cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7642295.v1
title: X-ray irradiation induces subtle changes in the genome-wide distribution of DNA hydroxymethylation with opposing trends in genic and intergenic regions

description: DNA hydroxymethylation has gained attention as an intermediate in the process of DNA demethylation. More recently, 5-hydroxymethylcytosine has been recognized as an independent epigenetic mark that can persist over time and that exerts influence on gene regulation and other biological processes. Deregulation of this DNA modification has been linked to tumorigenesis and a variety of other diseases. The impact of irradiation on DNA hydroxymethylation is poorly understood. In this study we exposed lung fibroblasts (IMR90) to 0.5 Gy and 2 Gy of X-rays, respectively. We characterized radiation induced changes of DNA hydroxymethylation 1 h, 6 h, 24 h and 120 h after exposure employing immunoprecipitation and subsequent deep sequencing of the genomic fraction enriched for hydroxymethylated DNA. Transcriptomic response to irradiation was analyzed for time points 6 h and 24 h post exposure by means of RNA sequencing. Irradiated and sham-irradiated samples shared the same overall distribution of 5-hydroxymethylcytosines with respect to genomic features such as promoters and exons. The frequency of 5-hydroxymethylcytosine peaks differentially detected in irradiated samples increased in genic regions over time, while the opposing trend was observed for intergenic regions. Onset and extent of this effect was dose dependent. Moreover, we demonstrated a biased distribution of 5-hmC alterations at CpG islands and sites occupied by the DNA binding protein CTCF. In summary, our study provides new insights into the epigenetic response to irradiation. Our data highlight genomic features more prone to irradiation induced changes of DNA hydroxymethylation, which might impact early and late onset effects of irradiation.
DOI: 10.6084/m9.figshare.24448663.v1
title: HaPy-Bug – Human Annotated Python Bug Resolution Dataset

description: We present HaPy-Bug, a curated dataset of 793 Python source code commits associated with bug fixes, with each line of code annotated by three domain experts. The annotations offer insights into the purpose of modified files, changes at the line level, and reviewers’ confidence levels. We analyze HaPy-Bug to examine the distribution of file purposes, types of modifications, and tangled changes. Additionally, we explore its potential applications in bug tracking, the analysis of bug-fixing practices, and the development of repository analysis tools. HaPy-Bug serves as a valuable resource for advancing research in software maintenance and security.
DOI: 10.6084/m9.figshare.7928813.v1
title: gVCF_HG02272

description: 1000 Genomes gVCF mapped to hs37d5 for HG02272. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.17632/jfpj77vs9k
title: Tongue Cancer Survival Data

description: Oral Tongue Cancer Survival from a low socioeconomic area, this contains the spss data sheet file
DOI: 10.6084/m9.figshare.7605509.v1
title: pipeline.json.gz

description: Gzipped JSON file of the output of the benchmarking pipeline. This has, for each sample, the resistance calls of each tool for that sample. It is the input file needed to generate all the results in the publication.
DOI: 10.17632/jfjts98y45
title: Matlab source code for: Hybrid Multi-objective Evolutionary Algorithm Based on Search Manager Framework for Big Data Optimization Problems

description: Matlab Code For Hybrid Multi-objective Evolutionary Algorithm Based on Search Manager Framework for Big Data Optimization Problems
DOI: 10.17632/m8pkzbktbk
title: Brunello Whole Genome Knock out library in BE(2)-C Neuroblastoma cells - NGS dataset of library population

description: NGS data to confirm representative and balanced creation of the Brunello whole genome knock out library in BE(2)-C neuroblastoma cells. 
Human Brunello CRISPR knockout pooled library was a gift from David Root and John Doench (Addgene #73178). 
BE(2)-C cells from ATCC CRL-2268.
DOI: 10.17632/pb8dk5vkgv
title: Cannabinoids: an effective treatment for chemotherapy-induced peripheral neurotoxicity?

description: materials and methods as supplementary data to the review "Cannabinoids: an effective treatment for chemotherapy-induced peripheral neurotoxicity?"
DOI: 10.17632/xc793ng42g
title: knowledge practice and attitude towards yoga therapy among regional university students in Haryana -An online cross sectional survey

description: Abstract Background: Yoga was an ancient day-to-day practice that was a key to healthy lifestyle. Yoga enhances musculoskeletal strength, flexibility, cardiopulmonary efficiency which helps improving quality of life. Yoga as a practice is beneficial when the user owns a complete knowledge and faith towards the ancient practice. Present study focuses on knowledge, practice and attitude of yoga among college going individuals. Methods: An approved Google form link was sent to 95 individuals and all 95 were received and analyzed. Out of 95 individuals, 27 respondents were males and 68 females. Inclusion criteria were both male and female aged 18-30 years from Haryana and non-internet users were excluded. Result: Outcome regarding yoga practice and awareness was 75% in college students who voluntarily participated in the study. Conclusion: The present study reveals that significant young population owes positive knowledge about various benefits of yoga. Keywords: Yoga, Students, Meditation, Quality of life.
DOI: 10.6084/m9.figshare.20277759.v5
title: Fungal genome size and composition reflect ecological strategies along soil fertility gradientsadd code and derived data

description: This dataset includes all data as well as the scripts used to produce figures from both the main text and the supporting information from Zhang et al. (2023) " Fungal genome size and composition reflect ecological strategies along soil fertility gradients". <br> Detailed description: genome_size_lifestyle.csv: the file containing genome size and lifestyles for all fungi. ncbi_fungi_GC_content.csv: files containing GC content data from NCBI. Fungi_all_gs_gc_match.csv: files containing fungal species that both have the GC and genome size values. genome_size_fungal_traits.csv: files containing other fungal traits data for species that have genome size data. <br> <br> All data above are the raw data files. By contrast, the following data files, including Australian_Microbiome_GC_CWM.csv, Australian_Microbiome_Genomesize_CWM.csv, Appendix_S1.csv, Appendix_S3.csv are derived data and the code Fig3.R can be used to generate these data files. Fig4_slope_data.csv was generated from FigS4_stats.R, FigS5_stats.R, FigS6_stats.R. <br> For each of these figures there is their respective R script and the reorganized dataset used to produce them. R scripts are responsible for the production of Figures 1-4 in the main text and most of the supplement respectively.
DOI: 10.6084/m9.figshare.21739745.v1
title: covid_19.xlsx

description: COVID-19 dataset
DOI: 10.6084/m9.figshare.23251661.v2
title: Padogobius bonelli 7-River Cerefone-Le Ville.tif

description: X-ray data set used in "Skeletal traits and otoliths can unravel the relationships within European Gobiidae (Gobius lineage sensu lato)" Bettina Reichenbacher, Jasna Vukić, Radek Šanda, Ulrich K. Schliewen, Hamid R. Esmaeili, Abderrahmane Kassar, IN: Zoological Journal of the Linnean Society, 2023, XX, 1–32 https://doi.org/10.1093/zoolinnean/zlad058 <br> scale bar of X-ray images = 1 cm
DOI: 10.6084/m9.figshare.28466243.v1
title: FRONTIERS_ID 1526236_DOI 10.3389/fphys.2025.1526236.xlsx

description: Data matrix of the study "Acute sonographic changes in common carotid artery after NESA neuromodulation intervention in healthy adults: a randomized controlled clinical trial" with DOI: 10.3389/fphys.2025.1526236. The general data matrix is ​​shown in tab 1, the reliability analysis assessment data by study variable.
DOI: 10.6084/m9.figshare.7804247.v1
title: PLSDB 2018_09_14

description: PLSDB data version 2018_09_14
DOI: 10.6084/m9.figshare.9199517.v1
title: Listado de programas grupales de parentalidad positiva identificados en la revisión sistemática

description: Listado de programas grupales de parentalidad positiva identificados en la revisión sistemática
DOI: 10.17632/3sv9tfsgdt
title: Drone Navigation Experiment Data

description: This dataset contain the measurement data in a drone navigation experiment. The experiment is conducted to test the performance of drone's navigation using pinhole model for distance prediction. The dataset contains two set of data. The first is statics experiment dataset. It contains the distance prediction between the drone with a certain target object, using pinhole model. The second set is dynamic experiment dataset. It contains the measurement data of a drone flight to reach certain area based on pinhole distance calculation model.
DOI: 10.6084/m9.figshare.22770105.v1
title: QSAR modeling approaches to identify a novel ACE2 inhibitor that selectively bind with the C and N terminals of the ectodomain

description: Due to the high rates of drug development failure and the massive expenses associated with drug discovery, repurposing existing drugs has become more popular. As a result, we have used QSAR modelling on a large and varied dataset of 657 compounds in an effort to discover both explicit and subtle structural features requisite for ACE2 inhibitory activity, with the goal of identifying novel hit molecules. The QSAR modelling yielded a statistically robust QSAR model with high predictivity (R<sup>2</sup><sub>tr</sub>=0.84, R<sup>2</sup><sub>ex</sub>=0.79), previously undisclosed features, and novel mechanistic interpretations. The developed QSAR model predicted the ACE2 inhibitory activity (<sub>P</sub>IC<sub>50</sub>) of 1615 ZINC FDA compounds. This led to the detection of a <sub>P</sub>IC<sub>50</sub> of 8.604 M for the hit molecule (ZINC000027990463). The hit molecule’s docking score is −9.67 kcal/mol (RMSD 1.4). The hit molecule revealed 25 interactions with the residue ASP40, which defines the N and C termini of the ectodomain of ACE2. The HIT molecule conducted more than thirty contacts with water molecules and exhibited polar interaction with the ARG522 residue coupled with the second chloride ion, which is 10.4 nm away from the zinc ion. Both molecular docking and QSAR produced comparable findings. Moreover, MD simulation and MMGBSA studies verified docking analysis. The MD simulation showed that the hit molecule-ACE2 receptor complex is stable for 400 ns, suggesting that repurposed hit molecule 3 is a viable ACE2 inhibitor.
DOI: 10.6084/m9.figshare.26840626.v1
title: <b>Characterizing dynamics of building height in China from 2005 to 2020 based on GEDI, Landsat, and PALSAR data</b>

description: The unprecedented urbanization in China has driven rapid urban and rural development in recent decades. While existing studies have extensively focused on horizontal urban expansion, research on vertical urban expansion patterns in China remains limited. To address this gap, we proposed a Multi-Temporal Building Height estimation network (MTBH-Net) to estimate building heights at a 30 m spatial resolution in China for 2005, 2010, 2015, and 2020 by integrating Global Ecosystem Dynamics Investigation (GEDI), Landsat, and PALSAR data. Specifically, we introduced sample migration to generate reference building height data and utilized the Continuous Change Detection and Classification (CCDC) disturbance feature to ensure consistency in unchanged built-up areas. Validation with GEDI L2A V2 data demonstrated that MTBH-Net achieved RMSEs of 5.38 m, 5.73 m, 6.26 m, and 6.36 m for the respective years. Further validation with field-measured data and GF-7 building height data yielded RMSEs of 9.13 m and 10.99 m, respectively. The proposed 30-m China Multi-Temporal Building Height (CMTBH-30) dataset reveals an increase in average building heights in China from 10.48 m in 2005 to 11.37 m in 2020, reflecting an upward trend in urban development. Additionally, the standard deviation of building heights rose from 3.87 m in 2005 to 6.35 m in 2020, indicating increased height variation nationwide. Regional analysis from 2005 to 2020 shows significant vertical growth on stable impervious surfaces in Chongqing (+3.6 m), Guizhou (+3.0 m), and Qinghai (+3.0 m), while Macau (+14.9 m), Hong Kong (+13.9 m), and Guangdong (+13.5 m) experienced notable growth on newly expanded impervious surfaces. Minimal growth was observed in Jilin, Heilongjiang, and Xinjiang. CMTBH-30 offers a more refined and accurate depiction of building heights, effectively capturing height variations and mitigating the underestimation of high-rise buildings. It fills the gap in multi-temporal building height products. Overall, this study provides a new dimension for urban research and is valuable for urban planning, disaster management, and environmental sustainability.
DOI: 10.6084/m9.figshare.5124166.v1
title: Supplementary Material for: Canonical Bcl-2 Motifs of the Na<sup>+</sup>/K<sup>+</sup> Pump Revealed by the BH3 Mimetic Chelerythrine: Early Signal Transducers of Apoptosis?

description: <b><i>Background/Aims: </i></b>Chelerythrine [CET], a protein kinase C [PKC] inhibitor, is a prop-apoptotic BH3-mimetic binding to BH1-like motifs of Bcl-2 proteins. CET action was examined on PKC phosphorylation-dependent membrane transporters (Na<sup>+</sup>/K<sup>+</sup> pump/ATPase [NKP, NKA], Na<sup>+</sup>-K<sup>+</sup>-2Cl<sup>+</sup> [NKCC] and K<sup>+</sup>-Cl<sup>-</sup> [KCC] cotransporters, and channel-supported K<sup>+</sup> loss) in human lens epithelial cells [LECs]. <b><i>Methods: </i></b>K<sup>+</sup> loss and K<sup>+</sup> uptake, using Rb<sup>+</sup> as congener, were measured by atomic absorption/emission spectrophotometry with NKP and NKCC inhibitors, and Cl<sup>-</sup> replacement by NO<sub>3</sub><sup>ˉ</sup> to determine KCC. <sup>3</sup>H-Ouabain binding was performed on a pig renal NKA in the presence and absence of CET. Bcl-2 protein and NKA sequences were aligned and motifs identified and mapped using PROSITE in conjunction with BLAST alignments and analysis of conservation and structural similarity based on prediction of secondary and crystal structures. <b><i>Results: </i></b>CET inhibited NKP and NKCC by &gt;90% (IC<sub>50</sub> values ∼35 and ∼15 µM, respectively) without significant KCC activity change, and stimulated K<sup>+</sup> loss by ∼35% at 10-30 µM. Neither ATP levels nor phosphorylation of the NKA α1 subunit changed. <sup>3</sup>H-ouabain was displaced from pig renal NKA only at 100 fold higher CET concentrations than the ligand. Sequence alignments of NKA with BH1- and BH3-like motifs containing pro-survival Bcl-2 and BclXl proteins showed more than one BH1-like motif within NKA for interaction with CET or with BH3 motifs. One NKA BH1-like motif (ARAAEILARDGPN) was also found in all P-type ATPases. Also, NKA possessed a second motif similar to that near the BH3 region of Bcl-2. <b><i>Conclusion: </i></b>Findings support the hypothesis that CET inhibits NKP by binding to BH1-like motifs and disrupting the α<sub>1</sub> subunit catalytic activity through conformational changes. By interacting with Bcl-2 proteins through their complementary BH1- or BH3-like-motifs, NKP proteins may be sensors of normal and pathological cell functions, becoming important yet unrecognized signal transducers in the initial phases of apoptosis. CET action on NKCC1 and K<sup>+</sup> channels may involve PKC-regulated mechanisms; however, limited sequence homologies to BH1-like motifs cannot exclude direct effects.
DOI: 10.17632/6x3jsjcc3r
title: Computational Study Instances of the Multi-visit Drone Pickup and Delivery Routing Problem Considering Time Windows

description: The set includes all instances used in the multi-visit drone pickup and delivery problem considering time windows:
1. Small instances 
2. Large instances
3. Instances for sensitivity analysis
4.Instances based on a real network
DOI: 10.17632/9dxgbgx86k
title: Arabic News Tweets

description: A great size collection of Arabic news tweets was collected from an official and verified users in Twitter that belongs to Saudi Arabia news. All data that is gathered was retrieved using specific time period and collected all news in that time. This dataset does not specify by keywords. Moreover, this news dataset can be valuable for diverse tasks in NLP, such as text classification and automated verification system. The dataset has been labeled as general news, regions news, sport news, economic news, and quality life news. In this data article, 89,179 original tweets have presented and fully labeled.
DOI: 10.17632/t58n75x5jb
title: Research Dataset-High-Performance Mid-Wave Infrared Metasurface for Broadband Linear-to-Circular Polarization Transformation

description: This dataset is a COMSOL simulation file that contains simulation performance data for converting linear polarization to circular polarization. Including simulation data such as reflection coefficient, phase difference, energy utilization efficiency, etc.
DOI: 10.6084/m9.figshare.12582632.v1
title: CPS list of papers and categories

description: this is the file containing the results of our mapping study on cognitive production systems conducted in 2019/2020<br>
DOI: 10.6084/m9.figshare.27919041.v1
title: FTIR, TGA and DSC characterisation

description: Raw material sulfated CNCs, Br-CNC macroinitiators and polyvinyl acetate-CNC copolymers were characterised with FTIR and TGA. DSC was used to characterise the polyvinyl acetate-CNC copolymers and the final composite.
DOI: 10.15482/usda.adc/1528072
title: Growth and Yield Data for the Bushland, Texas, Sunflower Datasets

description: This dataset consists of growth and yield data for each season when sunflower (Helianthus annuus L.) was grown for seed at the USDA-ARS Conservation and Production Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU) research weather station, Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL). In each season, sunflower was grown on two large, precision weighing lysimeters, each in the center of a 4.44 ha square field. The square fields are themselves arranged in a larger square with four fields in four adjacent quadrants of the larger square. Fields and lysimeters within each field are thus designated northeast (NE), southeast (SE), northwest (NW), and southwest (SW). Sunflower was grown in the NE and SE fields. Irrigation was by linear move sprinkler system. Irrigation protocols described as full were managed to replenish soil water used by the crop on a weekly or more frequent basis as determined by soil profile water content readings made with a neutron probe to 2.4-m depth in the field. Irrigation protocols described as deficit typically involved irrigations to establish the crop early in the season, followed by reduced or absent irrigations later in the season (typically in the later winter and spring).
    The growth and yield data include plant population density, height, plant row width, leaf area index, growth stage, total above-ground biomass, leaf and stem biomass, head mass (when present), kernel number, and final yield. Data are from replicate samples in the field and non-destructive (except for final harvest) measurements on the weighing lysimeters. In most cases yield data are available from both manual sampling on replicate plots in each field and from machine harvest.
    These datasets originate from research aimed at determining crop water use (ET), crop coefficients for use in ET-based irrigation scheduling based on a reference ET, crop growth, yield, harvest index, and crop water productivity as affected by irrigation method, timing, amount (full or some degree of deficit), agronomic practices, cultivar, and weather. Prior publications have focused on sunflower ET, crop coefficients, and crop water productivity. Crop coefficients have been used by ET networks. The data have utility for testing simulation models of crop ET, growth, and yield and have been used for testing, and calibrating models of ET that use satellite and/or weather data.
DOI: 10.6084/m9.figshare.12022737.v1
title: Supplementary Material for: Safety and Efficacy of Prasugrel in Elderly/Low Body Weight Japanese Patients with Ischemic Stroke: Randomized PRASTRO-II

description: <b><i>Introduction:</i></b> The safety of prasugrel in elderly and/or low body weight Japanese patients with ischemic stroke who have a relatively high bleeding risk with antiplatelet therapy remains unknown. <b><i>Objective:</i></b> We aimed to investigate the safety and efficacy of long-term prasugrel monotherapy for stroke prevention compared with clopidogrel in elderly and/or low body weight Japanese patients with non-cardioembolic ischemic stroke. <b><i>Methods:</i></b> In this randomized, double-blind, comparative, phase III study, elderly (age ≥75 years) and/or low body weight (≤50 kg) Japanese patients with a previous history of non-cardioembolic ischemic stroke were assigned to a prasugrel 3.75 mg (PRA3.75) group, a prasugrel 2.5 mg (PRA2.5) group, or a clopidogrel 50 mg (CLO50) group and followed up for 48 weeks. The primary safety endpoint was the combined incidence of primary safety events, defined as life-threatening, major, and other clinically relevant bleeding. The efficacy endpoint was a composite of ischemic stroke, myocardial infarction, and death from other vascular causes. <b><i>Results:</i></b> A total of 654 patients (age 76.4 ± 7.3 years, body weight 55.6 ± 9.3 kg, women 43.9%) from 74 medical institutions within Japan were enrolled. The combined incidence (95% CI) of primary safety events was 4.2% (1.9–7.8%), 1.9% (0.5–4.7%), and 3.6% (1.6–6.9%) in the PRA3.75 group (<i>n</i> = 216), PRA2.5 group (<i>n</i> = 215), and CLO50 group (<i>n</i> = 223), respectively (hazard ratios [HR] PRA3.75/CLO50, 1.13 [0.44–2.93]; PRA2.5/CLO50, 0.51 [0.15–1.69]). The incidences of bleeding leading to treatment discontinuation (95% CI) were 2.3% (0.8–5.3%), 0.9% (0.1–3.3%), and 2.2% (0.7–5.2%) in the PRA3.75, PRA2.5, and CLO50 groups, respectively (HRs PRA3.75/CLO50, 1.01 [0.29–3.48]; PRA2.5/CLO50, 0.41 [0.08–2.12]). There was no significant difference in all bleeding events between groups. The incidence of ischemic stroke, myocardial infarction, and death from other vascular causes was lower, but not significantly so, in patients treated with prasugrel than in patients treated with clopidogrel: PRA3.75, 0.0% (0/216); PRA2.5, 3.3% (7/215); and CLO50, 3.6% (8/223; HRs PRA3.75/CLO50, 0.00 [0.00–0.00]; PRA2.5/CLO50, 0.90 [0.32–2.47]). <b><i>Conclusions:</i></b> Elderly and/or low body weight ­Japanese patients with previous non-cardioembolic ischemic stroke who received PRA3.75 showed similar results in terms of primary safety endpoint, and a numerically lower incidence of ischemic stroke, myocardial infarction, and death from other vascular causes, compared with those who received CLO50.
DOI: 10.6084/m9.figshare.16661371.v2
title: Supporting Information: S1 Mu-RN DATASET & S2 the Walsh Hadamard calculation template

description: Datasets for growth rates of alleles across drug concentrations. Also the Walsh-Hadamard coefficient calculations.<br>Also a spreadsheet where Walsh-Hadamard calculations can be conducted.<br>
DOI: 10.6084/m9.figshare.21493725.v1
title: data.zip

description: Data for A1 Bioinformatica Training
DOI: 10.6084/m9.figshare.22557511.v1
title: BOLD Sequence and Metadata

description: Raw data from the Barcode of Life Database which was downloaded on 2023-11-19. It is formatted as a CSV file. It contains raw COI sequences, barcode identifiers, spatial coordinates, and other metadata reported by BOLD. <br> Necessary code for processing the raw data is available on https://github.com/connor-french/global-insect-macrogenetics, specifically the notebook <code>step-1_seq-filter-align-test.ipynb.</code>