cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25357988.v1
title: Additional file 2 of Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations

description: Additional file 2: Table S1. Symmetric f4-statistic testing. Table S2. Pairwise qpWave results indicated the genetic heterozygosity between GPH and East Asians. Table S3. Identification of modern Northern ancestral sources in the form of f4(reference populations, GPH; Northern ancestral sources, Mbuti). Table S4. Modern ancestral uniqueness of GPH determined by f4-statistic in the form f4(Northern ancestral sources, GPH; reference populations, Mbuti). Table S5. Pairwise qpWave results confirmed the genetic heterozygosity between GPH and ancestral sources in the distal qpAdm model. Table S6. Comparing genetic homogeneity between GPH and ancestral surrogate populations used in proximal qpAdm model using qpWave. Table S7. The three-population mixing model of GPH inferred by qpAdm. Table S8. Admixture times inferred from ALDER for GPH. Table S9. The population-specific adaptive signals using PBS in the form of (GPH/Miao/Yao/Zhuang/Sui/Jing_Guangxi-Han_Changchun-European). Table S10. The result of XPEHH of GXZ. Table S11. Frequency distribution of the three loci of FADS in ancient East Asians. Table S12. The regional-specific adaptive signals in the form of (GPH-Jing/Miao/Sui/Yao/Zhuang_Guangxi-Han_Changchun) using PBS.
DOI: 10.6084/m9.figshare.25357989
title: Additional file 2 of Resident-, prescriber-, and facility-level factors associated with antibiotic use in long-term care facilities: a systematic review of quantitative studies

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.25357989.v1
title: Additional file 2 of Resident-, prescriber-, and facility-level factors associated with antibiotic use in long-term care facilities: a systematic review of quantitative studies

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26689829
title: Additional file 3 of Resident-, prescriber-, and facility-level factors associated with antibiotic use in long-term care facilities: a systematic review of quantitative studies

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26689829.v1
title: Additional file 3 of Resident-, prescriber-, and facility-level factors associated with antibiotic use in long-term care facilities: a systematic review of quantitative studies

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.25357868
title: Additional file 1 of Clinical and genetic studies for a cohort of patients with congenital stationary night blindness

description: Supplementary Material 1: Links of fastq data
DOI: 10.6084/m9.figshare.25357868.v1
title: Additional file 1 of Clinical and genetic studies for a cohort of patients with congenital stationary night blindness

description: Supplementary Material 1: Links of fastq data
DOI: 10.15468/dl.avxppy
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mozambique",
 "OccurrenceStatus is Present",
 "TaxonKey is Monanthotaxis trichantha (Diels) Verdc."
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072850-240626123714530/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.26690021
title: Additional file 6 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.26690021.v1
title: Additional file 6 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.26690024
title: Additional file 7 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.26690024.v1
title: Additional file 7 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.26690030
title: Additional file 9 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 9
DOI: 10.6084/m9.figshare.26690030.v1
title: Additional file 9 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 9
DOI: 10.6084/m9.figshare.26690033
title: Additional file 10 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 10
DOI: 10.6084/m9.figshare.26690033.v1
title: Additional file 10 of KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome

description: Supplementary Material 10
DOI: 10.15468/dl.7m94ky
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Penicillium nucicola Visagie, Malloch & Seifert"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002243-250214102907787/datasets/export for details.
DOI: 10.15468/dl.gumupf
title: Occurrence Download

description: A dataset containing 1795 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Schistocerca gregaria (Forskål, 1775)"
 ]
}

 The dataset includes 1795 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002244-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q7qjc8
title: Occurrence Download

description: A dataset containing 219 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Prosopis cineraria (L.) Druce"
 ]
}

 The dataset includes 219 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002245-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13948742
title: A collection of high-quality human assemblies

description: A collection of high-quality human assemblies, including:



T2T-CHM13 v2.0 analysis set with HG002 chrY and rCRS chrM

GRCh38 no-alt analysis set with rCRS chrM

HG002 v1.1

CN1 v1.0.1

YAO v1.1

156 HPRC "r2-v1" samples (312 assemblies)


Use AGC to extract indivual genomes:



agc listset human320.agc   # list genomesagc getset human320.agc 400131_HG02615.pat > HG02615.pat.fa # extract one genome


Note: HPRC samples are already available from GenBank but are not formally published. You may use the data for algorithm development or performance evaluation. If you want to use the genomes for biological discovery, please contact HPRC.
DOI: 10.5281/zenodo.13953607
title: A collection of high-quality human assemblies

description: A collection of high-quality human assemblies, including:



T2T-CHM13 v2.0 analysis set with HG002 chrY and rCRS chrM

GRCh38 no-alt analysis set with rCRS chrM

HG002 v1.1

CN1 v1.0.1

YAO v1.1

156 HPRC "r2-v1" samples (312 assemblies)


Use AGC to extract indivual genomes and use ropebwt3 to query the FM-index:



agc listset human320.agc   # list genomesagc getset human320.agc 400131_HG02615.pat > HG02615.pat.fa # extract one genomegzip -d human320.fmr.gz     # decompress the incremental indexropebwt3 build -i human320.fmr -do human320.fmd  # convert to a faster query format


Note: HPRC samples are already available from GenBank but are not formally published. You may use the data for algorithm development or performance evaluation. If you want to use the genomes for biological discovery, please contact HPRC.
DOI: 10.5281/zenodo.13955431
title: A collection of high-quality human assemblies

description: A collection of high-quality human assemblies, including:



T2T-CHM13 v2.0 analysis set with HG002 chrY and rCRS chrM

GRCh38 no-alt analysis set with rCRS chrM

HG002 v1.1

CN1 v1.0.1

YAO v1.1

156 HPRC "r2-v1" samples (312 assemblies)


Use AGC to extract indivual genomes and use ropebwt3 to query the FM-index:



agc listset human320.agc   # list genomesagc getset human320.agc 400131_HG02615.pat > HG02615.pat.fa # extract one genomegzip -d human320.fmr.gz     # decompress the incremental indexropebwt3 build -i human320.fmr -do human320.fmd  # convert to a faster query format


Note: HPRC samples are already available from GenBank but are not formally published. You may use the data for algorithm development or performance evaluation. If you want to use the genomes for biological discovery, please contact HPRC.
DOI: 10.5281/zenodo.14511009
title: A collection of high-quality human assemblies

description: A collection of high-quality human assemblies, including:



T2T-CHM13 v2.0 analysis set with HG002 chrY and rCRS chrM

GRCh38 no-alt analysis set with rCRS chrM

HG002 v1.1

CN1 v1.0.1

YAO v1.1

195 HPRC "r2" samples (390 assemblies, excluding HG00272)


Use AGC to extract indivual genomes and use ropebwt3 to query the FM-index:



agc listset human398.agc   # list genomesagc getset human398.agc 400131_HG02615.pat > HG02615.pat.fa # extract one genomegzip -d human398.fmr.gz     # decompress the incremental indexropebwt3 build -i human398.fmr -do human398.fmd  # convert to a faster query formatgzip -d human398.fmd.ssa.gz  # decompress suffix array samplesecho CCAGGACCCCTGTCCAGTGTTAGACAGGAGCATGCAG | ropebwt3 sw -eN200 -Lm10 human398.fmd -


Note: The HPRC assemblies are already available from GenBank. This repository only provides a convenient way to download them. However, these assemblies are not formally published. You may use them for algorithm development or performance evaluation. If you want to use the genomes for biological discovery, please contact HPRC.
DOI: 10.5281/zenodo.14854401
title: A collection of high-quality human assemblies

description: A collection of high-quality human assemblies, including:



T2T-CHM13 v2.0 analysis set with HG002 chrY and rCRS chrM

GRCh38 no-alt analysis set with rCRS chrM

CN1 v1.0.1

YAO v1.1

KSA001 v1.1.0

232 HPRC r2/v0.6 samples (464 assemblies; HG00272 has a ~50Mb inversion misassembly)


Use AGC to extract indivual genomes and use ropebwt3 to query the FM-index:



agc listset human472.agc   # list genomesagc getset human472.agc 200149_HG02523.pat > HG02523.pat.fa # extract one genomegzip -d human472.fmr.gz     # decompress the incremental indexropebwt3 build -i human472.fmr -do human472.fmd  # convert to a faster query formatgzip -d human472.fmd.ssa.gz  # decompress suffix array samplesecho CCAGGACCCCTGTCCAGTGTTAGACAGGAGCATGCAG | ropebwt3 sw -eN200 -Lm10 human472.fmd -


Note: The HPRC assemblies are already available from GenBank. This repository only provides a convenient way to download them. However, these assemblies are not formally published. You may use them for algorithm development or performance evaluation. If you want to use the genomes for biological discovery, please contact HPRC.
DOI: 10.34740/kaggle/dsv/10768328
title: BOS Kemdikbud
DOI: 10.6084/m9.figshare.21454695
title: PPGL_scRNA_bulk_expression_data

description: Cell Ranger count data for single nuclei RNA seq data from PPGL, and normalised expression data from bulk expression compendium. Please note there is a typographical error in the folder naming for the snRNA count data, folder E326 should be named E236 to match the sample meta-data.
DOI: 10.15468/dl.5jx62y
title: Occurrence Download

description: A dataset containing 3207 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Sri Lanka",
 "TaxonKey is Pycnonotus penicillatus Blyth, 1851",
 "Year 2000-2025"
 ]
}

 The dataset includes 3207 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002247-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25439/rmt.26870314.v2
title: Internationally validated open access indicators of large public urban green space for healthy and climate resilient cities - supplementary materials

description: This data package contains supplementary materials related to large public urban green space (LPUGS) availability and accessibility indicator validation conducted for 13 diverse cities worldwide. This research was initiated by the Global Observatory of Healthy and Sustainable Cities for the 1000 Cities Challenge and inclusion in the Global Healthy & Sustainable City Indicators (GHSCI) open-source software.This data package contains the following:The Jupyter Notebook hosting a custom Python script that makes use of the Google Earth Engine API to apply Normalized Difference Vegetation Index (NDVI) filtering on areas of public open space derived from the GHSCI open-source software to identify LPUGS.A folder for each of the 13 cities involved in the study, containing spatial data in .shp format for the urban centre boundary, large public urban green spaces, accessibility grid, and pedestrian network. Additionally, official local reference data is included for the 4 select cities analysed.The instructional video provided to collaborators is also included as a .mp4 file, which outlines how to access the accessibility web map, how to perform the LACO-Wiki validation, and how to access and record comments in the live spreadsheet.The complete validation spreadsheet with comments is included as a .pdf file.A table of urban centre boundary source files used for each of the 13 cities included in a .pdf file.Additionally, please follow this link to the GitHub repository hosting the accessibility web maps used in the validation exercise for each city.
DOI: 10.5281/zenodo.14630150
title: The Artifacts for An Extensive Empirical Study of Nondeterministic Behavior in Static Analysis Tools.

description: This is the artifact for the ICSE 2025 paper, An Extensive Empirical Study of Nondeterministic Behavior in Static Analysis Tools. A pre-print of the original paper referencing this artifact can be found here: https://annabellam.github.io/docs/An_Extensive_Empirica_Study_of_Nondeterministic_Behavior_in_Static_A nalysis_Tools_-_Preprint.pdf. This artifact contains the code and data for the paper. The code contains the source code of the nondeterminism detection framework used in RQ2 as well as the instructions on how to run the framework to replicate the results reported in the paper. The data contains files that support the conclusions made in the two research questions (RQ1 and RQ2).

 

Changelog:



A Troubleshooting Section is added to address some potential issues, such as the docker permission issue Reviewer B encountered. We will continue updating this section whenever we notice any issues using our artifact.

A clarification is added to Section Data->RQ1 to avoid any confusion:



“There were 58 issues of Doop (as of the time this research was conducted) that are hosted on BitBucket, as stated at the beginning of Section III of our paper. These issues are not included in raw_data.zip as BitBucket requires administrative access to the repository to export the issues.”



The scripts to extract the GitHub issues and commits are included in our artifacts under the data/rq1/scripts folder.

A clarification is added to Section Detecting Nondeterminism Using Strategy I to avoid confusion when results_nondex/non_determinism folder is not generated:



"If no additional results are detected, the results_nondex/non_determinism folder will not be generated."
DOI: 10.5281/zenodo.14630151
title: The Artifacts for An Extensive Empirical Study of Nondeterministic Behavior in Static Analysis Tools.

description: This is the artifact for the ICSE 2025 paper, An Extensive Empirical Study of Nondeterministic Behavior in Static Analysis Tools. A pre-print of the original paper referencing this artifact can be found here: https://annabellam.github.io/docs/An_Extensive_Empirica_Study_of_Nondeterministic_Behavior_in_Static_A nalysis_Tools_-_Preprint.pdf. This artifact contains the code and data for the paper. The code contains the source code of the nondeterminism detection framework used in RQ2 as well as the instructions on how to run the framework to replicate the results reported in the paper. The data contains files that support the conclusions made in the two research questions (RQ1 and RQ2).
DOI: 10.5281/zenodo.14880152
title: The Artifacts for An Extensive Empirical Study of Nondeterministic Behavior in Static Analysis Tools.

description: This is the artifact for the ICSE 2025 paper, An Extensive Empirical Study of Nondeterministic Behavior in Static Analysis Tools. A pre-print of the original paper referencing this artifact can be found here: https://annabellam.github.io/docs/An_Extensive_Empirica_Study_of_Nondeterministic_Behavior_in_Static_A nalysis_Tools_-_Preprint.pdf. This artifact contains the code and data for the paper. The code contains the source code of the nondeterminism detection framework used in RQ2 as well as the instructions on how to run the framework to replicate the results reported in the paper. The data contains files that support the conclusions made in the two research questions (RQ1 and RQ2).

 

Changelog:



A Troubleshooting Section is added to address some potential issues, such as the docker permission issue Reviewer B encountered. We will continue updating this section whenever we notice any issues using our artifact.

A clarification is added to Section Data->RQ1 to avoid any confusion:



“There were 58 issues of Doop (as of the time this research was conducted) that are hosted on BitBucket, as stated at the beginning of Section III of our paper. These issues are not included in raw_data.zip as BitBucket requires administrative access to the repository to export the issues.”



The scripts to extract the GitHub issues and commits are included in our artifacts under the data/rq1/scripts folder.

A clarification is added to Section Detecting Nondeterminism Using Strategy I to avoid confusion when results_nondex/non_determinism folder is not generated:



"If no additional results are detected, the results_nondex/non_determinism folder will not be generated."
DOI: 10.15468/dl.wm8zxe
title: Occurrence Download

description: A dataset containing 1341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bactrocera dorsalis (Hendel, 1912)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 5000",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen)"
 ]
 }
 },
 {
 "not" : {
 "InstitutionCode" : [
 "is one of (iNaturalist)"
 ]
 }
 }
 ]
}

 The dataset includes 1341 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002250-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u9w3b2
title: Occurrence Download

description: A dataset containing 134268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "Geometry POLYGON((-12 20,60 20,60 75,-12 75,-12 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aesculus hippocastanum L.",
 "Year 1980-2024"
 ]
}

 The dataset includes 134268 records from 548 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002249-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14880148
title: Code and dataset for the WWW'25 paper: 'Digital Disparities: A Comparative Web Measurement Study Across Economic Boundaries.'

description: This repository contains the dataset and analysis code for our research paper "Digital Disparities: A Comparative Web Measurement Study Across Economic Boundaries," accepted at WWW'25. The study explores differences in web development practices across developed and developing countries, focusing on web size, complexity, security, privacy, technology adoption, and performance optimization.
DOI: 10.5281/zenodo.14880149
title: Code and dataset for the WWW'25 paper: 'Digital Disparities: A Comparative Web Measurement Study Across Economic Boundaries.'

description: This repository contains the dataset and analysis code for our research paper "Digital Disparities: A Comparative Web Measurement Study Across Economic Boundaries," accepted at WWW'25. The study explores differences in web development practices across developed and developing countries, focusing on web size, complexity, security, privacy, technology adoption, and performance optimization.
DOI: 10.17608/k6.auckland.28340441
title: Datasets used for performing Mendelian Randomisation analysis across eight tissues

description: This dataset includes the exposure, outcome, and harmonised data used for Mendelian Randomization (MR) analysis across eight tissues. The exposure dataset contains genetic variants associated with gene expression changes, while the outcome dataset includes genome-wide association study (GWAS) summary statistics for Parkinson's disease. The harmonised dataset ensures proper alignment of effect alleles between the exposure and outcome datasets, enabling robust MR analysis.
DOI: 10.17608/k6.auckland.28340441.v2
title: Datasets used for performing Mendelian Randomisation analysis across eight tissues

description: This dataset includes the exposure, outcome, and harmonised data used for Mendelian Randomization (MR) analysis across eight tissues. The exposure dataset contains genetic variants associated with gene expression changes, while the outcome dataset includes genome-wide association study (GWAS) summary statistics for Parkinson's disease. The harmonised dataset ensures proper alignment of effect alleles between the exposure and outcome datasets, enabling robust MR analysis.
DOI: 10.17608/k6.auckland.28340441.v1
title: Datasets used for performing Mendelian Randomisation analysis across eight tissues

description: This dataset includes the exposure, outcome, and harmonised data used for Mendelian Randomization (MR) analysis across eight tissues. The exposure dataset contains genetic variants associated with gene expression changes, while the outcome dataset includes genome-wide association study (GWAS) summary statistics for Parkinson's disease. The harmonised dataset ensures proper alignment of effect alleles between the exposure and outcome datasets, enabling robust MR analysis.
DOI: 10.15468/dl.auvcgy
title: Occurrence Download

description: A dataset containing 1073 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Sri Lanka",
 "TaxonKey is Elaphrornis palliseri (Blyth, 1851)",
 "Year 2000-2025"
 ]
}

 The dataset includes 1073 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002252-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.