cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/65fcympd2j
title: Sensitivity of genes, molecular pathways and disease related categories to chemical exposures

description: The goal of this project is to identify molecular mechanisms sensitive to chemical exposures in an unbiased way. Results of this project are published on preprints.org (doi: 10.20944/preprints202006.0261.v1).

The data-files described below represent major steps of our analysis:

1. Annotated chemical-gene interactions.xlsx 
The data on chemical-gene interactions obtained from high-throughput toxicological genomic experiments with human, mouse, or rat cells and tissues was extracted from Comparative Toxicogenomic Database (CTD, http://ctdbase.org/) on 08.24.2018. Genes not present in genomes of all three species were filtered out. Chemical compounds were annotated for major uses with information from Wikipedia, PubChem, and PubMed. Based on textual annotation every compound was assigned one to three annotation terms out of the following list: pharmaceutical, recreational drug, research, warfare, endobiotic, agricultural, cosmetics, environment, food components, industrial, and pollutant. All contributors annotated an equal numbers of chemicals, and AS checked every annotation to insure consistency of approaches. The resulting dataset includes 591,084 individual chemical-gene interactions. 

2. Number of chemical-gene interactions per gene.xlsx 
The dataset created at the previous step was used to determine number of chemical-gene annotations for every gene, including total number as well as number of activating and suppressive chemical-gene annotations. We hypothesize, that number of chemical gene interactions can be used as a measure of the gene sensitivity to chemical exposures. 

3. Enrichment of molecular pathways with genes sensitive to chemical exposures.xlsx 
The list of genes with the total number of chemical-gene interactions for every gene was used as an input for the Gene-Set Enrichment Analysis (GSEA, https://www.gsea-msigdb.org/gsea/index.jsp) against Hallmark, KEGG, and Reactome datasets, to identify molecular pathways highly enriched with genes sensitive to chemical exposures. We suggest, that normalized enrichment score (NES) for every enriched pathway is a measure of the pathway's sensitivity to chemical exposures. 

4. Diseases vs. chemically sensitive KEGG pathways matrix.xlsx and
5. Diseases vs. chemically sensitive Reactome pathways matrix.xlsx
To identify disease categories that are sensitive to chemical exposures, the lists of significantly enriched KEGG and Reactome pathways (false discovery rate (FDR) q &gt; 0.01 and normalized enrichment score (NES) &gt; 1.9) were submitted to the CTD to run pathway-disease association analysis. This analysis resulted in matrices of shared gene numbers between chemically sensitive pathways and disease states. Two numeric values indicate sensitivity of disease states to chemical exposures: the number of inferred pathways associated with the disease state and the sum of genes from every pathway overlapping with the disease (number of inference genes).
DOI: 10.6084/m9.figshare.23151947.v1
title: Supplementary materials to IRME 2023

description: The supplementary materials include the Psychopy file, the experimental item set, and the dataset analysed in this study.
DOI: 10.6084/m9.figshare.14285239.v1
title: PREVALENCE AND FACTORS ASSOCIATED WITH INJURIES IN RECREATIONAL RUNNERS: A CROSS-SECTIONAL STUDY

description: ABSTRACT Introduction The increased number of people who choose running as a form of exercise has been associated with a higher prevalence of musculoskeletal injuries. Objectives To determine the prevalence and the factors that could be correlated with injuries among amateur runners in Recife, in the State of Pernambuco (PE), Brazil. Methods An observational, cross-sectional study, in which 300 (three hundred) amateur runners answered a social demographic questionnaire, as well as questions about training characteristics, footstrike and landing pattern, and history of running injuries. The data were analyzed by descriptive statistics, the student-t test to compare means, and the Chi-squared to compare prevalences. Results The prevalence of injuries amongst runners in Recife-PE was 58.5% (n= 175), the knee being the most commonly injured site (37.3%). In both groups - runners with and without injuries – there was a higher number of male runners, with 72.4% and 72.6% respectively. There was no difference in relation to the weekly frequency of running between the groups (p&lt;0.63). However, runners with a history of injuries ran around 7 kmh a week more than the runners without injuries (p&lt;0.03). A neutral footstrike (F=0.87; p=0.99) and hindfoot landing (F=4.13; p=0.90) were the most reported running patterns in both groups. It was found that wear was the main criterion used for changing running shoes in both groups (F = 8.35, p = 0.4). Conclusion There was a high prevalence of musculoskeletal injuries among amateur runners in Recife-PE. Among the factors associated with the injuries, one variable was significant: a higher weekly volume of training. Level of evidence II; Study type: Cross-sectional study.
DOI: 10.17632/55fjm3zctn
title: High-energy blunt pelvic ring injury

description: Table 1: Patients’ demographic and injury characteristics
Table 2: Pelvic ring injuries type A, B & C and concomitant injuries
DOI: 10.17632/skndvrbdsb
title: Data for random forest

description: Data for random forest
DOI: 10.6084/m9.figshare.14773569.v2
title: Dataset for kinetic energy spectra from LLC4320 global ocean simulation

description: The dataset contains kinetic energy spectra and time series of various quantities in different regions of the oceans. The year-long LLC4320 simulation was used in these computations Python scripts that were used to generate this dataset are also included.
DOI: 10.17632/cm8tsd4d9v
title: Public Anxiety Around Monkeypox Outbreak: Detecting Emotional Distress From Bangla Instagram Posts

description: This dataset introduces a novel collection of Instagram posts related to Monkeypox, focusing on anxiety detection in Bangla language. Due to the scarcity of publicly available data on Monkeypox reactions in Bangla, around 2,000 posts, including 638 Bangla posts and 1,362 English posts (translated into Bangla), were gathered from hashtags like #Monkeypox, #Mpox, and others. The posts, published between January and July 2024, were labeled into two classes—non-anxiety and anxiety—verified by professional psychologists. The final dataset contains 791 anxiety samples and 783 non-anxiety samples, offering a balanced resource for further research.
DOI: 10.17632/6p9vpv3pjf
title: Simulated portfolio returns using dynamic risk allocation

description: This code simulates data for analyzing the performance of a dynamic risk allocation strategy over multiple time periods. Here's a breakdown of the data generation and analysis process:

Simulated Data:
Random returns are generated for a specified number of assets (3 in this case) over a certain number of time periods (100 in this case). These returns follow a normal distribution with a mean of 0.05 and a standard deviation of 0.1.
Simulated transaction costs, model complexity, data requirements, and scalability factors are generated to represent different aspects of the dynamic risk allocation strategy.
Dynamic Risk Allocation Strategy:
A function dynamic_risk_allocation is defined to implement the dynamic risk allocation strategy.
Within this function, portfolio weights are calculated based on the inverse of the standard deviation of returns and adjusted for model complexity.
Transaction costs are subtracted from the weights, and negative weights are set to zero to ensure non-negativity.
Finally, portfolio returns are calculated as the weighted sum of asset returns.
Portfolio Returns Visualization:
The calculated portfolio returns using the dynamic risk allocation strategy are plotted over time.
The plot provides insights into the performance of the portfolio strategy, showing how returns vary across different time periods.
DOI: 10.17632/fj8wn8wjxp
title: Data 10.7717/peerj.14975

description: The database contains information on 37 species and 7,506 individuals of dung beetles collected in northeastern Ecuador. It presents information on ecosystems, repetitions, and months of collection, as well as richness, abundance, and Shannon metrics. The data served as the basis for the article: Pozo-Rivera WE, Quiloango-Chimarro C, Paredes X, Landívar M, Chiriboga C, Hidalgo D, García K, Villacís J. 2023. Response of dung beetle diversity to remediation of soil ecosystems in the Ecuadorian Amazon. PeerJ 11:e14975 https://doi.org/10.7717/peerj.14975
DOI: 10.6084/m9.figshare.28742636.v1
title: Numerical source data.xlsx

description: Numerical source data for Figure 3H, 4D, 6E and 7J .
DOI: 10.17632/rrjnz8rwc8
title: Ghodke et. al.,Mol. cell_AHNAK controls 53BP1-mediated p53 response by restraining 53BP1 oligomerization and phase separation

description: Uncropped Western blots
DOI: 10.6084/m9.figshare.5826270.v1
title: Johnson_NEW SPSS version MCAR Combined data.sav

description: SPSS dataset for study entitled "Perfectionism, selective attention and subclinical body dysmorphic disorder in a community sample"
DOI: 10.17632/f6sp8v7xv7
title: Supplementary Material for Manuscript "Unraveling Dynamic Transcriptomic Changes in Sheep's Lactating Mammary Gland Following Escherichia coli Lipopolysaccharide Exposure” (JDS 25009)

description: In this dataset, we provide the supplementary material for the manuscript "Unraveling Dynamic Transcriptomic Changes in Sheep's Lactating Mammary Gland Following Escherichia coli Lipopolysaccharide Exposure" from the Journal of Dairy Science.
DOI: 10.6084/m9.figshare.14269247
title: Supplementary Material for: Differences in Acute Ischemic Stroke Management and Prognosis between Multiple Large-Vessel Occlusion and Single Large-Vessel Occlusion: Subanalysis of the RESCUE-Japan Registry 2

description: <b><i>Introduction:</i></b> The management and prognosis of acute ischemic stroke due to multiple large-vessel occlusion (LVO) (MLVO) are not well scrutinized. We therefore aimed to elucidate the differences in patient characteristics and prognosis of MLVO and single LVO (SLVO). <b><i>Methods:</i></b> The Recovery by Endovascular Salvage for Cerebral Ultra-Acute Embolism Japan Registry 2 (RESCUE-Japan Registry 2) enrolled 2,420 consecutive patients with acute LVO who were admitted within 24 h of onset. We compared patient prognosis between MLVO and SLVO in the favorable outcome, defined as a modified Rankin Scale (mRS) score ≤2, and in mortality at 90 days by adjusting for confounders. Additionally, we stratified MLVO patients into tandem occlusion and different territories, according to the occlusion site information and also examined their characteristics. <b><i>Results:</i></b> Among the 2,399 patients registered, 124 (5.2%) had MLVO. Although there was no difference between the 2 groups in terms of hypertension as a risk factor, the mean arterial pressure on admission was significantly higher in MLVO (115 vs. 107 mm Hg, <i>p</i> = 0.004). MLVO in different territories was more likely to be cardioembolic (42.1 vs. 10.4%, <i>p</i> = 0.0002), while MLVO in tandem occlusion was more likely to be atherothrombotic (39.5 vs. 81.3%, <i>p</i> &lt; 0.0001). Among MLVO, tandem occlusion had a significantly longer onset-to-door time than different territories (200 vs. 95 min, <i>p</i> = 0.02); accordingly, the tissue plasminogen activator administration was significantly less in tandem occlusion (22.4 vs. 47.9%, <i>p</i> = 0.003). However, interestingly, the endovascular thrombectomy (EVT) was performed significantly more in tandem occlusion (63.2 vs. 41.7%; adjusted odds ratio [aOR], 2.3; 95% confidence interval [CI], 1.1–5.0). The type of MLVO was the only and significant factor associated with EVT performance in multivariate analysis. The favorable outcomes were obtained less in MLVO than in SLVO (28.2 vs. 37.1%; aOR, 0.48; 95% CI, 0.30–0.76). The mortality rate was not significantly different between MLVO and SLVO (8.9 vs. 11.1%, <i>p</i> = 0.42). <b><i>Discussion/Conclusion:</i></b> The prognosis of MLVO was significantly worse than that of SLVO. In different territories, we might be able to consider more aggressive EVT interventions.
DOI: 10.17632/hf4xvtz8t4
title: Imprinted maternally-expressed microRNAs antagonize paternally-driven gene programs in neurons (Whipple et al.)

description: Files associated with Whipple et al. 2019
DOI: 10.6084/m9.figshare.21490059.v1
title: Dataset

description: Dataset for study
DOI: 10.17632/tcf5vdmfhz
title: Model data for Nested Machine Learning for Modelling Degradation and Drug Release of Bioresorbable Polymers

description: ANN structure, Matlab code and dataset for Nested machine learning for polymer degrdation
DOI: 10.6084/m9.figshare.19115018.v2
title: BL for CO2 storage

description: The excel file showing results of CMG simulation and the analytical solution is included.
DOI: 10.17632/y3rxs6984x
title: Spectral Data for 2-(4-fluorophenyl)-3-(5-methylisoxazol-3-yl)thiazolidin-4-one

description: Spectral Data for 2-(4-fluorophenyl)-3-(5-methylisoxazol-3-yl)thiazolidin-4-one
DOI: 10.6084/m9.figshare.c.3924763_d18.v1
title: Additional file 4: Table S3. of Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer

description: DE genes between TNBC and normal tissues (XLS 2099 kb)
DOI: 10.17632/jfkdznm29m
title: Data from: Mitogenomic data elucidate the phylogeny and evolution of life strategies of Dermestidae (Coleoptera)

description: Supplementary data
DOI: 10.25452/figshare.plus.27236764.v1
title: SMRT-seq for m6A methylation analysis dataset for <i>Pseudomonas aeruginosa </i>PAO1 37°C vs. 43°C

description: The data in this item includes Single-molecule real-time sequencing (SMRT-seq) data generated using PacBio Sequel I for high-resolution analysis of m6A methylation from post-43°C grown bacteria and during the recovery period.<b>Sample preparation: </b>Overall, 15 samples included 3 replicates of Pseudomonas aeruginosa after exposure to 37 °C (control) or 43 °C at 4 time points (T = 0 generations, T = 5 generations, T = 22 generations, and T = 54 generations). Samples from the T=0 groups are simply labeled “37” or “43”.<b>Analysis:</b> Pac Bio subreads were mapped to the reference genome Pseudomonas aeruginosa PAO1 GCA000006765, ASM676v1, for each sample separately, using the pbmm2 tool from the smrttools 10 toolkit (Pac Bio). m6A modifications were then inferred with the ipdSummary tools. The control model was used in two separate runs. In the first run samples from the group 43 were used as reference. In the second run, samples from the group 37 were used as reference. Sites with ipd-ratio with p-value &lt; 0.05 were considered to have a new modification in the sample, compared with the reference. Each sample was tested with the reference of the same line, e.g. 1_43_5g was tested against 1_43 or 1_37. 2_43_22g was tested against 2_43 or 2_37, and so on.
DOI: 10.6084/m9.figshare.19129844.v1
title: Simulation data for manuscript "A Simple Condensation Model for the H2SO4-H2O Gas-cloud System on Venus"

description: This is the data of our simulations and the observations and estimations.
DOI: 10.6084/m9.figshare.28541141.v1
title: Arvicolinae Proteomic Data Files

description: MALDI-TOF files of arvicoline rodents in ASCII format and <i>de novo </i>collagen(I) FASTA files produced for the manuscript titled, "Proteomic analysis resulting in species-level identification of recently diverged North American arvicoline rodents."
DOI: 10.17632/b8xf5jh5s8
title: cij: A Python code for quasiharmonic thermoelasticity

description: The Wu-Wentzcovitch semi-analytical method (SAM) is a concise and predictive formalism to calculate the high-pressure and high-temperature (high-PT) thermoelastic tensor (Cij) of crystalline materials. This method has been successfully applied to materials across different crystal systems in conjunction with ab initio calculations of static elastic coefficients and phonon frequencies. Such results have offered first-hand insights into the composition and structure of the Earth's mantle. Here we introduce the cij package, a Python implementation of the SAM-Cij formalism. It enables a thermoelasticity calculation to be initiated from a single command and fully configurable from a calculation settings file to work with solids within any crystalline system. These features allow SAM-Cij calculations to work on a personal computer and to be easily integrated as a part of high-throughput workflows. Here we show the performance of this code for three minerals from different crystal systems at their relevant PTs: diopside (monoclinic), akimotoite (trigonal), and bridgmanite (orthorhombic).
DOI: 10.6084/m9.figshare.3563646.v1
title: Supplement 2. Data used in meta-analyses for soil phosphatase, labile P, and total P under elevated CO2.

description: File List Supplement2a.csv (md5: a0b20dfc26e5fea9b85678b3003a8c9b) Supplement2b.csv (md5: 5a1c8d3f617c8e02975ff22f4efc8d41) Supplement2c.csv (md5: 425ee1370bfee92b76a9688bb2b6b303) Description Supplement2a.csv, Supplement2b.csv, Supplement2c.csv<br> This database includes three files with a total of 1168 records collected from 57 published articles (see Appendix B). All records include the reference, ecosystem type, experimental facility, experimental CO<sub>2</sub> concentration, plant species, CO<sub>2</sub> treatment, and N treatment. In addition, Supplement2a.csv includes phosphatase type and phosphatase activity (mean and standard error). Supplement2b.csv includes labile P (mean and standard error). Supplement2c.csv includes total P (mean and standard error).
DOI: 10.17632/pp8j9jtsyz
title: Data of the Impact of Aligning Business, IT, and Marketing Strategies on Firm Performance

description: This dataset represents assessments of triadic strategic alignment on organisational performance in Yemen. Survey data was collected using self-administered questionnaire during July 2014. The final data includes 208 complete cases.Data collected in a questionnaire survey of 242 Yemen managers.
DOI: 10.17632/ck6nzz8w5x
title: Probabilistic risk assessment of hydraulic discharge system by Bayesian Analysis

description: This dataset is uploaded for the support of the paper draft submitted to Water Research Resources titled "Probabilistic risk assessment of hydraulic discharge system by Bayesian Analysis". The dataset contains one file. The file contains information regarding the parameters as well as the data used in the paper, i.e., operation data and damage data.
DOI: 10.17632/cxr93w329w
title: Data for: An in situ 10Be production-rate calibration from a 14C-dated late-glacial moraine belt in Rannoch Moor, central Scottish Highlands

description: This file contains the input data for the Rannoch Moor production-rate calibration data set, to be used with the University of Washington Online Production-Rate Calculator (Ver. 3).
DOI: 10.6084/m9.figshare.6391226.v2
title: Supplementary Material for: Cognitive-Behavioral Analysis System of Psychotherapy, Drug, or Their Combination for Persistent Depressive Disorder: Personalizing the Treatment Choice Using Individual Participant Data Network Metaregression

description: <b><i>Background:</i></b> Persistent depressive disorder is prevalent, disabling, and often difficult to treat. The cognitive-behavioral analysis system of psychotherapy (CBASP) is the only psychotherapy specifically developed for its treatment. However, we do not know which of CBASP, antidepressant pharmacotherapy, or their combination is the most efficacious and for which types of patients. This study aims to present personalized prediction models to facilitate shared decision-making in treatment choices to match patients’ characteristics and preferences based on individual participant data network metaregression. <b><i>Methods:</i></b> We conducted a comprehensive search for randomized controlled trials comparing any two of CBASP, pharmacotherapy, or their combination and sought individual participant data from identified trials. The primary outcomes were reduction in depressive symptom severity for efficacy and dropouts due to any reason for treatment acceptability. <b><i>Results:</i></b> All 3 identified studies (1,036 participants) were included in the present analyses. On average, the combination therapy showed significant superiority over both monotherapies in terms of efficacy and acceptability, while the latter 2 treatments showed essentially similar results. Baseline depression, anxiety, prior pharmacotherapy, age, and depression subtypes moderated their relative efficacy, which indicated that for certain subgroups of patients either drug therapy or CBASP alone was a recommendable treatment option that is less costly, may have fewer adverse effects and match an individual patient’s preferences. An interactive web app (https://kokoro.med.kyoto-u.ac.jp/CBASP/prediction/) shows the predicted disease course for all possible combinations of patient characteristics. <b><i>Conclusions:</i></b> Individual participant data network metaregression enables treatment recommendations based on individual patient characteristics.
DOI: 10.17632/mz3c929xwr
title: Non-medical determinants of caesarean deliveries using logistic regression

description: The non-medical factors that influence expectant mothers to odecide for caesarean deliveries in Ghana were examined. Data on 395 expectant mothers across the ten regions of Ghana, located in urban, semi-rural and rural areas, and spanned a period of five years (2012 to 2016) were obtained from the Ghana Health Service. In fitting the logistic regression model, data on 355 expectant mothers (i.e. 89.9% of the data) was assigned to the analysis sample while 40 (i.e. 10.1%) was assigned to the hold-out sample. The hold-out sample together with other statistical measures of overall model fit, pseudo R^2 measures and classification accuracy were used to validate the results obtained from the analysis sample. Significance was tested at P=0.05. Determinants including, educational level of expectant mother, parity of expectant mother, baby’s birth weight, previous caesarean delivery, location of expectant mother, age of expectant mother and, period within the year of childbirth had a significant effect on caesarean delivery.
DOI: 10.6084/m9.figshare.25951450.v2
title: Data behind Figure 8

description: Example of N<sub>2</sub> dissolution into a sample with a composition of 0.29±0.03 r<sub>M </sub>(S<sub>E</sub>LL<sub>N</sub>V region of Figure 6).<b>LV_spec_0.79rM-fig8.csv:</b> Spectra as shown in Figure 8. These cover a range of 2300–3000 cm<sup>-1</sup>, are background removed, and normalized.<b>LV_spec_0.79rM-unprocessed.csv:</b> Spectra used to make Figure 8 in a range of 800–3200 cm<sup>-1</sup>. Background has been removed but the spectra are otherwise unprocessed.
DOI: 10.17632/9pn8ftswjb
title: Data for: End-User Development, End-User Programming and End-User Software Engineering: a Systematic Mapping Study

description: Papers found in literature through manual and automatic search and list of papers selected for the systematic mapping study on end-user development, end-user programming and end-user software engineering.