A program analysis framework for tccp based on abstract interpretation

[EN] The timed concurrent constraint language (tccp) is a timed extension of the concurrent constraint paradigm. tccp was defined to model reactive systems, where infinite behaviors arise naturally. In previous works, a semantic framework and abstract diagnosis method for the language have been defined. On the basis of that semantic framework, this paper proposes an abstract semantics that, together with a widening operator, is suitable for the definition of different analyses for tccp programs. The abstract semantics is correct and can be represented as a finite graph where each node represents a hypothetical (abstract) computational step of the program. The widening operator allows us to guarantee the convergence of the abstract fixpoint computation.This author has been supported by the Andalusian Excellence Project P11-TIC-7659. This work has been partially supported by the EU (FEDER) and the Spanish MINECO under grants TIN 2015-69175-C4-1-R and TIN 2013-45732-C4-1-P and by Generalitat Valenciana PROMETEOII/2015/013Comini, M.; Gallardo, M.; Titolo, L.; Villanueva, A. (2017). A program analysis framework for tccp based on abstract interpretation. Formal Aspects of Computing. 29(3):531-557. https://doi.org/10.1007/s00165-016-0409-8S531557293Alpuente M, Gallardo MM, Pimentel E, Villanueva A (2006) A semantic framework for the abstract model checking of tccp programs. Theor Comput Scie 346(1): 58–95Bagnara R, Hill PM., Ricci E, Zaffanella E (2005) Precise widening operators for convex polyhedra. Sci Comput Program 58(1–2):28–56Cousot P, Cousot R (1977) Abstract interpretation: a unified lattice model for static analysis of programs by construction or approximation of fixpoints. In: Proceedings of the 4th ACM SIGACT-SIGPLAN symposium on principles of programming languages, Los Angeles, California, January 17–19. ACM Press, New York, pp 238–252Clarke EM, Grumberg O, Jha S, Lu Y, Veith H (2000) Counterexample-guided abstraction refinement. In: CAV, Lecture Notes in Computer Science, vol 1855. Springer, pp 154–169Comini M, Gallardo MM, Titolo L, Villanueva A (2015) Abstract Analysis of Universal Properties for tccp. In: Falaschi M (ed) Logic-based Program Synthesis and Transformation, 25th International Symposium, LOPSTR 2015. Revised Selected Papers, Lecture Notes in Computer Science, vol 9527. Springer, pp 163–178Comini M, Titolo L, Villanueva A (2011) Abstract diagnosis for timed concurrent constraint programs. Theory Pract Logic Programm 11(4-5):487–502Comini M, Titolo L, Villanueva A (2013) A condensed goal-independent bottom-up fixpoint modeling the behavior of tccp. Technical report, DSIC, Universitat Politècnica de València. http://riunet.upv.es/handle/10251/34328de Boer FS, Gabbrielli M, Meo MC (2000) A timed concurrent constraint language. Inf Comput 161(1): 45–83Falaschi M, Gabbrielli M, Marriott K, Palamidessi C (1993) Compositional analysis for concurrent constraint programming. In: Proceedings of the eighth annual IEEE symposium on logic in computer science, Los Alamitos, CA, USA, IEEE Computer Society Press, pp 210–221Falaschi M, Olarte C, Palamidessi C (2015) Abstract interpretation of temporal concurrent constraint programs. Theory and Pract Logic Program (TPLP) 15(3): 312–357Falaschi M, Villanueva A (2006) Automatic verification of timed concurrent constraint programs. Theory Pract Logic Program 6(3): 265–300Gallardo MM, Merino P, Pimentel E (2002) Refinement of LTL formulas for abstract model checking. In: Static analysis, 9th international symposium, SAS 2002, Madrid, Spain, September 17–20, 2002, Proceedings, pp 395–410Saraswat VA (1993) Concurrent constraint programming. The MIT Press, CambridgeSaraswat VA, Rinard M, Panangaden P (1991) The semantic foundations of concurrent constraint programming. In: Proceedings of the 18th ACM SIGPLAN-SIGACT symposium on principles of programming languages. ACM, New York, pp 333–352Zaffanella E, Giacobazzi R, Levi G (1997) Abstracting synchronization in concurrent constraint programming. J Funct Logic Program (6

Sublittoral soft bottom communities and diversity of Mejillones Bay in northern Chile (Humboldt Current upwelling system)

The macrozoobenthos of Mejillones Bay (23°S; Humboldt Current) was quantitatively investigated over a 7-year period from austral summer 1995/1996 to winter 2002. About 78 van Veen grab samples taken at six stations (5, 10, 20 m depth) provided the basis for the analysis of the distribution of 60 species and 28 families of benthic invertebrates, as well as of their abundance and biomass. Mean abundance (2,119 individuals m-2) was in the same order compared to a previous investigation; mean biomass (966 g formalin wet mass m-2), however, exceeded prior estimations mainly due to the dominance of the bivalve Aulacomya ater. About 43% of the taxa inhabited the complete depth range. Mean taxonomic Shannon diversity (H', Log e) was 1.54 ± 0.58 with a maximum at 20 m (1.95 ± 0.33); evenness increased with depth. The fauna was numerically dominated by carnivorous gastropods, polychaetes and crustaceans (48%). About 15% of the species were suspensivorous, 13% sedimentivorous, 11% detritivorous, 7% omnivorous and 6% herbivorous. Cluster analyses showed a significant difference between the shallow and the deeper stations. Gammarid amphipods and the polychaete family Nephtyidae characterized the 5-mzone, the molluscs Aulacomya ater, Mitrella unifasciata and gammarids the intermediate zone, while the gastropod Nassarius gayi and the polychaete family Nereidae were most prominent at the deeper stations. The communities of the three depth zones did not appear to be limited by hypoxia during non-El Niño conditions. Therefore, no typical change in community structure occurred during El Niño 1997–1998, in contrast to what was observed for deeper faunal assemblages and hypoxic bays elsewhere in the coastal Humboldt Current system

Subtidal macrozoobenthos communities from northern Chile during and post El Niño 1997–1998

Despite a large amount of climatic and oceanographic information dealing with the recurring climate phenomenon El Niño (EN) and its well known impact on diversity of marine benthic communities, most published data are rather descriptive and consequently our understanding of the underlying mechanisms and processes that drive community structure during EN are still very scarce. In this study, we address two questions on the effects of EN on macrozoobenthic communities: (1) how does EN affect species diversity of the communities in northern Chile? and (2) is EN a phenomenon that restarts community assembling processes by affecting species interactions in northern Chile? To answer these questions, we compared species diversity and co-occurrence patterns of soft-bottoms macrozoobenthos communities from the continental shelf off northern Chile during (March 1998) and after (September 1998) the strong EN event 1997–1998. The methods used varied from species diversity and species co-occurrence analyses to multivariate ordination methods. Our results indicate that EN positively affects diversity of macrozoobenthos communities in the study area, increasing the species richness and diversity and decreasing the species dominance. EN represents a strong disturbance that affects species interactions that rule the species assembling processes in shallow-water, sea-bottom environments

The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins—including gene expression, chromatin occupancy and three-dimensional conformation—we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Oxygen: A Fundamental Property Regulating Pelagic Ecosystem Structure in the Coastal Southeastern Tropical Pacific

Background: In the southeastern tropical Pacific anchovy (Engraulis ringens) and sardine (Sardinops sagax) abundance have recently fluctuated on multidecadal scales and food and temperature have been proposed as the key parameters explaining these changes. However, ecological and paleoecological studies, and the fact that anchovies and sardines are favored differently in other regions, raise questions about the role of temperature. Here we investigate the role of oxygen in structuring fish populations in the Peruvian upwelling ecosystem that has evolved over anoxic conditions and is one of the world's most productive ecosystems in terms of forage fish. This study is particularly relevant given that the distribution of oxygen in the ocean is changing with uncertain consequences. Methodology/Principal Findings: A comprehensive data set is used to show how oxygen concentration and oxycline depth affect the abundance and distribution of pelagic fish. We show that the effects of oxygen on anchovy and sardine are opposite. Anchovy flourishes under relatively low oxygen conditions while sardine avoid periods/areas with low oxygen concentration and restricted habitat. Oxygen consumption, trophic structure and habitat compression play a fundamental role in fish dynamics in this important ecosystem. Conclusions/Significance: For the ocean off Peru we suggest that a key process, the need to breathe, has been neglected previously. Inclusion of this missing piece allows the development of a comprehensive conceptual model of pelagic fish populations and change in an ocean ecosystem impacted by low oxygen. Should current trends in oxygen in the ocean continue similar effects may be evident in other coastal upwelling ecosystems

Adverse Events Post Smallpox-Vaccination: Insights from Tail Scarification Infection in Mice with Vaccinia virus

Adverse events upon smallpox vaccination with fully-replicative strains of Vaccinia virus (VACV) comprise an array of clinical manifestations that occur primarily in immunocompromised patients leading to significant host morbidity/mortality. The expansion of immune-suppressed populations and the possible release of Variola virus as a bioterrorist act have given rise to concerns over vaccination complications should more widespread vaccination be reinitiated. Our goal was to evaluate the components of the host immune system that are sufficient to prevent morbidity/mortality in a murine model of tail scarification, which mimics immunological and clinical features of smallpox vaccination in humans. Infection of C57BL/6 wild-type mice led to a strictly localized infection, with complete viral clearance by day 28 p.i. On the other hand, infection of T and B-cell deficient mice (Rag1−/−) produced a severe disease, with uncontrolled viral replication at the inoculation site and dissemination to internal organs. Infection of B-cell deficient animals (µMT) produced no mortality. However, viral clearance in µMT animals was delayed compared to WT animals, with detectable viral titers in tail and internal organs late in infection. Treatment of Rag1−/− with rabbit hyperimmune anti-vaccinia serum had a subtle effect on the morbidity/mortality of this strain, but it was effective in reduce viral titers in ovaries. Finally, NUDE athymic mice showed a similar outcome of infection as Rag1−/−, and passive transfer of WT T cells to Rag1−/− animals proved fully effective in preventing morbidity/mortality. These results strongly suggest that both T and B cells are important in the immune response to primary VACV infection in mice, and that T-cells are required to control the infection at the inoculation site and providing help for B-cells to produce antibodies, which help to prevent viral dissemination. These insights might prove helpful to better identify individuals with higher risk of complications after infection with poxvirus

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

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