cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26232551
title: Data for the paper "Species distribution models built with local species data perform better for current time, but suffer from niche truncation".Historic (1989-2013) and future (2041-2060 for RCP4.5 and RCP8.5) distribution of tree species in the Alps and Piedmont, Italy.

description: Collection of raster related to the historic and future distribution of 22 tree species for Piedmont Region, Italy and the European Alps extent produced by using correlative species distribution models.Rasters are projected to EPSG:3034 with a spatial resolution of 1km, but originally available at 250m upon request.Files are provided as both binary maps (0 = absence, 1 = presence) or continuous probability of presence (0-1) in the GeoTiff format.The "Independent data" folder contains maps from Caudullo et al. (2017) and the csv file used for independent validation with LUCAS and GBIF occurrences.The EU-Trees4F dataset was very large and detailed, but can be fully downloaded at this link: https://springernature.figshare.com/collections/EU-Trees4F_A_dataset_on_the_future_distribution_of_European_tree_species_/5525688R code is available upon request.
DOI: 10.15468/dl.y5ujzb
title: Occurrence Download

description: A dataset containing 952 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is one of (USA.33_1, USA.31_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Crassostrea virginica (Gmelin, 1791)"
 ]
}

 The dataset includes 952 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028975-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j2h46a
title: Occurrence Download

description: A dataset listing the 6674 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.29225 41.02295,-8.35719 41.12366,-8.43932 41.16394,-8.58459 41.17254,-8.76598 41.18644,-8.76021 41.1064,-8.71719 40.97912,-8.58459 40.94939,-8.49797 40.92758,-8.38248 40.9194,-8.3139 40.95757,-8.29225 41.02295))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 6674 records were derived from 205 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028968-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48329/kbka-jh66
title: CPRD Aurum Small Area data (practice) November 2024

description: The general practice postcode linkages are available for all practices in CPRD GOLD and CPRD Aurum and use the general practice postcode which is linked via LSOA, SOA in Northern Ireland and datazone (DZ) in Scotland. The general practice postcode linkage includes several well-known area-based measures of deprivation, including the Index of Multiple Deprivation, Townsend Deprivation Index and Carstairs Index, and Rural-Urban Classification, which are available at the LSOA level for linkage to CPRD primary care data through the practice postcode. Additionally, Sub-Integrated Care Board Locations (Sub-ICB Locs) pseudonym (practice level, England-only) is available. Access is provided by CPRD subject to protocol approval. Further information is available at https://www.cprd.com/linked-data.
DOI: 10.5281/zenodo.14288914
title: Molecular dynamics and AlphaFold dataset of fluorinated protein variants

description: This dataset contains AlphaFold predictions and molecular dynamics (MD) trajectories of 50 fluorinated protein variants. Experimentally measured fluorine NMR chemical shifts are provided in the CSV file. Unless otherwise stated, secondary shifts were calculated using a random coil / reference chemical shift of -61.82 ppm. Proteins were labelled with 4-trifluoromethyl-L-phenylalanine (tfmF), modelled as a tyrosine residue in AlphaFold and explicitly in MD simulations with the CHARMM36m (C36m) and ff15ipq force fields. For each variant, ColabFold and AlphaFold 3 predictions (five models) are included. For MD, each variant contains three independent trajectories lasting one microsecond (150 microseconds total over the entire dataset per force field). Each simulation folder contains distance (in Å) and angle (in degrees) descriptors, which quantify the interaction of tfmF with nearby aromatic residues to predict ring current effects. Each folder also contains the solvent-accessible surface area of the trifluoromethyl group calculated over each trajectory, and the RMSD with respect to the starting structure. General template folders for each force field (and an additional template for HRAS due to custom GDP/ligand parameters) are also provided to allow for reproduction of the setup and production simulations for fluorinated protein variants. 

Excel files summarising the average distance and angle descriptors for each variant and their experimental chemical shifts are provided (averaged over all AlphaFold models or across all three trajectories, discarding the first 200 ns as equilibration). 

The dataset also includes six long MD trajectories (lasting 20 microseconds) of two HemK variants (N-terminal domain, residues 1-73) simulated with the DES-Amber protein force field, as proof-of-concept of fluorinated probes (38tfmF for HemK) reporting on mutation-induced conformational changes. Wild-type (K12 strain) and a mutant (I26V/R34K/Q46R) were simulated.  
description: This study was funded by a Wellcome Trust Investigator Award (to J.C., 206409/Z/17/Z). Computational resources were provided by 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 are also grateful to the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by the EPSRC (EP/T022213/1, EP/W032260/1 and EP/P020194/1), and the UCL Kathleen High Performance Computing Facility (Kathleen@UCL), and associated support services.
DOI: 10.5281/zenodo.14288915
title: Molecular dynamics and AlphaFold dataset of fluorinated protein variants

description: This dataset contains AlphaFold predictions and molecular dynamics (MD) trajectories of 50 fluorinated protein variants. Experimentally measured fluorine NMR chemical shifts are provided in the CSV file. Unless otherwise stated, secondary shifts were calculated using a random coil / reference chemical shift of -61.82 ppm. Proteins were labelled with 4-trifluoromethyl-L-phenylalanine (tfmF), modelled as a tyrosine residue in AlphaFold and explicitly in MD simulations with the CHARMM36m (C36m) and ff15ipq force fields. For each variant, ColabFold and AlphaFold 3 predictions (five models) are included. For MD, each variant contains three independent trajectories lasting one microsecond (150 microseconds total over the entire dataset per force field). Each simulation folder contains distance (in Å) and angle (in degrees) descriptors, which quantify the interaction of tfmF with nearby aromatic residues to predict ring current effects. Each folder also contains the solvent-accessible surface area of the trifluoromethyl group calculated over each trajectory, and the RMSD with respect to the starting structure. General template folders for each force field (and an additional template for HRAS due to custom GDP/ligand parameters) are also provided to allow for reproduction of the setup and production simulations for fluorinated protein variants. 

Excel files summarising the average distance and angle descriptors for each variant and their experimental chemical shifts are provided (averaged over all AlphaFold models or across all three trajectories, discarding the first 200 ns as equilibration). 

The dataset also includes six long MD trajectories (lasting 20 microseconds) of two HemK variants (N-terminal domain, residues 1-73) simulated with the DES-Amber protein force field, as proof-of-concept of fluorinated probes (38tfmF for HemK) reporting on mutation-induced conformational changes. Wild-type (K12 strain) and a mutant (I26V/R34K/Q46R) were simulated.  
description: This study was funded by a Wellcome Trust Investigator Award (to J.C., 206409/Z/17/Z). Computational resources were provided by 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 are also grateful to the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by the EPSRC (EP/T022213/1, EP/W032260/1 and EP/P020194/1), and the UCL Kathleen High Performance Computing Facility (Kathleen@UCL), and associated support services.
DOI: 10.15468/dl.mrcn9y
title: Occurrence Download

description: A dataset containing 162749 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is SBBG - Clifton Smith Herbarium, Santa Barbara Botanic Garden"
 ]
}

 The dataset includes 162749 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028949-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48329/2ahk-ys53
title: CPRD GOLD Small Area data (practice) November 2024

description: The general practice postcode linkages are available for all practices in CPRD GOLD and CPRD Aurum and use the general practice postcode which is linked via LSOA, SOA in Northern Ireland and datazone (DZ) in Scotland. The general practice postcode linkage includes several well-known area-based measures of deprivation, including the Index of Multiple Deprivation, Townsend Deprivation Index and Carstairs Index, and Rural-Urban Classification, which are available at the LSOA level for linkage to CPRD primary care data through the practice postcode. Additionally, Sub-Integrated Care Board Locations (Sub-ICB Locs) pseudonym (practice level, England-only) is available. Access is provided by CPRD subject to protocol approval. Further information is available at https://www.cprd.com/linked-data.
DOI: 10.34636/dmportal/pvydgz
title: Sample and Procedure Metadata of Whole-Genome Sequencing of 20 Rice Varieties

description: Within the scope of the TRACE-RICE project, samples of 20 rice varieties were collected and ordered to sequence by Whole-genome sequencing. This dataset contains metadata of the biological material used, the sequencing procedure and FastQC quality reports. The raw 20 pairs of FASTQ files (40 in total), generated by paired-end high-throughoutput Illumina sequencing, are deposited and annotated in ENA under the PRJEB64146 project ID, with each pair corresponding to one rice variety (e.g., Albatros, Manobi, etc.).
DOI: 10.34636/dmportal/pvydgz/pafrgg
title: MIAPPE_v1.1_TRACE-RICE.tab

description: :unav
DOI: 10.6084/m9.figshare.28001798.v1
title: Supplementary File 1 - Health Security Disparities in the Eastern Mediterranean Region

description: Summary: This supplementary document provides additional evidence for our research titled "Health Security Disparities in the Eastern Mediterranean Region: A Comparative Analysis Using an Integrated MCDM and Clustering Approach." It presents supplementary context and data tables to complement the primary analysis and results. This paper is structured into four sections. The first section delineates the primary health security criteria used to assess countries and their descriptions, which were applied to the decision matrices for 2019 and 2021. It also elucidates the information from the initial research phase, wherein decision matrices were constructed to establish health security criteria weights, ranks, and group countries. The second section presents the entropy calculation results employed to determine the significance of health security indicators for Eastern Mediterranean Region countries, including Gulf Cooperation Council (GCC) and non-GCC nations, for both 2019 and 2021. The third section examines the application of the Entropy-VIKOT model to rank these countries' health security performance during the aforementioned years. The final section presents the clustering analysis, which categorizes countries based on their health security performance scores derived from the Entropy-VIKOT model. This analysis identified distinct performance clusters and assigned grades, demonstrating the distribution of countries across regional groups (GCC and non-GCC countries) in both years.
DOI: 10.15468/dl.watck3
title: Occurrence Download

description: A dataset containing 2444 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 {
 "and" : [
 "Geometry POLYGON((-97.01028942240706 42.882851694986755,-97.01028942240706 33.77583663949228,-70.09064458193029 33.77583663949228,-70.09064458193029 42.882851694986755,-97.01028942240706 42.882851694986755))",
 "TaxonKey is one of (Myotis grisescens A.H.Howell, 1909)"
 ]
 }
 ]
}

 The dataset includes 2444 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028979-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7gyr4
title: Occurrence Download

description: A dataset containing 366 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 {
 "and" : [
 "Geometry POLYGON((-95.14785687579494 45.1316890986848,-95.14785687579494 34.9669292402162,-64.33238071683289 34.9669292402162,-64.33238071683289 45.1316890986848,-95.14785687579494 45.1316890986848))",
 "TaxonKey is one of (Myotis septentrionalis (Trouessart, 1897))"
 ]
 }
 ]
}

 The dataset includes 366 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028981-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ye684s
title: Occurrence Download

description: A dataset containing 1711 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 {
 "and" : [
 "Geometry POLYGON((-93.7044673445191 43.89825431577523,-93.7044673445191 34.27644395600696,-64.94963327376936 34.27644395600696,-64.94963327376936 43.89825431577523,-93.7044673445191 43.89825431577523))",
 "TaxonKey is one of (Myotis sodalis Miller & G.M.Allen, 1928)"
 ]
 }
 ]
}

 The dataset includes 1711 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028980-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a366kt
title: Occurrence Download

description: A dataset containing 98 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leontocebus fuscus (Lesson, 1840)"
 ]
}

 The dataset includes 98 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028982-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.raufhk
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((-84.78759 46.7842,-84.33289 46.7842,-84.33289 47.01352,-84.78759 47.01352,-84.78759 46.7842))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Parmotrema crinitum (Ach.) M.Choisy"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028985-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbj3wf
title: Occurrence Download

description: A dataset containing 276 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 {
 "and" : [
 "Geometry POLYGON((-91.4307677944354 43.6206022613857,-91.4307677944354 35.81556207657759,-67.91442572659919 35.81556207657759,-67.91442572659919 43.6206022613857,-91.4307677944354 43.6206022613857))",
 "TaxonKey is one of (Pleurobema clava (Lamarck, 1819))"
 ]
 }
 ]
}

 The dataset includes 276 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028986-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14364672
title: EPONYMS IN ONOMASTICS: LINGUISTIC, CULTURAL, AND HISTORICAL DIMENSIONS
DOI: 10.5281/zenodo.14364673
title: EPONYMS IN ONOMASTICS: LINGUISTIC, CULTURAL, AND HISTORICAL DIMENSIONS
DOI: 10.5281/zenodo.10647220
title: Simulation input scripts for "Resonant emittance mixing of flat beams in plasma accelerators"

description: This dataset presents the input scripts required to re-create the data of the figures in the article "Emittance mixing of flat beams in plasma accelerators".
DOI: 10.5281/zenodo.10647219
title: Simulation input scripts for "Resonant emittance mixing of flat beams in plasma accelerators"

description: This dataset presents the input scripts required to re-create the data of the figures in the article "Emittance mixing of flat beams in plasma accelerators".
DOI: 10.5281/zenodo.14364627
title: Simulation input scripts for "Resonant emittance mixing of flat beams in plasma accelerators"

description: This dataset presents the input scripts required to re-create the data of the figures in the article "Emittance mixing of flat beams in plasma accelerators".
DOI: 10.15468/dl.6djz95
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 {
 "and" : [
 "Geometry POLYGON((-101.30597691571612 44.457146452162846,-101.30597691571612 32.574545882786126,-66.03086178954109 32.574545882786126,-66.03086178954109 44.457146452162846,-101.30597691571612 44.457146452162846))",
 "TaxonKey is one of (Cyprogenia stegaria (Rafinesque, 1820))"
 ]
 }
 ]
}

 The dataset includes 306 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028987-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69uggc
title: Occurrence Download

description: A dataset containing 626 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 {
 "and" : [
 "Geometry POLYGON((-94.28690214503438 43.24331573567153,-94.28690214503438 34.49663390602332,-68.24045116980791 34.49663390602332,-68.24045116980791 43.24331573567153,-94.28690214503438 43.24331573567153))",
 "TaxonKey is one of (Fusconaia subrotunda (I.Lea, 1831))"
 ]
 }
 ]
}

 The dataset includes 626 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028989-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sx9utd
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cystodermella granulosa (Batsch) Harmaja"
 ]
}

 The dataset includes 100 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028988-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tt73nq
title: Occurrence Download

description: A dataset containing 8854 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Benthic biota of CIMAR-Fiordos and Southern Ice Field Cruises"
 ]
}

 The dataset includes 8854 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028990-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9yneh7
title: Occurrence Download

description: A dataset containing 494 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Epioblasma rangiana (I.Lea, 1838))"
 ]
}

 The dataset includes 494 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028991-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u3mqs7
title: Occurrence Download

description: A dataset containing 36515 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Taxon occurrence data for the FungalRoot database"
 ]
}

 The dataset includes 36515 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028992-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.