cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8056311
title: Role of lipid nanodomains for inhibitory FcγRIIb function

description: <strong>Dataset repository - Role of lipid nanodomains for inhibitory FcγRIIb function</strong> ============================== The repository contains setup files and parameter files for atomistic molecular dynamics (MD) simulations performed with the GROMACS 2021/2022 series. Modified trajectories for the post-processing analysis are further included. The repositiory corresponds to the following manuscript: Franziska Spiegel, Marius F.W. Trollmann, Sibel Kara, Matthias Pöhnl, Astrid F. Brandner, Falk Nimmerjahn, Anja Lux, Rainer A. Böckmann bioRxiv 2023.05.09.540011; doi: https://doi.org/10.1101/2023.05.09.540011 Corresponding authors: * Rainer A. Böckmann (rainer.boeckmann@fau.de) * Anja Lux (anja.lux@fau.de) ### XTC/TPRs Directories contain: * md.tpr: GROMACS run file for the whole system * md_nonsolvent.tpr: GROMACS run file for the non-solvent selection (Membrane-Protein only) * md_mol_center_dt10ns.xtc: GROMACS trajectories used during post-processing with a slightly larger spacing (10ns instead of 1ns). * topol.top: GROMACS topology file used for simulations * index.ndx: GROMACS index file used for simulations * toppar: Contains CHARMM36 forcefield parameters for lipids, protein and glycans in GROMACS readable format (.itp) * step6.6_equilibration.gro: Input structure of the last equilibration step (see step6.6_equilibration.mdp) that was used as inital structure for the production simulation * last_frame.gro: Output structure of the production simulation The preparation of the raw trajectories for post-processing was done with GROMACS using the commands: &gt;&gt; gmx trjconv -f md.xtc -s md.tpr -pbc mol -center -n md_traj.ndx -dt 1000 -o md_mol_center.xtc &gt;&gt; gmx trjconv -f md_mol_center.xtc -s md_nonsolvent.tpr -o md_mol_center_dt10ns.xtc -dt 10000 The group for centering was the transmembrane domain of the Fcg receptor, as output only the protein and the membrane was chosen. #### Wild type simulations (No Glycans) * wt_replica_0 * wt_replica_1 * wt_replica_2 * wt_replica_3 * wt_replica_4 * wt_replica_5 * wt_replica_6 * wt_replica_7 * wt_replica_8 #### Mutant simulations (No Glycans) * mut_replica_0 * mut_replica_1 * mut_replica_2 #### Wild type simulations (Glycans) * wt_glycan_replica_0 * wt_glycan_replica_1 * wt_glycan_replica_2 * wt_glycan_replica_3 ### Parameters Simulation parameter files (.mdp) are given for each equilibration step and the final production simulation. Initial input files are obtained from the CHARMM-GUI webserver. * simulation_parameters * mut_wt_no_glycans * wt_glycans ### Copyright This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
DOI: 10.34740/kaggle/dsv/5971694
title: Nigerian Presidential Election 2023 Tweets
DOI: 10.5281/zenodo.7794289
title: Windcrete Experimental Data

description: The shared folder contains the laboratory test data for the Windcrete platform, including results and experimental data. It also contains a report and a PowerPoint presentation as a schematic explanation of the data. <br> This data are an open experimental database for numerical modelling and future research. The context of this data is within the “corewind” project (D5.4).
DOI: 10.5281/zenodo.7794288
title: Windcrete Experimental Data

description: The shared folder contains the laboratory test data for the Windcrete platform, including results and experimental data. It also contains a report and a PowerPoint presentation as a schematic explanation of the data. <br> This data are an open experimental database for numerical modelling and future research. The context of this data is within the “corewind” project (D5.4).
DOI: 10.6084/m9.figshare.23541432.v3
title: ca51f

description: ca51f
DOI: 10.5281/zenodo.7794406
title: Mooring Tests Data

description: The shared folder contains the laboratory test data for the mooring lines. It includes the configurations carried out for the two types of lines: ALL-CHAIN configuration (regular, irregular and tension-deformation subfolders) and CHAIN-NYLON configuration (regular and tension-deformation subfolders). It also contains a “readme” file as a schematic explanation of the data. This data are an open experimental database for numerical modelling and future research. The context of this data is within the “corewind” project (D5.4). For further information check Deliverable 5.2: “Mooring and cable dynamic testing report” of the Corewind project.
DOI: 10.5281/zenodo.7794405
title: Mooring Tests Data

description: The shared folder contains the laboratory test data for the mooring lines. It includes the configurations carried out for the two types of lines: ALL-CHAIN configuration (regular, irregular and tension-deformation subfolders) and CHAIN-NYLON configuration (regular and tension-deformation subfolders). It also contains a “readme” file as a schematic explanation of the data. This data are an open experimental database for numerical modelling and future research. The context of this data is within the “corewind” project (D5.4). For further information check Deliverable 5.2: “Mooring and cable dynamic testing report” of the Corewind project.
DOI: 10.6084/m9.figshare.22223725
title: uce_baits_plus.fasta

description: Fasta formatted sequences of baits designed from pentatomomorphan taxa by Faircloth (2017) that target 103 UCE loci, which <strong>also</strong> have additional coreoid exon- or transcript-derived baits targeting them. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6084/m9.figshare.22223725.v1
title: uce_baits_plus.fasta

description: Fasta formatted sequences of baits designed from pentatomomorphan taxa by Faircloth (2017) that target 103 UCE loci, which <strong>also</strong> have additional coreoid exon- or transcript-derived baits targeting them. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6084/m9.figshare.22223716
title: uce_baits_only.fasta

description: Fasta formatted sequences of baits designed from pentatomomorphan taxa by Faircloth (2017) that target 2566 UCE loci, which <strong>do not</strong> have additional coreoid exon- or transcript-derived baits targeting them. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6084/m9.figshare.22223716.v1
title: uce_baits_only.fasta

description: Fasta formatted sequences of baits designed from pentatomomorphan taxa by Faircloth (2017) that target 2566 UCE loci, which <strong>do not</strong> have additional coreoid exon- or transcript-derived baits targeting them. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6084/m9.figshare.22223710
title: Coreoidea-transcripts-final.fasta

description: Fasta formatted sequences of baits designed from five Coreoidea transcriptomes that target 58 entire transcripts (RNAseq-derived sequences that may include more than one exon, with baits potentially spanning across one or more introns) not targeted by the other baits. We recommend refering to Forthman et al. (see reference below) regarding the utility of these particular baits in target capture studies. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6084/m9.figshare.22223710.v1
title: Coreoidea-transcripts-final.fasta

description: Fasta formatted sequences of baits designed from five Coreoidea transcriptomes that target 58 entire transcripts (RNAseq-derived sequences that may include more than one exon, with baits potentially spanning across one or more introns) not targeted by the other baits. We recommend refering to Forthman et al. (see reference below) regarding the utility of these particular baits in target capture studies. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6084/m9.figshare.22223704
title: Coreoidea-exons-final.fasta

description: Fasta formatted sequences of baits designed from five Coreoidea transcriptomes that target 376 individual exon regions not targeted by the other baits. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6084/m9.figshare.22223704.v1
title: Coreoidea-exons-final.fasta

description: Fasta formatted sequences of baits designed from five Coreoidea transcriptomes that target 376 individual exon regions not targeted by the other baits. When using this data, cite: Forthman, M., Gordon, E.R.L., Kimball, R.T. 2023. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). <em>R. Soc. Open Sci</em>.
DOI: 10.6073/pasta/6e56960bb43fbcb29859c9e7178b7881
title: NUT01 Nutrient Network: Investigating the roles of nutrient availability and vertebrate herbivory on grassland structure and function at Konza Prairie

description: The goals and focal research questions are copied below from the Nutrient Network website. More information can be found at nutnet.org. NutNet focal research questions: (1) How general is our current understanding of productivity-diversity relationships? (2) To what extent are plant production and diversity co-limited by multiple nutrients in herbacoues-dominated communities? (3) Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? NutNet goals: (1) To collect data from a broad range of sites in a consistent manner to allow direct comparisons of environment-productivity-diversity relationships among systems around the world. This is currently occurring at each site in the network and, when these data are compiled, will allow us to provide new insights into several important, unanswered questions in ecology. (2) To implement a cross-site experiment requiring only nominal investment of time and resources by each investigator, but quantifying community and ecosystem responses in a wide range of herbaceous-dominated ecosystems (i.e., desert grasslands to arctic tundra).
DOI: 10.5281/zenodo.8055023
title: Supporting data to reproduce figures and anaylisis presented in Bruciaferri et al. 2023 - submitted to Journal of Advances in Modeling Earth Systems (JAMES)

description: Data for reproducing figures and the analysis of Diego Bruciaferri, Catherine Guiavarc’h, Helene T. Hewitt, James Harle, Mattia Almansi and Pierre Mathiot. Localised general vertical coordinates for quasi-Eulerian ocean models: the Nordic overflows test-case, submitted to JAMES. Data includes (© Crown copyright Met Office): 1) models_geometry: bathymetry, horizontal grid and domain files needed to run the models and analyse their results. 2) hpge: output data from HPG error idealised test. 3) ideal_ovf: output data from the idealised overflow experiment 4) realistic: output data from the realistic simulations
DOI: 10.5281/zenodo.8055022
title: Supporting data to reproduce figures and anaylisis presented in Bruciaferri et al. 2023 - submitted to Journal of Advances in Modeling Earth Systems (JAMES)

description: Data for reproducing figures and the analysis of Diego Bruciaferri, Catherine Guiavarc’h, Helene T. Hewitt, James Harle, Mattia Almansi and Pierre Mathiot. Localised general vertical coordinates for quasi-Eulerian ocean models: the Nordic overflows test-case, submitted to JAMES. Data includes (© Crown copyright Met Office): 1) models_geometry: bathymetry, horizontal grid and domain files needed to run the models and analyse their results. 2) hpge: output data from HPG error idealised test. 3) ideal_ovf: output data from the idealised overflow experiment 4) realistic: output data from the realistic simulations
DOI: 10.15468/dl.buwc2v
title: Occurrence Download

description: A dataset containing 5938 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Issue is one of (Zero coordinate, Coordinate out of range, Coordinate invalid, Coordinate rounded, Geodetic datum invalid, Geodetic datum assumed WGS84, Coordinate reprojected, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate accuracy invalid, Coordinate precision invalid, Coordinate uncertainty meters invalid, Coordinate precision/uncertainty mismatch, Footprint SRS invalid, Footprint WKT mismatch, Footprint WKT invalid, Country coordinate mismatch, Country mismatch, Country invalid, Country derived from coordinates, Continent coordinate mismatch, Continent country mismatch, Continent invalid, Continent derived from country, Continent derived from coordinates, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Recorded date mismatch, Recorded date invalid, Recorded date unlikely, Taxon match fuzzy, Taxon match higher rank, Taxon match aggregate, The scientific name ID was not used in backbone matching, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, The scientific name ID was not found in the checklist, The taxon concept ID was not found in the checklist, The taxon ID was not found in the checklist, The scientific name differs on the record from that found in the checklist, Taxon match none, The backbone match found using the taxon IDs differs from what would be found if using the scientific names , Depth not metric, Depth unlikely, Depth min max swapped, Depth non numeric, Elevation unlikely, Elevation min max swapped, Elevation not metric, Elevation non numeric, Modified date invalid, Modified date unlikely, Identified date unlikely, Identified date invalid, Basis of record invalid, Type status invalid, Multimedia date invalid, Multimedia URI invalid, References URI invalid, Error during interpretation, Individual count invalid, Individual count conflicts with occurrence status, Occurrence status unparsable, Occurrence status inferred from individual count, ccurrence status inferred from basis of record, Georeferenced date unlikely, Georeferenced date invalid, Ambiguous institution, Ambiguous collection, Institution match none, Collection match none, Institution match fuzzy, Collection match fuzzy, Institution collection mismatch, Possibly on loan, Different owner institution)",
 "OccurrenceStatus is Present",
 "TaxonKey is Cabralea A.Juss."
 ]
}

 The dataset includes 5938 records from 212 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114972-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kafcmh
title: Occurrence Download

description: A dataset containing 4314 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Schoenoxiphium ecklonii var. ecklonii, Cyperus violifolius J.I.Rodr. & O.Alfonso, Carex viridula var. viridula, Mariscus phleoides Nees ex Kunth, Tetraria compar C.B.Clarke, 1894, Fimbristylis schulzii Boeckeler, Scirpus orbicephalus Beetle, Trichophorum bracteatum (Bigelow) V.I.Krecz. ex Kuseneva, Scirpus uniflorum T.V.Egorova, Blysmopsis exilis Ivanina)"
 ]
}

 The dataset includes 4314 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0114973-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e7rv5s
title: Occurrence Download

description: A dataset containing 302 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Agave fourcroydes Lem.",
 "Year 1981-2023"
 ]
}

 The dataset includes 302 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255569-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bk57n9
title: Occurrence Download

description: A dataset containing 21466 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Acacia pycnantha Benth.",
 "Year 1981-2023"
 ]
}

 The dataset includes 21466 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0254224-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mvc89
title: Occurrence Download

description: A dataset containing 1539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Austrocylindropuntia subulata (Muehlenpf.) Backeb.",
 "Year 1981-2023"
 ]
}

 The dataset includes 1539 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255687-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mnx383
title: Occurrence Download

description: A dataset containing 413 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Amaranthus emarginatus Salzm. ex Uline & W.L.Bray",
 "Year 1981-2023"
 ]
}

 The dataset includes 413 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255573-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfn7uq
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bidens vulgata Greene",
 "Year 1981-2023"
 ]
}

 The dataset includes 284 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255649-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3dpd9v
title: Occurrence Download

description: A dataset containing 837 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chasmanthe floribunda (Salisb.) N.E.Br.",
 "Year 1981-2023"
 ]
}

 The dataset includes 837 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255706-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfbse4
title: Occurrence Download

description: A dataset containing 4577 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anredera cordifolia (Ten.) Steenis",
 "Year 1981-2023"
 ]
}

 The dataset includes 4577 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255598-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6n6fk2
title: Occurrence Download

description: A dataset containing 1570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nelumbo nucifera Gaertn.",
 "Year 1981-2023"
 ]
}

 The dataset includes 1570 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255773-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jbwa8p
title: Occurrence Download

description: A dataset containing 4594 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1090.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gomphocarpus fruticosus (L.) W.T.Aiton",
 "Year 1981-2023"
 ]
}

 The dataset includes 4594 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0259327-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvvv75
title: Occurrence Download

description: A dataset containing 10359 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Agave americana L.",
 "Year 1981-2023"
 ]
}

 The dataset includes 10359 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0254203-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6y6fmp
title: Occurrence Download

description: A dataset containing 1179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1060.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cenchrus longisetus M.C.Johnst.",
 "Year 1981-2023"
 ]
}

 The dataset includes 1179 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255689-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.