Miracle-dz/UniFAR-FTUs huggingface dataset:
Code Refinement of Stencil Codes

A straightforward implementation of an algorithm in a general-purpose programming language does usually not deliver peak performance: Compilers often fail to automatically tune the code for certain hardware peculiarities like memory hierarchy or vector execution units. Manually tuning the code is firstly error-prone as well as time-consuming and secondly taints the code by exposing those peculiarities to the implementation. A popular method to avoid these problems is to implement the algorithm in a Domain-Specific Language (DSL). A DSL compiler can then automatically tune the code for the target platform. In this article we show how to embed a DSL for stencil codes in another language. In contrast to prior approaches we only use a single language for this task which offers explicit control over code refinement. This is used to specialize stencils for particular scenarios. Our results show that our specialized programs achieve competitive performance compared to hand-tuned CUDA programs while maintaining a convenient coding experience.
kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

Motifs of only 1–4 letters can play important roles when present at key locations within macromolecules. Because existing motif-discovery tools typically miss these position-specific short motifs, we developed kpLogo, a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs. kpLogo also overcomes the limitations of conventional motif-visualization tools in handling positional interdependencies and utilizing ranked or weighted sequences increasingly available from high-throughput assays.
Molecular Characterization of Infectious Clones of the Minute Virus of Canines Reveals Unique Features of Bocaviruses

ABSTRACT Minute virus of canines (MVC) is a member of the genus Bocavirus in the family Parvoviridae. We have molecularly cloned and sequenced the 5′- and 3′-terminal palindromes of MVC. The MVC genome, 5,404 nucleotides (nt) in length, shared an identity of 52.6% and 52.1% with that of human bocavirus and bovine parvovirus, respectively. It had distinct palindromic hairpins of 183 nt and 198 nt at the left-end and right-end termini of the genome, respectively. The left-end terminus was also found in two alternative orientations (flip or flop). Both termini shared extensive similarities with those of bovine parvovirus. Four full-length molecular clones constructed with different orientations of the left-end terminus proved to be infectious in Walter Reed canine cell/3873D (WRD) canine cells. Both MVC infection and transfection of the infectious clone in WRD cells revealed an identical RNA transcription profile that was similar to that of bovine parvovirus. Mutagenesis of the infectious clone demonstrated that the middle open reading frame encodes the NP1 protein. This protein, unique to the genus Bocavirus, was essential for MVC DNA replication. Moreover, the phospholipase A2 motif in the VP1 unique region was also critical for MVC infection. Thus, our studies revealed important information about the genus Bocavirus that may eventually help us to clone the human bocavirus and study its pathogenesis.
Motor abilities of children and adolescents with a psychiatric condition: A systematic literature review.

AIM To summarize research regarding the motor abilities of children and adolescents who suffer from a common psychiatric condition. METHODS In order to outline the current knowledge regarding the motor abilities of children and adolescents with autism spectrum disorders (ASD), attention deficit hyperactivity disorder (ADHD), disruptive behavior disorders (DBD) and depression, a comprehensive systematic literature search was carried out using PubMed, Medline and ERIC databases. The databases were searched for relevant English language articles published between January 1990 and April 2014. Only studies that conducted a quantitative evaluation of motor ability and concerned individuals aged 0-18 years were included. A separate search was conducted for each disorder (ASD, ADHD, DBD, depression) in conjunction with each of the following keywords: (psycho/perceptuo) motor/movement skill(s), (psycho/perceptuo) motor/movement abilities, (psycho/perceptuo) motor/movement impairment, (psycho/perceptuo) motor/movement problem(s), motor function, motor coordination, motor performance, motor deficit(s). To detect supplementary relevant literature, the reference lists of the retrieved articles were examined. RESULTS The search strategy yielded 51 studies meeting the inclusion criteria. In total, 28 studies were included that examined the motor abilities of children and adolescents with ASD. All studies indicated that they performed below average on various standardized motor assessment instruments. The overall prevalence rate for impairment in motor abilities ranged from 33% to 100%. Twenty-seven studies examined the motor abilities of children and adolescents with ADHD. Depending on the type of motor assessment tool and the cut-off points used by different researchers, prevalence rates of impairment in motor abilities are highly variable and ranged from 8% to 73%. Remarkably, there is a paucity of research addressing the motor abilities of individuals with DBD or depression. Furthermore, methodological problems, such as measurement and comorbidity issues, complicate the generalization of the findings. CONCLUSION Research suggests that motor impairment is highly prevalent in some psychiatric conditions, particularly ASD and ADHD. However, future work is necessary to draw sound conclusions.
Managing interference through space-time codes, lattice reduction and network coding

This paper studies the problem of providing a link between network coding and the signal space for interference management. The main idea is to find a correspondence at the relays, between the binary flows (at the network coding level) and the signal flows (at the physical layer), that is, to find a linear relation at the binary level that mimics the linear relation at the signal level. This has already been done but by neglecting the channel coefficients/matrices or considering some “perfect power control”. We show, in this paper how to find such a relation with any kind of channel by using an efficient channel quantization. As a corollary, such result can also be transposed to the so-called deterministic model of.
Atopic myelitis: first case report outside Japan?

episode of VTED in their follow up of 96 patients with CSS (4). Several factors may explain the association between CSS and VTED. First, VTED may be the mere consequence of classical thromboembolic risk factors such as heart failure, immobilization or hospitalization, as evidenced in our first and second cases. Secondly, inflammatory diseases may predispose to vascular thrombosis. For instance, it has been demonstrated that patients displaying inflammatory bowel disease have a threefold increased risk of developing acute VTED (5). More specifically, eosinophilic inflammation may be a risk factor for thrombotic events. Follow up of 15 patients with hypereosinophilic syndrome led to the description of 10 thromboembolic complications including two VTED (6). A possible explanation of this association could be the ability of eosinophil cationic protein to bind, in vitro, to Hageman factor (XII) and activate the intrinsic pathway of coagulation. In conclusion, we describe three episodes of severe VTED in a cohort of 10 CSS patients. It remains unclear whether VTED was the consequence of specific vascular lesions or the mere result of a combination of classical VTED risk factors.
Patient Experience with Conscious Sedation as a Method of Pain Relief for Transvaginal Oocyte Retrieval: A Cross Sectional Study

Aim: The aim of the study was to measure patient’s satisfaction level and acceptance of conscious sedation as a method of pain relief following transvaginal oocyte retrieval (TVOR) during assisted reproduction technology treatment. We also evaluated the factors that may influence the efficacy of conscious sedation method. Setting and Design: A prospective cross-sectional study. Materials and Methods: Prospective study was conducted from October 2015 to January 2016 at a university-level hospital and 100 women were recruited. Variables for analysis included woman age, duration of procedure, number of oocytes retrieved, and transmyometrial passage of the needle. Pain assessment was done by visual analog scale (VAS). Medical complications, and patient satisfaction score [Likert’s score and client satisfaction questionnaire (CSQ)] were recorded. Results: There was a moderate positive correlation between age and pain score on day 1 post-procedure. When the duration of procedure was >12 min, immediate post-procedure pain score was significantly higher compared to those whose procedure where duration was <12 min. There was no correlation between pain score and the number of oocytes retrieved (≤5, 6–15, and ≥16) and transmyometrial passage of needle. The VAS 10-point score immediately post-procedure, after 6 and 24 h post-procedure, and on day of embryo transfer was 2.83 (±1.67), 0.78 (±1.04), 0.39 (±1.09), and 0.14 (±0.58), respectively. The Likert’s score was 3.65 (±0.82) and mean CSQ was 27.04 (±3.01). Majority of the women (86%) preferred the same pain relief method for future analgesia. There were no major complications. Conclusion: Conscious sedation was associated with high satisfaction level and acceptance rate among patients undergoing TVOR.
Effect of Monascus-Fermented Soybean Extracts on Antioxidant and Skin Aging-Related Enzymes Inhibitory Activities

We investigated the in vitro inhibitory activity against skin aging-related enzymes and antioxidant activity of Monascus-fermented soybean extracts (MFSEs) obtained by using different solvents. The highest Trolox equivalent (TE) antioxidant capacity (3.13±0.06 mM TE/g) and oxygen radical absorbance capacity (2.79±0.09 mM TE/g) of MFSEs were evaluated for the methanol and 80% ethanol extracts, respectively. The antioxidant capacities increased with increasing concentration (0.5~50 mg/mL). In addition, the methanol and 80% ethanol extracts showed an effective inhibition against tyrosinase, hyaluronidase, and elastase compared with those of acetone and hot water extracts (P<0.05). Results indicate that the inhibitory activities against skin aging-related enzymes and antioxidant properties provide evidence for the nutricosmetic potentials of Monascus-fermented soybeans.
Mesenchymal Stromal Cells Can Regulate the Immune Response in the Tumor Microenvironment

The tumor microenvironment is a good target for therapy in solid tumors and hematological malignancies. Indeed, solid tumor cells’ growth and expansion can influence neighboring cells’ behavior, leading to a modulation of mesenchymal stromal cell (MSC) activities and remodeling of extracellular matrix components. This leads to an altered microenvironment, where reparative mechanisms, in the presence of sub-acute inflammation, are not able to reconstitute healthy tissue. Carcinoma cells can undergo epithelial mesenchymal transition (EMT), a key step to generate metastasis; these mesenchymal-like cells display the functional behavior of MSC. Furthermore, MSC can support the survival and growth of leukemic cells within bone marrow participating in the leukemic cell niche. Notably, MSC can inhibit the anti-tumor immune response through either carcinoma-associated fibroblasts or bone marrow stromal cells. Experimental data have indicated their relevance in regulating cytolytic effector lymphocytes of the innate and adaptive arms of the immune system. Herein, we will discuss some of the evidence in hematological malignancies and solid tumors. In particular, we will focus our attention on the means by which it is conceivable to inhibit MSC-mediated immune suppression and trigger anti-tumor innate immunity.
Partition Learning for Multiagent Planning

Automated surveillance of large geographic areas and target tracking by a team of autonomous agents is a topic that has received significant research and development effort. The standard approach is to decompose this problem into two steps. The first step is target track estimation and the second step is path planning by optimizing directly over target track estimation. This standard approach works well in many scenarios. However, an improved approach is needed for the scenario when general, nonparametric estimation is required, and the number of targets is unknown. The focus of this paper is to present a new approach that inherently handles the task to search for and track an unknown number of targets within a large geographic area. This approach is designed for the case when the search is performed by a team of autonomous agents and target estimation requires general, nonparametric methods. There are consequently very few assumptions made. The only assumption made is that a time-changing target track estimation is available and shared between the agents. This estimation is allowed to be general and nonparametric. Results are provided that compare the performance of this new approach with the standard approach. From these results it is concluded that this new approach improves search and tracking when the number of targets is unknown and target track estimation is general and nonparametric.
Limiting distribution of Lempel Ziv'78 redundancy

We show that the Lempel Ziv'78 redundancy rate tends to a Gaussian distribution for memoryless sources. We accomplish it by extending findings from our 1995 paper [3]. We present a new simplified proof of the Central Limit Theorem for the number of phrases in the LZ'78 algorithm. As in our 1995 paper, here we first analyze the asymptotic behavior of the total path length in a digital search tree (a DST) built from independent sequences. Then we present simplified proofs and extend our analysis of LZ'78 algorithm to include new results on the convergence of moments, moderate and large deviations, and redundancy analysis.
Collisional Snowbird tectonic zone resurrected: Growth of Laurentia during the 1.9 Ga accretionary phase of the Hudsonian orogeny

The ∼2800-km-long Snowbird tectonic zone is one of the most controversial tectonic features of the Canadian shield. Metamorphic and in situ geochronologic data reported here reveal that a 1.9 Ga medium- to high-pressure belt extends along most of this tectonic zone. In contrast to recent interpretations, a collisional origin is indicated by the length of this metamorphic belt, tectonic thickening documented in parts of it, geological contrasts across it, and subduction-type microdiamonds within it. This collisional event marks a pre–1.865 Ga phase of the Hudsonian orogeny involving microcontinent accretion that was fundamental to the growth of Laurentia.
Optogenetic neuronal stimulation promotes functional recovery after stroke

Significance Stroke is the leading cause of disability in the United States and has very limited treatment options. Brain stimulation techniques that promote recovery after stroke are a promising area of research; however, current stimulation techniques nonspecifically activate/inhibit the target area, which not only leads to undesired side effects but also makes it difficult to understand which cell types and mechanisms drive recovery. We used the optogenetic technique to specifically stimulate only neurons after stroke and demonstrate that selective neuronal stimulations can activate beneficial mechanisms and promote recovery. Understanding the cell type and mechanisms driving recovery may identify potential drug targets for stroke treatment, as well as ultimately help develop precise brain stimulation techniques for stroke therapy. Clinical and research efforts have focused on promoting functional recovery after stroke. Brain stimulation strategies are particularly promising because they allow direct manipulation of the target area’s excitability. However, elucidating the cell type and mechanisms mediating recovery has been difficult because existing stimulation techniques nonspecifically target all cell types near the stimulated site. To circumvent these barriers, we used optogenetics to selectively activate neurons that express channelrhodopsin 2 and demonstrated that selective neuronal stimulations in the ipsilesional primary motor cortex (iM1) can promote functional recovery. Stroke mice that received repeated neuronal stimulations exhibited significant improvement in cerebral blood flow and the neurovascular coupling response, as well as increased expression of activity-dependent neurotrophins in the contralesional cortex, including brain-derived neurotrophic factor, nerve growth factor, and neurotrophin 3. Western analysis also indicated that stimulated mice exhibited a significant increase in the expression of a plasticity marker growth-associated protein 43. Moreover, iM1 neuronal stimulations promoted functional recovery, as stimulated stroke mice showed faster weight gain and performed significantly better in sensory-motor behavior tests. Interestingly, stimulations in normal nonstroke mice did not alter motor behavior or neurotrophin expression, suggesting that the prorecovery effect of selective neuronal stimulations is dependent on the poststroke environment. These results demonstrate that stimulation of neurons in the stroke hemisphere is sufficient to promote recovery.
Detection of Recently Discovered Human Polyomaviruses in a Longitudinal Kidney Transplant Cohort

A large number of human polyomaviruses have been discovered in the last 7 years. However, little is known about the clinical impact on vulnerable immunosuppressed patient populations. Blood, urine, and respiratory swabs collected from a prospective, longitudinal adult kidney transplant cohort (n = 167) generally pre‐operatively, at day 4, months 1, 3, and 6 posttransplant, and at BK viremic episodes within the first year were screened for 12 human polyomaviruses using real‐time polymerase chain reaction. Newly discovered polyomaviruses were most commonly detected in the respiratory tract, with persistent shedding seen for up to 6 months posttransplant. Merkel cell polyomavirus was the most common detection, but was not associated with clinical symptoms or subsequent development of skin cancer or other skin abnormalities. In contrast, KI polyomavirus was associated with respiratory disease in a subset of patients. Human polyomavirus 9, Malawi polyomavirus, and human polyomavirus 12 were not detected in any patient samples.
Researcher Bias: The Use of Machine Learning in Software Defect Prediction

Background. The ability to predict defect-prone software components would be valuable. Consequently, there have been many empirical studies to evaluate the performance of different techniques endeavouring to accomplish this effectively. However no one technique dominates and so designing a reliable defect prediction model remains problematic. Objective. We seek to make sense of the many conflicting experimental results and understand which factors have the largest effect on predictive performance. Method. We conduct a meta-analysis of all relevant, high quality primary studies of defect prediction to determine what factors influence predictive performance. This is based on 42 primary studies that satisfy our inclusion criteria that collectively report 600 sets of empirical prediction results. By reverse engineering a common response variable we build a random effects ANOVA model to examine the relative contribution of four model building factors (classifier, data set, input metrics and researcher group) to model prediction performance. Results. Surprisingly we find that the choice of classifier has little impact upon performance (1.3 percent) and in contrast the major (31 percent) explanatory factor is the researcher group. It matters more who does the work than what is done. Conclusion. To overcome this high level of researcher bias, defect prediction researchers should (i) conduct blind analysis, (ii) improve reporting protocols and (iii) conduct more intergroup studies in order to alleviate expertise issues. Lastly, research is required to determine whether this bias is prevalent in other applications domains.
Canadian Academy of Sport and Exercise Medicine position statement: Neuromuscular training programs can decrease anterior cruciate ligament injuries in youth soccer players.

Cathy J. Campbell, BPE, MSc, MD, Dip Sport Med,* James D. Carson, MD, Dip Sport Med,* Elena D. Diaconescu, MD,† Rick Celebrini, PT, PhD,‡ Marc R. Rizzardo, Dip Sports Physio, BScPT, MPE, BPE,‡ Veronique Godbout, MD, Dip Sport Med, MA, MedEd, BSc,§ Jennifer A. Fletcher, MD, Dip Sport Med,¶ Robert McCormack, MD,k Ross Outerbridge, MD, Dip Sport Med,** Taryn Taylor, MSc, MD, Dip Sport Med,†† Naama Constantini, MD, DFM, Dip Sport Med,‡‡ and Manon Cote, MD, Dip Sport Med, BScPT§§
[Sensitivity of Corynebacterium diphtheriae isolated in Saint-Petersburg to antibacterial drugs].

One hundred and thirty strains of Corynebacterium diphtheriae isolated in St. Petersburg (42 toxigenic and 88 nontoxigenic) were tested with the method of serial dilutions in solid media for their susceptibility to 20 antibacterial drugs. The MICs of the drugs for the isolates ranged from < or = 0.015 to > or = 32.0 micrograms/ml. 13 per cent of the isolates was resistant at least to one antibacterial drug. The isolates resistant to erythromycin (11.5 per cent), lincomycin (11.5 per cent) and trimethoprim (8.5 per cent) were most frequent. 3 isolates (2.3 per cent) had multiple resistance to 8 drugs: benzylpenicillin, ampicillin, oxacillin, chloramphenicol, erythromycin, lincomycin, trimethoprim, and nitroxolin. No significant differences in the susceptibility of the toxigenic and nontoxigenic strains of C. diphtheriae were detected. Gentamicin, rifampicin, tetracycline, doxycycline and pefloxacin were the most active antibiotics.
The development and evaluation of a computer-adaptive testing application for English language

This paper reports on research undertaken at the University of Hertfordshire into the development and initial expert evaluation of a computer-adaptive testing programme based on Item Response Theory (IRT). The paper explains how the Three-Parameter Logistic model was implemented in the prototype. The underlying theory and assumptions of the model used in its development are also explained, along with the limitations and benefits of the computer-adaptive test (CAT) approach compared to traditional computer-based test (CBT) methods. In this paper use of the prototype as an alternative to the current method used by the University is evaluated by experts, and summaries of their reports and recommendations are presented. This paper also describes plans for developing this work further, including its use in computer-based student modelling where an accurate estimation of performance within a subject domain can be used to inform and adapt the choice of presentation of learning materials. Considerations for extending the CAT model to encompass other types of questions rather than multiple-choice or multiple-response questions are also presented.
Routing Issues in Transparent Optical Networks

Future optical networks are moving from static point-to-point connections towards dynamic wavelength-routed networks using all-optical, reconfigurable switching nodes. By doing so, lightpaths are dynamically routed/switched entirely over the optical layer, eliminating current expensive electronic regenerators. However, the lack of OEO transponders (i.e., transparency) makes it necessary to consider the degrading effects of the physical transmission of optical signals accumulated along the path. An efficient strategy to face up this problem and to provide quality-enabled services is to take into account physical impairments during the path computation process (ICBR algorithm). In the work we present a feasible solution which combines ICBR algorithms and the intelligence of a distributed GMPLS-based control plane to set up optical connections with the required QoS in the optical signal. In addition, analytical discussions are given for the assessment and validation of the solution