cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17312132
title: Profylo : benchmarking and application datas and scripts

description: This folder contains the experiment presented in the manuscript entitled "Profylo: a Python package for phylogenetic profile comparison and analysis" and published in the Journal of Molecular Evolution.Among other, it contains the phylogenetic profiles used in the analyses, the benchmarking results for the analyses and file describing the clusters of the the detailed use case, as well as some scripts needed to reproduce the results. The folder hierarchy is as follow:

Programming files- conda : Contains a file describing the set up of the conda environment use for the analysis- Notebooks : Contains the notebooks used for plotting the bencharmking results and to provide the analysis of the parsimony score.- scripts : Contains the python script that was used to obtain the benchmarking results from every distance matrix in this folder. The distance matricexs are located in distance_similarity_matrices and the benchmarking results in benchmark_results. Also contains the scripts used for KEGG module and pathway enrichment analysis.

Input files- datafiles : Contains external data file detailing KEGG pathways, GO terms for Human genes, paralogy relationship and any input files with information not containing in the profiles or the species tree. - profiles : Containe the phylogenetic files, as binary matrices, used in the paper on the three dataset described in the manuscript- trees : Contains the newick species tree used with the profiles in some of the analysis detailed in the paper

Output files- distance_similarity_matrices: Contains the files generated by using Profylo on the phylogenetic profiles in the profiles folder, with all methods available in profylo and for PCS and SVD, a variation of parameters.- benchmark_results : Contains the files generated by the script compute_kegg_precisons from the script folder, on the distance and similarity matrices from the folder distance_similarity_matrices. These results were used as benchmark for the different methods in Profylo.- application : Contains files corresponding to the human proteome case study (composition of clusters, enrichments, figures etc.).
DOI: 10.5281/zenodo.15224589
title: Profylo : benchmarking and application datas and scripts

description: This folder contains the experiment presented in the manuscript entitled "Profylo: a Python package for phylogenetic profile comparison and analysis" and published in the Journal of Molecular Evolution.Among other, it contains the phylogenetic profiles used in the analyses, the benchmarking results for the analyses and file describing the clusters of the the detailed use case, as well as some scripts needed to reproduce the results. The folder hierarchy is as follow:

Programming files- conda : Contains a file describing the set up of the conda environment use for the analysis- Notebooks : Contains the notebooks used for plotting the bencharmking results and to provide the analysis of the parsimony score.- scripts : Contains the python script that was used to obtain the benchmarking results from every distance matrix in this folder. The distance matricexs are located in distance_similarity_matrices and the benchmarking results in benchmark_results. Also contains the scripts used for KEGG module and pathway enrichment analysis.

Input files- datafiles : Contains external data file detailing KEGG pathways, GO terms for Human genes, paralogy relationship and any input files with information not containing in the profiles or the species tree. - profiles : Containe the phylogenetic files, as binary matrices, used in the paper on the three dataset described in the manuscript- trees : Contains the newick species tree used with the profiles in some of the analysis detailed in the paper

Output files- distance_similarity_matrices: Contains the files generated by using Profylo on the phylogenetic profiles in the profiles folder, with all methods available in profylo and for PCS and SVD, a variation of parameters.- benchmark_results : Contains the files generated by the script compute_kegg_precisons from the script folder, on the distance and similarity matrices from the folder distance_similarity_matrices. These results were used as benchmark for the different methods in Profylo.- application : Contains files corresponding to the human proteome case study (composition of clusters, enrichments, figures etc.).
DOI: 10.25549/maston-c31-347
title: School of Environmental Design, Cal Poly, Pomona, ca.1970, photographs

description: 35 photographs of the School of Environmental Design, California State Polytechnic University, Kellogg-Voorhis Pomona Campus, across the street from 45 South University Drive, Pomona, California, ca.1970. Designed by Carl Maston.
DOI: 10.15468/dl.c5g347
title: Occurrence Download

description: A dataset listing the 126740 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Animalia, Plantae)"
 ]
}

 The dataset's 126740 records were derived from 3209 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018200-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/uschist-c104-279723
title: Youth triumphant & Doheny Library, USC, 2017

description: 5 photographs of the Youth triumphant fountain with Edward L. Doheny Jr. Memorial Library, 3550 Trousdale Parkway, in the background, University of Southern California, Los Angeles, California, USA, 2017 February 1. One of the images is an interior of Doheny Library, the Los Angeles Times Reference Room.
DOI: 10.25549/uschist-c104-741
title: Five women runners just taking off from the starting line, Bovard Field track, USC, ca. 1920-1929

description: Photograph of five women runners just taking off from the starting line, Bovard Field track, USC, ca. 1920-1929. "Go! In bloomers and middy blouses, Trojan women off and running on Bovard Field track in this photo from the 1920s, Note upraised gun hand and starter, background" -- The Trojan gallery, p. 452.
DOI: 10.5281/zenodo.18706775
title: partial data(self-reports and test scores)

description: partial data
DOI: 10.5281/zenodo.18706776
title: partial data(self-reports and test scores)

description: partial data
DOI: 10.25549/uschist-c104-279459
title: Trojan Shrine & Wilson Student Union, USC, 2017

description: 5 photographs of the Trojan Shrine (Tommy Trojan) with the Gwynn Wilson Student Union, 3601 Trousdale Parkway, in the background, University of Southern California, Los Angeles, California, USA, 2017 February 1.
DOI: 10.25345/c5t727v9k
title: MassIVE MSV000100913 - Detection of Melanoma Using Deep Serum Proteome Profiling and Machine Learning
title: Early detection fundamentally determines melanoma outcomes, yet current screening relies on visual inspection that misses molecular changes preceding clinical diagnosis. Serum biomarkers offer objective, non-invasive detection but remain largely absent from clinical practice. To address this, we leveraged the Department of Defense Serum Repository containing longitudinal samples from military personnel to identify protein signatures of melanoma development. Using data-independent acquisition mass spectrometry with Seer Proteograph nanoparticle enrichment, we analyzed 390 serum samples from 73 melanoma cases and matched controls across four timepoints: 4 years prior, 2 years prior, diagnosis, and 2 years post-diagnosis. We quantified 3,364 proteins and employed machine learning analytical strategies involving cross-sectional case-control comparisons with longitudinal tracking of within-individual protein changes. Cross-sectional analysis at diagnosis achieved AUC 0.807 (95% CI: 0.701-0.914), identifying eight consensus protein features selected in &gt;50% of cross-validation folds: PRSS1, GSK3B, FAM20C, CES1, CCL14, EPHA10, LMAN2, and ITIH1. These results demonstrate proof-of-concept for serum-based melanoma detection and provide candidate biomarkers for validation. The identified protein signatures spanning proteases, immune activation, and extracellular matrix remodeling suggest measurable systemic responses preceding clinical disease diagnosis. Raw data were processed using Spectronaut 19.7 (Biognosys) in directDIA+ (Deep) mode with BGS Factory Settings. Briefly, peptides were identified using trypsin/P digestion (2 missed cleavages), with carbamidomethylation of cysteine as a fixed modification and acetylation (protein N-term) and oxidation (methionine) as variable modifications. Precursor and protein group FDR were controlled at 1% at both the run and experiment level. MS2 area-based quantification was performed using the top 3 peptides per protein group with automatic cross-run normalization and interference correction enabled.
DOI: 10.5281/zenodo.18706799
title: Artifact of LLM-Assisted Input-Requirement-Aware Differential Testing of Array Programming Frameworks

description: This artifact includes:

1. The Docker image containing the ArrayDiff prototype.

2. The experimental data.
DOI: 10.5281/zenodo.18706800
title: Artifact of LLM-Assisted Input-Requirement-Aware Differential Testing of Array Programming Frameworks

description: This artifact includes:

1. The Docker image containing the ArrayDiff prototype.

2. The experimental data.
DOI: 10.15468/dl.axp7md
title: Occurrence Download

description: A dataset containing 2896 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chrysopelea",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Brunei Darussalam, Cambodia, Indonesia, Lao People’s Democratic Republic, Myanmar, Malaysia, Philippines, Singapore, Thailand, Viet Nam, Timor-Leste, Chinese Taipei, China)",
 "Geometry POLYGON((90 -15, 90 35, 135 35, 135 -15, 90 -15))"
 ]
}

 The dataset includes 2896 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030911-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkn2pq
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "Geometry POLYGON((85.27771 0.51472,127.72229 0.51472,127.72229 17.48528,85.27771 17.48528,85.27771 0.51472))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Microchirita involucrata"
 ]
}

 The dataset includes 59 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030913-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jmt8pw
title: Occurrence Download

description: A dataset containing 3999 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhacophorus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Brunei Darussalam, Cambodia, Indonesia, Lao People’s Democratic Republic, Myanmar, Malaysia, Philippines, Singapore, Thailand, Viet Nam, Timor-Leste, Chinese Taipei, China)",
 "Geometry POLYGON((90 -15, 90 35, 135 35, 135 -15, 90 -15))"
 ]
}

 The dataset includes 3999 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030912-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.oftmjkiv
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.18706795
title: Supplementary material for: "Do human impacts and environmental factors shape intertidal meiobenthic communities across freshwater, estuarine, and oceanic beaches in Uruguay?"

description: This repository contains the supplementary material associated with the manuscript entitled "Do human impacts and environmental factors shape intertidal meiobenthic communities across freshwater, estuarine, and oceanic beaches in Uruguay?", accepted for publication in Ocean and Coastal Research.

The files include the main tables of the manuscript, supplementary figures and tables, and the corresponding figure legends related to the figures presented in the article.

This material is provided to ensure transparency, reproducibility, and long-term accessibility of the supporting data.
DOI: 10.5281/zenodo.18706796
title: Supplementary material for: "Do human impacts and environmental factors shape intertidal meiobenthic communities across freshwater, estuarine, and oceanic beaches in Uruguay?"

description: This repository contains the supplementary material associated with the manuscript entitled "Do human impacts and environmental factors shape intertidal meiobenthic communities across freshwater, estuarine, and oceanic beaches in Uruguay?", accepted for publication in Ocean and Coastal Research.

The files include the main tables of the manuscript, supplementary figures and tables, and the corresponding figure legends related to the figures presented in the article.

This material is provided to ensure transparency, reproducibility, and long-term accessibility of the supporting data.
DOI: 10.15468/dl.xukqzw
title: Occurrence Download

description: A dataset containing 134672 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lolium multiflorum"
 ]
}

 The dataset includes 134672 records from 1806 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030877-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r4y785
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calamagrostis contracta, Calamagrostis contracta, Calamagrostis freticola, Calamagrostis freticola, Calamagrostis fuegiana, Calamagrostis groenlandica, Calamagrostis groenlandica iljinii, Calamagrostis haenkeana, Calamagrostis hookeri, Calamagrostis inexpansa)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 43 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019006-250711103210423/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/12480027
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.6qkkkh
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Equus asinus",
 "Country is Ecuador",
 "HasCoordinate is true"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019007-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j6dj3p
title: Occurrence Download

description: A dataset containing 490 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Streptanthus lemmonii"
 ]
}

 The dataset includes 490 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019008-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5gqagj
title: Occurrence Download

description: A dataset containing 514 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mangifera indica",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 514 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019010-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kpwfe9
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ACL3731"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019011-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xa8ur8
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rattus rattus",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 39 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019009-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/7acj-b031
title: "Usability Study Data of a Shared Control-based Wheelchair for the Built Environment"

description: "As the global population of people with disabilities (PWD) continues to grow, so will the need for mobility solutions that promote independent living and social integration. Wheelchairs are vital for the mobility of PWD in both indoor and outdoor environments. The current state-of-the-art in powered wheelchairs are based on either manually controlled or fully autonomous modes of operation, offering limited flexibility and often proving difficult to navigate in spatially constrained environments. Moreover, research on robotic wheelchairs has focused predominantly on complete autonomy or improved manual control; approaches that can compromise efficiency and user trust. To overcome these challenges, this paper introduces the CoNav Chair\u2014a smart wheelchair based on the Robot Operating System (ROS) and features shared control navigation and obstacle avoidance capabilities that are intended to enhance navigational efficiency, safety, and ease fo use for the user. The paper outlines the CoNav Chair\u2019s design and presents a preliminary usability evaluation comparing three distinct navigation modes, namely, manual, shared, and fully autonomous, conducted with 21 healthy, unimpaired participants traversing an indoor building environment. Study findings indicated that the shared control navigation framework had significantly fewer collisions and performed comparably if not superior to the autonomous and manual modes on task completion time, trajectory length and smoothness; and was perceived as being safer and more efficient based on user-reported subjective assessments of usability. Overall, the CoNav system demonstrated acceptable safety and performance laying the foundation for subsequent usability testing with end users, namely, PWDs who rely on a powered wheelchair for mobility. "
DOI: 10.5281/zenodo.15876371
title: CJBS & MESM
DOI: 10.5281/zenodo.15876372
title: CJBS & MESM
DOI: 10.15468/dl.n3h8cy
title: Occurrence Download

description: A dataset containing 659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Festuca duriuscula, Festuca duriuscula, Festuca duriuscula rubra, Festuca duriuscula collina, Festuca duriuscula dumetorum, Festuca duriuscula glaucescens, Festuca duriuscula nemoralis, Festuca duriuscula pratensis, Festuca duriuscula rubra, Festuca duriuscula rubra)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 659 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019013-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5fh3y
title: Occurrence Download

description: A dataset containing 2694 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pedicularis palustris",
 "Geometry POLYGON((-8.00174339329464 54.1998526673513, 0.202120938926891 54.1998526673513, 0.202120938926891 61.2628565887411, -8.00174339329464 61.2628565887411, -8.00174339329464 54.1998526673513))",
 "CoordinateUncertaintyInMeters is 0,101",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2694 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019012-250711103210423/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.29577377
title: Data Availability Statement

description: This is the Data Availability Statement for my paper "DEVELOPMENT OF INDONESIAN LIVEWORKSHEET TO IMPROVE GRAMMAR MASTERY IN ELEMENTARY SCHOOL STUDENTS"
DOI: 10.6084/m9.figshare.29577377.v1
title: Data Availability Statement

description: This is the Data Availability Statement for my paper "DEVELOPMENT OF INDONESIAN LIVEWORKSHEET TO IMPROVE GRAMMAR MASTERY IN ELEMENTARY SCHOOL STUDENTS"
DOI: 10.15468/dl.guuafn
title: Occurrence Download

description: A dataset containing 2930 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Torilis scabra"
 ]
}

 The dataset includes 2930 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019014-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.petxnd
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Equus asinus",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 147 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019017-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.63uapp
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calamagrostis inexpansa micrantha, Calamagrostis jakutensis, Calamagrostis kolgujewensis, Calamagrostis laxiflora, Calamagrostis lucida, Calamagrostis magellanica, Calamagrostis micrantha, Calamagrostis micrantha micrantha, Calamagrostis neglecta borealis, Calamagrostis neglecta exserta)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019015-250711103210423/datasets/export for details.
DOI: 10.15468/dl.zy4nf9
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rorippa prolifera"
 ]
}

 The dataset includes 54 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019016-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.