Miracle-dz/UniFAR-FTUs huggingface dataset:
A radiomics model of contrast-enhanced computed tomography for predicting post-acute pancreatitis diabetes mellitus

Background Diabetes mellitus can occur after acute pancreatitis (AP), but the accurate quantitative methods to predict post-acute pancreatitis diabetes mellitus (PPDM-A) are lacking. This retrospective study aimed to establish a radiomics model based on contrast-enhanced computed tomography (CECT) for predicting PPDM-A. Methods A total of 374 patients with first-episode AP were retrospectively enrolled from two tertiary referral centers. There were 224 patients in the training cohort, 56 in the internal validation cohort, and 94 in the external validation cohort, and there were 86, 22, and 27 patients with PPDM-A in these cohorts, respectively. The clinical characteristics were collected from the hospital information system. A total of 2,398 radiomics features, including shape-based features, first-order histogram features, high order textural features, and transformed features, were extracted from the arterial- and venous-phase CECT images. Intraclass correlation coefficients were used to assess the intraobserver reliability and interobserver agreement. Random forest-based recursive feature elimination, collinearity analysis, and least absolute shrinkage and selection operator (LASSO) were used for selecting the final features. Three classification methods [eXtreme Gradient Boosting (XGBoost), Adaptive Boosting, and Decision Tree] were used to build three models and performances of the three models were compared. Each of the three classification methods were used to establish the clinical model, radiomics model, and combined model for predicting PPDM-A, resulting in a total of nine classifiers. The predictive performances of the models were evaluated by the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1-score. Results Eleven radiomics features were selected after a reproducibility test and dimensionality reduction. Among the three classification methods, the XGBoost classifier showed better and more consistent performances. The AUC of the XGBoost’s radiomics model to predict PPDM-A in the training, internal, and external cohorts was good (0.964, 0.901, and 0.857, respectively). The AUC of the XGBoost’s combined model to predict PPDM-A in the training, internal, and external cohorts was good (0.980, 0.901, and 0.882, respectively). The AUC of the XGBoost’s clinical model to predict PPDM-A in the training, internal, and external cohorts did not perform well (0.685, 0.733, and 0.619, respectively). In the external validation cohort, the AUC of the XGBoost’s radiomics model was significantly higher than that of the clinical model (0.857 vs. 0.619, P<0.001), but there was no significant difference between the combined and radiomics models (0.882 vs. 0.857, P=0.317). Conclusions The radiomics model based on CECT performs well and can be used as an early quantitative method to predict the occurrence of PPDM-A.
Relevance of histopathological findings for predictive scoring of short-term treatment response to plasma exchange in severe ANCA-associated renal vasculitides

Introduction Rapidly progressive glomerulonephritis (RPGN) is characterized by a rapid loss of kidney function, affecting both renal and overall patient survival. Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a small vessel vasculitis affecting multiple organ systems including the kidney, and among most frequent causes of RPGN. We here aimed to validate a recently described scoring system for short-term treatment response to therapeutic plasma exchange (PLEX) in a well-characterized and independent cohort of severe renal AAV presenting with RPGN. Furthermore, we compared this scoring with established classification systems in renal AAV including histopathological findings. Methods We here directly compare the scoring system with retrospective data about PLEX treatment in our own clinical practice and according to current recommendations in a cohort of 53 patients with severe AAV presenting with RPGN confirmed by kidney biopsy. Results We here confirm that PLEX scoring is capable to identify patients at risk for short-term poor outcome in severe AAV presenting with RPGN (p<0.0001). Furthermore, multiple stepwise regression analysis revealed that the PLEX score with renal biopsy performed best to predict poor outcome in this patient population (p<0.0001). Conclusion Our observations underscore the relevance of performing a kidney biopsy in this patient population that is often challenged in the setting of intensive care treatment, requirement of KRT with need for anticoagulation and bleeding risk. Therefore, validation of our observations and this recent scoring system for treatment response to PLEX in independent cohorts would be of great clinical relevance in the treatment of patients with severe AAV presenting with RPGN.
Stress and Deformation Analysis of Prestressed Wound Composite Components with an Arch-Shaped Metal Liner

The stress distribution in prestressed filament wound components plays a crucial role in determining the quality of these components during their operational lifespan. This article proposes a physical model to analyze the stress and deformation of prestressed wound composite components with arch-shaped sections. Drawing upon the principles of beam theory, we delve into the analysis of prestressed wound components with metal liners featuring arch-shaped sections. Our investigation revealed a noteworthy phenomenon termed the “additional bending moment effect” within prestressed wound components with arch-shaped sections. Furthermore, this study establishes a relationship between this additional bending moment and the external pressure. In addition, a 3D finite element (FE) model for prestressed wound components with arch-shaped sections incorporating metal liners was developed. The model’s accuracy was validated through a comparison with prestressed wound experiments, showcasing an error margin of less than 2%. In comparison with prestressed wound components with circular cross-sections under identical load and dimensional parameters, it was observed that prestressed wound components with arch-shaped sections exhibit stress distributions in the arc segments akin to their circular counterparts, with differences not exceeding 5%. Notably, when the ratio of the straight segment length to the inner diameter of the arc segment inner is less than 4, the deformation on the symmetric plane of the arc segment in an arch-shaped component can be effectively considered as the summation of deformations in equivalent-sized arc and straight segments under identical loading conditions. This yields an equivalent physical model and a streamlined analysis and design methodology for describing the deformation characteristics of prestressed wound components with arch-shaped sections.
MAVEN observations of a giant ionospheric flux rope near Mars resulting from interaction between the crustal and interplanetary draped magnetic fields

We present Mars Atmosphere and Volatile EvolutioN (MAVEN) observations of a giant magnetic flux rope in the Martian dayside ionosphere. The flux rope was observed at an altitude of <300 km, downstream from strong subsolar crustal magnetic fields. The peak field amplitude was ∼200 nT, resulting in the largest difference between the observed magnetic field strength and a model for crustal magnetic fields of the entire MAVEN primary science phase. MAVEN detected planetary ions, including H+, O+, and O2+ , across the structure. The axial orientation estimated for the flux rope indicates that it likely formed as a result of interactions between the local crustal and overlaid draped interplanetary magnetic fields. Pitch angle distributions of ionospheric photoelectrons imply that this structure is connected to the Martian upper atmosphere. However, the flux rope is not present in observations at the next commensurable orbit crossing (approximately two Martian days later), implying that it eventually detaches from the atmosphere and is carried downstream. The flux rope observations occurred during an interplanetary coronal mass ejection event at Mars, suggesting that the disturbed upstream state played a role in allowing the interplanetary magnetic field to penetrate deeper into the Martian ionosphere than is typical, allowing the formation of the flux rope.
Integrated Analysis of Single-Cell and Bulk RNA Sequencing Data Reveals Memory-like NK Cell Subset Associated with Mycobacterium tuberculosis Latency

Natural killer (NK) cells are innate-like lymphocytes that belong to the family of type-1 innate lymphoid cells and rapidly respond to virus-infected and tumor cells. In this study, we have combined scRNA-seq data and bulk RNA-seq data to define the phenotypic and molecular characteristics of peripheral blood NK cells. While the role of NK cells in immune surveillance against virus infections and tumors has been well established, their contribution to protective responses to other intracellular microorganisms, such as Mycobacterium tuberculosis (Mtb), is still poorly understood. In this study, we have combined scRNA-seq data and bulk RNA-seq data to illuminate the molecular characteristics of circulating NK cells in patients with active tuberculosis (TB) disease and subjects with latent Mtb infection (LTBI) and compared these characteristics with those of healthy donors (HDs) and patients with non-TB other pulmonary infectious diseases (ODs). We show here that the NK cell cluster was significantly increased in LTBI subjects, as compared to patients with active TB or other non-TB pulmonary diseases and HD, and this was mostly attributable to the expansion of an NK cell population expressing KLRC2, CD52, CCL5 and HLA-DRB1, which most likely corresponds to memory-like NK2.1 cells. These data were validated by flow cytometry analysis in a small cohort of samples, showing that LTBI subjects have a significant expansion of NK cells characterized by the prevalence of memory-like CD52+ NKG2C+ NK cells. Altogether, our results provide some new information on the role of NK cells in protective immune responses to Mtb.
Antidiabetic and antioxidant effects of Croton lobatus L. in alloxan-induced diabetic rats

Background: Croton lobatus contains a high amount of antioxidant phytochemicals that probably account for its wide use as food and medicine in the traditional communities of West Africa. Methods: The study evaluated the modulatory role of methanol extract of Croton lobatus leaf on alloxan-induced diabetes and associated cardiovascular complications. Male rats were randomly selected and assigned to one of six groups (A to F) of eight animals each: A (distilled water); B (corn oil); C (Alloxan); D (Alloxan + 100 mg kg-1 Croton lobatus); E: (Alloxan + 200 mg kg-1 C. lobatus); and F (Alloxan + 100 mg kg-1 glibenclamide). Results: Acute toxicity studies revealed no mortality of rats at the administration of different doses of extract up to the 5,000 mg kg-1 dose. Histology of the pancreas showed focal area of necrosis, and fatty infiltration in diabetic untreated rats, but these lesions were absent in pancreas of rats treated with C. lobatus extract. Conclusion: Methanol leaf extract of C. lobatus reduced arteriogenic risk factors, improved antioxidant status, restored the observable pathological lesions associated with experimental diabetes in rats, and thus offers a new therapeutic window as herbal therapy for the treatment of diabetes mellitus and associated cardiovascular complications.
Knowledge of Sexually Transmitted Infections and HIV among People Living with HIV: Should We Be Concerned?

Poor knowledge of sexually transmitted infections (STIs) and HIV among people with HIV (PLHIV) could worsen life quality. We aimed to investigate their STI and HIV knowledge, disclosure and undetectable = untransmittable (U=U). We proposed an anonymous questionnaire regarding STI and HIV to PLHIV attending ten Italian outpatient infectious diseases clinics. Moreover, disclosure and U=U were investigated. The calculated sample size was 178 people. Considering a missing response of 10%, the final sample size was 196. We enrolled 200 PLHIV (73.5% males), with a median age of 52.5 (IQR 41–59) years. The mean score was 7.61 ± 1.22 with no difference by gender, education, and employment. Significant statistical difference was observed by sexual orientation; bisexuals and those who preferred not to answer had a lower score than heterosexuals and MSM (p = 0.0032). PLHIV showed poor knowledge about HIV transmission (25% appropriately answered). Nearly 30% responded that virologically suppressed PLHIV could transmit the infection. Finally, 137 (68.5%) and 158 (79.0%) disclosed to the general practitioner and family and friends, respectively. Nearly 52.0% knew the meaning of U=U, and 83.6% highlighted its positive rebound. In conclusion, important knowledge gaps are present among PLHIV regarding U=U, and its implications are little-known. Improving PLHIVs’ awareness will undermine self-stigma and enhance life quality.
Combining Qualitative and Quantitative Methods for Soil Erosion Assessments: An Application in a Sloping Mediterranean Watershed, Cyprus

In arid and semi‐arid regions, water erosion is difficult to model because of highly irregular precipitation regimes and changes in vegetation cover. The application of quantitative, process‐based models at the catchment scale is often problematic because of large data requirements. Qualitative methods require less data and can be more easily performed in a relatively short time, but they are more subjective. The objective of this research is to develop an erosion assessment methodology that combines qualitative field surveys with quantitative model estimates. The qualitative World Overview of Conservation Approaches and Technologies (WOCAT) methodology is based on expert observations per mapping unit, while the Pan‐European Soil Erosion Risk Assessment (PESERA) model simulates hill slope soil loss based on land cover, soil texture, meteorological data and slope profile. This study was conducted in the 106·4‐km2 Peristerona watershed in Cyprus with a mean local slope higher than 40% in the mountainous upstream area and less than 8% in the plain. Out of 68 units, PESERA and WOCAT results were in agreement in 40 units, while PESERA results were lower in 25 and higher in 3 units. Both methods identified burnt areas and complex cultivation patterns as the most degraded. The total PESERA‐based sediment yield for the watershed was 1·2 Mg ha−1 y−1, which fell within the range of the sediment yield measured at the check‐dam downstream (0·2–2 Mg ha−1 y−1). This study provides a linkage between qualitative and quantitative soil erosion methods and helps to translate the outcomes of the former into the latter, thus providing a good tool for local erosion assessment. Copyright © 2016 John Wiley & Sons, Ltd.
DRY MATTER, NITROGEN, AND PHOSPHORUS CONTENT OF LITTERFALL AND BRANCHFALL IN PINUS RADIATA AND EUCALYPTUS FORESTS

The mass, nitrogen content, and phosphorus content of litterfall was estimated in five Pinus radiata D. Don and four Eucalyptus forests in Gippsland, Victoria. Litterfall in pines ranged from 258 to 386 g/m 2 /year, and in eucalypts from 388 to 686 g/m 2 /year. Dead foliage was the major component of litterfall in both forest types. Litterfall in eucalypts peaked in summer; in pines it peaked both in spring and in late summer to early autumn. Concentrations of nitrogen and phosphorus in dead foliage varied markedly between seasons but were consistently lowest at times of peak fall of dead foliage. The nutrient content of litterfall in pines ranged from 1400 to 2400 mg N/m 2 /year, and 97 to 230 mg P/m 2 /year. In eucalypts, the corresponding ranges were 2100 to 4600 mg N/m 2 /year and 94 to 200 mg P/m 2 /year. In comparison with litter­ fall, branchfall returned only small amounts of nitrogen and phosphorus to the forest floor. Concentrations of nitrogen in litterfall of pine and eucalypt forests were comparable; however, concentrations of phosphorus in pine litterfall were usually greater than those in eucalypt litterfall.
A reassessment of Hardy-Weinberg equilibrium filtering in large sample Genomic studies.

Hardy Weinberg Equilibrium (HWE) is a fundamental principle of population genetics. Adherence to HWE, using a p-value filter, is used as a quality control measure to remove potential genotyping errors prior to certain analyses. Larger sample sizes increase power to differentiate smaller effect sizes, but will also affect methods of quality control. Here, we test the effects of current methods of HWE QC filtering on varying sample sizes up to 486,178 subjects for imputed and Whole Exome Sequencing (WES) genotypes using data from the UK Biobank and propose potential alternative filtering methods. METHODS: Simulations were performed on imputed genotype data using chromosome 1. WES GWAS (Genome Wide Association Study) was performed using PLINK2. RESULTS: Our simulations on the imputed data from Chromosome 1 show a progressive increase in the number of SNPs eliminated from analysis as sample sizes increase. As the HWE p-value filter remains constant at p<1e-15, the number of SNPs removed increases from 1.66% at n=10,000 to 18.86% at n=486,178 in a multi-ancestry cohort and from 0.002% at n=10,000 to 0.334% at n=300,000 in a European ancestry cohort. Greater reductions are shown in WES analysis with a 11.91% reduction in analyzed SNPs in a European ancestry cohort n=362,192, and a 32.70% reduction in SNPs in a multi- ancestry dataset n=463,605. Using a sample size specific HWE p-value cutoff removes ~2.25% of SNPs in the all ancestry cohort across all sample sizes, but does not currently scale beyond 300,000 samples. A hard cutoff of +/- 20% deviation from HWE produces the most consistent results and scales across all sample sizes but requires additional user steps. CONCLUSION: Testing for deviance from HWE may still be an important quality control step in GWAS studies, however we demonstrate here that using an HWE p-value threshold that is acceptable for smaller sample sizes will be inappropriate for large sample studies due to an unnecessarily high number of variants removed prior to analysis. Rather than exclude variants that fail HWE prior to analysis it may be better to include all variants in the analysis and examine their deviation from HWE afterward. We believe that adjusting the cutoffs will be even more important for large whole genome sequencing results and more diverse population studies.
Reliance on vision for walking balance is related to somatosensory deficits in individuals with cerebral palsy

Aim: To investigate the relationship between somatosensory deficits, specifically ankle and hip joint position sense, two-point discrimination, and vibration on the (1) responses to visual perturbations during walking and (2) response improvements to visual perturbations while receiving a sensory-centric treatment, i.e., stochastic resonance (SR) stimulation, in individuals with and without cerebral palsy (CP). Methods: Twenty-eight individuals (14 CP, 14 age-and sex-matched controls) walked in a virtual reality cave while receiving visual perturbations. We applied SR to the ankle and hip joints. Data analysis consisted of bivariate correlations, and multiple regression analysis (MRA) using all four sensory tests as predictors with the responses to visual perturbation and the improvements in the responses when SR is applied as outcomes. Results: We found significant and strong correlations between performance on sensory tests and the responses to visual perturbations, and improvements in the responses with SR. Only one predictor could be entered into the MRA, indicating that performance on any of the sensory tests could predict the responses to visual perturbation and the improvements with SR. Interpretation: Individuals with sensory deficits are more responsive to sensory-centric interventions. This study is an initial step in identifying potential responders to sensory therapies in individuals with CP.
Breakfast Skipping and Associated Factors Among Jordanian University Students

Background: Although breakfast skipping among university students is a significant concern, its prevalence and the contributing factors among university students have received little attention in the literature. This study aims to determine the prevalence of skipping breakfast among Jordanian university students and examine the associated factors and variations in rates of skipping breakfast by day of the week. Materials and Methods: A cross-sectional study was conducted among undergraduate students between March and May 2022 through a self-questionnaire. A convenience sample of 891 students was chosen at four Jordanian public universities. The data were analyzed using descriptive and inferential statistics. Results: The prevalence of skipping breakfast among university students was 66%. The reasons for skipping breakfast were having no time due to oversleeping and having no feeling of hunger (59% for both), followed by having no energy to prepare the breakfast and making no difference (49% and 48%), and not being able to afford to eat or buy breakfast (19%). There is a strong correlation between eating fast food and skipping breakfast. With whom the student eats breakfast is significantly associated with breakfast skipping, revealing that the highest percentages of skipping occur with friends. About 63% of students skipped breakfast through university days compared with 37% on the weekend, while 37% of them had breakfast through university days compared with 67% on the weekend. Conclusions: A high percentage of university students in Jordan skip breakfast. More attention should be paid to correlating factors and developing interventions to help students adhere to the breakfast.
Creating a Medication Therapy Observational Research Database from an Electronic Medical Record: Challenges and Data Curation

Background Observational research has shown its potential to complement experimental research and clinical trials by secondary use of treatment data from hospital care processes. It can also be applied to better understand pediatric drug utilization for establishing safer drug therapy. Clinical documentation processes often limit data quality in pediatric medical records requiring data curation steps, which are mostly underestimated. Objectives The objectives of this study were to transform and curate data from a departmental electronic medical record into an observational research database. We particularly aim at identifying data quality problems, illustrating reasons for such problems and describing the systematic data curation process established to create high-quality data for observational research. Methods Data were extracted from an electronic medical record used by four wards of a German university children's hospital from April 2012 to June 2020. A four-step data preparation, mapping, and curation process was established. Data quality of the generated dataset was firstly assessed following an established 3 × 3 Data Quality Assessment guideline and secondly by comparing a sample subset of the database with an existing gold standard. Results The generated dataset consists of 770,158 medication dispensations associated with 89,955 different drug exposures from 21,285 clinical encounters. A total of 6,840 different narrative drug therapy descriptions were mapped to 1,139 standard terms for drug exposures. Regarding the quality criterion correctness, the database was consistent and had overall a high agreement with our gold standard. Conclusion Despite large amounts of freetext descriptions and contextual knowledge implicitly included in the electronic medical record, we were able to identify relevant data quality issues and to establish a semi-automated data curation process leading to a high-quality observational research database. Because of inconsistent dosage information in the original documentation this database is limited to a drug utilization database without detailed dosage information.