cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5128846.v1
title: Supplementary Material for: Plasma Xanthine Oxidase Activity Is Predictive of Cardiovascular Disease in Patients with Chronic Kidney Disease, Independently of Uric Acid Levels

description: <b><i>Background:</i></b> Chronic kidney disease (CKD) is associated with increased cardiovascular morbidity and mortality. Oxidative stress seems to play a pivotal role in this process, and purine metabolism may be involved in CKD-related oxidative stress. Xanthine oxidase (XO) is an enzyme involved in purine metabolism and is also responsible for the production of reactive oxygen species. <b><i>Methods:</i></b> This prospective study aimed to analyze the relation between plasma dosages of molecules involved in redox balance, purine metabolism and cardiovascular events in patients with non-diabetic CKD stages 3-5 or on chronic hemodialysis (HD). CKD (n = 51) and HD (n = 50) patients were compared to matched healthy controls (n = 38) and followed-up for 3 years. <b><i>Results:</i></b> Both CKD and HD patients had decreased plasma levels of antioxidants (selenium, zinc, vitamin C). HD patients had decreased levels of the antioxidant enzyme superoxide dismutase and increased levels of oxidation products (ischemia-modified albumin, malondialdehyde [MDA]). The following substrates and enzymes involved in purine metabolism were increased in the HD cohort: adenosine, adenosine deaminase and the pro-oxidant XO. XO activity was negatively correlated with super oxide dismutase and positively with MDA. Interestingly, XO activity was an independent predictor of cardiovascular events in CKD and HD patients, regardless of uric acid levels. Uric acid was not predictive of events. <b><i>Conclusion:</i></b> This highlights a possible role of XO itself in CKD-related cardiovascular disease (CVD) and raises the hypothesis that beneficial effects observed with XO inhibitors on CVD in CKD may also be due to the reduction of oxidative stress.
DOI: 10.6084/m9.figshare.14903909.v1
title: Additional file 2 of The infant gut resistome is associated with E. coli and early-life exposures

description: Additional file 2 Table S1: Baseline Characteristics by Single vs. Paired-end Reads. Table S2: Prevalence, Mean, and Median of ARGs by Sample Age. Table S3: Negative Binomial Regression of Unique ARG Markers. Table S4: Negative Binomial Regression of Relative Abundance of ARGs. Table S5: Analysis of 2 Infants with Overall ARG Relative Abundance &gt; 10,000 at 1 Year. Table S6: MaAsLin2 Analysis of Antimicrobial Resistance Genes Adjusted for Covariates and Early-life Exposures. Table S7: PERMANOVA of the Resistome. Table S8: Linear Models to Assess Difference between 1-Year and 6-Week Samples by Covariates. Table S9: MaAsLin2 Analysis of HUMAnN2 Gene Families Adjusted for Covariates and Early-life Exposures.
DOI: 10.6084/m9.figshare.3515585.v1
title: Appendix C. Figures showing population means for critical thermal minimum temperatures measured in the field and during the acclimation experiment, and hopping speeds at different temperatures for cane toads in Australia.

description: Figures showing population means for critical thermal minimum temperatures measured in the field and during the acclimation experiment, and hopping speeds at different temperatures for cane toads in Australia.
DOI: 10.23641/asha.20151842.v1
title: Effectiveness of the SCERTS Model for autism (Yi et al., 2022)

description: <strong>Purpose: </strong>This systematic review aimed to examine the effectiveness of the Social Communication, Emotional Regulation, and Transactional Support (SCERTS) Model–based interventions in supporting developmental skills of children who were diagnosed with or at increased likelihood of autism. <strong>Method: </strong>We searched six electronic databases, in addition to Google Scholar and the reference lists, using terms related to SCERTS, the Early Social Interaction project, and autism spectrum disorder. Of the 70 articles, six published between 2014 and 2021 (a total of 455 children) were eligible for inclusion and were analyzed in terms of study design, type of publication, participant characteristics, intervention procedures, and major findings. <strong>Results: </strong>Most reviewed studies that were relatively less vulnerable to the given risk of bias suggested that SCERTS may be an effective approach for promoting children’s social communication skills, and implementers were able to achieve an adequate level of intervention fidelity through training. Further implications could not be drawn concerning children’s language, reduction in restricted repetitive behaviors, emotional regulation, adaptive behavior, play, cognitive skills, academic competence, and motor skills due to contradicting findings within limited evidence. <strong>Conclusions:</strong> Although SCERTS is a promising intervention with emerging evidence, more methodologically rigorous studies are needed to progress the research base of SCERTS and draw firm conclusions about its effectiveness in improving a wide range of skills for children and implementers. Several areas for future research are discussed. <br> <strong>Supplemental Material S1. </strong>Critical appraisal of included studies of SCERTS using quality indicators. <br> Yi, J., Kim, W., & Lee, J. (2022). Effectiveness of the SCERTS Model–based interventions for autistic children: A systematic review. <em>Journal of Speech, Language, and Hearing Research</em>. Advance online publication. https://doi.org/10.1044/2022_JSLHR-21-00518
DOI: 10.6084/m9.figshare.12901928.v1
title: Breast cancer Qatar dataset RA-QA

description: RNASeq expression data and coded clinical annotation.
DOI: 10.6084/m9.figshare.9259103.v1
title: Table S8

description: Potential enzymes involved in lipid biosynthesis found encoded in Loki- and Thorarchaeota genomes. The protein identifiers of the enzymes from their respective genomes are listed. The Lokiarchaeota genomes are highlighted in green and Thorarchaea genomes are highlighted in blue.
DOI: 10.6084/m9.figshare.14872056.v1
title: Supplementary Material for: Interactions of Carbohydrate Intake and Physical Activity with Regulatory Genes Affecting Glycaemia: A Food4Me Study Analysis

description: <b><i>Introduction:</i></b> Carbohydrate intake and physical activity are related to glucose homeostasis, both being influenced by individual genetic makeup. However, the interactions between these 2 factors, as affected by genetics, on glycaemia have been scarcely reported. <b><i>Objective:</i></b> We focused on analysing the interplay between carbohydrate intake and physical activity levels on blood glucose, taking into account a genetic risk score (GRS), based on SNPs related to glucose/energy metabolism. <b><i>Methods:</i></b> A total of 1,271 individuals from the Food4Me cohort, who completed the nutritional intervention, were evaluated at baseline. We collected dietary information by using an online-validated food frequency questionnaire, a questionnaire on physical activity, blood biochemistry by analysis of dried blood spots, and by analysis of selected SNPs. Fifteen out of 31 SNPs, with recognized participation in carbohydrate/energy metabolism, were included in the component analyses. The GRS included risk alleles involved in the control of glycaemia or energy-yielding processes. <b><i>Results:</i></b> Data concerning anthropometric, clinical, metabolic, dietary intake, physical activity, and genetics related to blood glucose levels showed expected trends in European individuals of comparable sex and age, being categorized by lifestyle, BMI, and energy/carbohydrate intakes, in this Food4Me population. Blood glucose was inversely associated with physical activity level (β = −0.041, <i>p</i> = 0.013) and positively correlated with the GRS values (β = 0.015, <i>p</i> = 0.047). Interestingly, an interaction affecting glycaemia, concerning physical activity level with carbohydrate intake, was found (β = −0.060, <i>p</i> = 0.033), which also significantly depended on the genetic background (GRS). <b><i>Conclusions:</i></b> The relationships of carbohydrate intake and physical activity are important in understanding glucose homeostasis, where a role for the genetic background should be ascribed.
DOI: 10.6084/m9.figshare.6953294.v2
title: chick_NC-GRN_RData

description: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide <i>in vivo</i> reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering <i>in vivo</i>, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures allowing to reverse engineer the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits <i>in vivo</i>, has broad implications for GRN discovery and investigation.<br>
DOI: 10.6084/m9.figshare.c.3603782_d4.v1
title: Additional file 1: Table S1. of Emergence and evolution of yeast prion and prion-like proteins

description: List of fungal proteomes and their sources (weblinks). (XLS 37 kb)
DOI: 10.6084/m9.figshare.19203413.v1
title: Changes in Symptoms of Eustachian Tube Dysfunction after Nasal Surgery

description: Data from patients who underwent nasal surgery
DOI: 10.6084/m9.figshare.3580989.v1
title: Structural models of active and inactive structure of human High mobility group box 1 (HMGB1)

description: Structural models for the modelled HMGB1,HMGB1 without disulphide bond C23 and C45, HMGB1C23A, HMGB1C45A, HMGB1C106A, HMGB1SO3H.
DOI: 10.6084/m9.figshare.14330969.v1
title: genome assembly of A. venetum

description: genome assembly of A. venetum
DOI: 10.6084/m9.figshare.6669068.v1
title: PRStudy_Database.xlsx

description: This is a dataset that supports the findings of a research study.
DOI: 10.6084/m9.figshare.19787617.v1
title: LGBTQ.csv

description: This data is collected from the microblogging site, Twitter, for sentiment analysis.
DOI: 10.6084/m9.figshare.19583194.v1
title: Data and Code for "Adjusting agricultural emissions for trade matters for climate change mitigation"

description: This is a repository of the data and codes used for the paper Foong et al. (2022) published in Nature Communications, see reference below. It contains R scripts, processed data, data on countries and food items, and a readme file. All data are in CSV format. <br>
DOI: 10.6084/m9.figshare.25467826.v1
title: RDE-Dataset.zipRansomware Defense Empowered: Deep Learning for Real-Time Family Identification with a Proprietary Dataset

description: Ransomware, leveraging sophisticated encryption techniques, poses a significant threat by encrypting crucial data, thereby rendering it inaccessible. The proliferation of diverse ransomware variants has caused considerable harm to governments, corporations, and individual users alike. Despite the increasing prevalence of cyber threats, existing solutions often struggle with real-time detection and early identification of ransomware families. To address this challenge, we introduce FCG-RFD, a novel benchmark dataset featuring extensive Function Call Graphs (FCG) tailored for ransomware family detection. Given the constantly evolving nature of malware, antivirus scanners face ongoing challenges, necessitating access to recent and updated datasets. Our dataset comprises 8,095 samples sourced from reputable repositories including VirusSamples, Virusshare, VirusSign, the Zoo, and MalwareBazaar. Additionally, we include 8,020 normal files obtained from trusted sources such as the Microsoft Store and Softonic. Through FCG-RFD, we aim to facilitate more robust and timely detection of ransomware families, ultimately enhancing cybersecurity measures against this pervasive threat.
DOI: 10.6084/m9.figshare.3520061.v1
title: Appendix B. Observed and extrapolated species richness.

description: Observed and extrapolated species richness.
DOI: 10.6084/m9.figshare.21383715.v1
title: Elephant cascades in the savannas

description: Here is all the relevant data used in the paper titled “Cascading effects of elephant-human interactions and the role of space and mobility in sustaining biodiversity”. The description is given in the sheet names and highlighted inside the respective spread sheets. The analysis and graphics can easily be reproduced using any statistics software-Excell, R among others . More details can be discussed with the corresponding author, Victor N. Mose (vnmose@gmail.com | victor.mose@acc.or.ke).
DOI: 10.6084/m9.figshare.28007885.v1
title: MGIA_results

description: This dataset was generated with direct-to-PBMC Mtb killing assays using Bactec MGIT, in 3 groups of 20 samples. The aim was to compare the outcomes between COVID+ groups and COVID- groups.
DOI: 10.6084/m9.figshare.12579125.v1
title: JVASP-73866 to JVASP-74731

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.5480800.v2
title: Dataset S1 from Morphospaces of functionally analogous traits show ecological separation between birds and pterosaurs.

description: Measurements and data sources for pterosaurs
DOI: 10.6084/m9.figshare.24968601.v2
title: Crithidia kDNA annotations

description: This dataset describes the kDNA of Crithidia fasciculata.Cf.minicircles.fasta and Cf.maxicircles.fasta contain the assembled minicircle classes and maxicircle sequences.Cf_gRNAs lists the identified gRNAs. The fields specify: gRNA start position on minicircle, gRNA end position on minicircle, the minicircle class that encodes the gRNA, the mRNA edited by the gRNA, gRNA editing start position on mRNA, gRNA editing end position on mRNA.Cf.unedited.mRNAs.fasta contains unedited maxicircle genes, in which each heading indicates the gene location on the maxicircle contig and strand orientation.ND7_gRNA_alignment, A6_gRNA_alignment, and RPS12_gRNA_alignment visualizes the coverage of editing sites by predicted gRNAs on the edited mRNAs.kDNA annotation was performed with a custom version of the python package deposited on https://github.com/nicksavill/kDNA-annotation.restriction_site_presence shows the presence of restriction enzyme cutting sites on 18 minicircle classes and maxicircle.
DOI: 10.6084/m9.figshare.22644973.v2
title: dataset Hangzhou Sim

description: The simulated three-dimensional spatiotemporal trajectory dataset Hangzhou Sim, which consists of 8,000 trajectories that overlap in both space and time.
DOI: 10.6084/m9.figshare.8088302.v1
title: Demographics and Anthropometrics

description: File containing demographic and anthropometric features of 50 subjects
DOI: 10.6084/m9.figshare.7507586.v1
title: Paraendodontic surgery: case report

description: ABSTRACT Paraendodontic surgeries have been increasingly used to solve problems related to failures in conventional endodontic treatment. Better anatomical knowledge of the structures as well as the development of techniques and materials involved has resulted in substantial paraendodontic surgery increase and success. In some cases, teeth endodontic treatment highly benefits treatment accomplishment. This report describes a case of an endodontic treatment complemented by paraendodontic surgery in periapical region of 21, 22 and 23 of a female patient who had been treated at the clinic of the Brazilian Dental Association Dentistry - in the city of Cascavel, State of Parana, Brazil. The case presents a 12-month follow-up for the resolution of painful symptoms, lesion reduction, and bone formation. Literature review was performed regarding paraendodontic surgery in order to assess the determining factors, failure causes and procedure indications/contraindications, as well.
DOI: 10.6084/m9.figshare.19467269.v1
title: Finger Joints Angles ARAT

description: Finger Joints Angles during the performance of the ARAT<br>
DOI: 10.6084/m9.figshare.21859164.v1
title: Supplementary Material for: Asbestos Exposure and Malignant Pleural Mesothelioma: A Systematic Review of Literature

description: <b><i>Background:</i></b>The relationship between exposure to asbestos and malignant pleural mesothelioma (MPM) is already well established. Nevertheless, much remains to be known about exposure thereto and the incidence and mortality from MPM. <b><i>Objective:</i></b> This systematic review aims to map the relationship between asbestos and MPM by studying the exposure to asbestos and the incidence and mortality of MPM. <b><i>Methods:</i></b> A systematic review was conducted relating asbestos and MPM. Exposure to asbestos, incidence, and mortality by MPM was reviewed. PubMed, Web of Science, Cochrane Library, RCAAP, DART-Europe, and the reference lists of included studies were searched, from January 1, 1960, to December 31, 2020. Methodological quality was checked, the risk of bias analysis was performed, a level of evidence grade was assigned, and descriptive data analysis was performed. <b><i>Results:</i></b> 3,484 unique citations were identified, which included seventeen observational studies that met inclusion criteria with a total of 1,104 patients. Heterogeneity is present between the included studies which range from a case series of 16 retrospective studies and 1 prospective study. Studies were mostly conducted in Europe, particularly in Italy (6), and were published between 1969 and 2020. The mean age of patients is approximately 66 years with a latency period between the first exposure and diagnosis of approximately 42 years. 14 studies present data regarding the occupational context and chrysotile and crocidolite are the most studied types of fibre. The incidence of cases occurred between the interval 1966 and 2014 and in 9 studies the mortality rate was 100% of patients. <b><i>Conclusion:</i></b> There is high evidence to support the relationships between asbestos and MPM. However, the relatively scant information provided by the studies reinforces the need for well-conducted research and implementation of National Mesothelioma Surveillance Centres at a global level.
DOI: 10.6084/m9.figshare.3814275.v1
title: Systems response profiles to two Rehmanniae Radix formulae in metabolic syndrome patients

description: To explore the effects of two Rehmanniae Radix formulae in patients with metabolic syndrome (MetS), a randomized controlled study was conducted. MetS patients were randomly assigned to receive either a classic Rehmanniae Six Formula (R6, or ‘Liu Wei Di Huang Wan’) or a novel multi-herbal Rehmanniae Radix containing formula SUB889 for 8 weeks. Western medicine related clinical parameters, Chinese medicine defined symptoms and syndromes as well as metabolomic profiles were evaluated at different time points.
DOI: 10.6084/m9.figshare.25739727.v1
title: Citation Metadata Fields in the Bibliographic Database Schema

description: The Supplementary Material details the schema of our bibliographic database, focusing on the fields used for citations. This schema defines the specific information captured for each reference (e.g., author names, publication titles, keywords, citations, etc.)
DOI: 10.6084/m9.figshare.19071044.v2
title: Scripts and input files

description: These are the scripts to run the analysis and get the figures. get_models.R is an R script for the models and get_figures.R is an R script for the figures.
DOI: 10.6084/m9.figshare.1311757.v1
title: ELectronic Health Record

description: EHR Adoption
DOI: 10.6084/m9.figshare.24259993.v1
title: Supplementary Material for: An autopsy of ruptured hepatic angiosarcoma treated by transcatheter arterial embolization

description: An 80-year-old Japanese man presented to our hospital with intra-abdominal hemorrhage due to a ruptured liver tumor. His vital signs included depressed blood pressure (80/52 mmHg), tachycardia (111 bpm), and distended abdomen. CT scan showed ascites effusion with high density and 40 mm tumors in lateral segment and 40mm tumor in anterior segment of the liver. Transcatheter arterial embolization (TAE) temporarily achieved hemostasis, but he died following re-rupture 4 days later. Based on autopsy findings, the liver tumor was diagnosed as hepatic angiosarcoma. Embolic agents used during embolization were identified within the hepatic small interlobular arteries. However, there were no findings of tumor cell necrosis or ischemic change in the angiosarcoma. In the present case, TAE alone did not induce ischemia-induced tumor necrosis, suggesting that TAE might be unsuitable to treat hepatic angiosarcoma. Treatment optimization for ruptured hepatic angiosarcoma is desired.
DOI: 10.6084/m9.figshare.8869433.v1
title: On the development of sleep states in the first weeks of life

description: Related to https://www.biorxiv.org/content/10.1101/678144v1<br>
DOI: 10.6084/m9.figshare.21187033.v1
title: LUMIERE dataset - Pyradiomics features based on DeepBraTumIA segmentations

description: This CSV contains the radiomic features extracted for all study dates where all four MRI sequences and automated segmentation from DeepBraTumIA are available. The features were extracted from the images resampled to atlas space. Please note that features could not be extracted for studies where a given segmentation label was not found (or too small, see the minimum ROI size in the settings column). See our GitHub repository for a script to customize the extraction.
DOI: 10.6084/m9.figshare.5128045.v1
title: Supplementary Material for: White Rice Intake Varies in Its Association with Metabolic Markers of Diabetes and Dyslipidemia Across Region among Chinese Adults

description: <b><i>Background/Aims:</i></b> There are inconsistent associations between white rice consumption and diabetes and dyslipidemia, perhaps due to the nature of samples studied and quality of diet data. <b><i>Methods:</i></b> Using regionally diverse data from adults enrolled in the China Health and Nutrition Survey (n = 7,878) with diet data from three repeated 24-hour recalls and fasting blood to derive diabetes and dyslipidemia, we examined the odds of diabetes and dyslipidemia in participants across region-specific tertiles of percent energy from white rice consumption. <b><i>Results:</i></b> The prevalence of undiagnosed diabetes, high triglycerides, high low-density lipoprotein (LDL), low high-density lipoprotein (HDL), and atherogenic dyslipidemia (AD) was 4.7%, 31.8%, 31.3%, 25.9%, and 14.6%, respectively. We found an inverse association between the highest (versus lowest) tertile of rice intake and diabetes in Central China (odds ratio (OR): 0.59, 95% confidence interval (CI): 0.36-0.99). The highest rice consumption was also associated with high triglycerides (OR: 1.46, 95% CI: 1.09-1.95), low HDL (OR: 1.38, 95% CI: 1.03-1.85), and AD (OR: 1.63, 95% CI: 1.15-2.31) in North China, and low LDL (OR: 0.54, 95% CI: 0.42-0.69) in Central China. <b><i>Conclusions:</i></b> The association between white rice consumption and diabetes and dyslipidemia markers varied across regions of China, suggesting a role of other dietary and health-related exposures, beyond rice.
DOI: 10.6084/m9.figshare.9878360.v2
title: Retrospective Dataset for head and Neck Squamous cell carcinomas (2004-2009)

description: <b>Survival Rates of Head and Neck Cancers in Ghana. An 8-years retrospective data review at the Komfo Anokye Teaching Hospital cancer registry </b>
DOI: 10.6084/m9.figshare.3528383.v1
title: Appendix A. A list of all papers used in the meta-analytic calculations.

description: A list of all papers used in the meta-analytic calculations.