cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25239307.v1
title: The source data behind the graphs

description: Regulatory genetic variants repertoire in pig liver was expanded using RNA-seq, H3K27ac ChIP-seq, and DNA sequencing. These genetic foundations facilitate the dissection of molecular mechanisms underlying complex traits.
DOI: 10.6084/m9.figshare.4697605.v1
title: Time estimates using rho (ρ) and maximum likelihood (ML) and estimated migration times using founder analysis. from Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe

description: For time estimates, we used rho (ρ) and maximum likelihood (ML), with a mutation rate of one substitution every 3,624 years, corrected for purifying selection, and a synonymous rate of one substitution every 7,884 years. The full set of dated founders is shown for each model tested.
DOI: 10.6084/m9.figshare.14431301.v3
title: Fig. 4a

description: Raji cells and Raji cells expressing the MICA*001 allele were incubated for 1, 4 or 16 hours (overnight) with MICAB1 or isotype control mAbs coupled to a pH-sensitive cyanine dye (Cyp5). FACS profiles showing dye fluorescence upon anti-MICA mAb internalization are shown. Representative data from two independent experiments are shown<br>19E9 = MICAB1 antibody 15C11 = Control Antibody
DOI: 10.6084/m9.figshare.23104817.v2
title: Nocturnal Temperature Physiology Data - 2020-2022

description: All raw environmental and physiology data published in the article; <br> "Night-time warming in the field reduces nocturnal stomatal conductance and grain yield but does not alter daytime physiological responses" New Phytologist (2023) <br> The data includes; <br> - Field environmental data - T-FACE setup environmental data - Gas exchange data - Porometer data - Leaf water potential dta - Water-solube carbohydrate, carbon and nitrogen data - Harvest data <br>
DOI: 10.6084/m9.figshare.28440860.v1
title: Triplefin behaviour change full datasheet.xlsx

description: Full dataset of behaviour used in article titled Brain Control: Brain-Encysting Trematodes Increase the Frequency but Reduce the Repeatability of Surfacing Behaviour in Mottled Triplefin
DOI: 10.6084/m9.figshare.7795703.v1
title: Dataset before validations: Updating the global occurrence of Culicoides imicola, a vector for emerging viral diseases

description: The data contains an updated and comprehensive global database of Culicoides imicola occurrence, consisting of 2589 geo-positioned records from 50 countries around the world.
DOI: 10.6084/m9.figshare.20236509.v6
title: Single-nucleus and bulk ATAC-seq of liver from rat fed high fat diet

description: <strong>Background:</strong> Non-alcoholic fatty liver disease (NAFLD) develops from fatty liver to steatohepatitis during which multiple cell types may play different roles. Aiming to understand the tissue composition of cell types, their gene expression and global gene regulation in the development of NAFLD, we performed single-nucleus and bulk ATAC-seq on the liver of rats fed with a high-fat diet (HFD). <strong>Methods:</strong> Male Spontaneously Hypertensive Rats were fed a normal diet or a HFD. Rats fed HFD for 4 weeks developed fatty liver, and those fed HFD for 8 weeks further developed steatohepatitis. Under the washout condition, where 4 weeks of HFD is followed by 4 weeks of a normal diet, fatty liver was partially ameliorated. For each dietary condition, we performed single-nucleus ATAC-seq on one animal and bulk ATAC-seq on four animals. <strong>Results:</strong> In accordance with the pathological progression from fatty liver to steatohepatitis, the proportion of inflammatory macrophages dramatically increased. By machine learning, we divided the global gene expression into modules, such that transcription factors in a module regulate the genes in the same module. Consequently, many of the modules rediscovered known regulatory relationship between the transcription factors and biological processes. For the discovered biological processes, we searched core genes, which were defined as genes central regarding co-expression and protein-protein interaction. A large part of the core genes overlapped with previously implicated NAFLD genes. <strong>Conclusions:</strong> Single-nucleus ATAC-seq combined with data-driven statistical analysis help elucidate the global gene regulation <em>in vivo</em> as a combination of modules and discover core genes of the relevant biological processes.
DOI: 10.6084/m9.figshare.6713837.v1
title: tokenizer and word embeddings

description: Word tokenizer and precomputed word embeddings<br>
DOI: 10.6084/m9.figshare.7330304.v1
title: Human Convalescent Serum Sample after DENV3 seroconversion.

description: Human Convalescent Serum Sample collected after DENV3 seroconversion.
DOI: 10.6084/m9.figshare.3382837.v1
title: Data_Unconventional U-Turn Design Evaluation.xls

description: The data file includes two parts of data: 1) the field data collection at two intersections to calibrate the simulation model; and 2) the simulation results for the unconventional U-turn design. In the first part, data were collected from two sites in Nanchang, China. In sheet "Field data collection1", the data are used to calibrate the vehicle maneuvers at intersections in the Vissim. The data contains the following variables: No. (which is the vehicle number); Vehicle type; Turning start time; Turning end time; Turning time; Average distance of turning; Speed of turning; Type of maneuver (i.e., U-turn to left-most lane, U-turn to 2nd lane, or U-turn to 3rd lane); U-turn mode choice (i.e., straight-&gt;U-turn-&gt;turn right, or turn right-&gt;U-turn-&gt;straight). In the sheet "Field data collection2", the data are used as inputs in the simulation model. Those data are traffic parameters such as vehicle count and type in each turning-direction (i.e., left, straight, right) at each of the four intersection approaches. In the second part, data are those obtained from the simulation. Key information such as travel time, delay, and number of stops are provided. The comparison between UUT and DLT are also provided. We provide those data so that interested authors can better understand our U-turn design performance when combining the data with the contexts and figures/tables provided in the manuscript.
DOI: 10.6084/m9.figshare.26490157.v1
title: Impact of living with or without parents

description: This study investigates the effects of living arrangements on the social competencies and well-being of adolescents. Comparing high school students living with their families to those residing in bursas (boarding schools) in Warsaw and its suburbs, the research reveals significant differences in assertiveness, social exposure, and overall well-being. Adolescents in bursas show higher levels of assertiveness and social exposure, as well as greater emotional and social well-being. The study highlights the role of independence and structured environments in fostering social skills and mental health. The findings underscore the importance of targeted interventions to enhance social competencies and support adolescent well-being. Data was collected using the Social Competence Questionnaire (KKS) and the Mental Health Continuum-Short Form (MHC-SF).
DOI: 10.6084/m9.figshare.20489379.v1
title: The synthetic individual-level trip dataset

description: The synthetic vehicle individual-level dataset contains 1,829,218 trip records of 276,978 vehicle individuals in Xuancheng for one week. Each record of the dataset represents one trip of an individual, containing departure time at the minute level, trip origin, and destination represented by traffic zone, as well as the trip path that consists of a sequence of roads. Besides, there is a field to indicate the traveller type of the individual like commuter.
DOI: 10.6084/m9.figshare.4668508.v1
title: Introdução ao Planeta Terra e a Geologia

description: material didático para atividade de palavras cruzadas em aula de Geologia.
DOI: 10.6084/m9.figshare.c.3635324_d3.v1
title: Additional file 4: of FoCo: a simple and robust quantification algorithm of nuclear foci

description: CellProfiler pipeline for analyzing microscopy images. (CP 9 kb)
DOI: 10.6084/m9.figshare.19949717.v1
title: core_gene_alignment.aln.treefile

description: Newick format maximum-likelihood phylogenetic tree of the core genes of the <em>Vagococcus fluvialis</em> genome. This tree is illustrated in Figure 3
DOI: 10.6084/m9.figshare.28615994.v1
title: Supplementary Material for: Therapeutic Drug Monitoring in a Patient with Metastatic Renal Cell Carcinoma Who Achieved Long-Term Response to Cabozantinib in Third-Line Treatment: A Case Report

description: Introduction: Treatment strategies for metastatic renal cell carcinoma (mRCC) have advanced, and its prognosis has improved. However, the progression-free survival of patients with mRCC who have received prior treatment is approximately 8 months, and long-term responses are rare. We applied therapeutic drug monitoring to a case of mRCC in which a long-term response of more than 3 years was achieved after the administration of cabozantinib as third-line treatment. Here, we report the changes in the blood concentration of cabozantinib.
Case Presentation: The patient was a 67-year-old man who had received sunitinib as the first-line treatment and nivolumab as the second-line treatment for stage IV mRCC. However, the disease progressed, and cabozantinib (40 mg/day) was initiated. Three months after the initiation of cabozantinib, partial tumor shrinkage was achieved. In the sixth month, the dose was reduced to 20 mg/day because of severe palmar–plantar erythrodysesthesia syndrome and anorexia; however, further tumor shrinkage was achieved. Fourteen months after starting cabozantinib, the trough concentration of cabozantinib was 960 ng/mL. Thereafter, cabozantinib concentration was measured almost every month and was found to fluctuate between 583 and 1938 ng/mL; tumor shrinkage was maintained even at 39 months.
Conclusion: Cabozantinib provided long-term benefits for more than 3 years. We emphasize that the measurement of cabozantinib concentration in the blood may play a supporting role as an indicator of long-term response.
DOI: 10.6084/m9.figshare.5721052.v1
title: “Holographic” pyramid: conceptual errors and didactic potential

description: Allusion to holograms is identified in different contexts to refer to different devices and shows, like the images displayed by the pyramids “holographic”. However, as we pointed out in this article, the images displayed by these pyramids, besides not being holograms in fact, are just two-dimensional images. We identified, however, a rich didactic potential in “holographic” pyramids for the teaching of Physics, especially when we consider the transition from the student's naive curiosity to epistemological curiosity and the teaching of certain concepts of optics and mathematics. Therefore, we built a quadrangular pyramid using acrylic plates and we made discussions about their operation. Through this article, we hope, among other things, to promote the critical awareness of teachers and students in the face of technological artifacts in constant changes around them, especially those considered as holograms.
DOI: 10.17632/n5phxzxg4p
title: Virtual Work, Job Autonomy and Employee Performance

description: This dataset contains data on virtual work, job autonomy, and employee performance, which were collected from employees working in technology-based organizations in Ghana. It is an original dataset.
DOI: 10.6084/m9.figshare.21834939.v2
title: Data on study titled: Lycium barbarum (Goji berry) mouthwash is a viable alternative to 0.2% chlorhexidine gluconate for managing chronic periodontitis: a randomized clinical trial

description: Background: Removal of the microbial deposits (plaque and calculus) by performing effective scaling and root planing (SRP) is the primary and fundamental requirement for managing periodontal disease. Various adjuncts that have antimicrobial, antioxidant, and anti-inflammatory properties are used as adjuncts to SRP for managing chronic periodontitis. However, with the rapid rise in antimicrobial resistance to several antimicrobial agents along with the increased risk of adverse effects, the use the conventional chemotherapeutic agents for managing periodontal disease is slowly declining. Hence, there is a recent need to explore new plant-based products for treating periodontal disease. <em>Lycium barbarum (L. barbarum</em>), or goji berry, is recently gained popularity for managing chronic inflammatory and infectious diseases. However, its efficacy in managing periodontal diseases has never been explored. To evaluate the efficacy of <em>L. barbarum</em> mouthwash along with SRP compared to chlorhexidine for managing chronic periodontitis. Methods: The study is designed as a randomized clinical trial with 57 adult participants (Males:29; Females:28) with chronic periodontitis. The participants were divided randomly into two groups: One group used <em>L. barbarum</em> mouthwash and the other group used ‘0.2% chlorhexidine gluconate’ mouthwash. The changes in the gingival index (Gi), plaque index (Pi), bleeding on probing (BOP), clinical attachment loss (CAL), probing pocket depth (PPD), microbial load, and antioxidant levels (protein thiol levels) in saliva were noted at the baseline, at 15 days and one month. Results: A statistically significant difference was noted in the Pi (P-value = 0.791), Gi (P-value= 0.594), PPD (with P-value= 0.134), and microbial levels (P-value = 0.188) in both groups from the baseline. The protein thiol levels in saliva were increased only in the goji berry group. Conclusion: <em>L. barbarum</em> mouthwash along with SRP was found to be effective in managing periodontal disease. <br>
DOI: 10.6084/m9.figshare.26513404.v2
title: <b>Supplemental Data -</b><sub><strong> </strong></sub><b>Genetic Characterization of Wild </b><b><i>Vitis</i></b><b> Germplasm: Diversity Analysis and Identification of Disease Resistance Loci</b>

description: <b>Supplemental Table 1.</b> List of all genotypes used in this study: SSR allelic profiles of 323 wild grapevine samples genotyped at 29 SSR molecular markers and group assignments according to STRUCTURE and DAPC.<b>Supplemental Table 2.</b> Microsatellite markers used in this study.<b>Supplemental Table 3.</b> Characterization of resistance (<i>R</i>) loci in each studied accession based on the “all-vs.-all” approach: The occurrence of the <i>R</i>-locus is highlighted in red, while its absence is represented by an empty cell.<b>Supplemental Figure 1.</b> Representative accessions of the species groups used in the study.<b>Supplemental Figure 2.</b> The most likely number of genetic clusters (K) within the full dataset of 323 accessions based on the method described by Evanno et al. (2005). K values from ten separate runs, ranging from 1 to 15. The delta K graph shows the maximum value at K = 8.<b>Supplemental Figure 3.</b> Bayesian information criterion (BIC) values for different numbers of clusters. The accepted true number of clusters was nine.
DOI: 10.6084/m9.figshare.9461444.v1
title: mp_gap

description: <pre><pre>Matbench v0.1 test dataset for predicting DFT PBE band gap from structure. Adapted from Materials Project database. Removed entries having a formation energy (or energy above the convex hull) more than 150meV and those containing noble gases. Retrieved April 2, 2019.</pre></pre>
DOI: 10.6084/m9.figshare.12086724.v3
title: Supplementary Tables S1-S12

description: One pdf file explaining the content of Supplementary Tables and twelve Excel files containing Supplementary Tables 1 to 12 of the MS by Donal MacGrogan et al entitled: <br>" Identification of a peripheral blood gene signature predicting aortic valve calcification" (PG-00034-2020).
DOI: 10.6084/m9.figshare.22184158.v1
title: Supplementary Material for: Triglycerides and Renal Outcomes according to Albuminuria and in Consideration of other Metabolic Syndrome Components in Diabetic US Veterans

description: Objective: Hypertriglyceridemia, a component of the metabolic syndrome, is a known independent predictor of albuminuria and chronic kidney disease (CKD) in the general population. Previous studies have shown that the relationship of triglycerides with outcomes changes across stages of CKD. Our objective is to examine the association of triglycerides independent of other metabolic syndrome components with renal outcomes in diabetic patients with or without CKD. Research Design and Methods: This retrospective cohort study included diabetic US veteran patients with valid data on triglycerides (TG), estimated glomerular filtration rate (eGFR) and albuminuria (UACR), between fiscal years 2004 to 2006. Using Cox models adjusted for clinical characteristics and laboratory markers, we evaluated the relationship of TG with incident albuminuria (stratified by eGFR category) and based on eGFR (stratified by baseline albuminuria categories). To evaluate the relationship of TG with time to end-stage renal disease (ESRD), we stratified models by baseline CKD stage (eGFR category) and baseline albuminuria stage ascertained at time of TG measurement. Results: In a cohort of 138,675 diabetic veterans, the mean±SD age was 65±11 years old, and included 3% females and 14% African Americans. The cohort also included 28% of patients with non-dialysis dependent CKD (eGFR&lt;60 mL/min/173m2), as well as 28% of patients with albuminuria (≥30 mg/g). The median[IQR] of serum TG was 148[100, 222] mg/dL. We observed a slight positive linear association between TG and incident CKD after adjustment for case-mix and laboratory variables among non-albuminuric and microalbuminuric patients. High TG levels were associated with ESRD in CKD 3A non-albuminuric patients and in CKD 3A and 4/5 in patients with microalbuminuria. Conclusions: In a large cohort, we have shown that elevated TG are associated with all kidney outcomes tested independently of other metabolic syndrome components in diabetic patients with normal eGFR and normal albumin excretion rate, but the association is weaker in some groups of diabetic patients with pre-existing renal complications.
DOI: 10.6084/m9.figshare.9641999.v1
title: Dataset Nisa et al. 2019 NComms.xlsx

description: Presents the results of randomized controlled trials testing behavioral interventions to promote household action on climate change
DOI: 10.6084/m9.figshare.25392496.v1
title: Dataset for Fargeot et al_GENETIC DIVERSITY AFFECTS ECOSYSTEM FUNCTIONS ACROSS TROPHIC LEVELS AS MUCH AS SPECIES DIVERSITY, BUT IN AN OPPOSITE DIRECTION

description: The relative effects of intra- and interspecific diversity on ecosystem functions are poorly understood, especially under natural and multi-trophic conditions. Here, we investigated the interplay between species diversity, genetic diversity and ecosystem functions across three trophic levels (trees, shredders and fishes) in natural aquatic ecosystems. We estimated species diversity and genetic diversity within each trophic level, seven key ecosystem functions, and we assessed the strength of each possible relationship between biodiversity and ecosystem functions (BEFs). While the absolute effect sizes of BEFs were comparable at both the genetic and species levels, we observed a consistent positive association between genetic diversity and ecosystem functions, whereas species diversity exhibited a negative association. Notably, these contrasting effects of species and genetic diversity were evident solely when BEFs were assessed within trophic levels, rather than across them. This underscores the necessity of considering both species and genetic diversity lossto predictecosystem dynamics.This file synthesizes the data required for running the statistical models described in the MS
DOI: 10.6084/m9.figshare.8798096.v1
title: Proteogam02_Supplementary File 4__Transrate results

description: Raw results from Transrate
DOI: 10.6084/m9.figshare.23962830.v1
title: Supplementary Material for: Life's Essential 8 and Mortality in US Adults with Chronic Kidney Disease

description: Introduction: The current prevalence of chronic kidney disease (CKD) is substantial, and CKD individuals face a heightened risk of mortality, encompassing both all-cause and cause-specific outcomes. The current study aims to investigate the potential impact of adhering to Life Essential 8 (LE8) on reducing mortality among CKD individuals. Methods: Using the National Health and Nutrition Survey (NHANES) data from 2005 to 2018, we analyzed 22,420 United States adults (≥20 years old). CKD is defined by urinary albumin-to-creatinine ratio (≥30 mg/g or 3 mg/mmol) and estimated glomerular filtration rate (&lt;60 ml/min/1.73m2). The components of LE8, including diet, physical activity (PA), nicotine exposure, sleep, Body Mass Index, blood lipids, blood glucose, and blood pressure (BP) were measured and given a score of 0-100. The total LE8 score was the unweighted average of all components and was divided into low cardiovascular health (CVH) (0-49), moderate CVH (50-79), and high CVH (80-100). Cox proportional hazards regression model was used to explore the associations of LE8 with all-cause, cardiovascular disease (CVD), and cancer mortality, which were followed prospectively by the National Center for Health Statistics until December 31, 2019. Results: In the overall population, individuals with moderate CVH had a 47% lower risk of CKD, while high CVH was linked to a 55% lower risk compared to low CVH. During a median follow-up of 7.58 years, CKD individuals had a 93% higher all-cause mortality rate and a 149% higher CVD mortality rate compared to those without CKD. Among the CKD individuals, every 10-point increase in LE8 score was associated with reduced risks of 17% for all-cause mortality (especially PA, nicotine exposure, blood glucose, and BP), 18% for CVD mortality (especially PA), and 12% for cancer mortality (especially PA and sleep health). In additional and sensitivity analysis, the results remained significant after further consideration of potential confounding of renal function. Additionally, LE8 demonstrated superior risk stratification for CVD mortality among CKD patients compared with LS7. Interaction was observed between LE8 and age, education level, marital status, and drinking status. Conclusions: The current study demonstrates that adherence to higher LE8 levels within CKD individuals is associated with a reduced risk of both all-cause and cause-specific mortality.
DOI: 10.6084/m9.figshare.25605450.v3
title: <b>The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages</b>

description: Supplementary data for "The agglomeration of antibiotic resistance genes in resistance islands is biased towards specific large plasmid lineages".This folder contains the data of collinear syntenic blocks (CSBs) in the analysis of plasmid resistance islands in 2,441 genomes from Escherichia, Salmonella, and Klebsiella.csb.amr.ins0.q4.csb: CSB result file calculated using CSBFinder-Sinfo.csb.amr.fasta: Orthology information file of gene families as an optional input file for CSBFinder-Scsb.data.tsv: Gene content table for retrieving CSB sequence from the genomes in RefSeq database.GuideVideo: In this video, I show an example of how to use CSBFinder-S to explore CSB data for resistance island analysis.Supplementary Data 8 contains the phylogenetic data of five transposase gene families, Rop, and RepB.
DOI: 10.6084/m9.figshare.28816037.v1
title: Aligned BAM file for SRR3414629

description: mouse mm10 alignment, STAR