Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic approaches for increasing soundness and precision of static analyzers

Building static analyzers for modern programming languages is difficult. Often soundness is a requirement, perhaps with some well-defined exceptions, and precision must be adequate for producing useful results on realistic input programs. Formally proving such properties of a complex static analysis implementation is rarely an option in practice, which raises the challenge of how to identify causes and importance of soundness and precision problems. Through a series of examples, we present our experience with semi-automated methods based on delta debugging and dynamic analysis for increasing soundness and precision of a static analyzer for JavaScript. The individual methods are well known, but to our knowledge rarely used systematically and in combination.
Retroviral Env Glycoprotein Trafficking and Incorporation into Virions

Together with the Gag protein, the Env glycoprotein is a major retroviral structural protein and is essential for forming infectious virus particles. Env is synthesized, processed, and transported to certain microdomains at the plasma membrane and takes advantage of the same host machinery for its trafficking as that used by cellular glycoproteins. Incorporation of Env into progeny virions is probably mediated by the interaction between Env and Gag, in some cases with the additional involvement of certain host factors. Although several general models have been proposed to explain the incorporation of retroviral Env glycoproteins into virions, the actual mechanism for this process is still unclear, partly because structural data on the Env protein cytoplasmic tail is lacking. This paper presents the current understanding of the synthesis, trafficking, and virion incorporation of retroviral Env proteins.
Medial prefrontal cortex NMDA receptors and nitric oxide modulate the parasympathetic component of the baroreflex

The ventral portion of the medial prefrontal cortex (vMPFC) is involved in the modulation of the parasympathetic component of the baroreflex. In the present study, we verified the effect of blockade of vMPFC glutamatergic receptors and nitric oxide synthases (NOS) on the parasympathetic component of baroreflex in awake rats. Bilateral microinjection of the non‐selective ionotropic glutamate antagonist kynurenic acid (KYN) into the vMPFC caused a shift of the threshold of reflex bradycardia toward higher pressures in response to increases in mean arterial pressure (MAP) caused by intravenous infusion of phenylephrine, thus indicating a tonic facilitatory influence action of vMPFC glutamate receptors on the parasympathetic component of the baroreflex. The effect of blockade of vMPFC‐NMDA receptors by AP7 was similar to that observed after KYN, suggesting mediation via NMDA receptors. Pretreatment with the NOS inhibitor L‐NAME or the specific neural NOS (nNOS) Nω‐propyl‐l‐arginine microinjected in the vMPFC caused a shift of the reflex threshold toward higher pressures that was similar to that observed after blockade of NMDA receptors, thus indicating participation of the NO/NMDA‐receptor pathway in the vMPFC modulation of the parasympathetic component of the baroreflex. In conclusion, our data indicate that glutamatergic neurotransmission in the vMPFC has a tonic facilitatory influence on the parasympathetic component of the baroreflex. Because local treatment with either the nNOS inhibitor Nω‐propyl‐l‐arginine or the specific NMDA antagonist AP7 had similar effects on the baroreflex, it is also suggested that this modulation involves an NMDA–NO interaction within the vMPFC.
Modular Organization of the Phd Repressor/Antitoxin Protein

ABSTRACT The P1 plasmid addiction operon is a compact genetic structure consisting of promoter, operator, antitoxin gene (phd), and toxin gene (doc). The 73-amino-acid antitoxin protein, Phd, has two distinct functions: it represses transcription (by binding to its operator) and it prevents host death (by binding and neutralizing the toxin). Here, we show that the N terminus of Phd is required for repressor but not antitoxin activity. Conversely, the C terminus is required for antitoxin but not repressor activity. Only a quarter of the protein, the resolution limit of this analysis, was required for both activities. We suggest that the plasmid addiction operon is a composite of two evolutionarily separable modules, an operator-repressor module and an antitoxin-toxin module. Consideration of similar antitoxin proteins and their surroundings indicates that modular exchange may contribute to antitoxin and operon diversity.
A Reconfigurable MapReduce accelerator for multi-core all-programmable SoCs

Phoenix MapReduce is a programming framework for multi-core systems that is used to automatically parallelize and schedule the programs based on the MapReduce framework. This paper presents a novel reconfigurable MapReduce accelerator that can be augmented to multi-core SoCs and it can speedup the indexing and the processing of the MapReduce key-value pairs. The proposed architecture is implemented, mapped and evaluated to an all-programmable SoC with two embedded ARM cores (Zynq FPGA). Depending on the MapReduce application requirements, the user can dynamically reconfigure the FPGA with the appropriate version of the MapReduce accelerator. The performance evaluation shows that the proposed scheme can achieve up to 2.3x overall performance improvement in MapReduce applications.
Sensor Andrew: Large-scale campus-wide sensing and actuation

In this paper, we present Sensor Andrew, an infrastructure for Internet-scale sensing and actuation across a wide range of heterogeneous devices designed to facilitate application development. The goal of Sensor Andrew is to enable a variety of ubiquitous large-scale monitoring and control applications in a way that is extensible, easy to use, and secure while maintaining privacy. To illustrate the requirements of Sensor Andrew, as well as the capabilities and limitations of the system, we outline one such application in which multiple classes of energy sensors are combined with environmental sensors to not only monitor energy usage but also identify energy waste within buildings.
Processing strategies and transfer of heritage and non-heritage learners of Korean

What makes Heritage Language (HL) learners different from non-HL learners is the fact that HL learners possess both the linguistic characteristics of an L2 learner and of a native speaker. Like most HL learners, Korean HL learners have been known for their high command oflistening comprehension, vocabulary and cultural knowledge. Yet, studies in the field ofKorean language pedagogy have pointed out that HL learners also exhibit various significant weaknesses in other areas, such as productive skills and grammar competency, which tend to persist despite years of formal (college-level) instruction. As a result, identifying linguistic differences between HL and non-HL learners has been an ongoing and critical issue. This dissertation thus employs a design that empirically investigates the differences in language transfer and strategy when processing Korean relative clauses by using a picture-selection task. With varying degrees of language exposure and use, learners who participated in this experiment (N=128) were categorized into five subgroups based on their first language (Ll): HL learners who reported (i) Korean as Ll; (ii) both Korean & English as Ll; (iii) English as Ll; and non-HL learners who reported (iv) English as Ll; (v) Japanese as Ll. The results revealed that the Ll variable was crucial in determining the variability ofboth HL and non-HL learners. Furthermore, findings showed each sub-group ofHL and non-HL learners to be employing different processing transfer and strategies, which in tum shed light on pedagogical and theoretical issues on language acquisition as well as on domains of psycholinguistics.
Challenges of Analysing Gene-Environment Interactions in Mouse Models of Schizophrenia

The modelling of neuropsychiatric disease using the mouse has provided a wealth of information regarding the relationship between specific genetic lesions and behavioural endophenotypes. However, it is becoming increasingly apparent that synergy between genetic and nongenetic factors is a key feature of these disorders that must also be taken into account. With the inherent limitations of retrospective human studies, experiments in mice have begun to tackle this complex association, combining well-established behavioural paradigms and quantitative neuropathology with a range of environmental insults. The conclusions from this work have been varied, due in part to a lack of standardised methodology, although most have illustrated that phenotypes related to disorders such as schizophrenia are consistently modified. Far fewer studies, however, have attempted to generate a “two-hit” model, whereby the consequences of a pathogenic mutation are analysed in combination with environmental manipulation such as prenatal stress. This significant, yet relatively new, approach is beginning to produce valuable new models of neuropsychiatric disease. Focussing on prenatal and perinatal stress models of schizophrenia, this review discusses the current progress in this field, and highlights important issues regarding the interpretation and comparative analysis of such complex behavioural data.
Adaptation of stator and rotor resistances for the vector control of induction motors: A method based on reduced order current observer

This paper deals with the parameter adaptation problem of induction motors. It is well understood that the resistances of the stator and the rotor vary significantly in continuous operation. So, to prevent control performance degradation due to parameter error of the induction motor, online parameter adaptation is required. This paper proposes a new method, which is composed of two parts: a stator current observer and a parameter updating law. An outstanding feature of this method is that the rotor flux observer is not used. Instead, the flux reference value is used in the stator current observer which greatly simplifies the implementation. Simulations show that this method works satisfactorily.
ROLE OF REPLICATIVE SENESCENCE IN THE PROGRESSION OF FIBROSIS IN HEPATITIS C VIRUS (HCV) RECURRENCE AFTER LIVER TRANSPLANTATION

Background. Although hepatitis C virus (HCV) recurrence is almost universal after orthotopic liver transplantation (OLT), the impact of viral infection on liver graft is highly variable and difficult to predict. Because of the possible relationship between replicative senescence (RS) and the accelerated development of liver fibrosis, we aimed to assess the potential role of RS in the severity of HCV-related chronic hepatitis recurrence after OLT. Methods. One hundred three liver biopsies from 56 patients receiving transplants for HCV-related cirrhosis were studied, including 30 revascularization biopsies and 52 and 21 biopsies performed during and beyond the first year of OLT, respectively. The presence of senescent cells in liver grafts was assessed by the senescence-associated beta-galactosidase (SA-β-Gal) staining method. Chronic hepatitis was defined by fibrosis stage and necrotico-inflammatory activity grade using the METAVIR score. Results. A total of 34 of the 103 (33%) frozen liver biopsies displayed SA-β-Gal-positive cells, including 6 (20%) of the revascularization biopsies, 14 (34%) of the biopsies performed within the first year, and 10 (46%) of the biopsies performed beyond 1 year of follow-up. The presence of senescent cells in revascularization biopsies was significantly associated with the degree of ischemic necrosis at time of OLT (P = 0.01) and hepatitis C recurrence in the first year after OLT (P = 0.05). Furthermore, the presence of RS in the biopsy performed within the first year was associated with further development of fibrosis (P = 0.05). Conclusions. These data show that RS has a significant impact upon the course of liver transplantation, especially in the long-term progression of fibrosis observed in HCV-infected patients.
Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives

A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules.
Topographic Mapping of Large Dissimilarity Data Sets

Topographic maps such as the self-organizing map (SOM) or neural gas (NG) constitute powerful data mining techniques that allow simultaneously clustering data and inferring their topological structure, such that additional features, for example, browsing, become available. Both methods have been introduced for vectorial data sets; they require a classical feature encoding of information. Often data are available in the form of pairwise distances only, such as arise from a kernel matrix, a graph, or some general dissimilarity measure. In such cases, NG and SOM cannot be applied directly. In this article, we introduce relational topographic maps as an extension of relational clustering algorithms, which offer prototype-based representations of dissimilarity data, to incorporate neighborhood structure. These methods are equivalent to the standard (vectorial) techniques if a Euclidean embedding exists, while preventing the need to explicitly compute such an embedding. Extending these techniques for the general case of non-Euclidean dissimilarities makes possible an interpretation of relational clustering as clustering in pseudo-Euclidean space. We compare the methods to well-known clustering methods for proximity data based on deterministic annealing and discuss how far convergence can be guaranteed in the general case. Relational clustering is quadratic in the number of data points, which makes the algorithms infeasible for huge data sets. We propose an approximate patch version of relational clustering that runs in linear time. The effectiveness of the methods is demonstrated in a number of examples.
Board Composition, Political Connections and Performance in State-Owned Enterprises

This paper analyses the effects of board composition on the behaviour and performance of a sample of 114 Italian local public utilities, for which information about 1630 directors during 1994-2004 has been collected. This period is particularly interesting because of the legal changes that forced many firms to alter their juridical form and allowed the entrance of private investors. We investigate whether board size and/or board composition do affect decisions about employment and how they ultimately impact on performance. Our main findings indicate that politically connected directors, representing the state or the local municipality, dominate boards of directors in the Italian public utilities in the period under investigation. Politically connected directors exert a positive and significant effect on employment, while they impact negatively on performance.
Comparing proof systems for linear real arithmetic LFSC

LFSC is a high-level declarative language for defining proof systems and proof objects for virtually any logic. One of its distinguishing features is its support for computational side conditions on proof rules. Side conditions facilitate the design of proof systems that reflect closely the sort of high-performance inferences made by SMT solvers. This paper investigates the issue of balancing declarative and computational inference in LFSC focusing on (quantifier-free) Linear Real Arithmetic. We discuss a few alternative proof systems for LRA and report on our comparative experimental results on generating and checking proofs in them.
The Complexity of Ranking Hypotheses in Optimality Theory

Given a constraint set with k constraints in the framework of Optimality Theory (OT), what is its capacity as a classification scheme for linguistic data? One useful measure of this capacity is the size of the largest data set of which each subset is consistent with a different grammar hypothesis. This measure is known as the Vapnik-Chervonenkis dimension (VCD) and is a standard complexity measure for concept classes in computational learnability theory. In this work, I use the three-valued logic of Elementary Ranking Conditions to show that the VCD of Optimality Theory with k constraints is k-1. Analysis of OT in terms of the VCD establishes that the complexity of OT is a well-behaved function of k and that the hardness of learning in OT is linear in k for a variety of frameworks that employ probabilistic definitions of learnability.
Robots Interacting with Style

Our research goal is to identify ways to adapt non-verbal behavior and skills of a companion robot for children. We present an experiment considering parents' and children's perception of role changing and behavioral style in an interactive scenario with children. Behavioral styles being nonverbal parameters affect the way a robot expresses itself within a specific task. The results of this ongoing experiment aim to determine the influence of role changing and styles in term of perceived credibility and engagement of the child interacting with the robot.
Low exogenous lactate clearance as an early predictor of mortality in normolactatemic critically ill septic patients

ObjectiveTo evaluate the prognostic value of lactate clearance and lactate production in severely ill septic patients with normal or mildly elevated blood lactate concentration. DesignProspective, observational study. SettingNineteen-bed mixed medicosurgical intensive care unit. PatientsFifty-six patients with severe sepsis and blood lactate concentration <3 mmol/L. Measurements and Main ResultsLactate metabolism was evaluated in all patients. Lactate clearance was measured by modeling the change in arterial blood lactate over time induced by an infusion of 1 mmol/kg sodium lactate for 15 mins. Lactate production was calculated as the product of lactate clearance times the blood lactate concentration before the infusion. Outcome was taken to be mortality at 28 days after the beginning of the septic episode. A logistic regression model taking into account different risk factors was constructed. Among the 56 patients, 17 (30.3%) died before the 28th day. Basal blood lactate concentration was not different between survivors and nonsurvivors, whereas lactate clearance and production were higher in survivors (0.86 ± 0.32 vs. 0.58 ± 0.18 L/hr/kg, p < .005, and 1.19 ± 0.63 vs. 0.89 ± 0.24 mmol/hr/kg, p = .055, respectively). An increase in blood lactate 45 mins after the end of the lactate infusion (&Dgr;lact-T60) ≥0.6 mmol/L was predictive of 28-day mortality with 53% sensitivity and 90% specificity. Multivariate analysis showed that only three factors were independently and significantly correlated with 28-day mortality: presence of more than two organ failures (odds ratio, 27;p = .04), age >70 yrs (odds ratio, 5.7;p = .032), and &Dgr;lact-T60 ≥0.6 mmol/L (odds ratio, 14.2;p = .042). ConclusionLow lactate clearance in severely ill septic patients with normal or mildly elevated blood lactate is predictive of poor outcome independently of other known risk factors such as age and number of organ failures.
Selection in the presence of noise: the design of playoff systems

In every sport, playoffs and tournaments are used to select the best among a set of competing players or teams. In this paper we consider the optimal design of 6uch systems. We seek designs that are optimally efficient, in the sense that they minimize the number of rounds or the number of games needed to select the best player with a stated probabi1it.y. Our models reflect the fact that the better player in games between two players or teams does not always win. As a consequence, the problems we consider are not equivalent to choosing the smallest of n elements in the standard comparison model. We assume that there are n players. There is an initially unknown one-t+one correspondence between the set of players and the index set { 1.2,. -, n}. The player corresponding to index j is called Player j. Player 1 is the best player in the following sense: in any game between Player 1 and Player j, Player 1 wins with probability plj, where plj > l/2; draws are not allowed. The goal is to determine the identity of Player 1 with probabi1it.y at least 1 A, where A is a given constant. The games are played in rounds where,
Fewer Singles among Highly Educated Women: A Gender Reversal of Hypergamy Across Cohorts in France

Female hypergamy, defined as the propensity of individuals to form unions in which the woman is of lower status than the man, is a widely observed phenomenon. This article analyses first union formation in France using data from the 1999 family history survey (Étude de l’histoire familiale). In France, since the cohorts born in the late 1950s, couples where the woman is more educated than her partner are more frequent than the reverse. This trend is mainly attributable to the lengthening of female education – women are now more educated than men, even after controlling for changes in the educational distribution of the population (relative hypergamy) – and reflects a shift in individual preferences. Last, while the highest educated women in the pre-war birth cohorts were strongly disadvantaged on the marriage market, we observe that female permanent singlehood no longer increases with educational level. Conversely, permanent singlehood among low educated men has risen, reflecting the persistent negative effect of poor labour market outcomes on male union formation. These findings reveal a considerable weakening of the norm of female educational hypergamy, although the potential consequences of this change remain uncertain.
Molecular typing by random amplification of polymorphic DNA and M13 southern hybridization of related paired isolates of Aspergillus fumigatus

Three forms of DNA-based typing procedures for Aspergillus fumigatus isolates have been developed over the last five years. The procedures are random amplification of polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) detection, and Southern hybridizations with various repetitive sequence-based probes. Using two of these procedures, we compared 16 selected isolates, grouped into eight pairs on the basis of epidemiology or previously assigned RFLP types. RAPD with four primers (R108, RC08, 2, and 4), including three previously used with A. fumigatus, showed that one primer, R108, gave the best discrimination (8 types). Southern hybridization of total genomic DNA digested with HindIII and probed with the total bacteriophage M13 genome resulted in the highest overall level of discrimination. Combination of the RAPD and Southern hybridization with the previously assigned RFLP types discriminated 10 isolates of 16. Isolates closely linked epidemiologically could not be distinguished from each other. In addition, three pairs of isolates previously unlinked by epidemiology had the same overall types. Two pairs were obtained from the same hospital within 2 years of each other, whereas the third pair were isolated from California and Germany. A full understanding of the epidemiology and ecology of A. fumigatus requires multiple discriminatory typing procedures.