cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/8n5-flb-zr4
title: Oliva dactyliola Duclos, 1840

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l5m-9rp-2qy
title: Costellariidae MacDonald, 1860

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1d9-ptp-8a7
title: Folinella excavata (R. A. Philippi, 1836)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6tw-r3t-4dv
title: Littoraria pallescens (R. A. Philippi, 1846)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tan-56l-bex
title: Chondrula tridens (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6kg-p7q-01s
title: Pholadidea melanura (G. B. Sowerby I, 1834)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8ml-h7b-p49
title: Bulla Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bm5-0g4-8mf
title: Truncatellina claustralis (Gredler, 1856)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rql-ssm-7p4
title: Atys Montfort, 1810

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bs1-69x-g9v
title: Odostomia J. Fleming, 1813

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5n0-j6t-ddj
title: Decipifus sixaolus Olsson & McGinty, 1958

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/at9-7ay-nxg
title: Anachis miser (G. B. Sowerby I, 1844)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p08-rkj-gc9
title: Cochlodina fimbriata (Rossmässler, 1835)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s8y-1lq-8bb
title: Olivella mica (Duclos, 1835)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y51-57k-sn3
title: Opeatostoma pseudodon (Burrow, 1815)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1ht-9ay-y0n
title: Olivella mica (Duclos, 1835)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pmx-1ze-pxn
title: Atlantilux gemmata (G. B. Sowerby II, 1874)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lgt-th3-png
title: Bathyarca philippiana (Nyst, 1848)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.zpskn9
title: Occurrence Download

description: A dataset containing 1287255 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fagus sylvatica"
 ]
}

 The dataset includes 1287255 records from 2325 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006874-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26033/767a-xe38
title: Hi-Res Galileo Ida NIMS Spectral Image Cubes

description: This bundle contains 17 channel spectral image cubes of asteroid 243 Ida ranging from 0.7 to 5.2 micrometers in wavelength in cgs units of radiance. These data were obtained by the Galileo spacecraft Near Infrared Mapping Spectrometer on August 28, 1993. They were radiometrically calibrated using calibration measurements obtained by the Near Infrared Mapping Spectrometer during its observations of Europa on June 28, 1996.
DOI: 10.15468/dl.ek28h3
title: Occurrence Download

description: A dataset containing 119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Culex simpsoni Theobald, 1905"
 ]
}

 The dataset includes 119 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005324-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15304903
title: THE ROLE OF MOVAROUNNAHR IN ISLAMIC CIVILIZATION
DOI: 10.5281/zenodo.15304904
title: THE ROLE OF MOVAROUNNAHR IN ISLAMIC CIVILIZATION
DOI: 10.5281/zenodo.15173050
title: PGL-BCG-TUB

description: This repository contains all the data produced regarding the study of DIM PGL TUB and PGL BCG in a unique membrane environnement. The simulations of  phase transition of 4-membrane systems are gathered in different repositories :- DIM : https://doi.org/10.5281/zenodo.15276372- PGL TUB : https://doi.org/10.5281/zenodo.15276359- PGL BCG : https://doi.org/10.5281/zenodo.15276346It also contains the Scripts necessary to reproduce Fig2 Fig3 Fig4 of the corresponding article (DOI to come soon), and MARTINI3 parameters of DIM, PGL TUB and PGL BCG mycobacterial lipids.Below, a short description of the methodology : 

We conducted all simulations building on our previous work on PDIM . The atomistic MD simulations were carried out with the Amber16 software (http://ambermd.org) using the Lipid17 force field   in combination with the general AMBER force field (GAFF2) . Using the CHARMM-GUI server (https://www.charmm-gui.org) , we built systems containing a bilayer of 300 lipid molecules, DMPC or POPC, with either 1 or 10 embedded molecules of PGL. The systems were solvated with TIP3P water. The membrane models were minimized by executing 2500 iterations using the steepest descent method, followed by 7500 iterations with the conjugate gradient method, with weakly restrained solute (k = 10 kcal/mol/Å2). Next, a short 100 ps MD run was performed on weakly restrained solute with the temperature increasing linearly from 0 to 303 K. The temperature was controlled using Langevin dynamics with the collision frequency parameter γ set to 1.0 ps−1 and a time step of 1 fs. Throughout the calculations, a cutoff of 10 Å was used for electrostatic interactions. We then proceeded with the equilibration of the system, consisting of 10 consecutive MD runs of 500 ps each, progressively releasing the restraints, at a constant temperature of 303 K with a time step of 2 fs. We finally carried out a 1.4 µs production run at a temperature of 303 K and a pressure of 1 bar. Langevin dynamics was used to control the temperature, with γ = 1.0 ps−1, while the pressure was controlled by the anisotropic Monte Carlo semi-isotropic barostat with the pressure relaxation time τp = 2 ps, with csurften = 3 and gamma_ten = 0. Bonds involving hydrogen were constrained with the SHAKE algorithm.

We performed Coarse-Grained (CG) simulations using GROMACS 2020.2 with the Martini 3 force field . We built membrane systems made of pure DMPC, pure POPC or a mixture of DOPE/POPC (3:1), containing PDIM, PGL-BCG or PGL-Mtb, using the Martini insane tool. All systems were minimized and gradually equilibrated according to the protocol suggested by CHARMM-GUI Martini Maker  . Coulomb interactions were treated using the reaction-field potential, and Lennard–Jones interactions were treated using shifted potentials with a cutoff radius of 1.1 nm. Pressure was maintained at 1 bar using the Parrinello–Rahman algorithm with a semi-isotropic pressure control. The temperature was kept at 310 K using the v-rescale algorithm. A time step of 20 fs was used.
DOI: 10.5281/zenodo.15173051
title: PGL-BCG-TUB

description: This repository contains all the data produced regarding the study of DIM PGL TUB and PGL BCG in a unique membrane environnement. The simulations of  phase transition of 4-membrane systems are gathered in different repositories :- DIM : https://doi.org/10.5281/zenodo.15276372- PGL TUB : https://doi.org/10.5281/zenodo.15276359- PGL BCG : https://doi.org/10.5281/zenodo.15276346It also contains the Scripts necessary to reproduce Fig2 Fig3 Fig4 of the corresponding article (DOI to come soon), and MARTINI3 parameters of DIM, PGL TUB and PGL BCG mycobacterial lipids.Below, a short description of the methodology : 

We conducted all simulations building on our previous work on PDIM . The atomistic MD simulations were carried out with the Amber16 software (http://ambermd.org) using the Lipid17 force field   in combination with the general AMBER force field (GAFF2) . Using the CHARMM-GUI server (https://www.charmm-gui.org) , we built systems containing a bilayer of 300 lipid molecules, DMPC or POPC, with either 1 or 10 embedded molecules of PGL. The systems were solvated with TIP3P water. The membrane models were minimized by executing 2500 iterations using the steepest descent method, followed by 7500 iterations with the conjugate gradient method, with weakly restrained solute (k = 10 kcal/mol/Å2). Next, a short 100 ps MD run was performed on weakly restrained solute with the temperature increasing linearly from 0 to 303 K. The temperature was controlled using Langevin dynamics with the collision frequency parameter γ set to 1.0 ps−1 and a time step of 1 fs. Throughout the calculations, a cutoff of 10 Å was used for electrostatic interactions. We then proceeded with the equilibration of the system, consisting of 10 consecutive MD runs of 500 ps each, progressively releasing the restraints, at a constant temperature of 303 K with a time step of 2 fs. We finally carried out a 1.4 µs production run at a temperature of 303 K and a pressure of 1 bar. Langevin dynamics was used to control the temperature, with γ = 1.0 ps−1, while the pressure was controlled by the anisotropic Monte Carlo semi-isotropic barostat with the pressure relaxation time τp = 2 ps, with csurften = 3 and gamma_ten = 0. Bonds involving hydrogen were constrained with the SHAKE algorithm.

We performed Coarse-Grained (CG) simulations using GROMACS 2020.2 with the Martini 3 force field . We built membrane systems made of pure DMPC, pure POPC or a mixture of DOPE/POPC (3:1), containing PDIM, PGL-BCG or PGL-Mtb, using the Martini insane tool. All systems were minimized and gradually equilibrated according to the protocol suggested by CHARMM-GUI Martini Maker  . Coulomb interactions were treated using the reaction-field potential, and Lennard–Jones interactions were treated using shifted potentials with a cutoff radius of 1.1 nm. Pressure was maintained at 1 bar using the Parrinello–Rahman algorithm with a semi-isotropic pressure control. The temperature was kept at 310 K using the v-rescale algorithm. A time step of 20 fs was used.
DOI: 10.15468/dl.55y7zn
title: Occurrence Download

description: A dataset containing 5986 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Bufo americanus Holbrook, 1836)"
 ]
}

 The dataset includes 5986 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005326-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6mmqck
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Poa ×complanata Schur, Poa imbecilla Biehler, Poa pratensis subsp. turfosa (Litv.) Vorosch., Pogostemon pumilus (Graham) Press, Polycarpaea eriantha var. eriantha)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 96 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005329-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hfr4ym
title: Occurrence Download

description: A dataset containing 368 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Notophthalmus meridionalis (Cope, 1880))"
 ]
}

 The dataset includes 368 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005328-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3jyr3x
title: Occurrence Download

description: A dataset containing 28341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dermochelys coriacea (Vandelli, 1761)"
 ]
}

 The dataset includes 28341 records from 405 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005327-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7rc9wa
title: Occurrence Download

description: A dataset containing 167758 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Caretta caretta (Linnaeus, 1758)"
 ]
}

 The dataset includes 167758 records from 576 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005311-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jn4ndw
title: Occurrence Download

description: A dataset containing 321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "IucnRedListCategory is CR",
 "PublishingCountry is Hong Kong",
 "TaxonKey is Psittacidae",
 "Year 2023-2023"
 ]
}

 The dataset includes 321 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005330-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15297975
title: Mediciones de variables meteorológicas en Isla Guadalupe del 2009 al 2025

description: Datos con resolución horaria de las estaciones meteorológicas Bosque, Norte y Pista de Isla Guadalupe de 31-jul-2009 a 20-abr-2025. 
description: Esta es la versión 0.1.0 porque es la primera vez que lo subimos al Zenodo.



Correo: Respaldo y datos estaciones meteorológicas, Bosque, Norte y Pista
DOI: 10.15468/dl.8km3gw
title: Occurrence Download

description: A dataset containing 235661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Ixobrychus exilis (Gmelin, 1789)"
 ]
}

 The dataset includes 235661 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005302-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15276345
title: PGL-BCG_Phase_transition_CG

description: This work is based on the following repository : https://doi.org/10.5281/zenodo.15173051This repository contains all the data produced regarding phase transition of 4-membrane systems containing different concentrations of PGL_BCG lipid, at temperatures ranging from 280 to 350K. The folders contain the resulting xtc trajectories, gro files, and tpr files for reproduction of the calculations. Below, a short description of the methodology : 

All simulations were performed with GROMACS version 2020.2. We conducted CG simulations of stacked lipid membranes in close proximity using the MARTINI3 force field and home made parameters for the PGL_BCG molecule. We built a simulation system consisting of 4 stacked membranes. Each individual membrane contained 154 POPC molecules, 470 DOPE molecules (DOPE/POPC molar ratio 3.05:1) and either 6, 12 or 18 molecules PGL_BCG (PGL/lipid molar ratio 1%, 2%, 3%). The membranes were solvated with Martini 3 CG water (W) particles, with 3.33 W particles per lipid molecule, corresponding to about 13 atomistic water molecules per lipid. To preserve the lamellar membrane phase, the systems were equilibrated at 280 K, using the v-rescale thermostat with a time constant tT = 1.0 ps, and the Berendsen barostat with semi-isotropic pressure coupling, a reference pressure of 1.0 bar, a time constant tp = 5 ps, and a compressibility of 3 × 10-4 bar-1. Then 8 different simulations were launched, with temperatures ranging from 280 K to 350 K in 10 K increments. We executed the production runs in triplicate at each temperature, using a time step of 20 fs, for a total duration of 3 µs. The temperature was controlled using the Berendsen thermostat with a time constant tT = 1.0 ps, while the pressure was set using the Berendsen barostat with fully anisotropic pressure coupling, at a reference pressure of 1.0 bar, a time constant tp = 0.5 ps, and a compressibility of 1.0 × 10-5 bar-1. Constraints were imposed using the LINCS algorithm.The PGL_BCG force field parameters,  the Python and TCl files necessary to the reproduction of  figures are available in the parent repository.
DOI: 10.5281/zenodo.15276346
title: PGL-BCG_Phase_transition_CG

description: This work is based on the following repository : https://doi.org/10.5281/zenodo.15173051This repository contains all the data produced regarding phase transition of 4-membrane systems containing different concentrations of PGL_BCG lipid, at temperatures ranging from 280 to 350K. The folders contain the resulting xtc trajectories, gro files, and tpr files for reproduction of the calculations. Below, a short description of the methodology : 

All simulations were performed with GROMACS version 2020.2. We conducted CG simulations of stacked lipid membranes in close proximity using the MARTINI3 force field and home made parameters for the PGL_BCG molecule. We built a simulation system consisting of 4 stacked membranes. Each individual membrane contained 154 POPC molecules, 470 DOPE molecules (DOPE/POPC molar ratio 3.05:1) and either 6, 12 or 18 molecules PGL_BCG (PGL/lipid molar ratio 1%, 2%, 3%). The membranes were solvated with Martini 3 CG water (W) particles, with 3.33 W particles per lipid molecule, corresponding to about 13 atomistic water molecules per lipid. To preserve the lamellar membrane phase, the systems were equilibrated at 280 K, using the v-rescale thermostat with a time constant tT = 1.0 ps, and the Berendsen barostat with semi-isotropic pressure coupling, a reference pressure of 1.0 bar, a time constant tp = 5 ps, and a compressibility of 3 × 10-4 bar-1. Then 8 different simulations were launched, with temperatures ranging from 280 K to 350 K in 10 K increments. We executed the production runs in triplicate at each temperature, using a time step of 20 fs, for a total duration of 3 µs. The temperature was controlled using the Berendsen thermostat with a time constant tT = 1.0 ps, while the pressure was set using the Berendsen barostat with fully anisotropic pressure coupling, at a reference pressure of 1.0 bar, a time constant tp = 0.5 ps, and a compressibility of 1.0 × 10-5 bar-1. Constraints were imposed using the LINCS algorithm.The PGL_BCG force field parameters,  the Python and TCl files necessary to the reproduction of  figures are available in the parent repository.
DOI: 10.5281/zenodo.15304920
title: KURASH TURLARI: QIYOSIY TAHLIL
DOI: 10.5281/zenodo.15304921
title: KURASH TURLARI: QIYOSIY TAHLIL
DOI: 10.21227/dkbq-dn47
title: "some benchmark datasets for clustering"

description: "Pathbased\uff1bAggregation\uff1bR15\uff1bBanana\uff1bCMC\uff1bS1\uff1bMC\uff1bPearl\uff1bCth3\uff1bThreeCircles\uff1bTwoCluster\uff1bTwoMoons\uff1bD2\uff1bLs3"
DOI: 10.15468/dl.yx4k9f
title: Occurrence Download

description: A dataset containing 256 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-1.79025 37.2397,-5.51559 36.76543,-5.53854 35.95457,-2.39456 35.96987,-0.80345 36.59713,-1.79025 37.2397))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Elasmobranchii, Holocephali)"
 ]
}

 The dataset includes 256 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005331-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15276371
title: DIM_Phase_transition_CG

description: This work is based on the following repository : https://doi.org/10.5281/zenodo.15173051This repository contains all the data produced regarding phase transition of 4-membrane systems containing different concentrations of DIM lipid, at temperatures ranging from 280 to 350K. The folders contain the resulting xtc trajectories, gro files, and tpr files for reproduction of the calculations. Below, a short description of the methodology : 

All simulations were performed with GROMACS version 2020.2. We conducted CG simulations of stacked lipid membranes in close proximity using the MARTINI3 force field and home made parameters for the DIM molecule. We built a simulation system consisting of 4 stacked membranes. Each individual membrane contained 154 POPC molecules, 470 DOPE molecules (DOPE/POPC molar ratio 3.05:1) and either 6, 12 or 18 molecules PDIM (PGL/lipid molar ratio 1%, 2%, 3%). The membranes were solvated with Martini 3 CG water (W) particles, with 3.33 W particles per lipid molecule, corresponding to about 13 atomistic water molecules per lipid. To preserve the lamellar membrane phase, the systems were equilibrated at 280 K, using the v-rescale thermostat with a time constant tT = 1.0 ps, and the Berendsen barostat with semi-isotropic pressure coupling, a reference pressure of 1.0 bar, a time constant tp = 5 ps, and a compressibility of 3 × 10-4 bar-1. Then 8 different simulations were launched, with temperatures ranging from 280 K to 350 K in 10 K increments. We executed the production runs in triplicate at each temperature, using a time step of 20 fs, for a total duration of 3 µs. The temperature was controlled using the Berendsen thermostat with a time constant tT = 1.0 ps, while the pressure was set using the Berendsen barostat with fully anisotropic pressure coupling, at a reference pressure of 1.0 bar, a time constant tp = 0.5 ps, and a compressibility of 1.0 × 10-5 bar-1. Constraints were imposed using the LINCS algorithm.The DIM force field parameters,  the Python and TCl files necessary to the reproduction of  figures are available in the parent repository.