Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of complex modeling strategies for prediction of a binary outcome based on a few, highly correlated predictors

Motivated by a clinical prediction problem, a simulation study was performed to compare different approaches for building risk prediction models. Robust prediction models for hospital survival in patients with acute heart failure were to be derived from three highly correlated blood parameters measured up to four times, with predictive ability having explicit priority over interpretability. Methods that relied only on the original predictors were compared with methods using an expanded predictor space including transformations and interactions. Predictors were simulated as transformations and combinations of multivariate normal variables which were fitted to the partly skewed and bimodally distributed original data in such a way that the simulated data mimicked the original covariate structure. Different penalized versions of logistic regression as well as random forests and generalized additive models were investigated using classical logistic regression as a benchmark. Their performance was assessed based on measures of predictive accuracy, model discrimination, and model calibration. Three different scenarios using different subsets of the original data with different numbers of observations and events per variable were investigated. In the investigated setting, where a risk prediction model should be based on a small set of highly correlated and interconnected predictors, Elastic Net and also Ridge logistic regression showed good performance compared to their competitors, while other methods did not lead to substantial improvements or even performed worse than standard logistic regression. Our work demonstrates how simulation studies that mimic relevant features of a specific data set can support the choice of a good modeling strategy.
Flotillin: A Promising Biomarker for Alzheimer’s Disease

Alzheimer’s disease (AD) is characterized by the accumulation of beta amyloid (Aβ) in extracellular senile plaques and intracellular neurofibrillary tangles (NFTs) mainly consisting of tau protein. Although the exact etiology of the disease remains elusive, accumulating evidence highlights the key role of lipid rafts, as well as the endocytic pathways in amyloidogenic amyloid precursor protein (APP) processing and AD pathogenesis. The combination of reduced Aβ42 levels and increased phosphorylated tau protein levels in the cerebrospinal fluid (CSF) is the most well established biomarker, along with Pittsburgh compound B and positron emission tomography (PiB-PET) for amyloid imaging. However, their invasive nature, the cost, and their availability often limit their use. In this context, an easily detectable marker for AD diagnosis even at preclinical stages is highly needed. Flotillins, being hydrophobic proteins located in lipid rafts of intra- and extracellular vesicles, are mainly involved in signal transduction and membrane–protein interactions. Accumulating evidence highlights the emerging implication of flotillins in AD pathogenesis, by affecting APP endocytosis and processing, Ca2+ homeostasis, mitochondrial dysfunction, neuronal apoptosis, Aβ-induced neurotoxicity, and prion-like spreading of Aβ. Importantly, there is also clinical evidence supporting their potential use as biomarker candidates for AD, due to reduced serum and CSF levels that correlate with amyloid burden in AD patients compared with controls. This review focuses on the emerging preclinical and clinical evidence on the role of flotillins in AD pathogenesis, further addressing their potential usage as disease biomarkers.
Assessment of oral health literacy among patients attending Malabar dental college and research centre in Kerala: A cross sectional survey

Introduction: Oral health literacy is relatively a new, but critical concept to decrease disparities and increase oral health for all. Low oral health literacy contributes to oral disease which results in increased cost for vulnerable population such as poor, those with low levels of education, minorities, and the elderly. Aim: To assess oral health literacy among patients attending Malabar dental college and research centre in Kerala. Materials and Methods: Health literacy in dentistry scale questionnaire with 29 items was administered by the investigator to collect data related to oral health literacy among 272 patients attending Malabar Dental College and Research Centre. The collected data were compiled and statistically analyzed using Chi-square test. Results: The oral health literacy was assessed based on the interquartile range, of 272 patients, 23.9% of patients had poor oral health literacy, 57% were found to have moderate oral health literacy, and 19.1% patients were found to have good oral health literacy. The results were significant at P < 0.001. Conclusion: Oral health literacy was found to be moderate among patients attending Malabar Dental College and Research Centre.
HIV-2: A summary of present standard of care and treatment options for HIV-2 infected individuals living in Western Europe.

HIV-2 infection is endemic in some countries in West Africa. Due to the lower prevalence in industrialized countries, there is limited experience and knowledge on management of HIV-2 infected individuals in Europe. Compared to HIV-1, there are differential characteristics of HIV-2 regarding diagnostic procedures, clinical course and, most importantly, antiretroviral therapy. We integrated the published literature on HIV-2 (studies and reports on epidemiology, diagnostics, clinical course, treatment) as well as expert experience in diagnosing and clinical care of HIV-2 infected to provide recommendations for a present standard of medical care of HIV- infected in Western European countries, including an overview of strategies for diagnosis, monitoring and treatment, with suggestions for effective drug combinations for first- and second line treatment, post-exposure prophylaxis and prevention of mother-to-child transmission as well as listings of mutations related to HIV-2 drug resistance- and CCR5/CRCX4 co-receptor tropism.
A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models

MOTIVATION Epistasis reflects the distortion on a particular trait or phenotype resulting from the combinatorial effect of two or more genes or genetic variants. Epistasis is an important genetic foundation underlying quantitative traits in many organisms as well as in complex human diseases. However, there are two major barriers in identifying epistasis using large genomic data sets. One is that epistasis analysis will induce over-fitting of an over-saturated model with the high-dimensionality of a genomic dataset. Therefore, the problem of identifying epistasis demands efficient statistical methods. The second barrier comes from the intensive computing time for epistasis analysis, even when the appropriate model and data are specified. RESULTS In this study, we combine statistical techniques and computational techniques to scale up epistasis analysis using empirical Bayesian Elastic Net (EBEN) models. Specifically, we first apply a matrix manipulation strategy for pre-computing the correlation matrix and pre-filter to narrow down the search space for epistasis analysis. We then develop a parallelized approach to further accelerate the modeling process. Our experiments on synthetic and empirical genomic data demonstrate that our parallelized methods offer tens of fold speed-up in comparison with the classical EBEN method which runs in a sequential manner. We applied our parallelized approach to a yeast dataset, and we were able to identify both main and epistatic effects of genetic variants associated with traits such as fitness. AVAILABILITY The software is available at github.com/shilab/parEBEN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Chemical Bleaching to Minimize Fluorescence Interference in Raman Spectroscopic Measurements for Sulfonated Polystyrene Solutions

Auto-fluorescence is a significant challenge for Raman spectroscopic analyses. Since fluorescence is a much stronger phenomenon than Raman scattering, even trace fluorescent impurities can overwhelm the Raman signal. Strategies to minimize fluorescence interference in Raman measurements include either an instrumental-based approach or treatment of the sample itself to minimize fluorescence. Efforts focused on sample-based treatments to reduce fluorescence interferences have generally focused on sample purification and photobleaching methodologies. In this work, we present a sample treatment approach based upon chemical bleaching to remove fluorescence from Raman measurements of aqueous solutions of sulfonated polystyrene (SPS). Synthetic batches of SPS are characterized by a wide variation in fluorescence from minimum to a catastrophic level, which greatly limits the use of Raman spectroscopy. We systematically investigate the efficacy of various sample-based treatments of the SPS samples. An important acceptance criterion is that the procedure effectively and reliably removes fluorescence without damaging the SPS component. The chemical bleaching, which involves the addition of hydrogen peroxide and incubation at 60 ℃, is found to be highly effective. The parameters affecting the bleaching efficacy are studied, including temperature, hydrogen peroxide dosage, and bleaching time. Classification models are then developed based on the drastically diverse fluorescence background levels in Raman spectra of SPS to help optimize bleaching time for each specific sample. This work serves as an example of using chemical bleaching to remove fluorescence, which is inexpensive and readily available. It can facilitate a broader use of Raman spectroscopy as a quantitative qualitative control method in industrial settings.
Mindfulness-based cognitive therapy reduces clinical symptoms, but do not change frontal alpha asymmetry in people with major depression disorder

Abstract Objectives Mindfulness-based cognitive therapy (MBCT) has demonstrated to be successful in the reduction of relapse rates in patients with recurrent major depressive disorder (MDD). Little is known if MBCT is effective for treating individuals with current MDD episode and about underlying psychophysiological mechanisms of symptoms reduction. The aim of the present study was to assess effects of MBCT on depressed individuals in terms of reduction of depressive and anxiety symptoms and to evaluate if this therapeutic improvement would be reflected on neurophysiological level by shift in frontal alpha asymmetry (FAA). Participants We studied 20 individuals with current MDD. Design Participants were randomly assigned either to waiting list or 8-week MBCT. Before and after the treatment we have assessed depression, anxiety, and FAA in resting-state electroencephalogram (EEG) – an indicator of approach vs. withdrawal-related response dispositions and a vulnerability factor of MDD. Results In line with previous findings, reduction of depressive and anxiety symptoms, but no change in mean values of FAA in MBCT group was found. Conclusions These results provide a support for the beneficial effects of MBCT in current MDD treatment, however, they do not support the hypothesis on alpha asymmetry change as a neural correlate of MDD improvement.
Structure-Based Design of Antivirals against Envelope Glycoprotein of Dengue Virus

Dengue virus (DENV) presents a significant threat to global public health with more than 500,000 hospitalizations and 25,000 deaths annually. Currently, there is no clinically approved antiviral drug to treat DENV infection. The envelope (E) glycoprotein of DENV is a promising target for drug discovery as the E protein is important for viral attachment and fusion. Understanding the structure and function of DENV E protein has led to the exploration of structure-based drug discovery of antiviral compounds and peptides against DENV infections. This review summarizes the structural information of the DENV E protein with regards to DENV attachment and fusion. The information enables the development of antiviral agents through structure-based approaches. In addition, this review compares the potency of antivirals targeting the E protein with the antivirals targeting DENV multifunctional enzymes, repurposed drugs and clinically approved antiviral drugs. None of the current DENV antiviral candidates possess potency similar to the approved antiviral drugs which indicates that more efforts and resources must be invested before an effective DENV drug materializes.
Screen Exposure during Early Life and the Increased Risk of Astigmatism among Preschool Children: Findings from Longhua Child Cohort Study

Screen media usage has become increasingly prevalent in daily life with children being exposed to screens at an early age. This is a growing public health concern with evidence linking screen exposure to detrimental health outcomes, whereas relationship between screen exposure and the presence of astigmatism among preschoolers remains unknown, thus we aimed to resolve this issue. During the 2017 survey of the Longhua Child Cohort Study, data of 29,595 preschoolers were collected via a caregiver-reported questionnaire regarding socio-demographics, screen exposure and refraction. Cox regression models were adopted to generate adjusted prevalence ratios (APR) and 95% confidence intervals (CI) to estimate the association between early screen exposure and astigmatism. 28,029 preschoolers were included in the final analysis. After adjustment for potential confounders, screen exposure during early life was significantly associated with the increased risk of astigmatism (APR and 95% CI: 2.25, 1.76–2.88), and the greatest risk was observed in the period from birth to 1-year (APR and 95% CI: 3.10, 2.41–3.98). The risk of astigmatism increased with both the total years of exposure and the average daily duration of screen exposure. Our findings suggested that preschoolers who were exposed to screens during early life might have an increased risk of astigmatism.
Contribution of Accessibility & Convenience as Adoption Tool of e-Banking in Ghana .

 Abstract— The aim of the study is to identify the determinants of adoption rate of e banking in Ghana. The data were collected with self-administered questionnaire and interview. The Questionnaires were distributed to only current account holders of commercial banks and who visit the bank at least twice in a week in the greater Accra region of Ghana and 310 out of 500 completed questionnaires were collected from the respondents. Descriptive analysis, mean, standard deviation, Cronbach’s Alpha, Pearson correlation and regression analysis, were performed to analyze the data. The findings revealed that both dimensions: convenience and accessibility had a significant and positive relationship with adoption rate. The study suggested that Managements of commercial banks in Ghana should strive to introduce banking through constant communication of its benefit to clients.
Predicting Developers' Negative Feelings about Code Review

During code review, developers critically examine each others' code to improve its quality, share knowledge, and ensure conformance to coding standards. In the process, developers may have negative interpersonal interactions with their peers, which can lead to frustration and stress; these negative interactions may ultimately result in developers abandoning projects. In this mixed-methods study at one company, we surveyed 1,317 developers to characterize the negative experiences and cross-referenced the results with objective data from code review logs to predict these experiences. Our results suggest that such negative experiences, which we call “pushback”, are relatively rare in practice, but have negative repercussions when they occur. Our metrics can predict feelings of pushback with high recall but low precision, making them potentially appropriate for highlighting interactions that may benefit from a self-intervention.
Structure for Dynamic Facet Ordering in E-commerce

— faceted scrutinizing is broadly utilized in Web shops and item examination destinations. In these cases, a fixed arranged rundown of aspects is frequently utilized. This methodology experiences two fundamental issues. Initial, one needs to contribute a lot of time to devise a viable rundown. Second, with a fixed rundown of aspects it can happen that a feature winds up futile if all items that match the inquiry are related to that specific aspect. In this work, we present a structure for dynamic feature requesting in web based business. In view of measures for particularity and scattering of feature esteems, the completely robotized calculation positions those properties and aspects on top that lead to a brisk drill-down for any conceivable target item. As opposed to existing arrangements, the structure tends to online business explicit viewpoints, for example, the likelihood of various snaps, the gathering of aspects by their comparing properties, and the wealth of numeric features. In an enormous scale reenactment and client consider, our methodology was, by and large, positively contrasted with a feature rundown made by space specialists, a ravenous methodology as gauge, and a cutting edge entropy-based arrangement.
Carboxylated Chitosan Nanocrystals: Novel Synthetic Route and Application as Superior Support for Gold-Catalyzed Reactions

Chitin nanocrystals (ChNCs) were prepared by partial cleavage of glycosidic bonds in chitin with concurrent oxidation of chitin C6 primary alcohols to produce carboxylate groups on the surface of the ChNCs. Following alkaline deacetylation of the ChNCs in the presence of NaBH4 to inhibit “end-peeling” afforded chitosan nanocrystals (ChsNCs) with a degree of deacetylation (DDA) >80%. Transmission electron microscopy (TEM), X-ray diffraction (XRD) and Fourier-transform Infrared (FTIR) spectroscopy were used to determine the morphology and composition of these carboxylated ChNCs and ChsNCs. Subsequently, two methods were used to deposit Au onto the nanocrystals, and the catalytic activities of the resulting biomass-based nanocatalysts were tested for the 4-nitrophenol reduction and the aldehyde-amine-alkyne (A3) coupling reaction. In particular, Au nanoparticles over ChsNCs featured the highest turnover frequency value for the 4-nitrophenol reduction reported to date. Spectroscopic and imaging techniques confirmed the importance of controlling precisely the redox state of Au as it is being deposited to afford highly disperse active site on the bio-nano-support.
GENETIC ENHANCEMENT OF MICRONUTRIENT CONTENT IN CEREALS

ICAR-Indian Agricultural Research Institute’s Regional Research Centre, Dharwad, 580 005, Karnataka, India ICARIndian Institute of Millets Research(IIMR), Hyderabad, Telangana, 500030, India ICAR-Indian Agricultural Research Institute (IARI), Maize Genetics Unit, New Delhi, 110012, India ICAR-Indian Agricultural Research Institute (IARI), Pearl millet Unit, New Delhi, 110012, India ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, Haryana, 132 001, India ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, 753 006, India. JN Medical College, KLE Academy of Higher Education & Research, Belagavi, 590010, India Karnataka University, Dharwad (KUD), 580 003, Karnataka, India ICAR Research Complex for Eastern Region (RCER), Patna 800 014, Bihar, India *Corresponding author’s email: jsbhat73@gmail.com Email addresses of coauthors: bs_patil2000@yahoo.com, hariprasannak@yahoo.com, fh_gpb@yahoo.com, pmvignesh@yahoo.co.in, ganapati4121@gmail.com, MG.Mallikarjuna@icar.gov. in, raj_gpb@yahoo.com, sumerpalsingh@yahoo.com, mukeshsankar@gmail.com, triptisinghal16@gmail.com, kv4515gpb@gmail.com, vikasdwr@gmail.com, mriduliari@gmail.com, krishnenducrri@gmail.com, shridhar.kleskf@gmail.com, murigendra@gmail.com, akicar1968@gmail.com
Modeling of surface tension of microdroplets with surfactants

This research work investigates the modeling of surface tension and surfactant of micro droplets. A parallel volume of fluid code has been developed to simulate interfacial flows with surface tension and surfactant. The continuity, momentum and energy equations were used to formulate the governing equations for the problem. The governing equations were dimensionalised and the resulting equations were solved with variable separable and Eigen function expansion method. Pressure gradient was varied and also considered with and without surfactants. The results obtained shows that harmonic pressure gradient with more concentration of surfactant is smooth, more stable and shows good agreement with experimental data and theory.
NCCRP-1 Might Not be a Marker of so Called NCC Cells in Common Carp (Cyprinus carpio) Leukocytes

The purpose of this study was to verify whether NCCRP-1 is a marker of a unique type of cells in teleost, so-called NCC, or an ubiquitin, like in cytotoxic cells. Therefore, common carp peripheral blood leukocytes were isolated and tested for the binding of fluorescent NCCRP-1 antibody to stained MAIT, γδ T and T cells following stress treatments. The results were analyzed by a confocal microscope. The results revealed the presence of NCCRP-1 in γδ T, MAIT and T cells in more than one type of leukocytes. γδ T cells were the dominant population in carp leukocytes. Therefore, it was concluded that there might be no presence of NCC cells in the common carp leukocytes and that the NCC marker,NCCRP-1, acts probably as an ubiquitin in cytotoxic cells such as γδ T and MAIT cells, which were abundant in peripheral blood leukocytes of common carp.
Evaluation of Adherence to Drug Treatment in Patients with Rheumatoid Arthritis

Objectives: The aim of this study was to measure the frequency of medication adherence in rheumatoid arthritis (RA)patients and to assess factors affecting it, deal with some factors to improve adherence and reevaluate after six months.Methods: A prospective cohort interventional study of 100 patients with RA under treatment fulfilled the American Collegeof Rheumatology / European League against Rheumatism (ACR/EULAR) criteria. All patients subjected to full historytaking including socio-demographic data, medication and clinical examination, Assessment of disease activity by DAS28,functional ability by Health Assessment Questionnaire (HAQ) score, pain by Visual Analogue Scale (VAS) scale, adherenceto treatment by Compliance Questionnaire of Rheumatology (CQR) and Power Doppler U/S for both metacarophalangealand wrist joints were done at baseline and after 6 months at the end of the study. Analysis of factors of non-adherence was done at baseline before intervention. Results: The baseline adherence rate (CQR80) was 37%. The cost of medication (62%), non-availability of medication in pharmacy (59%), lack of belief in the benefit of treatment (38%) forgetting the medication (37%) ,poor provider-patient relationship (25%), inadequate follow up (23%) and polypharmacy (20%) were the most common causes of non adherence in non adherent patients (p 0.05). Adherent patients to drug treatment were younger, living inside Cairo, with higher level of education and nonsmoker. Non-adherent patients had longer morning stiffness duration (p=0.013), more tender joints, higher DAS28 and HAQ scores, higher ESR and CRP titer (p<0.001) and higher frequency of active synovitis in Doppler ultrasound. They also had significantly more frequency of having medications on their expense (p<0.001). After 6 months of follow up and trying to correct the causes of non-adherence, the adherence rate increased to 69% and this associated with improvement in disease activity, functional state and ultrasongraphic findings. Conclusion: Adherence rate to drug treatment in RA patients at baseline was low (37%). It was associated with higher disease activity, functional disability. Patient education, financial support, good physician-patient relationship and simplification of the prescription were found to improve the patient adherence to treatment and to control disease activity after follow up. [Egypt J Rheumatology & Clinical Immunology, 2016; 4(1): 81-92]