Miracle-dz/UniFAR-FTUs huggingface dataset:
Combined assessment of tuberculosis case notification rate and infection control at health facilities of Dale districts, Sidama Zone, Southern Ethiopia

Background Mycobacterium tuberculosis (TB) is the deadliest disease that claims millions of deaths globally. Ethiopia is among the countries heavily hit by the disaster. Despite the effective directly observed treatment and TB infection control (TBIC) measures provided by the world health organization (WHO), the rate of new cases increased daily throughout the country. Healthcare workers (HCWs) are at highest risk serving without having the necessary facility in place while overcrowding of patients exacerbated TB transmission. The study aimed to assess TBIC implementation and analyze case notification rate (CNR) of smear-positive pulmonary TB in the selected health facilities at Dale district, Sidama Zone, Southern Ethiopia. Methods Seven health care facilities have been visited in the study area and smear-positive pulmonary TB notification rate was determined retrospectively during the years 2012 to 2014. Data on smear positive test results and demographic characteristics were collected from the TB unit registries. A structured questionnaire, facility survey, and observation checklists were used to assess the presence of TBIC plans at the health care facilities. Results The overall case notification rate of smear-positive pulmonary tuberculosis was 5.3% among all 7696 TB suspected patients. The odds of being diagnosed with smear-positive TB were 24% more in males than in females (adj OR = 1.24, 95% CI: (1.22, 1.55). Moreover, in the study area, only 28% of the facilities have been practiced TB infection control and 71% of the facilities assigned a focal person for the TBIC plan. The implementation of environmental control measures in the facilities was ranged between 16–83%. N95 particulate respirators were found only in 14% of the facilities. Conclusion TB CNR in Dale district was low. Moreover, implementations of TBIC in Dale district health facilities were poor when the survey was done. Hence, urgent measures should be taken to reverse the burden of TB.
Measurement Invariance of Perfectionism Measures in Students with and without a History of Non-Suicidal Self-Injury

Perfectionism is a transdiagnostic process which may be implicated in the onset and maintenance of non-suicidal self-injury. No study has evaluated whether reported differences in perfectionism between individuals with and without a history of self-injury represent genuine group differences or measurement artefacts. The present study reports an investigation of the measurement invariance of two common scales of perfectionism, the Frost Multidimensional Perfectionism Scale-Brief (FMPS-Brief) and the Clinical Perfectionism Questionnaire (CPQ), among university students (Mage = 20.48, SDage = 2.22, 75.3% female, 22.8% male) with and without a history of self-injury (total n = 711). Results revealed full residual error invariance for the two-factor model of FMPS-Brief, while the bifactor model of the FMPS-Brief and the two-factor model of the CPQ demonstrated partial metric invariance. Accounting for partial metric invariance, the bifactor model of the FMPS-Brief also demonstrated partial residual error invariance. The current findings suggest that observed differences using the FMPS-Brief reflect genuine differences in perfectionism between individuals with and without a history of self-injury. Further, while researchers using the bi-factor model can have confidence that the general factor can adequately assess group differences, differential item functioning should be considered if using the strivings and concerns factors. Finally, in the current data, the CPQ did not perform as expected in baseline model fit and future research should replicate assessments of measurement invariance in this measure.
MicroRNAs and Calcium Signaling in Heart Disease

In hearts, calcium (Ca2+) signaling is a crucial regulatory mechanism of muscle contraction and electrical signals that determine heart rhythm and control cell growth. Ca2+ signals must be tightly controlled for a healthy heart, and the impairment of Ca2+ handling proteins is a key hallmark of heart disease. The discovery of microRNA (miRNAs) as a new class of gene regulators has greatly expanded our understanding of the controlling module of cardiac Ca2+ cycling. Furthermore, many studies have explored the involvement of miRNAs in heart diseases. In this review, we aim to summarize cardiac Ca2+ signaling and Ca2+-related miRNAs in pathological conditions, including cardiac hypertrophy, heart failure, myocardial infarction, and atrial fibrillation. We also discuss the therapeutic potential of Ca2+-related miRNAs as a new target for the treatment of heart diseases.
Potential Biomarkers Associated with Multiple Sclerosis Pathology

Multiple sclerosis (MS) is a complex disease of the central nervous system (CNS) that involves an intricate and aberrant interaction of immune cells leading to inflammation, demyelination, and neurodegeneration. Due to the heterogeneity of clinical subtypes, their diagnosis becomes challenging and the best treatment cannot be easily provided to patients. Biomarkers have been used to simplify the diagnosis and prognosis of MS, as well as to evaluate the results of clinical treatments. In recent years, research on biomarkers has advanced rapidly due to their ability to be easily and promptly measured, their specificity, and their reproducibility. Biomarkers are classified into several categories depending on whether they address personal or predictive susceptibility, diagnosis, prognosis, disease activity, or response to treatment in different clinical courses of MS. The identified members indicate a variety of pathological processes of MS, such as neuroaxonal damage, gliosis, demyelination, progression of disability, and remyelination, among others. The present review analyzes biomarkers in cerebrospinal fluid (CSF) and blood serum, the most promising imaging biomarkers used in clinical practice. Furthermore, it aims to shed light on the criteria and challenges that a biomarker must face to be considered as a standard in daily clinical practice.
Selenium and the 15kDa Selenoprotein Impact Colorectal Tumorigenesis by Modulating Intestinal Barrier Integrity

Selenoproteins play important roles in many cellular functions and biochemical pathways in mammals. Our previous study showed that the deficiency of the 15 kDa selenoprotein (Selenof) significantly reduced the formation of aberrant crypt foci (ACF) in a mouse model of azoxymethane (AOM)-induced colon carcinogenesis. The objective of this study was to examine the effects of Selenof on inflammatory tumorigenesis, and whether dietary selenium modified these effects. For 20 weeks post-weaning, Selenof-knockout (KO) mice and littermate controls were fed diets that were either deficient, adequate or high in sodium selenite. Colon tumors were induced with AOM and dextran sulfate sodium. Surprisingly, KO mice had drastically fewer ACF but developed a similar number of tumors as their littermate controls. Expression of genes important in inflammatory colorectal cancer and those relevant to epithelial barrier function was assessed, in addition to structural differences via tissue histology. Our findings point to Selenof’s potential role in intestinal barrier integrity and structural changes in glandular and mucin-producing goblet cells in the mucosa and submucosa, which may determine the type of tumor developing.
Concordance between Different Criteria for Self-Reported Physical Activity Levels and Risk Factors in People with High Blood Pressure in a Rural District in Bangladesh

Self-reported assessment of physical activity (PA) is commonly used in public health research. The present study investigated the concordance of self-reported PA assessed using the global physical activity questionnaire (GPAQ) and two different measurement approaches. Participants (n = 307, aged 30–75 years with hypertension) were recruited from a rural area in Bangladesh. We analyzed the difference between the World Health Organization (WHO) recommendations of more than 600 metabolic-equivalent time-minutes (MET-min) and the self-reported active hours, at least 2.5 h per week. Tests of sensitivity and specificity were conducted to determine concordance between the two measures. According to the WHO criteria, 255 (83%) participants were active more than 600 MET-min per week and 172 (56%) people were physically active 2.5 h or more per week, indicating a 27% difference in self-reported PA. The sensitivity, specificity, positive and negative predictive values and concordance between the two measures were 64%, 92%, 98%, 34% and 70%, respectively. Considering the WHO MET-min as the appropriate measure, 89 (35%) were false negative (FN). Older age, professionals and businesspersons were associated with a higher proportion of FN. There is a gap between self-reported PA, thus a better estimate of PA may result from combining two criteria to measure PA levels.
The Role of Physical Activity-Related Health Competence and Leisure-Time Physical Activity for Physical Health and Metabolic Syndrome: A Structural Equation Modeling Approach for German Office Workers

Office workers (OWs) are prone to insufficient physical activity (PA), which increases their risk of metabolic syndrome (MetS) and impaired physical health. The Physical Activity-related Health Competence (PAHCO) model holds the potential to facilitate a healthy physically active lifestyle. Therefore, in this study, we investigate the interplay between PAHCO, leisure-time PA, physical health, and MetS in OWs in Germany. In a cross-sectional study, OWs (N = 316, 25% female) completed self-report questionnaires along with an occupational health checkup to examine their Metabolic Syndrome Severity Score (MetSSS) values. Structural equation modeling indicated a strong positive association between PAHCO and leisure-time PA and a small positive association with physical health. PAHCO showed a considerable negative association with the MetSSS. Leisure-time PA was a positive mediator for the PAHCO–physical health association but was not a significant mediator for the association between PAHCO and the MetSSS. These findings underscore the importance of PAHCO in the context of leisure-time PA, physical health, and MetS in OWs. Furthermore, our findings highlight the health-enhancing value of the qualitative aspects of PA, such as motivational and volitional components in PA participation, with respect to physical health and MetS.
Structural and Kinetic Insights Into the Molecular Basis of Salt Tolerance of the Short-Chain Glucose-6-Phosphate Dehydrogenase From Haloferax volcanii

Halophilic enzymes need high salt concentrations for activity and stability and are considered a promising source for biotechnological applications. The model study for haloadaptation has been proteins from the Halobacteria class of Archaea, where common structural characteristics have been found. However, the effect of salt on enzyme function and conformational dynamics has been much less explored. Here we report the structural and kinetic characteristics of glucose-6-phosphate dehydrogenase from Haloferax volcanii (HvG6PDH) belonging to the short-chain dehydrogenases/reductases (SDR) superfamily. The enzyme was expressed in Escherichia coli and successfully solubilized and refolded from inclusion bodies. The enzyme is active in the presence of several salts, though the maximum activity is achieved in the presence of KCl, mainly by an increment in the kcat value, that correlates with a diminution of its flexibility according to molecular dynamics simulations. The high KM for glucose-6-phosphate and its promiscuous activity for glucose restrict the use of HvG6PDH as an auxiliary enzyme for the determination of halophilic glucokinase activity. Phylogenetic analysis indicates that SDR-G6PDH enzymes are exclusively present in Halobacteria, with HvG6PDH being the only enzyme characterized. Homology modeling and molecular dynamics simulations of HvG6PDH identified a conserved NLTX2H motif involved in glucose-6-phosphate interaction at high salt concentrations, whose residues could be crucial for substrate specificity. Structural differences in its conformational dynamics, potentially related to the haloadaptation strategy, were also determined.
Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis

While horizontally transferred transposable elements (TEs) have been reported in several groups of plants, their importance for genome evolution remains poorly understood. To understand how horizontally transferred TEs contribute to plant genome evolution, we investigated the composition and activity of horizontally transferred TEs in the genomes of four Vitis species. A total of 35 horizontal transfer (HT) events were identified between the four Vitis species and 21 other plant species belonging to 14 different families. We determined the donor and recipient species for 28 of these HTs, with the Vitis species being recipients of 15 of them. As a result of HTs, 8–10 LTR retrotransposon clusters were newly formed in the genomes of the four Vitis species. The activities of the horizontally acquired LTR retrotransposons differed among Vitis species, showing that the consequences of HTs vary during the diversification of the recipient lineage. Our study provides the first evidence that the HT of TEs contributes to the diversification of plant genomes by generating additional TE subfamilies and causing their differential proliferation in host genomes.
Assessment of Force Production in Parkinson’s Disease Subtypes

Muscle weakness is a secondary motor symptom of Parkinson’s disease (PD), especially in the subtype characterized by postural instability and gait difficulty (PIGD). Since the PIGD subtype also presents worse bradykinesia, we hypothesized that it also shows a decreased rate of force development, which is linked to an increased risk of falling in PD. Therefore, we investigated the effects of PD and PD subtypes on a force production profile and correlated the force production outcomes with clinical symptoms for each PD subtype. We assessed three groups of participants: 14 healthy older adults (OA), 10 people with PD composing the PIGD group, and 14 people with PD composing the tremor-dominant group. Three knee extension maximum voluntary isometric contractions were performed in a leg extension machine equipped with a load cell to assess the force production. The outcome measures were: peak force and rate of force development (RFD) at 50 ms (RFD50), 100 ms (RFD100), and 200 ms (RFD200). We observed lower peak force, RFD50, RFD100, and RFD200 in people with PD, regardless of subtypes, compared with the OA group (p < 0.05 for all comparisons). Together, our results indicated that PD affects the capacity to produce maximal and rapid force. Therefore, future interventions should consider rehabilitation programs for people with PD based on muscle power and fast-force production, and consequently reduce the likelihood of people with PD falling from balance-related events, such as from an unsuccessful attempt to avoid a tripping hazard or a poor and slower stepping response.
Thrombosis of Bilateral Profunda Femoris, Anterior Tibial, and Tibioperoneal Arteries in a Patient With COVID-19 Infection

COVID-19, also known as severe acute respiratory distress syndrome coronavirus 2, mostly affects the respiratory system causing acute respiratory syndrome. It not only targets lungs but also causes vascular endothelial disruption, which can lead to arterial or venous thrombosis causing ischemia, which increases the morbidity and mortality in some patients, if not recognized and treated in a timely manner. We present an interesting case of a patient recovering from COVID-19 pneumonia , who developed bilateral foot ischemia due to thrombosis of bilateral profunda femoris, bilateral anterior tibial, and tibioperoneal arteries. A 44-year-old gentleman presented to the emergency department complaining of severe bilateral foot pain, which progressively got worse. Upon examination he had blue toes bilaterally with absent dorsalis pedis and posterior tibial pulse. CT angiogram was performed, which showed severe multilevel lower limb arterial occlusions involving bilateral profunda femoris, bilateral anterior tibial, and tibioperoneal arteries. The patient was initially thrombolyzed and later underwent thrombectomy with the assistance of interventional radiologist. Hospital course was uneventful, and the patient was discharged on warfarin following complete resolution of symptoms.
Prevalence of Peripheral Arterial Disease and Associated Vascular Risk Factors in 65-Years-Old People of Northern Barcelona

Objective: To determine the prevalence and risk factors associated with peripheral arterial disease (PAD) in Northern Barcelona at 65 years of age. Methods: A single-center, cross-sectional study, including males and females 65 years of age, health care cardholders of Barcelona Nord. PAD was defined as an ankle–brachial index (ABI) < 0.9. Attending subjects were evaluated for a history of common cardiovascular risk factors. A REGICOR score was obtained, as well as a physical examination and anthropometric measurements. Results: From November 2017 to December 2018, 1174 subjects were included: 479 (40.8%) female and 695 (59.2%) male. Overall prevalence of PAD was 6.2% (95% CI: 4.8–7.6%), being 7.9% (95% CI: 5.9–9.9%) in males and 3.8% (95% CI: 2.1–5.5%) in females. An independent strong association was seen in male smokers and diabetes, with ORs pf 7.2 (95% CI: 2.8–18.6) and 1.8 (95% CI: 1.0–3.3), respectively, and in female smokers and hypertension, with ORs of 5.2 (95% CI: 1.6–17.3) and 3.3 (95% CI: 1.2–9.0). Male subjects presented with higher REGICOR scores (p < 0.001). Conclusion: Higher-risk groups are seen in male subjects with a history of smoking and diabetes and female smokers and arterial hypertension, becoming important subgroups for our primary healthcare centers and should be considered for ABI screening programs.
Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding

Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the TYRP1 gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indolequinone-2-carboxylic acid (IQCA). Here, for the first time, four OCA3-causing mutations of Tyrp1, C30R, H215Y, D308N, and R326H, were investigated computationally to understand Tyrp1 protein stability and catalytic activity. Using the Tyrp1 crystal structure (PDB:5M8L), global mutagenesis was conducted to evaluate mutant protein stability. Consistent with the foldability parameter, C30R and H215Y should exhibit greater instability, and two other mutants, D308N and R326H, are expected to keep a native conformation. SDS-PAGE and Western blot analysis of the purified recombinant proteins confirmed that the foldability parameter correctly predicted the effect of mutations critical for protein stability. Further, the mutant variant structures were built and simulated for 100 ns to generate free energy landscapes and perform docking experiments. Free energy landscapes formed by Y362, N378, and T391 indicate that the binding clefts of C30R and H215Y mutants are larger than the wild-type Tyrp1. In docking simulations, the hydrogen bond and salt bridge interactions that stabilize DHICA in the active site remain similar among Tyrp1, D308N, and R326H. However, the strengths of these interactions and stability of the docked ligand may decrease proportionally to mutation severity due to the larger and less well-defined natures of the binding clefts in mutants. Mutational perturbations in mutants that are not unfolded may result in allosteric alterations to the active site, reducing the stability of protein-ligand interactions.
Autism Spectrum Disorder and Duchenne Muscular Dystrophy: A Clinical Case on the Potential Role of the Dystrophin in Autism Neurobiology

A diagnosis of autism spectrum disorder is reported in up to 19% of dystrophinopathies. However, over the last ten years, only a few papers have been published on this topic. Therefore, further studies are required to analyze this association in depth and ultimately to understand the role of the brain dystrophin isoform in the pathogenesis of ASD and other neurodevelopmental disorders. In this paper, we report a clinical case of a patient affected by ASD and Duchenne muscular dystrophy, who carries a large deletion of the dystrophin gene. Then we present a brief overview of the literature about similar cases and about the potential role of the dystrophin protein in the neurobiology of autism spectrum disorder.
Genome-Wide Identification, Evolution, and Comparative Analysis of B-Box Genes in Brassica rapa, B. oleracea, and B. napus and Their Expression Profiling in B. rapa in Response to Multiple Hormones and Abiotic Stresses

The B-box zinc-finger transcription factors are important for plant growth, development, and various physiological processes such as photomorphogenesis, light signaling, and flowering, as well as for several biotic and abiotic stress responses. However, there is relatively little information available regarding Brassica B-box genes and their expression. In this study, we identified 51, 52, and 101 non-redundant genes encoding B-box proteins in Brassica rapa (BrBBX genes), B. oleracea (BoBBX genes), and B. napus (BnBBX genes), respectively. A whole-genome identification, characterization, and evolutionary analysis (synteny and orthology) of the B-box gene families in the diploid species B. rapa (A genome) and B. oleracea (C genome) and in the allotetraploid species B. napus (AC genome) revealed segmental duplications were the major contributors to the expansion of the Brassica BBX gene families. The Brassica BBX genes were classified into five subgroups according to phylogenetic relationships, gene structures, and conserved domains. Light-responsive cis-regulatory elements were detected in many of the BBX gene promoters. Additionally, BrBBX expression profiles in different tissues and in response to various abiotic stresses (heat, cold, salt, and drought) or hormones (abscisic acid, methyl jasmonate, and gibberellic acid) were analyzed by qRT-PCR. The data indicated that many B-box genes (e.g., BrBBX13, BrBBX15, and BrBBX17) may contribute to plant development and growth as well as abiotic stress tolerance. Overall, the identified BBX genes may be useful as functional genetic markers for multiple stress responses and plant developmental processes.