Miracle-dz/UniFAR-FTUs huggingface dataset:
From Runtime Failures to Patches: Study of Patch Generation in Production. (De l'erreur d'exécution aux correctifs: étude de la génération de correctifs en production)

Patch creation is one of the most important actions in the life cycle of an application. Creating patches is a time-consuming task. Not only because it is difficult to create a sound and valid patch, but also because it requires the intervention of humans. Indeed, a user must report the bug, and a developer must reproduce it and fix it, which takes much time. To address this problem, techniques that automate this task have been created. However, those techniques still require a developer to reproduce the bug and encode it as a failing test case. This requirement drastically reduces the applicability of the approaches since it still relies on humans. This thesis proposes new patch generation techniques that remove the human intervention for the patch generation. Our idea is to put as close as possible the patch generation in the production environment. We adopt this approach because the production environment contains all the data and human interactions that lead to the bug. In this thesis, we show how to exploit this data to detect bugs, generate and validate patches. We evaluate this approach on seven different benchmarks of real bugs collected from open-source projects. During the evaluation, we are particularly attentive to the number of generated patches, to their correctness, readability and to the time required for generating them. Our evaluation shows the applicability and feasibility of our approach to generate patches in the production environment without the intervention of a developer.
XPA: An Open Soruce IDE for XACML Policies (S)

This paper presents XPA (XACML Policy Analyzer), an open source IDE (Integrated Development Environment) for testing, debugging, and mutating XACML 3.0 policies. XACML is an OASIS standard for specifying attributebased access control policies. XPA provides a variety of new techniques for generating test cases from policies, localizing bugs in faulty policies, and repairing faulty policy elements. XPA has been applied to numerous XACML policies from the literature and real-world applications. These policies have been used to quantitatively evaluate the effectiveness of various testing and debugging methods. For system developers and administrators, XPA is a practical IDE for developing dependable XACML policies. For access control researchers, XPA offers a versatile toolkit for studying and evaluating new testing, debugging, and verification techniques. Keywords—access control, XACML, testing, fault localization,
Assessment of the potential allergenicity of genetically-engineered food crops

Abstract An extensive safety assessment process exists for genetically-engineered (GE) crops. The assessment includes an evaluation of the introduced protein as well as the crop containing the protein with the goal of demonstrating the GE crop is “as-safe-as” non-GE crops in the food supply. One of the evaluations for GE crops is to assess the expressed protein for allergenic potential. Currently, no single factor is recognized as a predictor for protein allergenicity. Therefore, a weight-of-the-evidence approach, which accounts for a variety of factors and approaches for an overall assessment of allergenic potential, is conducted. This assessment includes an evaluation of the history of exposure and safety of the gene(s) source; protein structure (e.g. amino acid sequence identity to human allergens); stability of the protein to pepsin digestion in vitro; heat stability of the protein; glycosylation status; and when appropriate, specific IgE binding studies with sera from relevant clinically allergic subjects. Since GE crops were first commercialized over 20 years ago, there is no proof that the introduced novel protein(s) in any commercialized GE food crop has caused food allergy.
Automated staging for virtual cinematography

While the topic of virtual cinematography has essentially focused on the problem of computing the best viewpoint in a virtual environment given a number of objects placed beforehand, the question of how to place the objects in the environment with relation to the camera (referred to as staging in the film industry) has received little attention. This paper first proposes a staging language for both characters and cameras that extends existing cinematography languages with multiple cameras and character staging. Second, the paper proposes techniques to operationalize and solve staging specifications given a 3D virtual environment. The novelty holds in the idea of exploring how to position the characters and the cameras simultaneously while maintaining a number of spatial relationships specific to cinematography. We demonstrate the relevance of our approach through a number of simple and complex examples.
Efficient Basis Pursuit DeNoising via Active Sets and Homotopy

The Basis Pursuit DeNoising problem is a variant of the well-known lasso method for obtaining sparse least-squares approximations, which can be represented as the minimization problem minβ 1 2 ‖Aβ − y‖ 2 + λ ‖β‖ 1 . In this paper the problem is treated as a parametric quadratic program with parameter λ ≥ 0. By this technique, very large scale problems can be essentially solved exactly for a range of values of λ, as long as the number of non-zero components of β is small to modest.
Genetic variants in CCL5 and CCR5 genes and serum VEGF‐A levels predict efficacy of bevacizumab in metastatic colorectal cancer patients

Early VEGF‐A reduction (EVR) by targeting abundant VEGF‐A is a potential predictive marker of bevacizumab (BEV). The CCL5/CCR5 axis modulates VEGF‐A production via endothelial progenitor cells migration. We tested whether genetic polymorphisms in the CCL5/CCR5 pathway could predict efficacy of BEV in patients with metastatic colorectal cancer (mCRC) in a first‐line setting. Genomic DNA was extracted from 215 samples from three independent cohorts: 61 patients receiving FOLFOX+BEV (evaluation cohort); 83 patients receiving FOLFOX (control cohort); 71 patients receiving FOLFOX/XELOX+BEV (exploratory cohort) for validation and serum biochemistry assay (n = 48). Single nucleotide polymorphisms of genes in the CCL5/CCR5 pathway were analyzed by PCR‐based direct sequencing. Considering the unbalanced distribution of patient baseline characteristics between the evaluation and control cohorts, propensity score matching analysis was performed. Serum VEGF‐A levels during treatment were measured using ELISA. Among the evaluation and control cohorts, patients with any CCL5 rs2280789 G allele had longer progression‐free survival (PFS) and overall survival (OS) when receiving FOLFOX+BEV than FOLFOX (PFS: 19.8 vs. 11.0 months, HR 0.44, 95%CI: 0.24–0.83, p = 0.004; OS: 41.8 vs. 24.5 months, HR: 0.50, 95%CI: 0.26–0.95, p = 0.024). No significant difference was shown in patients with the A/A variant. In the exploratory cohort, CCL5 rs2280789 G alleles were associated with higher VEGF‐A levels at baseline and a greater decrease in VEGF‐A levels at day 14 compared to the A/A variant. CCL5 and CCR5 impact the angiogenic environment, and the genotypes in CCL5/CCR5 genes may identify specific populations who will benefit from BEV in first‐line treatment for mCRC.
Ghost Infarct Core and Admission Computed Tomography Perfusion: Redefining the Role of Neuroimaging in Acute Ischemic Stroke

Background: Determining the size of infarct extent is crucial to elect patients for reperfusion therapies. Computed tomography perfusion (CTP) based on cerebral blood volume may overestimate infarct core on admission and consequently include ghost infarct core (GIC) in a definitive lesional area. Purpose: Our goal was to confirm and better characterize the GIC phenomenon using CTP cerebral blood flow (CBF) as the reference parameter to determine infarct core. Methods: We performed a retrospective, single-center analysis of consecutive thrombectomies of middle cerebral or intracranial internal carotid artery occlusions considering noncontrast CT Alberta Stroke Program Early CT Score ≥6 in patients with pretreatment CTP. We used the RAPID® software to measure admission infarct core based on initial CBF. The final infarct was extracted from follow-up CT. GIC was defined as initial core minus final infarct > 10 mL. Results: A total of 123 patients were included. The median National Institutes of Health Stroke Scale score was 18 (13–20), the median time from symptoms to CTP was 188 (67–288) min, and the recanalization rate (Thrombolysis in Cerebral Infarction score 2b, 2c, or 3) was 83%. Twenty patients (16%) presented with GIC. GIC was associated with shorter time to recanalization (150 [105–291] vs. 255 [163–367] min, p = 0.05) and larger initial CBF core volume (38 [26–59] vs. 6 [0–27] mL, p < 0.001). An adjusted logistic regression model identified time to recanalization < 302 min (OR 4.598, 95% CI 1.143–18.495, p = 0.032) and initial infarct volume (OR 1.01, 95% CI 1.001–1.019, p = 0.032) as independent predictors of GIC. At 24 h, clinical improvement was more frequent in patients with GIC (80 vs. 49%, p = 0.01). Conclusions: CTP CBF < 30% may overestimate infarct core volume, especially in patients imaged in the very early time window and with fast complete reperfusion. Therefore, the CTP CBF technique may exclude patients who would benefit from endovascular treatment.
Information diffusion through blogspace

We study the dynamics of information propagation in environments of low-overhead personal publishing, using a large collection of WebLogs over time as our example domain. We characterize and model this collection at two levels. First, we present a macroscopic characterization of topic propagation through our corpus, formalizing the notion of long-running "chatter" topics consisting recursively of "spike" topics generated by outside world events, or more rarely, by resonances within the community. Second, we present a microscopic characterization of propagation from individual to individual, drawing on the theory of infectious diseases to model the flow. We propose, validate, and employ an algorithm to induce the underlying propagation network from a sequence of posts, and report on the results.
Therapeutic targeting of transcriptional cyclin-dependent kinases

ABSTRACT The fact that many cancer types display transcriptional addiction driven by dysregulation of oncogenic enhancers and transcription factors has led to increased interest in a group of protein kinases, known as transcriptional cyclin dependent kinases (tCDKs), as potential therapeutic targets. Despite early reservations about targeting a process that is essential to healthy cell types, there is now evidence that targeting tCDKs could provide enough therapeutic window to be effective in the clinic. Here, we discuss recent developments in this field, with an emphasis on highly-selective inhibitors and the challenges to be addressed before these inhibitors could be used for therapeutic purposes. Abbreviations: CAK: CDK-activating kinase;CDK: cyclin-dependent kinase;CMGC group: CDK-, MAPK-, GSK3-, and CLK-like;CTD: C-terminal repeat domain of the RPB1 subunit of RNA polymerase II;DRB: 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole;mCRPC: metastatic castration-resistant prostate cancer;NSCLC: non-small cell lung cancer;P-TEFb: positive elongation factor b;RNAPII: RNA polymerase II;S2: serine-2 of CTD repeats;S5: serine-5 of CTD repeats;S7: serine-7 of CTD repeats;SEC: super elongation complex;tCDK: transcriptional cyclin-dependent kinase;TNBC: triple-negative breast cancer
Visualizing Interactions in AngularJS-based Single Page Web Applications

AngularJS is a popular framework for single page web applications. In AngularJS applications, the programming logic is implemented in Javascript, while the layout is defined separately in HTML files. Due to this separation, data and control flow is usually hard to track. We propose a method to visualize the data and control flow in AngularJS-based single page web applications and separate interactions from each other. Our method helps to get a better understanding of the application’s work flow, to realize the boundaries of the interactions, and to know what is updated in an interaction and what is not.
Diversity Patterns of Hematophagous Insects in Atlantic Forest Fragments and Human-Modified Areas of Southern Bahia, Brazil

ABSTRACT: There have been several important outbreaks of mosquito-borne diseases in the Neotropics in recent years, particularly in Brazil. Some taxa are also considered to be indicators of environmental health. Despite the importance of understanding insect abundance and distribution to the understanding of disease dynamics and design strategies to manage them, very little is known about their ecology in many tropical regions. We studied the abundance and diversity of mosquitoes and sand flies in the Bahia State of Brazil, a point of origin for arbovirus outbreaks, including Zika and Chikungunya fever. During 2009-2014, 51 mosquito taxa were identified, belonging to three dipteran families, Ceratopogonidae, Culicidae, and Psychodidae. The family Culicidae, including the Sabethini tribe, were the most abundant (81.5%) and most taxa-rich (n=45). While season (winter and summer) was a strong factor determinant of the occurrence of the most abundant taxa, the stratification level in the forest (ground or tree level) had a strong effect and the dominant taxa at ground level were completely different from the dominant species collected at tree level. We suggest that sites with a mix of forest and agroforestry systems support the highest biodiversity of hematophagous insects as compared to highly disturbed landscapes.
Principle and Analysis of Doubly Salient PM Motor With Π-Shaped Stator Iron Core Segments

This paper investigates a novel three-phase doubly salient permanent magnet (DSPM) motor. Because of the adoption of Π-shaped stator iron core segments, the asymmetrical magnetic circuit among different phases occurring in conventional DSPM motors with E-shaped stator iron core segments can be avoided, so that balanced and sinusoidal three-phase PM flux linkage and no-load electromotive force (EMF) can be achieved. First, based on a 12/7 stator/rotor pole combination, the operation principle of Π-core DSPM motor is discussed using the least magnetic reluctance principle. Then, the general airgap field modulation theory is extended to the Π-core DSPM motor for explaining its operation principle further and armature winding connection. The finite element analysis is used to validate theoretical analysis, as well as to calculate its electromagnetic performances. The results show that the 12/7-pole Π-core DSPM motor possesses higher average torque output capability and lower torque ripple compared with the 12/8-pole E-core counterpart. Finally, a 12/7-pole Π-core DSPM motor is built and tested so as to experimentally verify the theoretical analysis.
Efficient error estimating coding: feasibility and applications

Motivated by recent emerging systems that can leverage partially correct packets in wireless networks, this paper investigates the novel concept of error estimating codes (EEC). Without correcting the errors in the packet, EEC enables the receiver of the packet to estimate the packet's bit error rate, which is perhaps the most important meta-information of a partially correct packet. Our EEC algorithm provides provable estimation quality, with rather low redundancy and computational overhead. To demonstrate the utility of EEC, we exploit and implement EEC in two wireless network applications, Wi-Fi rate adaptation and real-time video streaming. Our real-world experiments show that these applications can significantly benefit from EEC.
MatchPy: Pattern Matching in Python

Pattern matching is a powerful tool for symbolic computations. Applications include symbolic integration, term rewriting systems, theorem proving and the manipulation of abstract syntax trees. Given a pattern and an expression, the goal of pattern matching is to find a substitution for all the variables in the pattern such that the pattern becomes the expression. As an example, consider the pattern f(x) , where x is a variable, and the expression f(a) . Then the substitution that replaces x with a is a match. In practice, functions can also be associative and/or commutative, which makes matching more complicated and can lead to multiple possible matches. Among existing systems, Mathematica (Wolfram Research n.d.) arguably offers the most expressive pattern matching. Unfortunately, no lightweight implementation of pattern matching as general and flexible as Mathematica exists for Python. The purpose of MatchPy (Krebber 2018; Krebber, Barthels, and Bientinesi 2017a) is to provide this functionality in Python. While the pattern matching in SymPy (Meurer et al. 2017) can work with associative/commutative functions, it does not support finding multiple matches, which is relevant in some applications. Furthermore, SymPy does not support sequence variables and is limited to a predefined set of mathematical operations.
Risk Factor Modeling for Cardiovascular Disease in Type 1 Diabetes in the Pittsburgh Epidemiology of Diabetes Complications (EDC) Study: A Comparison With the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Study (DCCT/EDIC)

In a recent Diabetes Control and Complications Trial (DCCT)/Epidemiology of Diabetes Interventions and Complications (EDIC) study report, mean HbA1c was the strongest predictor of cardiovascular disease (CVD) after age. In DCCT/EDIC, mean diabetes duration was 6 years (median 4) at baseline and those with high blood pressure or cholesterol were excluded. We now replicate these analyses in the Pittsburgh Epidemiology of Diabetes Complications (EDC) prospective cohort study of childhood-onset (at <17 years of age) type 1 diabetes, with similar age (mean 27 years in both studies) but longer diabetes duration (mean 19 years and median 18 years) and no CVD risk factor exclusion at baseline. CVD incidence (CVD death, myocardial infarction (MI), stroke, revascularization, angina, or ischemic electrocardiogram) was associated with diabetes duration, most recent albumin excretion rate (AER), updated mean triglycerides, baseline hypertension, baseline LDL cholesterol, and most recent HbA1c. Major atherosclerotic cardiovascular events (CVD death, MI, or stroke) were associated with diabetes duration, most recent AER, baseline systolic blood pressure, baseline smoking, and updated mean HbA1c. Compared with findings in DCCT/EDIC, traditional risk factors similarly predicted CVD; however AER predominates in EDC and HbA1c in DCCT/EDIC. Thus, the relative impact of HbA1c and kidney disease in type 1 diabetes varies according to diabetes duration.
To identify predictors of relapse in cases of alcohol dependence syndrome in relation to life events

Background and Objectives: Relapse is a complex and dynamic phenomenon that appears to be determined by biological, psychological, and social factors and an interaction among these. This study examined the association between demographic variables, clinical parameters, and psychosocial factors that predict the vulnerability to relapse in cases of alcohol dependence syndrome. Materials and Methods: Structured assessments of clinical/demographic parameters, relapse precipitants, life events, and dysfunction were carried out among patients with alcohol dependence syndrome (n = 100) who had relapsed and compared with those (n = 100) who had managed to remain abstinent. Results: Patients who had relapsed were found to have significantly more positive family history of substance use, past history of alcohol-related comorbidity, experienced a higher number of undesirable life events, and higher negative mood states and social anxiety and dysfunction in social, vocational, personal, family, and cognitive spheres compared to patients who had remained abstinent. Conclusions: Relapse in alcohol dependents is an interaction of many factors, and multiple layers of assessment may be required to predict relapse. This study provided further evidence in support of the importance of certain clinical/psychosocial factors in relapse in substance dependence. It provides the basis for investigating the correlates of relapse in a wide range of behavioral and substance use problems.
Acceptability and efficacy of partner notification for curable sexually transmitted infections in sub-Saharan Africa: A systematic review

Comprehensive case management of sexually transmitted infections (STIs) includes partner notification. We reviewed the recent literature evaluating the acceptability and efficacy of partner notification strategies (i.e. direct patient referral, provider referral, or expedited partner treatment) for curable STIs in sub-Saharan Africa. We conducted a systematic search following PRISMA guidelines: published January 2008 to June 2017 in the English language, study in sub-Saharan Africa, and discussion of any curable STI with an outcome on partner notification. We searched six electronic databases, conference abstracts, online clinical trial registries, and article bibliographies. The results showed that out of the 74 identified articles, 55 did not meet inclusion criteria. Of the 11 studies evaluating direct patient referral, the proportion of index cases (n = 4163) who successfully notified sex partner(s) was 53% (range 23-95%). Among those who notified (n = 1727), 25% (range 0–77%) had partner(s) that sought evaluation (95% CI 0.51–0.54; 95% CI 0.23–0.27). Both provider referral and expedited partner treatment had higher proportions of partner(s) who sought treatment (n = 208, 69% and n = 44, 84%, respectively). Direct patient referral is the most commonly used and evaluated partner notification strategy for STIs in sub-Saharan Africa with mixed success. We recommend future research to investigate other strategies such as expedited partner treatment.
Perplexity-free t-SNE and twice Student tt-SNE

In dimensionality reduction and data visualisation, t-SNE has become a popular method. In this paper, we propose two variants to the Gaussian similarities used to characterise the neighbourhoods around each high-dimensional datum in t-SNE. A first alternative is to use t distributions like already used in the low-dimensional embedding space; a variable degree of freedom accounts for the intrinsic dimensionality of data. The second variant relies on compounds of Gaussian neighbourhoods with growing widths, thereby suppressing the need for the user to adjust a single size or perplexity. In both cases, heavy-tailed distributions thus characterise the neighbourhood relationships in the data space. Experiments show that both variants are competitive with t-SNE, at no extra cost