Miracle-dz/UniFAR-FTUs huggingface dataset:
Ceramide Suppresses Influenza A Virus Replication In Vitro

Understanding the effect of sphingolipid metabolism on viral pathogenesis provide important insights into the development of therapeutic strategies against microbial infections. In this study, we demonstrate a critical role of ceramide during influenza A virus infection. We demonstrate that ceramide produced through de novo biosynthesis possess an antiviral role. These observations unlock new opportunities for the development of novel antiviral therapies against influenza. ABSTRACT Annual influenza outbreaks are associated with significant morbidity and mortality worldwide despite the availability of seasonal vaccines. Influenza pathogenesis depends on the manipulation of host cell signaling to promote virus replication. Ceramide is a sphingosine-derived lipid that regulates diverse cellular processes. Studies highlighted the differential role of ceramide de novo biosynthesis on the propagation of various viruses. Whether ceramide plays, a role in influenza virus replication is not known. In this study, we assessed the potential interplay between the influenza A (IAV) and ceramide biosynthesis pathways. The accumulation of ceramide in human lung epithelial cells infected with influenza A/H1N1 virus strains was evaluated using thin-layer chromatography and/or confocal microscopy. Virus replication was assessed upon the regulation of the de novo ceramide biosynthesis pathway. A significant increase in ceramide accumulation was observed in cells infected with IAV in a dose- and time-dependent manner. Inoculating the cells with UV-inactivated IAV did not result in ceramide accumulation in the cells, suggesting that the induction of ceramide required an active virus replication. Inhibiting de novo ceramide significantly decreased ceramide accumulation and enhanced virus replication. The addition of exogenous C6-ceramide prior to infection mediated an increase in cellular ceramide levels and significantly attenuated IAV replication and reduced viral titers (≈1 log10 PFU/ml unit). Therefore, our data demonstrate that ceramide accumulation through de novo biosynthesis pathway plays a protective and antiviral role against IAV infection. These findings propose new avenues for development of antiviral molecules and strategies. IMPORTANCE Understanding the effect of sphingolipid metabolism on viral pathogenesis provide important insights into the development of therapeutic strategies against microbial infections. In this study, we demonstrate a critical role of ceramide during influenza A virus infection. We demonstrate that ceramide produced through de novo biosynthesis possess an antiviral role. These observations unlock new opportunities for the development of novel antiviral therapies against influenza.
Next-Generation Sequencing and CRISPR/Cas13 Editing in Viroid Research and Molecular Diagnostics

Viroid discovery as well as the economic significance of viroids and biological properties are presented. Next-generation sequencing (NGS) technologies combined with informatics have been applied to viroid research and diagnostics for almost a decade. NGS provides highly efficient, rapid, low-cost high-throughput sequencing of viroid genomes and of the 21–24 nt vd-sRNAs generated by the RNA silencing defense of the host. NGS has been utilized in various viroid studies which are presented. The discovery during the last few years that prokaryotes have heritable adaptive immunity mediated through clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins, have led to transformative advances in molecular biology, notably genome engineering and most recently molecular diagnostics. The potential application of the CRISPR-Cas13a system for engineering viroid interference in plants is suggested by targeting specific motifs of three economically important viroids. The CRISPR-Cas13 system has been utilized recently for the accurate detection of human RNA viruses by visual read out in 90 min or less and by paper-based assay. Multitarget RNA tests by this technology have a good potential for application as a rapid and accurate diagnostic assay for known viroids. The CRISPR/Cas system will work only for known viroids in contrast to NGS, but it should be much faster.
Mouse Model of Tracheal Replacement With Electrospun Nanofiber Scaffolds

Objectives: The clinical experience with tissue-engineered tracheal grafts (TETGs) has been fraught with graft stenosis and delayed epithelialization. A mouse model of orthotopic replacement that recapitulates the clinical findings would facilitate the study of the cellular and molecular mechanisms underlying graft stenosis. Methods: Electrospun nanofiber tracheal scaffolds were created using nonresorbable (polyethylene terephthalate + polyurethane) and co-electrospun resorbable (polylactide-co-caprolactone/polyglycolic acid) polymers (n = 10/group). Biomechanical testing was performed to compare load displacement of nanofiber scaffolds to native mouse tracheas. Mice underwent orthotopic tracheal replacement with syngeneic grafts (n = 5) and nonresorbable (n = 10) and resorbable (n = 10) scaffolds. Tissue at the anastomosis was evaluated using hematoxylin and eosin (H&E), K5+ basal cells were evaluated with the help of immunofluorescence testing, and cellular infiltration of the scaffold was quantified. Micro computed tomography was performed to assess graft patency and correlate radiographic and histologic findings with respiratory symptoms. Results: Synthetic scaffolds were supraphysiologic in compression tests compared to native mouse trachea (P < .0001). Nonresorbable scaffolds were stiffer than resorbable scaffolds (P = .0004). Eighty percent of syngeneic recipients survived to the study endpoint of 60 days postoperatively. Mean survival with nonresorbable scaffolds was 11.40 ± 7.31 days and 6.70 ± 3.95 days with resorbable scaffolds (P = .095). Stenosis manifested with tissue overgrowth in nonresorbable scaffolds and malacia in resorbable scaffolds. Quantification of scaffold cellular infiltration correlated with length of survival in resorbable scaffolds (R2 = 0.95, P = .0051). Micro computed tomography demonstrated the development of graft stenosis at the distal anastomosis on day 5 and progressed until euthanasia was performed on day 11. Conclusion: Graft stenosis seen in orthotopic tracheal replacement with synthetic tracheal scaffolds can be modeled in mice. The wide array of lineage tracing and transgenic mouse models available will permit future investigation of the cellular and molecular mechanisms underlying TETG stenosis.
Out of the Cube: Augmented Rubik's Cube

Computer gaming habits have a tendency to evolve with technology, the best being ones that immerse both our imagination and intellect. Here, we describe a new game platform, an Augmented Reality Rubik's cube. The cube acts simultaneously as both the controller and the game board. Gameplay is controlled by the cube, and game assets are rendered on top of it. Shuffling and tilting operations on the cube are mapped to game interaction. We discuss the game design decisions involved in developing a game for this platform, as well as the technological challenges in implementing it. Ultimately, we describe two games and discuss the conclusions of an informal user study based on those games.
23-year dynamics (1994-2016) relationships to its health, behavioral characteristics and  prevention of cardiovascular diseases among women 25-44 years in Russia /Siberia.

AIM To determine the 23-year dynamics (1994-2016) of attitudes toward one's health, behavioral characteristics and the prevention of cardiovascular diseases in an open population among women 25-44 years old in Russia / Siberia (Novosibirsk). MATERIALS AND METHODS In the framework of the third screening of the MONICA program for the study of trends and control of cardiovascular diseases and the MONICA-psychosocial (MOPSY) subprogram, in 1994 a random representative sample of women aged 25-64 years of age from one from the districts of Novosibirsk (n = 870, the average age is 45.4±0.4 years); in the age group 25-44 years - 284 persons. In 2016 years. in the framework of screening studies on the budgetary issue of NIITPM No. gos. reg. 01201282292, a random representative sample of women aged 25-44 years old in the same district of Novosibirsk (n = 540) was examined. Attitude to their health, behavioral characteristics and the prevention of cardiovascular diseases were studied using the "Knowledge and attitude to their health" scale, validated for the Russian population under the WHO "MONICA" program. The chi-square test (x2) was used to calculate the indices. The criterion of statistical significance was the reliability of the result at p<0.05. RESULTS The analysis showed that in the open population among women aged 25-44 years, there is a positive dynamics in assessing their health (21% and 50.7%, respectively). But, despite this, 50% of women negatively assess their health and 96% note the probability of getting a serious illness for 5-10 years. Most women believe in the ability of medicine to successfully prevent and treat heart disease, but the proportion of people using health resources for preventive purposes remains extremely low and does not exceed 10%. In the open population among women aged 25-44 years for 23 years there is an increase in stress in the workplace and the trend of growth in changes in marital status. Recorded in the period 1994-2016 gg. changes in the behavior of women associated with health: increased the proportion of people who gave up smoking and regularly doing physical exercises, and improved eating behavior. CONCLUSION It was found that among women aged 25-44 years there is a positive dynamics in relation to the prevention of behavioral risk factors for CVD. But despite this, half of women negatively assess their health and use health resources only slightly.
Estimating blood pressure trends and the nocturnal dip from photoplethysmography

Objective. Evaluate a method for the estimation of the nocturnal systolic blood pressure (SBP) dip from 24 h blood pressure trends using a wrist-worn photoplethysmography (PPG) sensor and a deep neural network in free-living individuals, comparing the deep neural network to traditional machine learning and non-machine learning baselines. Approach. A wrist-worn PPG sensor was worn by 106 healthy individuals for 226 d during which 5111 reference values for blood pressure (BP) were obtained with a 24 h ambulatory BP monitor and matched with the PPG sensor data. Features based on heart rate variability and pulse morphology were extracted from the PPG waveforms. Long- and short term memory (LSTM) networks, dense networks, random forests and linear regression models were trained and evaluated in their capability of tracking trends in BP, as well as the estimation of the SBP dip. Main results. Best performance for estimating the SBP dip were obtained with a deep LSTM neural network with a root mean squared error (RMSE) of 3.12 2.20 mmHg and a correlation of 0.69 . This dip was derived from trend estimates of BP which had an RMSE of 8.22 1.49 mmHg for systolic and 6.55 1.39 mmHg for diastolic BP (DBP). While other models had similar performance for the tracking of relative BP, they did not perform as well as the LSTM for the SBP dip. Significance: The work provides first evidence for the unobtrusive estimation of the nocturnal SBP dip, a highly prognostic clinical parameter. It is also the first to evaluate unobtrusive BP measurement in a large data set of unconstrained 24 h measurements in free-living individuals and provides evidence for the utility of LSTM models in this domain.
On Parsing Visual Sequences with the Hidden Markov Model

Hidden Markov Models have been employed in many vision applications to model and identify events of interest. Their use is common in applications where HMMs are used to classify previously divided segments of video as one of a set of events being modelled. HMMs can also simultaneously segment and classify events within a continuous video, without the need for a separate first step to identify the start and end of the events. This is significantly less common. This paper is an exploration of the development of HMM frameworks for such complete event recognition. A review of how HMMs have been applied to both event classification and recognition is presented. The discussion evolves in parallel with an example of a real application in psychology for illustration. The complete videos depict sessions where candidates perform a number of different exercises under the instruction of a psychologist. The goal is to isolate portions of video containing just one of these exercises. The exercise involves rotating the head of a kneeling subject to the left, back to centre, to the right, to the centre, and repeating a number of times. By designing a HMM system to automatically isolate portions of video containing this exercise, issues such as the strategy of choice of event to be modelled, feature design and selection, as well as training and testing are reviewed. Thus this paper shows how HMMs can be more extensively applied in the domain of event recognition in video.
Feature extraction of four-class motor imagery EEG signals based on functional brain network

Objective. A motor-imagery-based brain–computer interface (MI-BCI) provides an alternative way for people to interface with the outside world. However, the classification accuracy of MI signals remains challenging, especially with an increased number of classes and the presence of high variations with data from multiple individual people. This work investigates electroencephalogram (EEG) signal processing techniques, aiming to enhance the classification performance of multiple MI tasks in terms of tackling the challenges caused by the vast variety of subjects. Approach. This work introduces a novel method to extract discriminative features by combining the features of functional brain networks with two other feature extraction algorithms: common spatial pattern (CSP) and local characteristic-scale decomposition (LCD). After functional brain networks are established from the MI EEG signals of the subjects, the measures of degree in the binary networks are extracted as additional features and fused with features in the frequency and spatial domains extracted by the CSP and LCD algorithms. A real-time BCI robot control system is designed and implemented with the proposed method. Subjects can control the movement of the robot through four classes of MI tasks. Both the BCI competition IV dataset 2a and real-time data acquired in our designed system are used to validate the performance of the proposed method. Main results. As for the offline data experiment results, the average classification accuracy of the proposed method reaches 79.7%, outperforming the majority of popular algorithms. Experimental results with real-time data also prove the proposed method to be highly promising in its real-time performance. Significance. The experimental results show that our proposed method is robust in extracting discriminative brain activity features when performing different MI tasks, hence improving the classification accuracy in four-class MI tasks. The high classification accuracy and low computational demand show a considerable practicality for real-time rehabilitation systems.
Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome

Protein tyrosine phosphatases (PTPs) fulfil multiple key regulatory functions. Within the group of PTPs, the atypical lipid phosphatases (ALPs) are known for their role as virulence factors associated with human pathogens. Another group of PTPs, which is capable of using inositol-hexakisphosphate (InsP6) as substrate, are known as phytases. Phytases play major roles in the environmental phosphorus cycle, biotechnology, and pathogenesis. So far, all functionally characterized PTPs, including ALPs and PTP-phytases, have been derived exclusively from isolated microorganisms. In this study, screening of a soil-derived metagenomic library resulted in identification of a gene (pho16B), encoding a PTP, which shares structural characteristics with the ALPs. In addition, the characterization of the gene product (Pho16B) revealed the capability of the protein to use InsP6 as substrate, and the potential of soil as a source of phytases with so far unknown characteristics. Thus, Pho16B represents the first functional environmentally derived PTP-phytase. The enzyme has a molecular mass of 38 kDa. The enzyme is promiscuous, showing highest activity and affinity toward naphthyl phosphate (Km 0.966 mM). Pho16B contains the HCXXGKDR[TA]G submotif of PTP-ALPs, and it is structurally related to PtpB of Mycobacterium tuberculosis. This study demonstrates the presence and functionality of an environmental gene codifying a PTP-phytase homologous to enzymes closely associated to bacterial pathogenicity.
Bcd1p controls RNA loading of the core protein Nop58 during C/D box snoRNP biogenesis

Biogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins (C/D snoRNPs) is guided by conserved trans-acting factors that act collectively to assemble the core proteins SNU13/Snu13, NOP58/Nop58, NOP56/Nop56, FBL/Nop1, and box C/D small nucleolar RNAs (C/D snoRNAs), in human and in yeast, respectively. This finely elaborated process involves the sequential interplay of snoRNP-related proteins and RNA through the formation of transient pre-RNP complexes. BCD1/Bcd1 protein is essential for yeast cell growth and for the specific accumulation of box C/D snoRNAs. In this work, chromatin, RNA, and protein immunoprecipitation assays revealed the ordered loading of several snoRNP-related proteins on immature and mature snoRNA species. Our results identify Bcd1p as an assembly factor of C/D snoRNP biogenesis that is likely recruited cotranscriptionally and that directs the loading of the core protein Nop58 on RNA.
E-cigarette use (vaping) is associated with illicit drug use, mental health problems, and impulsivity in university students.

BACKGROUND This study examined the prevalence of e-cigarette use ("vaping") among university students and its associations with psychosocial correlates. METHODS In this study, 9,449 students received a 156-item anonymous online survey assessed the use of e-cigarettes (ever or past year), alcohol and drug use, mental health issues, and impulsive and compulsive traits. RESULTS In total, 3,572 university students (57.1% female) responded to the survey. The prevalence of past 12-month e-cigarette use was 9.2%, with 9.8% reporting having used more than 12 months ago. E-cigarette use was associated with the use of multiple other drugs (eg, alcohol, opiates). Those who used e-cigarettes were significantly more likely to have mental health histories of attention-deficit/hyperactivity disorder, posttraumatic stress disorder, gambling disorder, and anxiety, to report low self-esteem, and to endorse traits of impulsivity. CONCLUSIONS Use of e-cigarettes is common in university students and appears to be associated with a variety of mental health and drug use problems. Clinicians should be aware that certain mental health conditions are more common in e-cigarette users. This study indicates the need for longitudinal research into the effects of chronic nicotine consumption on brain function and mental health, especially in young people, since such effects would be common to conventional tobacco smoking and vaping.
Similarity Grouping as Feature-Based Selection

Across the natural world as well as the artificial worlds of maps, diagrams, and data visualizations, feature similarity (e.g., color and shape) links spatially separate areas into sets. Despite a century of study, it is yet unclear what mechanism underlies this gestalt similarity grouping. One recent proposal is that similarity grouping—for example, seeing a red, vertical, or square group—is just global selection of those features. Although parsimonious, this account makes the counterintuitive prediction that similarity grouping is strictly serial: A green group cannot be constructed at the same time as a red group. We tested this prediction with a novel measure—a grouping illusion within number-estimation tasks that should work only if participants simultaneously construct groups—and found the strongest evidence yet in favor of serial feature-based attention (Ns = 14, 12, and 12 for Experiment 1, Experiment 2, and Experiment 3, respectively).
Complete mitochondrial genome of sterlet (Acipenser ruthenus)

Abstract The complete mitochondrial genome of sterlet (Acipenser ruthenus) was determined in this study. The mitogenome is 16,790 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (the control region and the putative origin of the light strand replication) with a typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand is 30.26% for A, 29.00% for C, 16.23% for G and 24.51% for T, with a slight AT bias of 54.77%.
In silico Identification of Novel Toxin Homologs and Associated Mobile Genetic Elements in Clostridium perfringens

Clostridium perfringens causes a wide range of diseases in a variety of hosts, due to the production of a diverse set of toxins and extracellular enzymes. The C. perfringens toxins play an important role in pathogenesis, such that the presence and absence of the toxins is used as a typing scheme for the species. In recent years, several new toxins have been discovered that have been shown to be essential or highly correlated to diseases; these include binary enterotoxin (BecAB), NetB and NetF. In the current study, genome sequence analysis of C. perfringens isolates from diverse sources revealed several putative novel toxin homologs, some of which appeared to be associated with potential mobile genetic elements, including transposons and plasmids. Four novel toxin homologs encoding proteins related to the pore-forming Leukocidin/Hemolysin family were found in type A and G isolates. Two novel toxin homologs encoding proteins related to the epsilon aerolysin-like toxin family were identified in Type A and F isolates from humans, contaminated food and turkeys. A novel set of proteins related to clostridial binary toxins was also identified. While phenotypic characterisation is required before any of these homologs can be established as functional toxins, the in silico identification of these novel homologs on mobile genetic elements suggests the potential toxin reservoir of C. perfringens may be much larger than previously thought.