cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ny55jz
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scoloplax dicra",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 43 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012970-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g59dvk
title: Occurrence Download

description: A dataset containing 21130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Micropterus punctulatus",
 "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 21130 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012969-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n5ppdd
title: Occurrence Download

description: A dataset containing 1636 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trichostigma octandrum",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 1636 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012971-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5683/sp3/iaxg9q
title: Replication Code for: Of hired guns and ideologues: why would a law firm ever retain an honest expert witness?

description: The programs replicate figures from "Of hired guns and ideologues: why would a law firm ever retain an honest expert witness?", by Martin Richardson and Jose Rodrigues-Neto. Please see the ReadMe file for additional details.
description: GAUSS, 24.03
DOI: 10.15468/dl.jg8t9k
title: Occurrence Download

description: A dataset containing 2304 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solanum granulosoleprosum",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 2304 records from 133 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012972-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gg9fxc
title: Occurrence Download

description: A dataset containing 1107369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Belgium, Germany, Netherlands)",
 "TaxonKey is one of (Ondatra zibethicus, Myocastor coypus)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1107369 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012882-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w5xbhz
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polymorphus contortus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 24 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012973-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3p8u8s
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schlechterella abyssinica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012974-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8yrnj2
title: Occurrence Download

description: A dataset containing 124589 species occurrences available in GBIF matching the query:
{
 "and" : [
 "KingdomKey is Plantae",
 "Country is Guatemala",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Machine Observation)"
 ]
}

 The dataset includes 124589 records from 212 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012918-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzngqg
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scoloplax dolicholophia",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 45 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012976-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e245216
title: Minimum Data Set Frequency

description: The Minimum Data Set (MDS) Frequency data summarizes health status indicators for active residents currently in nursing homes. The MDS is part of the Federally-mandated process for clinical assessment of all residents in Medicare and Medicaid certified nursing homes. This process provides a comprehensive assessment of each resident's functional capabilities and helps nursing home staff identify health problems. Care Area Assessments (CAAs) are part of this process, and provide the foundation upon which a resident's individual care plan is formulated. MDS assessments are completed for all residents in certified nursing homes, regardless of source of payment for the individual resident. MDS assessments are required for residents on admission to the nursing facility, periodically, and on discharge. All assessments are completed within specific guidelines and time frames. In most cases, participants in the assessment process are licensed health care professionals employed by the nursing home. MDS information is transmitted electronically by nursing homes to the national MDS database at CMS.<br><br>This dataset is based on the resident's MDS assessment record. The MDS assessment information for each active nursing home resident is consolidated to create a profile of the most recent standard information for the resident.
DOI: 10.3886/e245216v1
title: Minimum Data Set Frequency

description: The Minimum Data Set (MDS) Frequency data summarizes health status indicators for active residents currently in nursing homes. The MDS is part of the Federally-mandated process for clinical assessment of all residents in Medicare and Medicaid certified nursing homes. This process provides a comprehensive assessment of each resident's functional capabilities and helps nursing home staff identify health problems. Care Area Assessments (CAAs) are part of this process, and provide the foundation upon which a resident's individual care plan is formulated. MDS assessments are completed for all residents in certified nursing homes, regardless of source of payment for the individual resident. MDS assessments are required for residents on admission to the nursing facility, periodically, and on discharge. All assessments are completed within specific guidelines and time frames. In most cases, participants in the assessment process are licensed health care professionals employed by the nursing home. MDS information is transmitted electronically by nursing homes to the national MDS database at CMS.<br><br>This dataset is based on the resident's MDS assessment record. The MDS assessment information for each active nursing home resident is consolidated to create a profile of the most recent standard information for the resident.
DOI: 10.15468/dl.999vgb
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polymorphus minutus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 28 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012981-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frk647
title: Occurrence Download

description: A dataset containing 1102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apeiba glabra",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 1102 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012977-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.79whwa
title: Occurrence Download

description: A dataset containing 16317 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trema micranthum",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 16317 records from 502 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012979-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.29annq
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bothrops sazimai"
 ]
}

 The dataset includes 15 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012982-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sktddw
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Corallus batesii"
 ]
}

 The dataset includes 270 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012983-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mny2ye
title: Occurrence Download

description: A dataset containing 211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Secamone schweinfurthii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 211 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012984-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18626136
title: Trajectory for MD simulation on EGFR in the fluid membrane

description: Trajectory for MD simulation on EGFR TM-JM sequence in the fluid membrane.

Protein:

- Source: PDB entry (EGFR transmembrane-juxtamembrane domain structure)

- Number of copies: 2

- Chains labeled A, B

- Conversion: martinize2 version 2.6 with elastic network constraints

 

Membrane:

- Box dimensions: 10 × 10 × 15 nm³

 

Upper leaflet (analyzed):

- DIPC: 100 mol% 

Lower leaflet (not analyzed):



DIPC: 70 mol%

DIPS (dilinoleoyl phosphatidylserine): 30mol%


 

Force field: MARTINI 2.2 with MARTINI protein model

Electrostatics:

- Method: Reaction-field

- Cutoff: 1.2 nm

- Relative dielectric constant (εᵣ): 15 (MARTINI standard)

 

Van der Waals:

- Method: Shifted potential

- Cutoff: 1.2 nm

- Switch: 1.0 nm (shifted to zero at cutoff)

 

Constraints:

- Protein elastic network: Enabled (maintains secondary structure)

- Cutoff: 0.9 nm (backbone beads)

- Force constant: 500 kJ mol⁻¹ nm⁻²

- Bond constraints: None (MARTINI uses harmonic bonds)

 

Lipid parameters:

- DIPC: MARTINI lipid type "C1A" headgroup, "C1" tail beads

- DOPS: MARTINI lipid type "C1A" headgroup with charge

 

S2.3 Simulation Protocols

S2.3.1 Energy Minimization

- Algorithm: Steepest descent

- Convergence criterion: Maximum force < 10 kJ mol⁻¹ nm⁻¹

- Typical steps: 5,000-10,000

- Purpose: Remove steric clashes from initial structure

 

S2.3.2 Equilibration

Duration: 100 ns

Ensemble: NPT (constant number, pressure, temperature)

Temperature control:

- Target: 298 K

- Thermostat: Velocity-rescale (v-rescale, modified Berendsen)

- Time constant: 1.0 ps

- Coupling groups: Protein, lipids, solvent (separately coupled)

Pressure control:

- Target: 1 bar

- Barostat: Semi-isotropic Berendsen

- Time constant: 5.0 ps

- Compressibility: 3 × 10⁻⁴ bar⁻¹

- Semi-isotropic: xy plane coupled, z independent

Integration:

- Time step: 20 fs (0.020 ps, standard for MARTINI)

- Neighbor list update: every 10 steps

Position restraints:

- Protein backbone: 1000 kJ mol⁻¹ nm⁻² (first 50 ns)

- Released gradually over 50-100 ns

Output:

- Coordinates: every 1 ns

- Energies: every 100 ps

 

S2.3.3 Production Run

Duration: 10 μs total for all systems

Ensemble: NPT

Temperature control:

- Same as equilibration (298 K, v-rescale, τ = 1.0 ps)

Pressure control:

- Target: 1 bar

- Barostat: Parrinello-Rahman (more accurate than Berendsen for production)

- Time constant: 12.0 ps (longer than equilibration to reduce fluctuations)

- Compressibility: 3 × 10⁻⁴ bar⁻¹

- Semi-isotropic: xy plane coupled, z independent

Integration:

- Time step: 20 fs

- Neighbor list update: every 10 steps (with Verlet scheme)

Output frequencies:

- Coordinates: every 100 ps (5000 steps)

- Energies: every 100 ps

- Velocities: not saved (to reduce file size)

- Forces: not saved

Periodic boundary conditions: xyz (all dimensions)

Neighbor searching:

- Method: Verlet cutoff scheme

- Cutoff: 1.4 nm

- Update frequency: automatically determined by GROMACS
DOI: 10.5281/zenodo.18626137
title: Trajectory for MD simulation on EGFR in the fluid membrane

description: Trajectory for MD simulation on EGFR TM-JM sequence in the fluid membrane.

Protein:

- Source: PDB entry (EGFR transmembrane-juxtamembrane domain structure)

- Number of copies: 2

- Chains labeled A, B

- Conversion: martinize2 version 2.6 with elastic network constraints

 

Membrane:

- Box dimensions: 10 × 10 × 15 nm³

 

Upper leaflet (analyzed):

- DIPC: 100 mol% 

Lower leaflet (not analyzed):



DIPC: 70 mol%

DIPS (dilinoleoyl phosphatidylserine): 30mol%


 

Force field: MARTINI 2.2 with MARTINI protein model

Electrostatics:

- Method: Reaction-field

- Cutoff: 1.2 nm

- Relative dielectric constant (εᵣ): 15 (MARTINI standard)

 

Van der Waals:

- Method: Shifted potential

- Cutoff: 1.2 nm

- Switch: 1.0 nm (shifted to zero at cutoff)

 

Constraints:

- Protein elastic network: Enabled (maintains secondary structure)

- Cutoff: 0.9 nm (backbone beads)

- Force constant: 500 kJ mol⁻¹ nm⁻²

- Bond constraints: None (MARTINI uses harmonic bonds)

 

Lipid parameters:

- DIPC: MARTINI lipid type "C1A" headgroup, "C1" tail beads

- DOPS: MARTINI lipid type "C1A" headgroup with charge

 

S2.3 Simulation Protocols

S2.3.1 Energy Minimization

- Algorithm: Steepest descent

- Convergence criterion: Maximum force < 10 kJ mol⁻¹ nm⁻¹

- Typical steps: 5,000-10,000

- Purpose: Remove steric clashes from initial structure

 

S2.3.2 Equilibration

Duration: 100 ns

Ensemble: NPT (constant number, pressure, temperature)

Temperature control:

- Target: 298 K

- Thermostat: Velocity-rescale (v-rescale, modified Berendsen)

- Time constant: 1.0 ps

- Coupling groups: Protein, lipids, solvent (separately coupled)

Pressure control:

- Target: 1 bar

- Barostat: Semi-isotropic Berendsen

- Time constant: 5.0 ps

- Compressibility: 3 × 10⁻⁴ bar⁻¹

- Semi-isotropic: xy plane coupled, z independent

Integration:

- Time step: 20 fs (0.020 ps, standard for MARTINI)

- Neighbor list update: every 10 steps

Position restraints:

- Protein backbone: 1000 kJ mol⁻¹ nm⁻² (first 50 ns)

- Released gradually over 50-100 ns

Output:

- Coordinates: every 1 ns

- Energies: every 100 ps

 

S2.3.3 Production Run

Duration: 10 μs total for all systems

Ensemble: NPT

Temperature control:

- Same as equilibration (298 K, v-rescale, τ = 1.0 ps)

Pressure control:

- Target: 1 bar

- Barostat: Parrinello-Rahman (more accurate than Berendsen for production)

- Time constant: 12.0 ps (longer than equilibration to reduce fluctuations)

- Compressibility: 3 × 10⁻⁴ bar⁻¹

- Semi-isotropic: xy plane coupled, z independent

Integration:

- Time step: 20 fs

- Neighbor list update: every 10 steps (with Verlet scheme)

Output frequencies:

- Coordinates: every 100 ps (5000 steps)

- Energies: every 100 ps

- Velocities: not saved (to reduce file size)

- Forces: not saved

Periodic boundary conditions: xyz (all dimensions)

Neighbor searching:

- Method: Verlet cutoff scheme

- Cutoff: 1.4 nm

- Update frequency: automatically determined by GROMACS
DOI: 10.15468/dl.dsdku5
title: Occurrence Download

description: A dataset containing 172845 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Eucalyptus viminalis, Gleditsia triacanthos, Salix cantabrica)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 172845 records from 637 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012924-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id332089.1
title: StrainInfo SI-ID 332089.1

description: StrainInfo dataset 332089 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332090.1
title: StrainInfo SI-ID 332090.1

description: StrainInfo dataset 332090 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332091.1
title: StrainInfo SI-ID 332091.1

description: StrainInfo dataset 332091 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332092.1
title: StrainInfo SI-ID 332092.1

description: StrainInfo dataset 332092 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332172.1
title: StrainInfo SI-ID 332172.1

description: StrainInfo dataset 332172 about a strain of Neurospora tetrasperma. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332173.1
title: StrainInfo SI-ID 332173.1

description: StrainInfo dataset 332173 about a strain of Neurospora tetrasperma. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332174.1
title: StrainInfo SI-ID 332174.1

description: StrainInfo dataset 332174 about a strain of Neurospora sitophila. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332175.1
title: StrainInfo SI-ID 332175.1

description: StrainInfo dataset 332175 about a strain of Fusarium solani. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332017.1
title: StrainInfo SI-ID 332017.1

description: StrainInfo dataset 332017 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332018.1
title: StrainInfo SI-ID 332018.1

description: StrainInfo dataset 332018 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332019.1
title: StrainInfo SI-ID 332019.1

description: StrainInfo dataset 332019 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332020.1
title: StrainInfo SI-ID 332020.1

description: StrainInfo dataset 332020 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332093.1
title: StrainInfo SI-ID 332093.1

description: StrainInfo dataset 332093 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332094.1
title: StrainInfo SI-ID 332094.1

description: StrainInfo dataset 332094 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id332095.1
title: StrainInfo SI-ID 332095.1

description: StrainInfo dataset 332095 about a strain of Fusarium verticillioides. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.