cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23514531
title: Data accompanying the paper 'Mechanisms underlying pathological cortical bursts during metabolic depletion'.

description: Processed EEG data, and the source data for the figures included in the manuscript "Dutta, S., Iyer, K.K., Vanhatalo, S., Breakspear, M., Roberts, J.A. (2023). Mechanisms underlying pathological cortical bursts during metabolic depletion. <em>Nature Communications</em>.".
DOI: 10.6084/m9.figshare.23514531.v1
title: Data accompanying the paper 'Mechanisms underlying pathological cortical bursts during metabolic depletion'.

description: Processed EEG data, and the source data for the figures included in the manuscript "Dutta, S., Iyer, K.K., Vanhatalo, S., Breakspear, M., Roberts, J.A. (2023). Mechanisms underlying pathological cortical bursts during metabolic depletion. <em>Nature Communications</em>.".
DOI: 10.6084/m9.figshare.22699282
title: Supplementary Material for: A common variant of ARRB2 promoter region Associated with the Prognosis of Heart Failure

description: Introduction The role of ARRB2 in cardiovascular disease has recently gained increasing attention. However, the association between ARRB2 polymorphisms and heart failure (HF) has not yet been investigated. Methods A total of 2386 hospitalized patients with chronic heart failure were enrolled as the first cohort and followed up for a mean period of 20.2 months. Meanwhile, ethnically and geographically matched 3000 individuals without evidence of HF were included as healthy controls. We genotyped the common variant in ARRB2 gene to identify the association between variant and HF. A replicated independent cohort enrolling 837 patients with chronic HF was applied to validate the observed association. A series of function analysis were conducted to illuminate the underlying mechanism. Results We identified a common variant rs75428611 associated with the prognosis of HF in two-stage population: adjusted P = 0.001, HR = 1.31 (1.11-1.54) in additive model and adjusted P = 0.001, HR = 1.39 (1.14-1.69) in dominant model in first-stage population; adjusted P = 0.04, HR = 1.41 (1.02-1.95) in additive model and adjusted P = 0.03, HR = 1.51 (1.03-2.20) in dominant model in replicated stage. However, rs75428611 did not significantly associate with the risk of HF. Functional analysis indicated that rs75428611‐G allele increased the promoter activity and the mRNA expression level of ARRB2 by facilitating transcription factor SRF binding, but not the A allele. Conclusions Our findings demonstrate that rs75428611 in promoter of ARRB2 is associated with the risk of HF mortality. It is a promising potential treatment target for HF.
DOI: 10.17632/3skw27c5k2.1
title: Extreme Copper Isotope Fractionation Driven By Redox Oscillation During Gleysols Weathering in Mun River Basin, Northeast Thailand

description: This dataset includes the location of samples, sand, clay, silt contents, soil organic carbon (SOC) contents, major and trace elements contents (Na, Mg, Al, Ca, Ti, K, Fe, Mn, Cu, Ce), the chemical index of alteration (CIA) values, mafic index of alteration (MIA) values, and Cu isotope fractionation data from two low-humic gleysol profiles (S1 and S2) from the Mun river basin Thailand.
DOI: 10.17632/k85nv2j2p5.1
title: Dataset - Changes in plasticity of the pelvic girdle from infancy to late adulthood in Homo sapiens

description: Dataset used in the article:
Kubicka AM. 2023. Changes in plasticity of the pelvic girdle from infancy to late adulthood in Homo sapiens. Scientific Reports. 
Abstract
Previous research on the effects of body mass on the pelvic girdle focused mostly on adult females and males. Because the ontogenetic plasticity level in the pelvis remains largely unknown, this study investigated how the association between body mass index (BMI) and pelvic shape changes during development. It also assessed how the large variation in pelvic shape could be explained by the number of live births in females. 
Data included CT scans of 308 humans from infancy to late adulthood with known age, sex, body mass, body stature, and number of live births (for adult females). 3D reconstruction and geometric morphometrics was used to analyze pelvic shape. Multivariate regression showed a significant association between BMI and pelvic shape in young females and old males. The association between the number of live births and pelvic shape in females was not significant. 
Less plasticity in pelvis shape in adult females than during puberty, perhaps reflects adaptation to support the abdominopelvic organs and the fetus during pregnancy. Non-significant susceptibility to BMI in young males may reflect bone maturation accelerated by excessive body mass. Hormonal secretion and biomechanical loading associated with pregnancy may not have a long-term effect on the pelvic morphology of females.
DOI: 10.17632/pszc85djcx.1
title: Linseed protein concentrate

description: Data regarding the evaluation of the substitution of fish meal for linseed protein concentrate in diets for Rhamdia quelen
DOI: 10.5281/zenodo.6795945
title: Offshore British Columbia microseismicity

description: Initial and relocations of microseismicity in the Queen Charlotte triple junction and Explorer microplate region offshore British Columbia, Canada from 1995-2021. These data include detections using the Regressive Estimator (REST) algorithm and those from network analysts at the Geological Survey of Canada (GSC). The files include earthquake locations, origin times, and P and S wave travel/arrival times. Centroid moment tensor solutions from the Geological Survey of Canada. 1. comb_all_event_4pr_final.dat<br> All (63,566) 4-pair initial data (Unique GSC, REST, and matched events.)<br> Event header format: YYYY MM DD HH MM SC LAT LON DEP 0 0 0 0 ID 2. phase_REST_initial_all.dat<br> Detections and locations for all REST events from 1995-2021. Excludes 9,929 events matched with the GSC.<br> Event header format: YYYY MM DD HH MM SC LAT LON DEP 0 0 0 0 ID<br> Phase detection format:<br> Station Traveltime Quality Phase 3. phase_matchGSC_initial.dat<br> 9,929 events matched between REST-GSC detections from 1995-2021. Locations and phase detections from the GSC.<br> Event header format: YYYY MM DD HH MM SC LAT LON DEP 0 0 0 0 ID<br> Phase detection format:<br> Station Traveltime Quality Phase 4. phase_GSC_initial_all_mag_ml.dat<br> 40,839 events from the GSC catalog from 1995-2021. Includes local (ML) magnitudes.<br> Event header format: YYYY MM DD HH MM SC LAT LON DEP MAG 0 0 0 ID<br> Phase detection format:<br> Station Traveltime Quality Phase 5. hypreloc_fix5_4pr_all.reloc<br> 18,441 final hypoDD relocations in hypoDD file format. 6. PGC_CMT.tgz<br> .tgz file includes Geological Survey of Canada centroid moment tensor solutions and associated README file.
description: {"references": ["Kao, H., Shan, S., Bent, A., Woodgold, C., Rogers, G., Cassidy, J. F., and Ristau, J. (2012). Regional centroid-moment-tensor analysis for earthquakes in Canada and adjacent regions: An update. Seismological Research Letters, 83(5), 505-988515. doi: https://doi.org/10.1785/gssrl.83.3.505"]}
DOI: 10.5281/zenodo.7764879
title: Streamflow drought hazard indicators for monitoring drought hazard for human water supply and river ecosystems at the global scale (WaterGAP 2.2d, WFDEI-GPCC)

description: <strong>1) Streamflow drought hazard indicators (SDHIs) as computed by WaterGAP 2.2d (climate data WFDEI-GPCC) for the whole globe except Antarctica, spatial resolution: 0.5°, monthly data for the reference period 1986-2015:</strong> <strong>Indicators of drought magnitude: </strong>SSI1, SSI12, EP1, RDQI1 <strong>Indicators of drought severity: </strong> CDQI1-Q50, CDQI1-Q50_f, CDQI1-Q80, CDQI1-Q80_f, CDQI1-Q80-HS, CDQI6-Q80, CDQI6-Q80_f, CDQI1-WUs, CDQI1-WUs-EFR, CDQI1-WUs-EFR_f, CEP1(20%), CEP1(20%)_f, CRDQI1(-50%), CRDQI1(-50%)_f <strong>2) WaterGAP grid cell IDs ("arcid") with longitude and latitude:</strong> (WaterGAP_ArcID_lon_lat.txt) <strong>3) Streamflow observations at 220 GRDC gauging stations and list of the 220 GRDC station numbers with related WaterGAP grid cell ID ("arcid"):</strong> Observed_monthly_streamflow_km3month_220_calstations_1986_2015.txt GRDC_number_WaterGAP_ArcID_220_stations.txt <strong>4) SDHIs for four GRDC gauging stations:</strong> time_series_danube_river.txt, time_series_angara_river.txt, time_series_white_river.txt, time_series_orange_river.txt <strong>5) WaterGAP output: Mean monthly surface water abstractions in km3 per month: </strong>Mean_monthly_WUs_km3_per_month_WFDEI_GPCC_ant_22d_1986_2015.txt
DOI: 10.5281/zenodo.7826238
title: Regional distribution of annual sea-to-air OCS fluxes for the present day atmosphere with 500 ppt OCS and the two OCS geoengineering scenarios with 4.8 ppb and 35.5 ppb.

description: This dataset was prepared for a publication by von Hobe et al. (2023): <strong>Comment on “An approach to sulfate geoengineering with surface emissions of carbonyl sulfide” by Quaglia et al. (2022)</strong> In that publication, the data are displayed in Figure 3. Average annual sea-to-air OCS fluxes on a 2.8 ° latitude x 2.8 ° longitude grid for the present day atmosphere and for the two OCS emission scenarios considered by Quaglia et al. (2022) were obtained from a 2003 - 2019 simulation, using a model described in Lennartz et al. (2021). - - - - - - - - - - - File format: netCDF Index Variables: latitude longitude Parameters: ocsem500: mean annual sea-to-air OCS flux calculated for an atmospheric OCS mole fraction of 500 ppt ocsem4800: mean annual sea-to-air OCS flux calculated for an atmospheric OCS mole fraction of 4.8 ppb ocsem35500: mean annual sea-to-air OCS flux calculated for an atmospheric OCS mole fraction of 35.5 ppb - - - - - - - - - - - <strong>References:</strong> Lennartz, S. T., Gauss, M., von Hobe, M., and Marandino, C. A.: Monthly resolved modelled oceanic emissions of carbonyl<br> sulphide and carbon disulphide for the period 2000–2019, Earth Syst. Sci. Data, 13, 2095-2110, 10.5194/essd-13-2095-2021, 2021. Quaglia, I., Visioni, D., Pitari, G., and Kravitz, B.: An approach to sulfate geoengineering with surface emissions of carbonyl<br> sulfide, Atmos. Chem. Phys., 22, 5757-5773, 10.5194/acp-22-5757-2022, 2022. von Hobe, M., Brühl, C., Lennartz, S. T., Whelan, M. E., and Kaushik, A.: Comment on “An approach to sulfate geoengineering with surface emissions of carbonyl sulfide” by Quaglia et al. (2022) , EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-268, 2023.
description: Sinikka Lennartz acknowledges funding from Ministry for Education and Research (BMBF, grant 16TTP079) and the Ministry for Research and Culture in Lower-Saxony (MWK 'Niedersächsisches Vorab', grant VWZN3421).
DOI: 10.5281/zenodo.7826422
title: Top-of-the-atmosphere radiative forcing by aerosol due to continuous OCS injection near the tropical tropopause simulated by EMAC

description: This dataset was prepared for a publication by von Hobe et al. (2023): <strong>Comment on “An approach to sulfate geoengineering with surface emissions of carbonyl sulfide” by Quaglia et al. (2022)</strong> In that publication, the data are displayed in Figure 4. The dataset contains additional stratospheric aerosol forcing for injections of 6 Tg S a<sup>-1</sup> OCS for several years over 5 tropical cities at the tropopause (97 hPa) calculated with the EMAC (ECHAM5/MESSy Atmospheric Chemistry) CCM (e.g. Brühl et al., 2018; Schallock et al., 2023). Data are given for a four year time series starting in January 2017. - - - - - - - - - - - - File format: netCDF Index Variables: time, 10 hourly, as 'day since 1997-01-01' (note that the two variables named time4 and time6 are identical) Parameters: SOLFORCCSO: instantaneous solar radiative forcing at the top of the atmosphere by aerosol due to continuous OCS injection near the tropical tropopause with surface mixing ratios of OCS were fixed to observations TOTFORCCSO: instantaneous total radiative forcing at the top of the atmosphere by aerosol due to continuous OCS injection near the tropical tropopause with surface mixing ratios of OCS were fixed to observations SOLFORCCSO_FREE: instantaneous solar radiative forcing at the top of the atmosphere by aerosol due to continuous OCS injection near the tropical tropopause with surface mixing ratios of OCS allowed to increase from downward transport TOTFORCCSO_FREE: instantaneous total radiative forcing at the top of the atmosphere by aerosol due to continuous OCS injection near the tropical tropopause with surface mixing ratios of OCS allowed to increase from downward transport - - - - - - - - - - - - <strong>References:</strong> Brühl, C., Schallock, J., Klingmüller, K., Robert, C., Bingen, C., Clarisse, L., Heckel, A., North, P., and Rieger, L.: Stratospheric aerosol radiative forcing simulated by the chemistry climate model EMAC using Aerosol CCI satellite data, Atmos. Chem. Phys., 18, 12845-12857, 10.5194/acp-18-12845-2018, 2018 Quaglia, I., Visioni, D., Pitari, G., and Kravitz, B.: An approach to sulfate geoengineering with surface emissions of carbonyl<br> sulfide, Atmos. Chem. Phys., 22, 5757-5773, 10.5194/acp-22-5757-2022, 2022. Schallock, J., Brühl, C., Bingen, C., Höpfner, M., Rieger, L., and Lelieveld, J.: Reconstructing volcanic radiative forcing since 1990, using a comprehensive emission inventory and spatially resolved sulfur injections from satellite data in a chemistry climate model, Atmos. Chem. Phys., 23, 1169-1207, 10.5194/acp-23-1169-2023, 2023. von Hobe, M., Brühl, C., Lennartz, S. T., Whelan, M. E., and Kaushik, A.: Comment on “An approach to sulfate geoengineering with surface emissions of carbonyl sulfide” by Quaglia et al. (2022) , EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-268, 2023.
DOI: 10.6084/m9.figshare.21687686.v1
title: PLOS Open Science Indicators

description: This dataset contains article metadata and information about Open Science Indicators for approximately 61,000 research articles published in PLOS from 1 January 2019 to 30 June 2022 and a set of approximately 6,500 comparator articles published in non-PLOS journals. This is the first release of this dataset, which will be updated with new versions as newly published content is analysed. This version of the Open Science Indicators dataset focuses on detection of three Open Science practices by analysing the XML of published research articles: Sharing of research data, in particular data shared in data repositories Sharing of code Posting of preprints The dataset provides data and code generation and sharing rates, the location of shared data and code (whether in Supporting Information or in an online repository). It also provides preprint sharing rates as well as details of the shared preprint, such as publication date, URL and preprint server used. Additional data fields are also provided for each article analysed, such as geographic information (‘Country’) and research topics (‘Discipline’). Further information on the methods used to collect and analyse the data can be found in OSI-Methods-Statement_v1_Dec22.pdf with accompanying information in OSI-Column-Descriptions_v1_Dec22.pdf and OSI-Repository-List_v1_Dec22.xlsx. Further information on the principles and requirements for developing Open Science Indicators is available in https://doi.org/10.6084/m9.figshare.21640889. The data files PLOS-Dataset_v1_Dec22.csv and Comparator-Dataset_v1_Dec22.csv contain descriptive metadata, e.g. article title, publication data, author countries, is taken from the article .xml files additional information around the Open Science Indicators derived algorithmically, using Natural Language Processing. The OSI-Summary-statistics_v1_Dec22.xlsx file contains the summary data for both PLOS-Dataset_v1_Dec22.csv and Comparator-Dataset_v1_Dec22.csv used in https://theplosblog.plos.org/2022/12/open-science-indicators-first-dataset. <br> <strong>Contact details for further information:</strong> Iain Hrynaszkiewicz, Director, Open Research Solutions, PLOS, ihrynaszkiewicz@plos.org / plos@plos.org Lauren Cadwallader, Open Research Manager, PLOS, lcadwallader@plos.org / plos@plos.org <br> <strong>Acknowledgements:</strong> Thanks to Allegra Pearce and Tim Vines of DataSeer for contributing to data acquisition and supporting information.
DOI: 10.6084/m9.figshare.22099580.v1
title: Dataset

description: This contains OTD raw data and questionnaire
DOI: 10.6084/m9.figshare.22361818
title: Supplementary Material for: Tryptophol acetate and tyrosol acetate, small molecule metabolites identified in a probiotic mixture, inhibit hyperinflammation

description: Probiotic fermented foods are perceived as contributing to human health, however solid evidence for their presumptive therapeutic systemic benefits is generally lacking. Here we report that tryptophol acetate and tyrosol acetate, small molecule metabolites secreted by the probiotic milk-fermented yeast Kluyveromyces marxianus inhibit hyperinflammation (e.g., “cytokine storm”). Comprehensive in vivo and in vitro analyses, employing LPS-induced hyperinflammation models, reveal dramatic effects of the molecules, added in tandem, on mice morbidity, laboratory parameters, and mortality. Specifically, we observed attenuated levels of the pro-inflammatory cytokines IL-6, IL-1α, IL-1β and TNF-α, and reduced reactive oxygen species. Importantly, tryptophol acetate and tyrosol acetate did not completely suppress pro-inflammatory cytokine generation, rather brought their concentrations back to baseline levels thus maintaining core immune functions, including phagocytosis. The anti-inflammatory effects of tryptophol acetate and tyrosol acetate were mediated through downregulation of TLR4, IL-1R, and TNFR signaling pathways and increased A20 expression, leading to NF-kB inhibition. Overall, this work illuminates phenomenological and molecular details underscoring anti-inflammatory properties of small molecules identified in a probiotic mixture, pointing to potential therapeutic avenues against severe inflammation.
DOI: 10.6084/m9.figshare.23267021
title: Supplementary Material for: Urea Reduction in Acute Kidney Injury and Mortality Risk

description: <b><i>Introduction:</i></b> Urea is a toxin present in acute kidney injury (AKI). We hypothesize that reduction in serum urea levels might improve clinical outcomes. We examined the association between the reduction in urea and mortality. <b><i>Methods:</i></b> Patients with AKI admitted to the Hospital Civil de Guadalajara were enrolled in this retrospective cohort study. We create 4 groups of urea reduction ratio (UXR) stratified by their decrease in urea from the highest index value in comparison to the value on day 10 (0%, 1–25%, 26–50%, and &gt;50%), or at the time of death or discharge if prior to 10 days. Our primary endpoint was to observe the association between UXR and mortality. Secondary observations included determination of which types of patients achieved a UXR &gt;50%, whether the modality of kidney replacement therapy (KRT) effected changes in UXR, and if serum creatinine (sCr) value changes were similarly associated with patient mortality. <b><i>Results:</i></b> A total of 651 AKI patients were enrolled. The mean age was 54.1 years, and 58.6% were male. AKI 3 was present in 58.5%; the mean admission urea was 154 mg/dL. KRT was started in 32.4%, and 18.9% died. A trend toward decreased risk of death was observed in association with the magnitude of UXR. The best survival (94.3%) was observed in patients with a UXR &gt;50%, and the highest mortality (72.1%) was observed in patients achieving a UXR of 0%. After adjusting for age, sex, diabetes mellitus, CKD, antibiotics, sepsis, hypovolemia, cardio-renal syndrome, shock, and AKI stage, the 10-day mortality was higher in groups that did not achieve a UXR of at least 25% (OR: 1.20). Patients achieving a UXR &gt;50% were most likely initiated on dialysis due to a diagnosis of the uremic syndrome or had a diagnosis of obstructive nephropathy. Percentage change in sCr was also associated with increased mortality risk. <b><i>Conclusions:</i></b> In our retrospective cohort of AKI patients, the percent decrease in UXR from admission was associated with a stratified risk of death. Patients with a UXR &gt;25% had the best associated outcomes. Overall, a greater magnitude in UXR was associated with improved patient survival.
DOI: 10.5281/zenodo.7803017
title: The oxidation state of sulfur in apatite of Martian meteorite- Shergotty

description: S-XANES data of Shergotty apatite.
DOI: 10.17189/1519502
title: MSL DYNAMIC ALBEDO OF NEUTRONS LEVEL 3/4 RDR V1.0
DOI: 10.17632/jbxtx2p6r9.1
title: Low-temperature thermochronology

description: The Huangling dome is one of the largest tectonic domes in the South China continent. According to previous geological mapping results, the dome was formed between the Late Jurassic and Early Cretaceous, when regional compression was eventually replaced by regional extension. This transition fuels a dispute about whether the dome was generated by compression or extension. This study carried out single-grain zircon (U–Th)/He (ZHe) dating for samples collected from the dome and adjacent synclines. All measured  ZHe ages are  younger than the depositional or crystallization ages of the sampled rocks, and the western and eastern dome sides have much older ZHe mean ages than those of the dome and synclines' cores. These reflect  an complex interactions between uplift, denudation and heating processes during dome formation. 
In order to explore the exhumation history of the dome, we developed one-dimensional heat-conduction models that cover a wide range of heating and exhumation scenarios (assuming that uplift rate equals denudation rate) within an interval of 152.1–121.4 Ma. These models were solved and searched for the predictions of the measured ages. The best models have a fast decrease in uplift rate with time and a constant heating rate, indicative of an early-interval shaping of the dome in a compressional setting.
DOI: 10.5281/zenodo.3699950
title: The Research Software Alliance (ReSA) and the community landscape

description: The Research Software Alliance (ReSA)’s mission is to bring research software communities together to collaborate on the advancement of research software. ReSA has formed taskforces and one of them revolves around a <strong>software landscape analysis</strong> aiming to answer the question "How can we identify the different communities and topics of interest for the research software community (e.g., preservation, RSEs, citation, productivity, sustainability)?" Here we include text describing the work of the taskforce to date (see 2020-03-11-ReSA-landscape.md), as well as plans for the future, and an invitation to readers to contribute to the ReSA list of research software communities. We are a;sp including the current version of the list in a CSV file (see 2020-03-11-ReSA-landscape.csv ), and we welcome contributions on the live spreadsheet that can be found via this link.
DOI: 10.5281/zenodo.4456701
title: Customized gtf file from Ensembl version 98 mm10

description: The gtf from Ensembl version 98 (mm10) was filtered to remove readthrough transcripts and all non-coding transcripts from a protein-coding gene. In addition, all genes with the same gene name which overlaps were merged under the same gene id to avoid ambiguous reads.
DOI: 10.5281/zenodo.6576495
title: chr2 of mutant genomes used in Rekaik et al. 2022

description: Fasta file for ch2 of the Del(d1-d4), Del(sub-TAD1) and Ins(2xCBS-d4d8) mutant ES cell lines used in Rekaik et al., 2022. In Del(d1-d4) mutant, the deletion includes bases between mm10:74,719,771 and 74,765,994. The Del(sub-TAD1) chr2 contains the deletion of mm10:74768588 to 75133800. In Ins(2xCBS-d4d8), a 900bp cassette was inserted between bases mm10:74,716,919 and 74,717,063. The insertion contains 2 CTCF binding sites, both cloned from the endogenous CBS1 sequence at the position mm10: 74,715,687-74,716,136 and mm10: 74,715,717-74,716,166, respectively. The fasta files were generated from the chr2 of the mm10 genome (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/chromosomes/chr2.fa.gz).