Miracle-dz/UniFAR-FTUs huggingface dataset:
The Investigation of Promoter Sequences of Marseilleviruses Highlights a Remarkable Abundance of the AAATATTT Motif in Intergenic Regions

ABSTRACT Viruses display a wide range of genomic profiles and, consequently, a variety of gene expression strategies. Specific sequences associated with transcriptional processes have been described in viruses, and putative promoter motifs have been elucidated for some nucleocytoplasmic large DNA viruses (NCLDV). Among NCLDV, the Marseilleviridae is a well-recognized family because of its genomic mosaicism. The marseilleviruses have an ability to incorporate foreign genes, especially from sympatric organisms inhabiting Acanthamoeba, its main known host. Here, we identified for the first time an eight-nucleotide A/T-rich promoter sequence (AAATATTT) associated with 55% of marseillevirus genes that is conserved in all marseilleviruses lineages, a higher level of conservation than that of any giant virus described to date. We instigated our prediction about the promoter motif by biological assays and by evaluating how single mutations in this octamer can impact gene expression. The investigation of sequences that regulate the expression of genes relative to lateral transfer revealed that the promoter motifs do not appear to be incorporated by marseilleviruses from donor organisms. Indeed, analyses of the intergenic regions that regulate lateral gene transfer-related genes have revealed an independent origin of the marseillevirus intergenic regions that does not match gene-donor organisms. About 50% of AAATATTT motifs spread throughout intergenic regions of the marseilleviruses are present as multiple copies. We believe that such multiple motifs are associated with increased expression of a given gene or are related to incorporation of foreign genes into the mosaic genome of marseilleviruses. IMPORTANCE The marseilleviruses draw attention because of the peculiar features of their genomes; however, little is known about their gene expression patterns or the factors that regulate those expression patterns. The limited published research on the expression patterns of the marseilleviruses and their unique genomes has led us to study the promoter motif sequences in the intergenic regions of the marseilleviruses. This work is the first to analyze promoter sequences in the genomes of the marseilleviruses. We also suggest a strong capacity to acquire foreign genes and to express those genes mediated by multiple copies of the promoter motifs available in intergenic regions. These findings contribute to an understanding of genomic expansion and plasticity observed in these giant viruses.
Scalable Parallel Mining for Frequent Patterns from Dense Datasets Using a Cluster of PCs

− Parallelizing computation intensive data mining tasks provides an excellent means of meeting their everincreasing processing needs. Connecting several off-the-shelf PCs in a cluster is an effective and efficient way to harness their combined computing power for parallel processing. This paper describes the design and implementation of a parallel data mining algorithm on a PC cluster. The architecture of the system and its implementation are described first. Then the performance results for different configurations of processors using various dense databases are presented and compared with theoretically optimal performance.
Safety and efficacy of low intensity shockwave (LISW) treatment in patients with erectile dysfunction

ABSTRACT The primary goal in the management strategy of a patient with ED would be to determine its etiology and cure it when possible, and not just to treat the symptoms alone. One of the new therapeutic strategies is the use of low intensity extracorporeal shockwave (LISW) therapy. The mechanism of shockwave therapy is not completely clear. It is suggested that LISW induces neovascularization and improvement of cavernosal arterial flow which can lead to an improvement of erectile function by releasing NO, VEGF and PCNA. Materials and Methods: 31 patients between February and June 2013 with mild to severe ED and non-Phosphodiesterase 5 inhibitors responders were enrolled. Patients underwent four weekly treatment sessions. During each session 3600 shocks at 0.09mJ/ mm2 were given, 900 shocks at each anatomical area (right and left corpus cavernosum, right and left crus). Improvement of the erectile function was evaluated using the International Index of Erectile Function (IIEF-EF), the Sexual Encounter Profile (SEP) diaries (SEP-Questions 2 and 3) and Global Assessment Questions (GAQ-Q1 and GAQ-Q2). Results: At 3-month follow-up IIEF-EF scores improved from 16.54±6.35 at baseline to 21.03±6.38. Patients answering ‘yes’ to the SEP-Q2 elevated from 61% to 89% and from 32% to 62% in the SEP-Q3. A statistically significant improvement was reported to the Global Assessment Questions (GAQ-Q1 and GAQ-Q2). Conclusion: In conclusion, we can affirm that LISW is a confirmed therapeutic approach to erectile dysfunction that definitely needs more long-term trials to be clarified and further verified.
Flipped Learning With Simulation in Undergraduate Nursing Education.

BACKGROUND Flipped learning has proliferated in various educational environments. This study aimed to verify the effects of flipped learning on the academic achievement, teamwork skills, and satisfaction levels of undergraduate nursing students. METHOD For the flipped learning group, simulation-based education via the flipped learning method was provided, whereas traditional, simulation-based education was provided for the control group. After completion of the program, academic achievement, teamwork skills, and satisfaction levels were assessed and analyzed. RESULTS The flipped learning group received higher scores on academic achievement, teamwork skills, and satisfaction levels than the control group, including the areas of content knowledge and clinical nursing practice competency. In addition, this difference gradually increased between the two groups throughout the trial. CONCLUSION The results of this study demonstrated the positive, statistically significant effects of the flipped learning method on simulation-based nursing education. [J Nurs Educ. 2017;56(6):329-336. ].
Pain Catastrophizing, Subjective Outcomes, and Inflammatory Assessments Including Ultrasound: Results From a Longitudinal Study of Rheumatoid Arthritis Patients

Pain catastrophizing is conceptualized as a negative cognitive–affective response to anticipated or actual pain and has been associated with important pain‐related outcomes. The objective of this prospective study of established rheumatoid arthritis (RA) patients was to explore how pain catastrophizing was related to patient‐reported outcomes (PROs), composite scores, and assessments of inflammatory activity.
Wolbachia Modulates Lipid Metabolism in Aedes albopictus Mosquito Cells

ABSTRACT Certain strains of the intracellular endosymbiont Wolbachia can strongly inhibit or block the transmission of viruses such as dengue virus (DENV) by Aedes mosquitoes, and the mechanisms responsible are still not well understood. Direct infusion and liquid chromatography-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry-based lipidomics analyses were conducted using Aedes albopictus Aa23 cells that were infected with the wMel and wMelPop strains of Wolbachia in comparison to uninfected Aa23-T cells. Substantial shifts in the cellular lipid profile were apparent in the presence of Wolbachia. Most significantly, almost all sphingolipid classes were depleted, and some reductions in diacylglycerols and phosphatidylcholines were also observed. These lipid classes have previously been shown to be selectively enriched in DENV-infected mosquito cells, suggesting that Wolbachia may produce a cellular lipid environment that is antagonistic to viral replication. The data improve our understanding of the intracellular interactions between Wolbachia and mosquitoes. IMPORTANCE Mosquitoes transmit a variety of important viruses to humans, such as dengue virus and Zika virus. Certain strains of the intracellular bacterial genus called Wolbachia found in or introduced into mosquitoes can block the transmission of viruses, including dengue virus, but the mechanisms responsible are not well understood. We found substantial shifts in the cellular lipid profiles in the presence of these bacteria. Some lipid classes previously shown to be enriched in dengue virus-infected mosquito cells were depleted in the presence of Wolbachia, suggesting that Wolbachia may produce a cellular lipid environment that inhibits mosquito-borne viruses.
Potential Use of Dimethyl Sulfoxide in Treatment of Infections Caused by Pseudomonas aeruginosa

ABSTRACT Dimethyl sulfoxide (DMSO) is commonly used as a solvent to dissolve water-insoluble drugs or other test samples in both in vivo and in vitro experiments. It was observed during our experiment that DMSO at noninhibitory concentrations could significantly inhibit pyocyanin production in the human pathogen Pseudomonas aeruginosa. Pyocyanin is an important pathogenic factor whose production is controlled by a cell density-dependent quorum-sensing (QS) system. Investigation of the effect of DMSO on QS showed that DMSO has significant QS antagonistic activities and concentrations of DMSO in the micromolar range attenuated a battery of QS-controlled virulence factors, including rhamnolipid, elastase, and LasA protease production and biofilm formation. Further study indicated that DMSO inhibition of biofilm formation and pyocyanin production was attained by reducing the level of production of an autoinducer molecule of the rhl QS system, N-butanoyl-l-homoserine lactone (C4-HSL). In a mouse model of a burn wound infection with P. aeruginosa, treatment with DMSO significantly decreased mouse mortality compared with that for mice in the control group. The capacity of DMSO to attenuate the pathogenicity of P. aeruginosa points to the potential use of DMSO as an antipathogenic agent for the treatment of P. aeruginosa infection. As a commonly used solvent, however, DMSO's impact on bacterial virulence calls for cautionary attention in its usage in biological, medicinal, and clinical studies.
Assessing the External Validity of an Experimental Wage Subsidy

In Canada, a policy aiming at helping single parents on social assistance become self-reliant was implemented on an experimental basis. The Self-Sufficiency Entry Effects Demonstration randomly selected a sample of 4,134 single parents who had applied for welfare between January 1994 and March 1995. It turned out only 3,315 took part in the experiment despite a 50% chance of receiving a generous, time-limited, earnings supplement conditional on finding a full-time job and leaving income assistance within a year. The purpose of this paper is to determine whether a non-response rate of 20% is likely to harm the external validity of the experiment. We compare the estimated impact of the program using experimental data only to that obtained using additional data on individuals not taking part in the experiment. We find strong evidence of non-response bias in the data. When we correct for the bias, we find that estimates that rely on experimental data only significantly underestimate the true impact of the program.
Phase 1 Study of the Safety, Tolerability, and Pharmacokinetics of the β-Lactamase Inhibitor Vaborbactam (RPX7009) in Healthy Adult Subjects

ABSTRACT Vaborbactam (formerly RPX7009) is a member of a new class of β-lactamase inhibitor with pharmacokinetic properties similar to those of many β-lactams, including carbapenems. The pharmacokinetics and safety of vaborbactam were evaluated in 80 healthy adult subjects in a first-in-human randomized, placebo-controlled, double-blind, sequential single- and multiple-ascending-dose study. A total of 10 dose cohorts were enrolled in the study, with 6 subjects randomized to receive 250 to 2,000 mg of vaborbactam and 2 subjects randomized to receive placebo in each cohort. Maximum concentrations for vaborbactam were achieved at the end of the 3-h infusion. Vaborbactam exposure (Cmax and area under the concentration-time curve [AUC]) increased in a dose-proportional manner following multiple doses. There was no evidence of accumulation with multiple doses, consistent with the terminal half-life of ∼2 h. Both the volume of distribution (Vss) and plasma clearance were independent of dose. For the 2,000-mg dose, the plasma clearance was 0.17 ± 0.03 liters/h, the AUC from 0 h to infinity (AUC0–∞) was 144.00 ± 13.90 mg · h/liter, and the Vss was 21.80 ± 2.26 mg · h/liter. Urinary recovery was 80% or greater over 48 h across all dose groups. No subjects discontinued the study due to adverse events (AEs), and no serious AEs (SAEs) were observed. All AEs were mild to moderate and similar among the vaborbactam- and placebo-treated subjects, with mild lethargy as the only unique AE reported with the high dose of vaborbactam. Overall, this study revealed the safety, tolerability, and pharmacokinetic profile of vaborbactam and formed the basis for advancement into patient studies in combination with meropenem, including treatment of patients with carbapenem-resistant Enterobacteriaceae (CRE) infections. (This study is registered at ClinicalTrials.gov under identifier NCT01751269.)
Who SKIPS? Using Temperament to Explain Differential Outcomes of a Motor Competence Intervention for Preschoolers

ABSTRACT Purpose: Although motor skill interventions often improve fundamental motor skills (FMS) during preschool, the extent of individual children’s success in development of FMS still varies among children receiving the same intervention. Temperament is multifaceted and includes negative affect (high levels of frustration or anger), effortful control (focus, self-regulation, and concentration), and surgency (energy and activity level). Temperament often influences cognitive, social, and behavioral outcomes and may be a significant factor in the development of FMS. The purpose of this study was to examine the influence of temperament on children’s improvement in FMS within a gross motor intervention. Method: Participants (N = 80; Mage = 55.36 months, SD = 6.99 months) completed the Test of Gross Motor Development-Second Edition prior to and after intervention. Teachers completed the Child Behavior Questionnaire-Very Short Form to examine each child’s temperament. To account for possibility of a Type 1 error, we conducted 6 separate 2 (temperament variable: high, low) × 2 (treatment: intervention, control) analyses of covariance and examined posttest scores for locomotor and object-control skills with pretest scores as covariates among participants with high and low surgency, negative affect, and effortful control. Results: Results revealed children with low levels of negative affect and surgency and high levels of effortful control demonstrated greater gains (ηp2 = .05–.34) in both locomotor and object-control skills during motor skill intervention compared with their peers. Conclusion: Providing interventions tailored to temperamental profiles could maximize gains in FMS through intervention.
Model-Based Action Exploration for Learning Dynamic Motion Skills

Deep reinforcement learning has achieved great strides in solving challenging motion control tasks. Recently, there has been significant work on methods for exploiting the data gathered during training, but there has been less work on how to best generate the data to learn from. For continuous action domains, the most common method for generating exploratory actions involves sampling from a Gaussian distribution centred around the mean action output by a policy. Although these methods can be quite capable, they do not scale well with the dimensionality of the action space, and can be dangerous to apply on hardware. We consider learning a forward dynamics model to predict the result, $(x_{t+1})$, of taking a particular action, ($u$), given a specific observation of the state, $(x_{t})$. With this model we perform internal lookahead predictions of outcomes and seek actions we believe have a reasonable chance of success. This method alters the exploratory action space, thereby increasing learning speed and enables higher quality solutions to difficult problems, such as robotic locomotion and juggling.
Scalable Parallel Algorithm of Multiple-Relaxation-Time Lattice Boltzmann Method with Large Eddy Simulation on Multi-GPUs

The lattice Boltzmann method (LBM) has become an attractive and promising approach in computational fluid dynamics (CFD). In this paper, parallel algorithm of D3Q19 multi-relaxation-time LBM with large eddy simulation (LES) is presented to simulate 3D flow past a sphere using multi-GPUs (graphic processing units). In order to deal with complex boundary, the judgement method of boundary lattice for complex boundary is devised. The 3D domain decomposition method is applied to improve the scalability for cluster, and the overlapping mode is introduced to hide the communication time by dividing the subdomain into two parts: inner part and outer part. Numerical results show good agreement with literature and the 12 Kepler K20M GPUs perform about 5100 million lattice updates per second, which indicates considerable scalability.
Interference from 24-GHz automotive radars to passive microwave earth remote sensing satellites

The automotive industry is currently considering the introduction of short-range radars (SRR) operating near 24 GHz for improving road traffic safety. SSRs are intended to observe the full azimuthal space cover around a vehicle using up to eight sensors. The sensors would operate in an ultrawideband (UWB) mode, occupying 3-5 GHz of bandwidth. Interference from SRR transmitters with passive microwave remote sensing satellites used for weather and climate monitoring could occur as the result of several coupling mechanisms, including direct coupling via the transmit antenna beam and scattering and diffraction of the transmitted signals from leading vehicles, buildings, and other nearby objects. In this study, we estimate the amount of coupling anticipated to occur from SRRs, including the direct and scattered contributions. The calculations are based on bistatic scattering measurements of a typical automobile and ray optical simulations of reflection and propagation in an urban environment. Using these calculations, the maximum allowable SRR transmitted power for interference levels acceptable for meteorological and climatological remote sensing applications are quantified. The study provides criteria for SRR operation with the Earth Exploration Satellite Service on a noninterference basis.
Automated detection of focal cortical dysplasia type II with surface‐based magnetic resonance imaging postprocessing and machine learning

Focal cortical dysplasia (FCD) is a major pathology in patients undergoing surgical resection to treat pharmacoresistant epilepsy. Magnetic resonance imaging (MRI) postprocessing methods may provide essential help for detection of FCD. In this study, we utilized surface‐based MRI morphometry and machine learning for automated lesion detection in a mixed cohort of patients with FCD type II from 3 different epilepsy centers.
Brain Connectivity

It has been well known that gender plays a critical role in the anatomy and function of the human brain, as well as human behaviors. Recent neuroimaging studies have demonstrated gender effects on not only focal brain areas but also the connectivity between areas. Specifically, structural MRI and diffusion MRI data have revealed substantial gender differences in white matter–based anatomical connectivity. Structural MRI data further demonstrated gender differences in the connectivity revealed by morphometric correlation among brain areas. Functional connectivity derived from functional neuroimaging (e.g., functional MRI and PET) data is also modulated by gender. Moreover, male and female human brains display differences in the network topology that represents the organizational patterns of brain connectivity across the entire brain. In this review, the authors summarize recent findings in the multimodal brain connectivity/network research with gender, focusing on large-scale data sets derived from modern neuroimaging techniques. The literature provides convergent evidence for a substantial gender difference in brain connectivity within the human brain that possibly underlies gender-related cognitive differences. Therefore, it should be mandatory to take gender into account when designing experiments or interpreting results of brain connectivity/network in health and disease. Future studies will likely be conducted to explore the interdependence between gender-related brain connectivity/network and the gender-specific nature of brain diseases as well as to investigate gender-related characteristics of multimodal brain connectivity/network in the normal brain.
Low-grade Epstein-Barr virus positive plasma cell proliferations of precursor plasma cell origin: Report of two cases

B cell lymphoproliferative disorders with plasmacytic differentiation are a spectrum of neoplasms arising from B cells in different stages of maturation, which include marginal zone lymphoma, plasmablastic lymphoma, ALK-positive diffuse large B cell lymphoma, primary effusion lymphoma, and plasma cell neoplasms. Within this group, Epstein-Barr virus (EBV) is mostly linked to plasmablastic lymphoma and primary effusion lymphoma. EBV has only rarely been associated with the remaining entities and occurs almost exclusively in immunocompromised patients. We report two cases of EBV positive, mature appearing plasma cell proliferations without previously identified immunodeficiency. The proliferating plasma cells showed co-expression of CD19, CD38, and CD138 with monotypic surface light chain expression suggesting a plasmablastic origin. The neoplastic plasma cells were positive for EBV RNA by in situ hybridization (EBER) in both cases, and showed a low proliferation index (Ki-67 10-20%). Such lesions could be easily mistaken for plasmacytomas and low grade B cell non-Hodgkin lymphomas with extensive plasmacytic differentiation without detailed immunophenotyping and EBV studies, if the diagnosis is solely based on the morphologic features and the low proliferation index. Increased awareness of this rare or under recognized entity is necessary to better characterize this group of neoplasms and determine the best treatment approach for these patients.
Fast Learning of Clusters and Topics via Sparse Posteriors

Mixture models and topic models generate each observation from a single cluster, but standard variational posteriors for each observation assign positive probability to all possible clusters. This requires dense storage and runtime costs that scale with the total number of clusters, even though typically only a few clusters have significant posterior mass for any data point. We propose a constrained family of sparse variational distributions that allow at most $L$ non-zero entries, where the tunable threshold $L$ trades off speed for accuracy. Previous sparse approximations have used hard assignments ($L=1$), but we find that moderate values of $L>1$ provide superior performance. Our approach easily integrates with stochastic or incremental optimization algorithms to scale to millions of examples. Experiments training mixture models of image patches and topic models for news articles show that our approach produces better-quality models in far less time than baseline methods.