Miracle-dz/UniFAR-FTUs huggingface dataset:
Finite Mixture Model of Bounded Semi-Naive Bayesian Networks for Classification

The Naive Bayesian (NB) network classifier, a probabilistic model with a strong assumption of conditional independence among features, shows a surprisingly competitive prediction performance even when compared with some state-of-the-art classifiers. With a looser assumption of conditional independence, the Semi-Naive Beyesian (SNB) network classifier is superior to NB classifiers when features are combined. However, the problem for SNB is that its structure is still strongly constrained which may generate inaccurate distributions for some datasets. A natural progression to improve SNB is to extend it using the mixture approach. However, in obtaining the final structure, traditional SNBs use the heuristic approaches to learn the structure from data locally. On the other hand, ExpectationMaximization (EM) method is used in the mixture approach to obtain the structure iteratively. The extension is difficult to integrate the local heuristic into the maximization step since it may not convergence. In this paper we firstly develop a Bounded Semi-Naive Bayesian network (B-SNB) model, which contains the restriction on the number of variables that can be joined in a combined feature. As opposed to local property of the traditional SNB models, our model enjoys a global nature and maintains a polynomial time cost. Overcoming the difficulty of integrating SNBs into the mixture model, we then propose an algorithm to extend it into a finite mixture structure, named Mixture of Bounded Semi-Naive Bayesian network (MBSNB). We give theoretical derivations, outline of the algorithm, analysis of algoTO SUBMIT TO IEEE TRANSACTION ON NEURAL NETWORKS — [ 1.5] 2 rithm and a set of experiments to demonstrate the usefulness of MBSNB in some classification tasks. The novel finite MBSNB network shows good speed up, ability to converge and an increase in prediction accuracy.
Expression and Evaluation of Recombinant Plasmodium knowlesi Merozoite Surface Protein-3 (MSP-3) for Detection of Human Malaria

Malaria remains a major health threat in many parts of the globe and causes high mortality and morbidity with 214 million cases of malaria occurring globally in 2015. Recent studies have outlined potential diagnostic markers and vaccine candidates one of which is the merozoite surface protein (MSP)-3. In this study, novel recombinant Plasmodium knowlesi MSP-3 was cloned, expressed and purified in an Escherichia coli system. Subsequently, the recombinant protein was evaluated for its sensitivity and specificity. The recombinant pkMSP-3 protein reacted with sera from patients with P. knowlesi infection in both Western blot (61%) and ELISA (100%). Specificity-wise, pkMSP-3 did not react with healthy donor sera in either assay and only reacted with a few non-malarial parasitic patient sera in the ELISA assay (3 of 49). In conclusion, sensitivity and specificity of pkMSP-3 was found to be high in the ELISA and Western Blot assay and thus utilising both assays in tandem would provide the best sero-diagnostic result for P. knowlesi infection.
Initial findings from an observational study of software engineers

For the last 30 years, several empirical studies have been conducted to understand how software engineers work. However, during this period, many changes occurred in the context of software development: new communication technologies like instant messaging appeared as well as new quality models to evaluate the work being conducted. Despite this new context, much of the research in the collaborative aspects of software design is based on research that does not reflect these new aspects of work. Thus, a more up-to-date understanding of the nature of software engineering work - as a type of information work - is necessary. The purpose of this paper is to present the initial findings of an observational study to understand how software developers' time is distributed during their workday. The main results are related to aspects of collaboration observed in 55% of their time, information seeking consuming 31,90% of developers' time, and poor use of software process tools in 5% of the time observed. In particular, this last result is different from what one would expect and which has been previously been reported in the literature.
Factor Analysis With Validity And Reliability And For Highschool And University Students Of Zung Depression

Depression, is an important psychologic disorder. So, it is of importance early diagnose (Oskay,1997). Various depression scales are used the measurement of depression. Although Zung Depression Scale, which is one of these, is used in researches especially psychiatry branch, validity and reliability studies were done only by Ceyhun and Akca in psychiatric patients. There is a need for valid and reliable tools to determine degree of depression in the young. So, validity and reliability studies are needed so that It could be used Zung Depression Scale in adolescents. This research covers a total of 1221 students, 767 “normal” university students and 212 patient university students and 242 highschool students. “Structure and alike scale” validity methods and “depression” sub-scale of SCL-90R scale with Beck Depression Inventory were used. In determining of the reliability of scale two half validity-Cronbach Alfa Coefficient and Gutman Split-half and Spearman Brown were used. Besides, Kaiser-Meyer-Olkin Sampling Adequecy and Berlett’s Test of Sphericity analysises were administered to determine factor structure of scale then the factor analysises were done separately for highschool, university patient student groups. In terms of depression points averages of highschool and university students, as there was no significant difference in the alpha level of p<0.05 in terms of Zung Depression Scale points between high students and university normal students group, there was a significant difference on behalf of the high students. There was significant difference on behalf of the normal students in terms of depression point averages. Consequently, it is said that Zung Depression Scale is applicable in respect of validity and reliable for depression levels of normal and patient students in highschool and university students. In this context, it could be suggested that the scale be used as a validity and reliability means in the measurement of depression levels of normal and patient students and researches
Computing Semantic Similarity Measure between Words Using Web Search Engine

Semantic Similarity measures between words plays an important role in information retrieval, natural language processing and in various tasks on the web. In this paper, we have proposed a Modified Pattern Extraction Algorithm to compute the supervised semantic similarity measure between the words by combining both page count method and web snippets method. Four association measures are used to find semantic similarity between words in page count method using web search engines. We use a Sequential Minimal Optimization (SMO) support vector machines (SVM) to find the optimal combination of page counts-based similarity scores and top-ranking patterns from the web snippets method. The SVM is trained to classify synonymous word-pairs and non-synonymous word-pairs. The proposed Modified Pattern Extraction Algorithm outperforms by 89.8 percent of correlation value.
Improving the proportion of at-speed tests in scan BIST

A method to select the lengths of functional sequences in a BIST scheme for scan designs is proposed in this paper. A functional sequence is a sequence of primary input vectors applied when the circuit operates as a sequential circuit, without using scan. These sequences can be applied at-speed, i.e., at the normal circuit clock speed. The objectives set for choosing the lengths of the functional sequences are to increase the number of vectors applied at-speed, and to reduce the number of settings of functional sequence lengths, without compromising the fault coverage achieved. The experimental results presented demonstrate that compared to earlier methods, the proposed method achieves the above objectives while also achieving higher fault coverages for most of the benchmark circuits considered.
Comparison of Different Rowing Exercises: Trunk Muscle Activation and Lumbar Spine Motion, Load, and Stiffness

Fenwick, CMJ, Brown, SHM, and McGill, SM. Comparison of different rowing exercises: Trunk muscle activation and lumbar spine motion, load and stiffness. J Strength Cond Res 23(5): 1408-1417, 2009-The objective of this study was to investigate 3 different rowing exercises and quantify the muscle activation of the torso and the hip musculature, together with the corresponding spinal loading and stiffness. Seven healthy male subjects from a university population were instrumented to obtain surface electromyography of selected trunk and hip muscles and to obtain spine position using an electromagnetic spine position sensor, together with video analysis to calculate joint moments. The 3 rowing exercises investigated are the inverted row, standing bent-over row, and the standing 1-armed cable row. The inverted row elicited the highest activation of the latissimus dorsi muscles, upper back, and hip extensor muscles. The lower activation of the lumbar erector spinae muscles during the inverted row corresponded to the lower-spine load measured. The standing bent-over row produced large activation symmetrically across the back but produced the largest lumbar spine load. The 1-armed cable row challenged the torsional capabilities of the trunk musculature. Some “core” exercises may be better for rehabilitation (e.g., having the training goals of modest muscle activation with low spine load), while other exercises may be better for athletic training (e.g., resulting in higher muscle activation and larger spine load). When prescribing “core” exercises, those wishing to spare the low back may choose the inverted row given the lowest spine load exercise. The standing bent-over row elicited large muscle activation symmetrically from the upper to lower back, however induced larger spine loads, but not surprisingly the highest spine stiffness. If torsional endurance or strength is the training goal, the 1-armed cable row might be considered.
c-Src activation promotes nasopharyngeal carcinoma metastasis by inducing the epithelial-mesenchymal transition via PI3K/Akt signaling pathway: a new and promising target for NPC

Aberrant activation of cellular Src (c-Src), a non-receptor tyrosine kinase, could promote cancer progression through activating its downstream signaling pathways. However, the roles of c-Src and phosphorylated-Src (p-Src) in nasopharyngeal carcinoma (NPC) progression are rarely investigated. Herein, we have identified high c-Src concentrations in the serum of NPC patients with distant metastasis using high-throughput protein microarrays. Levels of c-Src in serum and p-Src in human primary NPC samples were unfavorable independent prognostic factors for cancer-specific survival, disease-free survival, and distant metastasis-free survival. Depletion or inactivation of c-Src in NPC cells using sgRNA with CRISPR/Cas9 system or PP2 decreased cell viability, colony formation, migration and invasion in vitro and metastasis in vivo. In contrast, these malignancies could be up-regulated by overexpressed c-Src in a NPC cell line with low-metastasis potential. Furthermore, p-Src was involved in promoting NPC cell metastasis by inducing the epithelial-mesenchymal transition (EMT) process via activating the PI3K/Akt pathway and cytoskeleton remodeling. The p-Src-induced EMT process could be retarded by PP2, which mediated by down-regulating the PI3K/Akt pathway. In conclusion, elevated levels of c-Src in serum and p-Src in primary NPC tissue correlated with poor outcomes of NPC patients. And aberrant activation of c-Src facilitated NPC cells with malignant potential, especially metastasis ability, which mediated by the PI3K/Akt pathway activation and sequentially induced the EMT process. These findings unveiled a promising approach for targeted therapy of advanced NPC.
Advances in Internet Quality of Service

We describe recent advances in theories and architecture that support performance guarantees needed for quality of service networks. We start with deterministic computations and give applications to integrated services, differentiated services, and playback delays. We review the methods used for obtaining a scalable integrated services support, based on the concept of a stateless core. New probabilistic results that can be used for a statistical dimensioning of differentiated services are explained; some are based on classical queuing theory, while others capitalize on the deterministic results. Then we discuss performance guarantees in a best effort context; we review: methods to provide some quality of service in a pure best effort environment; methods to provide some quality of service differentiation without access control, and methods that allow an application to control the performance it receives, in the absence of network support.
A General Framework for Shape Similarity

We propose a formal framework to clarify the import of and the relationship among different notions of similarity. The framework, borrowing from the general E-connections approach, allows to use multiple similarity notions in the same system by relating the domain of discourse to specialized sets of entities even across different logics. In practice, we start form the assumption that (Leibnizian) relative identity is the only local form of similarity, and show that more sophisticated notions can be conceptually understood as the result of transformations across heterogeneous logics. These transformations, called global similarities, are usually motivated by arguments external to the starting system, and can be intertwined to generate a prolific family of similarity relations. We exemplify this framework in the context of shape similarity whose comprehension motivated our work. Finally, the approach developed in this paper sets the basis for a general study of similarity as a group of transformations generated by (primitive) global similarity relations.
Influence of ATP-Binding Cassette Transporter 1 R219K and M883I Polymorphisms on Development of Atherosclerosis: A Meta-Analysis of 58 Studies

Background Numerous epidemiological studies have evaluated the associations between ATP-binding cassette transporter 1 (ABCA1) R219K (rs2230806) and M883I (rs4149313) polymorphisms and atherosclerosis (AS), but results remain controversial. The purpose of the present study is to investigate whether these two polymorphisms facilitate the susceptibility to AS using a meta-analysis. Methods PubMed, Embase, Web of Science, Medline, Cochrane database, Clinicaltrials.gov, Current Controlled Trials, Chinese Clinical Trial Registry, CBMdisc, CNKI, Google Scholar and Baidu Library were searched to get the genetic association studies. All statistical analyses were done with Stata 11.0. Results Forty-seven articles involving 58 studies were included in the final meta-analysis. For the ABCA1 R219K polymorphism, 42 studies involving 12,551 AS cases and 19,548 controls were combined showing significant association between this variant and AS risk (for K allele vs. R allele: OR = 0.77, 95% CI = 0.71–0.84, P<0.01; for K/K vs. R/R: OR = 0.60, 95% CI = 0.51–0.71, P<0.01; for K/K vs. R/K+R/R: OR = 0.69, 95% CI = 0.60–0.80, P<0.01; for K/K+R/K vs. R/R: OR = 0.74, 95% CI = 0.66–0.83, P<0.01). For the ABCA1 M883I polymorphism, 16 studies involving 4,224 AS cases and 3,462 controls were combined. There was also significant association between the variant and AS risk (for I allele vs. M allele: OR = 0.85, 95% CI = 0.77–0.95, P<0.01). Conclusions The present meta-analysis suggested that the ABCA1 R219K and M883I polymorphisms were associated with the susceptibility to AS. However, due to the high heterogeneity in the meta-analysis, the results should be interpreted with caution.
Unique Mutational Patterns in the Envelope α2 Amphipathic Helix and Acquisition of Length in gp120 Hypervariable Domains Are Associated with Resistance to Autologous Neutralization of Subtype C Human Immunodeficiency Virus Type 1

ABSTRACT Autologous neutralizing antibodies (NAb) against human immunodeficiency virus type 1 generate viral escape variants; however, the mechanisms of escape are not clearly defined. In a previous study, we determined the susceptibilities of 48 donor and 25 recipient envelope (Env) glycoproteins from five subtype C heterosexual transmission pairs to NAb in donor plasma by using a virus pseudotyping assay, thereby providing an ideal setting to probe the determinants of susceptibility to neutralization. In the present study, acquisition of length in the Env gp120 hypervariable domains was shown to correlate with resistance to NAb in donor plasma (P = 0.01; Kendall's tau test) but not in heterologous plasma. Sequence divergence in the gp120 V1-to-V4 region also correlated with resistance to donor (P = 0.0002) and heterologous (P = 0.001) NAb. A mutual information analysis suggested possible associations of nine amino acid positions in V1 to V4 with NAb resistance to the donor's antibodies, and five of these were located within an 18-residue amphipathic helix (α2) located on the gp120 outer domain. High nonsynonymous-to-synonymous substitution (dN/dS) ratios, indicative of positive selection, were also found at these five positions in subtype C sequences in the database. Nevertheless, exchange of the entire α2 helix between resistant donor Envs and sensitive recipient Envs did not alter the NAb phenotype. The combined mutual information and dN/dS analyses suggest that unique mutational patterns in α2 and insertions in the V1-to-V4 region are associated with NAb resistance during subtype C infection but that the selected positions within the α2 helix must be linked to still other changes in Env to confer antibody escape. These findings suggest that subtype C viruses utilize mutations in the α2 helix for efficient viral replication and immune avoidance.
Forage Species Suitability Mapping for China Using Topographic, Climatic and Soils Spatial Data and Quantitative Plant Tolerances

Selecting plants adapted to the climatic and soil conditions of specific locations is essential for environmental protection and economic sustainability of agricultural and pastoral systems. This is particularly true for countries like China with a diversity of climates and soils and intended uses. Currently, proper species selection is difficult due to the absence of computer-based selection tools. Climate and soil GIS layers, matched with a matrix of plant characteristics through rules describing species tolerances would greatly improve the selection process. Better matching will reduce environmental hazards and economic risks associated with sub-optimal plant selection and performance. GIS-based climate and soil maps have been developed for China. A matrix of quantitative species tolerances has been developed for example forage species and used in combination with an internet map server that allows customized map creation. A web-based decision support system has been developed to provide current information and links to original data sources, supplementary materials, and selection strategies.
MIGRATION OF TWO MASSIVE PLANETS INTO (AND OUT OF) FIRST ORDER MEAN MOTION RESONANCES

We consider the dynamical evolution of two planets with nearly circular and nearly coplanar orbits undergoing eccentricity damping and convergent migration in the vicinity of a first order mean motion resonance. Following Goldreich & Schlichting, we include a coupling between the dissipative semimajor axis evolution and the damping of the eccentricities. In agreement with past studies, we find that this coupling can lead to instability of the resonance and that for a certain range of parameters capture into resonance is only temporary. Using a more general model, we show that whether escape from resonance can occur depends in a characteristic way on the mass ratio between the two planets as well as their relative eccentricity damping timescales. In particular, systems undergoing Type I migration with a more massive inner planet typically result in permanent capture. Additionally, we show that even when escape from resonance does occur, the timescale for escape is long enough such at any given time a pair of planets is more likely to be found in a low-order resonance rather than migrating between them. Thus, we argue that intrinsic instability of resonances cannot singlehandedly reconcile convergent migration with the observed lack of Kepler planet pairs found near resonances.
K-Viz: KEGG Based Bisualization for Comparing Metabolic Pathways

The comparison of metabolic pathway in different species is important in detecting a missing gene. There are many visualizations for metabolic pathway. However, Biologists need not only a simple path but also a visualization for comparison. K-Viz is a tool for visualization of metabolic pathway based on KEGG. To compare pathways in different species, K-Viz uses different color for path such as PathComp in KEGG and shows the table of path in pathway. K-Viz helps biologists to understand the comparison of metabolic pathways in different species.
An Affect-based Approach for QoE evaluation in VoIP Systems

The success of VoIP systems such as Skype, Google Talk, MSN Messenger, etc. have inspired the migration of voice communication from the Public Switched Telephone Network (PSTN) to the Internet. The inherent challenges for designing VoIP systems are due to the particular characteristics of voice communication such as low volume, burstiness and stringent delay/loss requirements which is different from the best-effort data delivery model of Internet. Effective evaluation frameworks are important for further refinement of these systems by adopting user feedback based requirements. Most of the VoIP evaluation models are system-centric (Quality of Service or QoS-based), which questioned us to explore for an user-centric (Quality of Experience or QoE-based) approach as a step towards the human-centric paradigm. We research an affect-based QoE evaluation framework which tries to capture user’s perception while they are using VoIP applications along multiple dimensions. Our experimental methodology is illustrated in depth and we provide detailed results.
On the LQ-based optimization techniques for impulsive hybrid control systems

This paper deals with a quadratic optimization problem for linear impulsive hybrid systems. We study a class of LQ-type impulsive hybrid optimal control problems (OCPs) and consider the application of the hybrid Maximum Principle (MP). Our aim is to investigate the natural relationship between the Pontryagin-type MP and the Bellman Dynamic Programming (DP) approach. As next we develop the “hybrid” Riccati formalism and discuss some related computational aspects.
Ring of Fire : Near-Infrared and X-ray Quasi-Periodic Oscillations in Numerical Models of Sgr A *

We report transient quasi-periodic oscillations (QPOs) on minute timescales in relativistic, radiative models of the galactic center source Sgr A*. The QPOs result from nonaxisymmetric m = 1 structure in the accretion flow excited by MHD turbulence. Near-infrared (NIR) and X-ray power spectra show significant peaks at frequencies comparable to the orbital frequency at the innermost stable circular orbit (ISCO) fo. The excess power is associated with inward propagating magnetic filaments inside the ISCO. The amplitudes of the QPOs are sensitive to the electron distribution function. We argue that transient QPOs appear at a range of frequencies in the neighborhood of fo and that the power spectra, averaged over sufficiently long times, likely show a broad bump near fo rather than distinct, narrow QPO features. Subject headings: accretion, accretion disks — black hole physics — Galaxy: center — magnetohydrodynamics (MHD) — methods: numerical — radiative transfer Physics Department, University of Illinois, Urbana, IL 61801