cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28130837.v2
title: Equivalent Mutants Analysed via Deductive Verification

description: This is the reproduction package complementing the paper "Equivalent Mutants: Deductive Verification to the Rescue" accepted at the Mutation 2025 Workshop.In the paper we investigate the (supposedly) equivalent mutants from, MutantBench an open-source dataset designed for comparing the performance of tools for detecting equivalent mutants [https://github.com/MutantBench/]. The dataset comes with 4,400 mutants injected into 18 C and 18 Java programs where 1,416 are marked as equivalent. The equivalence status itself was drawn from previously published papers concerning tools that detect equivalent mutants. This status has not been confirmed by independent authors and as we show in our analysis, several equivalent mutants were in fact false positives.Below we list the mutants in this dataset; 30 mutants applied on 10 systems under testCode # loc # mutants<br>-------------------------------<br>Day 59 4 / 14<br>Defroster 160 1 / 147<br>MathUtils (distance) 33 1 / 0<br>Mid 59 5 / 5<br>Min 23 9 / 9<br>Quicksort 96 1 / 322<br>Triangle 89 5 / 706<br>BinarySearch. 37 1 / n.a.<br>FindLast 22 1 / n.a.<br>FindMin 40 2 / n.a.<br>#loc = lines of code of the program and mutant under test including self composition# mutants = the number of mutants analyzed versus the total number of mutants for the given system in the MutantBench dataset<br>The code in the MutantBench dataset required some adaptation to be amenable for the analysis by means of Contract Schemas (the technique proposed in the paper). In particular, the code under test must satisfy the RIPR criterion (reach - infect - propagate - reveal); where the reveal part means we should be able to manipulate the result via the output of a function. Many of the programs under test wrote the result to the console via *print* statements; we replaced those with *return* statements. Other programs just used a single *main()* method; we replaced it with a standard method declared on a class named after the file of the program under test.For MathUtils, the benchmark covers only the uninteresting *gcd*, instead we supplied a mutant for *distance*.Most of the samples selected above lacked loops. We therefore added three search algorithms: BinarySearch, FindLast and FindMin.
DOI: 10.6084/m9.figshare.12295466.v1
title: Factors associated with health facility delivery in Kitui County; A cross sectional study

description: Data of women of reproductive age interviewed during a cross section study carried out in Kitui county-Kenya
DOI: 10.6084/m9.figshare.13347443.v1
title: Supplementary Material for: Switching Monopolar No-Touch Radiofrequency Ablation Using Octopus Electrodes for Small Hepatocellular Carcinoma: A Randomized Clinical Trial

description: <b><i>Introduction:</i></b> A switching monopolar no-touch radiofrequency ablation (RFA) technique is used for small hepatocellular carcinoma (HCC); however, there have not been any randomized clinical trials comparing this technique to the conventional RFA technique. <b><i>Objective:</i></b>This study aims to compare the results of two RFA techniques, and to comparatively identify more effective methods to reduce the progression of local tumors associated with small HCC (≤2.5 cm). <b><i>Methods:</i></b> This prospective randomized clinical trial (NCT03375281) recruited a total of 116 participants (M:F, 93:23; 68.3 ± 8.4 years) between October 2016 and September 2017. The primary outcome was the cumulative incidence of local tumor progression (LTP) after RFA. Secondary outcomes included technical success rate, technique efficacy, and RFA procedure characteristics. Kaplan-Meier analysis and the Cox proportional hazard regression model were used. <b><i>Results:</i></b> The mean follow-up period was 24.1 months. A sufficient ablative margin was more frequently achieved in the no-touch RFA group (57/60 = 95%) than in the conventional RFA group (50/64 = 78.1%) on immediate follow-up CT (<i>p</i> = 0.01). The cumulative incidence of LTP in the no-touch RFA group was significantly lower than that in the conventional RFA group (<i>p</i> = 0.02). In multivariable analysis, no-touch RFA was the only predictive factor for LTP (<i>p</i> = 0.04, hazard ratio = 0.2, 95% confidence interval = 0.04–0.94). <b><i>Conclusions:</i></b> A switching monopolar no-touch RFA technique is a favorable treatment option and provides lower LTP after RFA compared with conventional RFA for small HCC.
DOI: 10.6084/m9.figshare.5122498.v1
title: Supplementary Material for: The Effect of HMGB1, a Damage-Associated Molecular Pattern Molecule, on Polymorphonuclear Neutrophil Migration Depends on Its Concentration

description: Polymorphonuclear neutrophils (PMN) play a key role in host defenses against invading microorganisms but also potentiate inflammatory reactions in case of excessive or misdirected responses. Release of the alarmin high-mobility group box 1 (HMGB1) by cells that die at an inflammatory site may act as an alert signal for the immune system. We studied the effect of HMGB1 on human PMN migration, using whole-blood samples to avoid cell activation associated with isolation procedures. HMGB1 50–100 ng/ml reduced baseline PMN migration as well as formyl-methionyl-leucyl-phenylalanine- and IL-8-induced PMN chemotaxis. This inhibitory effect was mediated by the RAGE receptor. In contrast, a higher HMGB1 concentration (5,000 ng/ml) had a chemoattractant effect on PMN through IL-8 production. This effect required the engagement of Toll-like receptors 2 and 4 in addition to the RAGE receptor. The A box component of HMGB1, which antagonizes the endogenous protein, reduced chemotaxis and also strongly inhibited the enhancement of PMN migration observed with the highest HMGB1 concentration. In contrast, the B box, reported to be the active form of HMGB1, exerted a chemoattractant effect. These results strongly point to a key regulatory role of HMGB1 in PMN recruitment to inflammatory tissues. The A box component could potentially serve to inhibit inappropriate PMN recruitment during chronic inflammatory disorders associated with excessive HMGB1 release.
DOI: 10.6084/m9.figshare.9800636.v2
title: Complete phylogenies and alignment files

description: Complete phylogenies, alignment files and trimmed files referring to "Multi-layered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts"
DOI: 10.6084/m9.figshare.24783867.v1
title: Supplemental Material for Exposome and Metabolome Analysis of Sugarcane Workers Reveals Predictors of Kidney Injury

description: Supplemental Material for Exposome and Metabolome Analysis of Sugarcane Workers Reveals Predictors of Kidney InjurySupplemental Table 1: Complete raw ICPMS elemental analysis table.Supplemental Table 2: Complete raw metabolomic results table.Supplemental Table 3: Significantly impacted pathways based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) with p values from pathway enrichment analysis and pathway impact values from pathway topology analysis.Supplemental Table 4: Complete raw pesticide metabolomic results table.
DOI: 10.6084/m9.figshare.28716044.v1
title: recombination

description: This repositiory contains the scripts and datasets used to perform the recombination (recombination.py) and sterility (sterility.py) analyses in Kapperud (2023) and in an upcoming paper (in press). I refer to these for further details.Kapperud, Ø (2023) Recombination and sterility in inversion homo- and heterokaryotypes under a general counting model of chiasma interference. Genetics. 225.Kapperud, Ø (in press) Breakpoint-chiasma interference in pericentric inversion heterokaryotypes. Genetics
DOI: 10.6084/m9.figshare.27868785.v1
title: readme

description: This folder contains results from the GWAS fine-mapping (SAFFARI pipeline results) and MHC fine-mapping from the PGC3 BIP fine-mapping preprint. Link: https://www.medrxiv.org/content/10.1101/2024.02.12.24302716v1
DOI: 10.6084/m9.figshare.6949604.v1
title: Supplementary Material for: Order of Treatment Matters in Ischemic Stroke: Mechanical Thrombectomy First, Then Carotid Artery Stenting for Tandem Lesions of the Anterior Circulation

description: <b><i>Background:</i></b> One endovascular treatment option of acute ischemic stroke due to tandem occlusion (TO) comprises intracranial thrombectomy and acute extracranial carotid artery stenting (CAS). In this setting, the order of treatment may impact the clinical outcome in this stroke subtype. <b><i>Methods:</i></b> Retrospective analysis was performed on data prospectively collected in 4 international stroke centers between 2013 and 2017. One hundred sixty-five patients with anterior TO were treated by endovascular therapy. Clinical and procedural data were evaluated. Favorable clinical outcome was defined as modified Rankin Scale (mRS) ≤2 at 90 days. Propensity score matching was performed for different treatment strategies. <b><i>Results:</i></b> Patients’ mean age was 65 ± 11 years and 118 were male (69%). The median admission National Institutes of Health Stroke Scale was 15 (interquartile range 8). In 59% of the patients (<i>n</i> = 101), the antegrade strategy (first stenting, then thrombectomy) was ­performed, in 41% (<i>n</i> = 70) retrograde treatment (first thrombectomy, then stenting). Successful reperfusion (mTICI ≥2b) was achieved in 128 patients (75%). Fifty-nine patients (39%) showed a favorable clinical outcome after 90 days. After propensity score matching, data of 100 patients could be analyzed. Analysis revealed that the retrograde strategy yielded a significantly higher rate of successful reperfusion compared to the antegrade strategy (92 vs. 56%; <i>p</i> &lt; 0.001). The rate of favorable clinical outcome after 90 days (mRS ≤2) was consistently higher (44 vs. 30%; <i>p</i> &lt; 0.05) in the retrograde strategy group. <b><i>Conclusion:</i></b> Mechanical thrombectomy prior to acute CAS in TO is a predictive factor for favorable clinical outcome at 90 days.
DOI: 10.6084/m9.figshare.23806098.v1
title: A Semantic Comparative Analysis of Agile Teamwork QualityInstruments in Agile Software Development -DATASET

description: This dataset have eight teamwork quality instruments semantically compared in the article <b>A Semantic Comparative Analysis of Agile Teamwork Quality Instruments in Agile Software Development</b>
DOI: 10.6084/m9.figshare.14986587.v1
title: Supplementary Material for: Mapping Angiopoietin1 expression in the developing and adult brain

description: Medicine
DOI: 10.6084/m9.figshare.24123111.v6
title: Raw Data from Manuscript "A genetic screen of transcription factors in the <i>Drosophila melanogaster</i> abdomen performed in an undergraduate laboratory course"

description: The raw image files and supplemental material for the manuscript "A genetic screen of transcription factors in the <i>Drosophila melanogaster</i> abdomen identifies novel pigmentation genes", are included here. This manuscript details a genetic screen in which we targeted 71 transcription factor genes in the <i>Drosophila </i>abdomen, either overexpressing or knocking out the target gene. In our screen, we used a transgenic CRISPR/Cas9 approach to overexpress or knockout a transcription factor gene in the<i> pannier</i> expression domain, which drives expression in the middle of the abdomen and thorax.Supplemental material includes Figures S1, S2, and S3; Tables S1 and S2; and Supplementary File 1.Image files are named to include 1) the gene being targeted, indicated by its abbreviation; 2) whether the treatment is overexpression (e) or knockout (ko); 3) the Bloomington ID numbers of the parents; and 4) whether the fly is male or female.For example, if a file is named "ab_e_67040_83608_f0001", the "ab" indicates the gene targeted, in this case, <i>abrupt</i>; the "e" indicates that this was an overexpression cross; 67040 is the Bloomington ID for the female parent of the cross; 83608 is the Bloomington ID for the male parent of the cross; and the "f0001" indicates that the fly in the image is female.The numbers 67040 and 67077 are the IDs for the overexpression and knockout lines, respectively. In all cases, the female parent was the one that contained the <i>pannier-</i>Gal4 driver. The male parent contained the guide RNAs for the target genes.For the controls, overexpression controls are labeled "gof_control_f/m", and knockout controls are labeled "lof_control_f/m".Raw numerical measurements of these images is included in file Supplementary File 1. Measurements from overexpression experiments and from knockout experiments are on separate, labeled tabs. In this file, the darkness measurement has been converted to percent darkness using the following formula:(255 - x) / 255where x is the "mean A4 darkness" value.
DOI: 10.6084/m9.figshare.22581913.v1
title: Whole transcriptomic analysis identified differentially dysregulated immune and neurological pathways in relapse and remission phases of experimental autoimmune encephalomyelitis

description: Multiple sclerosis (MS) is a neurodegenerative disorder that is characterized by chronic inflammation and demyelination of the central nervous system (CNS). Most affected patients undergo relapse and remission stages. Relapse episodes represent one of the most challenges in the treatment of MS as overtime frequent relapses result in the accumulation of unreversed damage in the CNS. Relapse is correlated with genetic and environmental factors, however, the molecular mechanisms that are associated with it are still unclear. This study aims to investigate the mechanisms of MS relapse and remission using its animal model experimental autoimmune encephalomyelitis (EAE). via transcriptomic analysis was used, and several factors were found to participate in the initiation of the relapse in EAE disease, including dysregulation of signalling pathways such as PI3K/Akt, MAPK, and JAK/STAT pathways. In addition, increased numbers of immune cells such as activated natural killer (NK) cells were observed in relapse. whereas other properties characterize the remission including high percentages of Tregs, B and T CD8+ lymphocytes, and increased expression of prolactin (Prl) hormone. Taken together, dysregulation of these molecular pathways may potentially contribute to decreased inflammation and myelin repair and regeneration in the remission EAE phase
DOI: 10.6084/m9.figshare.28683512.v1
title: Supplementary Material for: The Spanish GIRO guideline: a paradigm shift in the management of obesity in adults.

description: Introduction: Current obesogenic environments, along with intrinsic factors, contribute to the obesity pandemic, which impacts the quality of life and healthcare for individuals with obesity. In addition, discrimination and stigma related to obesity remain widespread in our society. In this scenario, the Spanish Society for the Study of Obesity (SEEDO), in collaboration with 38 recognized scientific societies and 12 patients’ organisation, have elaborated the Spanish guideline for obesity management in adults, referred to as the GIRO guideline. GIRO aims to drive a shift in obesity management and serve as a guide for healthcare professionals (HCPs) to address this chronic and multifactorial disease. Methods: A comprehensive systematic review was conducted and completed with experts’ contribution, with a particular focus on Spanish society. The quality of evidence was assessed using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) system. Experts selected the recommendations and determined their strength through consensus. Results: A total of 121 recommendations were proposed, including 32 adopted from the Canadian Adult Obesity Clinical Practice Guidelines and 89 specific recommendations created for the Spanish context, distributed across five areas of application: 1) Recognition of obesity as a chronic disease; 2) Obesity assessment; 3) Multidisciplinary approach to obesity treatment; 4) Recommendations for obesity management in special populations; and 5) Implementation of the GIRO guideline and future challenges. Conclusion: The GIRO recommendations are intended to serve as a useful and interactive tool for HCPs, policymakers and other stakeholders to ensure access to and quality of healthcare for individuals living with obesity.
DOI: 10.6084/m9.figshare.26127244.v2
title: Bases de datos de encuestas docentes no universitarios en España 2021-2022, sobre diversidad, interculturalidad, estereotipos y aculturación

description: Bases de datos de encuestas docentes no universitarios en España 2021-2022, recabado en el marco del proyecto Diverprof (https://diverprof.es/). Se incluye informe de variables iniciales y ad-hoc elaboradas para analizar las actitudes hacia la aculturación y la diversidad cultural en el profesorado a nivel de educación obligatoria en España.Proyecto (PP-2022-06), financiado por la Universidad Internacional de La Rioja.<br>
DOI: 10.6084/m9.figshare.13064231.v1
title: Fragment Library of Natural Products and Compound Databases for Drug Discovery

description: Natural products and semi-synthetic compounds continue to be a significant source of drug candidates for a broad range of diseases, including the current pandemic caused by COVID-19. Besides being attractive sources of bioactive compounds for further development or optimization, natural products are excellent candidates of unique substructures for fragment-based drug discovery inspired on natural products. To this end, fragment libraries are required that can be incorporated into automated drug design pipelines. However, it is still scarce to have public fragment libraries based on extensive collections of natural products. Herein we report the generation and analysis of a fragment library of natural products derived from a database with more than 400,000 compounds. We also report fragment libraries of food chemical databases and other compound data sets of interest in drug discovery, including compound libraries relevant for COVID-19 drug discovery. The fragment libraries were characterized in terms of contents and diversity.<br><br>Sopporting information contains: <br>COCONUT_COMPOUNDS.csv, FooDB_COMPOUNDS.csv, DCM_COMPOUNDS.csv, CAS_COMPOUNDS.csv, 3CLP_COMPOUNDS.csv. All datasets contain the curated structures and the following information: identicator number (ID), simplified molecular input line entry system (Smiles), Average Molecular Weight (AMW), number of carbons, oxygens, nitrogens, heavy atoms, aliphatic rings, aromatic rings, heterocycles, bridgehead atoms, fraction of sp3 carbon atoms and chiral carbons, and a list of fragments generated from each compound. FRAGMENTS_COCONUT.csv, FRAGMENTS_FooDB.csv, FRAGMENTS_DCM.csv, FRAGMENTS_CAS.csv, FRAGMENTS_3CLP.csv. All libraries contain structures generated (Fragments) from each compound library (Dataset) and the following information: number of compounds that contain that fragment in a dataset (Count) and fraction of them (Proportion), average Molecular Weight (AMW), number of carbons, oxygens, nitrogens, heavy atoms, aliphatic rings, aromatic rings, heterocycles, bridgehead atoms, fraction of sp3 carbon atoms and chiral carbons. <br>
DOI: 10.6084/m9.figshare.28711079.v1
title: Supplemental Figure-

description: Endothelial-to-mesenchymal transition (EndMT) is a biological process that converts endothelial cells to mesenchymal cells with increased proliferative and migrative abilities. EndMT has been implicated in the development of pulmonary vascular remodeling in pulmonary arterial hypertension (PAH), a fatal and progressive lung vascular disease. Transforming growth factor β<sub>1</sub> (TGF-β<sub>1</sub>), an inflammatory cytokine, is known to induce EndMT in many types of endothelial cells including lung vascular endothelial cells (LVEC). An increase in cytosolic free Ca<sup>2+</sup> concentration ([Ca<sup>2+</sup>]<sub>cyt</sub>) is a major stimulus for cellular proliferation and phenotypic transition, but it is unknown whether Ca<sup>2+</sup> signaling is involved in EndMT. In this study we tested the hypothesis that TGF-β<sub>1</sub>-induced EndMT in human LVEC is Ca<sup>2+</sup>-dependent. Treatment of LVEC with TGF-β<sub>1</sub> for 5-7 days resulted in increase in SNAI1/2 expression, induction of EndMT, upregulation of STIM/Orai1 and enhancement of store-operated Ca<sup>2+</sup> entry (SOCE). Removal (or chelation) of extracellular or intracellular Ca<sup>2+</sup> with EGTA or BAPTA-AM respectively abolished EndMT in response to TGF-β<sub>1</sub>. Moreover, EGTA diminished TGF-β<sub>1</sub>-induced increase in SNAI in a dose-dependent manner. Knockdown of either STIM1 or Orai1 was sufficient to prevent TGF-β-mediated increase in SNAI1/2 and EndMT, but did not rescue the continuous adherent junctions. Blockade of Orai1 channels by AnCoA4 inhibited TGF-β-mediated EndMT and restored PECAM1-positive continuous adherent junctions. In conclusion, intracellular Ca<sup>2+</sup> signaling plays a critical role in TGF-β-associated EndMT through enhanced SOCE and STIM1-Orai1 interaction. Thus, targeting Ca<sup>2+</sup> signaling pathways regulating EndMT may be a novel therapeutic approach to treat PAH and other forms of pre-capillary pulmonary hypertension.
DOI: 10.6084/m9.figshare.24722232.v4
title: Microservices Dataset - Filtered version

description: This is a microservices dataset. For an exclusive explanation, please take a look at the <b>paper</b> and at the <b>online appendix</b>: https://github.com/darioamorosodaragona-tuni/Microservices-Dataset<br><br>In particular, this file contains all the projects labeled as:<br>- <i>Is it a microservices?:</i> <i>Yes</i><br>- <i>Archived:</i> <i>No</i><br><br><b>Copyright:</b><br><i>Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the owner/author(s). MSR ’24, April 15–16, 2024, Lisbon, Portugal © 2024 Copyright held by the owner/author(s). ACM ISBN 979-8-4007-0587-8/24/04</i><i> </i><i>https://doi.org/10.1145/3643991.3644890</i>
DOI: 10.6084/m9.figshare.28537421.v1
title: 16S04813-001.ndpi

description: Whole Slide Images of Gastric Cancer
DOI: 10.6084/m9.figshare.25316452.v1
title: Suppl. Files

description: Supplementary data files for:<br><b>Rinker et al.</b><b> </b><b>Strain heterogeneity in a non-pathogenic fungus highlights factors associated with virulence. </b><b><i>Communications Biology</i></b><b>, 2024</b><b>.</b><br>
DOI: 10.6084/m9.figshare.27215724.v1
title: Data File 1.csv

description: Phantom Phase values (rad)
DOI: 10.6084/m9.figshare.7492664.v1
title: Human sperm image data - brightfield and fluorescence images from acridine orange

description: Image data for Wang Y., ... Sinton D. et al. "A single-sperm DNA fragmentation index assay and the prediction of DNA integrity from morphological parameters" (under review)<br>Donor# = respective donor sample anonymizedbrightfield = images acquired via confocal microscopy at 100x magnification - unprocessed data are raw images - processed data contains images after processing in ImageJ via "ImageJ_brightness_adj_full_macro.txt" red = fragmented single-stranded DNAfluorescence - fluorescence emission filtered between 598-660nm from acridine orange stain (488 nm excitation wavelength)<br>green = double-stranded DNA - fluorescence emission filtered between 500-550nm from acridine orange stain (488 nm excitation wavelength)<br>