DQ286010DQ220684Cyathodium aureonitens IXiang et al. 20160709-98 (HSNU)China, SichuanPQ768093PQ768071PQ768082C. aureonitens IIXiang et al. 20161103-20 (HSNU)China, SichuanPQ768094PQ768072PQ768083C. aureonitens IIIXiang et al. 20161109-39 (HSNU)China, YunnanPQ768095PQ768073PQ768084C. aureonitens IVZhu et al. 20150824-24 (HSNU)China, YunnanPQ768096PQ768074PQ768085C. cavernarum ISalazar Allen 20698 (PMA)Costa RicaKT793467KT793565KT793712C. cavernarum IICuadra, Pacheco & Montenegro (PMA)PanamaKT793468KT793566KT793713C. cavernarum IIIXiang et al. 20161109-46 (HSNU)China, YunnanPQ768097PQ768075PQ768086C. cavernarum IVLong 28255 (E)BangladeshKT793466KT793564KT793711C. foetidissimum ISalazar Allen 20635 (PMA)Costa RicaKJ590868KJ590911KJ590954C. foetidissimum IISalazar Allen et al. 20627 (PMA)Costa RicaKT793469KT793567KT793714C. indicum IXiang et al. 20161107-35 (HSNU)China, YunnanPQ768098PQ768076PQ768087C. indicum IIXiang 20160917-12 (HSNU)China, Yunnan–PQ768077PQ768088C. spruceanumSalazar Allen & Lepiz 20916 (PMA)Costa RicaKT356963KT356973KT356983C. tuberosum IXiang 20160922-31 (HSNU)China, SichuanPQ768099PQ768078PQ768089C. tuberosum IIWei & Shu 20151012-4 (HSNU)China, SichuanPQ768100PQ768079PQ768090C. tuberosum IIILong 30558 (E)NepalDQ265752DQ286008DQ220682C. tuberosum IVYin et al. 20160712-51 (HSNU)China, SichuanPQ768101PQ768080PQ768091C. tuberosum VXiang et al. 20161107-36 (HSNU)China, YunnanPQ768102PQ768081PQ768092
description: Published as part of Xiang, You-Liang, Xu, Hao & Zhu, Rui-Liang, 2026, Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads, pp. 121 in European Journal of Taxonomy 1034 on page 121, DOI: 10.5852/ejt.2026.1034.3145, http://zenodo.org/record/18685583
DOI: 10.5281/zenodo.18685615
title: Table 1 in Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads

description: Table 1. Sequences used in the phylogenetic tree of Cyathodium Kunze ex Lehm., including taxa, vouchers, locations, and GenBank accession numbers. ‘–’ missing data.
TaxonVoucher informationLocalitiesGenBank accessionpsb A- trn Hrbc Lrps4Corsinia coriandrina ISchill 9 (E)PortugalDQ265750DQ286006DQ220680C. coriandrina IILong 35445 (E)ItalyKT793462KT793560KT793710Cronisia fimbriata IPeralta 10276 (E)BrazilKT793463KT793561–C. fimbriata IIPeralta 10272 (E)BrazilKT793464KT793562–C. weddelliiPeralta 10213 (E)BrazilKT793465KT793563–Exormotheca pustulosaSchill 8 (E)PortugalDQ265754DQ286010DQ220684Cyathodium aureonitens IXiang et al. 20160709-98 (HSNU)China, SichuanPQ768093PQ768071PQ768082C. aureonitens IIXiang et al. 20161103-20 (HSNU)China, SichuanPQ768094PQ768072PQ768083C. aureonitens IIIXiang et al. 20161109-39 (HSNU)China, YunnanPQ768095PQ768073PQ768084C. aureonitens IVZhu et al. 20150824-24 (HSNU)China, YunnanPQ768096PQ768074PQ768085C. cavernarum ISalazar Allen 20698 (PMA)Costa RicaKT793467KT793565KT793712C. cavernarum IICuadra, Pacheco & Montenegro (PMA)PanamaKT793468KT793566KT793713C. cavernarum IIIXiang et al. 20161109-46 (HSNU)China, YunnanPQ768097PQ768075PQ768086C. cavernarum IVLong 28255 (E)BangladeshKT793466KT793564KT793711C. foetidissimum ISalazar Allen 20635 (PMA)Costa RicaKJ590868KJ590911KJ590954C. foetidissimum IISalazar Allen et al. 20627 (PMA)Costa RicaKT793469KT793567KT793714C. indicum IXiang et al. 20161107-35 (HSNU)China, YunnanPQ768098PQ768076PQ768087C. indicum IIXiang 20160917-12 (HSNU)China, Yunnan–PQ768077PQ768088C. spruceanumSalazar Allen & Lepiz 20916 (PMA)Costa RicaKT356963KT356973KT356983C. tuberosum IXiang 20160922-31 (HSNU)China, SichuanPQ768099PQ768078PQ768089C. tuberosum IIWei & Shu 20151012-4 (HSNU)China, SichuanPQ768100PQ768079PQ768090C. tuberosum IIILong 30558 (E)NepalDQ265752DQ286008DQ220682C. tuberosum IVYin et al. 20160712-51 (HSNU)China, SichuanPQ768101PQ768080PQ768091C. tuberosum VXiang et al. 20161107-36 (HSNU)China, YunnanPQ768102PQ768081PQ768092
description: Published as part of Xiang, You-Liang, Xu, Hao & Zhu, Rui-Liang, 2026, Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads, pp. 121 in European Journal of Taxonomy 1034 on page 121, DOI: 10.5852/ejt.2026.1034.3145, http://zenodo.org/record/18685583
DOI: 10.5281/zenodo.18685618
title: Table 2 in Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads

description: Table 2. Infraspecific (INT, bold) and interspecific p -distances of psb A- trn H-region, rbc L-region, and rps 4-region (%) of species of Cyathodium Kunze ex Lehm ..
No. and taxonINT1234561. C. aureonitens1.1/1.1/1.6––––––2. C. cavernarum0.8/0.7/0.85.1/5.9/11.4–––––3. C. foetidissimum0/5.7/0.36.2/8.7/16.76.9/9.1/16.6––––4. C. indicumnc/0.3/0.12.4/2.7/6.13.9/5.8/11.75.1/8.1/16.6–––5. C. spruceanumnc/nc/nc6.5/5.6/13.37.0/6.7/13.63.0/0.4/10.55.4/5.3/12.4––6. C. tetrasporanc/nc/nc1.5/2.5/6.34.2/5.5/11.25.6/7.9/16.51.3/1.8/5.65.7/4.7/12.7–7. C. tuberosum1.3/1.4/1.62.9/2.9/5.45.5/6.1/10.05.9/8.5/16.52.4/2.4/4.96.3/5.5/13.21.4/2.0/4.1
description: Published as part of Xiang, You-Liang, Xu, Hao & Zhu, Rui-Liang, 2026, Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads, pp. 124 in European Journal of Taxonomy 1034 on page 124, DOI: 10.5852/ejt.2026.1034.3145, http://zenodo.org/record/18685583
DOI: 10.5281/zenodo.18685619
title: Table 2 in Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads

description: Table 2. Infraspecific (INT, bold) and interspecific p -distances of psb A- trn H-region, rbc L-region, and rps 4-region (%) of species of Cyathodium Kunze ex Lehm ..
No. and taxonINT1234561. C. aureonitens1.1/1.1/1.6––––––2. C. cavernarum0.8/0.7/0.85.1/5.9/11.4–––––3. C. foetidissimum0/5.7/0.36.2/8.7/16.76.9/9.1/16.6––––4. C. indicumnc/0.3/0.12.4/2.7/6.13.9/5.8/11.75.1/8.1/16.6–––5. C. spruceanumnc/nc/nc6.5/5.6/13.37.0/6.7/13.63.0/0.4/10.55.4/5.3/12.4––6. C. tetrasporanc/nc/nc1.5/2.5/6.34.2/5.5/11.25.6/7.9/16.51.3/1.8/5.65.7/4.7/12.7–7. C. tuberosum1.3/1.4/1.62.9/2.9/5.45.5/6.1/10.05.9/8.5/16.52.4/2.4/4.96.3/5.5/13.21.4/2.0/4.1
description: Published as part of Xiang, You-Liang, Xu, Hao & Zhu, Rui-Liang, 2026, Cyathodium tetrasporum (Cyathodiaceae, Marchantiopsida), a new species of liverworts with spores permanently united in tetrads, pp. 124 in European Journal of Taxonomy 1034 on page 124, DOI: 10.5852/ejt.2026.1034.3145, http://zenodo.org/record/18685583
DOI: 10.15468/dl.s5j9ax
title: Occurrence Download

description: A dataset containing 565 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 1900",
 "TaxonKey is Suaeda fruticosa"
 ]
}

 The dataset includes 565 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028045-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6v8db
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "InstitutionCode is PSM",
 "OccurrenceStatus is Present",
 "TaxonKey is Oryctolagus cuniculus"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028044-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e237677v1
title: Transcending COVID-19 barriers to pain care in rural America: Pragmatic comparative effectiveness trial of evidence-based, on-demand, digital behavioral treatments for chronic pain

description: This
randomized comparative effectiveness trial compared two at-home, digital pain-management programs for rural adults
living with chronic pain during and after the COVID-19 pandemic. One
program (<b>painTRAINER</b>) delivered an 8-week behavioral pain-skills curriculum on a regular
screen (phone/computer). The other delivered an 8-week curriculum using <b>skills-based virtual
reality (VR) </b>headsets to create an immersive 3D environment. We enrolled 330 and analyzed 329 participants from from 3 large health networks (Cedars-Sinai Medical Center; the
University of Alabama in Birmingham and its affiliated ENRICH network; Ochsner
Health System) and
randomly assigned each person to one of the two programs. Over 8 weeks,
participants completed brief online surveys about pain (PROMIS-PI, pain
intensity) and distress (including COVID-related anxiety). The primary outcome of this study was to compare the difference in numeric pain score rating between the active VR and comparator 2D arm at week 8 of the intervention. A final Week 12 survey measured coping skill use 4 weeks after the completion of the assigned intervention. <br><br>Clinicaltrials.gov (NCT04933474): https://clinicaltrials.gov/study/NCT04933474.<br>
description: Response Rates: Of 2,804 participants screened, 367 underwent the informed eConsent process and enrolled in the Screening Week. Of these, 329 successfully met inclusion criteria and were randomized to one of two treatment arms.<br><br>All randomized participants provided baseline data. 125 / 161 (77.6%) of individuals randomized to the painTRAINER arm were included in primary ITT analyses compared to 153/168 (91.1%) in the Skills-Based VR arm.
description: Presence of Common Scales: Several Likert-type scales were used and are included in documentation via "Assessments.pdf"
description: The sample contains individuals recruited randomly from patients lists generated by querying participatory health systems and research networks (Cedars-Sinai Medical Center; the University of Alabama in Birmingham and
its affiliated ENRICH network; Ochsner Health System) for individuals meeting inclusion criteria.
description: Individuals aged ≥14 years residing in U.S. rural ZIP codes (Federal Office of Rural Health Policy definition; RUCA 4–10) who can read and write English, have access to a personal computer, tablet, or smartphone, and experience chronic pain from any underlying condition—operationalized via ICD-10 G89.x or one of the 134 chronic overlapping pain condition (COPC) codes as standardized by an expert panel—and reported average pain &gt;3/10 in the prior week..
description: remote sensing; web-based survey;
DOI: 10.6084/m9.figshare.30753135
title: Association of glycemic control and chronic kidney disease with hospitalization in type 2 diabetes in a cross-sectional study in Region Halland

description: To examine the separate associations of glycemic control and chronic kidney disease with hospitalization days over one year in patients with type 2 diabetes (T2D). A cross-sectional study using retrospective data on T2D patients in Region Halland, Sweden, during 2020. Data from the Region Halland database included hospitalizations, emergency visits, primary care encounters, glycemic control, estimated glomerular filtration rate (eGFR), comorbidities, pharmacotherapy and healthcare encounters. Negative binomial regression was used to assess associations with healthcare utilization. A total of 12,689 patients participated, with an average age of 66.0 years (67.1 years for women and 65.2 years for men, <i>p</i> = 0.010). Higher glycated hemoglobin (HbA1c) and elevated blood glucose levels were associated with increased hospitalization days. Relative risks (RRs) for hospitalization days were higher for HbA1c 52–70 mmol/mol (RR 1.08, 95% CI 1.01–1.15) and &gt;70 mmol/mol (RR 1.24, 95% CI 1.12–1.37). Elevated blood glucose levels ≥7.8 mmol/L had an RR of 1.17 (95% CI 1.04–1.32), while &lt;7.8 mmol/L had an RR of 0.85 (95% CI 0.76–0.96). Patients with an eGFR between 30 and 60 mL/min had a RR of hospitalization of 1.35 (95% CI 1.26–1.44) compared to those with an eGFR &gt;60 mL/min. For patients with an eGFR &lt;30 mL/min, the RR of hospitalization was 3.36 (95% CI 3.00–3.77). Both poor glycemic control and decreased kidney function were associated with higher hospitalization rates in T2D patients. These findings emphasize the need for effective management of glycemic control and renal function to reduce the healthcare burden in this patient population.