cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13813360
title: Benchmarking Turbulence Models to Represent Cloud-Edge Mixing

description: This is the simulation output of the submitted manuscript "Benchmarking Turbulence Models to Represent Cloud-Edge Mixing" to the Journal of Atmospheric Sciences. 

Abstract: Considering turbulence is crucial to understand clouds. However, covering all scales involved in the turbulent mixing of clouds with their environment is computationally challenging, urging the need for simple models to represent some of the involved processes. By using full direct numerical simulations as a reference, this study compares several statistical approaches for representing small-scale turbulent mixing. All models use a comparable Lagrangian representation of cloud microphysics, and simulate the same cases of cloud edge mixing, covering different ambient humidities and turbulence intensities. It is demonstrated that all statistical models represent the evolution of thermodynamics successfully, but not all models capture the changes in cloud microphysics (cloud droplet number concentration, droplet mean radius, and spectral width). Implications of these results for using the presented models as subgrid-scale schemes are discussed.

The raw data presented here was produced by five different models and is completely available. For information on how the dataset is structured, see the readme.txt.
DOI: 10.15468/dl.3dxv6w
title: Occurrence Download

description: A dataset containing 1700 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Chrysodeixis chalcites (Esper, 1789)",
 "PhylumKey is Arthropoda",
 "Year is greater than or equal to 1992",
 "Year is less than or equal to 2012",
 "Geometry POLYGON((-26 34, 42 34, 42 70, -26 70, -26 34))"
 ]
}

 The dataset includes 1700 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020256-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aeurt3
title: Occurrence Download

description: A dataset containing 595 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is La liste (3) Rouge des plantes menacées de la Guinée"
 ]
}

 The dataset includes 595 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020259-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vtvxjf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Columba livia J.F.Gmelin, 1789)",
 "Country is one of (Spain)",
 "Year is greater than 2023",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020258-241007104925546/datasets/export for details.
DOI: 10.15468/dl.tdpar4
title: Occurrence Download

description: A dataset containing 30868 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-13.062 12.408,-10.26 12.408,-10.26 15.151,-13.062 15.151,-13.062 12.408))",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 30868 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020257-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y6tvz6
title: Occurrence Download

description: A dataset containing 608500 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Triticum aestivum L."
 ]
}

 The dataset includes 608500 records from 1078 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020240-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c94ysv
title: Occurrence Download

description: A dataset containing 595 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is La liste (3) Rouge des plantes menacées de la Guinée"
 ]
}

 The dataset includes 595 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020261-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fxjj3h
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Scoparia semiamplalis Warren, 1905",
 "PhylumKey is Arthropoda",
 "Year is greater than or equal to 1992",
 "Year is less than or equal to 2012",
 "Geometry POLYGON((-26 34, 42 34, 42 70, -26 70, -26 34))"
 ]
}

 The dataset includes 23 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020262-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mjt6rq
title: Occurrence Download

description: A dataset containing 595 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is La liste (3) Rouge des plantes menacées de la Guinée"
 ]
}

 The dataset includes 595 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020263-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ewwnqd
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Lepinotus reticulatus Enderlein, 1904",
 "PhylumKey is Arthropoda",
 "Year is greater than or equal to 1992",
 "Year is less than or equal to 2012",
 "Geometry POLYGON((-26 34, 42 34, 42 70, -26 70, -26 34))"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020265-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13946137
title: Data for: A computational pipeline to observe the flexibility and dynamics of (plant) cytochrome P450 binding sites

description: Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on human CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. Firstly, we use molecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyse a number of binding site properties - size, flexibility, shape, hydrophobicity, and accessibility - using the fpocket and mdpocket packages on MD-generated trajectories. This led to a first categorization of 15 chosen plant CYPs based on their binding site's (dis)similarities. The workflow was tested and verified on human CYPs 1A2, 2A6, and 3A4 as their binding site characteristics are well known. In addition to confirming known binding site properties, we identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. This study gives initial insights into the largely uncharted fields plant CYP substrate specificity and facilitates a more precise understanding of their largely unknown specific biological functions. It offers new insights into the structural and functional dynamics of plant CYPs, which may facilitate a more accurate understanding of the fate of agrochemicals or the biotechnological design and exploitation of enzymes with specific functions. Additionally, it serves as a reference for future structural-functional analyses of CYP enzymes across various biological kingdoms.
DOI: 10.5281/zenodo.13870508
title: Data for: A computational pipeline to observe the flexibility and dynamics of (plant) cytochrome P450 binding sites

description: Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on human CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. Firstly, we use molecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyse a number of binding site properties - size, flexibility, shape, hydrophobicity, and accessibility - using the fpocket and mdpocket packages on MD-generated trajectories. This led to a first categorization of 15 chosen plant CYPs based on their binding site's (dis)similarities. The workflow was tested and verified on human CYPs 1A2, 2A6, and 3A4 as their binding site characteristics are well known. In addition to confirming known binding site properties, we identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. This study gives initial insights into the largely uncharted fields plant CYP substrate specificity and facilitates a more precise understanding of their largely unknown specific biological functions. It offers new insights into the structural and functional dynamics of plant CYPs, which may facilitate a more accurate understanding of the fate of agrochemicals or the biotechnological design and exploitation of enzymes with specific functions. Additionally, it serves as a reference for future structural-functional analyses of CYP enzymes across various biological kingdoms.
DOI: 10.5281/zenodo.13870509
title: Data for: A computational pipeline for observing the flexibility and dynamics of (plant) cytochrome P450 binding sites

description: Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate sub-strates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on hu-man CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. Firstly, we use mo-lecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyse a number of binding site properties - size, flexibility, shape, hydrophobicity, and accessibility - us-ing the fpocket and mdpocket packages on MD-generated trajectories. This led to the categoriza-tion of 15 chosen plant CYPs based on their binding site’s (dis)similarities. The workflow was tested and verified on human CYPs 1A2, 2A6, and 3A4 as their binding site characteristics are well known. In addition to confirming known binding site properties, we identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. The results of this study lead a way to evaluate the substrate specificity of plant CYPs and to describe their interactions more precisely. It offers new insights into the structural and functional dynamics of plant CYPs, facili-tating the development of CYP-targeted applications in biotechnology and agriculture. Addition-ally, it serves as a reference for future structural-functional analyses of CYP enzymes across vari-ous biological kingdoms.
DOI: 10.15468/dl.max3x9
title: Occurrence Download

description: A dataset containing 6311 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "GadmGid is PRT.5_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ardea cinerea Linnaeus, 1758"
 ]
}

 The dataset includes 6311 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020266-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/9650855
title: EmotionalTurk
DOI: 10.15468/dl.q8zxpr
title: Occurrence Download

description: A dataset containing 4744642 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 "Continent is Europe",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Turdus merula Linnaeus, 1758",
 "Year 1974-2023"
 ]
}

 The dataset includes 4744642 records from 3069 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240324-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.myui8a
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Donax asper Hanley, 1845",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024731-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hz7a7d
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gnidia scabra Thunb."
 ]
}

 The dataset includes 92 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015208-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6s3ppg
title: Occurrence Download

description: A dataset containing 2515 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polybia occidentalis (Olivier, 1791)",
 "Year 1970-2024"
 ]
}

 The dataset includes 2515 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038511-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n2e865
title: Occurrence Download

description: A dataset containing 536 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plethodon amplus Highton & Peabody, 2000"
 ]
}

 The dataset includes 536 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011466-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.l5rzzg
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Espeletia barclayana Cuatrec.",
 "Country is Colombia",
 "Geometry POLYGON((-85.51 -2.11,-85.51 12.24,-62.82 12.24,-62.82 -2.11,-85.51 -2.11))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 122 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024733-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pasxj5
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium vinaceiforme Johanss. & Sam."
 ]
}

 The dataset includes 32 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021489-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9dcxkp
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is South America",
 "Country is Argentina",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Condylocarpon isthmicum (Vell.) A.DC."
 ]
}

 The dataset includes 56 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011446-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ldeqgu
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Donax asper Hanley, 1845",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024734-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.646zse
title: Occurrence Download

description: A dataset containing 3233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solanum melongena L.",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3233 records from 194 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015217-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8a7cce
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bathyraja richardsoni (Garrick, 1961)"
 ]
}

 The dataset includes 97 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011493-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bcrtrt
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Donax asper Hanley, 1845",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024735-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ddymcz
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Habenaria elongata R.Br."
 ]
}

 The dataset includes 120 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015225-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hxndaf
title: Occurrence Download

description: A dataset containing 5282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Trametes versicolor (L.) Lloyd",
 "Year 2022-2022"
 ]
}

 The dataset includes 5282 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015285-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.utwrnw
title: Occurrence Download

description: A dataset containing 360 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyura praeputialis (Heller, 1878)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 360 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071794-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vydqe1
title: Occurrence Download

description: A dataset containing 1758 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fregata magnificens Mathews, 1914",
 "Country is Colombia",
 "Geometry POLYGON((-85.51 -2.11,-85.51 12.24,-62.82 12.24,-62.82 -2.11,-85.51 -2.11))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1758 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024736-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4723gp
title: Occurrence Download

description: A dataset containing 36181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Luzula spicata (L.) DC.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 36181 records from 353 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003282-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hctyrq
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Habenaria excelsa S.Thomas & P.J.Cribb"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015275-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0nxn5c
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Donax punctatostriatus Hanley, 1843",
 "HasCoordinate is true"
 ]
}

 The dataset includes 42 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024737-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.