cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15747940
title: Proton transfer through a charged conduit in respiratory complex I - long range effects and conformational gating

description: If the data and/or scripts supplied in this dataset are used, please cite the following references:

 



Simsive et al., Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating, JCIM (2025), https://doi.org/10.1021/acs.jcim.5c01365

Zdorevskyi et al. Catalytic relevance of quinol anion in biological energy conversion by respiratory complex I, bioRxiv (2024), https://doi.org/10.1101/2024.09.06.611712

Zdorevskyi et al. Horizontal proton transfer across the antiporter-like subunits in mitochondrial respiratory complex I, Chem. Sci. (2023), https://doi.org/10.1039/d3sc01427d


####################################################################################################################

The dataset lists all input files necessary for launching classical and QM/MM molecular dynamics simulations published in  "Proton transfer through a charged conduit in respiratory complex I - long range effects and conformational gating" by Luka Simsive, Oleksii Zdorevskyi and Vivek Sharma (UH, Finland), https://doi.org/10.1021/acs.jcim.5c01365. Every folder of the dataset represents the respective setup described in Tables S2-S5. Output trajectory files are also uploaded for the selected setups.

Dataset structure

Classical_MD

     500ns_propka

     500ns_L3

QM_MM_MD

     L

     L_US

     M

     M_prime

     M_prime_US

     M_US

     R_prime

    R_prime_US



The simulation protocol is outlined in the Methods section. The folder “Classical_MD” contains 2 subfolders: 500ns_propka (classical MD simulations of the system with the protonation sates obtained from pKa estimates), and 500ns_L3, where protonation states correspond to setup L3, Table S2.

Each subdirectory of “QM_MM_MD” contains the respective QM region: L (Table S2), M (Table S3), M_prime (Table S4), R_prime (Table S5). Subfolders “*_US” contain data from umbrella sampling simulations of the respective region.
DOI: 10.15468/dl.d79sgm
title: Occurrence Download

description: A dataset containing 4423 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 PRINTF('%04d-%02d', "year", "month") yearmonth,
 GBIF_EQDGCODE(6, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)) eqdcellcode,
 COUNT(*) occurrences
FROM
 occurrence
WHERE
 occurrence.countrycode = 'ZA'
 AND (CAST(occurrence.taxonkey AS INTEGER) = 2931469 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 2931469 OR CAST(occurrence.kingdomkey AS INTEGER) = 2931469 OR CAST(occurrence.phylumkey AS INTEGER) = 2931469 OR CAST(occurrence.classkey AS INTEGER) = 2931469 OR CAST(occurrence.orderkey AS INTEGER) = 2931469 OR CAST(occurrence.familykey AS INTEGER) = 2931469 OR CAST(occurrence.genuskey AS INTEGER) = 2931469 OR CAST(occurrence.specieskey AS INTEGER) = 2931469)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence."month" IS NOT NULL AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 PRINTF('%04d-%02d', "year", "month"),
 GBIF_EQDGCODE(6, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000))

 The dataset's 4423 records were derived from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003809-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/wwdqqv
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1989

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/e632qe
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1990

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/2tvjjp
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1991

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/pn53m8
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1993

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/y58htk
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1992

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/t6xmrm
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1994

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.17632/vktn6sfbr2
title: Novel relationships between the ICAD, CD53, GRM1, and GSTmu protein levels and atherosclerosis and cardiovascular outcomes

description: The levels of glutathione S-transferase Mu1 (GSTmu), DNA fragmentation factor subunit (DFF45/ICAD), interleukin-6 (IL-6), leukocyte surface antigen (CD53), and metabotropic glutamate receptor 1 (GRM1) were shown to differ between the small selected groups of patients with severe and minor coronary lesions by microarray assays. In the total cohort, only ICAD was linked to type 2 diabetes and presence of coronary artery stenosis regardless of the severity of stenosis. CD53 was specifically associated with severe degree of coronary stenosis. GRM1 was associated with the presence of coronary stenosis and cardiovascular outcomes. IL6 was associated with femoral stenosis &gt;70% and with diabetes, and GSTmu was associated with brachiocephalic stenosis &gt;60% and with diabetes. Only GRM1 was a predictor of surrogate endpoint outcome, with inverse associations with coronary stenosis and surrogate endpoint outcome (r= -0.24 and P=0.025 and r= -0.31 and P=0.007, respectively).
DOI: 10.15468/dl.dw6fuj
title: Occurrence Download

description: A dataset containing 8843 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Otaria"
 ]
}

 The dataset includes 8843 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003844-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/vktn6sfbr2.1
title: Novel relationships between the ICAD, CD53, GRM1, and GSTmu protein levels and atherosclerosis and cardiovascular outcomes

description: The levels of glutathione S-transferase Mu1 (GSTmu), DNA fragmentation factor subunit (DFF45/ICAD), interleukin-6 (IL-6), leukocyte surface antigen (CD53), and metabotropic glutamate receptor 1 (GRM1) were shown to differ between the small selected groups of patients with severe and minor coronary lesions by microarray assays. In the total cohort, only ICAD was linked to type 2 diabetes and presence of coronary artery stenosis regardless of the severity of stenosis. CD53 was specifically associated with severe degree of coronary stenosis. GRM1 was associated with the presence of coronary stenosis and cardiovascular outcomes. IL6 was associated with femoral stenosis &gt;70% and with diabetes, and GSTmu was associated with brachiocephalic stenosis &gt;60% and with diabetes. Only GRM1 was a predictor of surrogate endpoint outcome, with inverse associations with coronary stenosis and surrogate endpoint outcome (r= -0.24 and P=0.025 and r= -0.31 and P=0.007, respectively).
DOI: 10.15468/mu43hd
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1995

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/ye33ga
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1996

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/dl.8d7rac
title: Occurrence Download

description: A dataset containing 705 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cherax quadricarinatus (von Martens, 1868)"
 ]
}

 The dataset includes 705 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041136-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/93p7xv
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1997

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/zfs5ue
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1998

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/twfju9
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2000

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/zby4kb
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 1999

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/ccgzba
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2001

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/eynh4n
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2002

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/vup3z6
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2003

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/yaa9h8
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2004

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/jwhgwy
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2005

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/v62fy8
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2006

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/v47rhn
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2007

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/4fzqkf
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2008

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/746za3
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2009

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/nwpby7
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2010

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/vkxa3p
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2011

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.15468/mndqyv
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2012

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.17632/wxv79vrd9w
title: HUS-ACC

description: Bases de datos del diseño y validación de la herramienta para autoevaluar el cuidado compasivo de enfermería en instituciones de salud (HUS-ACC)
DOI: 10.17632/wxv79vrd9w.1
title: HUS-ACC

description: Bases de datos del diseño y validación de la herramienta para autoevaluar el cuidado compasivo de enfermería en instituciones de salud (HUS-ACC)
DOI: 10.15468/vs82hr
title: Semi-quantitive microplankton analysis (Sylt Roads Time Series) in the Wadden Sea off List, Sylt, North Sea in 2013

description: Presence absence data of microplankton in the Wadden Sea off List, Sylt, North Sea.
DOI: 10.17632/w3ffky29k6.3
title: Isotope of the North Plain Groundwater

description: This dataset is based on the research of groundwater circulation in the North China Plain. The dataset shows the oxygen isotope signature of groundwater in different aquifers. The results of the data show that there is inter-basin groundwater flow in the North China Plain.
DOI: 10.17632/272gcrr4fs
title: Physical Activity Incentive Program for Older People: Cost-Utility and Quality-Adjusted Life Years (QALYs)

description: This dataset refers to the study “Physical Activity Incentive Program for Older People: Cost-Utility and Quality-Adjusted Life Years (QALYs)”, published in the Pan-American Journal of Aging Research (PAJAR). Data were collected over 12 months from 300 older adults (≥60 years) enrolled in the PIAFI program, including attendance records for exercise sessions, quarterly health reassessments, quality of life measures (EQ-5D), functional independence (CPF), physical activity level (IPAQ), and costs of program implementation. These data enabled the calculation of QALYs, cost-utility, and program effectiveness, demonstrating positive impacts on quality of life, functional independence, and healthcare cost reduction.
DOI: 10.17632/272gcrr4fs.1
title: Physical Activity Incentive Program for Older People: Cost-Utility and Quality-Adjusted Life Years (QALYs)

description: This dataset refers to the study “Physical Activity Incentive Program for Older People: Cost-Utility and Quality-Adjusted Life Years (QALYs)”, published in the Pan-American Journal of Aging Research (PAJAR). Data were collected over 12 months from 300 older adults (≥60 years) enrolled in the PIAFI program, including attendance records for exercise sessions, quarterly health reassessments, quality of life measures (EQ-5D), functional independence (CPF), physical activity level (IPAQ), and costs of program implementation. These data enabled the calculation of QALYs, cost-utility, and program effectiveness, demonstrating positive impacts on quality of life, functional independence, and healthcare cost reduction.
DOI: 10.17632/854pn8b3kv
title: Does Public Data Openness Reduce Boundary Pollution? Evidence from Interprovincial Neighboring Cities in China

description: Description:
This repository contains the replication materials for the study investigating the impact of public data openness on boundary pollution and firm performance in China. The main analysis is based on a panel dataset of inter-provincial boundary cities. The files included are:

do: A Stata DO file containing the complete code for data processing and regression analysis.

city_border: A panel dataset of inter-provincial boundary cities (2008–2021), used for the main empirical analysis.

city_all: A panel dataset covering all prefecture-level cities in China.

firm_border: A panel dataset of industrial firms located in boundary regions.

These materials are provided to ensure the transparency and reproducibility of the study.
DOI: 10.17632/854pn8b3kv.3
title: Does Public Data Openness Reduce Boundary Pollution? Evidence from Interprovincial Neighboring Cities in China

description: Description:
This repository contains the replication materials for the study investigating the impact of public data openness on boundary pollution and firm performance in China. The main analysis is based on a panel dataset of inter-provincial boundary cities. The files included are:

do: A Stata DO file containing the complete code for data processing and regression analysis.

city_border: A panel dataset of inter-provincial boundary cities (2008–2021), used for the main empirical analysis.

city_all: A panel dataset covering all prefecture-level cities in China.

firm_border: A panel dataset of industrial firms located in boundary regions.

These materials are provided to ensure the transparency and reproducibility of the study.
DOI: 10.25345/c5v11vz97
title: MassIVE MSV000099167 - Lipidomics analysis of senescent SK-MEL103 cells
title: Lipidomics analysis of senescent SK-MEL103 cells and cells treated with GPX4 inhibitor RSL3 or SCLA2 (n=3). RAW datafiles were centroided and converted using MSConvert to mzXML format.
DOI: 10.6084/m9.figshare.30100762.v2
title: <b>Enhanced Carboniferous Magmatism Reveals a Dual Subduction System of the Paleo-Tethys: New Detrital Zircon Evidence from Western Türkiye</b>

description: We present new detrital zircon U-Pb geochronology and trace element data from Mesozoic-Cenozoic sandstones in western Türkiye to investigate the distribution and tectonic significance of Carboniferous magmatic arcs in the Pontides and the Anatolide-Tauride Block.
DOI: 10.5281/zenodo.16751886
title: Dataset for the Experimental Verification of a DNN-Based Horizontal Two-Dimensional Inverse Model of Turbidity Current

description: This record includes the training and test datasets for DNN-based horizontal 2D inverse models of turbidity currents, the corresponding inversion results, flume experiment datasets used to verify the performance of the model, and scripts for generating figures from the data. The data in this record used in https://doi.org/10.22541/essoar.175525655.54389731/v1.
DOI: 10.15468/dl.csu3ch
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Cardinalis cardinalis)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003851-250914085247600/datasets/export for details.
DOI: 10.15468/dl.tqngn9
title: Occurrence Download

description: A dataset containing 1424 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Andropogon bicornis"
 ]
}

 The dataset includes 1424 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003849-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bsmpza
title: Occurrence Download

description: A dataset containing 2884 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Hyaena hyaena (Linnaeus, 1758)"
 ]
}

 The dataset includes 2884 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064630-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.np443f
title: Occurrence Download

description: A dataset containing 819 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Chrysocyon brachyurus (Illiger, 1815)"
 ]
}

 The dataset includes 819 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075996-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.