A formal soundness proof of region-based memory management for object-oriented paradigm.

Region-based memory management has been proposed as a viable alternative to garbage collection for real-time applications and embedded software. In our previous work we have developed a region type inference algorithm that provides an automatic compile-time region-based memory management for object-oriented paradigm. In this work we present a formal soundness proof of the region type system that is the target of our region inference. More precisely, we prove that the object-oriented programs accepted by our region type system achieve region-based memory management in a safe way. That means, the regions follow a stack-of-regions discipline and regions deallocation never create dangling references in the store and on the program stack. Our contribution is to provide a simple syntactic proof that is based on induction and follows the standard steps of a type safety proof. In contrast the previous safety proofs provided for other region type systems employ quite elaborate techniques

Decision Procedure for Entailment of Symbolic Heaps with Arrays

This paper gives a decision procedure for the validity of en- tailment of symbolic heaps in separation logic with Presburger arithmetic and arrays. The correctness of the decision procedure is proved under the condition that sizes of arrays in the succedent are not existentially bound. This condition is independent of the condition proposed by the CADE-2017 paper by Brotherston et al, namely, one of them does not imply the other. For improving efficiency of the decision procedure, some techniques are also presented. The main idea of the decision procedure is a novel translation of an entailment of symbolic heaps into a formula in Presburger arithmetic, and to combine it with an external SMT solver. This paper also gives experimental results by an implementation, which shows that the decision procedure works efficiently enough to use

Serological Survey of Antibodies to Mannheimia haemolytica and Pasteurella multocida in Camelids from Argentina

South American camelids are a source of livestock wealth in Andean countries. In Argentina,there is little information about camelid pathogens, and most of the literature data available areseroprevalence works against virus. Besides, little is known about the immunological status againstbacterial agents affecting these animals. In an effort to explore the serological status of Argentineancamelids, we evaluated the presence of serum antibodies against bacterial pathogens involved inpneumonic diseases (Pasteurella multocida and Mannheimia haemolytica) in llamas from differentregions of the country. By ELISA, a high seroprevalence for both pathogens was found in the serumsamples; higher optical density (OD) values were obtained when the sera were incubated with heatkilledP. multocida as coating antigen compared to M. haemolytica. In addition, a large number ofsera analyzed presented high OD values for both microorganisms independently of their originregion. Serum avidity was also evaluated, by means of an assay based on antibody desorption byurea. No correlation was found between the high ODs obtained for P. multocida and the serumavidity. On the other hand, samples reacting with M. haemolytica had lower OD values but higheravidity index. The antigenic recognition pattern for both microorganisms was determined bywestern blot. Unlike P. multocida, the antigenic recognition pattern of M. haemolytica did not differamong serum samples obtained from animals living in different areas. In summary, we found thatcamelids can synthetize antibodies that recognize M. haemolytica with high avidity for differentantigens of the bacterium, suggesting that Argentinean camelids are in contact with M. haemolyticawhich is probably a causative agent of subclinical infections. Conversely, specific antibodies forP. multocida were also found, but these sera presented low avidity that is probably the result of acolonization process by this bacterium, or else, to be a consequence of cross-reactivity phenomenaFil: Díaz, Ailén Magalí. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni; ArgentinaFil: Ledesma, Martin Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni; ArgentinaFil: Calcagno, M. L.. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Físico Matemática. Cátedra de Matemáticas; ArgentinaFil: Leoni, Juliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni; ArgentinaFil: Manghi, Marcela Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni; ArgentinaFil: Canellada, Andrea Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni; ArgentinaFil: Castro, Marisa Silvia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Estudios de la Inmunidad Humoral Prof. Ricardo A. Margni; Argentin

What Developers Want and Need from Program Analysis: An Empirical Study

Program Analysis has been a rich and fruitful field of research for many decades, and countless high quality program analysis tools have been produced by academia. Though there are some well-known examples of tools that have found their way into routine use by practitioners, a common challenge faced by researchers is knowing how to achieve broad and lasting adoption of their tools. In an effort to understand what makes a program analyzer most attractive to developers, we mounted a multi-method investigation at Microsoft. Through interviews and surveys of developers as well as analysis of defect data, we provide insight and answers to four high level research questions that can help researchers design program analyzers meeting the needs of software developers. First, we explore what barriers hinder the adoption of program analyzers, like poorly expressed warning messages. Second, we shed light on what functionality developers want from analyzers, including the types of code issues that developers care about. Next, we answer what non-functional characteristics an analyzer should have to be widely used, how the analyzer should fit into the development process, and how its results should be reported. Finally, we investigate defects in one of Microsoft's flagship software services, to understand what types of code issues are most important to minimize, potentially through program analysis

The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 Å resolution

AbstractBackground: The allosteric hexameric enzyme glucosamine-6-phosphate deaminase from Escherichia coli catalyses the regulatory step of N-acetylglucosamine catabolism, which consists of the isomerisation and deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonia. The reversibility of the catalysis and its rapid-equilibrium random kinetic mechanism, among other properties, make this enzyme a good model for studying allosteric processes.Results: Here we present the structure of P6322 crystals, obtained in sodium acetate, of GlcN6P deaminase in its ligand-free T state. These crystals are very sensitive to X-ray radiation and have a high (78%) solvent content. The active-site lid (residues 162–185) is highly disordered in the T conformer; this may contribute significantly to the free-energy change of the whole allosteric transition. Comparison of the structure with the crystallographic coordinates of the R conformer (Brookhaven Protein Data Bank entry 1dea) allows us to describe the geometrical changes associated with the allosteric transition as the movement of two rigid entities within each monomer. The active site, located in a deep cleft between these two rigid entities, presents a more open geometry in the T conformer than in the R conformer.Conclusions: The differences in active-site geometry are related to alterations in the substrate-binding properties associated with the allosteric transition. The rigid nature of the two mobile structural units of each monomer seems to be essential in order to explain the observed kinetics of the deaminase hexamer. The triggers for both the homotropic and heterotropic allosteric transitions are discussed and particular residues are assigned to these functions. A structural basis for an entropic term in the allosteric transition is an interesting new feature that emerges from this study

Verifying linearizability on TSO architectures

Linearizability is the standard correctness criterion for fine-grained, non-atomic concurrent algorithms, and a variety of methods for verifying linearizability have been developed. However, most approaches assume a sequentially consistent memory model, which is not always realised in practice. In this paper we define linearizability on a weak memory model: the TSO (Total Store Order) memory model, which is implemented in the x86 multicore architecture. We also show how a simulation-based proof method can be adapted to verify linearizability for algorithms running on TSO architectures. We demonstrate our approach on a typical concurrent algorithm, spinlock, and prove it linearizable using our simulation-based approach. Previous approaches to proving linearizabilty on TSO architectures have required a modification to the algorithm's natural abstract specification. Our proof method is the first, to our knowledge, for proving correctness without the need for such modification

The chitinases expression is related to Simian Immunodeficiency Virus Encephalitis (SIVE) and in HIV encephalitis (HIVE)

OBJECTIVES: Human Immunodeficiency Virus (HIV) infection can induce neurocognitive complications classified as HIV-associated neurocognitive disorder (HAND). The chitinase family is associated with innate immunity cells and many infectious diseases. METHODS: We analyzed microarray datasets obtained from NCBI in order to verify the expression of chitinase family genes in hippocampus of uninfected rhesus macaques versus those with histopathologic evidence of Simian Immunodeficiency Virus Encephalitis (SIVE). Moreover, we have analysed two human microarray datasets to verify the results obtained in macaques hippocampus affected by SIVE. For these studies, we have also used the open source tools Genome-scale Integrated Analysis of gene Networks in Tissues (GIANT) to identify the chitinase genes network. RESULTS: CHIT1, CHI3L1 and CHI3L2 levels were significantly increased in SIVE hippocampus as compared to non-infected control specimens. Furthermore, we found a negative correlation between CHIA vs. Brain Viral Load (BVL). These data was confirmed partially in human brain section of HAD/HIVE subjects. Also, we showed that HIV-1 was able to modulate the expression of CHIT1, CHI3L1, CHI3L2 and CHID1 in human macrophages. CONCLUSIONS: These results suggest that chitinase gene expression is altered in SIVE and in HAD/HIVE brain sections and call for more studies examining whether this is a protective immunological reaction or a destructive tissue response to encephalitis

Admit your weakness: Verifying correctness on TSO architectures

“The final publication is available at http://link.springer.com/chapter/10.1007%2F978-3-319-15317-9_22 ”.Linearizability has become the standard correctness criterion for fine-grained non-atomic concurrent algorithms, however, most approaches assume a sequentially consistent memory model, which is not always realised in practice. In this paper we study the correctness of concurrent algorithms on a weak memory model: the TSO (Total Store Order) memory model, which is commonly implemented by multicore architectures. Here, linearizability is often too strict, and hence, we prove a weaker criterion, quiescent consistency instead. Like linearizability, quiescent consistency is compositional making it an ideal correctness criterion in a component-based context. We demonstrate how to model a typical concurrent algorithm, seqlock, and prove it quiescent consistent using a simulation-based approach. Previous approaches to proving correctness on TSO architectures have been based on linearizabilty which makes it necessary to modify the algorithm’s high-level requirements. Our approach is the first, to our knowledge, for proving correctness without the need for such a modification

Physical exercise in major depression: Reducing the mortality gap while improving clinical outcomes

Major depression shortens life while the effectiveness of frontline treatments remains modest. Exercise has been shown to be effective both in reducing mortality and in treating symptoms of major depression, but it is still underutilized in clinical practice, possibly due to prevalent misperceptions. For instance, a common misperception is that exercise is beneficial for depression mostly because of its positive effects on the body (\u201cfrom the neck down\u201d), whereas its effectiveness in treating core features of depression (\u201cfrom the neck up\u201d) is underappreciated. Other long-held misperceptions are that patients suffering from depression will not engage in exercise even if physicians prescribe it, and that only vigorous exercise is effective. Lastly, a false assumption is that exercise may be more harmful than beneficial in old age, and therefore should only be recommended to younger patients. This narrative review summarizes relevant literature to address the aforementioned misperceptions and to provide practical recommendations for prescribing exercise to individuals with major depression