Miracle-dz/UniFAR-FTUs huggingface dataset:
ICTV virus taxonomy profile: Picobirnaviridae.

Picobirnaviridae is a family of viruses with bi-segmented (rarely unsegmented) dsRNA genomes comprising about 4.4 kbp in total, with small, non-enveloped spherical virions. The family includes one genus (Picobirnavirus) grouping three genetic clusters with high sequence variability, two defined by viruses infecting vertebrates and a third with viruses found in invertebrates. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Picobirnaviridae, which is available at www.ictv. global/report/picobirnaviridae.
Metformin induces significant reduction of body weight, total cholesterol and LDL levels in the elderly – A meta-analysis

Background Metformin is the first-choice drug for patients with Type 2 diabetes, and this therapy is characterized by being weight neutral. However, in the elderly an additional unintentional weight loss could be considered as an adverse effect of the treatment. Objectives We aimed to perform a meta-analysis of placebo-controlled studies investigating the body weight changes upon metformin treatment in participants older than 60 years. Materials and methods PubMed, EMBASE and the Cochrane Library were searched. We included at least 12 week-long studies with placebo control where the mean age of the metformin-treated patients was 60 years or older and the body weight changes of the patients were reported. We registered our protocol on PROSPERO (CRD42017055287). Results From the 971 articles identified by the search, 6 randomized placebo-controlled studies (RCTs) were included in the meta-analysis (n = 1541 participants). A raw difference of -2.23 kg (95% CI: -2.84 –-1.62 kg) body weight change was detected in the metformin-treated groups as compared with that of the placebo groups (p<0.001). Both total cholesterol (-0.184 mmol/L, p<0.001) and LDL cholesterol levels (-0.182 mmol/L, p<0.001) decreased upon metformin-treatment. Conclusions Our meta-analysis of RCTs showed a small reduction of body weight together with slight improvement of the blood lipid profile in patients over 60 years. With regard to the risk of unintentional weight loss, metformin seems to be a safe agent in the population of over 60 years. Our results also suggest that metformin treatment may reduce the risk of major coronary events (-4-5%) and all-cause mortality (-2%) in elderly diabetic populations.
NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies

The increasing number of OMICs studies demands bioinformatic tools that aid in the analysis of large sets of genes or proteins to understand their roles in the cell and establish functional networks and pathways. In the last decade, over-representation or enrichment tools have played a successful role in the functional analysis of large gene/protein lists, which is evidenced by thousands of publications citing these tools. However, in most cases the results of these analyses are long lists of biological terms associated to proteins that are difficult to digest and interpret. Here we present NeVOmics, Network-based Visualization for Omics, a functional enrichment analysis tool that identifies statistically over-represented biological terms within a given gene/protein set. This tool provides a hypergeometric distribution test to calculate significantly enriched biological terms, and facilitates analysis on cluster distribution and relationship of proteins to processes and pathways. NeVOmics is adapted to use updated information from the two main annotation databases: Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). NeVOmics compares favorably to other Gene Ontology and enrichment tools regarding coverage in the identification of biological terms. NeVOmics can also build different network-based graphical representations from the enrichment results, which makes it an integrative tool that greatly facilitates interpretation of results obtained by OMICs approaches. NeVOmics is freely accessible at https://github.com/bioinfproject/bioinfo/.
Two new species of Geejayessia (Hypocreales) from Asia as evidenced by morphology and multi-gene analyses

Abstract Two new species of Geejayessia are introduced, based on materials collected from central China. Geejayessiaclavatasp. nov. is characterised by gregarious, red brownish to dark red, oval-subglobose to globose perithecia that are formed on a basal stroma; (4–7-)8-spored cylindrical asci; ellipsoidal or rarely broadly ellipsoidal, uniseptate, smooth or finely verruculose ascospores; clavate, aseptate microconidia and absence of macroconidia. Geejayessiasinicasp. nov. is characterised by red to bright red, pyriform, subglobose to globose, perithecia on a basal stroma, collapsing laterally when dry; subcylindrical to clavate asci with a rounded apex; ellipsoidal, uniseptate ascospores; and falcate, multiseptate macroconidia with an arcuate tip. Morphological distinctions of the new species from the related fungi are discussed. This is the first report of Geejayessia from Asia.
Shift Work Related to Stress, Health and Mood States

This article has two main objectives. The first is to examine the extent of stress, negative mental health outcomes and variations in mood states experienced by shift workers (N = 100) and a control group of day workers (N = 100) employed in Feeder Balancing Dairy, Ramnagar Varanasi and Kanpur, Dugdth Utpadak Sahakari Sangh (brand name Parag, Ltd. for both organisations). Second, to find out the relative contribution of stress variables and mood states in the prediction of mental health outcomes separately for both shift workers and a control group of day workers. Our overall findings concur with other studies and provide evidence that shift workers significantly experienced higher levels of job and life stress, higher indices of negative mental health outcomes (as measured by GHQ – 28) and variations in mood states as compared to day workers. The results of the present study established some significant relationships between stress and negative mental health outcomes among both shift and day group of workers. However, the magnitude of correlation coefficients is slightly higher in the day worker group. For both groups of workers significant positive correlations were found between all the dimensions of negative mental health and mood states of tense arousal, anger, energetic arousal and general arousal. The findings of step-wise multiple regression analysis indicated that amount of life stress and role conflicts were the two major predictors of negative mental health outcomes among shift workers. The results of a similar analysis carried out on day workers indicated that in the prediction of mental health of day workers, job related stressors (role ambiguity, role conflict and role overload) played a significant role. The findings further indicated that shift workers’ mood states such as anger, tense arousal and hedonic tone were also significant predictors of mental health outcomes. In day group of workers, anger coupled with low level of energetic arousal influenced their mental health. It is interesting to note, however, that in both groups of workers anger was the strongest predictor of all indices of negative mental health outcomes. Thus, the present study adds additional support to the notion that shift and night shift work is a potent source of stress. Shift work is opposed to the human circadian system and this conflict creates multiple physiological, psychological and psychosocial problems for shift workers.
The study of colliding molecular clumps evolution

The results of study of the gravitational fragmentation in the interstellar medium (ISM) by clump-clump collisions are presented. We suggest, that collision of clumps, that are subparts of Giant Molecular Clouds (GMC) may be on of the basic mechanism, which result to ISM fragmentation and define the dynamical as well as statistical characteristics (e.g. the mass spectra) of protostellar condensation. In the present paper, we describe our 3D SPH-modeling, in isothermal approximation, of supersonic collisions of two identical clumps with a few variants of initial impact parameters (β), that cover the wide range. Our results shown, that at all β in system began intensive fragmentation. The resulting fragments mass function depend from initial impact parameter. The obtained mass spectra have the slopes in a good enough agreement with observational data for our Galaxy–especially for large impact parameters, which are more realistic as for large clumps ensembles.
Carfilzomib vs bortezomib in patients with multiple myeloma and renal failure: a subgroup analysis of ENDEAVOR.

In ENDEAVOR, carfilzomib (56 mg/m2) and dexamethasone (Kd56) demonstrated longer progression-free survival (PFS) over bortezomib and dexamethasone (Vd) in patients with relapsed/refractory multiple myeloma (RRMM). Here we evaluated Kd56 vs Vd by baseline renal function in a post hoc exploratory subgroup analysis. The intent-to-treat population included 929 patients (creatinine clearance [CrCL] ≥15 to <50 mL/min, n = 85 and n = 99; CrCL 50 to <80 mL/min, n = 186 and n = 177; and CrCL ≥80 mL/min, n = 193 and n = 189 for Kd56 and Vd arms, respectively). In these respective subgroups, median PFS was 14.9 vs 6.5 months (hazard ratio [HR], 0.49; 95% confidence interval [CI], 0.320-0.757), 18.6 vs 9.4 months (HR, 0.48; 95% CI, 0.351-0.652), and not reached (NR) vs 12.2 months (HR, 0.60; 95% CI, 0.434-0.827) for those receiving Kd56 vs Vd, respectively; median overall survival (OS) was 42.1 vs 23.7 months (HR, 0.66; 95% CI, 0.443-0.989), 42.5 vs 32.8 months (HR, 0.83; 95% CI, 0.626-1.104), and NR vs 42.3 months (HR, 0.75; 95% CI, 0.554-1.009). Complete renal response (ie, CrCL improvement to ≥60 mL/min in any 2 consecutive visits if baseline CrCL <50 mL/min) rates were 15.3% (95% CI, 8.4-24.7) and 14.1% (95% CI, 8.0-22.6) for those receiving Kd56 vs Vd, respectively. In a combined Kd56 and Vd analysis, complete renal responders had longer median PFS (14.1 vs 9.4 months; HR, 0.805; 95% CI, 0.438-1.481) and OS (35.3 vs 29.7 months; HR, 0.91; 95% CI, 0.524-1.577) vs nonresponders. Grade ≥3 adverse event rates in the respective subgroups were 87.1% vs 79.4%, 84.4% vs 71.8%, and 77.1% vs 65.9% for those receiving Kd56 vs Vd, respectively. Thus, Kd56 demonstrated PFS and OS improvements over Vd in RRMM patients regardless of their baseline renal function. The ENDEAVOR trial was registered at www.clinicaltrials. gov as #NCT01568866.
Optimal duration of DAPT after second-generation drug-eluting stent in acute coronary syndrome

Background We evaluated optimal duration of dual antiplatelet therapy (DAPT) after second-generation drug-eluting stent (DES) implantation in acute coronary syndrome (ACS). Material and methods From pooled analysis of three randomized clinical trials (EXCELLENT, IVUS-XPL, RESET), a total of 2,216 patient with ACS undergoing second-generation DES implantation were selected. Each study randomized patients to a short-duration DAPT arm (n = 1119; ≤6 months) or a standard-duration DAPT arm (n = 1097; ≥12 months). Two-thirds of patients were male, and their mean age was 63 years. Mean DAPT durations were 164 ±76 and 359 ±68 days, respectively. The primary endpoint was composite of cardiac death, myocardial infarction, stent thrombosis, stroke or major bleeding during the first 12 months after implantation, analyzed according to the intention-to-treat population. Results Demographic characteristics were balanced between groups. Mean DAPT duration was 164 and 359 days, respectively. Primary endpoint occurred in 22 patients with short-DAPT and 21 patients with standard-DAPT (2.0% versus 1.9%; hazard ratio [HR] 1.03; 95% confidence interval [CI] 0.56–1.86; p = 0.94). Landmark analysis after six-months, no significant difference in primary endpoint between short and standard duration DAPT (1.0% versus 0.8%; HR 1.22; 95% CI 0.51–2.95; p = 0.66). Conclusions Short-duration DAPT (≤6 months) demonstrated a similar incidence of net adverse cardiovascular and clinical events at 12 months after second-generation DES in ACS compared with standard duration DAPT (≥12 months). Clinical trial registration EXCELLENT (ClinicalTrials.gov, NCT00698607), RESET (ClinicalTrials.gov, NCT01145079), IVUS-XPL (ClinicalTrials.gov, NCT01308281)
Are There Limitations to Exercise Benefits in Peripheral Arterial Disease?

Substantial evidence exists indicating that inactivity contributes to the progression of chronic disease, and conversely, that regular physical activity can both prevent the onset of disease as well as delay the progression of existing disease. To that end “exercise as medicine” has been advocated in the broad context as general medical care, but also in the specific context as a therapeutic, to be considered in much the same way as other drugs. As there are non-responders to many medications, there also are non-responders to exercise; individual who participate but do not demonstrate appreciable improvement/benefit. In some settings, the stress induced by exercise may aggravate an underlying condition, rather than attenuate chronic disease. As personalized medicine evolves with ready access to genetic information, so too will the incorporation of exercise in the context of those individual genetics. The focus of this brief review is to distinguish between the inherent capacity to perform, as compared to adaptive response to active exercise training in relation to cardiovascular health and peripheral arterial disease.
Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial.

Background Although preliminary evidence suggests that intermittent calorie restriction (ICR) exerts stronger effects on metabolic parameters, which may link obesity and major chronic diseases, compared with continuous calorie restriction (CCR), there is a lack of well-powered intervention studies. Objective We conducted a randomized controlled trial to test whether ICR, operationalized as the "5:2 diet," has stronger effects on adipose tissue gene expression, anthropometric and body composition measures, and circulating metabolic biomarkers than CCR and a control regimen. Design One hundred and fifty overweight and obese nonsmokers [body mass index (kg/m2) ≥25 to <40, 50% women], aged 35-65 y, were randomly assigned to an ICR group (5 d without energy restriction and 2 d with 75% energy deficit, net weekly energy deficit ∼20%), a CCR group (daily energy deficit ∼20%), or a control group (no advice to restrict energy) and participated in a 12-wk intervention phase, a 12-wk maintenance phase, and a 26-wk follow-up phase. Results Loge relative weight change over the intervention phase was -7.1% ± 0.7% (mean ± SEM) with ICR, -5.2% ± 0.6% with CCR, and -3.3% ± 0.6% with the control regimen (Poverall < 0.001, PICR vs. CCR = 0.053). Despite slightly greater weight loss with ICR than with CCR, there were no significant differences between the groups in the expression of 82 preselected genes in adipose tissue implicated in pathways linking obesity to chronic diseases. At the final follow-up assessment (week 50), weight loss was -5.2% ± 1.2% with ICR, -4.9% ± 1.1% with CCR, and -1.7% ± 0.8% with the control regimen (Poverall = 0.01, PICR vs. CCR = 0.89). These effects were paralleled by proportional changes in visceral and subcutaneous adipose tissue volumes. There were no significant differences between ICR and CCR regarding various circulating metabolic biomarkers. Conclusion Our results on the effects of the "5:2 diet" indicate that ICR may be equivalent but not superior to CCR for weight reduction and prevention of metabolic diseases. This trial was registered at clinicaltrials.gov as NCT02449148.
Towards the Quantification of Peggy Babcock: Speech Errors and Their Position within the Word

Abstract Sequences of similar (i.e., partially identical) words can be hard to say, as indicated by error frequencies, longer reaction and execution times. This study investigates the role of the location of this partial identity and the accompanying differences, i.e. whether errors are more frequent with mismatches in word onsets (top cop), codas (top tock) or both (pop tot). Number of syllables (tippy ticky) and empty positions (top ta) were also varied. Since the gradient nature of errors can be difficult to determine acoustically, articulatory data were investigated. Articulator movements were recorded using electromagnetic articulography, for up to 9 speakers of American English repeatedly producing 2-word sequences to an accelerating metronome. Most word pairs showed more intrusions and greater variability in coda than in onset position, in contrast to the predominance of onset position errors in corpora from perceptual observation.
ABR streaming of VBR-encoded videos: characterization, challenges, and solutions

Adaptive Bitrate (ABR) video streaming is widely used for over-the-top (OTT) video delivery. Recently, streaming providers have been moving towards using Variable Bitrate (VBR) encodings for the video content, spurred by the potential of improving user QoE (Quality of Experience) and reducing network bandwidth requirements compared to Constant Bitrate (CBR) encodings. However VBR introduces new challenges for ABR streaming, whose nature and implications are little understood. We explore these challenges across diverse video genres, encoding technologies, and platforms. We identify distinguishing characteristics of VBR encodings that impact user QoE and should be factored in any ABR adaptation decision. Traditional ABR adaptation strategies designed for the CBR case are not adequate for VBR. We develop novel best practice design principles to guide ABR rate adaptation for VBR encodings. As a proof of concept, we design a novel and practical control-theoretic rate adaptation scheme, CAVA (Control-theoretic Adaption for VBR-based ABR streaming), incorporating these concepts. Extensive evaluations show that CAVA substantially outperforms existing state-of-the-art adaptation techniques, validating the importance of these design principles.
The new definition of effective emissivity of non-isothermal rough surface and its approximate expression for continuous canopy vegetation

In order to determine surface temperature at large scale from space, a new definition of effective emissivity has been proposed for the whole pixel area for heterogeneous and non-isothermal surfaces. This new effective emissivity depends on the structure of the whole pixel, the optical features of components in the pixel. In order to further illustrate the new effective emissivity, the continuous canopy vegetation is taken as an example, its approximate expression of effective emissivity has been studied by the aid of the Monte Carlo algorithm.
Design and Analysis of Distributed State Estimation Algorithms Based on Belief Propagation and Applications in Smart Grids

We present a detailed study on application of factor graphs and the belief propagation (BP) algorithm to the power system state estimation (SE) problem. We start from the BP solution for the linear DC model, for which we provide a detailed convergence analysis. Using BP-based DC model we propose a fast real-time state estimator for the power system SE. The proposed estimator is easy to distribute and parallelize, thus alleviating computational limitations and allowing for processing measurements in real time. The presented algorithm may run as a continuous process. Using insights from the DC model, we use two different approaches to derive the BP algorithm for the non-linear model. The first method directly applies BP methodology, however, providing only approximate BP solution for the non-linear model. In the second approach, we make a key further step by providing the solution in which the BP is applied sequentially over the non-linear model, akin to what is done by the Gauss-Newton method. The resulting iterative Gauss-Newton belief propagation (GN-BP) algorithm can be interpreted as a distributed Gauss-Newton method with the same accuracy as the centralized SE.
A Study of the Properties of Eaton ’ s Primary Atypical Pneumonia Organism

Some of the recorded properties of a filterable organism (the PAP organism) isolated by Eaton and colleagues from cases of human primary atypical pneumonia suggest that it may be related biologically to the Mycoplasma (pleuropneumonia-like) group. In further investigation of this possibility now reported it was found that the organic gold salt, sodium aurothiomalate, which is known to inhibit certain mycoplasmas, would also inhibit infection with the PAP organism in the hamster and chick embryo lung. Some accepted viruses of a similar order of size to the PAP organism -namely, Nigg’s pneumonitis virus of mice (psittacosis group), three strains of influenza virus A, vaccinia and variola viruses-were not inhibited by sodium aurothiomalate. On the other hand, grey lung virus of mice, an organism with some properties resembling those of the PAP organism, was strongly inhibited. Diethyl ether and the antibiotic kanamycin sulphate both inhibited the growth of the PAP organism in chick embryo lung. An intensified Giemsa-staining method revealed small red-purple coccobacillary bodies (later called elementary bodies, EB) in the lungs of chick embryos infected with three different strains of PAP organism isolated, respectively, in 1944, 1954 and 1960 in different parts of the United States. The EB were not seen in uninfected chick embryo lungs. The EB and the antigen of the PAP organism stained by the fluorescent antibody technique occupied essentially the same position in relation to the mesobronchial epithelial cells of chick embryo lung. The formation of both was suppressed in parallel by treatment of inoculum or eggs with diethyl ether, kanamycin sulphate or sodium aurothiomalate. There was a good but not absolute correlation between the presence or absence of EB and antigen in experiments on the growth or survival of the P,4P organism in chick embryos, in cell-free media, and in titrations in eggs.
Sampling can be faster than optimization

Significance Modern large-scale data analysis and machine learning applications rely critically on computationally efficient algorithms. There are 2 main classes of algorithms used in this setting—those based on optimization and those based on Monte Carlo sampling. The folk wisdom is that sampling is necessarily slower than optimization and is only warranted in situations where estimates of uncertainty are needed. We show that this folk wisdom is not correct in general—there is a natural class of nonconvex problems for which the computational complexity of sampling algorithms scales linearly with the model dimension while that of optimization algorithms scales exponentially. Optimization algorithms and Monte Carlo sampling algorithms have provided the computational foundations for the rapid growth in applications of statistical machine learning in recent years. There is, however, limited theoretical understanding of the relationships between these 2 kinds of methodology, and limited understanding of relative strengths and weaknesses. Moreover, existing results have been obtained primarily in the setting of convex functions (for optimization) and log-concave functions (for sampling). In this setting, where local properties determine global properties, optimization algorithms are unsurprisingly more efficient computationally than sampling algorithms. We instead examine a class of nonconvex objective functions that arise in mixture modeling and multistable systems. In this nonconvex setting, we find that the computational complexity of sampling algorithms scales linearly with the model dimension while that of optimization algorithms scales exponentially.