cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17456214
title: Supplemental Notes

description: Appendix figures supporting the results reported in paper "Exploring Functional Insights into the Human Gut Microbiome via the Structural Proteome".
description: The human gut microbiome contains numerous proteins whose functions remain elusive yet are pivotal for host health. Sequence-based methods often falter when attempting to infer functions within this microbial proteome due to evolutionary divergence. To address this challenge, we develop the Human Gut Microbial Protein Structure Database, which incorporates ~2.7 million predicted protein structures. Our findings reveal that structural analogy enhances the annotation of phage proteins. We detail the structural diversification of phage endolysins and confirm their potential in eliminating gut pathobionts. Furthermore, our structure-guided approach is effective in the identification of microbial-host isozymes. By employing structural alignments, we identify previously unrecognized bacterial enzymes involved in melatonin biosynthesis. Finally, we present an alignment-free method, Dense Enzyme Retrieval, based on structure-encoded protein language models for ultrafast and sensitive detection of remote homologs. Our research underscores the value of computational structural genomics in elucidating the functional landscape of the human gut microbiome.
DOI: 10.6084/m9.figshare.30515837
title: Kanki Diabetes Manuscript 2025 Supplementary Tables 20-23

description: Kanki Diabetes Manuscript 2025 Supplementary Tables 20-23
DOI: 10.6084/m9.figshare.30515837.v1
title: Kanki Diabetes Manuscript 2025 Supplementary Tables 20-23

description: Kanki Diabetes Manuscript 2025 Supplementary Tables 20-23
DOI: 10.5281/zenodo.17498125
title: E3SMv2 climatology and time series output for analysis of ocean-atmosphere turbulent flux parameterization (pt 1)

description: This upload contains climatology and time series data of various variables resulting from several E3SMv2 model runs:



Control run without modifications to the ocean-atmosphere turbulent flux algorithm.

Test run using regularized neutral heat exchange coefficient and adaptive Obukhov stability limiter to address solution non-existence and non-uniqueness issues. 

Sensitivity runs varying various regularization and limiter parameters.
DOI: 10.5281/zenodo.17498126
title: E3SMv2 climatology and time series output for analysis of ocean-atmosphere turbulent flux parameterization (pt 1)

description: This upload contains climatology and time series data of various variables resulting from several E3SMv2 model runs:



Control run without modifications to the ocean-atmosphere turbulent flux algorithm.

Test run using regularized neutral heat exchange coefficient and adaptive Obukhov stability limiter to address solution non-existence and non-uniqueness issues. 

Sensitivity runs varying various regularization and limiter parameters.
DOI: 10.15468/dl.t5dxnd
title: Occurrence Download

description: A dataset containing 14562 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "Year is 2017",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 14562 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012361-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ycxzz
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Buceros bicornis"
 ]
}

 The dataset includes 273 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012362-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5c8njv
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Asia",
 "OccurrenceStatus is Present",
 "TaxonKey is Botryococcus",
 "Year 1000-2025"
 ]
}

 The dataset includes 79 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012363-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ay2wfh
title: Occurrence Download

description: A dataset containing 939 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((57.17989 35.71651,77.18951 -3.8147,125.99346 -12.43672,125.99346 9.85041,107.60429 18.65411,109.71734 20.88455,139.41733 16.89324,155.97929 46.23617,102.8012 67.77859,94.8144 34.64815,57.17989 35.71651))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Limnophila sessiliflora"
 ]
}

 The dataset includes 939 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012364-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7pqa94
title: Occurrence Download

description: A dataset containing 12313 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((107.69 33.83,107.86 33.83,107.86 34.14,107.69 34.14,107.69 33.83))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 12313 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012365-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.auzatk
title: Occurrence Download

description: A dataset containing 16802 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "Year is 2018",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 16802 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012367-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15591084
title: Prevalence of neuropathic pain: additional data

description: This repository contains two zip files that allow for analytical reproducibility. Each of the zip files contain 10 binary files with an '.rds' extension, which were written in R using the saveRDS function with 'xz' compression.

Nine of the 10 files are 'prev' objects generated using the prevalence::truePrev function in R. In both zip files, the names of the 'prev' objects are:



baskozos.rds

bouhassira.rds

dibonaventura.rds

harifi.rds

hebert.rds

toth.rds

vandenkerkhof_dn4.rds

vandenkerkhof_lanss.rds

yawn.rds


The tenth file (data_plot.rds) is a large R dataframe in which true prevalence data from the 9 'prev' objects have been collated for plotting the data by ggplot2 in R.

The files in the 'prevalence_true_uninformative.zip' file were generated using an uniformative prior [Beta(1, 1)], while the files in the 'prevalence_true_informative.zip' file were generated using an informative prior [Beta(4.389, 29.522)].

To use the data, using the following proceedures:



Clone the associated GitHub repository locally 

git clone https://github.com/kamermanpr/neuropathic-pain_prevalence.git


Download the two zip files contained in this repository to the home directory of the cloned repository and unzip the files. Unzipping the files will generate two new directories ('/prevalence_true_uninformative' and '/prevalence_true_informative'). These two directories contain the additional data that was too large to upload to GitHub, and which allow all scripts in the cloned repository to run in a reproducible manner.
DOI: 10.5281/zenodo.15591085
title: Prevalence of neuropathic pain: additional data

description: This repository contains two zip files that allow for analytical reproducibility. Each of the zip files contain 10 binary files with an '.rds' extension, which were written in R using the saveRDS function with 'xz' compression.

Nine of the 10 files are 'prev' objects generated using the prevalence::truePrev function in R. In both zip files, the names of the 'prev' objects are:



baskozos.rds

bouhassira.rds

dibonaventura.rds

harifi.rds

hebert.rds

toth.rds

vandenkerkhof_dn4.rds

vandenkerkhof_lanss.rds

yawn.rds


The tenth file (data_plot.rds) is a large R dataframe in which true prevalence data from the 9 'prev' objects have been collated for plotting the data by ggplot2 in R.

The files in the 'prevalence_true_uninformative.zip' file were generated using an uniformative prior [Beta(1, 1)], while the files in the 'prevalence_true_informative.zip' file were generated using an informative prior [Beta(4.389, 29.522)].

To use the data, using the following proceedures:



Clone the associated GitHub repository locally 

git clone https://github.com/kamermanpr/neuropathic-pain_prevalence.git


Download the two zip files contained in this repository to the home directory of the cloned repository and unzip the files. Unzipping the files will generate two new directories ('/prevalence_true_uninformative' and '/prevalence_true_informative'). These two directories contain the additional data that was too large to upload to GitHub, and which allow all scripts in the cloned repository to run in a reproducible manner.
DOI: 10.15468/dl.xyzs8d
title: Occurrence Download

description: A dataset containing 2070 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diabrotica barberi"
 ]
}

 The dataset includes 2070 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012368-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.82201/fhx4rx
title: BSC Dataverse - Introduction and organization

description: This dataset provides the support material for the BSC Dataverse training session. The session introduces participants to the BSC Dataverse platform, explains who can use it, and guides them through its structure, workflows, and best practices. It also presents real-world use cases from current BSC Dataverse users. The material helps both users and data stewards understand their roles and learn how to efficiently upload, manage, and share datasets.
DOI: 10.4121/6b79dc99-b55d-44eb-80d2-c66001de3a45
title: Data underlying the study of vertical drain method to improve soft soil using sand-filled perforated bamboos.

description: Data were collected to evaluate the performance of an eco-friendly, innovative vertical drain technique designed to improve soft soil using end-bearing, sand-filled perforated bamboo drains. Laboratory tests were conducted to determine the properties of the soil, sand, and perforated bamboo. The results are summarized in the given tables. Soft soil is idealized with modified Cam-Clay and sand is modified as Mohr-Coulomb constitutive model in the numerical analysis performed in the study.
DOI: 10.5281/zenodo.12686566
title: Raw data
DOI: 10.5281/zenodo.12686567
title: Raw data
DOI: 10.15468/dl.q36uuj
title: Occurrence Download

description: A dataset containing 28798 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "Year is 2019",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 28798 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012369-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/6b79dc99-b55d-44eb-80d2-c66001de3a45.v1
title: Data underlying the study of vertical drain method to improve soft soil using sand-filled perforated bamboos.

description: Data were collected to evaluate the performance of an eco-friendly, innovative vertical drain technique designed to improve soft soil using end-bearing, sand-filled perforated bamboo drains. Laboratory tests were conducted to determine the properties of the soil, sand, and perforated bamboo. The results are summarized in the given tables. Soft soil is idealized with modified Cam-Clay and sand is modified as Mohr-Coulomb constitutive model in the numerical analysis performed in the study.
DOI: 10.15468/dl.9pqk36
title: Occurrence Download

description: A dataset containing 4087 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Asia",
 "OccurrenceStatus is Present",
 "TaxonKey is Brassica",
 "Year 1000-2025"
 ]
}

 The dataset includes 4087 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012370-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u5hykx
title: Occurrence Download

description: A dataset containing 154 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)"
 ]
 }
 },
 "TaxonKey is one of (Abies chensiensis)",
 "Geometry POLYGON((72.2 56, 137.5 56, 137.5 0, 72.2 0, 72.2 56))",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 }
 ]
}

 The dataset includes 154 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012371-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fc48su
title: Occurrence Download

description: A dataset containing 870794 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((105.49789 9.86977,110.59058 9.86977,110.59058 17.76946,105.49789 17.76946,105.49789 9.86977))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 870794 records from 780 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012333-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2956yz
title: Occurrence Download

description: A dataset containing 25161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "Year is 2020",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 25161 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012372-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ugyx4x
title: Occurrence Download

description: A dataset containing 423105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is d5ef14a1-5177-4547-9ce2-46d84a4214eb",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 423105 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012366-251025141854904/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/13595092
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5281/zenodo.17498146
title: E3SMv2 climatology and time series output for analysis of ocean-atmosphere turbulent flux parameterization (pt 2)

description: This upload contains climatology and time series data of various variables resulting from several E3SMv2 model runs:



Control run without modifications to the ocean-atmosphere turbulent flux algorithm.

Test run using regularized neutral heat exchange coefficient and adaptive Obukhov stability limiter to address solution non-existence and non-uniqueness issues. 

Sensitivity runs varying various regularization and limiter parameters.
DOI: 10.5281/zenodo.17498147
title: E3SMv2 climatology and time series output for analysis of ocean-atmosphere turbulent flux parameterization (pt 2)

description: This upload contains climatology and time series data of various variables resulting from several E3SMv2 model runs:



Control run without modifications to the ocean-atmosphere turbulent flux algorithm.

Test run using regularized neutral heat exchange coefficient and adaptive Obukhov stability limiter to address solution non-existence and non-uniqueness issues. 

Sensitivity runs varying various regularization and limiter parameters.
DOI: 10.15468/dl.vm3qzd
title: Occurrence Download

description: A dataset containing 20270 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "Year is 2021",
 "InstitutionCode is iNaturalist"
 ]
}

 The dataset includes 20270 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012373-251025141854904/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.30514943
title: Defects4C: Benchmarking Large Language Model Repair Capability with C/C++ Bugs

description: Automated Program Repair (APR) plays a critical role in enhancing the quality and reliability of software systems. While substantial progress has been made in Java-based APR, largely facilitated by benchmarks like Defects4J, there remains a significant gap in research on C/C++ program repair, despite the widespread use of C/C++ and the prevalence of associated vulnerabilities. This gap is primarily due to the lack of high-quality, open-source benchmarks tailored for C/C++. To address this issue, we introduce Defects4C, a comprehensive and executable benchmark specifically designed for C/C++ program repair. Our dataset is constructed from real-world C/C++ repositories and includes a large collection of bug-relevant commits (9M in total), 248 high-quality buggy functions, and 102 vulnerable functions, all paired with test cases for reproduction. These resources enable rigorous evaluation of repair techniques and support the retraining of learning-based approaches for enhanced performance. Using Defects4C, we conduct a comprehensive empirical study evaluating the effectiveness of 24 state-of-the-art large language models (LLMs) in repairing C/C++ faults. Our findings offer valuable insights into the strengths and limitations of current LLM-based APR techniques in this domain, highlighting both the need for more robust methods and the critical role of Defects4C in advancing future research
DOI: 10.6084/m9.figshare.30514943.v1
title: Defects4C: Benchmarking Large Language Model Repair Capability with C/C++ Bugs

description: Automated Program Repair (APR) plays a critical role in enhancing the quality and reliability of software systems. While substantial progress has been made in Java-based APR, largely facilitated by benchmarks like Defects4J, there remains a significant gap in research on C/C++ program repair, despite the widespread use of C/C++ and the prevalence of associated vulnerabilities. This gap is primarily due to the lack of high-quality, open-source benchmarks tailored for C/C++. To address this issue, we introduce Defects4C, a comprehensive and executable benchmark specifically designed for C/C++ program repair. Our dataset is constructed from real-world C/C++ repositories and includes a large collection of bug-relevant commits (9M in total), 248 high-quality buggy functions, and 102 vulnerable functions, all paired with test cases for reproduction. These resources enable rigorous evaluation of repair techniques and support the retraining of learning-based approaches for enhanced performance. Using Defects4C, we conduct a comprehensive empirical study evaluating the effectiveness of 24 state-of-the-art large language models (LLMs) in repairing C/C++ faults. Our findings offer valuable insights into the strengths and limitations of current LLM-based APR techniques in this domain, highlighting both the need for more robust methods and the critical role of Defects4C in advancing future research
DOI: 10.34740/kaggle/dsv/13595119
title: e-IPO Indonesia Data - Investment
DOI: 10.15468/dl.6prw39
title: Occurrence Download

description: A dataset containing 14672 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Diabrotica barberi, Epitrix tuberis, Diabrotica undecimpunctata, Epitrix cucumeris, Crioceris asparagi, Diabrotica virgifera)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 14672 records from 272 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012374-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21979/n9/xuk1jt
title: Replication data for: Brillouin zone folding driven bound states in the continuum

description: This dataset contains all the data used in the paper, titled 'Brillouin zone folding driven bound states in the continuum'.
DOI: 10.15468/dl.v5cjtg
title: Occurrence Download

description: A dataset containing 11182 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((138.16002 -10.73083,173.14072 64.93552,77.31514 52.81964,59.91298 29.93201,73.27463 -0.64912,119.28802 -17.6427,117.93095 11.72337,107.74867 17.90815,108.05037 20.92513,118.00638 18.059,138.16002 -10.73083))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantago asiatica"
 ]
}

 The dataset includes 11182 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012375-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.