Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis C virus genotype analysis in patients with chronic hepatitis in North Eastern Bulgaria

Abstract Background: The main objective of this study was to analyse the spread of hepatitis C virus (HCV) genotype in patients with chronic liver disease; commenting on the molecular characterization of HCV and gender and age in Varna, Bulgaria. Across Europe and the world, HCV is a significant economic concern and public health crisis. Defined by genotype variations, HCV is the leading cause of chronic liver disease, liver related morbidity, and mortality worldwide. Active examination for asymptomatic patients is essential, initiating early treatment aimed at the specific HCV genotype, effective outcomes, and reducing transmission and mortality in Bulgaria. Methods and materials: Nucleic acid extraction and amplification were performed with commercially available test kits on 115 patients blood samples collected from March 2018 to October 2018. Male (n = 58) (50.43%, 95% CI = 41.29%–59.57%) and female (n = 57) (49.57%, 95% CI = 41.29%–59.57%) samples were equally distributed (mean age = 51.4 years; SD = ±16.5 years; range = 17–87 years old). Results: Genotype 1b predominated (73%, 95% CI = 64.89%–81.11%), followed by high prevalence of 1a (13.9%, 95% CI = 7.58%–20.22%) and 3 genotypes (11.3%, 95% CI = 5.51%–17.09%). Genotypes 2 and 4 were equally the least prevalent (0.9%, 95% CI = −0.83%–2.63%). In genotype 1b, 60.7% were women and 39.3% were men; in genotype 1a, 25% were women and 75% were men; and in genotype 3, only 7.7% were women and 92.3% were men. Males were most prevalent in genotypes 1a (75%) and 3 (92.3%), while women were most prevalent in genotype 1b (60.7%). Conclusions: HCV genotype lb is the predominant variant within the epidemiological pattern of HCV genotypes in patients with chronic liver diseases in North Eastern Bulgaria.
On Secure Simple Pairing in Bluetooth Standard v5.0-Part I: Authenticated Link Key Security and Its Home Automation and Entertainment Applications

Bluetooth is an important technical standard for short-range and low-power wireless communication. The home automation and entertainment (HAE) systems often make use of Bluetooth technology to link different Bluetooth devices and form Bluetooth networks. The security concerns of the HAE systems are raised due to massive deployment of the Bluetooth devices. The Bluetooth standard mainly depends on the secure simple pairing (SSP) solution to protect the Bluetooth devices. Hence, we investigate the SSP solution according to the Bluetooth standard v5.0. The contributions are threefold. (1) A formal security model is proposed to evaluate SSP’s association models and authenticated link key. (2) We formally analyze two SSP protocols and present the security requirements for basic cryptographic modules in these SSP protocols. (3) We discuss the typical SSP applications in the HAE systems. Our results are useful to not only evaluating and designing the SSP protocols but also enhancing the security of the HAE systems in which the Bluetooth access is available.
The Magnitude and Duration of the Effect of Intra-articular Corticosteroid Injections on Pain Severity in Knee Osteoarthritis

Supplemental digital content is available in the text. Objectives The aims of the study were to clarify the evidence on the magnitude and duration of treatment effect of intra-articular corticosteroid injections for knee osteoarthritis compared with placebo, to evaluate a treatment effect by steroid type, and to describe the reported adverse effects. Design Cochrane Controlled Trials Register, Medline, Embase, CINAHL, Scopus, and Web of Science databases were searched. The risk of systematic bias was assessed according to the Cochrane Collaboration’s domain-based evaluation framework. Results The final sample included eight randomized controlled studies with follow-ups from 1 to 26 wks. The risk of systematic bias was considered low in five and high in three studies. The pooled standardized mean difference was −0.58 (95% confidence interval = −0.88 to −0.27) and number needed to treat 5.1 (95% confidence interval = 10.0 to 3.7). The heterogeneity was considerable. The pooled effect size approached the level of statistical insignificance at 4 mos. The pooled risk ratio of adverse effects was insignificant 0.95 (95% confidence interval = 0.34 to 2.55). Conclusions The intra-articular corticosteroid had a mild to moderate effect on pain severity up to 3 mos after the injection—much longer than it had previously been reported. The effect may vary substantially in different patient groups and appropriate patient selection is important. The risk of adverse effects was low.
Association Between Sleep Duration, Obesity, and School Failure Among Adolescents

The aim of this study was to investigate the association between sleep duration, overweight/obesity, and school failure using data obtained from self-reported questionnaires completed by 13- to 15-year-olds in Sweden (n = 1,363; 50.7% female). The height and weight of the participants were measured by school nurses. A multiple logistic regression analysis was used to analyze the association between sleep duration and overweight/obesity, school failure, and perceived economic situation. A short sleep duration (<7 hr) was associated with overweight/obesity (p = .001), school failure (p = .007), and poorer perceived economic situation (p = .004). Modifying the sleep habits of adolescents is a potential target for obesity intervention as well as for improving school success. This information is particularly well suited for school nurses to disseminate to students and their parents.
Upper and lower limb performance fatigability in people with multiple sclerosis investigated through surface electromyography: a pilot study

Objective: Fatigue experienced by people with multiple sclerosis (pwMS) is multidimensional, consisting of different components, such as perceived, physical and cognitive fatigue and performance fatigability. At present, there is no gold standard to assess performance fatigability in pwMS; therefore, we aimed to determine whether, during a fatiguing task, average rectified value (ARV), mean frequency of the power spectrum (MNF), muscle fiber conduction velocity (CV) and fractal dimension (FD) of surface electromyography (sEMG) may be used as indirect indices of performance fatigability. Moreover, we analyzed whether a three-week rehabilitation program impacts on performance fatigability in pwMS, and whether a relationship between sEMG parameters and trait levels of perceived fatigability, before and after rehabilitation, does exist. Approach: Twenty-one pwMS performed a 20% maximal voluntary contraction (MVC) of 1 min, and afterwards a 60% MVC held until exhaustion. sEMG signals were detected from the biceps brachii, vastus medialis and vastus lateralis. Performance fatigability was determined at entry to (t0) and discharge from (t1) rehabilitation. Perceived fatigability was measured at t0 and t2, one month after rehabilitation. Main results: ARV, MNF, CV and FD rates of change showed significant changes at t0 and t1 (p < 0.05) during the high-level contraction in the BB, but rather limited in the vastii muscles. Moreover, rehabilitation did not induce any reductions in either perceived or performance fatigability. No significant correlations between ARV, MNF, CV and FD rates of change during the 60% MVC and perceived fatigability, at t0 and t2, were found. Significance: Our findings suggest that the sEMG parameters are useful for indirectly assessing performance fatigability in pwMS during sub-maximal fatiguing contractions, particularly in the biceps brachii.
Predicting and mapping human risk of exposure to Ixodes ricinus nymphs using climatic and environmental data, Denmark, Norway and Sweden, 2016

Background Tick-borne diseases have become increasingly common in recent decades and present a health problem in many parts of Europe. Control and prevention of these diseases require a better understanding of vector distribution. Aim Our aim was to create a model able to predict the distribution of Ixodes ricinus nymphs in southern Scandinavia and to assess how this relates to risk of human exposure. Methods We measured the presence of I. ricinus tick nymphs at 159 stratified random lowland forest and meadow sites in Denmark, Norway and Sweden by dragging 400 m transects from August to September 2016, representing a total distance of 63.6 km. Using climate and remote sensing environmental data and boosted regression tree modelling, we predicted the overall spatial distribution of I. ricinus nymphs in Scandinavia. To assess the potential public health impact, we combined the predicted tick distribution with human density maps to determine the proportion of people at risk. Results Our model predicted the spatial distribution of I. ricinus nymphs with a sensitivity of 91% and a specificity of 60%. Temperature was one of the main drivers in the model followed by vegetation cover. Nymphs were restricted to only 17.5% of the modelled area but, respectively, 73.5%, 67.1% and 78.8% of the human populations lived within 5 km of these areas in Denmark, Norway and Sweden. Conclusion The model suggests that increasing temperatures in the future may expand tick distribution geographically in northern Europe, but this may only affect a small additional proportion of the human population.
Investigating the Effect of Short Term Responsive VNS Therapy on Sleep Quality Using Automatic Sleep Staging

Objective: The goal of this work is to objectively evaluate the effectiveness of responsive (or closed-loop) Vagus nerve stimulation (VNS) therapy in sleep quality in patients with medically refractory epilepsy. Methods: Using quantitative features obtained from electroencephalography, we first developed a new automatic sleep-staging framework that consists of a multi-class support vector machine (SVM) classification, based on a decision tree approach. To train and evaluate the performance of the framework, we used polysomnographic data of 23 healthy subjects from the PhysioBank database where the sleep stages have been visually annotated. We then used the trained classifier to label the sleep stages using data from 22 patients with epilepsy, treated with short term responsive VNS therapy during an epilepsy-monitoring unit visit, one month after VNS implantation, and ten VNS-naïve patients with epilepsy. Results: Application of multi-class SVM classifier to classify the three sleep stages of awake, light sleep + rapid eye movement, and deep sleep achieved a classification accuracy of 90%. Results of the application of this methodology to VNS-treated and VNS-naïve patients revealed that the patients treated with short term responsive VNS therapy showed significant increase in sleep efficiency, and significant decrease in seizures plus interictal epileptiform discharges and awakenings. Conclusion: These results indicate that VNS treatment can reduce the epileptiform activities and thus help in achieving better sleep quality for patients with epilepsy. Significance: The proposed approach can be used to investigate the effect of long-term VNS therapy on sleep quality.
Health Literacy and Outcomes of a Community-Based Self-Help Intervention

Background Although scientific reports increasingly document the negative impact of inadequate health literacy on health-seeking behaviors, health literacy’s effect on health outcomes in patients with diabetes is not entirely clear, owing to insufficient empirical studies, mixed findings, and insufficient longitudinal research. Objective The aim of this study was to empirically examine underlying mechanisms of health literacy’s role in diabetes management among a group of Korean Americans with Type 2 diabetes mellitus. Methods Data from a randomized clinical trial of a health literacy-focused Type 2 diabetes self-management intervention conducted during 2012–2016 in the Korean American community were collected at baseline and at 3, 6, 9, and 12 months. A total of 250 Korean Americans with Type 2 diabetes participated (intervention, 120; control, 130). Participants were first-generation Korean American immigrants. Health literacy knowledge was measured with the original Rapid Estimate of Adult Literacy in Medicine and the diabetes mellitus-specific Rapid Estimate of Adult Literacy in Medicine. Functional health literacy was measured with the numeracy subscale of the Test of Functional Health Literacy in Adults and the Newest Vital Sign screening instrument, which also uses numeracy. Primary outcomes included glucose control and diabetes quality of life. Multivariate analyses included latent variable modeling. Results A series of path analyses identified self-efficacy and self-care skills as significant mediators between health literacy and glucose control and quality of life. Education and acculturation were the most significant correlates of health literacy. Discussion Despite inconsistent findings in the literature, this study indicates that health literacy may indirectly influence health outcomes through mediators such as self-care skills and self-efficacy. The study highlights the importance of health literacy, as well as underlying mechanisms with which health literacy influences processes and outcomes of diabetes self-management.
Automatic and label‐free identification of blood vessels in gliomas using the combination of multiphoton microscopy and image analysis

Currently, the targeted treatment of tumor based on the tumor microenvironment is newly developed. Blood vessels are the key parts in the tumor microenvironment, which is taken as a new visible target for tumor therapy. Multiphoton microscopy (MPM), based on the second harmonic generation and two‐photon excited fluorescence, is available to make the label‐free analysis on the blood vessels in human gliomas. MPM can reveal the vascular morphological characteristics in gliomas, including vascular malformation, intense vascular proliferation, perivascular collagen deposition, perivascular lymphocytes aggregation and microvascular proliferation. In addition, the image analysis algorithms were developed to automatically calculate the perivascular collagen content, vascular cavity area, lumen area, wall area and vessel number. Thus, the vascular morphology, the perivascular collagen deposition and intense vascular proliferation degree can be further quantitatively characterized. Compared with the pathological analysis, the combination of MPM and image analysis has potential advantages in making a quantitative and qualitative analyzing on vascular morphology in glioma microenvironment. As micro‐endoscope and two‐photon fiberscope are technologically improved, this combined method will be a useful imaging way to make the real‐time research on the targeting tumor microenvironment in gliomas.
A Feasibility Study

Background: Pediatric blood and marrow transplant (PBMT) patients experience significant symptom distress. Mobile health (mHealth) technologies can be leveraged to improve understanding of the patient’s symptom experience by providing continuous, real-time, in situ, patient-generated symptom data. This rich data stream can subsequently enhance symptom management strategies. However, limited research has been conducted in this area.
Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer

As a noninvasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma has raised an increasing interest due to diagnostic applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. In this study, we investigated the cfDNA methylation patterns in lung cancer patients by MeDIP-seq. Compared with the healthy individuals, 330 differentially methylated regions (DMRs) at gene promoters were identified in lung cancer patients with 33 hypermethylated and 297 hypomethylated regions, respectively. Moreover, these hypermethylated genes were validated with the publicly available DNA methylation data, yielding a set of ten significant differentially methylated genes in lung cancer, including B3GAT2, BCAR1, HLF, HOPX, HOXD11, MIR1203, MYL9, SLC9A3R2, SYT5, and VTRNA1-3. Our study demonstrated MeDIP-seq could be effectively used for cfDNA methylation profiling and identified a set of potential biomarker genes with clinical application for lung cancer.
Sclerostin antibody treatment rescues the osteopenic bone phenotype of TGFβ inducible early gene‐1 knockout female mice

Deletion of TGFβ inducible early gene‐1 (TIEG) in mice results in an osteopenic phenotype that exists only in female animals. Molecular analyses on female TIEG knockout (KO) mouse bones identified increased expression of sclerostin, an effect that was confirmed at the protein level in serum. Sclerostin antibody (Scl‐Ab) therapy has been shown to elicit bone beneficial effects in multiple animal model systems and human clinical trials. For these reasons, we hypothesized that Scl‐Ab therapy would reverse the low bone mass phenotype of female TIEG KO mice. In this study, wildtype (WT) and TIEG KO female mice were randomized to either vehicle control (Veh, n = 12/group) or Scl‐Ab therapy (10 mg/kg, 1×/wk, s.c.; n = 12/group) and treated for 6 weeks. Following treatment, bone imaging analyses revealed that Scl‐Ab therapy significantly increased cancellous and cortical bone in the femur of both WT and TIEG KO mice. Similar effects also occurred in the vertebra of both WT and TIEG KO animals. Additionally, histomorphometric analyses revealed that Scl‐Ab therapy resulted in increased osteoblast perimeter/bone perimeter in both WT and TIEG KO animals, with a concomitant increase in P1NP, a serum marker of bone formation. In contrast, osteoclast perimeter/bone perimeter and CTX‐1 serum levels were unaffected by Scl‐Ab therapy, irrespective of mouse genotype. Overall, our findings demonstrate that Scl‐Ab therapy elicits potent bone‐forming effects in both WT and TIEG KO mice and effectively increases bone mass in female TIEG KO mice.
Direct removal of RNA polymerase barriers to replication by accessory replicative helicases

Abstract Bacterial genome duplication and transcription require simultaneous access to the same DNA template. Conflicts between the replisome and transcription machinery can lead to interruption of DNA replication and loss of genome stability. Pausing, stalling and backtracking of transcribing RNA polymerases add to this problem and present barriers to replisomes. Accessory helicases promote fork movement through nucleoprotein barriers and exist in viruses, bacteria and eukaryotes. Here, we show that stalled Escherichia coli transcription elongation complexes block reconstituted replisomes. This physiologically relevant block can be alleviated by the accessory helicase Rep or UvrD, resulting in the formation of full-length replication products. Accessory helicase action during replication-transcription collisions therefore promotes continued replication without leaving gaps in the DNA. In contrast, DinG does not promote replisome movement through stalled transcription complexes in vitro. However, our data demonstrate that DinG operates indirectly in vivo to reduce conflicts between replication and transcription. These results suggest that Rep and UvrD helicases operate on DNA at the replication fork whereas DinG helicase acts via a different mechanism.
Construction and dissection of the ceRNA-ceRNA network reveals critical modules in depression

The prevalence of mental health disorders such as depression is high. Depression is a multifactorial disorder and its underlying mechanisms remain unclear. Competing endogenous RNA (ceRNA) regulation has been reported to serve important roles in human disease. In the present study, ceRNA networks for depression and the corresponding normal physiological states were constructed. Further analysis of the ceRNA networks revealed that ceRNA regulation may be important for depression. Hub ceRNAs including high mobility group nucleosomal binding domain 3, peroxisome proliferator-activated receptor-γ coactivator 1β and leukemia inhibitory factor receptor-α were associated with depression. A common core ceRNA network was identified by comparison analysis. Functional analysis suggested that these ceRNAs may be implicated in depression. Differential expression analysis revealed that ceRNAs in the obtained ceRNA interaction networks were significantly enriched with significantly differentially expressed genes. A total of 8 key functional modules for depression were identified, and small target molecules were screened. ceRNA protocadherin-α subfamily C2 in module 1 and ceRNA Cyclin-dependent kinase 6 in module 3 were reported to be implicated in the occurrence and development of depressive disorders. Thus, the present analysis may provide insight into the pathogenesis of depression and improve its treatment.
Self-managed programmes in homeless care as (reinvented) institutions

ABSTRACT Purpose: Self-managed institutional homeless programmes started as an alternative to regular shelters. Using institutional theory as a lens, we aim to explore the experiences of stakeholders with the institutional aspects of a self-managed programs. Method: The data we analysed (56 interviews, both open and semi-structured) were generated in a longitudinal participatory case-study into JES, a self-managed homeless shelter. In our analysis we went back and forth between our empirical data and theory, using a combination of systematic coding and interpretation. Participants were involved in all stages of the research. Results: Our analysis revealed similarities between JES and regular shelters, stemming from institutional similarities. Participants shared space and facilities with sixteen people, which caused an ongoing discussion on (enforcement of) rules. Participants loathed lack of private space. However, participants experienced freedom of choice over both their own life and management of JES and structures were experienced more fluid than in regular care. Some structures also appeared stimulated self-management. Conclusion: Our analysis showed how an institutional context influences self-management and suggested opportunities for introducing freedom and fluidity in institutional care.
Primary bacillary resistance in multidrug-resistant tuberculosis and predictive factors associated with cure at a referral center in São Paulo, Brazil

ABSTRACT Objective: To identify transmitted or primary resistance among cases of multidrug-resistant tuberculosis and predictive factors for cure in multidrug-resistant tuberculosis after the first treatment. Method: Descriptive study of a cohort from 2006 to 2010, in a reference unit of tuberculosis in São Paulo, Brazil. The data were obtained by the revision of medical records. Clinical criteria were used to classify transmitted and acquired resistance. Extended primary resistance was also defined, in this study, as cases initially treated with a standardized scheme, but with no therapeutic success, and the pre-treatment drug susceptibility test (DST) showed presence of resistance. Results: 156 patients with multidrug-resistant tuberculosis and their respective sputum samples were eligible for the study. Only 7% of the patients were positive for the human immunodeficiency virus (HIV). Previous treatment occurred in 95% of the sample. The cure rate after the first treatment was 54%. The median bacteriological conversion time of those who healed was one month. Bacillary resistance was considered acquired resistance in 100 (64%) and transmitted resistance in 56 (36%). By logistic regression, patients who presented primary multidrug-resistant tuberculosis (odds ratio-OR = 6,29), without comorbidity (OR = 3,37) and with higher initial weight (OR = 1.04) were associated with cure after the first treatment. Conclusion: The early detection of bacillary resistance and appropriate treatment are in favor of healing. Thus, it is crucial to know exactly the primary resistance rate avoiding the use of inadequate treatments, amplification of bacillary resistance and its transmission.