cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24137880
title: Supplementary Material for: Characteristics of severe asthma patients and predictors of asthma control in the Swiss Severe Asthma Registry (SSAR)

description: Background: Asthma is a chronic airway disease, affecting over 300 million people worldwide. 5-10% of patients suffer from severe asthma and account for 50% of asthma related financial burden. Availability of real-life data about the clinical course of severe asthma is insufficient. Objectives: To characterise patients with severe asthma in Switzerland, enrolled in the Swiss Severe Asthma Registry (SSAR) and evaluate predictors for asthma control. Method: A descriptive characterisation of 278 patients was performed, who were prospectively enrolled in the registry until January 2022. Socio-demographic variables, comorbidities, diagnostic values, asthma treatment and healthcare utilisation were evaluated. Groups of controlled and uncontrolled asthma according to the Asthma Control Test were compared. Results: 48% of patients were female and the mean age was 55.8 years (range 13-87). The mean BMI was 27.4 kg/m2 (±6). 10.8% of patients were current smokers. Allergic comorbidities occurred in 54.3% of patients, followed by chronic rhinosinusitis (46.4%) and nasal polyps (34.1%). According to the ACT score, 54.7% had well controlled, 16.2% partly controlled and 25.9% uncontrolled asthma. The most common inhalation therapy was combined ICS/LABA (78.8%). Biologics were administered to 81.7% of patients and 19.1% received oral steroids. The multivariable analysis indicated that treatment with biologics was positively associated with asthma control whereas higher BMI, oral steroids, exacerbations and COPD were negative predictors for asthma control. Conclusion: Biologics are associated with improved control in severe asthma. Further studies are required to complete the picture of severe asthma in order to provide improved care for those patients.
DOI: 10.7488/ds/2800
title: Variant effect predictions for human, yeast, bacterial and viral proteins

description: Variant effect predictions made by DEOGEN2, Envision, FATHMM, Fathmm-MKL, FathmmXF, MPC, MutationTaster, MutPred, NetDiseaseSNP, PhD_SNP, PolyPhen2 (HumDiv and HumVar), PonPS, PonP2, PrimateAI, S3D-PROF, SNAP2, SNPs&GO, SNP&GOs3D, SuSPect, VEST4, DeepSequence, fitCons, GenoCanyon, PANTHER, phastCons, PROVEAN, MutationAssessor, BLOSUM62, GERP++, Grantham, LRT, phyloP, SIFT, SIFT4G, SiPhy, CADD, CONDEL, DANN, Eigen, M-CAP, MetaLR, MetaSVM, MVP, PAPI and REVEL. Predictions are made for UBE2I, SUMO1, TPK1, CALM1, BRCA1, P53, HRAS, MAPK1, PTEN, TPMT, ADRB2, HSP82, UBI4, PAB1, GAL4, infA, GmR, bla, ccdB, haeIIIM, Cas9, env, HA-H1N1, HA-H3N2 and PA.
DOI: 10.25582/data.2021-07.2283817/2044513
title: Data for EMSL Project 51127 from July 2021
DOI: 10.25582/data.2021-07.2283626/2044514
title: Data for EMSL Project 51127 from July 2021
DOI: 10.25582/data.2021-07.2279882/2044515
title: Data for EMSL Project 51127 from July 2021
DOI: 10.18728/557.0
title: Lake Tegel physico-chemical data
DOI: 10.5281/zenodo.7350265
title: H-gradient

description: It is the data and code (data analysis and data visualization) used in the creation of the manuscript Modifications to Three-Dimensional Turbulence Parameterization for Tropical Cyclone Simulation at Convection-Permitting Resolution
DOI: 10.5281/zenodo.8295790
title: Neutronic Analysis of the BYU MSMR - Data

description: Supporting data for the Neutronic Analysis of the BYU MSMR. Within these data files, the reactor geometries, materials, settings, and tallies can be found. The scripts and data used to generate graphs for feedbacks, power profile, and flux profile are also included.
DOI: 10.5281/zenodo.8351732
title: 'Extended Data' :Evaluation of knowledge and awareness of pediatric oral health among school teachers of Hazaribag before and after oral health education.

description: Extended data: 1. Questionnaire 2. Dental Quiz 3. Topic Guide 4. Training Program
DOI: 10.6084/m9.figshare.23668272
title: Supplementary Material for: Genome-Wide Association Studies for Albuminuria of non-Diabetic Taiwanese Population

description: Background Chronic renal disease (CKD), defined by reduced estimated glomerular filtration rate (eGFR) and albuminuria, imposes huge health burden worldwide. Ethnicity-specific associations were frequently observed in genome-wide association studies (GWAS). In this research, we conducted GWAS of albuminuria in the non-diabetic population of Taiwan. Subjects and Methods Non-diabetic individuals aged 30 to 70 years and without cancer history were enrolled from the Taiwan Biobank. A total of 6,768 subjects received spot urine examination. After quality control with PLINK and imputation with SHAPEIT and IMPUTE2, a total of 3,638,350 single nucleotide polymorphisms (SNPs) remained for testing. SNPs with minor allele frequency low than 0.1% were excluded. We applied linear regression for analyzing associations between SNPs and log UACR. Results We identified six loci in or near the FCRL3 (P = 2.56 × 10−6), TMEM161(P = 4.43 × 10−6), EFCAB1 (P = 2.03 × 10−6), ELMOD1 (P = 2.97 × 10−6), RYR3 (P = 1.34 × 10−6), and PIEZO2 (P = 2.19 × 10−7) as candidate. Genetic variants in the FCRL3 gene that encodes a secretory IgA receptor were found to be associated with IgA nephropathy, which might manifest proteinuria. The PIEZO2 gene encodes a sensor for mechanical forces in mesangial cells and renin-producing cells. Conclusion We identified five new loci and one known suggestive loci for albuminuria in the non-diabetic Taiwanese population.
DOI: 10.6084/m9.figshare.23723754
title: Supplementary Material for: A novel mutation of UMOD in a Chinese family with IgA nephropathy: a case report

description: IgA nephropathy (IgAN) is the most prevalent primary glomerulonephritis worldwide, with varying clinical presentations. The hereditary susceptibility to IgAN is rather complex. In this report, a Chinese case of IgAN was recruited. Renal biopsy showed the tubular atrophy and dilatation, but the glomerular lesions were rather weak except slight mesangial hyperplasia. Immunological staining of kidney tissue revealed the positive immunological staining of IgA and C3. By using whole exome sequencing (WES), a heterozygous variant in UMOD gene was found and was confirmed by Sanger sequencing. The variants in UMOD gene might contribute to the disease and this case help to understand the correlation of genotype and phenotypes of UMOD mutations.
DOI: 10.6084/m9.figshare.24032010
title: Supplementary Material for: Primary Cutaneous Marginal Zone Lymphoma Following Repeated Inflammation Caused by Hair Dyeing

description: Primary cutaneous marginal zone lymphoma (PCMZL) is a rare form of B-cell lymphoma that primarily affects the skin. Chronic antigen stimulation has been implicated in its development, with cases associated with various triggers. We present a case of PCMZL following chronic inflammation caused by long-term hair dyeing. A 75-year-old woman with a history of repeated inflammation and itching after hair dyeing for 30 years presented with persistent red-to-violaceous patches and plaques on her scalp. Despite receiving topical corticosteroid treatment for ten years, the lesions remained. Pathological examinations confirmed the diagnosis of PCMZL. The patient achieved complete remission after radiotherapy. This case underscores the potential link between chronic inflammation and the development of PCMZL.
DOI: 10.6084/m9.figshare.24211053
title: Supplementary Material for: Risk factors for acute kidney injury after hematopoietic stem cell transplantation: A systemic review and meta-analysis

description: Aims The aim of this study was to identify risk factors associated with acute kidney injury (AKI) after hematopoietic stem cell transplantation (HSCT) by systematically reviewing the relevant literature. Methods This meta-analysis surveyed relevant articles published in PubMed, EMBASE, and the Cochrane Library up to December 2022 to identify the reliable risk factors for AKI after HSCT, calculating odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Results Twenty studies with 4378 patients were included. Umbilical cord blood transplantation (OR = 2.36; 95% CI: 1.77–3.15; P &lt;0.00001), calcineurin inhibitors (OR = 1.97; 95% CI: 1.06–3.67; P = 0.03), sinusoidal obstruction syndrome (OR = 5.80; 95% CI: 3.96–8.51; P &lt;0.00001), allogeneic transplantation (OR = 4.27; 95% CI: 1.83–9.95; P = 0.0008), hypertension (OR = 2.07; 95% CI: 1.16–3.69; P = 0.01), amphotericin B (OR = 4.03; 95% CI: 2.54–6.40; P &lt;0.00001), vancomycin (OR = 2.19; 95% CI: 1.24–3.87; P = 0.007), and total body irradiation (OR = 1.81; 95% CI: 1.27–2.57; P = 0.001) were risk factors for AKI. Conclusion Umbilical cord blood transplantation, calcineurin inhibitors. sinusoidal obstruction syndrome, allogeneic transplantation, hypertension, amphotericin B, vancomycin and total body irradiation were risk factors for AKI. It is important for clinical staff to be aware of these risk factors in their treatment planning with patients undergoing HSCT.
DOI: 10.5281/zenodo.6561068
title: A dataset for comparing filtering methods used to separate balanced and unbalanced flow at the surface of the Agulhas region

description: This dataset comprises sea surface height (SSH) and velocity data at the ocean surface in two small regions near the Agulhas retroflection. The unfiltered SSH and a horizontal velocity field are provided, along with the same fields after various kinds of filtering, as described in the accompanying manuscript, <em>Separating balanced and unbalanced flow at the surface of the Agulhas region using Lagrangian filtering. </em>The code repository for this work is https://github.com/cspencerjones/separating-balanced . Two time-resolutions are provided: two weeks of hourly data and 70 days of daily data. See the manuscript for more information. This work was supported by NASA award 80NSSC20K1142.
DOI: 10.5281/zenodo.8004129
title: Evaluation of knowledge and awareness of pediatric oral health among school teachers of Hazaribag before and after oral health education.

description: This study was done to assess the knowledge of school teachers regarding child dental health. The number of subjects participated in research were more than 150. . A self‑administered, 30‑item questionnaire was designed in English language on clinical pediatric oral health. After receiving google forms, all the participants participated in oral health education webinar program using a web based online education training protocol on ZOOM platform. Post training assessment of the oral health knowledge scores was done using the same online semi‑structured self‑administered questionnaire. The inadequacy in knowledge of school teachers was evident and they need to be trained in varied areas of pediatric oral health.
DOI: 10.5281/zenodo.8033965
title: Data of smoothed particle hydrodynamic giant impact simulations for the paper "A super-massive Neptune-sized planet"

description: This dataset contains data from the article: L. Naponiello et al. 2023 "A super-massive Neptune-sized planet". DOI: https://doi.org/10.1038/s41586-023-06499-2 The dataset comprises initial conditions and final snapshots of the smoothed particle hydrodynamics simulations selected in the paper. All the simulations were performed using SWIFT with initial condtions generated using WoMa. The planets are modeled with forsterite core (see Link), water middle layer (see link), and H&He mixture atmosphere top layer (see link). We simulated three different pre-impact compositions: water-rich by mass (22.5 % rock, 67.5 % water, 10 % H/He), equal rock and water (45 % rock, 45 % water, 10 % H/He), and rock-rich (67.5 % rock, 22.5 % water, 10 % H/He). These are located in the "data.zip" file under the folders "water rich", "equal_water_rock", and "rock_rich", respectively. In each simulation subfolder, "snapshot_0000.hdf5" is the initial condition file, where the target and impactor are separated by a distance that allows contact to occur 1 hour after the start of the simulation. "snapshot_00xx.hdf5" is the final snapshot of that simulation, where "xx" is the simulation time in hours. For example, "snapshot_0015.hdf5" is the snapshot taken after 15 hours of the simulation.
DOI: 10.6084/m9.figshare.12759833
title: Metadata record for: HyperKvasir, A comprehensive multi-class image and video dataset for gastrointestinal endoscopy

description: This dataset contains key characteristics about the data described in the Data Descriptor HyperKvasir, A comprehensive multi-class image and video dataset for gastrointestinal endoscopy. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.23607030
title: Supplementary Material for: Case Report: Vision Loss Induced by Capecitabine in Patient with Preexisting Left Eyes Blind

description: Capecitabine is an orally administered fluoropyrimidine carbamate antineoplastic agent, widely used to treat different tumor types. Eye toxicity is not well established with this type of drug. Here, we report the case of a 57-year-old man with a low rectal cancer whose vision decreased 3 weeks after starting a daily treatment of capecitabine and radiotherapy. After eliminating all other diagnoses, toxicity of antineoplastic agents remains the most likely hypothesis, making it the first case of vision loss induced by this capecitabine.
DOI: 10.6084/m9.figshare.23792265
title: Supplementary Material for: Assessment of Developmental Language Disorder in Multilingual Children: Results from an International Survey

description: Introduction: The Multilingual-Multicultural Affairs Committee of the International Association of Communication Disorders (IALP) conducted a Survey of Diagnostic Criteria for Developmental Language Disorder (DLD) in Multilingual Children to discover how clinicians apply terminology and diagnostic criteria to multilingual children in different parts of the world. Methods: An international web survey was used to survey 354 participants from 44 countries about their assessment practices, and clinical opinions about assessing multilingual children for DLD. Results: The findings show that most clinicians felt confident in assessing multilingual children, and they applied the DLD terminology and inclusionary criteria to multilingual children with difficulty learning language. Clinicians used different procedures to assess heritage and societal languages. Barriers to access to services included a lack of knowledge by parents and referral sources about services available and typical multilingual development, with additional reasons differing by geographical region. Discussion/Conclusion: Speech pathologists across the globe have many similarities in the way that they assess multilingual children. Differences may be attributed to clinical experience, professional education, the clinician’s role, the system they work in, and the clinician’s own language skills. This paper advances knowledge of current clinical practices, which can be used to evaluate frameworks in international and national contexts, with implications for policy and practice to improve access to clinical services.
DOI: 10.6084/m9.figshare.24032436
title: Supplementary Material for: Pediatric Macrocorticotropinoma: Do They Differ from Microcorticotropinoma?

description: Introduction: Cushing’s disease (CD) due to macrocorticotropinoma (MC) in children and adolescents is a rare entity with limited information regarding its characteristics. The objective of the study is to describe the clinical, biochemical, imaging, management, outcome and genetic characteristics of children and adolescents with CD due to MC and compare them with those of microcorticotropinoma (mc). Methods: This retrospective study was conducted in a single tertiary care center. 32 patients of CD with MC (maximum tumor dimension ≥ 10 mm on imaging) and 65 patients with mc (&lt;10 mm on imaging) aged ≤20 years at presentation were enrolled. Results: Nineteen girls and 13 boys with MC presented at a median (IQR) age of 14.5 (12.0-17.9) years. Patients with MC had higher body mass index-standard deviation score (BMI-SDS) (3.70±2.60 vs 2.59±2.01, p=0.04), more frequent neuro-ophthalmic symptoms (25% vs 9% p=0.04) and short stature (59% vs 34%, p=0.049) but less frequent livid striae (53% vs 77%, p 0.01), and hypokalemia (12% vs 36%, p=0.04) and lower cortisol (nmol/l) to corticotropin (pmol/l) ratio (41.20 vs. 55.74, p=0.05) than those with mc. The remission (59% vs 64% p=1.0) and relapse (53% vs 37% p=0.26) rates after first-line surgery and remission rate after radiotherapy (RT) were comparable between the two cohorts whereas time to remission after RT (27 vs 13 months, p=0.05) was longer in the MC group. A patient with MC had a pathogenic germ line variant in CDH23. Conclusion: In this large monocentric series of pediatric CD, frequent mass effect symptoms and short stature, higher BMI-SDS, less frequent livid striae and hypokalemia with lower effective cortisol secretion characterize the MC cohort. The outcomes of surgery and RT were similar between the groups except for a longer time to remission after RT in the MC cohort.
DOI: 10.6084/m9.figshare.24086985
title: Supplementary Material for: A 4-variable model to predict cardio-kidney events and mortality in chronic kidney disease: The Chronic Renal Insufficiency Cohort (CRIC) Study

description: Introduction Current prognostic models for CKD are complex and were designed to predict one single outcome. We aimed to develop and validate a simple and parsimonious prognostic model to predict cardio-kidney events and mortality. Methods Patients from the CRIC Study (n=3718) were randomly divided into derivation (n=2478) and validation (n=1240) cohorts. Twenty-nine candidate variables were pre-selected. Multivariable Cox regression models were developed using stepwise selection for various cardio-kidney endpoints, namely: i) the primary composite outcome of 50% decline in eGFR from baseline, end-stage renal disease or cardiovascular mortality; ii) hospitalization for heart failure (HHF) or cardiovascular mortality; iii) 3-point major CV endpoints (3P-MACE); iv) all-cause death. Results During a median follow-up of 9 years, the primary outcome occurred in 977 patients of the derivation cohort and 501 patients of the validation cohort. Log-transformed NT-proBNP, log-transformed hs-cTnT, log-transformed albuminuria and eGFR were the dominant predictors. The primary outcome risk score discriminated well (c-statistic=0.83) with a proportion of events of 11.4% in the lowest tertile of risk and 91.5% in the highest tertile at 10 years. The risk model presented good discrimination for HHF or cardiovascular mortality, 3P-MACE and all-cause death (c-statistic=0.80, 0.75 and 0.75, respectively). The 4-variable risk model achieved similar c-statistics for all tested outcomes in the validation cohort. The discrimination of the 4-variable risk model was mostly superior to that of published models. Conclusion The combination of NT-proBNP, hs-cTnT, albuminuria and eGFR in a single 4-variable model provides a unique individual prognostic assessment of multiple cardio-kidney outcomes in CKD.
DOI: 10.6084/m9.figshare.24126180
title: Supplementary Material for: Pan-Cancer Analysis of the Prognostic and Immunological Role of SMG5: A biomarker for cancers

description: Introduction: SMG5 is involved in tumor cell development and viewed as a potential target for immunotherapy. The purpose of this study was to systematically analyze the expression level, function and prognostic value of SMG5 in pan-cancers. Methods: Differential expression of SMG5 in normal and tumor tissues was analyzed using The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression database (GTEx) data. Survival analysis was performed by Kaplan-Meier (KM) method and Cox risk regression. The relationship between SMG5 expression and lymphocyte abundance, tumor cell immune infiltration level, molecular and immune subtypes, as well as immune checkpoints were analyzed by Tumor-immune system interactions database (TISIDB), Tumor Immune Estimation Resource (TIMER) and Sangerbox databases. The correlation between SMG5 and immune scores was studied using the Estimation of Stromal and Immune cells in Malignant Tumours using Expression data (ESTIMATE) algorithm. Further, drug sensitivity analysis of SMG5 with low-grade glioma (LGG) was conducted using the CellMiner database. Results: SMG5 was highly expressed in 23 tumors and only had a significant impact on the prognosis of patients with LGG only. In addition, in tumor microenvironment and tumor immune analysis, we found that the level of immune infiltration, tumor mutational load (TMB), microsatellite instability (MSI) and immune checkpoints of LGG were significantly correlated with SMG5 expression. Furthermore, SMG5 was significantly associated with immune scores, stromal scores and sensitivity of some drugs in LGG. Conclusion: SMG5 is differentially expressed in several cancers and is significantly associated with prognosis, immune microenvironment and immune checkpoints in LGG patients. Therefore, SMG5 could be a potential pan-cancer biomarker and an immunotherapeutic target for LGG.
DOI: 10.25582/data.2021-07.2279843/2044516
title: Data for EMSL Project 51127 from July 2021
DOI: 10.25582/data.2021-07.2283538/2044517
title: Data for EMSL Project 51127 from July 2021
DOI: 10.25582/data.2021-07.2283665/2044518
title: Data for EMSL Project 51127 from July 2021
DOI: 10.6084/m9.figshare.22696309
title: Ketamine evoked disruption of entorhinal and hippocampal spatial maps

description: <em>Companion code located at https://github.com/GiocomoLab/Masuda_et_al_2023</em> MEC_Neuropixels.zip <em>MEC spike times and behavior from acute Neuropixels insertions during a 1D VR linear track task</em> File names: [animal name]_[date]_baseline1_controlinjx1_ketamine1fr_corr.mat lickt = lick timestamps, of IR beam breaks lickx = position of animal at lick times post = timestamps of 50 Hz VR frames posx = position of animal at each VR frame speed = speed of animal at each VR frame trial = trial at each VR frame spike_depth: depth along electrode of peak channel of each cell all_cellCorrScore = correlation score between a trial and the baseline spatial template all_cellStabilityScore = spatial stability for each cell on each trial all_corrmatrix = firing correlation of each cell between each pair of trials all_drugEffectScores = [ketamine FR diff, control FR diff, ketamine FR effect score, ketamine corr effect score, spike depth] for each cell FR effect score = the ratio ketamine vs control of the differences between the avg FR of the pre-injection trials and the the avg FR of the equivalent number of trials post-injection corr effect score = difference between the average of the corrScore in the 25 trials before ketamine and the average of the corrScore in the 25 trials after ketamine appication all_fr = mean firing rate per cell per trial per spatial bin all_fr_smoothed = save as all_fr, smoothed with Gaussian kernel all_frTime = firing rate of each cell averaged over each VR frame all_peakiness = mean crest factor of each cell all_spatialinfo = mean spatial information of each cell all_spatialInfoCurve = spatial information of each cell on each trial all_spike_idx = spike times for each cell, in VR bins all_waveforms = waveforms of each cell avg_all_cellCorrScore = avarge cellCorrScores curves for each trial avg_all_corrmatrix = trial by trial correlation for all cells avg_all_fr: mean firing rate per position bin per trial over all cells avg_cell_fr: mean firing rate over full session per cell CA1_miniscope.zip <em>CA1 calcium transients from 1-photon imaging during a freely moving context exploration</em> Folder names: M[mouse number][F for female, nothing for male] behavIndividualsf.mat neuronIndivisualsf.mat sessions.mat thresh.mat