cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7276981
title: 25ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the a99SB-disp Forcefield

description: Molecular dynamics simulation trajectory and for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the a99SB-disp force field published by Maxwell et al. The simulation was run for 25 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K. This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers. The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).
description: This trajectory is provided to support Jupyter Notebooks and CoLabs demonstrating the free and open-source software, SPEADI, developed by the authors.
description: {"references": ["Tucker, M. R., Piana, S., Tan, D., LeVine, M. V., & Shaw, D. E. (2022). Development of force field parameters for the simulation of single- and double-stranded dna molecules and dna-protein complexes. The Journal of Physical Chemistry B, 126(24), 4442\u20134457. http://dx.doi.org/10.1021/acs.jpcb.1c10971", "Abraham, M. J., Murtola, T., Schulz, R., Szil\u00e1rd P\u00e1ll, Smith, J. C., Hess, B., & Lindahl, E. (2015). Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2(nil), 19\u201325. http://dx.doi.org/10.1016/j.softx.2015.06.001", "Wang, L., Friesner, R. A., & Berne, B. J. (2011). Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (rest2). The Journal of Physical Chemistry B, 115(30), 9431\u20139438. http://dx.doi.org/10.1021/jp204407d", "Alvarez, D. (2021). Juwels cluster and booster: Exascale pathfinder with modular supercomputing architecture at J\u00fclich Supercomputing Centre. Journal of large-scale research facilities JLSRF, 7, 183. http://dx.doi.org/10.17815/jlsrf-7-183"]}
DOI: 10.5883/bold:aag3557
title: Overview of Barcode Index Number - BOLD:AAG3557

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3558
title: Overview of Barcode Index Number - BOLD:AAG3558

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5281/zenodo.13892825
title: Molecular Dynamics Trajectories Exploring the Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution

description: Primary data for the publication "Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution" by de Bruyn, Dorn, Rossetti, Fernandez, Outeiro, Schulz and Carloni. Submitted to the Journal of Chemical Information and Modeling.

Included are all GROMACS input files, parameterised topologies, starting and final configurations, and trajectories for the lowest temperature replica (at 300 K, lowest of 32 replicas between 300-500 K exchanging according to the REST2 algorithm (Wang et al. 2011)). The data is split into three archives:



all_atom_trajectories.zip



contains all input files and all atom trajectories including solvent

trajectories written at 100 ps intervals



protein+ion_trajectories.zip



contains configuration/non-parameterised topologies and trajectories excluding solvent, but including ions

trajectories written at 10 ps intervals



additional_simulations.zip



contains the all atom trajectories and input files, and

solvent-free trajectories above,

for the additional simulations in the Supplemental Information of the article:



includes the DES-Amber-based simulations with 64 replicas between 300-600 K, and

a99SB-disp-based simulations






 

Folders are named according to the following top level scheme:



DES-Amber simulations/ Simulations created using the DES-Amber force field (Tucker et al. 2022)

a99SB-disp simulations/ SImulations created using the a99SB-disp force field for Intrinsically Disordered Proteins (IDPs) (Robustelli et al. 2018)


Sub-folders follow the following scheme:



AS/ Simulations of the physiological form of wild-type Human α-Synuclein



unphosphorylated



pAS/ Simulations of the physiological form of wild-type Human α-Synuclein



phosphorylated at S129

with double negative charge



pASH/ Simulations of the physiological form of wild-type Human α-Synuclein (a99SB-disp simulations only)



phosphorylated at S129

with a single negative charge (monoprotonated)
DOI: 10.5883/bold:aag3559
title: Overview of Barcode Index Number - BOLD:AAG3559

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3560
title: Overview of Barcode Index Number - BOLD:AAG3560

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3565
title: Overview of Barcode Index Number - BOLD:AAG3565

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3566
title: Overview of Barcode Index Number - BOLD:AAG3566

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3568
title: Overview of Barcode Index Number - BOLD:AAG3568

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3569
title: Overview of Barcode Index Number - BOLD:AAG3569

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3571
title: Overview of Barcode Index Number - BOLD:AAG3571

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3572
title: Overview of Barcode Index Number - BOLD:AAG3572

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3574
title: Overview of Barcode Index Number - BOLD:AAG3574

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3575
title: Overview of Barcode Index Number - BOLD:AAG3575

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.15468/dl.gfqm8b
title: Occurrence Download

description: A dataset containing 3290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Apis cerana Fabricius, 1793"
 ]
}

 The dataset includes 3290 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008047-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5883/bold:aag3577
title: Overview of Barcode Index Number - BOLD:AAG3577

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3583
title: Overview of Barcode Index Number - BOLD:AAG3583

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3584
title: Overview of Barcode Index Number - BOLD:AAG3584

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3594
title: Overview of Barcode Index Number - BOLD:AAG3594

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3602
title: Overview of Barcode Index Number - BOLD:AAG3602

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3609
title: Overview of Barcode Index Number - BOLD:AAG3609

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3614
title: Overview of Barcode Index Number - BOLD:AAG3614

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3619
title: Overview of Barcode Index Number - BOLD:AAG3619

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3621
title: Barcode Index Number BOLD:AAG3621

description: A cluster of barcode records associated with a Barcode Index Number(BIN). Each cluster is a proxy for a named or unnamed species. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3622
title: Overview of Barcode Index Number - BOLD:AAG3622

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3624
title: Overview of Barcode Index Number - BOLD:AAG3624

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3625
title: Overview of Barcode Index Number - BOLD:AAG3625

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3626
title: Barcode Index Number BOLD:AAG3626

description: A cluster of barcode records associated with a Barcode Index Number(BIN). Each cluster is a proxy for a named or unnamed species. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3628
title: Overview of Barcode Index Number - BOLD:AAG3628

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3629
title: Overview of Barcode Index Number - BOLD:AAG3629

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3630
title: Overview of Barcode Index Number - BOLD:AAG3630

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3631
title: Overview of Barcode Index Number - BOLD:AAG3631

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aag3633
title: Overview of Barcode Index Number - BOLD:AAG3633

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.14278/rodare.3541
title: (Data set) Fermi-liquid behavior of non-altermagnetic RuO2

description: 1) Data set of the figures in main text and supplementary - Originlab format (Origin Viewer can be used to open these files).

2) FPLO calculations for the representation of the nodal line.
DOI: 10.14278/rodare.3542
title: (Data set) Fermi-liquid behavior of non-altermagnetic RuO2

description: 1) Data set of the figures in main text and supplementary - Originlab format (Origin Viewer can be used to open these files).

2) FPLO calculations for the representation of the nodal line.
DOI: 10.5281/zenodo.14725514
title: Graced plasmo-photonic sensors characterization data
DOI: 10.5281/zenodo.14725515
title: Graced plasmo-photonic sensors characterization data
DOI: 10.34740/kaggle/dsv/10559158
title: Limpopo Mankweng HIV dataset
DOI: 10.5281/zenodo.13928396
title: Chronic Imaging of ferret 2181

description: Calcium Imaging Experiments for one animal (F2181) imaged on 5 imaging sessions. Experiments were performed every two days, starting two days prior to the natural time of eye opening (EO-2) until six days after eye opening (EO+6).

Imaging experiments were performed by Jeremy T. Chang and David E. Whitney in the lab of David Fitzpatrick at the Max Planck Florida Institute. The data were used in (Chang, Whitney, Fitzpatrick, 2020) and (Trägenap et al., 2025).

Each folder contains:



large scale spontaneous events extracted from 10 min of imaging without visual stimulation (see Smith et al., 2018) in shape (#events, #X-Dim, #Y-dim)

trials recorded for 16 moving grating stimuli and one blank, response measures at different timepoint after stimulus onset (0.5 s interval from 0s to 3.5s) in shape (#timepoints, #trials, #stim, #X-Dim, #Y-dim)



for binocular, contralateral, and ipsilateral stimulation




The file 'commonROI.npy' contains a mask outlining the region of high GCaMP6s expression and excluded bloodvessels.
DOI: 10.5281/zenodo.13928397
title: Chronic Imaging of ferret 2181

description: Calcium Imaging Experiments for one animal (F2181) imaged on 5 imaging sessions. Experiments were performed every two days, starting two days prior to the natural time of eye opening (EO-2) until six days after eye opening (EO+6).

Imaging experiments were performed by Jeremy T. Chang and David E. Whitney in the lab of David Fitzpatrick at the Max Planck Florida Institute. The data were used in (Chang, Whitney, Fitzpatrick, 2020) and (Trägenap et al., 2025).

Each folder contains:



large scale spontaneous events extracted from 10 min of imaging without visual stimulation (see Smith et al., 2018) in shape (#events, #X-Dim, #Y-dim)

trials recorded for 16 moving grating stimuli and one blank, response measures at different timepoint after stimulus onset (0.5 s interval from 0s to 3.5s) in shape (#timepoints, #trials, #stim, #X-Dim, #Y-dim)



for binocular, contralateral, and ipsilateral stimulation




The file 'commonROI.npy' contains a mask outlining the region of high GCaMP6s expression and excluded bloodvessels.
DOI: 10.5281/zenodo.14720035
title: Raw data metagenomic analysis and aroma profile
DOI: 10.5281/zenodo.14720036
title: Raw data metagenomic analysis and aroma profile
DOI: 10.15468/dl.728x34
title: Occurrence Download

description: A dataset containing 5715 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euglandina rosea (A.Férussac, 1821)"
 ]
}

 The dataset includes 5715 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002591-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zucf28
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Copiapoa decorticans N.P.Taylor & G.J.Charles"
 ]
}

 The dataset includes 20 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002594-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bvw8fq
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Living Specimen, Machine Observation)",
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Puma concolor (Linnaeus, 1771)"
 ]
}

 The dataset includes 28 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002595-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14724868
title: Convective organisation indices based on 3D radar reflectivities

description: This repository accompanies the article "A ML-based perspective on deep convective clouds and their organisation in 3D. Part II: Spatial-temporal patterns of convective organisation" by Sarah Brüning and Holger Tost, which is to be submitted to ACP. 

The datasets here are used to create the plots from the study using code from https://doi.org/10.5281/zenodo.14710228. They contain the convective organisation indices associated to each convective cloud trajectory. The data cover March - August 2019 for a region over tropical West Africa (30° N - 30° S, 30° E -  30° W). Within the folder, one file contains the trajectories aggregated by the cloud ID (agg) and one zip-folder with monthly files for all unique observations of the trajectories.
DOI: 10.15468/dl.pfrzkq
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pleurothallis carvalhoi Luer & Toscano"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002596-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26037646
title: Wikipedia Trust Survey Data_2024

description: The use of Wikipedia citations in scholarly research has been the topic of much inquiry over the past decade. A cross-publisher study (Taylor & Francis and University of Michigan Press) convened by Digital Science was established in late 2022 to explore author sentiment towards Wikipedia as a trusted source of information. A short survey was designed to poll published authors about views and uses of Wikipedia and explore how the increased addition of research citations in Wikipedia might help combat misinformation in the context of increasing public engagement with and access to validated research sources.With 21,854 surveys sent, targeting 40,402 papers mentioned in Wikipedia, a total of 750 complete surveys from 60 countries were included in this analysis. In general, responses revealed a positive sentiment towards research citation in Wikipedia and the researcher engagement practices. However, our sub analysis revealed statistically significant differences when comparison articles vs books and across disciplines, but not open vs closed access. This study will open the door to further research and deepen our understanding of authors perceived trustworthiness of the representation of their research in Wikipedia.
DOI: 10.6084/m9.figshare.26037646.v2
title: Wikipedia Trust Survey Data_2024

description: The use of Wikipedia citations in scholarly research has been the topic of much inquiry over the past decade. A cross-publisher study (Taylor & Francis and University of Michigan Press) convened by Digital Science was established in late 2022 to explore author sentiment towards Wikipedia as a trusted source of information. A short survey was designed to poll published authors about views and uses of Wikipedia and explore how the increased addition of research citations in Wikipedia might help combat misinformation in the context of increasing public engagement with and access to validated research sources.With 21,854 surveys sent, targeting 40,402 papers mentioned in Wikipedia, a total of 750 complete surveys from 60 countries were included in this analysis. In general, responses revealed a positive sentiment towards research citation in Wikipedia and the researcher engagement practices. However, our sub analysis revealed statistically significant differences when comparison articles vs books and across disciplines, but not open vs closed access. This study will open the door to further research and deepen our understanding of authors perceived trustworthiness of the representation of their research in Wikipedia.
DOI: 10.6084/m9.figshare.26037646.v1
title: Wikipedia_surveydata_for submission_no pubs.xlsx

description: The use of Wikipedia citations in scholarly research has been the topic of much inquiry over the past decade. A cross-publisher study (Taylor & Francis and University of Michigan Press) convened by Digital Science was established in late 2022 to explore author sentiment towards Wikipedia as a trusted source of information. A short survey was designed to poll published authors about views and uses of Wikipedia and explore how the increased addition of research citations in Wikipedia might help combat misinformation in the context of increasing public engagement with and access to validated research sources.With 21,854 surveys sent, targeting 40,402 papers mentioned in Wikipedia, a total of 750 complete surveys from 60 countries were included in this analysis. In general, responses revealed a positive sentiment towards research citation in Wikipedia and the researcher engagement practices. However, our sub analysis revealed statistically significant differences when comparison articles vs books and across disciplines, but not open vs closed access. This study will open the door to further research and deepen our understanding of authors perceived trustworthiness of the representation of their research in Wikipedia.
DOI: 10.5281/zenodo.14725576
title: Simulation data for photonic to plasmonic interface for Graced sensors
DOI: 10.5281/zenodo.14725577
title: Simulation data for photonic to plasmonic interface for Graced sensors
DOI: 10.15468/dl.cj8zyv
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rattus rattus (Linnaeus, 1758)",
 "Country is New Caledonia",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 110 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002601-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14720092
title: Raw data OD growth curve
DOI: 10.5281/zenodo.14720093
title: Raw data OD growth curve