Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteochemometric Modeling of the Susceptibility of Mutated Variants of the HIV-1 Virus to Reverse Transcriptase Inhibitors

Background Reverse transcriptase is a major drug target in highly active antiretroviral therapy (HAART) against HIV, which typically comprises two nucleoside/nucleotide analog reverse transcriptase (RT) inhibitors (NRTIs) in combination with a non-nucleoside RT inhibitor or a protease inhibitor. Unfortunately, HIV is capable of escaping the therapy by mutating into drug-resistant variants. Computational models that correlate HIV drug susceptibilities to the virus genotype and to drug molecular properties might facilitate selection of improved combination treatment regimens. Methodology/Principal Findings We applied our earlier developed proteochemometric modeling technology to analyze HIV mutant susceptibility to the eight clinically approved NRTIs. The data set used covered 728 virus variants genotyped for 240 sequence residues of the DNA polymerase domain of the RT; 165 of these residues contained mutations; totally the data-set covered susceptibility data for 4,495 inhibitor-RT combinations. Inhibitors and RT sequences were represented numerically by 3D-structural and physicochemical property descriptors, respectively. The two sets of descriptors and their derived cross-terms were correlated to the susceptibility data by partial least-squares projections to latent structures. The model identified more than ten frequently occurring mutations, each conferring more than two-fold loss of susceptibility for one or several NRTIs. The most deleterious mutations were K65R, Q151M, M184V/I, and T215Y/F, each of them decreasing susceptibility to most of the NRTIs. The predictive ability of the model was estimated by cross-validation and by external predictions for new HIV variants; both procedures showed very high correlation between the predicted and actual susceptibility values (Q 2 = 0.89 and Q2ext = 0.86). The model is available at www.hivdrc. org as a free web service for the prediction of the susceptibility to any of the clinically used NRTIs for any HIV-1 mutant variant. Conclusions/Significance Our results give directions how to develop approaches for selection of genome-based optimum combination therapy for patients harboring mutated HIV variants.
Analyzing Exploratory Talk as a Socio-Cognitive Practice: Identity, Group Argumentation, and Class Debate Quality

This paper addresses the appraisal of the quality of student debate about a socio-scientific issue, with a focus on the interactional factor. The “scientific cafe” pedagogical situation offers an opportunity for observing the circulation of arguments from small group to class-level debate, indicating the quality of group reasoning. We use Mercer and Wegerif’s typology of student talk (exploratory, cumulative, disputational) and study the attitude toward self-identity needed to engage in exploratory talk. Such a positioning is conceptualized as being associated to specific politeness rules and face-preservation system. Three case studies held in an American and a French high schools explore the boundaries between those 3 categories and questions which units of analysis are relevant for assessing students’ argumentation. The paper provides methodological tools to apply this typology to authentic students’ interactions, where students’ engagement in a specific group talk type is both a matter of cognitive skills and perceived relevancy in a given social context. We propose a refinement of the analytical categories that allows studying students’ argumentation at different time scales (interactional phase, sequence, subsequence) and social levels (group talk, individual self-identity footing, and repercussions on class debate).
GPUML : Graphical processors for speeding up kernel machines

Algorithms based on kernel methods play a central role in statistical machine learning. At their core are a number of linear algebra operations on matrices of kernel functions which take as arguments the training and testing data. These range from the simple matrix-vector product, to more complex matrix decompositions, and iterative formulations of these. Often the algorithms scale quadratically or cubically, both in memory and operational complexity, and as data sizes increase, kernel methods scale poorly. We use parallelized approaches on a multi-core graphical processor (GPU) to partially address this lack of scalability. GPUs are used to scale three different classes of problems, a simple kernelmatrix-vector product, iterative solution of linear systems of kernel function and QR and Cholesky decomposition of kernel matrices. Application of these accelerated approaches in scaling several kernel based learning approaches are shown, and in each case substantial speedups are obtained. The core software is released as an open source package, GPUML.
DCC association with lipid rafts is required for netrin-1-mediated axon guidance

During development, axons migrate long distances in responses to attractive or repulsive signals that are detected by their growth cones. One of these signals is mediated by netrin-1, a diffusible laminin-related molecule that both attracts and repels growth cones via interaction with its receptor DCC (deleted in colorectal cancer). Here we show that DCC in both commissural neurons and immortalized cells, is partially associated with cholesterol- and sphingolipid-enriched membrane domains named lipid rafts. This localization of DCC in lipid rafts is mediated by the palmitoylation within its transmembrane region. Moreover, this raft localization of DCC is required for netrin-1-induced DCC-dependent ERK activation, and netrin-1-mediated axon outgrowth requires lipid raft integrity. Thus, the presence of axon guidance-related receptors in lipid rafts appears to be a crucial pre-requisite for growth cone response to chemo-attractive or repulsive cues.
Rethinking corruption: hocus-pocus, locus and focus

Although there has been a significant increase in research on the phenomenon of corruption over the last quarter-century, there is little evidence that this has resulted in effective policy interventions, nor in any significant reduction in its scope and extent. This article argues that three main reasons account for this failure to develop effective anti-corruption measures. First, the dominance of economistic analyses of the role of incentives in decision-making has given rise to proposed institutional fixes that are too abstracted from reality to gain purchase. That dominance was partly prompted by a misplaced assumption that market-based liberal democracies would become the modal regime type following the collapse of communism. Second, an emphasis on the nation state as the primary unit of analysis has not kept pace with significant changes in how some forms of corruption operate in practice, nor with the changing nature of states themselves. Third, different types of corruption are insufficiently disaggregated according not just to kind and form, but also to the locations in which they occur (sectoral, organisational, geographical), the actors involved, and the dependencies that enable them. This reflects an overuse of the term ‘corruption’ in both academic literature and policy recommendations; insufficient attention is paid to what exactly is being addressed and ultimately, the notion of corruption, without adjectives, is a poor guide both to analysis and to policy prescription.
Research on the comprehensive evaluation for competition ability of private hospital

In order to optimize and dispatch the resources in hospital appropriately, this article evaluated the competition ability of private hospital comprehensively by the combination of principal component analysis and Choquet integral, which could prevent the waste of resources and build a comprehensive evaluation model for private hospital about the competition ability. Measures of association among various factors are a key step in the process of modeling. This article obtained the fuzzy measure of each factor by principal component analysis, and calculated the measures of association by Sugeno measure. Then the expert experience was used to calculate the conformity of each factor, and the Choquet integral was used to calculate the competition ability of the hospital.
ProTailor: A Parallel Operator for Extremely Fast Shape Analysis in Bioinformatics Applications

The geometric shape of molecular surfaces strongly influences the docking processes where, although electrostatic, hydrophobic and van der Waals interactions affect greatly the binding affinity of the molecules, shape complementarity is a necessary condition. The vast majority of molecular docking algorithms uses a brute force enumeration of the transformation space, which requires extremely long running times. Few other methods use local shape feature matching to reduce the search to those relative positions which satisfy geometric constraints.Based on a shape analysis tool developed in Computer Graphics, in this paper we introduce ProTailor, a parallel algorithm for efficient multi-scale detection of morphological features on molecular surfaces. Thanks to an almost linear speed-up, we show how ProTailor is well suited to efficiently identify salient features like cavities and depressions, saddle areas or bridges. Feature identification may serve as a powerful tool to automatically locate potential binding sites or as a pre-processing step for efficient shape complementarity assessment in docking prediction.
Community assembly during secondary forest succession in a Chinese subtropical forest

Subtropical broad-leaved forests in southeastern China support a high diversity of woody plants. Using a comparative study design with 30 × 30 m plots (n = 27) from five successional stages ( 1 m in height in each plot and counted all woody recruits (bank of all seedlings ≤1 m in height) in each central 10 × 10 m quadrant of each plot. In addition, we measured a number of environmen.
Investigating the Roles of Time Perspective and Emerging Adulthood in Predicting Driving Behavior

INVESTIGATING THE ROLES OF TIME PERSPECTIVE AND EMERGING ADULTHOOD IN PREDICTING DRIVING BEHAVIOR Kristie L. Johnson Old Dominion University, 2012 Director: Dr. Bryan E. Porter In the U.S., motor vehicle crashes are the leading cause of death for individuals 2 to 34 years of age (National Highway Traffic Safety Administration, 2009c). Of particular interest are 18 to 25 year olds or emerging adults because of their increased crash risk. The prevalence of crashes attributable to the combination of driving inexperience and risky behaviors creates the necessity to identify predictors of crash likelihoods. While there are known personality variables that predict risky driving, time perspective as an additional one was suggested. Time perspective pertains to how the past, present, and future influence an individual's actions. Zimbardo, Keough, and Boyd (1997) investigated the relationship between time perspective and risky driving behavior as part of a larger health behavior study. The current research focused on replicating and extending their initial endeavor. Proposed improvements included expanding the risky driving outcome questionnaire from Zimbardo's five items to include scales more commonly used in the traffic research field (e.g., the Driver Behavior Questionnaire: Lajunen, Parker, & Summala, 2004; the Driving Anger Expression Inventory: Deffenbacher, Lynch, Oetting, & Swaim, 2002). Second, the two separate present time perspective subscales of the Zimbardo Time Perspective Inventory (ZTPI), which have not been used in driving risk research, were employed to better reflect differing driving behaviors and characteristics associated with fatalism and hedonism (Zimbardo & Boyd, 1999). Third, the role of positive driving behaviors seemed important given its recent focus in the literature. Thus, both risky and positive driving behaviors were investigated (Ozkan & Lajunen, 2005). Based on previous research, hypotheses were tested among the various time perspective orientations and risky and positive driving behaviors. The utility of time perspective as a predictor of driving behavior is discussed. In addition to studying the relationship between time perspective and driving behaviors, the influence of emerging adulthood were explored. Today many individuals are extending the time between adolescence and adulthood (Arnett, 2000). This intermediate stage where individuals are taking more time to explore their options before making long-term commitments was tested for its unique contribution toward predicting driving behavior. Specifically, it was hypothesized that those who score lower on the emerging adult factor would display more risky driving behaviors and fewer positive driving behaviors. Emerging adulthood was also tested in an overall model of risky driving which includes the time perspectives of interest and the control variables of sensation seeking and anger.
ADAPTIVE DIFFERENTIAL EVOLUTION BASED ON THE CONCEPT OF POPULATION DIVERSITY APPLIED TO SIMULTANEOUS ESTIMATION OF RADIATION PHASE FUNCTION , ALBEDO AND OPTICAL THICKNESS

Differential Evolution Algorithm (DE) has shown to be a powerful evolutionary algorithm for global optimization in a variety of real world problems. DE differs from other evolutionary algorithms in the mutation and recombination phases. Unlike some meta-heuristic techniques such as genetic algorithms and evolutionary strategies, where perturbation occurs in accordance with a random quantity, DE uses weighted differences between solution vectors to perturb the population. Although the efficiency of DE algorithm has been proven in the literature, studies indicate that the efficiency of the DE methods is sensitive to its control parameters (perturbation rate and crossover rate) and there is not any guarantee that premature convergence will be avoided. To overcome this problem, the present work proposes an Adaptive Differential Evolution as based on the concept of population diversity aiming at dynamically updating the control parameters. The methodology proposed is applied to the simultaneous estimation of the radiation phase function of anisotropic scattering, albedo and optical thickness in an inverse radiative transfer problem. The results show that the procedure represents a promising alternative for the type of problem presented above.
Angular Differential Imaging: A Powerful High-Contrast Imaging Technique

Angular differential imaging is a high-contrast imaging technique that reduces quasistatic speckle noise and facilitates the detection of nearby companions. A sequence of images is acquired with an altitude/azimuth telescope while the instrument field derotator is switched off. This keeps the instrument and telescope optics aligned and allows the field of view to rotate with respect to the instrument. For each image, a reference point-spread function (PSF) is constructed from other appropriately selected images of the same sequence and subtracted to remove quasistatic PSF structure. All residual images are then rotated to align the field and are combined. Observed performances are reported for Gemini North data. It is shown that quasistatic PSF noise can be reduced by a factor ~5 for each image subtraction. The combination of all residuals then provides an additional gain of the order of the square root of the total number of acquired images. A total speckle noise attenuation of 20-50 is obtained for a 1 hr long observing sequence compared to a single 30 s exposure. A PSF noise attenuation of 100 was achieved for a 2 hr long sequence of images of Vega, reaching a 5 σ contrast of 20 mag for separations greater than 8''. For a 30 minute long sequence, ADI achieves signal-to-noise ratios 30 times better than a classical observation technique. The ADI technique can be used with currently available instruments to search for ~1MJup exoplanets with orbits of radii between 50 and 300 AU around nearby young stars. The possibility of combining the technique with other high-contrast imaging methods is briefly discussed.
Photopic ERG negative response from amacrine cell signaling in RCS rat retinal degeneration.

PURPOSE The authors investigated photopic electroretinographic changes during degeneration in the Royal College of Surgeons (RCS) and transgenic P23H rhodopsin rat models, including the cellular origins of a large corneal-negative component that persists in the RCS rat. METHODS Photopic and scotopic electroretinograms (ERGs) were recorded from dystrophic RCS (RCS-p(+)/Lav) rats (4-18 weeks old) and transgenic rhodopsin Pro23His line 1 (P23H) rats (4-30 weeks old). Age-matched congenic (RCS-rdy(+)p(+)/Lav) and Sprague-Dawley rats were used as controls. N-methyl-DL-aspartic acid (NMA), dopamine, and gamma-aminobutyric acid (GABA) were injected intravitreally, and optic nerve sectioning (ONS) was performed to suppress or remove inner retinal neuron activity. Retinal morphology for cone cell counts and immunohistochemistry for quantification of Kir4.1 channels were performed at various stages of degeneration. RESULTS As degeneration progressed, the photopic ERG of RCS dystrophic rats was distinctly different from that of P23H rats, primarily because of the growth of a corneal-negative response (RCS-NPR) after the b-wave in RCS rats. This response had a peak time similar to the photopic negative response (PhNR) in controls but with a more gradual recovery phase, and it was not affected by ONS. The PhNR in P23H rats declined linearly with the b-wave. NMA and GABA eliminated the RCS-NPR and uncovered a larger b-wave in RCS rats at late stages of degeneration, but NMA had little effect on the ERG in P23H rats. The NMA-sensitive negative response in RCS rats declined with age more slowly than did the NMA-isolated b-wave. The density of Kir4.1 channels at the endfeet of Müller cells and in the proximal retina increased significantly between 6 to 10 weeks and 14 weeks of age in the RCS rat retina but not in the P23H rat retina. CONCLUSIONS The photopic ERG of the dystrophic RCS rat retina becomes increasingly electronegative because of an aberrant negative response, originating from amacrine cell activity, which declines more slowly than the b-wave with degeneration. The absence of this response in the P23H rat indicates that the inner retinal cone pathway pathology is different in the two models. A relative increase in Kir4.1 channels on Müller cells of RCS retina may contribute to the enhanced negative ERG response in the RCS rat.
LA DIFFÉRENCIATION PÉDAGOGIQUE : REPRÉSENTATIONS ET PRATIQUES RAPPORTÉES D’ENSEIGNANTES DU PRIMAIRE

La differenciation pedagogique compte parmi les mesures censees ameliorer la reussite scolaire de tous les eleves. Toutefois, le construit theorique reste flou et les enseignants y recourent rarement de facon systematique. Dans ce contexte, cet article vise a apporter des eclaircissements theoriques, en operant tout d’abord la distinction entre differenciation pedagogique et pratique de differenciation. Une conceptualisation de la differenciation pedagogique appuyee sur le construit d’intentionnalite d’action est proposee. Des caracteristiques des pratiques de differenciation sont decrites afin de contribuer a leur operationnalisation. Les resultats presentes proviennent d’une recherche qui s’est deroulee aupres de 24 enseignants du primaire au Quebec, qui a compris une etape d’exploration de leurs representations relatives a la differenciation pedagogique et une deuxieme etape d’observation des pratiques effectives. DIFFERENTIATED INSTRUCTION: REPRESENTATIONS AND REPORTED PRACTICES OF ELEMENTARY SCHOOL TEACHERS Differentiated instruction is one of the measures intended to improve academic achievement for all students. However, its theoretical construct remains unclear and teachers rarely use it systematically. In this context, this article aims to provide theoretical clarification by first operating a distinction between differentiated instruction and the practice of differentiation. A conceptualization of differentiated instruction based on the construct of intentionality of action is then proposed. Features of practices of differentiation are also described in order to contribute to their operationalization. The results presented stem from a research conducted with 24 elementary teachers in Quebec, which included a first phase of exploration of their representations concerning differentiated instruction and a second phase of observation of actual practices.
Cascaded Multilevel Inverter With Series Connection of Novel H-Bridge Basic Units

In this paper, a new single-phase cascaded multilevel inverter based on novel H-bridge units is proposed. In order to generate all voltage levels (even and odd) at the output, nine different algorithms are proposed to determine the magnitudes of dc voltage sources. Then, the proposed algorithms are compared to investigate their advantages and disadvantages. This topology is able to increase the number of output voltage levels by using a lower number of power electronic devices such as switches, power diodes, driver circuits, and dc voltage sources that lead to reduction in installation space and cost of the inverter. In addition, in the proposed cascaded multilevel inverter, not only the number of required power electronic devices is reduced, but also the amount of the blocked voltage by switches, and the number of different voltage amplitudes of the used sources is decreased. These features are some of the most important advantages of the proposed topology. These features are obtained via the comparison of the proposed topology and its proposed algorithms with the conventional cascaded multilevel inverters that have been presented in the literatures. The operation and performances of the proposed topology with its presented algorithms in generating all voltage levels have been verified by using the experimental results of a 49-level single-phase inverter.
Towards a pattern language for model-based GUI testing

Graphical user interfaces (GUIs) have become popular as they appear in everydays' software. GUIs have become an ideal way of interacting with computer programs, making the software friendlier to its users. GUIs have grown, and so has the usage of UI Patterns featured in GUIs. UI Patterns are recurring solutions to solve common GUI design problems. We developed the notion of UI Test Patterns that, are able to test different implementations of UI Patterns. Therefore, we created a new methodology called Pattern-Based GUI Testing (PBGT) that aims at systematizing and automating the GUI testing process. PBGT samples the input space using UI Test Patterns, which provide a reusable and configurable test strategy, in order to test a GUI that was implemented using a set of UI Patterns. In this paper we present three UI Test Patterns: Login, Master/Detail and Sort.
Transport-layer assisted vertical traffic balanced routing for thermal-aware three-dimensional Network-on-Chip systems

The thermal problem of three-dimensional Network-on-Chip (3D NoC) is severer than 2D NoC because chip stacking. To keep the temperature below a certain thermal limit, the near-overheat routers are throttled and the 3D topology becomes Non-Stationary Irregular Mesh (NSI-Mesh). To ensure the successful packet delivery in the NSI-Mesh, Transport Layer Assisted Routing (TLAR) scheme was proposed. It has better performance than the conventional routing approaches for NSI-Mesh. However, it still suffers significant traffic congestion in the bottom chip layer and extremely traffic unbalance between vertical chip layers. In this paper, we propose a transport layer assisted Vertical Traffic Balance Routing (VTBR) scheme. It can be applied to any routing approaches for NSI-Mesh. The experimental results show that the proposed VTBR can achieve more balanced traffic in the vertical direction and improve 35.3% ~ 40% network throughput.