cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17054942
title: Simulation data related to the shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

description: This record contains the MD simulation dataset for the paper with the title:

Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

Authors

Thijs W. Ettema 1#, Satomi Inaba-Inoue 2,3,#,†, Chancievan Thangaratnarajah 1,#,‡, Leticia Alves da Silva 4, Nikas Senning 4, Amy Clarke 4, Piotr Stepien 5,§, Anokhi Shah 6,7, Yue Ma 6,7, Katie Hardman 8, Sophia David 9, Hassane El Mkami 10, Jonathan G. Heddle 5,§, Norimichi Nomura 11, Satoshi Ogasawara 11, So Iwata 11, Dmitry Ghilarov 5,12,*, Christos Pliotas 6,7,*, Thomas Stockner 4,*, Dirk J. Slotboom 1,*, Konstantinos Beis 2,3,*

 

Affiliations

1 Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands

2 Department of Life Sciences, Imperial College London; Exhibition Road, London, South Kensington, SW7 2AZ, UK.

3 Rutherford Appleton Laboratory, Research Complex at Harwell; Didcot, Oxfordshire OX11 0FA, UK.

4 Institute of Pharmacology, Medical University of Vienna; 1090 Vienna, Austria

5 Malopolska Centre of Biotechnology, Jagiellonian University; Krakow, Poland.

6 BioEmPiRe Centre for Structural Biological EPR Spectroscopy, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.

7 Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK

8 Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.

9 Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, OX3 7DQ, UK.

10 School of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK

11 Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.

12 Department of Molecular Microbiology, John Innes Centre; Norwich Research Park, Norwich NR4 7UH, UK
DOI: 10.5281/zenodo.17143299
title: Data and scripts supporting "Evaluating the sensitivity of an air quality model to emission changes: lessons learned from COVID-19"

description: This repository contains the code and data supporting the paper “Evaluating the sensitivity of an air quality model to emission changes: lessons learned from COVID-19”.

It includes:





CHIMERE model simulation control file (*.par) and procesed outputs, for different emission scenarios.




Scripts for estimating Business-as-Usual (BAU) predictions using Generalized Additive Model (GAM), integrating ERA5 reanalysis, surface observations, and synoptic data.




Post-processing scripts for calculating different metrics. 


2020 Business-as-Usual (BAU) daily predictions for NO2 and O3
description: CHIMERE model simulations are based on the version provided here: https://doi.org/10.5281/zenodo.17064716
DOI: 10.5281/zenodo.17143300
title: Data and scripts supporting "Evaluating the sensitivity of an air quality model to emission changes: lessons learned from COVID-19"

description: This repository contains the code and data supporting the paper “Evaluating the sensitivity of an air quality model to emission changes: lessons learned from COVID-19”.

It includes:





CHIMERE model simulation control file (*.par) and procesed outputs, for different emission scenarios.




Scripts for estimating Business-as-Usual (BAU) predictions using Generalized Additive Model (GAM), integrating ERA5 reanalysis, surface observations, and synoptic data.




Post-processing scripts for calculating different metrics. 


2020 Business-as-Usual (BAU) daily predictions for NO2 and O3
description: CHIMERE model simulations are based on the version provided here: https://doi.org/10.5281/zenodo.17064716
DOI: 10.4121/08c1ce13-63d0-4950-bb0f-93fd72c894e0
title: Data underlying the publication: Mapping spatial organization of in vitro neuronal networks using high-content imaging

description: This dataset was generated to study neuronal organization in complete cell culture wells using automated high-content imaging. Primary cortical, hippocampal, and cerebellar cells from mouse brain tissue were plated in 24- or 96-well plates, fixed at 7, 10, or 14 days in vitro (DIV), and stained for neuronal markers. Cortical and hippocampal neurons were labelled with DAPI (nuclei), MAP2 (soma and dendrites), and Ankyrin-G (axon initial segment), while cerebellar Purkinje neurons were identified with Calbindin. Whole wells were imaged via automated confocal microscopy (400 images/well at 10× for 24-well plates; 225 images/well at 20× for 96-well plates). Individual maximum intensity projection images were stitched into full-well reconstructions using an adapted ImageJ plugin.<br>Scripts and code used for generating and analyzing this dataset are available through Zenodo (see at references)
DOI: 10.4121/08c1ce13-63d0-4950-bb0f-93fd72c894e0.v1
title: Data underlying the publication: Mapping spatial organization of in vitro neuronal networks using high-content imaging

description: This dataset was generated to study neuronal organization in complete cell culture wells using automated high-content imaging. Primary cortical, hippocampal, and cerebellar cells from mouse brain tissue were plated in 24- or 96-well plates, fixed at 7, 10, or 14 days in vitro (DIV), and stained for neuronal markers. Cortical and hippocampal neurons were labelled with DAPI (nuclei), MAP2 (soma and dendrites), and Ankyrin-G (axon initial segment), while cerebellar Purkinje neurons were identified with Calbindin. Whole wells were imaged via automated confocal microscopy (400 images/well at 10× for 24-well plates; 225 images/well at 20× for 96-well plates). Individual maximum intensity projection images were stitched into full-well reconstructions using an adapted ImageJ plugin.<br>Scripts and code used for generating and analyzing this dataset are available through Zenodo (see at references)
DOI: 10.5281/zenodo.17143737
title: Continuous data used in the publication "Automatic earthquake catalogs from a permanent DAS offshore network".

description: This repository contains 20 hours of raw DAS data recorded on the 27th of September 2024 on the CCN.N fiber during the ABYSS project. This data was part, and is representative, of the larger dataset used to obtain the results in the scientific paper "Automatic earthquake catalogs from a permanent DAS offshore network". The data has been acquired with an OptoDAS interrogator made by Alcatel Submarine Networks (ASN), the sampling frequency is 62.5 Hz, the spatial sampling is 15 m and the gauge length is 30 m for a fiber length of 153.179 km. 

Each zip file contains 2 hours of data and is named with the start and end times of the data it contains. File 00_02.zip contains data dated from midnight to 2 a.m., while the file 14_16.zip contains data dated from 2 p.m. to 4 p.m.

In each zip file, the file names refer to the start time of the data in the folder with the form HHMMSS.hdf5. This means that a file named 202444.hdf5 has a first time sample equal to 2024-09-27T20:24:44 (UTC time). All the metadata including the data unit, conversion factors, instrument parameters and many others, are available through the headers of each individual files.
DOI: 10.5281/zenodo.17143738
title: Continuous data used in the publication "Automatic earthquake catalogs from a permanent DAS offshore network".

description: This repository contains 20 hours of raw DAS data recorded on the 27th of September 2024 on the CCN.N fiber during the ABYSS project. This data was part, and is representative, of the larger dataset used to obtain the results in the scientific paper "Automatic earthquake catalogs from a permanent DAS offshore network". The data has been acquired with an OptoDAS interrogator made by Alcatel Submarine Networks (ASN), the sampling frequency is 62.5 Hz, the spatial sampling is 15 m and the gauge length is 30 m for a fiber length of 153.179 km. 

Each zip file contains 2 hours of data and is named with the start and end times of the data it contains. File 00_02.zip contains data dated from midnight to 2 a.m., while the file 14_16.zip contains data dated from 2 p.m. to 4 p.m.

In each zip file, the file names refer to the start time of the data in the folder with the form HHMMSS.hdf5. This means that a file named 202444.hdf5 has a first time sample equal to 2024-09-27T20:24:44 (UTC time). All the metadata including the data unit, conversion factors, instrument parameters and many others, are available through the headers of each individual files.
DOI: 10.15468/dl.nutku6
title: Occurrence Download

description: A dataset listing the 14528 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Taxon occurrence data for the FungalRoot database"
 ]
}

 The dataset's 14528 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015121-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48623/aperta.286270
title: The Theoretical Investigation Of The Stability And The Racemization Of Pristine, Functionalized And Doped Expanded Helicenes

description: This supporting information file contains necessary information on the geometrical data of the studied molecules.
DOI: 10.15468/dl.98bw2b
title: Occurrence Download

description: A dataset containing 6750 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Veronica filiformis",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6750 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015151-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s9uhpc
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Veronica filiformis",
 "Country is Latvia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 47 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015150-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17153213
title: Supplementary data 1. TF ChIP-seq peaks, motif enrichment and HDMB03/MB3W1 bulk-RNA-seq data

description: ## ChIP-seq analysis

1. Individual peak summits. Each peak summit was extended to a 100bp window aroung the summit,filtered for non-canonical chromosomes and black-listed regions.

MB129_CRX_summits.fil.ext.bedMB129_EOMES_summits.fil.ext.bedMB129_PAX6_summits.fil.ext.bedMB165_EOMES_summits.fil.ext.bedMB297_CRX_summits.fil.ext.bedMB297_EOMES_summits.fil.ext.bedMB96_CRX_summits.fil.ext.bed

2. Merged peak summits per TF.Peak summits from multiple samples were merged to obtain consensus peak summits. This data was used as input for HOMER motif enrichment analysis

CRX.com.bedEOMES.com.bedPAX6.bed

3. Overlap of peak summits between consensus EOMES and CRX binding sites.EOMES_CRX.ov.bed

4. HOMER output foldersCRXEOMESPAX6

5. MEME motif analysis reports

## HDMB03 and MB3W1 cell line and PDX RNA-seq 

6. Gene count matricesCell line:HDMB03_CL_mat.txtMB3W1_CL_mat.txtPDX:HDMB03_PDX_mat.txtMB3W1_PDX_mat.txt

7. Metadata excel fileHDMB03 and MB3W1 RNA-seq metadata.xlsx
DOI: 10.17877/tudodata-2025-m8hi5xtm
title: Optimization results for axially variable metal felt regenerators in Stirling engines

description: This data set contains simulation results generated with the numerical simulation code kpsim &lt;a href="https://doi.org/10.1016/j.applthermaleng.2016.09.176"&gt;[1]&lt;/a&gt;, which was developed at the Laboratory of Thermodynamics of TU Dortmund University. It is a one-dimensional differential, so-called “third-order” model for regenerative gas cycles, which is organized in a modular way, so that almost any such cycle may be mapped by combining various components from a library. The cycle modelled within this contribution corresponds to Stirling-mode operation of a convertible experimental machine, which was also designed, realized and investigated at this laboratory &lt;a href="https://doi.org/10.2514/1.B34726"&gt;[2]&lt;/a&gt;. The numerical results are discussed in the related publication, which focuses on efficiency enhancements by regenerators with axially varying matrix structures in Stirling engines.
DOI: 10.15468/dl.vv98n8
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Veronica filiformis",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 62 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015149-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17153279
title: The Medical Metaphors Corpus (MMC)
DOI: 10.15468/dl.ucwr8a
title: Occurrence Download

description: A dataset containing 195481 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Poland",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Neovison vison, Podiceps cristatus, Podiceps grisegena, Podiceps nigricollis, Tachybaptus ruficollis, Fulica atra, Aythya ferina, Aythya fuligula, Vanellus vanellus, Tringa totanus, Limosa limosa)"
 ]
}

 The dataset includes 195481 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015076-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pqxn2e
title: Occurrence Download

description: A dataset containing 93 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhaponticoides centaurium"
 ]
}

 The dataset includes 93 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015152-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/25735
title: Chandra X-ray Observatory ObsId 25735

description: Post-outburst evolution of the high-magnetic field pulsar PSR J1846-0258
DOI: 10.15468/dl.ebm2a7
title: Occurrence Download

description: A dataset containing 87958 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dryopteris affinis"
 ]
}

 The dataset includes 87958 records from 656 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015047-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15159816
title: TABLE 1 in Taxonomic redescription and molecular confirmation of Lutjanus rufolineatus (Acanthuriformes: Lutjanidae) from the Andaman Islands, India

description: TABLE 1. Meristic counts of Lutjanus rufolineatus from Andaman waters.
MeristicsPresent Study (n=6)Dorsal fin- SpineXIDorsal fin- Soft rays13–14Pectoral fin rays15–16Anal fin-SpineIIIAnal fin-Soft rays8Caudal fin rays17Pelvic fin-SpineIPelvic fin- Soft rays5Lateral line count47–49Scale row above the lateral line8–9Scale row below the lateral line16–19Scale row on Cheek7–8Gill raker upper6–7Gill raker lower13–14
description: Published as part of Ps, Fahmeeda Parveen, Venu, Sasidharan, Eranhottu, Shibin, Ummath, Ameen, Kalita, Samrat, Pv, Mohammed Ramees & Sadaka, Shehin, 2025, Taxonomic redescription and molecular confirmation of Lutjanus rufolineatus (Acanthuriformes: Lutjanidae) from the Andaman Islands, India, pp. 374 in Zootaxa 5566 (2) on page 374, DOI: 10.11646/zootaxa.5566.2.7, http://zenodo.org/record/14703020
DOI: 10.15468/dl.77mct9
title: Occurrence Download

description: A dataset containing 4072 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plantago depressa Willd."
 ]
}

 The dataset includes 4072 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001558-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.us7cbu
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Entomological Collection (GNM)",
 "OccurrenceStatus is Present",
 "TaxonKey is Eristalis tenax (Linnaeus, 1758)",
 "Year 1000-1864"
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0210320-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.auyzhr
title: Occurrence Download

description: A dataset containing 577 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plectranthus verticillatus (L.f.) Druce"
 ]
}

 The dataset includes 577 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001581-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m6we4s
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Furcifer petteri (Brygoo & Domergue, 1966)"
 ]
}

 The dataset includes 21 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0275618-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ap4mum
title: Occurrence Download

description: A dataset containing 923 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plectranthus fruticosus L'Hér."
 ]
}

 The dataset includes 923 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001571-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98cy36
title: Occurrence Download

description: A dataset containing 46971 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lonicera japonica Thunb."
 ]
}

 The dataset includes 46971 records from 572 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0210315-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ubfynx
title: Occurrence Download

description: A dataset listing the 14872 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diplopoda"
 ]
}

 The dataset's 14872 records were derived from 1035 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022827-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5883/bold:aab7780
title: Overview of Barcode Index Number - BOLD:AAB7780

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:aab7781
title: Overview of Barcode Index Number - BOLD:AAB7781

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:aab7782
title: Overview of Barcode Index Number - BOLD:AAB7782

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:aab7783
title: Overview of Barcode Index Number - BOLD:AAB7783

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:aab7785
title: Overview of Barcode Index Number - BOLD:AAB7785

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:aab7786
title: Overview of Barcode Index Number - BOLD:AAB7786

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:aab7787
title: Overview of Barcode Index Number - BOLD:AAB7787

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:aab7788
title: Overview of Barcode Index Number - BOLD:AAB7788

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:aab7789
title: Overview of Barcode Index Number - BOLD:AAB7789

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:aab7790
title: Overview of Barcode Index Number - BOLD:AAB7790

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:aab7791
title: Overview of Barcode Index Number - BOLD:AAB7791

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:aab7794
title: Barcode Index Number BOLD:AAB7794

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:aab7798
title: Overview of Barcode Index Number - BOLD:AAB7798

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:aab7799
title: Overview of Barcode Index Number - BOLD:AAB7799

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:aab7801
title: Overview of Barcode Index Number - BOLD:AAB7801

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:aab7802
title: Overview of Barcode Index Number - BOLD:AAB7802

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:aab7803
title: Overview of Barcode Index Number - BOLD:AAB7803

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:aab7805
title: Overview of Barcode Index Number - BOLD:AAB7805

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.