cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15188642
title: Human brain cell-type-specific aging clocks based on single-nuclei transcriptomics - Supplementary Data

description: Additional Data for: "Human brain cell-type-specific aging clocks based on single-nuclei transcriptomics" (DOI: https://doi.org/10.1002/advs.202506109)

All supplementary data corresponding to the article can be found in the compressed file, "Supplementary_Data.zip". The contents include the following:

Supplementary Data 1: Sample information and distribution of cells from different cell types.Supplementary Data 2: Gene expression in each cell type in the training dataset.Supplementary Data 3: Differential gene expression analysis results from all major cell Types across all age-group comparisons.Supplementary Data 4: Gene over-representation test results from all comparisons.Supplementary Data 5: Aging clocks: regression models of each of the 27 aging clocks.Supplementary Data 6: Predicted age from the testing rounds of each of the 27 aging clocks.Supplementary Data 7: Summary of aging clock performances in the training dataset.Supplementary Data 8: Summary of ExtraTrees Regressor model performances in the training dataset.Supplementary Data 9: Gene over-representation test results for clock-selected feature genesSupplementary Data 10: Label transfer prediction results in the external datasets.Supplementary Data 11: Predicted age given by the 27 aging clocks in the control cohort of Fröhlich et al. dataset.Supplementary Data 12: Predicted age given by the 27 aging clocks in Velmeshev et al. dataset.Supplementary Data 13: Summary of aging clock performances in the external validation datasets.Supplementary Data 14: Age correlation results of clock-selected feature genes in the training and the external validation datasets.Supplementary Data 15: Predicted age given by the top aging clocks in the Schizophrenia cohort of Frohlich et al. dataset.Supplementary Data 16: Summary of age acceleration comparison in the Fröhlich et al. dataset.Supplementary Data 17: Predicted age given by the top aging clocks in the Gabitto et al. dataset.Supplementary Data 18: Summary of age acceleration comparison in the Gabitto et al. dataset.

Further, the following files are included for reproducing the code/figures and as an additional resource for exploring the original human postmortem prefrontal cortex dataset:

training_cohort_metadata.csv: Metadata of the training cohort.

training_data_so_qc.rds: Contains Seurat object with unfiltered data along with basic qc parameters.

training_data_so_final.rds: Contains Seurat object with final filtered data, assays, reductions and cell type annotations.
DOI: 10.5281/zenodo.12646467
title: Source data for the kinetic assays in publication "Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase"

description: Datasets of enzyme kinetics related to the publication "Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase", published in Nature Communications with DOI: https://doi.org/10.1038/s41467-024-50933-6 

Individual files contain raw kinetic reaction data of the mycobacterial IMPDHs (wild type and mutant forms Mycobacterium smegmatis or wild type Mycobacterium tuberculosis) as a function of IMP, NAD+, GTP, ATP, ppGpp and Mg2+ concentration.

Individual data sets are presented as time data points of the absorbance at 340 nm in an Excel file with a linked Graphpad graphical link. Detailed experimental conditions are available in the related publication.
DOI: 10.5281/zenodo.12646468
title: Source data for the kinetic assays in publication "Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase"

description: Datasets of enzyme kinetics related to the publication "Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase", published in Nature Communications with DOI: https://doi.org/10.1038/s41467-024-50933-6 

Individual files contain raw kinetic reaction data of the mycobacterial IMPDHs (wild type and mutant forms Mycobacterium smegmatis or wild type Mycobacterium tuberculosis) as a function of IMP, NAD+, GTP, ATP, ppGpp and Mg2+ concentration.

Individual data sets are presented as time data points of the absorbance at 340 nm in an Excel file with a linked Graphpad graphical link. Detailed experimental conditions are available in the related publication.
DOI: 10.5281/zenodo.15362411
title: Datafiles - Hierarchical beyond-vacuum-GR effects

description: Datafiles for the analysis done in the paper "Hierarchical modeling of gravitational-wave populations for disentangling beyond-vacuum-GR effects".
DOI: 10.5281/zenodo.16066307
title: Datafiles - Hierarchical beyond-vacuum-GR effects

description: Datafiles for the analysis done in the paper "Hierarchical modeling of gravitational-wave populations for disentangling beyond-vacuum-GR effects".
DOI: 10.15468/dl.4j2yst
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chiloglanis carnosus, Chiloglanis congicus, Chiloglanis deckenii, Chiloglanis devosi, Chiloglanis dialloi, Chiloglanis disneyi, Chiloglanis elisabethianus, Chiloglanis emarginatus, Chiloglanis fasciatus, Chiloglanis harbinger, Chiloglanis kabaensis, Chiloglanis kalambo, Chiloglanis kerioensis, Chiloglanis kolente, Chiloglanis lamottei, Chiloglanis loffabrevum, Chiloglanis longibarbis, Chiloglanis lufirae, Chiloglanis lukugae, Chiloglanis macropterus, Chiloglanis marlieri, Chiloglanis mbozi, Chiloglanis microps, Chiloglanis modjensis, Chiloglanis mongoensis, Chiloglanis neumanni, Chiloglanis niger, Chiloglanis niloticus, Chiloglanis normani, Chiloglanis nzerekore, Chiloglanis occidentalis, Chiloglanis paratus, Chiloglanis pezoldi, Chiloglanis pojeri, Chiloglanis polyodon, Chiloglanis polypogon, Chiloglanis pretoriae, Chiloglanis reticulatus, Chiloglanis rukwaensis, Chiloglanis ruziziensis, Chiloglanis sanagaensis, Chiloglanis sardinhai, Chiloglanis somereni, Chiloglanis swierstrai, Chiloglanis trilobatus, Chiloglanis tweddlei, Chiloglanis voltae, Chiloglanis waterloti, Chilotilapia euchilus, Chilotilapia rhoadesii, Chindongo ater, Chindongo bellicosus, Chindongo cyaneus, Chindongo demasoni, Chindongo flavus, Chindongo heteropictus, Maylandia heteropicta, Chindongo longior, Chindongo minutus, Chindongo saulosi, Chromidotilapia cavalliensis, Chromidotilapia elongata, Chromidotilapia guntheri, Chromidotilapia kingsleyae, Chromidotilapia linkei, Chromidotilapia mamonekenei, Chromidotilapia melaniae, Chromidotilapia mrac, Chromidotilapia nana, Chromidotilapia regani, Chromidotilapia schoutedeni, Chrysichthys aluuensis, Chrysichthys ansorgii, Chrysichthys auratus, Chrysichthys bocagii, Chrysichthys brachynema, Chrysichthys brevibarbis, Chrysichthys cranchii, Chrysichthys dageti, Chrysichthys delhezi, Chrysichthys dendrophorus, Chrysichthys duttoni, Chrysichthys furcatus, Chrysichthys nigrodigitatus, Chrysichthys grandis, Chrysichthys graueri, Chrysichthys habereri, Chrysichthys helicophagus, Chrysichthys hildae, Chrysichthys johnelsi, Chrysichthys laticeps, Chrysichthys levequei, Chrysichthys longibarbis, Chrysichthys longidorsalis, Chrysichthys longipinnis, Chrysichthys mabusi, Chrysichthys macropterus, Chrysichthys maurus, Chrysichthys nyongensis)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((6.524 -0.514,7.0065 -0.2456,7.2624 0.2943,7.123 0.7051,6.6607 0.9135,6.1391 0.6726,5.9617 0.2289,6.1206 -0.3209,6.524 -0.514))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006725-250827131500795/datasets/export for details.
DOI: 10.21954/ou.rd.30005917
title: REDEFINE (Hungary): Interview with Former Hungarian Minister B

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with a former Hungarian minister B. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.21954/ou.rd.30005917.v1
title: REDEFINE (Hungary): Interview with Former Hungarian Minister B

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with a former Hungarian minister B. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.21954/ou.rd.30005836.v1
title: REDEFINE (Hungary): Interview with a Hungarian trade unionist

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with a Hungarian trade unionist. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.21954/ou.rd.30005836
title: REDEFINE (Hungary): Interview with a Hungarian trade unionist

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with a Hungarian trade unionist. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.15468/dl.9s5h4f
title: Occurrence Download

description: A dataset containing 4207984 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)"
 ]
}

 The dataset includes 4207984 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006697-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21954/ou.rd.30005827
title: REDEFINE (Hungary): Interview with an Investigative Journalist B

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with an investigative journalist B. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.21954/ou.rd.30005827.v1
title: REDEFINE (Hungary): Interview with an Investigative Journalist B

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with an investigative journalist B. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.18150/2dope1
title: Mechanism and energetics of JDP induced Hsp70’s conformational transition towards catalytically active state

description: This dataset contains files supporting the analyses presented in "Mechanism and energetics of JDP induced Hsp70’s conformational transition towards catalytically active state."It includes:(1) Contact analysis of unbiased MD trajectories for DnaK and the DnaK-J-domain complex, including contact frequencies and analysis scripts;(2) Dynamic network analysis results for the DnaK-J-domain complex detailing network topology and individual trajectory analyses;(3) Free energy profiles from umbrella sampling simulations, characterizing NBD-SBD distance, DnaK-JD distance, and T199-γ-phosphate distance;(4) Torsion angle values for the NBD;(5) Reduced-frame trajectories of the unbiased simulations;(6) Full-system PDB structures of DnaK and the DnaK-J-domain complex;(7) PDB structure of the DnaK-D35A J-domain variant complex;(8) PDB structures of isolated J-domain simulations, wild type and P34A variant;(9) PDB structure of the Thr-close state for the compensatory mutant DnaK R167A + J-domain D35N; and(10) Final structures from each umbrella sampling simulation window for DnaK, DnaK+J-domain, DnaK with disrupted beta-sheet, and DnaK+J-domain with intact beta-sheet.Deposited files are in pdb, tsv, dat, xtc, format and can be processed with MD software like Gromacs, VMD. Custom software is written in Python and deposited in py or npy format.
DOI: 10.15468/dl.mmmdjg
title: Occurrence Download

description: A dataset containing 3064 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 PRINTF('%04d-%02d-%02d', "year", "month", "day") yearmonthday,
 GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)) eeacellcode,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), PRINTF('%04d-%02d-%02d', "year", "month", "day"))) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 GBIF_WITHIN('POLYGON((-26.55752 25.35509,106.37856 25.35509,106.37856 78.50676,-26.55752 78.50676,-26.55752 25.35509))', occurrence.decimallatitude, occurrence.decimallongitude) = TRUE
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (CAST(occurrence.taxonkey AS INTEGER) = 4451511 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 4451511 OR CAST(occurrence.kingdomkey AS INTEGER) = 4451511 OR CAST(occurrence.phylumkey AS INTEGER) = 4451511 OR CAST(occurrence.classkey AS INTEGER) = 4451511 OR CAST(occurrence.orderkey AS INTEGER) = 4451511 OR CAST(occurrence.familykey AS INTEGER) = 4451511 OR CAST(occurrence.genuskey AS INTEGER) = 4451511 OR CAST(occurrence.specieskey AS INTEGER) = 4451511)
 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.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL AND occurrence."month" IS NOT NULL AND occurrence."day" 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-%02d', "year", "month", "day"),
 GBIF_EEARGCODE(1000, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000))

 The dataset's 3064 records were derived from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006692-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21954/ou.rd.30005821.v1
title: REDEFINE (Hungary): Interview with Transport Planning Specialist

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with a transport planning specialist. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.21954/ou.rd.30005821
title: REDEFINE (Hungary): Interview with Transport Planning Specialist

description: This document forms part of the REDEFINE research project (ERC Grant No. 885475), funded by the European Research Council. REDEFINE focuses on the dynamics and effects of China’s large-scale infrastructure investments in Europe, with a focus on Germany, Greece, Hungary, and the UK. Through multi-sited fieldwork and interdisciplinary analysis, the project seeks to understand the evolving relations between China and Europe and to assess what this means for politics, economic growth and development more broadly.This anonymised transcript presents a semi-structured interview conducted with a transport planning specialist. The conversation contributes to REDEFINE’s case study of Chinese investment in Budapest-Belgrade Railway upgrade. All identifying details have been removed, and informed consent for participation and data use was obtained.
DOI: 10.15468/dl.e5ymw2
title: Occurrence Download

description: A dataset containing 182 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sphaerichthys osphromenoides"
 ]
}

 The dataset includes 182 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006728-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygemct
title: Occurrence Download

description: A dataset containing 93413 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-96.7888719208969 28.362410434745147, -96.79816677036483 28.363320268117523, -96.8074836019274 28.362607602860066, -96.81646370432829 28.360299897377303, -96.82476140256061 28.356486057320588, -96.83205742959674 28.351312985165148, -96.83807125521622 28.344979883183417, -96.8425718890627 28.33773053663701, -96.8453867393898 28.32984388313796, -96.84640818987397 28.321623240061243, -96.84559765031563 28.313384612086985, -96.8429869385488 28.305444533692768, -96.83867695586612 28.298107915851986, -96.83283372234649 28.29165636229207, -96.82568193765154 28.286337399147012, -96.81749632368003 28.28235502405453, -96.80859108510342 28.27986192855683, -96.79930789004102 28.278953683290222, -96.79000282434372 28.27966510137406, -96.78103280801953 28.281968914274895, -96.77274198056074 28.285776808952143, -96.76544856298268 28.290942788061162, -96.75943268824133 28.297268729181788, -96.75492565865528 28.304511937228384, -96.75210103966518 28.31239440911946, -96.75106793478422 28.320613464091405, -96.75186670848638 28.328853339238467, -96.75446733418059 28.336797310212475, -96.75877044608647 28.3441398734305, -96.76461107013932 28.350598520035803, -96.77176490394704 28.35592464404278, -96.779956913654 28.359913157637227, -96.7888719208969 28.362410434745147))",
 "Year is one of (2019, 2020, 2021, 2022, 2023, 2024, 2025)",
 "KingdomKey is one of (Animalia, Fungi, Plantae)"
 ]
}

 The dataset includes 93413 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006688-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.