cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fvcjxq
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((149.186973 -36.33756, 149.186973 -36.339806, 149.182481 -36.339806, 149.182481 -36.342051, 149.180235 -36.342051, 149.180235 -36.348789, 149.182481 -36.348789, 149.182481 -36.346543, 149.186973 -36.346543, 149.186973 -36.342051, 149.19371 -36.342051, 149.19371 -36.348789, 149.198202 -36.348789, 149.198202 -36.342051, 149.195956 -36.342051, 149.195956 -36.339806, 149.19371 -36.339806, 149.19371 -36.33756, 149.186973 -36.33756))"
 ]
}

 The dataset includes 67 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054555-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2akfq3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((146.218026 -36.342051, 146.218026 -36.346543, 146.220272 -36.346543, 146.220272 -36.342051, 146.218026 -36.342051))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054557-240626123714530/datasets/export for details.
DOI: 10.6073/pasta/5b94fc55e546e3e364a5fae35526194a
title: Factors Influencing Aboveground Carbon Storage in Mixed Oak-Pine Forests: USDA FIA Data from Southeastern U.S. (2009-2019)

description: This study explores factors affecting aboveground carbon (AGC) storage in mixed oak-pine forests across the Southeastern United States. Utilizing USDA Forest Inventory and Analysis (FIA) data from 2009 to 2019, the research spans nine states: Alabama, Mississippi, Florida, Georgia, North Carolina, South Carolina, Texas, Louisiana, and Virginia. Data processing in R included converting units to the metric system and calculating structural diversity using Shannon diversity indices. Climate data from the PRISM Climate Group were integrated with FIA data using longitude and latitude. The research aims to uncover how various factors influence AGC storage and contribute to informed forest management practices.
DOI: 10.15468/dl.wp5q7r
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.827645 -36.342051, 148.827645 -36.348789, 148.834382 -36.348789, 148.834382 -36.346543, 148.829891 -36.346543, 148.829891 -36.342051, 148.827645 -36.342051))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054559-240626123714530/datasets/export for details.
DOI: 10.15468/dl.utbqbd
title: Occurrence Download

description: A dataset containing 33395 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asclepias incarnata L."
 ]
}

 The dataset includes 33395 records from 260 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054558-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12803606
title: Postfire flood simulation data

description: Simulation results of rainfall-runoff events over the upper Cañada del Oro (CDO) watershed using KINEROS2 described in the paper "Temporal persistence of postfire flood hazards under present and future climate conditions in southern Arizona, USA" by Tao Liu, Luke A. McGuire, Ann M. Youberg, Charles J. Abolt, Adam L. Atchley.
DOI: 10.5281/zenodo.12803607
title: Postfire flood simulation data

description: Simulation results of rainfall-runoff events over the upper Cañada del Oro (CDO) watershed using KINEROS2 described in the paper "Temporal persistence of postfire flood hazards under present and future climate conditions in southern Arizona, USA" by Tao Liu, Luke A. McGuire, Ann M. Youberg, Charles J. Abolt, Adam L. Atchley.
DOI: 10.5281/zenodo.11618749
title: The ribosome lowers the entropic penalty of protein folding

description: This dataset contains concatenated MD trajectories for unfolded, isolated FLN5 A3A3 (iso.pdb and iso_traj.xtc) and the unfolded FLN5+31 A3A3 ribosome-nascent chain complex (RNC, nc.pdb and nc_traj.xtc). A representative structure of the ribosome model used in the simulations is also provided (ribosome_sim.pdb). Numpy array files (ending in .npy) contain the weights obtained for every frame in the ensembles after reweighting with PRE-NMR data. Text files including the trajectory frames (1-indexed, frames_nc.ndx and frames_iso.ndx) corresponding to the weights are also included (a few frames were removed because MTSL/spinlabel rotamers could not be accomdated sterically to allow for PRE calculations at protein labelling sites of interest). Both ensembles consist of ~100,000 frames. The FLN5 A3A3 ensemble was generated from ten independent MD trajectories of 2 microseconds, and FLN5+31 A3A3 consists of ten independent simulations lasting 1.5 microseconds (20 and 15 microseconds total, respectively).  Independent simulations were initiated from different starting structures. The *.tar files contain initial coordinate files, MD input files and topologies. 
description: This work was supported by a Wellcome Trust Investigator Award (to J.C., 206409/Z/17/Z) and by the Francis Crick Institute through provision of access to the MRC Biomedical NMR Centre. The Francis Crick Institute receives its core funding from Cancer Research UK (FC001029), the UK Medical Research Council (FC001029) and the Wellcome Trust (FC001029). This project made use of time on HPC resources on Archer2 (ARCHER2 UK National Supercomputing service, https://www.archer2.ac.uk) granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1 and EP/X035603/1). We also acknowledge the EuroHPC Joint Undertaking for awarding this project access to the EuroHPC supercomputer LUMI, hosted by CSC (Finland) and the LUMI consortium through a EuroHPC Regular Access call and the Baskerville Tier 2 HPC service (https://www.baskerville.ac.uk/). Baskerville was funded by the EPSRC and UKRI through the World Class Labs scheme (EP/T022221/1) and the Digital Research Infrastructure programme (EP/W032244/1) and is operated by Advanced Research Computing at the University of Birmingham. We additionally acknowledge the use of the UCL Myriad and Kathleen High Performance Computing Facility (Myriad@UCL and Kathleen@UCL), and associated support services, in the completion of this work.
DOI: 10.5281/zenodo.13257324
title: Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA

description: Data deposition for "Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA" published in Nucleic Acids Research. Data includes custom paramaterized nucleobase residues for use in AMBER molecular dyanmics simulations. Initial structures and setup code along with starting structures for generation of simulations in AMBER (pmemd.cuda). A in-house "MD-Generator" script to create nessessary files with our select simulation settings. Lastly, also included are CPPTRAJ analysis commands and scripts with visualizion scripts for use in Pymol 2.5 and above.
DOI: 10.5281/zenodo.13257325
title: Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA

description: Data deposition for "Unravelling the Dependence of Aptamer–Target Binding Orientation and Strength on Nucleotide Modification Size, Position, and Number: A Computational Case Study of TBA" published in Nucleic Acids Research. Data includes custom paramaterized nucleobase residues for use in AMBER molecular dyanmics simulations. Initial structures and setup code along with starting structures for generation of simulations in AMBER (pmemd.cuda). A in-house "MD-Generator" script to create nessessary files with our select simulation settings. Lastly, also included are CPPTRAJ analysis commands and scripts with visualizion scripts for use in Pymol 2.5 and above.
DOI: 10.15468/dl.9kqau5
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (ARG, CHL, PRY, URY, FLK, BRA.21_1, BRA.16_1, BRA.24_1)",
 "TaxonKey is Paradisanthus Rchb.f."
 ]
}

 The dataset includes 48 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054562-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w9k2pp
title: Occurrence Download

description: A dataset containing 4177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Asclepias incarnata L."
 ]
}

 The dataset includes 4177 records from 138 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054563-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xmjsbc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((149.272313 -36.333068, 149.272313 -36.339806, 149.27905 -36.339806, 149.27905 -36.333068, 149.272313 -36.333068)), ((149.27905 -36.339806, 149.27905 -36.342051, 149.272313 -36.342051, 149.272313 -36.346543, 149.26333 -36.346543, 149.26333 -36.35328, 149.265576 -36.35328, 149.265576 -36.348789, 149.274559 -36.348789, 149.274559 -36.35328, 149.281296 -36.35328, 149.281296 -36.339806, 149.27905 -36.339806)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054564-240626123714530/datasets/export for details.
DOI: 10.15468/dl.56e68a
title: Occurrence Download

description: A dataset containing 99399 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Plantae",
 "Year 2024-2024"
 ]
}

 The dataset includes 99399 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054561-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7cukec
title: Occurrence Download

description: A dataset containing 6101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-32.3877 62.53418,-21.31348 59.37012,-12.34863 34.76074,8.9209 37.9248,22.2649 34.63368,25.26855 39.24316,27.36694 41.45142,36.16699 44.16504,41.96777 48.99902,32.91504 54.00879,29.83887 57.78809,31.68457 71.7627,-17.18262 71.14746,-24.64766 66.91871,-32.3877 62.53418))",
 "HasCoordinate is true",
 "TaxonKey is Dianthus seguieri Vill.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6101 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023817-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tddt57
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "InstitutionKey is 1be3aa67-8f90-4309-92f4-bd55426a8c09",
 "TaxonKey is Verbesina arborea Kunth"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0112063-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0r1apn
title: Occurrence Download

description: A dataset containing 5955 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Buceros bicornis Linnaeus, 1758",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5955 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005046-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5q48wk
title: Occurrence Download

description: A dataset containing 15411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Celosia argentea L.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 15411 records from 204 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036075-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vsobms
title: Occurrence Download

description: A dataset containing 13597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Aedes aegypti (Linnaeus, 1762)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13597 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014235-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4xfxqf
title: Occurrence Download

description: A dataset containing 399 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1970-2000",
 "HasCoordinate is true",
 "TaxonKey is Triticum durum Desf.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 399 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015165-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8md55
title: Occurrence Download

description: A dataset containing 344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((125.48437 10.91285,125.89676 10.91285,125.89676 11.22284,125.48437 11.22284,125.48437 10.91285))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 344 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0411738-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xfjmeu
title: Occurrence Download

description: A dataset containing 478 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chamaecrista basifolia (Vogel) H.S.Irwin & Barneby"
 ]
}

 The dataset includes 478 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027436-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8s6nuk
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Shorea curtisii Dyer ex King"
 ]
}

 The dataset includes 126 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021524-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t9bt2r
title: Occurrence Download

description: A dataset containing 634990 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cirsium arvense (L.) Scop.",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 634990 records from 984 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036081-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gpi1lj
title: Occurrence Download

description: A dataset containing 1066 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Cystoseira compressa (Esper) Gerloff & Nizamuddin, 1975"
 ]
}

 The dataset includes 1066 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004124-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fsq4xh
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apteronotus brasiliensis (Reinhardt, 1852)"
 ]
}

 The dataset includes 34 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021532-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dyamrp
title: Occurrence Download

description: A dataset containing 163358 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maianthemum F.H.Wigg."
 ]
}

 The dataset includes 163358 records from 488 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004063-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15095699
title: 9-cis-retinoic acid improves disease modelling in iPSC-derived liver organoids

description: Liver fibrosis majorly impacts global health, necessitating development of in vitro models to study disease mechanisms and develop drug therapies. Relevant models should at least include hepatocytes and hepatic stellate cells (HSCs) and ideally use three-dimensional cultures to mimic in vivo conditions. Induced pluripotent stem cells (iPSCs) allow patient-specific liver modelling, but current models based on iPSC-derived hepatocytes (iHepatocytes) and HSCs (iHSCs) still lack key functions. We developed organoids of iHepatocytes and iHSCs, and compared them to HepaRG and primary HSC organoids. RNA-sequencing analysis comparison of these cultures identified a potential role for the transcription factor RXRA  in hepatocyte  differentiation and HSC quiescence. Treating cells with the RXRA ligand 9-cis-retinoic acid (9CRA) promoted iHepatocyte metabolism and iHSC quiescence. In organoids, 9CRA enhanced fibrotic response to TGF-β and acetaminophen, highlighting its potential for refining iPSC-based liver fibrosis models to more faithfully replicate human drug-induced liver injury and fibrotic conditions.
DOI: 10.5281/zenodo.15095698
title: 9-cis-retinoic acid improves disease modelling in iPSC-derived liver organoids

description: Liver fibrosis majorly impacts global health, necessitating development of in vitro models to study disease mechanisms and develop drug therapies. Relevant models should at least include hepatocytes and hepatic stellate cells (HSCs) and ideally use three-dimensional cultures to mimic in vivo conditions. Induced pluripotent stem cells (iPSCs) allow patient-specific liver modelling, but current models based on iPSC-derived hepatocytes (iHepatocytes) and HSCs (iHSCs) still lack key functions. We developed organoids of iHepatocytes and iHSCs, and compared them to HepaRG and primary HSC organoids. RNA-sequencing analysis comparison of these cultures identified a potential role for the transcription factor RXRA  in hepatocyte  differentiation and HSC quiescence. Treating cells with the RXRA ligand 9-cis-retinoic acid (9CRA) promoted iHepatocyte metabolism and iHSC quiescence. In organoids, 9CRA enhanced fibrotic response to TGF-β and acetaminophen, highlighting its potential for refining iPSC-based liver fibrosis models to more faithfully replicate human drug-induced liver injury and fibrotic conditions.
DOI: 10.25345/c5d50g956
title: MassIVE MSV000098311 - GNPS-butyrolactol B high-resolution mass spectrum
title: We purified butyrolactol B from Streptomyces and determined its high-resolution mass using an Agilent 1290 Infinity II HPLC system coupled to a 6550 Q-TOF ESI/MS. Here, we deposit the high-resolution electrospray ionization mass spectrum of butyrolactol B to GNPS for public access and reference.
DOI: 10.15468/dl.5nr6an
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is Participation aux politiques publiques départementales de l'environnement-Données CEN L-R départements",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0208021-230224095556074/datasets/export for details.
DOI: 10.15468/dl.9s2xyw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is Plan d'actions du Canal des Deux mers en Midi Pyrénées-Données patrimoine naturel Canal des deux mers et Canal du Midi",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0208033-230224095556074/datasets/export for details.
DOI: 10.15468/dl.tm42mz
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Justicia hilsenbeckii T.F.Daniel"
 ]
}

 The dataset includes 96 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0260305-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4v72u2
title: Occurrence Download

description: A dataset containing 118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Aves marinas de la Isla Cayo Serranilla durante la Expedición Seaflower 2017 - Proyecto Colombia BIO"
 ]
}

 The dataset includes 118 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231349-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9kfp9n
title: Occurrence Download

description: A dataset containing 1052 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hygrophila polysperma (Roxb.) T.Anderson"
 ]
}

 The dataset includes 1052 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0249903-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.