Ilinva: Using Abduction to Generate Loop Invariants

International audienceWe describe a system to prove properties of programs. The key feature of this approach is a method to automatically synthesize in-ductive invariants of the loops contained in the program. The method is generic, i.e., it applies to a large set of programming languages and application domains; and lazy, in the sense that it only generates invariants that allow one to derive the required properties. It relies on an existing system called GPiD for abductive reasoning modulo theories [14], and on the platform for program verification Why3 [16]. Experiments show evidence of the practical relevance of our approach

Invariant Synthesis for Incomplete Verification Engines

We propose a framework for synthesizing inductive invariants for incomplete verification engines, which soundly reduce logical problems in undecidable theories to decidable theories. Our framework is based on the counter-example guided inductive synthesis principle (CEGIS) and allows verification engines to communicate non-provability information to guide invariant synthesis. We show precisely how the verification engine can compute such non-provability information and how to build effective learning algorithms when invariants are expressed as Boolean combinations of a fixed set of predicates. Moreover, we evaluate our framework in two verification settings, one in which verification engines need to handle quantified formulas and one in which verification engines have to reason about heap properties expressed in an expressive but undecidable separation logic. Our experiments show that our invariant synthesis framework based on non-provability information can both effectively synthesize inductive invariants and adequately strengthen contracts across a large suite of programs

Verified lifting of stencil computations

This paper demonstrates a novel combination of program synthesis and verification to lift stencil computations from low-level Fortran code to a high-level summary expressed using a predicate language. The technique is sound and mostly automated, and leverages counter-example guided inductive synthesis (CEGIS) to find provably correct translations. Lifting existing code to a high-performance description language has a number of benefits, including maintainability and performance portability. For example, our experiments show that the lifted summaries can enable domain specific compilers to do a better job of parallelization as compared to an off-the-shelf compiler working on the original code, and can even support fully automatic migration to hardware accelerators such as GPUs. We have implemented verified lifting in a system called STNG and have evaluated it using microbenchmarks, mini-apps, and real-world applications. We demonstrate the benefits of verified lifting by first automatically summarizing Fortran source code into a high-level predicate language, and subsequently translating the lifted summaries into Halide, with the translated code achieving median performance speedups of 4.1X and up to 24X for non-trivial stencils as compared to the original implementation.United States. Department of Energy. Office of Science (Award DE-SC0008923)United States. Department of Energy. Office of Science (Award DE-SC0005288

Evaluation of Biological Properties of New Selective Differential Medium for Cholera Vibrios Isolation Based on the Results of Laboratоry Trials

Previously developed selective differential medium for V. cholerae growth was modernized. The modernized medium called SDMV-M was shown to possess the required sensitivity and germination index. The growth of E. coli was entirely inhibited, that of P. vulgaris was inhibited considerably. The medium possessed good differentiating ability: orange V. cholerae colonies were clearly distinguished from concomitant microorganisms. In the laboratory trials SDMV-M demonstrated some advantages as regards V. cholerae isolation from contaminated faeces in comparison with the reference medium TCBS

«Кинурениновый переключатель» и ожирение

Aim. To assess the concentrations of bacterial and eukaryotic metabolites mainly involved in indole, kynurenine, and serotonin pathways of tryptophan metabolism in a cohort of patients with obesity. Materials and methods. Using high-performance liquid chromatography with mass spectrometric detection, the concentrations of several serum metabolites, such as kynurenine, kynurenic acid, anthranilic acid, xanthurenic acid, quinolinic acid, 5-hydroxyindole-3-acetate, tryptamine, serotonin, indole-3-lactate, indole-3-acetate, indole-3- butyrate, indole-3-carboxaldehyde, indole-3-acrylate, and indole-3-propionate, were analyzed in a cohort of obese patients compared with healthy volunteers.Results. It was found that serum levels of tryptophan metabolites of microbial and eukaryotic origin were significantly increased in obese patients. Therefore, the concentration of kynurenine in the blood serum in obese patients was 2,413 ± 855 nmol / l, while in healthy volunteers of the same age group, the level of kynurenine in the blood serum was 2,122 ± 863 nmol / l. In obese patients, two acids formed due to kynurenine metabolism; the concentrations of kynurenic and quinolinic acids were increased in the blood serum. The concentration of kynurenic acid in the blood serum in obese patients was 21.1 ± 9.26 nmol / l, and in healthy patients, it was 16.8 ± 8.37 nmol / l. At the same time, the level of quinolinic acid in the blood serum in obese patients was 73.1 ± 54.4 nmol / l and in healthy volunteers – 56.8 ± 34.1 nmol / l. Normally, the level of quinolinic acid is 3.4 times higher than the concentration of kynurenic acid, and in case of obesity, there is a comparable increase in these acids in the blood serum.From indole derivatives, mainly of microbial origin, the concentrations of indole-3-lactate, indole-3-butyrate, and indole-3-acetate were significantly increased in the blood serum of obese patients. In obese patients, the serum concentration of 5-hydroxyindole-3-acetate was elevated to 74.6 ± 75.8 nmol / l (in healthy volunteers – 59.4 ± 36.6 nmol / l); indole-3-lactate – to 523 ± 251 nmol / l (in healthy volunteers – 433 ± 208 nmol / l); indole-3-acetate – to 1,633 ± 1,166 nmol / l (in healthy volunteers – 1,186 ± 826 nmol / l); and indole-3-butyrate – to 4.61 ± 3.31 nmol / l (in healthy volunteers – 3.85 ± 2.51 nmol / l).Conclusion. In case of obesity, the utilization of tryptophan was intensified by both the microbiota population and the macroorganism. It was found that obese patients had higher concentrations of kynurenine, quinolinic and kynurenic acids, indole-3-acetate, indole-3-lactate, indole-3-butyrate, and 5-hydroxyindole-3-acetate. Apparently, against the background of increased production of proinflammatory cytokines by adipocytes in obese patients, the “kynurenine switch” was activated which contributed to subsequent overproduction of tryptophan metabolites involved in the immune function of the macroorganism. Цель. Изучить содержание метаболитов бактериального и эукариотического происхождения индольного, кинуренинового и серотонинового путей обмена триптофана у пациентов с ожирением.Материалы и методы. Методом высокоэффективной жидкостной хроматографии с масс-спектрометрическим детектированием изучили концентрации сывороточных метаболитов: кинуренина, кинуреновой кислоты, антраниловой кислоты, ксантуреновой кислоты, хинолиновой кислоты, 5-гидросииндол-3-ацетата, триптамина, серотонина, индол-3-лактата, индол-3-ацетата, индол-3-бутирата, индол-3-карбоксальдегида, индол-3-акрилата, индол-3-пропионата у пациентов с ожирением в сравнении с группой здоровых добровольцев.Результаты. Установлено, что у пациентов с ожирением в сыворотке крови статистически значимо повышен уровень метаболитов триптофанового обмена микробиотического и эукариотического происхождения. Концентрация кинуренина в сыворотке крови у больных с ожирением составляла 2 413 ± 855 нмоль/л, тогда как у здоровых добровольцев такой же возрастной группы – 2 122 ± 863 нмоль/л. Также у пациентов с ожирением в сыворотке крови были повышены две кислоты, которые образуются в результате метаболизма кинуренина – кинуреновая и хинолиновая. Концентрация кинуреновой кислоты в сыворотке крови у пациентов с ожирением составляла 21,1 ± 9,26 нмоль/л, а у здоровых 16,8 ± 8,37 нмоль/л соответственно. Тогда как концентрация хинолиновой кислоты в сыворотке крови при ожирении – 73,1 ± 54,4 нмоль/л, а у здоровых добровольцев – 56,8 ± 34,1 нмоль/л. В норме концентрация хинолиновой кислоты в 3,4 раза выше, чем концентрация кинуреновой кислоты, а при ожирении происходит сопоставимое их повышение. Из производных индола, которые имеют преимущественно микробиотическое происхождение, в сыворотке крови пациентов с ожирением статистически значимо повышена концентрация индол-3-лактата, индол-3-бутирата и индол-3-ацетата. У пациентов с ожирением концентрация в сыворотке крови метаболита серотонина – 5-гидроксииндол-3-ацетата – была повышена и составляла 74,6 ± 75,8 нмоль/л (у здоровых добровольцев – 59,4 ± 36,6 нмоль/л); индол-3-лактата – 523 ± 251 нмоль/л (у здоровых добровольцев 433 ± 208 нмоль/л); индол-3-ацетата – 1 633 ± 1166 нмоль/л (у здоровых добровольцев 1 186 ± 826 нмоль/л); индол-3-бутирата – 4,61 ± 3,31 нмоль/л (у здоровых добровольцев 3,85 ± 2,51 нмоль/л).Заключение. При ожирении происходит интенсификация утилизации триптофана как микробиотической популяцией кишечника, так и макроорганизмом. Установлено, что больные с ожирением имеют более высокие концентрации кинуренина, хинолиновой и кинуреновой кислот, индол-3-ацетата, индол-3-лактата, индол-3-бутирата и 5-гидроксииндол-3-ацетата. Видимо, на фоне гиперпродукции провоспалительных цитокинов адипоцитами у пациентов с ожирением срабатывает «кинурениновый переключатель», что и обеспечивает гиперпродукцию метаболитов триптофанового обмена, которые вовлечены в иммунологическую функцию макроорганизма.

Молекулярный портрет рака желудка, ассоциированного с вирусом Эпштейна–Барр

Epstein–Barr virus (EBV) associated gastric carcinoma is a special form of gastric adenocarcinoma that arises against the background of clonal growth of EBV-infected epithelial cells of the gastric mucosa. This subtype of tumors has unique genetic and epigenetic features that determine its characteristic phenotype. Determination of the molecular features of EBV-associated gastric cancer made it possible to identify potential targets for drug therapy of this subtype of tumors. The review presents modern data on the epidemiology and pathogenesis of EBVassociated gastric cancer, describes its unique pathomorphological and molecular features. Particular attention is paid to the prognostic role of EBV infection and drug therapy potentially applicable to the treatment of EBV-positive gastric cancer.Рак желудка, ассоциированный с вирусом Эпштейна–Барр (ВЭБ), – особая форма онкологического заболевания, возникающая в результате клональной пролиферации ВЭБ-инфицированных эпителиоцитов слизистой оболочки желудка. Данный подтип опухолей имеет уникальные генетические и эпигенетические особенности, определяющие его характерный фенотип. Выявление широкого спектра молекулярных особенностей ВЭБ-ассоциированного рака желудка позволяет описать потенциальные мишени, перспективные для лекарственной терапии данного подтипа опухолей. В обзоре представлены современные данные об эпидемиологии и патогенезе ВЭБ-ассоциированного рака желудка, описаны его уникальные патоморфологические и молекулярные особенности. Особое внимание уделено прогностической роли ВЭБ-инфекции и лекарственной терапии, потенциально применимой для лечения ВЭБ-положительного рака желудка

How to Win First-Order Safety Games

First-order (FO) transition systems have recently attracted attention for the verification of parametric systems such as network protocols, software-defined networks or multi-agent workflows like conference management systems. Functional correctness or noninterference of these systems have conveniently been formulated as safety or hypersafety properties, respectively. In this article, we take the step from verification to synthesis---tackling the question whether it is possible to automatically synthesize predicates to enforce safety or hypersafety properties like noninterference. For that, we generalize FO transition systems to FO safety games. For FO games with monadic predicates only, we provide a complete classification into decidable and undecidable cases. For games with non-monadic predicates, we concentrate on universal first-order invariants, since these are sufficient to express a large class of properties---for example noninterference. We identify a non-trivial sub-class where invariants can be proven inductive and FO winning strategies be effectively constructed. We also show how the extraction of weakest FO winning strategies can be reduced to SO quantifier elimination itself. We demonstrate the usefulness of our approach by automatically synthesizing nontrivial FO specifications of messages in a leader election protocol as well as for paper assignment in a conference management system to exclude unappreciated disclosure of reports

P68

Transmembrane prostate androgen-induced protein 1 (TMEPAI) is a membrane protein that has attracted significant attention of many researchers its involvement in TGF-β signaling pathway which involved in malignant transformation and metastatic tumor progression. We investigated the TMEPAI expression level in gastric adenocarcinomas in comparison to non-tumor mucosa samples and determined its potential prognostic significance. Materials and methods: Fresh and paraffin-embedded gastric adenocarcinoma samples and paired adjacent normal tissues were collected from gastric cancer patients. Evaluation of the PMEPA 1 gene expression was carried out using RT-PCR. For evaluation of TMEPAI protein expression, monoclonal antibodies (mAbs) were developed by using hybridoma techniques. Specificity of prepared monoclonal antibodies against recombinant TMEPAI and evaluation of its expression in the clinical samples using selected mAbs were performed using immunoblotting and immunohistochemistry. Results: We have identified more than two-fold increase in gene expression of PMEPA1 in tumor tissue in 44% of patients. The monoclonal antibodies have shown the capacity to specifically recognize the recombinant TMEPAI in HEK293T cell lysates. We also evaluate the ability of the selected antibodies to recognize the target protein in fixed cells by immunocytochemistry. The evaluation of TMEPAI in adenocarcinoma samples collected from gastric cancer patients revealed decreased protein expression. We have observed pronounced expression of TMEPAI in normal gastric epithelial cells, while tumor cells from gastric adenomas and adenocarcinomas samples were mostly negative for target protein expression. We found that gastric epithelium cells lose the TMEPAI expression concurrent with severe dysplasia. Conclusion: Apparently, the TMEPAI may be a potential biomarker of malignant transformation risk of the stomach epithelium. The presented study was financially supported by Grants from the Russian Fund for Basic Research (14-04-31500) and Tomsk State University Competitiveness Improvement Program

Development of novel monoclonal antibodies for evaluation of transmembrane prostate androgen-induced protein 1 (TMEPAI) expression patterns in gastric cancer.

Transmembrane prostate androgen-induced protein 1 (TMEPAI) is a single-span membrane protein, functionally involved in transforming growth factor beta signaling pathway. The particular protein presented in cells in three isoforms, which differs in the length of the soluble N-terminal extracellular domain, making it challenging for the immunochemical recognition. By using quantitative real-time polymerase chain reaction, we identified significant upregulation of PMEPA1 gene expression in malignant tissues of patients with gastric adenocarcinoma. The main part of commercially available anti-TMEPAI antibodies are having polyclonal nature or not suitable for immunocytochemical localization of target protein in tissue specimens. Hence, we decide to generate a set of novel rat monoclonal antibodies (mAb) directed against conservative C-terminal cytoplasmic epitope. Immunoblotting analysis showed that monoclonal antibodies, 2E1, 6C6, and 10A7 were able to recognize specifically target protein in transiently transfected HEK293T and CHO-K1 cells. Especially established mAb, named 10A7, showed the excellent binding ability to target protein in immunohistochemistry. By using developed antibodies, we observed pronounced expression of TMEPAI in normal gastric epithelial cells while tumor cells from gastric adenomas, and adenocarcinoma samples were mostly negative for target protein expression. Also, we found that gastric epithelium cells lose the TMEPAI expression concurrently with severe dysplasia progression, which probably caused by a mechanism involving specific microRNA