cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.334qa3
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oreochromis mossambicus",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009650-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ja6hes
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pycnoplinthopsis bhutanica"
 ]
}

 The dataset includes 31 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009651-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b738vy
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Batrachochytrium dendrobatidis",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 156 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009652-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u44a3j
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus hybridus",
 "Country is Nauru",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009654-250717081556266/datasets/export for details.
DOI: 10.15468/dl.5rafm3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudotocinclus intermedius"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009657-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkdc8y
title: Occurrence Download

description: A dataset containing 29817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (North America, South America)",
 "TaxonKey is Euterpe precatoria"
 ]
}

 The dataset includes 29817 records from 206 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009655-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2nq6u
title: Occurrence Download

description: A dataset containing 800 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Lithobates heckscheri)"
 ]
}

 The dataset includes 800 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009658-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/kdk-s76-f4q
title: Dicotyledoneae DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.15468/dl.rk82wh
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Odontarrhena samia"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009665-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b7ynt3
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oreochromis mossambicus",
 "Country is Guatemala",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009663-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hgnzx8
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lysichiton camtschatcensis",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 111 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009667-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xuvbxh
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Physaria cinerea"
 ]
}

 The dataset includes 168 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009668-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syy63b
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus hybridus",
 "Country is Nepal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009666-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8ajqr
title: Occurrence Download

description: A dataset containing 13296 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinguicula grandiflora"
 ]
}

 The dataset includes 13296 records from 321 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009660-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m7d3fx
title: Occurrence Download

description: A dataset containing 192805 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 192805 records from 171 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009631-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j996em
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Aquarana)"
 ]
}

 The dataset includes 62 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009671-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bh89m9
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psilorhynchus balitora"
 ]
}

 The dataset includes 96 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009669-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7wx25f
title: Occurrence Download

description: A dataset containing 3072 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus hybridus",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3072 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009670-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vyucdz
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Muscari armeniacum",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 94 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009673-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fzk43m
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus hybridus",
 "Country is Pakistan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 121 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009672-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aa53ww
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cardamine cheotaiyienii"
 ]
}

 The dataset includes 126 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009674-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/2xg-w0w-kf2
title: Rumex angustifolius Campd.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.15468/dl.t3bvtr
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oreochromis mossambicus",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 83 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009675-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dmdybm
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Matthiola daghestanica"
 ]
}

 The dataset includes 25 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009676-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xuge5v
title: Occurrence Download

description: A dataset containing 458 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus luchuensis"
 ]
}

 The dataset includes 458 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009677-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fduj78
title: Occurrence Download

description: A dataset containing 492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Lithobates kauffeldi)"
 ]
}

 The dataset includes 492 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009679-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pb9qfq
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ADR6531"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009680-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kb86jq
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oreochromis mossambicus",
 "Country is Indonesia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 41 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009681-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15238548
title: Coarse-Grained Molecular Dynamics Simulations of SARS-CoV-2 E Protein embedded in 100% POPC membrane

description: Coarse-grained MD simulations of the SARS-CoV-2 E protein (PDB ID: 5X29) embedded in 100% POPC lipids. 

Unless otherwise noted, all simulations were performed using GROMACS 2016 and the Martini 2.2 force field. The Berendsen thermostat was set to 313 K and a semi-isotropic Berendsen barostat was set to 1 bar in both directions. The compressibility modulus in both dimensions was 3 × 10−5 bar−1 with time constant 3 ps. Electrostatics and van der Waals (vdW) were shifted with a cutoff r-value of 1.2 nm. All systems underwent 100,000 steps of steepest-descent energy minimization prior to MD simulation with a timestep of 0.025 ps.

Comparisons of different combinations of restraint scheme and run-time parameters took place in a 100% POPC membrane with E protein embedded. In two simulations, protein back-bone beads were restrained to their initial coordinates via harmonic potential with a force constant of 2,000 kJ mol−1 nm−1. We describe this style of restraint as “absolute position restraints". We performed two different simulations: one with run-time parameter refcoord_scaling set to all, and one with the setting turned off (refcoord_scaling no). Both simulations were then simulated in the NPT ensemble. The refcoord_scaling no simulation used GROMACS version 2021.6 and the v-rescale thermostat, but all other settings remained the same.

We also performed two simulations with elastic network restraints instead of absolute position restraints. In our elastic networks, all protein backbone bead pairs within 1.4 nm of one another were bonded together with force constants of 5,000 kJ mol−1 nm−1 using the Martinize tool. One of these simulations (NPT ensemble) had identical settings to those listed in Common Settings. The second elastic network simulation (NVT ensemble) used GROMACS version 2021.6, the v-rescale thermostat, and utilized restraints to prevent diffusion, rotation, and tilt of the protein. Restraints were parameterized using the Colvars Dashboard. 

The absolute position restraint simulation with refcoord_scaling all ran for over 50 μs, with the membrane adopting a metastable conformation before 10 μs. The absolute position restraint simulation with refcoord_scaling no and the NPT elastic network simulation ran for at least 10 μs, which was more than sufficient for area per lipid (Σ) to converge. The NVT elastic network simulation ran for 2 μs.
DOI: 10.5281/zenodo.15238549
title: Coarse-Grained Molecular Dynamics Simulations of SARS-CoV-2 E Protein embedded in 100% POPC membrane

description: Coarse-grained MD simulations of the SARS-CoV-2 E protein (PDB ID: 5X29) embedded in 100% POPC lipids. 

Unless otherwise noted, all simulations were performed using GROMACS 2016 and the Martini 2.2 force field. The Berendsen thermostat was set to 313 K and a semi-isotropic Berendsen barostat was set to 1 bar in both directions. The compressibility modulus in both dimensions was 3 × 10−5 bar−1 with time constant 3 ps. Electrostatics and van der Waals (vdW) were shifted with a cutoff r-value of 1.2 nm. All systems underwent 100,000 steps of steepest-descent energy minimization prior to MD simulation with a timestep of 0.025 ps.

Comparisons of different combinations of restraint scheme and run-time parameters took place in a 100% POPC membrane with E protein embedded. In two simulations, protein back-bone beads were restrained to their initial coordinates via harmonic potential with a force constant of 2,000 kJ mol−1 nm−1. We describe this style of restraint as “absolute position restraints". We performed two different simulations: one with run-time parameter refcoord_scaling set to all, and one with the setting turned off (refcoord_scaling no). Both simulations were then simulated in the NPT ensemble. The refcoord_scaling no simulation used GROMACS version 2021.6 and the v-rescale thermostat, but all other settings remained the same.

We also performed two simulations with elastic network restraints instead of absolute position restraints. In our elastic networks, all protein backbone bead pairs within 1.4 nm of one another were bonded together with force constants of 5,000 kJ mol−1 nm−1 using the Martinize tool. One of these simulations (NPT ensemble) had identical settings to those listed in Common Settings. The second elastic network simulation (NVT ensemble) used GROMACS version 2021.6, the v-rescale thermostat, and utilized restraints to prevent diffusion, rotation, and tilt of the protein. Restraints were parameterized using the Colvars Dashboard. 

The absolute position restraint simulation with refcoord_scaling all ran for over 50 μs, with the membrane adopting a metastable conformation before 10 μs. The absolute position restraint simulation with refcoord_scaling no and the NPT elastic network simulation ran for at least 10 μs, which was more than sufficient for area per lipid (Σ) to converge. The NVT elastic network simulation ran for 2 μs.
DOI: 10.15468/dl.j4tenf
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus hybridus",
 "Country is Peru",
 "HasCoordinate is true"
 ]
}

 The dataset includes 69 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009683-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jbexy9
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Othocallis siberica",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 83 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009682-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k58dqx
title: Occurrence Download

description: A dataset containing 873289 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 873289 records from 187 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009653-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eav689
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oreochromis mossambicus",
 "Country is Jamaica",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009684-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8bdd4
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sterigmostemum billardierei"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009685-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uryt99
title: Occurrence Download

description: A dataset containing 7166 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Piper auritum"
 ]
}

 The dataset includes 7166 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009686-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8axt74
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus hybridus",
 "Country is Poland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 101 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009689-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.882eeg
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Lithobates okaloosae)"
 ]
}

 The dataset includes 61 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009687-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymqnpa
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AAH7984"
 ]
}

 The dataset includes 16 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009688-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tcqt6h
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oreochromis mossambicus",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009691-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekhgdw
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erucastrum palustre"
 ]
}

 The dataset includes 29 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009690-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9hp53n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus hybridus",
 "Country is Qatar",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009694-250717081556266/datasets/export for details.