Concurrency and static analysis

The thesis describes three important contributions developed during my doctoral course, all involving the use and the verification of concurrent Java code: Binary decision diagrams, or BDDs, are data structures for the representation of Boolean functions. These functions are of great importance in many fields. It turns out that BDDs are the state-of-the-art representation for Boolean functions, and indeed all real world applications use a BDD library to represent and manipulate Boolean functions. It can be desirable to perform Boolean operations from different threads at the same time. In order to do this, the BDD library in use must allow threads to access BDD data safely, avoiding race conditions. We developed a Java BDD library, that is fast in both single and multi-threaded applications, that we use in the Julia static program analyzer. We defined a sound static analysis that identifies if and where a Java bytecode program lets data flow from tainted user input (including servlet requests) into critical operations that might give rise to injections. Data flow is a prerequisite to injections, but the user of the analysis must later gage the actual risk of the flow. Namely, analysis approximations might lead to false alarms and proper input validation might make actual flows harmless. Our analysis works by translating Java bytecode into Boolean formulas that express all possible explicit flows of tainted data. The choice of Java bytecode simplifies the semantics and its abstraction (many high-level constructs must not be explicitly considered) and lets us analyze programs whose source code is not available, as is typically the case in industrial contexts that use software developed by third parties, such as banks. The standard approach to prevent data races is to follow a locking discipline while accessing shared data: always hold a given lock when accessing a given shared datum. It is all too easy for a programmer to violate the locking discipline. Therefore, tools are desirable for formally expressing the locking discipline and for verifying adherence to it. The book Java Concurrency in Practice (JCIP) proposed the @GuardedBy annotation to express a locking discipline. The original @GuardedBy annotation was designed for simple intra-class synchronization policy declaration. @GuardedBy fields and methods are supposed to be accessed only when holding the appropriate lock, referenced by another field, in the body of the class (or this). In simple cases, a quick visual inspection of the class code performed by the programmer is sufficient to verify the synchronization policy correctness. However, when we think deeper about the meaning of this annotation, and when we try to check and infer it, some ambiguities rise. Given these ambiguities of the specification for @GuardedBy, different tools interpret it in different ways. Moreover, it does not prevent data races, thus not satisfying its design goals. We provide a formal specification that satisfies its design goals and prevents data races. We have also implemented our specification in the Julia analyzer, that uses abstract interpretation to infer valid @GuardedBy annotations for unannotated programs. It is not the goal of this implementation to detect data races or give a guarantee that they do not exist. Julia determines what locking discipline a program uses, without judging whether the discipline is too strict or too lax for some particular purpose

A higher Angiogenin expression is associated with a non-nuclear Maspin location in laryngeal carcinoma

Objectives. In numerous malignancies, angiogenin (ANG) and Maspin are important proangiogenic and antiangiogenic regulators, respectively. The aim of this study was to identify potential relationships between the biological roles of these two proteins in laryngeal squamous cell carcinoma (LSCC). Methods. Immunohistochemical staining for ANG and Maspin was performed on specimens from 76 consecutive LSCC patients treated with surgery alone, considering the subcellular pattern of Maspin expression. Univariate and multivariate statistical models were used for prognostic purposes. Results. On univariate analysis, a different level of ANG expression was seen for patients stratified by subcellular Maspin expression pattern: the mean ANG expression was higher in cases with a nonnuclear MASPIN expression than in those with a nuclear pattern (P=0.002). Disease-free survival (DFS; in months) differed significantly when patients were stratified by N stage (P=0.01). Patients whose Maspin expression was nonnuclear (i.e., it was cytoplasmic or there was none) had a significantly higher recurrence rate (P<0.001), and shorter DFS (P=0.01) than those with a nuclear Maspin pattern. The mean ANG expression was significantly higher in cases with loco-regional recurrent disease (P=0.007); and patients with an ANG expression 655.0% had a significantly shorter DFS than those with an ANG expression <5.0% (P=0.007). On multivariate analysis, ANG expression 655.0% was a significant, independent, negative prognostic factor in terms of DFS (P=0.041). Conclusion. Our results support the hypothesis that a higher ANG expression is associated with a nonnuclear Maspin expression pattern in patients with LSCC. Further studies are needed to clarify the relationship between the ANG and Maspin pathways, and their potential diagnostic and therapeutic role in LSCC

General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species

<p>Abstract</p> <p>Background</p> <p>Downy mildew is a destructive grapevine disease caused by <it>Plasmopara viticola </it>(Berk. and Curt.) Berl. and de Toni, which can only be controlled by intensive fungicide treatments. Natural sources of resistance from wild grapevine (<it>Vitis</it>) species are used in conventional breeding approaches, but the signals and effectors involved in resistance in this important crop species are not well understood.</p> <p>Results</p> <p>Early transcriptional changes associated with <it>P. viticola </it>infection in susceptible <it>V. vinifera </it>and resistant <it>V. riparia </it>plants were analyzed using the Combimatrix microarray platform. Transcript levels were measured 12 and 24 h post-inoculation, reflecting the time points immediately preceding the onset of resistance in <it>V. riparia</it>, as determined by microscopic analysis. Our data indicate that resistance in <it>V. riparia </it>is induced after infection, and is not based on differences in basal gene expression between the two species. The strong and rapid transcriptional reprogramming involves the induction of pathogenesis-related proteins and enzymes required for the synthesis of phenylpropanoid-derived compounds, many of which are also induced, albeit to a lesser extent, in <it>V. vinifera</it>. More interestingly, resistance in <it>V. riparia </it>also involves the specific modulation of numerous transcripts encoding components of signal transduction cascades, hypersensitive reaction markers and genes involved in jasmonate biosynthesis. The limited transcriptional modulation in <it>V. vinifera </it>represents a weak attempted defense response rather than the activation of compatibility-specific pathways.</p> <p>Conclusions</p> <p>Several candidate resistance genes were identified that could be exploited in future biotechnological approaches to increase disease resistance in susceptible grapevine species. Measurements of jasmonic acid and methyl jasmonate in infected leaves suggest that this hormone may also be involved in <it>V. riparia </it>resistance to <it>P. viticola</it>.</p

Microwave-assisted solvothermal : an efficient and new method to obtain hydrophobic wood surfaces

The objective of this work was to form a hydrophobic surface in a highly porous wood by coating and incorporating TiO2 micro/nano structures through the microwave-assisted solvotermal method, without need any pre- or post-modification of the wood substrate, using low temperatures and short times. The behavior and morphology of the TiO2-treated surfaces was characterized using scanning electron microscopy (SEM), while the elemental composition was determined via energy-dispersive X-ray spectroscopy and X-ray diffraction analysis. The results indicated that the crystallization of the TiO2 anatase phase was efficient and fully coated the wood surface during the solvothermal process. The treated wood contained TiO2 particles agglomerate with an average diameter of 200 nm that also allowed to coat an abundant fraction of tracheids cell walls. When investigated through X-ray spectroscopy-mapping, the element titanium appeared abundantly throughout the wood. After TiO2 growth in wood through the microwave-assisted solvotermal method, a roughness at the micro/ nano scales structures was created on the wood surface, originating an increase in the contact angle up to 137°, which characterizes the appearance of a hydrophobic surface. The TiO2-treated wood demonstrated 85% of water absorption after 400 h of immersion, while untreated wood reached 160%, suggesting that the microwave-assisted solvotermal process promotes a delay in the progression of water absorption. This feature can improve the dimensional stability of wood, contributing to the increase of its durability and applications

Locking Discipline Inference and Checking

Concurrency is a requirement for much modern software, but the implementation of multithreaded algorithms comes at the risk of errors such as data races. Programmers can prevent data races by documenting and obeying a locking discipline, which indicates which locks must be held in order to access which data. This paper introduces a formal semantics for locking specifications that gives a guarantee of race freedom. The paper also provides two implementations of the formal semantics for the Java language: one based on abstract interpretation and one based on type theory. To the best of our knowledge, these are the first tools that can soundly infer and check a locking discipline for Java. Our experiments com-pare the implementations with one another and with annotations written by programmers

An updated portrait of monocyte-macrophages in classical Hodgkin lymphoma

Classical Hodgkin lymphoma (cHL) is a unique neoplastic ecosystem characterized by a heterogeneous immune infiltrate surrounding the rare malignant Hodgkin Reed-Sternberg cells. Though less abundant than T-cells, tumor-infiltrating macrophages play a pivotal role in supporting HRS survival through cell-to-cell and paracrine interactions. Traditional immunohistochemistry based upon the M1-M2 dichotomy yielded controversial results about the composition, functional role and prognostic impact of macrophages in cHL. More recent studies exploiting single-cell technologies and image analyses have highlighted the heterogeneity and the peculiar spatial arrangement of the macrophagic infiltrate, with the most immunosuppressive subpopulations lying in close proximity of HRS cells and the most tumor-hostile subsets kept far away from the neoplastic niches. High-throughput analysis of peripheral blood mononuclear cells in cHL patients have also identified a novel, potentially cytotoxic, subpopulation predicting better response to PD-1 blockade. This review examines the phenotypic profile, spatial localization and clinical impact of tumor-infiltrating macrophages and circulating monocytes in cHL, providing an up-do-date portrait of these innate immune cells with possible translational applications

Modelo dinámico de un reactor de ultrasonido continuo en la degradación de anaranjado de metilo

Se analiza la degradación de soluciones acuosas del colorante azoico anaranjado de metilo en un reactor sonoquímico de flujo continuo. Las determinaciones de los tiempos de residencia en cada una de las cuatro unidades del reactor muestran que los mismos no difieren de los tiempos espaciales, por lo que el reactor puede considerarse un reactor continuo de mezcla completa sin volúmenes muertos ni cor-tocircuitos.Mediante la simulación dinámica se desarrollan modelos de funcionamiento del reactor. Los resultados tanto en el estado transiente como en el estacionario no presentan diferencias estadísticamente significativas con los obtenidos analíticamente.Fil: Kieffer, Luis Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química. Universidad Nacional del Litoral. Instituto de Desarrollo Tecnológico para la Industria Química; ArgentinaFil: de la Sierra, Patricia Monica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química. Universidad Nacional del Litoral. Instituto de Desarrollo Tecnológico para la Industria Química; ArgentinaFil: Luna, Julio Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química. Universidad Nacional del Litoral. Instituto de Desarrollo Tecnológico para la Industria Química; ArgentinaFil: Lovato, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química. Universidad Nacional del Litoral. Instituto de Desarrollo Tecnológico para la Industria Química; ArgentinaFil: Claret, Maria. Provincia de Santa Fe. Fundación Para la Promoción y Des.tec.del Litoral; Argentin

Efeito de plantas de cobertura de inverno sobre cultivo de milho em sistema de plantio direto.

Com o objetivo de avaliar a viabilidade do plantio direto sem herbicidas, foram testadas misturas de centeio, ervilhaca e nabo forrageiro para controle de plantas espontâneas e promoção do rendimento de milho em plantio direto. Mediram-se cobertura do solo e biomassa de plantas de cobertura e espontâneas durante o inverno, rendimento do milho e massa de espontâneas durante o ciclo da cultura de verão. A cobertura do solo durante o período de crescimento das culturas de inverno foi superior a 80%, embora os tratamentos não apresentassem diferenças nas variáveis medidas. As plantas de cobertura proporcionaram boas condições para a cultura comercial, que teve rendimentos entre 6,0 e 6,7 t.ha-1, acima da média da região produtora, sem diferenças entre os tratamentos. Analisando-se valor de grãos colhidos e gastos com sementes das plantas de cobertura, demonstrou-se a viabilidade econômica do plantio direto sem herbicidas para o milho, em sucessão a diferentes coberturas de inverno

Microwave-assisted solvothermal: An efficient and new method to obtain hydrophobic wood surfaces

The objective of this work was to form a hydrophobic surface in a highly porous wood by coating and incorporating TiO2 micro/nano structures through the microwave-assisted solvotermal method, without need any pre- or post-modification of the wood substrate, using low temperatures and short times. The behavior and morphology of the TiO2-treated surfaces was characterized using scanning electron microscopy (SEM), while the elemental composition was determined via energy-dispersive X-ray spectroscopy&nbsp; and X-ray diffraction analysis. The results indicated that the crystallization of the TiO2 anatase phase was efficient and fully coated the wood surface during the solvothermal process. The treated wood contained TiO2 particles with an average diameter of 200 nm that also allowed to coat an abundant fraction of tracheids cell walls. When investigated through X-ray spectroscopy-mapping, the element titanium&nbsp; appeared abundantly throughout the wood. After TiO2 growth in wood through the microwave-assisted solvotermal method, a roughness at the micro/nano scales structures was created on the wood surface, originating an increase in the contact angle up to 137°, which characterizes the appearance of a hydrophobic surface.&nbsp; The TiO2-treated wood demonstrated 85% of water absorption after 400 hours of immersion, while untreated wood reached 160%, suggesting that the microwave-assisted solvotermal process promotes a delay in the progression of water absorption. This feature can improve the dimensional stability of wood, contributing to the increase of its durability and applications