cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14003790
title: Data from: A fixed mutation in the respiratory complex I impairs mitochondrial bioenergetics in the endangered Apennine brown bear

description: Description

This dataset contains all molecular dynamics (MD) simulation post-processed data supporting the analysis presented in our study on the impact of the G527E mutation in the ND5 subunit of mitochondrial Complex I from the endangered Apennine brown bear (Ursus arctos marsicanus). The simulations compare three systems: the naturally occurring Apennine variant, a control variant (CTRL), and the engineered G527E variant (E527).

The data are organized into directories corresponding to the main analyses reported in the manuscript and supplementary materials:

Figure_4/:



A_RMSF/: Root Mean Square Fluctuation data for selected backbone atoms across systems.

B_Contacts/: Atomic contact profiles (within 15 Å) across three replicates for each system.

D_Water/: Time-resolved hydration data in key subunit interfaces for the ND5-ND4 channel.


Starting_coordinates/:



GROMACS coordinate files (.gro) for three simulation replicates per system, capturing representative snapshots used as MD input.


Supplementary_Figure_S3, S4, S5/:



These folders include projection of the backbone trajectories along the first eigenvector of the motion obtained by PCA (.pdb files) of the ND5 subunit and hydration profiles (.dat files) corresponding to key water channels within Complex I. Each file is systematically named to specify the system (i.e., Apennine, E527, or CTRL), the type of measurement, and the replicate number.


Applications:

This dataset is intended to support the validation and reproducibility of our structural and functional findings.

File formats:

Includes .xvg, .dat, .pdb, and .gro files compatible with GROMACS, VMD, and standard scientific plotting tools.

Keywords:

ND5, Complex I, G527E mutation, Apennine brown bear, mitochondrial bioenergetics, molecular dynamics, hydration, respiratory chain, GROMACS
DOI: 10.15468/dl.jxz2dm
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tagetes minuta",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013706-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mprcqw
title: Occurrence Download

description: A dataset containing 240 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Avena alba barbata, Avena alba hirtula, Avena alba wiestii, Avena almeriensis, Avena atherantha, Avena atheranthera, Avena barbata, Avena barbata, Avena barbata colorata, Avena barbata triflora)",
 "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 240 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013708-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6jmtnu
title: Occurrence Download

description: A dataset containing 212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Batrachoseps robustus)"
 ]
}

 The dataset includes 212 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013710-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.acknmu
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trichomycterus amazonicus"
 ]
}

 The dataset includes 5 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013711-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fsq9en
title: Occurrence Download

description: A dataset containing 9244 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Flagellaria indica"
 ]
}

 The dataset includes 9244 records from 176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013709-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bv8uft
title: Occurrence Download

description: A dataset containing 1898 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynodon dactylon",
 "Country is Switzerland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1898 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013712-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x27ycz
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynodon dactylon",
 "Country is Tajikistan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013714-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m6hmeb
title: Occurrence Download

description: A dataset containing 7789 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidium nitidum"
 ]
}

 The dataset includes 7789 records from 129 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013713-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15884622
title: IBD Research Data
title: IBD RS

description: Inflammatory bowel disease data, including treatment type and CXCL8 with Hs-CRP
DOI: 10.5281/zenodo.15884623
title: IBD Research Data
title: IBD RS

description: Inflammatory bowel disease data, including treatment type and CXCL8 with Hs-CRP
DOI: 10.15468/dl.p36rp8
title: Occurrence Download

description: A dataset containing 819 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Avena barbata atherantha, Avena barbata atheranthera, Avena barbata castellana, Avena barbata hirtula, Avena barbata hirtula, Avena barbata hirtula, Avena barbata hoppeana, Avena barbata lusitanica, Avena barbata subtypica, Avena barbata weistii)",
 "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 819 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013717-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.32ux2n
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynodon dactylon",
 "Country is Thailand",
 "HasCoordinate is true"
 ]
}

 The dataset includes 31 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013718-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.74789s
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Draba pickeringii"
 ]
}

 The dataset includes 20 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013716-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9e9snw
title: Occurrence Download

description: A dataset containing 119 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Streptoloma desertorum"
 ]
}

 The dataset includes 119 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013720-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ja96yx
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ADL3225"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013721-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p6kuu4
title: Occurrence Download

description: A dataset containing 170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Batrachoseps simatus)"
 ]
}

 The dataset includes 170 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013719-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15685926
title: The Cosmic Evolution of CIV Absorbers at 1.4 < z < 4.5 : Insights from 100,000 Systems in DESI Quasars

description: This Zenodo link provides the data used to reproduce the plots in the results section of the paper titled The Cosmic Evolution of CIV absorbers at 1.4 < z < 4.5 : Insights from 100,000 Systems in DESI Quasars . The DESI DR2 raw data used to generate this dataset will be released publicly in the future. However, the DR1 CIV catalog is publicly available at: https://github.com/abhi0395/desi-dr1-civ .DESI-DR1 VAC will also be available on : https://data.desi.lbl.gov/doc/releases/dr1/#value-added-catalogs

The paper is available at: https://arxiv.org/abs/2504.20299The associated code that was used to build the catalog is available at: 10.5281/zenodo.15685771
DOI: 10.15468/dl.suxawn
title: Occurrence Download

description: A dataset containing 224 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tagetes minuta",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 224 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013724-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aejsvm
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynodon dactylon",
 "Country is Trinidad and Tobago",
 "HasCoordinate is true"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013723-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qcmr9s
title: Occurrence Download

description: A dataset containing 2917 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Flaveria linearis"
 ]
}

 The dataset includes 2917 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013722-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15880965
title: LLM-Generated Library Imports

description: This is the replication package for the paper "How Robust are LLM-Generated Library Imports? An Empirical Study using Stack Overflow" submitted to TSE. 

Preprint on arXiv. 

Abstract: 

Software libraries are central to the functionality, security, and maintainability of modern code. As developers increasingly turn to Large Language Models (LLMs) to assist with programming tasks, understanding how these models recommend libraries is essential. In this paper, we conduct an empirical study of six state-of-the-art LLMs, both proprietary and open-source, by prompting them to solve real-world Python problems sourced from Stack Overflow. We analyze the types of libraries they import, the characteristics of those libraries, and the extent to which the recommendations are usable out of the box. Our results show that LLMs predominantly favour third-party libraries over standard ones, and often recommend mature, popular, and permissively licensed dependencies. However, we also identify gaps in usability: 4.6% of the libraries could not be resolved automatically due to structural mismatches between import names and installable packages, and few models provided installation guidance. While the generated code is technically valid, the lack of contextual support places the burden of manually resolving dependencies on the user. Our findings offer actionable insights for both developers and researchers, and highlight opportunities to improve the reliability and usability of LLM-generated code in the context of software dependencies.
DOI: 10.15468/dl.nwakvr
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Avena barbata wiestii, Avena barbata wiestii, Avena barbata atherantha, Avena barbata atherantha, Avena barbata atheranthera, Avena barbata caspica, Avena barbata frutescens, Avena barbata hirtula, Avena barbata media, Avena barbata minor)",
 "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 4 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013727-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.maguk3
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynodon dactylon",
 "Country is Turkmenistan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013725-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5z60cf33
title: MassIVE MSV000098513 - Initial M.Mesophilicum growth MM1 and MM2
title: M. Mesophilicum MM1 and MM2 initial growth and metabolite profiles. DDA.
DOI: 10.57748/de2b-fc72
title: Auckland_soil_metagenomes
DOI: 10.15468/dl.kw8zuc
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nasturtium floridanum"
 ]
}

 The dataset includes 145 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013728-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wvdbgc
title: Occurrence Download

description: A dataset containing 32920 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((-172.5 53.27,-144.63 53.27,-144.63 64.31,-172.5 64.31,-172.5 53.27))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 32920 records from 121 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013726-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57748/q89d-d037
title: Puketi_soil_metagenomes
DOI: 10.15468/dl.sffu53
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AER9412"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013730-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.erc3b4
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Batrachoseps stebbinsi)"
 ]
}

 The dataset includes 151 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013731-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w2awzs
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tagetes minuta",
 "Country is Kenya",
 "HasCoordinate is true"
 ]
}

 The dataset includes 82 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013735-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4q5yh5
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Camelina neglecta"
 ]
}

 The dataset includes 39 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013732-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57748/2gh6-3644
title: Aotea_soil_metagenomes
DOI: 10.15468/dl.u2p4f7
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tagetes minuta",
 "Country is Lesotho",
 "HasCoordinate is true"
 ]
}

 The dataset includes 26 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013737-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7c26zd
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013740-250711103210423/datasets/export for details.
DOI: 10.15468/dl.ya8n69
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parolinia ornata"
 ]
}

 The dataset includes 140 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013739-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4cjxxa
title: Occurrence Download

description: A dataset containing 16812 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Flueggea virosa"
 ]
}

 The dataset includes 16812 records from 254 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013736-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7w4nsh
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Avena barbata solida, Avena barbata subtypica, Avena barbata subtypica, Avena barbata triflora, Avena barbata wiestii, Avena bolivaris, Avena cypria, Avena damascena, Avena deusta, Avena fatua barbata)",
 "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 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013738-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8cp553
title: Occurrence Download

description: A dataset containing 78244 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arundo donax, Arundo donax, Arundo donax)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 78244 records from 794 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013715-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/rbm-c58-6526
title: Man in pelvis cloth lifting weight and posing

description: Men in pelvis cloth lifting weight and posing. This is plate 321, captioned "A: Lifting a 50-lb. dumbbell. B: Posing" from Eadweard Muybridge. Animal locomotion: an electro-photographic investigation of consecutive phases of animal movements. 1872-1885 / published under the auspices of the University of Pennsylvania. Plates. The plates printed by the Photo-Gravure Company. Philadelphia, 1887.
DOI: 10.25549/rbm-c58-6529
title: Man in pelvis cloth lifting weight and posing

description: Men in pelvis cloth lifting weight and posing. This is plate 321, captioned "A: Lifting a 50-lb. dumbbell. B: Posing" from Eadweard Muybridge. Animal locomotion: an electro-photographic investigation of consecutive phases of animal movements. 1872-1885 / published under the auspices of the University of Pennsylvania. Plates. The plates printed by the Photo-Gravure Company. Philadelphia, 1887.