HeteroGenius: A Framework for Hybrid Analysis of Heterogeneous Software Specifications

Nowadays, software artifacts are ubiquitous in our lives being an essential part of home appliances, cars, cell phones, and even in more critical activities like aeronautics and health sciences. In this context software failures may produce enormous losses, either economical or, in the worst case, in human lives. Software analysis is an area in software engineering concerned with the application of diverse techniques in order to prove the absence of errors in software pieces. In many cases different analysis techniques are applied by following specific methodological combinations that ensure better results. These interactions between tools are usually carried out at the user level and it is not supported by the tools. In this work we present HeteroGenius, a framework conceived to develop tools that allow users to perform hybrid analysis of heterogeneous software specifications. HeteroGenius was designed prioritising the possibility of adding new specification languages and analysis tools and enabling a synergic relation of the techniques under a graphical interface satisfying several well-known usability enhancement criteria. As a case-study we implemented the functionality of Dynamite on top of HeteroGenius.Comment: In Proceedings LAFM 2013, arXiv:1401.056

On the construction of explosive relation algebras

Fork algebras are an extension of relation algebras obtained by extending the set of logical symbols with a binary operator called fork. This class of algebras was introduced by Haeberer and Veloso in the early 90's aiming at enriching relation algebra, an already successful language for program specification, with the capability of expressing some form of parallel computation. The further study of this class of algebras led to many meaningful results linked to interesting properties of relation algebras such as representability and finite axiomatizability, among others. Also in the 90's, Veloso introduced a subclass of relation algebras that are expansible to fork algebras, admitting a large number of non-isomorphic expansions, referred to as explosive relation algebras. In this work we discuss some general techniques for constructing algebras of this type

Time-Course Analysis of Brain Regional Expression Network Responses to Chronic Intermittent Ethanol and Withdrawal: Implications for Mechanisms Underlying Excessive Ethanol Consumption

Long lasting abusive consumption, dependence, and withdrawal are characteristic features of alcohol use disorders (AUD). Mechanistically, persistent changes in gene expression are hypothesized to contribute to brain adaptations leading to ethanol toxicity and AUD. We employed repeated chronic intermittent ethanol (CIE) exposure by vapor chamber as a mouse model to simulate the cycles of ethanol exposure and withdrawal commonly seen with AUD. This model has been shown to induce progressive ethanol consumption in rodents. Brain CIE-responsive expression networks were identified by microarray analysis across five regions of the mesolimbic dopamine system and extended amygdala with tissue harvested from 0-hours to 7-days following CIE. Weighted Gene Correlated Network Analysis (WGCNA) was used to identify gene networks over-represented for CIE-induced temporal expression changes across brain regions. Differential gene expression analysis showed that long-lasting gene regulation occurred 7-days after the final cycle of ethanol exposure only in prefrontal cortex (PFC) and hippocampus. Across all brain regions, however, ethanol-responsive expression changes occurred mainly within the first 8-hours after removal from ethanol. Bioinformatics analysis showed that neuroinflammatory responses were seen across multiple brain regions at early time-points, whereas co-expression modules related to neuroplasticity, chromatin remodeling, and neurodevelopment were seen at later time-points and in specific brain regions (PFC or HPC). In PFC a module containing Bdnf was identified as highly CIE responsive in a biphasic manner, with peak changes at 0 hours and 5 days following CIE, suggesting a possible role in mechanisms underlying long-term molecular and behavioral response to CIE. Bioinformatics analysis of this network and several other modules identified Let-7 family microRNAs as potential regulators of gene expression changes induced by CIE. Our results suggest a complex temporal and regional pattern of widespread gene network responses involving neuroinflammatory and neuroplasticity related genes as contributing to physiological and behavioral responses to chronic ethanol

Distributed acoustic sensing for seismic activity monitoring

Continuous, real-time monitoring of surface seismic activity around the globe is of great interest for acquiring new insight into global tomography analyses and for recognition of seismic patterns leading to potentially hazardous situations. The already-existing telecommunication fiber optic network arises as an ideal solution for this application, owing to its ubiquity and the capacity of optical fibers to perform distributed, highly sensitive monitoring of vibrations at relatively low cost (ultra-high density of point sensors available with minimal deployment of new equipment). This perspective article discusses early approaches on the application of fiber-optic distributed acoustic sensors (DASs) for seismic activity monitoring. The benefits and potential impact of DAS technology in these kinds of applications are here illustrated with new experimental results on teleseism monitoring based on a specific approach: the so-called chirped-pulse DAS. This technology offers promising prospects for the field of seismic tomography due to its appealing properties in terms of simplicity, consistent sensitivity across sensing channels, and robustness. Furthermore, we also report on several signal processing techniques readily applicable to chirped-pulse DAS recordings for extracting relevant seismic information from ambient acoustic noise. The outcome presented here may serve as a foundation for a novel conception for ubiquitous seismic monitoring with minimal investment

A mathematical model for optimizing the indications of liver transplantation in patients with hepatocellular carcinoma

Abstract Background The criteria for organ sharing has developed a system that prioritizes liver transplantation (LT) for patients with hepatocellular carcinoma (HCC) who have the highest risk of wait-list mortality. In some countries this model allows patients only within the Milan Criteria (MC, defined by the presence of a single nodule up to 5 cm, up to three nodules none larger than 3 cm, with no evidence of extrahepatic spread or macrovascular invasion) to be evaluated for liver transplantation. This police implies that some patients with HCC slightly more advanced than those allowed by the current strict selection criteria will be excluded, even though LT for these patients might be associated with acceptable long-term outcomes. Methods We propose a mathematical approach to study the consequences of relaxing the MC for patients with HCC that do not comply with the current rules for inclusion in the transplantation candidate list. We consider overall 5-years survival rates compatible with the ones reported in the literature. We calculate the best strategy that would minimize the total mortality of the affected population, that is, the total number of people in both groups of HCC patients that die after 5 years of the implementation of the strategy, either by post-transplantation death or by death due to the basic HCC. We illustrate the above analysis with a simulation of a theoretical population of 1,500 HCC patients with tumor size exponentially. The parameter λ obtained from the literature was equal to 0.3. As the total number of patients in these real samples was 327 patients, this implied in an average size of 3.3 cm and a 95% confidence interval of [2.9; 3.7]. The total number of available livers to be grafted was assumed to be 500. Results With 1500 patients in the waiting list and 500 grafts available we simulated the total number of deaths in both transplanted and non-transplanted HCC patients after 5 years as a function of the tumor size of transplanted patients. The total number of deaths drops down monotonically with tumor size, reaching a minimum at size equals to 7 cm, increasing from thereafter. With tumor size equals to 10 cm the total mortality is equal to the 5 cm threshold of the Milan criteria. Conclusion We concluded that it is possible to include patients with tumor size up to 10 cm without increasing the total mortality of this population

Ibudilast reduces alcohol drinking in multiple animal models of alcohol dependence

Neuroinflammatory signaling pathways in the central nervous system are of current interest as potential pharmacotherapy targets for alcohol dependence. In this study, we examined the ability of ibudilast, a non-selective phosphodiesterase inhibitor, to reduce alcohol drinking and relapse in alcohol-preferring P rats, high-alcohol drinking HAD1 rats, and in mice made dependent on alcohol through cycles of alcohol vapor exposure. When administered twice daily, ibudilast reduced alcohol drinking in rats by approximately 50% and reduced drinking by alcohol-dependent mice at doses which had no effect in non-dependent mice. These findings support the viability of ibudilast as a possible treatment for alcohol dependence

Distributed acoustic sensing for seismic activity monitoring

Continuous, real-time monitoring of surface seismic activity around the globe is of great interest for acquiring new insight into global tomography analyses and for recognition of seismic patterns leading to potentially hazardous situations. The already-existing telecommunication fiber optic network arises as an ideal solution for this application, owing to its ubiquity and the capacity of optical fibers to perform distributed, highly sensitive monitoring of vibrations at relatively low cost (ultra-high density of point sensors available with minimal deployment of new equipment). This perspective article discusses early approaches on the application of fiber-optic distributed acoustic sensors (DASs) for seismic activity monitoring. The benefits and potential impact of DAS technology in these kinds of applications are here illustrated with new experimental results on teleseism monitoring based on a specific approach: the so-called chirped-pulse DAS. This technology offers promising prospects for the field of seismic tomography due to its appealing properties in terms of simplicity, consistent sensitivity across sensing channels, and robustness. Furthermore, we also report on several signal processing techniques readily applicable to chirped-pulse DAS recordings for extracting relevant seismic information from ambient acoustic noise. The outcome presented here may serve as a foundation for a novel conception for ubiquitous seismic monitoring with minimal investment

Natural genetic diversity of nutritive value traits in the genus Cynodon

The Cynodon spp. collection maintained by United States Department of Agriculture National Plant Germplasm System (USDA-NPGS) has limited information on nutritive value (NV) traits. In this study, crude protein (CP), phosphorous concentration (P), in vitro digestible organic matter (IVDOM), and neutral detergent fiber (NDF) were determined to (i) estimate genetic parameters for NV, (ii) obtain genetic values for the whole population across two harvests, (iii) estimate genotype by harvest interaction (GHI) for NV traits, and (iv) select accessions exhibiting improved NV traits compared to ‘Tifton 850 . The experiment was setup as a row-column design with two replicates and augmented representation of controls: Tifton 85, ‘Jiggs’, and ‘Coastal’. The whole-population was harvested twice, and data were analyzed using linear mixed models with repeated measures. In addition, a selected population of 15 genotypes were evaluated across 11 harvests to determine the extent of GHI. Genetic parameters revealed the presence of significant genetic variability, indicating potential improvements for NV through breeding. Specifically, P and IVDOM presented large variation, while NDF had lower diversity but some accessions exhibited lower NDF than Tifton 85. Low GHI, except for IVDOM, indicated genotypic stability and potential for selecting improved accessions under fewer harvests. Breeding line 240, PI-316510, and PI-3166536 presented superior NV than Tifton 85

Age and regional differences in clinical presentation and risk of hospitalization for dengue in Brazil, 2000-2014

OBJECTIVES: Dengue cases range from asymptomatic to severe, eventually leading to hospitalization and death. Timely and appropriate management is critical to reduce morbidity. Since 1980, dengue has spread throughout Brazil, affecting an increasing number of individuals. This paper describes age and regional differences in dengue’s clinical presentation and associated risk of hospitalization based on more than 5 million cases reported to the Brazilian Ministry of Health from 2000-2014. METHODS: We performed a retrospective analysis of ∼5,450,000 dengue cases, relating clinical manifestations and the risk of hospitalization to age, gender, previous infection by dengue, dengue virus serotype, years of formal education, delay to first attendance and the occurrence of dengue during outbreaks and in different Brazilian regions. RESULTS: Complicated forms of dengue occurred more frequently among those younger than 10 years (3.12% vs 1.92%) and those with dengue virus 2 infection (7.65% vs 2.42%), with a delay to first attendance >;2 days (3.18% vs 0.82%) and with ≤4 years of formal education (2.02% vs 1.46%). The risk of hospitalization was higher among those aged 6-10 years old (OR 4.57; 95% CI 1.43-29.96) and those who were infected by dengue virus 2 (OR 6.36; 95% CI 2.52-16.06), who lived in the Northeast region (OR 1.38; 95% CI 1.11-2.10) and who delayed first attendance by >;5 days (composite OR 3.15; 95% CI 1.33-8.9). CONCLUSIONS: In Brazil, the occurrence of severe dengue and related hospitalization is associated with being younger than 10 years old, being infected by dengue virus 2 or 3, living in the Northeast region (the poorest and the second most populated) and delaying first attendance for more than 2 days