cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.zck7e2
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptopsammia pruvoti Lacaze-Duthiers, 1897",
 "HasGeospatialIssue is true",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014330-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p38gr9
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Ecuador",
 "TaxonKey is Tapirus terrestris (Linnaeus, 1758)"
 ]
}

 The dataset includes 159 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194819-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pwmtjh
title: Occurrence Download

description: A dataset containing 1284897 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2024-04-04",
 "EventDate is less than or equal to 2024-05-04",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 1284897 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049985-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.93w4ky
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Ethiopia",
 "HasCoordinate is true",
 "TaxonKey is Pelomys Peters, 1852",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014057-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bctcy2
title: Occurrence Download

description: A dataset containing 2168 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "TaxonKey is Lomatium macrocarpum (Hook. & Arn.) J.M.Coult. & Rose"
 ]
}

 The dataset includes 2168 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0227939-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17118845
title: Data for ''Finite steady-state current defies non-Hermitian many-body localization"

description: The datafiles collect the numerical simulations for the steady state current, the steady state gap and the dynamical current.

Each dataset corresponds to a value of h and contains the result for the various disorder realizations.

The TEBD data report the current in the middle of the chain, namely in the central 25-50 sites, depending on the disorder strength. The plateaus are obtained by averaging in time over long time windows t = 100-800.

Data were obtained at the Vienna Scientific Cluster (VSC).  This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/COE1,Grant Agreement No. 10.55776/ESP9057324].
DOI: 10.5281/zenodo.17118846
title: Data for ''Finite steady-state current defies non-Hermitian many-body localization"

description: The datafiles collect the numerical simulations for the steady state current, the steady state gap and the dynamical current.

Each dataset corresponds to a value of h and contains the result for the various disorder realizations.

The TEBD data report the current in the middle of the chain, namely in the central 25-50 sites, depending on the disorder strength. The plateaus are obtained by averaging in time over long time windows t = 100-800.

Data were obtained at the Vienna Scientific Cluster (VSC).  This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/COE1,Grant Agreement No. 10.55776/ESP9057324].
DOI: 10.15468/dl.mdwsxv
title: Occurrence Download

description: A dataset containing 997 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atheta trinotata (Kraatz, 1856))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 997 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071113-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7pmmgv
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year is 2003",
 "TaxonKey is Vulpes Frisch, 1775",
 "Geometry MULTIPOLYGON (((-8.161857 41.85906, -8.527224 42.07702, -8.880565 41.752, -8.644973 41.01597, -9.077983 39.58985, -9.365945 39.34838, -9.48594 38.71047, -8.825615 38.0493, -8.807188 37.41877, -8.60226 37.12299, -7.897836 36.96982, -7.406357 37.17109, -7.522943 37.55345, -7.202615 38.00281, -7.317024 38.43926, -6.981906 39.0884, -7.295541 39.45596, -6.874204 39.99583, -6.860683 40.94946, -6.189352 41.57505, -6.516733 41.8729, -8.161857 41.85906)))"
 ]
}

 The dataset includes 21 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071114-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10813969
title: Choice of the right supporting electrolyte in electrochemical reductions: a principal component analysis

description: Introduction

This dataset contains the raw data as well as an HTML-based visualization of our dataset using Python Bokeh. We have also added a feature to highlight commercially available supporting electrolytes. The data is taken from the PubChem database. For each of the 6650 cations, the known neutral compounds in the PubChem dataset were identified with their corresponding anions. For each of these compounds, the vendor information stored in PubChem was queried.

Directory structure



Raw Data



[raw_data.tar.xz] Compressed directory with the output from the automated feature calculation.

[raw_data.csv] CSV file with the values of the calculated properties of all cations.



Visualization



[pca_qac_tool_QC.html] HTML page with Javascript to display PC1 and PC2 for the quantum chemical PCA model.

[pca_qac_tool_RDKit.html] HTML page with Javascript to display PC1 and PC2 for the PCA model based on non empirical RDKit descriptors.



Tools



[pca_qac_tool.py] Python script to generate the HTML output using Bokeh. Depends on the data_pca_qac.csv and the data_commercial.json file.

[PubChem_get_Vendor_information.py] Crawler that checks a list of PubChem CIDs for net-neutral compounds and whether they are commercially available.

[RDKit_Descriptor-2D.py] Python script to calculate all available 2D RDkit descriptors based on a list of SMILES strings.

[RDKit_Descriptor-3D.py] Python script to calculate the RDKit 3D descriptors based on the CREST and ORCA GeoOpt geometries.
DOI: 10.5281/zenodo.10478550
title: Choice of the right supporting electrolyte in electrochemical reductions: a principal component analysis

description: Introduction

This dataset contains the raw data as well as an HTML-based visualization of our dataset using Python Bokeh. We have also added a feature to highlight commercially available supporting electrolytes. The data is taken from the PubChem database. For each of the 6650 cations, the known neutral compounds in the PubChem dataset were identified with their corresponding anions. For each of these compounds, the vendor information stored in PubChem was queried.

Directory structure



Raw Data



[raw_data.tar.xz] Compressed directory with the output from the automated feature calculation.

[raw_data.csv] CSV file with the values of the calculated properties of all cations.



Visualization



[pca_qac_tool_QC.html] HTML page with Javascript to display PC1 and PC2 for the quantum chemical PCA model.

[pca_qac_tool_RDKit.html] HTML page with Javascript to display PC1 and PC2 for the PCA model based on non empirical RDKit descriptors.



Tools



[pca_qac_tool.py] Python script to generate the HTML output using Bokeh. Depends on the data_pca_qac.csv and the data_commercial.json file.

[PubChem_get_Vendor_information.py] Crawler that checks a list of PubChem CIDs for net-neutral compounds and whether they are commercially available.

[RDKit_Descriptor-2D.py] Python script to calculate all available 2D RDkit descriptors based on a list of SMILES strings.

[RDKit_Descriptor-3D.py] Python script to calculate the RDKit 3D descriptors based on the CREST and ORCA GeoOpt geometries.
DOI: 10.15468/dl.mggz97
title: Occurrence Download

description: A dataset containing 536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gyrophaena joyioides Wüsthoff, 1937)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 536 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071115-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11615993
title: Growth, nutrient uptake, blood metabolites and bone properties in broilers consuming feed with mineral-enriched whole black soldier fly larvae

description: Recycling critical minerals like phosphorus is essential for future circular agriculture. This study explored adding mineral-enriched black soldier fly larvae (BSFL), grown on substrates with sewage sludge recyclates (SSR), to broiler feed to reintroduce minerals from restricted waste streams into the nutrient cycle. Results showed that including 15% mineral-enriched BSFL in broiler diets for 42 days had no adverse effects on growth, nutrient intake, or bone condition, and maintained acceptable levels of heavy metals.
DOI: 10.5281/zenodo.11615994
title: Growth, nutrient uptake, blood metabolites and bone properties in broilers consuming feed with mineral-enriched whole black soldier fly larvae

description: Recycling critical minerals like phosphorus is essential for future circular agriculture. This study explored adding mineral-enriched black soldier fly larvae (BSFL), grown on substrates with sewage sludge recyclates (SSR), to broiler feed to reintroduce minerals from restricted waste streams into the nutrient cycle. Results showed that including 15% mineral-enriched BSFL in broiler diets for 42 days had no adverse effects on growth, nutrient intake, or bone condition, and maintained acceptable levels of heavy metals.
DOI: 10.25625/47scuz/kayjsx
title: Plot_info_and_covariables.tab

description: Plot covariables
Summary of environemtal and animal varaibles per plot
DOI: 10.25625/47scuz/tn4bsz
title: ReadMe _Beech_seedfate and plot covariables.docx

description: Description of variables in dataset beech seedfate and plot_info_and_covariables
DOI: 10.25625/47scuz/fsyr0i
title: 2021-Beech_seedfate.tab

description: Information about the fate of beech seeds - Fagus sylvatica - placed in the Unterluss, Goehrede, Winnefeld and Nienover in 2021
DOI: 10.25625/47scuz
title: Data from "Forest composition shapes seed-rodent interactions in a gradient of broadleaves and conifers"

description: Data from "Forest composition shapes seed-rodent interactions in a gradient of broadleaves and conifers" Information about the fate of beech seeds - Fagus sylvatica - placed in the Unterluss, Goehrede, Winnefeld and Nienover in 2021 and 2022, and all variables that might affect seed fate: Seed production, mice and vole densities,understory vegetation, basal areas of Norway Spruce European beech and Douglas fir&gt; Please check Readme for detailed inforamtion on varaibles
DOI: 10.25625/47scuz/ic4sgn
title: 2022-Beech_seedfate.tab

description: Information about the fate of beech seeds - Fagus sylvatica - placed in the Unterluss, Goehrede, Winnefeld and Nienover in 2022
DOI: 10.6084/m9.figshare.26022460
title: PCCP_Khodov.zip

description: These files are for Data availability statements in the PCCP.
DOI: 10.6084/m9.figshare.26022460.v1
title: PCCP_Khodov.zip

description: These files are for Data availability statements in the PCCP.
DOI: 10.5281/zenodo.11582347
title: Complete Data Set, Raman spectra for strains A/Nebraska/14/2019 and A/Hawaii/47/2014 collected at 785 nm and 532 nm

description: This data contains Raman spectra for two different strains of Influenza A;  A/Nebraska/14/2019 which is an H1N1 subtype and A/Hawaii/47/2014 which is an H3N2 subtype. There contains data for 10 separate growth cultures (i.e. 10 files) for each subtype, collected at two different wavelengths; 785 nm and 532 nm. This makes a total of 40 files. Each file has 400 spectra collected. All spectra were collected at 100x with a 5 second accumulation time.
DOI: 10.5281/zenodo.11615634
title: Dataset S4-6: Leveraging co-evolutionary insights and AI-based structural modeling to unravel receptor-peptide ligand-binding mechanisms

description: Significance statement:

This study presents proof-of-concept for a rapid and inexpensive alternative to classical structure-based approaches for resolving ligand-receptor binding mechanisms. It relies on a multilayered bioinformatic approach that leverages genomic data across diverse species in combination with AI-based structural modeling to identify true ligand and receptor homologues, and subsequently predict their binding mechanisms. In silico findings were validated by multiple experimental approaches, which investigated the effect of amino acid changes in the proposed binding pockets on ligand-binding, complex formation with a co-receptor essential for downstream signaling, and activation of downstream signaling. Our analysis combining evolutionary insights, in silico modeling and functional validation provides a framework for structure-function analysis of other peptide-receptor pairs, which could be easily implemented by most laboratories.

Zip file contains:

Dataset S4: Plasmid maps of constructs used in this study.

Dataset S5: AFM and AF3 predicted structures (.pdb) and AFM confidence metrics (.pae)

Dataset S6: Unedited files (.tiff) of co-IP and western blotting.
DOI: 10.5281/zenodo.11615633
title: Dataset S4-6: Leveraging co-evolutionary insights and AI-based structural modeling to unravel receptor-peptide ligand-binding mechanisms

description: Significance statement:

This study presents proof-of-concept for a rapid and inexpensive alternative to classical structure-based approaches for resolving ligand-receptor binding mechanisms. It relies on a multilayered bioinformatic approach that leverages genomic data across diverse species in combination with AI-based structural modeling to identify true ligand and receptor homologues, and subsequently predict their binding mechanisms. In silico findings were validated by multiple experimental approaches, which investigated the effect of amino acid changes in the proposed binding pockets on ligand-binding, complex formation with a co-receptor essential for downstream signaling, and activation of downstream signaling. Our analysis combining evolutionary insights, in silico modeling and functional validation provides a framework for structure-function analysis of other peptide-receptor pairs, which could be easily implemented by most laboratories.

Zip file contains:

Dataset S4: Plasmid maps of constructs used in this study.

Dataset S5: AFM and AF3 predicted structures (.pdb) and AFM confidence metrics (.pae)

Dataset S6: Unedited files (.tiff) of co-IP and western blotting.
DOI: 10.15468/dl.5wjpkf
title: Occurrence Download

description: A dataset containing 824 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myioborus albifrons (P.L.Sclater & Salvin, 1871)"
 ]
}

 The dataset includes 824 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071116-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnczgt
title: Occurrence Download

description: A dataset containing 241 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acrotona parens (Mulsant & Rey, 1851))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 241 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071117-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qeysw3
title: Occurrence Download

description: A dataset containing 192657 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ireland, Svalbard and Jan Mayen, Norway, Sweden, Finland, Estonia, Latvia, Denmark, Portugal, Spain, France, Germany, Netherlands, Switzerland, Austria, Italy, Greece, Türkiye, Russian Federation, Belarus, Ukraine, Poland, Czechia, Slovakia, Hungary, Romania, Bulgaria, Albania, Serbia, Slovenia, Bosnia and Herzegovina)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Epilobium montanum L."
 ]
}

 The dataset includes 192657 records from 750 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071112-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wxc7gh
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dienerella argus (Reitter, 1884))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 27 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071118-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9288k5
title: Occurrence Download

description: A dataset containing 976 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lessingianthus buddlejifolius (Mart. ex DC.) H.Rob."
 ]
}

 The dataset includes 976 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071119-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26022454
title: fmig-line.sgy

description: Seismic line
DOI: 10.15468/dl.dsde7g
title: Occurrence Download

description: A dataset containing 215892 records in GBIF matching the query:

SELECT 
 GBIF_EEARGCode(
 10000, 
 decimalLatitude,
 decimalLongitude,
 COALESCE(coordinateUncertaintyInMeters, 0) 
 ) AS cellcode,
 COUNT(DISTINCT speciesKey) AS unique_species_count
FROM
 occurrence
GROUP BY
 cellcode


 The dataset's 215892 records were derived from 74244 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071101-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5yu6r
title: Occurrence Download

description: A dataset containing 1441 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pinus koraiensis Siebold & Zucc."
 ]
}

 The dataset includes 1441 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071120-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f7qnf6
title: Occurrence Download

description: A dataset containing 306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dienerella filum (Aubé, 1850))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 306 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071121-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qu9ks
title: Occurrence Download

description: A dataset containing 1216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dipelta yunnanensis Franch., Dipelta yunnanensis var. brachycalyx Hand.-Mazz.)"
 ]
}

 The dataset includes 1216 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071122-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r56bdm
title: Occurrence Download

description: A dataset containing 207 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dienerella ruficollis (Marsham, 1802))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 207 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071123-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26019280.v1
title: Files

description: <br>This readme file was generated on 2024-06 by GABRIEL S. VICENTE FERREIRA<br>GENERAL INFORMATION<br>Title of Dataset: Body shape in colubrid snakes<br>Author/Principal Investigator InformationName: GABRIEL S. VICENTE FERREIRAORCID: https://orcid.org/0000-0002-0909-3579Institution: UNIVERSIDADE ESTADUAL DE CAMPINASAddress: Email: spangheri@gmail.com<br>Author/Associate or Co-investigator InformationName: Tiana KohlsdorfORCID: https://orcid.org/0000-0002-3873-2042Institution: UNIVERSIDADE DE SAO PAULOAddress: Email: <br>Date of data collection: 2018 - 2020<br>Geographic location of data collection: Brazil<br><br>DATA & FILE OVERVIEW<br>File List: traits: data table with ecological categories and morphological means for each speciestree: phylogenetic tree trimmed from Zaher (2019) with only the species that we had morphological data.code: code for comparative methods analyses<br>Relationship between files, if important: all files are need to conduct the analyses<br><br>METHODOLOGICAL INFORMATION<br>Instrument- or software-specific information needed to interpret the data: R Core Team version 4.3.2<br>People involved with sample collection, processing, analysis and/or submission: Gabriel Spanghero Vicente-Ferreira, Melissa Bars-Closel, Fábio Cury de Barros, Wilfried Klein, Tiana Kohlsdorf<br>
DOI: 10.48544/3421edb3-bcd1-497d-8e44-8fd324d7f540
title: Onderzoek Den Haag Seniorvriendelijke Stad 2022