Miracle-dz/UniFAR-FTUs huggingface dataset:
Directed test generation to detect loop inefficiencies

Redundant traversal of loops in the context of other loops has been recently identified as a source of performance bugs in many Java libraries. This has resulted in the design of static and dynamic analysis techniques to detect these performance bugs automatically. However, while the effectiveness of dynamic analyses is dependent on the analyzed input tests, static analyses are less effective in automatically validating the presence of these problems, validating the fixes and avoiding regressions in future versions. This necessitates the design of an approach to automatically generate tests for exposing redundant traversal of loops. In this paper, we design a novel, scalable and automatic approach that addresses this goal. Our approach takes a library and an initial set of coverage-driven randomly generated tests as input and generates tests which enable detection of redundant traversal of loops. Our approach is broadly composed of three phases – analysis of the execution of random tests to generate method summaries, identification of methods with potential nested loops along with the appropriate context to expose the problem, and test generation to invoke the identified methods with the appropriate parameters. The generated tests can be analyzed by existing dynamic tools to detect possible performance issues. We have implemented our approach on top of the SOOT bytecode analysis framework and validated it on many open-source Java libraries. Our experiments reveal the effectiveness of our approach in generating 224 tests that reveal 46 bugs across seven libraries, including 34 previously unknown bugs. The tests generated using our approach significantly outperform the randomly generated tests in their ability to expose the inefficiencies, demonstrating the usefulness of our design. The implementation of our tool, named Glider, is available at http://drona.csa. iisc.ac. in/~sss/tools/glider.
The Geographic Synchrony of Seasonal Influenza: A Waves across Canada and the United States

Background As observed during the 2009 pandemic, a novel influenza virus can spread globally before the epidemic peaks locally. As consistencies in the relative timing and direction of spread could form the basis for an early alert system, the objectives of this study were to use the case-based reporting system for laboratory confirmed influenza from the Canadian FluWatch surveillance program to identify the geographic scale at which spatial synchrony exists and then to describe the geographic patterns of influenza A virus across Canada and in relationship to activity in the United States (US). Methodology/Principal Findings Weekly laboratory confirmations for influenza A were obtained from the Canadian FluWatch and the US FluView surveillance programs from 1997/98 to 2006/07. For the six seasons where at least 80% of the specimens were antigenically similar, we identified the epidemic midpoint of the local/regional/provincial epidemics and analyzed trends in the direction of spread. In three out of the six seasons, the epidemic appeared first in Canada. Regional epidemics were more closely synchronized across the US (3–5 weeks) compared to Canada (5–13 weeks), with a slight gradient in timing from the southwest regions in the US to northeast regions of Canada and the US. Cities, as well as rural areas within provinces, usually peaked within a couple of weeks of each other. The anticipated delay in peak activity between large cities and rural areas was not observed. In some mixed influenza A seasons, lack of synchronization sub-provincially was evident. Conclusions/Significance As mixing between regions appears to be too weak to force a consistency in the direction and timing of spread, local laboratory-based surveillance is needed to accurately assess the level of influenza activity in the community. In comparison, mixing between urban communities and adjacent rural areas, and between some communities, may be sufficient to force synchronization.
Selection of the learning gain matrix of an iterative learning control algorithm in presence of measurement noise

Arbitrary high precision output tracking is one of the most desirable control objectives found in industrial applications regardless of measurement errors. The main purpose of this paper is to supply to the iterative learning control (ILC) designer guidelines to select the corresponding learning gain in order to achieve this control objective. For example, if certain conditions are met, then it is necessary for the learning gain to converge to zero in the learning iterative domain. In particular, this paper presents necessary and sufficient conditions for boundedness of trajectories and uniform tracking in presence of measurement noise and a class of random reinitialization errors for a simple ILC algorithm. The system under consideration is a class of discrete-time affine nonlinear systems with arbitrary relative degree and arbitrary number of system inputs and outputs. The state function does not need to satisfy a Lipschitz condition. This work also provides a recursive algorithm that generates the appropriate learning gain functions that meet the arbitrary high precision output tracking objective. The resulting tracking output error is shown to converge to zero at a rate inversely proportional to square root of the number of learning iterations in presence of measurement noise and a class of reinitialization errors. Two illustrative numerical examples are presented.
8 Image coding using redundant dictionaries

This chapter discusses the problem of coding images using very redundant libraries of waveforms, also referred to as dictionaries. We start with a discussion of the shortcomings of classical approaches based on orthonormal bases. More specifically, we show why these redundant dictionaries provide an interesting alternative for image representation. We then introduce a special dictionary of 2-D primitives called anisotropic refinement atoms that are well suited for representing edge-dominated images. Using a simple greedy algorithm, we design an image coder that performs very well at low bit rate. We finally discuss its performance and particular features such as geometric adaptativity and rate scalability.
Assessing process-centered software engineering environments

Process-centered software engineering environments (PSEEs) are the most recent generation of environments supporting software development activities. They exploit an representation of the process (called the process model that specifies how to carry out software development activities, the roles and tasks of software developers, and how to use and control software development tools. A process model is therefore a vehicle to better understand and communicate the process. If it is expressed in a formal notation, it can be used to support a variety of activities such as process analysis, process simulation, and process enactment. PSEEs provide automatic support for these activities. They exploit languages based on different paradigms, such as Petri nets and rule-based systems. They include facilities to edit and analyze process models. By enacting the process model, a PSEE provides a variety of services, such as assistance for software developers, automation of routine tasks, invocation and control of software development tools, and enforcement of mandatory rules and practices. Several PSEEs have been developed, both as research projects and as commercial products. The initial deployment and exploitation of this technology have made it possible to produce a significant amount of experiences, comments, evaluations, and feedback. We still lack, however, consistent and comprehensive assessment methods that can be used to collect and organize this information. This article aims at contributing to the definition of such methods, by providing a systematic comparison grid and by accomplishing an initial evaluation of the state of the art in the field. This evaluation takes into account the systems that have been developed by the authors in the past five years, as well as the main characteristics of other well-known environments
Simultaneous stability and sensitivity in model cortical networks is achieved through anti-correlations between the in- and out-degree of connectivity

Neuronal networks in rodent barrel cortex are characterized by stable low baseline firing rates. However, they are sensitive to the action potentials of single neurons as suggested by recent single-cell stimulation experiments that reported quantifiable behavioral responses in response to short spike trains elicited in single neurons. Hence, these networks are stable against internally generated fluctuations in firing rate but at the same time remain sensitive to similarly-sized externally induced perturbations. We investigated stability and sensitivity in a simple recurrent network of stochastic binary neurons and determined numerically the effects of correlation between the number of afferent (“in-degree”) and efferent (“out-degree”) connections in neurons. The key advance reported in this work is that anti-correlation between in-/out-degree distributions increased the stability of the network in comparison to networks with no correlation or positive correlations, while being able to achieve the same level of sensitivity. The experimental characterization of degree distributions is difficult because all pre-synaptic and post-synaptic neurons have to be identified and counted. We explored whether the statistics of network motifs, which requires the characterization of connections between small subsets of neurons, could be used to detect evidence for degree anti-correlations. We find that the sample frequency of the 3-neuron “ring” motif (1→2→3→1), can be used to detect degree anti-correlation for sub-networks of size 30 using about 50 samples, which is of significance because the necessary measurements are achievable experimentally in the near future. Taken together, we hypothesize that barrel cortex networks exhibit degree anti-correlations and specific network motif statistics.
A Comparative Study of Four Hierarchy Browsers using the Hierarchical Visualisation Testing Environment (HVTE)

Four hierarchy browsers were compared in a counterbalanced repeated measures study with 32 test users. The four browsers tested were in-house implementations of 1) a Windows Explorer style tree view, 2) an information pyramids browser, 3) a treemap browser, and 4 ) a hyperbolic browser. Each user performed eight tasks with each browser. Task completion time, subjective ratings, and overall preference data were collected. Almost no significant differences in performance were found, but users significantly preferred the tree view browser. The four browsers are implemented as part of the hierarchical visualisation system (HVS), a Java framework for visualising hierarchies. The hierarchical visualisation testing environment (HVTE) is a semi-automated testing environment built on top of HVS, which presents a sequence of tasks from a test case database to the user, together with an associated browser and test hierarchy, and automates the collection of timing data.
Flocking for multi-agent dynamic systems: algorithms and theory

In this paper, we present a theoretical framework for design and analysis of distributed flocking algorithms. Two cases of flocking in free-space and presence of multiple obstacles are considered. We present three flocking algorithms: two for free-flocking and one for constrained flocking. A comprehensive analysis of the first two algorithms is provided. We demonstrate the first algorithm embodies all three rules of Reynolds. This is a formal approach to extraction of interaction rules that lead to the emergence of collective behavior. We show that the first algorithm generically leads to regular fragmentation, whereas the second and third algorithms both lead to flocking. A systematic method is provided for construction of cost functions (or collective potentials) for flocking. These collective potentials penalize deviation from a class of lattice-shape objects called /spl alpha/-lattices. We use a multi-species framework for construction of collective potentials that consist of flock-members, or /spl alpha/-agents, and virtual agents associated with /spl alpha/-agents called /spl beta/- and /spl gamma/-agents. We show that migration of flocks can be performed using a peer-to-peer network of agents, i.e., "flocks need no leaders. " A "universal" definition of flocking for particle systems with similarities to Lyapunov stability is given. Several simulation results are provided that demonstrate performing 2-D and 3-D flocking, split/rejoin maneuver, and squeezing maneuver for hundreds of agents using the proposed algorithms.
Degree dependence in rates of transcription factor evolution explains the unusual structure of transcription networks

Transcription networks have an unusual structure. In both prokaryotes and eukaryotes, the number of target genes regulated by each transcription factor, its out-degree, follows a broad tailed distribution. By contrast, the number of transcription factors regulating a target gene, its in-degree, follows a much narrower distribution, which has no broad tail. We constructed a model of transcription network evolution through trans- and cis-mutations, gene duplication and deletion. The effects of these different evolutionary processes on the network structure are enough to produce an asymmetrical in- and out-degree distribution. However, the parameter values required to replicate known in- and out-degree distributions are unrealistic. We then considered variation in the rate of evolution of a gene dependent upon its position in the network. When transcription factors with many regulatory interactions are constrained to evolve more slowly than those with few interactions, the details of the in- and out-degree distributions of transcription networks can be fully reproduced over a range of plausible parameter values. The networks produced by our model depend on the relative rates of the different evolutionary processes. By determining the circumstances under which the networks with the correct degree distributions are produced, we are able to assess the relative importance of the different evolutionary processes in our model during evolution.
A Simple Test of Abortion and Crime

I first replicate Donohue and Levitt's results for violent and property crime arrest rates. I apply their data and specification to an analysis of age-specific homicide rates and murder arrest rates. The coefficients on the abortion rate have the wrong sign for two of the four measures of crime and none is statistically significant at conventional levels. I then use the legalization of abortion in 1973 to exploit two sources of variation: between-state changes in abortion rates before and after Roe, and cross-cohort differences in exposure to legalized abortion. I find no meaningful association between abortion and age-specific crime rates.
Apathy in Parkinson's Disease: An Electrophysiological Study

In Parkinson's disease (PD), apathy (or loss of motivation) is frequent. Nevertheless, the contribution of attentional disorders to its genesis is still not clearly known. We want to determine the relation existing between apathy and attentional disorders by using P300a (or novelty P3) as a marker of the attentional process. The study included 25 patients (13 women and 12 men) with PD for whom we have determined the relationship between automatic attention (represented by P300a) and motor status, apathy, executive dysfunction, mental flexibility, inhibitory control, and depression/anxiety. We have found a correlation between the apathy score and amplitude of novelty P300 during the ON period and also a correlation of the apathy score with a decrease in amplitude of P300 during the OFF period. In a linear regression model, changes in the P300a predicted the severity of apathy independently of any other variable. We concluded firstly that the reduction in amplitude of the P300a wave was a neurophysiological marker of apathy in PD and secondly that apathy led to both dopaminergic denervation (mesolimbic) and nondopaminergic (dorsolateral prefrontal-subcortical) dysfunction.
Submillimeter functional localization in human striate cortex using BOLD contrast at 4 Tesla: Implications for the vascular point‐spread function

Using multislice segmented echoplanar imaging at 4 T, we have measured an upper bound to the cortical vasculature point‐spread function (PSF) using functional magnetic resonance imaging (fMRI) in humans. Our experiments demonstrate that cortical subunits that are approximately 700 μm apart can be resolved using the early part of the hyperoxygenation phase of the blood oxygenation level‐dependent (BOLD) effect. This was accomplished using brief (4 sec) single trials of monocular and binocular stimulation of ocular dominance columns in human primary visual cortex. The data suggest that at even higher magnetic fields, the cortical vasculature PSF may be limited by the extent and nature of horizontal connections and not signal‐to‐noise ratio. Magn Reson Med 41:230–235, 1999. © 1999 Wiley‐Liss, Inc.
Predicting Reading Fluency in Patients with Macular Disease

Purpose. Difficulty in reading is the most frequent complaint of patients with macular disease (MD). This article assesses whether clinical variables measured at the onset of MD can be used to predict patients’ future reading ability. Methods. Twenty-five patients with MD were recruited within 4 weeks of the onset of symptoms in their second affected eye. Clinical and demographic features were recorded at baseline and at the exit point of the study 3 to 12 months later. Odds ratios (OR’s) were constructed to assess the predictive value of these variables in terms of reading fluency and any change in reading speed at the exit point of the study. Results. Baseline contrast sensitivity was associated with future fluent reading (OR, 2.40; interval size, 0.15; 95% confidence interval, 1.13 to 5.07). Age, sex, scotoma size, disease type, visual acuity, and reading speed were not statistically significant predictors of future fluent reading. It was not possible to predict fully in which patients reading speed improved or deteriorated. Conclusions. Contrast sensitivity can predict the likelihood of future fluent reading in patients with MD. Baseline reading speed, visual acuity, age, disease type, and scotoma size are poor predictors of future reading performance.
Induction of a Specific Strong Polyantigenic Cellular Immune Response after Short-Term Chemotherapy Controls Bacillary Reactivation in Murine and Guinea Pig Experimental Models of Tuberculosis

ABSTRACT RUTI is a therapeutic vaccine that is generated from detoxified and liposomed Mycobacterium tuberculosis cell fragments that has demonstrated its efficacy in the control of bacillus reactivation after short-term chemotherapy. The aim of this study was to characterize the cellular immune response generated after the therapeutic administration of RUTI and to corroborate the lack of toxicity of the vaccine. Mouse and guinea pig experimental models were infected with a low-dose M. tuberculosis aerosol. RUTI-treated animals showed the lowest bacillary load in both experimental models. RUTI also decreased the percentage of pulmonary granulomatous infiltration in the mouse and guinea pig models. This was not the case after Mycobacterium bovis BCG treatment. Cellular immunity was studied through the characterization of the intracellular gamma interferon (IFN-γ)-producing cells after the splenocytes' stimulation with M. tuberculosis-specific structural and growth-related antigens. Our data show that the difference between the therapeutic administration of BCG and RUTI resides mainly in the stronger activation of IFN-γ+ CD4+ cells and CD8+ cells against tuberculin purified protein derivative, ESAT-6, and Ag85B that RUTI generates. Both vaccines also triggered a specific immune response against the M. tuberculosis structural antigens Ag16kDa and Ag38kDa and a marked mRNA expression of IFN-γ, tumor necrosis factor, interleukin-12, inducible nitric oxide synthase, and RANTES in the lung. The results show that RUTI's therapeutic effect is linked not only to the induction of a Th1 response but also to the stimulation of a quicker and stronger specific immunity against structural and growth-related antigens that reduces both the bacillary load and the pulmonary pathology.
Patient Reported Outcomes of Eat, Walk, Sleep: A Cardiometabolic Lifestyle Program for Cambodian Americans Delivered by Community Health Workers

Background. This study investigated a community health worker-delivered lifestyle intervention for prevention of cardiometabolic disease, called Eat, Walk, Sleep. It was designed for traumatized, low-literacy Cambodian American refugees. Methods. We used a single group, pre-post design to evaluate the effects of the program on self-reported health behaviors. As a control for threats to internal validity, we also measured a nonequivalent dependent variable, i.e., perceived discrimination by health care providers. Results. Of 140 participants enrolled, 114 completed one-year assessments. In intent-to-treat analysis with correction for multiple comparisons, compared with baseline, participants at one year scored higher on cardiometabolic prevention knowledge, self-rated health, physical activity, medication compliance, and preventive screenings, and they reported improved sleep, a modest shift from white to brown rice, and reduced barriers to care. As expected, perceptions of discrimination by health care providers did not change. Conclusions. Self-reported behavioral risk factors improved. A randomized, controlled study with objective measures is warranted.