cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9253130.v1
title: formation_energy.extxyz

description: Dataset containing atomic geometries and formation energies for inorganic crystals extracted from OQMD 1.1.
DOI: 10.17632/jj95n45h3v
title: The impact of divestiture transactions on the market value of a company in emerging markets

description: The model of the impact of divestiture transactions on the market value of a company in emerging markets
DOI: 10.6084/m9.figshare.28715621.v2
title: Open Reading Frame prediction

description: <b>Open reading frame (ORF) predicted by </b><b>TransDecoder (v5.7.1) for 25 grassland plant species. </b><b>Species list:</b>Species_code Species_nameGerPra Geranium pratenseLeuVul Leucanthemum vulgare agg.TriFla Trisetum flavescensLotCor Lotus corniculatusCreBie Crepis biennisBelPer Bellis perennisDauCar Daucus carotaPruVul Prunella vulgarisTriPra Trifolium pratensePriVer Primula verisHolLan Holcus lanatusAloPra Alopecurus pratensisGalMol Galium mollugo agg.KnaArv Knautia arvensisMedVar Medicago x variaPlaLan Plantago lanceolataLuzCam Luzula campestrisVerCha Veronica chamaedrysArrEla Arrhenatherum elatiusTriDub Trifolium dubiumLatPra Lathyrus pratensisVicCra Vicia craccaRanAcr Ranunculus acrisPlaMed Plantago mediaAjuRep Ajuga reptans<br><br><b>Analyse pseudo code:</b>#! /usr/binLongOrf='path/to/TransDecoder-TransDecoder-v5.7.1/TransDecoder.LongOrfs'Predict='path/to/TransDecoder-TransDecoder-v5.7.1/TransDecoder.Predict'<br>for i in {01..25}; do# the number corresponding to a particular speciescd path/to/isoSeqData/BMK230426-BJ202-01P000$i;$LongOrf -t BMK230426-BJ202-01P000$i.flnc.clustered.isoforms.fa;$Predict -t BMK230426-BJ202-01P000$i.flnc.clustered.isoforms.fa;done<br>
DOI: 10.6084/m9.figshare.11914380.v3
title: The Use of a Variable Representing Compliance Improves Accuracy of Estimation of the Effect of Treatment Allocation Regardless of Discontinuation in Trials with Incomplete Follow-up

description: <i>Abstract–</i>In Clinical Trials, not all randomized patients follow the course of treatment they are allocated to. The potential impact of such deviations is increasingly recognized, and it has been one of the reasons for a redefinition of the targets of estimation (“Estimands”) in the ICH E9 draft Addendum. Among others, the effect of treatment assignment, regardless of the adherence, appears an Estimand of practical interest, in line with the intention-to-treat principle. This study aims at evaluating the performance of different estimation techniques in trials with incomplete post-discontinuation follow-up when a “treatment-policy” strategy is implemented. To achieve that, we have (i) modeled and visualized as directed acyclic diagram a reasonable data-generating model; (ii) investigated which set of variables allows identification and estimation of such effect; (iii) simulated 10,000 trials in Major Depressive Disorder, with varying real treatment effects, proportions of patients discontinuing the treatment, and incomplete follow-up. Our results suggest that, at least in a “Missing at Random” setting, all studied estimation methods increase their performance when a variable representing compliance is used. This effect is more pronounced the higher the proportion of post-discontinuation follow-up is.
DOI: 10.6084/m9.figshare.5619436.v1
title: Small Cell Lung Cancer

description: These data are described in (Ying et al., 1995) and originally collected in (Maksymuik et al., 1994). The patients were randomly assigned to one of two treatments referred to as Arm A and Arm B. Arm A patients received cisplatin (P) followed by etoposide (E), while Arm B patients received (E) followed by (P). There were a total of 62 patients in Arm A with 15 right censored survival times, while Arm B consisted of 59 patients with 8 right censored survival times.<br><br>The variables recorded in the dataset(s) are:<br>- age: age of the patient upon entry (in years)<br>- time: survival time of the patient (in days)<br>- cens: indicator for survival time - 0 if observed, 1 if right censored<br><br>We analyze these data using a Dirichlet Process Mixture Model with a Gamma kernel distribution (Poynor and Kottas, 2017). The primary emphasis of our work is to obtain inference for the mean residual life function. Our code is shared through github (see link in references). <br><br>Journal References:<br><i><br></i><i>Jett, R, J D Earle, J Q Su, F A Diegert, J A Mailliard, C G Kardinal, J E Krook, M H Veeder, and M Wiesenfeld. Sequencing and schedule effects of cisplatin plus etoposide in small-cell lung cancer: results of a North Central Cancer Treatment Group randomized clinical trial</i>. A W Maksymiuk, J Journal of Clinical Oncology 1994 12:1, 70-76<br><br>Poynor V. and Kottas A. (2017). <i>Nonparametric Bayesian Inference for Mean Residual Life Functions in Survival Analysis</i>. Submitted to Biostatistics. arXiv:1411.7481 [stat.ME]. <br><br><i>Ying, Z., S. H. Jung and L. J. Wei. Survival Analysis with Median Regression Models. </i>Journal of the American Statistical Association, Vol. 90, No. 429 (Mar., 1995), pp.178-184<br> <br><br>
DOI: 10.6084/m9.figshare.7969502.v1
title: Supplementary Material for: Human Mast Cell Sensitization with IgE Increases miRNA-210 Expression

description: <b><i>Background:</i></b> MicroRNAs (miRNAs) represent important post-transcriptional regulators with a dynamic expression profile during health and disease. <b><i>Objectives:</i></b> We explored the miRNA profile of human mast cells (MCs) during sen­sitization with IgE, during activation through IgE, and relat ed it to prostaglandin D<sub>2</sub> synthesis and histamine release. <b><i>Method:</i></b> We investigated the expression pattern of 762 miRNAs during the IgE-mediated sensitization and activation of MCs cultured from CD133+ stem cells that were isolated from allergic asthmatic patients and nonatopic controls. <b><i>Results:</i></b> IgE-mediated sensitization increased the expression of miRNA-210 eight-fold. This increase was sustained during IgE-mediated MC activation. Furthermore, we confirmed the increase of the miRNA-132/212 cluster after MC activation. Predicted target genes of miRNA-210/132/212 were enriched in several pathways known to be involved in MC activation. Histamine release was significantly higher in MCs from allergic patients when compared to controls, and a number of miRNAs correlated with histamine release and prostaglandin D<sub>2</sub> synthesis during MC activation. <b><i>Conclusion:</i></b> The miRNAs and analysis presented here can help to elucidate the role of miRNAs in mediator release during MC activation. We speculate that miRNA-210 could be important in MC sensitization that leads to allergic symptoms.
DOI: 10.17632/hkj4z5h84p
title: Evaluation of the performance capability of remote visual inspection of concrete structures using drones

description: Scoring data for participants from remote visual inspection (RVI) trials involving the inspection of a concrete block wall using unmanned aerial vehicles (UAVs)
DOI: 10.6084/m9.figshare.1499145.v1
title: 16S rRNA amplicon data from the paper : "The outer mucus layer hosts a distinct intestinal microbial niche"

description: The 16S rRNA gene segments spanning the variable V5 and V6 regions were amplified from DNA from mucus, contents, or mouse faecal samples using a multiplex approach with barcoded primers. The PCR amplified 16S V5-V6 amplicons were purified and prepared for sequencing on the Ion torrent PGM system according to the manufacturer’s instructions (Life Technologies). The FASTQ files provided correspond to the two microbial diversity status tested in the study: SPF (2 files) and sDMDMm2 defined flora (1 file). Each file corresponds to an Ion torrent chip.The corresponding mapping files (containing barcodes and sample metadata) are also provided in TXT format. These files can be used directly for analysis (eg. using the Qiime pipeline).
DOI: 10.6084/m9.figshare.19106825.v1
title: Impact of a phantom decoy on foraging decisions by free-ranging herbivore shifts over time

description: R script used for data analysis in manuscript. Also includes accompanying csv files. af_diets has the composition of the diets used in the experiment. artificial_food_behaviour_all_visits_data has the raw data for the whole experiment.
DOI: 10.6084/m9.figshare.22548736.v1
title: Italian hydrogeological emergencies 2013-2022

description: This dataset collects tabular and geographical information about all hydrogeological disasters (landslides and floods) that occurred in Italy from 2013 to 2022 that caused such severe impacts to require the declaration of national-level emergencies. The severity and spatiotemporal extension of each emergency is characterized in terms of duration and timing, funds requested by local administrations, funds approved by the national government, and municipalities and provinces hit by the event (further subdivided between those included in the emergency and those not, depending on whether relevant impacts were ascertained).
DOI: 10.6084/m9.figshare.25551138.v2
title: Revisión bibliográfica sobre requisitos para la selección de software de gestión para bibliotecas y colecciones digitales patrimoniales

description: Este conjunto de datos recoge una recopilación de requisitos extraídos de la literatura científica, así como del análisis de las prestaciones de algunas de las aplicaciones más populares en diferentes sectores: DSpace-GLAM, Omeka Classic, Omeka S, Artefactual y ArchivesSpace. Se incluye también la lista de referencias utilizadas para el análisis. Todo este material forma parte del trabajo publicado como informe bajo el título: <i>A</i><i>nálisis de requisitos para la selección de software de gestión para bibliotecas y colecciones digitales patrimoniales</i>. Barcelona: Universitat de Barcelona.
DOI: 10.6084/m9.figshare.26793622.v1
title: LNCTVSeg-DataSet.zip

description: We retrospectively collected 440 computed tomography (CT) images from 262 patients with different imaging modalities, disease stages and treatment strategies. To protect the patients' private information, we first blurred the face region and removed all metadata about clinical and personal. Then, all files are stored with the format NIfTI-1 (32-bit floating point). Each cohort is stored as a folder and named "Internal\_Cohort", and "Testing\_Cohort\_X" ("X" is from 1 to 4), Raw CT images in the training or testing sets are stored in the "imagesTr" or "imagesTs" folders of each cohort with the name "lnctvseg\_cx\_xxxx\_yyyy.nii.gz", respectively, where "cx" denotes the center number x is the digit number from 1 to 4, "xxxx" is the index number of each patient the range is 1 to the total number of patients in "cx", "yyyy" is set to "0000" (non-contrast CT) or "0001" (contrast-enhanced CT). The corresponding labels are stored in the "labelsTr" and "labelsTs" folders with the name "lnctvseg\_cx\_xxxx.nii.gz", respectively.
DOI: 10.6084/m9.figshare.19922096.v1
title: Supplementary Material for: Validation of a Protocol for Continuous Hemodiafiltration with Regional Citrate Anticoagulation with Omni®

description: <b><i>Introduction:</i></b> Omni® (B Braun, Melsungen, Germany) is able to run continuous renal replacement therapy (CRRT) in continuous veno-venous hemofiltration (CVVH), hemodialysis (CVVHD), and hemodiafiltration (CVVHDF) modes. However, to date, there is no validated protocol to guide the use of Omni® in CVVHDF mode with regional citrate anticoagulation (RCA). <b><i>Methods:</i></b> We designed a protocol for CVVHDF-RCA tailored for Omni®. This protocol was tested in patients included in an observational study conducted in our center between January and March 2021. For all study patients, we collected baseline characteristics, laboratory results, CRRT circuit lifespan as well as plasma and effluent samples at 12, 24, 48, and 72 h of CRRT circuit initiation. At each study time point, we computed urea, creatinine, and β2-microglobulin clearance as well as effluent/blood ratios. Data from circuits in CVVHDF-RCA mode are compared with those in standard therapy (CVVHD-RCA) with the same device. <b><i>Results:</i></b> We analyzed ten circuits (5 patients) in CVVHDF-RCA mode and 32 (13 patients) in CVVHD-RCA mode. No adverse events related to the therapy were observed. In CVVHDF-RCA mode, median circuit running time was 68 (IQR 8.1) hours versus 46 (IQR 9.0) in CVVHD mode, <i>p</i> = 0.053. Therapy adaptations (dialysate rate and/or blood flow) were required in one (10%) circuit (15.6% in CVVHD mode, <i>p</i> = 0.56). Compared to CVVHD, CVVHDF was able to achieve similar clearance and effluent/blood ratio for urea, creatinine, and β2-microglobulin across the entire duration of circuit lifetime. <b><i>Conclusion:</i></b> The proposed protocol for CVVHDF-RCA for Omni® was associated with similar circuit lifetime, number of required adaptations and clearances to standard CVVHD-RCA. It appears to be safe and feasible.
DOI: 10.6084/m9.figshare.24100590.v1
title: Supplementary Material for: Comparisons of insulin resistance- and steatosis-based scores in monitoring metabolic associated fatty liver disease treatment response

description: Background: Quantitative measurements of liver fat contents (LFCs) by magnetic resonance imaging derived-proton density fat fraction (MRI-PDFF) are accurate but limited by availability, convenience, and expense in the surveillance of metabolic associated fatty liver (MAFLD). Insulin resistance (IR) and steatosis-associated serum indices are useful in screening for MAFLD, but their value in monitoring MAFLD with or without chronic hepatitis B virus (CHB) infection remains unclear and we aimed to evaluate these scores in predicting changes in LFC. Methods: We conducted a prospective study between January, 2015 and December, 2021 with 620 consecutive participants with MAFLD (212 participants with CHB) who received a 24-week lifestyle intervention. The homeostasis model assessment of insulin resistance (HOMA-IR), HOMA2 index, Glucose insulin ratio, Quantitative Insulin Sensitivity Check Index, Fasting Insulin Resistance Index, Fatty liver index (FLI), Hepatic steatosis index (HSI), Liver fat score (LFS), Visceral Adiposity Index, and Triglycerides * Glucose were calculated. Results: When using endpoints such as LFS improvements of ≥5% or 10% or escalations of ≥5%, LFS had the highest area under the curve (AUC) values at all endpoints for MAFLD alone (0.756, 95% CI: 0.707–0.805; 0.761, 95% CI: 0.705–0.818; 0.807, 95% CI: 0.713–0.901, all P&lt;0.05, respectively). With CHB, the FLI (AUC=0.750) and HIS (AUC=0.770) exhibited the highest AUCs between the former two outcomes, respectively, but no score could predict LFC escalation of ≥5%. Conclusion: Among IR and steatosis scores, changes in LFC through lifestyle interventions can be captured with LFS possessing moderate precision but not in those with CHB.
DOI: 10.17632/6ym99x2y8d
title: A mathematical model to predict Transition-to-Fatigueduring isometric exercise on muscles of the lower extremities

description: Some students have request the data set for this research published on Scientific Research as free download in the link: https://www.scirp.org/journal/PaperInformation.aspx?PaperID=26740.  To re-create the importance to identify transitional muscle fatigue stage, because make possible to predict when muscle fatigue will occur, which provides the foundation of the automated system that has the potential to aid in many applications of our lives, including sports, rehabilitation, ergonomics and even neuropathy formation on legs.
DOI: 10.17632/wfcbfy29wm
title: Small Corpus of Colombian English as a Second Language Essays (SCoCESLE)

description: The Small Corpus of Colombian English as a Second Language Essays (SCoCESLE) can be classified as a small learner corpus. SCoCESLE is made up of 272 argumentative essays written by Colombian English as a Second Language (ESL) learners. It has a total of 81,994 tokens, 6,057 types, and 5,161 lemmas. Each essay has an average length of about 270 words. Essay topics include gender-related issues, education, information technology, environmental problems, personality traits, poverty, genetic engineering, globalisation, pets ownership, compulsory vaccination, transportation, compulsory military conscription, immigration, job satisfaction, economy, foreign language learning, and employees working conditions. The texts in the corpus were written by male (n=157), female (n=114) and gender fluid (n=1) adult learners (i.e., 18+). The learners’ first language is Colombian Spanish. The corpus is unannotated and is divided into a lower proficiency sub-corpus (n=133) and a higher proficiency one (n=139). The data presented here includes: 1. The corpus manual (.pdf) 2. The corpus metadata (.xls) 3. The corpus of 272 unannotated plain texts (.txt) 4. The sub-corpus of 133 lower proficiency texts (.txt) 5. The sub-corpus of 139 higher proficiency texts (.txt)
DOI: 10.6084/m9.figshare.16558032.v1
title: Supplementary Material for: Inverted Internal Limiting Membrane Flap Technique versus Internal Limiting Membrane Peeling for Large Macular Holes: A Meta-Analysis of Randomized Controlled Trials

description: <b><i>Background:</i></b> Vitrectomy with internal limiting membrane (ILM) peeling is an effective surgical procedure for the treatment of macular holes (MHs). However, there is a possibility of poor postoperative anatomical closure with conventional ILM peeling for MHs larger than 400 μm. Therefore, a novel inverted ILM flap technique was developed for such cases. <b><i>Objectives:</i></b> This meta-analysis study was performed to evaluate and compare the anatomical and visual outcomes of the inverted ILM flap technique and ILM peeling in large MHs. <b><i>Methods:</i></b> The Cochrane Library, PubMed, and Embase databases were searched to identify randomized controlled trials (RCTs). The trial eligibility and risk of bias were assessed according to Cochrane review methods. The primary outcome measures included MH closure rate and postoperative visual acuity (VA). Subgroup analysis of postoperative VA based on follow-up time was also conducted. Pooled odds ratios (ORs), weighted mean difference (WMD), and 95% confidence intervals (CIs) were calculated. Statistical analysis was performed using RevMan 5.3 software. <b><i>Results:</i></b> Five RCTs with a total of 155 eyes in the inverted ILM flap group and 161 eyes in the ILM peeling group were included in this meta-analysis. Statistical meta-analysis revealed that the overall MH closure rate in the inverted ILM flap group was significantly higher than that in the ILM peeling group (OR = 3.10; 95% CI: 1.25–7.66; <i>p</i> = 0.01). The postoperative VA was significantly better in the inverted ILM flap group than the ILM peeling group (WMD = −0.14; 95% CI: −0.21 to −0.07; <i>p</i> = 0.0002). The subgroup meta-analysis indicated that the postoperative VA was significantly better in the inverted ILM flap group than the ILM peeling group (WMD = −0.17; 95% CI: −0.26 to −0.08; <i>p</i> = 0.0004) at the 3-month follow-up. However, no significant difference was observed between the 2 groups at the 6-month follow-up (WMD = −0.09; 95% CI: −0.20 to 0.02; <i>p</i> = 0.10). <b><i>Conclusions:</i></b> Vitrectomy with the inverted ILM flap technique showed a higher anatomical closure rate as well as visual gain – although only in the short term as no difference in visual recovery was found at the 6-month follow-up – than did ILM peeling in large MHs. The inverted ILM flap technique should be considered as a preferred and routine procedure for the treatment of patients with MHs larger than 400 µm.
DOI: 10.6084/m9.figshare.11777727.v1
title: Evolution of Android applications layouts [Thesis Appendix 1]

description: This is a .csv file reporting data about the evolution of Android applications layouts. In particular, it focuses on added, deleted and modified lines of xml layout files in each transition from a release of the app to the following one.This dataset contains data about 705 Android projects found on github.
DOI: 10.6084/m9.figshare.5436136.v7
title: 1000 Empirical Time series

description: A diverse selection of 1000 empirical time series, along with results of an <i>hctsa</i> feature extraction, using v1.03 of <i>hctsa</i> and Matlab 2019b, computed on a linux server at Sydney University.<br>The results of the computation are in the <i>hctsa</i> file, <b>HCTSA_Empirical1000.mat</b> for use in Matlab using v1.03 of <i>hctsa</i>.<br><b><br></b>The same data is available in <b>.csv</b> format (e.g., for use with non-Matlab computing environments) for the <b>hctsa_datamatrix.csv</b> (results of feature computation), with information about rows (time series) in <b>hctsa_timeseries-info.csv</b>, information about columns (features) in <b>hctsa_features.csv</b> and the data of individual time series (each line a time series, for time series described in <b>hctsa_timeseries-info.csv</b>) is in <b>hctsa_timeseries-data.csv</b>. Note that these files were produced by running <b>&gt;&gt;OutputToCSV(HCTSA_Empirical1000.mat,true);</b> in <i>hctsa</i>.<b><br></b>The input file, <b>INP_Empirical1000.mat</b>,<b> </b>is for use with <i>hctsa</i>, and contains the time-series data and metadata for the 1000 time series. For example, massive feature extraction from these data on the user's machine, using <i>hctsa</i>, can proceed as<b>&gt;&gt; TS_Init('INP_Empirical1000.mat');</b><br>Some visualizations of the dataset are in <b>CarpetPlot.png </b>(first 1000 samples of all time series as a carpet (color) plot) and <b>150TS-250samples.png</b> (conventional time-series plots of the first 250 samples of a sample of 150 time series from the dataset). More visualizations can be performed by the user using <b>TS_PlotTimeseries</b> from the <i>hctsa</i> package.<br><br>See links in references for more comprehensive documentation for performing methodological comparison using this dataset, and on how to download and use v1.03 of <i>hctsa</i>.
DOI: 10.6084/m9.figshare.9753848.v1
title: Panc-1 NMR data

description: Raw Data for Panc-1 cell line for <b>Influence of Drying Method on NMR-Based Metabolic Profiling of Human Cell Lines</b> project.
DOI: 10.6084/m9.figshare.c.3605579_d2.v1
title: MOESM2 of Caseâ  control study of diarrheal disease etiology in individuals over 5Â years in southwest China

description: Additional file 2: The information of all subjects recruited in the study.
DOI: 10.6084/m9.figshare.19126985.v1
title: Determination of differentiated expression states occurs after seeding of hiPS cells for cardiac directed differentiation

description: Single cell RNA sequencing (10X Genomics single-cell RNA-seq kit v3) of barcoded hiPS cell-derived cardiomyocytes and hiPS cells. hiPS cells were lentivirally transduced with barcode libraries consisting of random 100-mers in the 3’ untranslated region of a green fluorescent protein (GFP) transgene after which they were permitted to divide approximately three times before being split and seeded for two parallel differentiations. On day 14 of differentiation (16 days after seeding), we used fluorescent activated cell sorting (FACS) gated for GFP positivity to enrich for barcode-containing cells on which we performed single cell RNA sequencing. As transcripts of the GFP transgene are captured by single cell RNA sequencing, we were also able to recover barcodes through a separate “side reaction” cDNA sequencing run and connect them to individual cells through analysis of GFP transcript 10x sequencing reads. Separately, we also transduced hiPS cells, allowed them to divide approximately six times before harvesting them for GFP sorting and sequencing. See Jiang et al. citation for additional details and GEO accession GSE198729 for single cell RNA sequencing raw/processed data (also available on Dropbox).