Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid genomic first- and second-line drug resistance prediction from clinical Mycobacterium tuberculosis specimens using Deeplex-MycTB

The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis complex (Mtbc) isolates challenges tuberculosis (TB) control worldwide [1] and requires the rapid determination of extensive resistance profiles [2], enabling prompt initiation of effective treatment regimens. Phenotypic drug susceptibility testing (pDST) takes up to 6 weeks [3], and is unreliable and/or not standardised for several drugs, according to World Health Organization (WHO) guidelines [4]. Molecular DST (mDST) assays, like Xpert MTB/RIF (Cepheid) or MTBDRplus/sl line probe assays (LPAs; Hain Lifesciences) can be performed directly from clinical specimens, but only target a limited number of resistance variants [5]. Targeted next generation sequencing using the Deeplex-MycTB assay can rapidly generate comprehensive drug resistance profiles from Mycobacterium tuberculosis complex cultures and directly from tuberculosis patient samples to guide personalised treatment https://bit.ly/3dP1eIp
Statistical properties of scale-invariant helical magnetic fields and applications to cosmology

We investigate the statistical properties of isotropic, stochastic, Gaussian distributed, helical magnetic fields characterized by different shapes of the energy spectra at large length scales and study the associated realizability condition. We discuss smoothed magnetic fields that are commonly used when the primordial magnetic field is constrained by observational data. We are particularly interested in scale-invariant magnetic fields that can be generated during the inflationary stage by quantum fluctuations. We determine the correlation length of such magnetic fields and relate it to the infrared cutoff of perturbations produced during inflation. We show that this scale determines the observational signatures of the inflationary magnetic fields on the cosmic microwave background. At smaller scales, the scale-invariant spectrum changes with time. It becomes a steeper weak-turbulence spectrum at progressively larger scales. We show numerically that the critical length scale where this happens is the turbulent-diffusive scale, which increases with the square root of time.
A Regularized LDA Approach for AD, MCI and Normal Subjects Classification Using Resting-State fMRI Data

This paper conducts the Alzheimer’s Disease (AD), mild cognitive impairment (MCI) and normal control (NC) subject classification, by exploiting brain network connectivity pattern analysis. More specifically, we propose a regularized linear discriminant analysis (LDA) approach to reduce the noise effect (including both biological variability and measurement errors) under size limited functional magnetic resonance imaging (fMRI) data samples. The proposed approach is shown to be effective in increasing the classification accuracy significantly.
Prevalence of overweight/obesity among the adult population in Ethiopia: a systematic review and meta-analysis

Background Overweight and obesity are emerging public health problems in Ethiopia. However, primary study findings on the prevalence of overweight and obesity in Ethiopia are inconsistent. Therefore, this study aimed to estimate the pooled prevalence of overweight and obesity among adults in Ethiopia. Methods Studies that looked at overweight and obesity among adults were searched from four international databases. The search involved articles published from 1 January 2010 to 10 March 2020. The Cochran’s Q χ2 and the I2 test statistics were used to check heterogeneity among the studies. The funnel plot and Egger’s regression tests were also used to assess the presence of publication bias. Subgroup analysis was performed by residence, study setting, sample size and year of study. Sensitivity analysis was also done to assess the effect of a single study on the pooled estimates. Data analysis was done using STATA V.14 software program. Results A total of 16 studies with 19 527 study participants were included in this systematic review and meta-analysis. The estimated pooled prevalence of overweight among adults in Ethiopia was 20.4%, and after adjustment for publication bias with the trim-and-fill analysis, the estimated prevalence rate was changed to 19%. Besides, the estimated pooled prevalence of obesity was 5.4%. The prevalence of overweight was higher, 22.6% in studies published since 2015, 22.4% in studies conducted only in urban settings and 24.4% in studies with small sample size (≤384 participants). Similarly, the prevalence of obesity was 6.9% in studies published since 2015, 6.2% in studies conducted only in urban settings, 6.4% in institution-based settings and 9.6% in studies with small sample size. Conclusion The prevalence of overweight and obesity is high in Ethiopia compared with previous studies. This needs large scale awareness creation campaigns and situation-based and context-specific prevention strategies.
Motor outcome measures in patients with FKRP mutations

Objective To test the hypothesis that we will be able to detect change in motor outcome measures over time in a cohort with mutations in FKRP. Methods Individuals with documented FKRP mutations were evaluated annually with a battery of established motor outcome measures including limited quantitative myometry and timed function measures. Results were analyzed using random coefficient regression to determine annual change in each measure. Due to the nonlinear progression through the lifespan of the study participants, pediatric (<19 years) and adult (≥19 years) cohorts were analyzed separately. Effect of genotype was evaluated in each cohort. Results Sixty-nine participants (30 pediatric, 44 adult) with at least 2 evaluations were included. There was a small but statistically significant decline in timed motor function measures in both pediatric and adult cohorts. Genotype significantly affected rate of decline in the pediatric but not the adult cohort. Some pediatric patients who are homozygous for the c.826C>A mutation showed improving motor performance in adolescence. Performance on the 10-meter walk/run was highly correlated with other timed function tests. Conclusions There is a slow annual decline in motor function in adults with FKRP mutations that can be detected with standard motor outcome measures, while the results in the pediatric population were more variable and affected by genotype. Overall, these analyses provide a framework for development of future clinical trials. The dystroglycanopathies natural history study (Clinical Trial Readiness for the Dystroglycanopathies) may be found on clinicaltrials.gov (NCT00313677).
Are the shots predictive for the football results

In modelling football outcomes, scores’ data are regularly used for the estimation of the attack and the defence strength of each team. However, these teams’ abilities are quite complex and are correlated with many quantities inherent to the game. Additional available information, relevant for their estimation, are shots, both made and conceded. For such a reason, we propose a hierarchical model that incorporates this information in three stages for each game and each team: number of scores, number of shots on target and number of total shots. We fit the model on English Premier League data and obtained predictions for future matches. Abstract Nel modellare i risultati calcistici, i dati sui goal sono solitamente utilizzati per stimare le abilità di attacco e difesa di ogni squadra. Tuttavia, queste abilità hanno una natura complessa e sono correlate con molte quantità inerenti al gioco. Un’ulteriore informazione disponibile, rilevante per stimare questi parametri, è data dai tiri, sia quelli realizzati che quelli concessi. A tale scopo proponiamo un modello gerarchico che incorpora questa informazione in tre stadi per ogni partita e ogni squadra: numero di goal, numero di tiri nello specchio e numero di tiri totali. Abbiamo applicato il modello sui dati della Premier League inglese e ottenuto previsioni per partite future.
A simple nomogram score for screening patients with type 2 diabetes to detect those with hypertension: A cross-sectional study based on a large community survey in China

Objectives Compared with unaffected individuals, patients with type 2 diabetes (T2DM) have higher risk of hypertension, and diabetes combined with hypertension can lead to server cardiovascular disease. Therefore, the purpose of this study was to establish a simple nomogram model to identify the determinants of hypertension in patients with T2DM and to quickly calculate the probability of hypertension in individuals with T2DM. Materials and methods A total of 643,439 subjects participating in the national physical examination has been recruited in this cross-sectional study. After excluding unqualified subjects, 30,507 adults with T2DM were included in the final analysis. 21,355 and 9,152 subjects were randomly assigned to the model developing group and validation group, respectively, with a ratio of 7:3. The potential risk factors used in this study to assess hypertension in patients with T2DM included questionnaire investigation and physical measurement variables. We used the least absolute shrinkage and selection operator models to optimize feature selection, and the multivariable logistic regression analysis was for predicting model. Discrimination and calibration were assessed using the receiver operating curve (ROC) and calibration curve. Results The results showed that the major determinants of hypertension in patients with T2DM were age, gender, drinking, exercise, smoking, obesity and atherosclerotic vascular disease. The area under ROC curve of developing group and validation group are both 0.814, indicating that the prediction model owns high disease recognition ability. The p values of the two calibration curves are 0.625 and 0.445, suggesting that the nomogram gives good calibration. Conclusion The individualized nomogram model can facilitate improved screening and early identification of patients with hypertension in T2DM. This procedure will be useful in developing regions with high epidemiological risk and poor socioeconomic status just like Urumqi, in Northern China.
Clump mass function at an early stage of molecular cloud evolution – I. A statistical approach

We derive the mass function of condensations (clumps) which were formed through a turbulent cascade over a range of spatial scales L≤ 20 pc during early, predominantly turbulent evolution of a molecular cloud. The approach rests upon the assumption of a statistical clump mass–density relationship n∝mx with a scale dependence of the exponent x obtained from equipartition relations between various forms of energy of clumps. The derived clump mass function (ClMF) could be represented by series of two or three power laws, depending on the chosen equipartition relation, the velocity scaling index and the type of turbulent forcing. The high-mass ClMF exhibits an average slope Γ≃−1, typical for fractal clouds, whereas its intermediate-mass part is shallower or flattened, in agreement with some observational studies.
Medicinal plant extracts protect epithelial cells from infection and DNA damage caused by colibactin‐producing Escherichia coli, and inhibit the growth of bacteria

To investigate the biological activity of Thai medicinal plant extracts and their active substances on the inhibition of growth and the transcription of colibactin genes of colibactin‐producing Escherichia coli, and effect on the pathogenesis from colibactin toxin including transient infections and colibactin‐induced DNA damage.
The value of chosen diagnostic tools in evaluating myocarditis in children and adolescents

Introduction: Myocarditis is an inflammatory disease of the myocardium. Paediatric myocarditis is frequently overlooked due a misleading presentation when characteristic symptoms are lacking. Aim of the study: The aim of our study was to assess the clinical presentation of myocarditis in children, and the sensitivity and usefulness of chosen tests for diagnosing this disease. Material and methods: A retrospective chart review of paediatric patients with myocarditis was performed, where electrocardiography (ECG) and biomarker test results (leucocytes number, creatine kinase – CK, creatine kinase myocardial band – CKMB, troponin I, C-reactive protein – CRP, N-terminal precursor of natriuretic peptide type B – NT-proBNP) at admission and discharge were analysed along with echocardiography and cardiac magnetic resonance (CMR). Results: Thirty-one cases were gathered, of which the majority presented with cardiac (90.3%) or respiratory (61.3%) symptoms. In most cases, normal or only slightly lowered ejection fraction (EF) was observed (mean 62.9%, 95% CI 60.6–65.1%). ECG changes, cardiac troponin I, and CMR proved the most sensitive tests with respective sensitivities of 96.8% (95% CI 83.3–99.9%), 96.7% (95% CI 82.78–99.9%), and 100% (95% CI 83.2–100%). At discharge, levels of inflammatory and myocardial necrosis marker concentrations were significantly lower, and ejection fraction was significantly improved compared to ejection fraction at admission. CMR changes (i.e. signs of inflammation, delayed enhancement) were usually located in the inferolateral basal and mid-ventricular segments of the left ventricle. CRP, CK, and CKMB at admission correlated with the length of hospital stay. Conclusions: Cardiac troponin, ECG changes, and cardiac magnetic resonance are highly sensitive tests for myocarditis in children. The initial values of biomarkers (concentration of CRP and activities of CK and CKMB) correlate with the length of hospital stay. Myocarditis in children is most commonly located in the inferolateral wall of the left ventricle.
Induced Knockdown of Decorin, Alone and in Tandem with Biglycan Knockdown, Directly Increases Aged Tendon Viscoelasticity.

Tendon injuries increase with age, yet the age-associated changes in tendon properties remain unexplained. Decorin and biglycan are two matrix proteoglycans that play complex roles in regulating tendon formation, maturation, and aging, most notably in extracellular matrix assembly and maintenance. However, the roles of decorin and biglycan have not been temporally isolated in a homeostatic aged context. The goal of this work was to temporally isolate and define the roles of decorin and biglycan in regulating aged murine patellar tendon mechanical properties. We hypothesized that decorin would have a larger influence than biglycan on aged tendon mechanical properties and that biglycan would have an additive role in this regulation. When decorin and biglycan were knocked down in aged tendons, minimal changes in gene expression were observed, implying that these models directly define the role of decorin and biglycan in regulating tendon mechanical properties. Knockdown of decorin or biglycan led to minimal changes in quasi-static mechanical properties. However, decorin deficiency led to increases in stress relaxation and phase shift that were exacerbated when coupled with biglycan deficiency. This study highlights an important role for decorin, alone and in tandem with biglycan, in regulating aged tendon viscoelastic properties.
Association of Lifestyle Factors and Neuropsychological Development of 4-Year-Old Children

Background: We aimed to assess how lifestyle factors such as diet, sleep, screen viewing, and physical activity, individually, as well as in a combined score, were associated with neuropsychological development in pre-school age children. Methods: We conducted a cross-sectional study in 1650 children of 4 years of age, from the Environment and Childhood Project (INMA) population-based birth cohorts in four regions of Spain. Children were classified per a childhood healthy lifestyle score (CHLS) with a range of 0 to 4 that included eating in concordance with the Mediterranean diet (1 point); reaching recommended sleep time (1 point); watching a maximum recommended screen time (1 point); and being physically active (1 point). The McCarthy Scales of Children’s Abilities (MSCA) were used to test neuropsychological development. Multi-adjusted linear regression models were created to assess the association with the lifestyle factors individually and as a combined score. Results: CHLS was not associated with MSCA general cognitive score (1-point increment = −0.5, 95% CI: −1.2, 0.2). Analyzed by separate lifestyle factors, physical activity had a significant negative association with MSCA score and less TV/screen time had a negative association with MSCA score. Conclusion: In this cross-sectional study, a combined score of lifestyle factors is not related to neuropsychological development at pre-school age.
Development of an Audio Transmission System Through an Indoor Visible Light Communication Link

This study presents an approach to develop an indoor visible light communication system capable of transmitting audio signal over light beam within a short distance. Visible Light Communication (VLC) is a pretty new technology which used light sources to transmit data for communication. In any communication system, both analog and digital signal transmission are possible, though, due to having the capability of providing a faithful quality of signal regeneration after the transmission process, digital communication system is much more popular than the analog one. In the current project, digital communication process was adopted also. To convert the analog audio signal into the digital transmission signal and vice versa, Pulse Width Modulation (PWM) was used as the signal encoding strategy. As the light emitter, white Light Emitting Diodes (LEDs) were used and as photo sensor, a solar cell was used instead of a photodiode to obtain greater signal power and sensitivity. In the system, the carrier signal for transmission was chosen to have a frequency of 50 KHz. At the receiving end, a 4th order Butterworth lowpass filter having a cutoff frequency of 8 KHz was used to demodulate the audio signal. Using only 2 white LEDs, the indoor transmission range of this visible light communication system was found to be 5 meters while reproducing a satisfactory quality audio.
Resolution and Efficiency of Large Area Picosecond PhotoDetectors

This paper presents large area picosecond photo-detectors (LAPPD) as compelling detectors for neutrino, collider, and medical imaging experiments. The design and functionality of these detectors is described with emphasis on the process of computing the horizontal position of an event, known as second localization. An experimental study of this process in a prototype detector is presented. Ultimately, the prototype is shown to be error prone. An analysis of design space shows begins to characterize future detectors.
In Vitro Study of Extracellular Vesicles Migration in Cartilage-Derived Osteoarthritis Samples Using Real-Time Quantitative Multimodal Nonlinear Optics Imaging

Mesenchymal stromal cells (MSCs)-derived extracellular vesicles (EVs) are promising therapeutic nano-carriers for the treatment of osteoarthritis (OA). The assessment of their uptake in tissues is mandatory but, to date, available technology does not allow to track and quantify incorporation in real-time. To fill this knowledge gap, the present study was intended to develop an innovative technology to determine kinetics of fluorescent MSC-EV uptake by means of time-lapse quantitative microscopy techniques. Adipose-derived mesenchymal stromal cells (ASCs)-EVs were fluorescently labeled and tracked during their uptake into chondrocytes micromasses or cartilage explants, both derived from OA patients. Immunofluorescence and time-lapse coherent anti-Stokes Raman scattering, second harmonic generation and two-photon excited fluorescence were used to follow and quantify incorporation. EVs penetration appeared quickly after few minutes and reached 30–40 μm depth after 5 h in both explants and micromasses. In explants, uptake was slightly faster, with EVs signal overlapping both extracellular matrix and chondrocytes, whereas in micromasses a more homogenous diffusion was observed. The finding of this study demonstrates that this innovative technology is a powerful tool to monitor EVs migration in tissues characterized by a complex extracellular network, and to obtain data resembling in vivo conditions.
LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events

Mounting evidence has shown the involvement of long non-coding RNAs (lncRNAs) during various cancer metastatic events (abbreviated as CMEs, e.g. cancer cell invasion, intravasation, extravasation, proliferation, etc.) that may cooperatively facilitate malignant tumor spread and cause massive patient deaths. The study of lncRNA-CME associations might help understand lncRNA functions in metastasis and present reliable biomarkers for early dissemination detection and optimized treatment. Therefore, we developed a database named 'lncR2metasta' by manually compiling experimentally supported lncRNAs during various CMEs from existing studies. LncR2metasta documents 1238 associations between 304 lncRNAs and 39 CMEs across 54 human cancer subtypes. Each entry of lncR2metasta contains detailed information on a lncRNA-CME association, including lncRNA symbol, a specific CME, brief description of the association, lncRNA category, lncRNA Entrez or Ensembl ID, lncRNA genomic location and strand, lncRNA experiment, lncRNA expression pattern, detection method, target gene (or pathway) of lncRNA, lncRNA regulatory role on a CME, cancer name and the literature reference. An easy-to-use web interface was deployed in lncR2metasta for its users to easily browse, search and download as well as to submit novel lncRNA-CME associations. LncR2metasta will be a useful resource in cancer research community. It is freely available at http://lncR2metasta.wchoda. com.
Intervening to enhance collaboration in translational research: A relational coordination approach

Introduction A core challenge of a multidisciplinary and multi-organizational translational research enterprise such as a Clinical and Translational Research Award (CTSA) is coordinating and integrating the work of individuals, workgroups, and organizations accustomed to working independently and autonomously. Tufts Clinical and Translational Science Institute (CTSI) undertook and studied a multifacted intervention to address this challenge and to create a culture of systems thinking, process awareness, responsive to others' needs, and shared decision-making. Intervention The intervention, based on relational coordination, included 1) relational interventions, in three staff retreats and a diagnostic survey to provide feedback on the current quality of relational coordination, and 2) structural interventions, in the launching of five new cross-functional teams with regular meeting structures. Methods A mixed-methods evaluation yielded quantitative data via two types of team surveys and qualitative data via interviews and meeting observations. Results The findings suggest that interventions to improve relational coordination are feasible for CTSAs, including good fidelity to the model and staff/physician engagement. Survey and interview data suggest model improvements in coordination and alignment. Further research about their optimal design is warranted.