Miracle-dz/UniFAR-FTUs huggingface dataset:
Implementing the concept of refactoring in software development

According to the changes that were made to existing software the quality of the code is known to impair in quality, which is complex for editing or adding new changes in future. In real when the changes that are done to the existing code it may not be optimal. Refactoring is a recognized solution for deteriorating code, and by implementing it the future changes to the code base will be easier. Refactoring is largely practiced by experienced developers in the industry wide. As there is still some reluctance with the management to support it, because it is not a productive effort as no behavior is added or altered. The code is merely reshaped so why not spend that effort on doing something productive instead? In this paper we have conducted an experiment to make even the most narrow-minded manager a spokesman for the use of refactoring.
A STUDY ON SIMULATION AND OPTIMIZATION FOR PERSONNEL AND VEHICLE COORDINATION EVACUATION IN CASE OF EMERGENCY

A novel approach is proposed in this paper for personnel and vehicle iterative evacuation optimization to tackle crowd evacuation problem in emergency. The paper analyzes the mechanism to coordinate people flow evacuation with traffic stream evacuation, and explores optimization model from a personnel and vehicle coordination evacuation perspective. The evacuation is classified as two categories, namely evacuation with intervention and evacuation without intervention, which depends on whether intervention can be applied to path selection for evacuees. Scheduling scheme of evacuation vehicles is derived from improved ant colony algorithm, and then we integrate personnel evacuation simulation with micro traffic simulation system based on distributed collaborative simulation platform. Finally the optimal scheduling solution of system is searched out through constantly modifying evacuation plan by improved genetic algorithm.
On the admissible equilibrium points of nonlinear dynamical systems affected by parametric uncertainty: Characterization via LMIs

This paper investigates the set of admissible equilibrium points of nonlinear dynamical systems affected by parametric uncertainty. As it is well-known, determining this set is a difficult problem since one should compute the solutions of a system of nonlinear equations for all the admissible values of the uncertainty, which typically amounts to an infinite number of times. In order to address this problem, this paper proposes a characterization of this set via convex optimization for the case of polynomial nonlinearities and uncertainty constrained in a polytope. Specifically, it is shown that an upper bound of the smallest outer estimate with a freely selectable fixed shape can be obtained by solving a linear matrix inequality (LMI) problem built through the square matrix representation (SMR). Then, a necessary and sufficient condition is provided for establishing the tightness of the found upper bound. The proposed methodology and its benefits are illustrated through several numerical examples.
The Cyanobacterial Hepatotoxin Microcystin Binds to Proteins and Increases the Fitness of Microcystis under Oxidative Stress Conditions

Microcystins are cyanobacterial toxins that represent a serious threat to drinking water and recreational lakes worldwide. Here, we show that microcystin fulfils an important function within cells of its natural producer Microcystis. The microcystin deficient mutant ΔmcyB showed significant changes in the accumulation of proteins, including several enzymes of the Calvin cycle, phycobiliproteins and two NADPH-dependent reductases. We have discovered that microcystin binds to a number of these proteins in vivo and that the binding is strongly enhanced under high light and oxidative stress conditions. The nature of this binding was studied using extracts of a microcystin-deficient mutant in vitro. The data obtained provided clear evidence for a covalent interaction of the toxin with cysteine residues of proteins. A detailed investigation of one of the binding partners, the large subunit of RubisCO showed a lower susceptibility to proteases in the presence of microcystin in the wild type. Finally, the mutant defective in microcystin production exhibited a clearly increased sensitivity under high light conditions and after hydrogen peroxide treatment. Taken together, our data suggest a protein-modulating role for microcystin within the producing cell, which represents a new addition to the catalogue of functions that have been discussed for microbial secondary metabolites.
Efficiently updating IDE-based data-flow analyses in response to incremental program changes

Most application code evolves incrementally, and especially so when being maintained after the applications have been deployed. Yet, most data-flow analyses do not take advantage of this fact. Instead they require clients to recompute the entire analysis even if little code has changed—a time consuming undertaking, especially with large libraries or when running static analyses often, e.g., on a continuous-integration server. In this work, we present Reviser, a novel approach for automatically and e ciently updating inter-procedural dataflow analysis results in response to incremental program changes. Reviser follows a clear-and-propagate philosophy, aiming at clearing and recomputing analysis information only where required, thereby greatly reducing the required computational e↵ort. The Reviser algorithm is formulated as an extension to the IDE framework for Inter-procedural Finite Distributed Environment problems and automatically updates arbitrary IDE-based analyses. We have implementedReviser as an open-source extension to the Heros IFDS/IDE solver and the Soot program-analysis framework. An evaluation of Reviser on various client analyses and target programs shows performance gains of up to 80% in comparison to a full recomputation. The experiments also show Reviser to compute the same results as a full recomputation on all instances tested.
New Insights into the Genetic Diversity of Clostridium botulinum Group III through Extensive Genome Exploration

Animal botulism is caused by group III Clostridium botulinum strains producing type C and D toxins, or their chimeric forms C/D and D/C. Animal botulism is considered an emerging disease in Europe, notably in poultry production. Before our study, 14 genomes from different countries were available in the public database, but none were from France. In order to investigate the genetic relationship of French strains with different geographical areas and find new potential typing targets, 17 strains of C. botulinum group III were sequenced (16 from France and one from New Caledonia). Fourteen were type C/D strains isolated from chickens, ducks, guinea fowl and turkeys and three were type D/C strains isolated from cattle. The New Caledonian strain was a type D/C strain. Whole genome sequence analysis showed the French strains to be closely related to European strains from C. botulinum group III lineages Ia and Ib. The investigation of CRISPR sequences as genetic targets for differentiating strains in group III proved to be irrelevant for type C/D due to a deficient CRISPR/Cas mechanism, but not for type D/C. Conversely, the extrachromosomal elements of type C/D strains could be used to generate a genetic ID card. The highest level of discrimination was achieved with SNP core phylogeny, which allowed differentiation up to strain level and provide the most relevant information for genetic epidemiology studies and discrimination.
Model-guided Evolution Strategies for Dynamically Balancing Exploration and Exploitation

Wide exploration of high-dimensional, multimodal design spaces is required for uncovering alternative solutions in the conceptual phase of design optimization tasks. We present a general framework for balancing exploration and exploitation during the course of the optimization that induces sequential exploitation of different optima in the search space by selecting on a solution’s fitness and a dynamic criterion termed interestingness. We use a fitness approximation model as a memory representing the parts of the search space that have been visited before. It guides the optimizer toward those areas that require additional sampling to be correctly modeled, and are hence termed interesting. Next to applying the prediction error of the model as a measure of interestingness, we consider the statistical variation in the predictions made by multiple parallel models as an alternative approach to quantify interestingness. On three artificial test functions we compare these setups running on a canonical ES to the same ES extended with either archive-based novelty, niching, or restarting, and to simply evaluating a Latin Hypercube set of sample points.
Structural Mechanisms and Drug Discovery Prospects of Rho GTPases

Rho GTPases regulate cellular morphology and dynamics, and some are key drivers of cancer progression. This superfamily offers attractive potential targets for therapeutic intervention, with RhoA, Rac1 and Cdc42 being prime examples. The challenges in developing agents that act on these signaling enzymes include the lack of obvious druggable pockets and their membrane-bound activities. However, progress in targeting the similar Ras protein is illuminating new strategies for specifically inhibiting oncogenic GTPases. The structures of multiple signaling and regulatory states of Rho proteins have been determined, and the post-translational modifications including acylation and phosphorylation points have been mapped and their functional effects examined. The development of inhibitors to probe the significance of overexpression and mutational hyperactivation of these GTPases underscores their importance in cancer progression. The ability to integrate in silico, in vitro, and in vivo investigations of drug-like molecules indicates the growing tractability of GTPase systems for lead optimization. Although no Rho-targeted drug molecules have yet been clinically approved, this family is clearly showing increasing promise for the development of precision medicine and combination cancer therapies.
Efficient soft-output detectors: Multi-core and GPU implementations in MIMOPack library

Error control coding ensures the desired quality of service for a given data rate and is necessary to improve re-laibility of Multiple-Input Multiple-Output (MIMO) communication systems. Therefore, a good combination of detection MIMO schemes and coding schemes has drawn attention in recent years. The most promising coding schemes are Bit-Interleaved Coded Modulation (BICM). At the transmitter the information bits are encoded using an error-correction code. The soft demodulator provides the reliability information in form of real valued log-likehood ratios (LLR). These values are used by the channel decoder to make final decisions on the transmitted coded bits. Nevertheless, these sophisticated techniques produce a significant increase in the computational cost and require large computational power. This paper presents a set of Soft-Output detectors implemented in CUDA and OpenMP, which allows to considerably decrease the computational time required for the data detection stage in MIMO systems. These detectors will be included in the future MIMOPack library, a High Performance Computing (HPC) library for MIMO Communication Systems. Experimental results confirm that these implementations allow to accelerate the data detection stage for different constellation sizes and number of antennas.
More is less: reducing latency via redundancy

Low latency is critical for interactive networked applications. But while we know how to scale systems to increase capacity, reducing latency --- especially the tail of the latency distribution --- can be much more difficult. We argue that the use of redundancy in the context of the wide-area Internet is an effective way to convert a small amount of extra capacity into reduced latency. By initiating redundant operations across diverse resources and using the first result which completes, redundancy improves a system's latency even under exceptional conditions. We demonstrate that redundancy can significantly reduce latency for small but critical tasks, and argue that it is an effective general-purpose strategy even on devices like cell phones where bandwidth is relatively constrained.
MTHFR 677TT genotype and disease risk: is there a modulating role for B-vitamins?

Methylenetetrahydrofolate reductase (MTHFR) is a critical folate-metabolising enzyme which requires riboflavin as its co-factor. A common polymorphism (677C→T) in the MTHFR gene results in reduced MTHFR activity in vivo which in turn leads to impaired folate metabolism and elevated homocysteine concentrations. Homozygosity for this polymorphism (TT genotype) is associated with an increased risk of a number of conditions including heart disease and stroke, but there is considerable variability in the extent of excess risk in various reports. The present review will explore the evidence which supports a role for this polymorphism as a risk factor for a number of adverse health outcomes, and the potential modulating roles for B-vitamins in alleviating disease risk. The evidence is convincing in the case which links this polymorphism with hypertension and hypertensive disorders of pregnancy, particularly preeclampsia. Furthermore, elevated blood pressure was found to be highly responsive to riboflavin intervention specifically in individuals with the MTHFR 677TT genotype. Future intervention studies targeted at these genetically predisposed individuals are required to further investigate this novel gene–nutrient interaction. This polymorphism has also been associated with an increased risk of neural tube defects (NTD) and other adverse pregnancy outcomes; however, the evidence in this area has been inconsistent. Preliminary evidence has suggested that there may be a much greater need for women with the MTHFR 677TT genotype to adhere to the specific recommendation of commencing folic acid prior to conception for the prevention of NTD, but this requires further investigation.
This Paper Is Included in the Proceedings of the 12th Usenix Symposium on Operating Systems Design and Implementation (osdi '16). Simplifying Datacenter Network Debugging with Pathdump Simplifying Datacenter Network Debugging with Pathdump

Datacenter networks continue to grow complex due to larger scales, higher speeds and higher link utilization. Existing tools to manage and debug these networks are even more complex, requiring in-network techniques like collecting per-packet per-switch logs, dynamic switch rule updates, periodically collecting data plane snapshots, packet mirroring, packet sampling, traffic replay, etc. This paper calls for a radically different approach to network management and debugging: in contrast to implementing the functionality entirely in-network, we should carefully partition the debugging tasks between the edge devices and the network elements. We present the design, implementation and evaluation of PathDump, a minimalistic tool that utilizes resources at edge devices for network debugging. PathDump currently runs over a real network comprising only of commodity hardware, and yet, can support a surprisingly large class of network debugging problems. Evaluation results show that Path-Dump requires minimal switch and edge resources, while enabling network debugging at fine-grained time scales.
Social grouping for target handover in multi-view video

This paper uses a social grouping model to improve target handover across multiple non-overlapping cameras to enable wide-area video understanding. Prior work focuses on modeling appearance and spatial-temporal cues for target handover. In cameras with different conditions, these cues are weak, at best. We provide a complete generative social grouping model which generalizes a recent single-camera case. Our extension requires strengthening the probabilistic interpretations and the resulting optimization over track handovers and social groupings can be formulated in terms of standard fast algorithms. We demonstrate the effectiveness of the method over existing techniques on challenging real-world multi-camera video.
Family Environment and Psychiatric History in Women with Binge-eating Disorder and Obese Controls

We examined the prevalence of comorbid psychopathology, family psychiatric history, and perceptions of family environment in 20 women with binge-eating disorder (BED) and 20 non-binge-eating obese controls. Women with BED were significantly more likely to report current or lifetime affective and anxiety disorders as well as family histories of BED. Family histories of substance abuse did not differ across groups. Significantly more women with BED rated their parents' parenting style as consistent with “affectionless control” on the Parental Bonding Instrument, and reported significantly lower cohesion, expressiveness, conflict, independence, intellectual-cultural orientation, and active-recreational orientation on the Family Environment Scale.
Biotic Control over the Functioning of Ecosystems

Changes in the abundance of species — especially those that influence water and nutrient dynamics, trophic interactions, or disturbance regime — affect the structure and functioning of ecosystems. Diversity is also functionally important, both because it increases the probability of including species that have strong ecosystem effects and because it can increase the efficiency of resource use. Differences in environmental sensitivity among functionally similar species give stability to ecosystem processes, whereas differences in sensitivity among functionally different species make ecosystems more vulnerable to change. Current global environmental changes that affect species composition and diversity are therefore profoundly altering the functioning of the biosphere.
Evolution of Recombination Due to Random Drift

In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts independently (i.e., multiplicatively) upon all loci. Negative disequilibrium reduces the variance in fitness and hence, by Fisher's (1930) fundamental theorem, slows the rate of increase in mean fitness. Modifiers that increase recombination eliminate the negative disequilibria that impede selection and consequently increase in frequency by “hitchhiking. ” Thus, stochastic fluctuations in linkage disequilibrium in finite populations favor the evolution of increased rates of recombination, even in the absence of epistatic interactions among loci and even when disequilibrium is initially absent. The method developed within this article allows us to quantify the strength of selection acting on a modifier allele that increases recombination in a finite population. The analysis indicates that stochastically generated linkage disequilibria do select for increased recombination, a result that is confirmed by Monte Carlo simulations. Selection for a modifier that increases recombination is highest when linkage among loci is tight, when beneficial alleles rise from low to high frequency, and when the population size is small.
Les écarts salariaux de genre au Cameroun

L’objectif de cette etude est d’analyser les ecarts salariaux de genre au Cameroun. Plus precisement, il s’agit d’apprecier les principaux aspects de la discrimination de genre sur le fonctionnement du marche du travail au Cameroun. Partant des theories des ecarts salariaux et d’une analyse descriptive, nous parcourons les facteurs qui determinent les salaires des individus. Notre approche methodologique s’acheve par l’estimation des modeles sur la base de la troisieme enquete camerounaise aupres des menages.
Particle Swarm Algorithm for Classification Rules Generation

It is the core problem in building a fuzzy classification system to extract an optimal group of fuzzy classification rules from fuzzy data set. A new kind of algorithm is proposed for fuzzy rules' generating in this work. The idea behind the algorithm is mainly based on both, concepts of data mining and particle swarm optimization (PSO) algorithm. A fuzzy information entropy based measure which generalizes the one used in crisp domain is introduced to measure fuzzy rule's interestingness, and it combines with other two measures, accuracy and coverage, to construct the composite objective function which is called fitness function in the algorithm. Finally, the algorithm is utilized to solve the famous Saturday morning problem. The result is compared with that of fuzzy decision tree induction method
Taxing working memory with syntax: Bihemispheric modulations

Motivated by claims that relegate the syntactic functions of Broca's region to working memory (WM) and not to language‐specific mechanisms, we conducted an fMRI and an aphasia study that featured two varieties of intrasentential dependency relations: One was syntactic movement (e.g., Which boy does the girl think ◂ examined Steven? ), the other was antecedent–reflexive binding (e.g., Jill thinks the boy examined himself). In both, WM is required to link two nonadjacent positions. Syntactically, they are governed by distinct rule systems. In health, the two dependencies modulated activity in distinct brain regions within the left inferior frontal gyrus and the left middle temporal gyrus. Binding uniquely modulated activation in the right frontal lobe. Receptive abilities in brain damaged patients likewise distinguished among these syntactic types. The results indicate that sentence comprehension is governed by syntactically carved neural chunks and provide hints regarding a language related region in the right hemisphere. Hum Brain Mapp 2006. © 2006 Wiley‐Liss, Inc.
Bond order solid of two-dimensional dipolar fermions.

The recent experimental realization of dipolar Fermi gases near or below quantum degeneracy provides an opportunity to engineer Hubbard-like models with long-range interactions. Motivated by these experiments, we chart out the theoretical phase diagram of interacting dipolar fermions on the square lattice at zero temperature and half filling. We show that, in addition to p-wave superfluid and charge density wave order, two new and exotic types of bond order emerge generically in dipolar fermion systems. These phases feature homogeneous density but periodic modulations of the kinetic hopping energy between nearest or next-nearest neighbors. Similar, but manifestly different, phases of two-dimensional correlated electrons have previously only been hypothesized and termed "density waves of nonzero angular momentum. " Our results suggest that these phases can be constructed flexibly with dipolar fermions, using currently available experimental techniques.
On Computing a Multiple of an Elliptic Curve Point

We describe an improved algorithm for computing a multiple of a point on elliptic curves deened over nite elds of characteristic greater than three. The proposed algorithm is based on new formulae for computing repeated doubling points with only one eld inversion, and the signed-digit exponent recoding algorithm. The new algorithm is shown to be faster than M uller's method 7]. Our new formulae for repeated doubling points can also be used to speed up algorithms such as the k-ary method and the signed binary window method.