Answer Sets for Logic Programs with Arbitrary Abstract Constraint Atoms

In this paper, we present two alternative approaches to defining answer sets for logic programs with arbitrary types of abstract constraint atoms (c-atoms). These approaches generalize the fixpoint-based and the level mapping based answer set semantics of normal logic programs to the case of logic programs with arbitrary types of c-atoms. The results are four different answer set definitions which are equivalent when applied to normal logic programs. The standard fixpoint-based semantics of logic programs is generalized in two directions, called answer set by reduct and answer set by complement. These definitions, which differ from each other in the treatment of negation-as-failure (naf) atoms, make use of an immediate consequence operator to perform answer set checking, whose definition relies on the notion of conditional satisfaction of c-atoms w.r.t. a pair of interpretations. The other two definitions, called strongly and weakly well-supported models, are generalizations of the notion of well-supported models of normal logic programs to the case of programs with c-atoms. As for the case of fixpoint-based semantics, the difference between these two definitions is rooted in the treatment of naf atoms. We prove that answer sets by reduct (resp. by complement) are equivalent to weakly (resp. strongly) well-supported models of a program, thus generalizing the theorem on the correspondence between stable models and well-supported models of a normal logic program to the class of programs with c-atoms. We show that the newly defined semantics coincide with previously introduced semantics for logic programs with monotone c-atoms, and they extend the original answer set semantics of normal logic programs. We also study some properties of answer sets of programs with c-atoms, and relate our definitions to several semantics for logic programs with aggregates presented in the literature

S-Net for multi-memory multicores

Copyright ACM, 2010. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Proceedings of the 5th ACM SIGPLAN Workshop on Declarative Aspects of Multicore Programming: http://doi.acm.org/10.1145/1708046.1708054S-Net is a declarative coordination language and component technology aimed at modern multi-core/many-core architectures and systems-on-chip. It builds on the concept of stream processing to structure dynamically evolving networks of communicating asynchronous components. Components themselves are implemented using a conventional language suitable for the application domain. This two-level software architecture maintains a familiar sequential development environment for large parts of an application and offers a high-level declarative approach to component coordination. In this paper we present a conservative language extension for the placement of components and component networks in a multi-memory environment, i.e. architectures that associate individual compute cores or groups thereof with private memories. We describe a novel distributed runtime system layer that complements our existing multithreaded runtime system for shared memory multicores. Particular emphasis is put on efficient management of data communication. Last not least, we present preliminary experimental data

A Constraint Solver for Flexible Protein Models

This paper proposes the formalization and implementation of a novel class of constraints aimed at modeling problems related to placement of multi-body systems in the 3-dimensional space. Each multi-body is a system composed of body elements, connected by joint relationships and constrained by geometric properties. The emphasis of this investigation is the use of multi-body systems to model native conformations of protein structures---where each body represents an entity of the protein (e.g., an amino acid, a small peptide) and the geometric constraints are related to the spatial properties of the composing atoms. The paper explores the use of the proposed class of constraints to support a variety of different structural analysis of proteins, such as loop modeling and structure prediction. The declarative nature of a constraint-based encoding provides elaboration tolerance and the ability to make use of any additional knowledge in the analysis studies. The filtering capabilities of the proposed constraints also allow to control the number of representative solutions that are withdrawn from the conformational space of the protein, by means of criteria driven by uniform distribution sampling principles. In this scenario it is possible to select the desired degree of precision and/or number of solutions. The filtering component automatically excludes configurations that violate the spatial and geometric properties of the composing multi-body system. The paper illustrates the implementation of a constraint solver based on the multi-body perspective and its empirical evaluation on protein structure analysis problems

MICROMORPHOLOGICAL PROPERTIES OF COLLUVIUMS IN HILLSLOPE IN THE MIDDLE VALLEY OF MARRECAS RIVER (SOUTH-WEST OF PARANÁ STATE) - BASIS FOR DISTINCTION OFALLOCHTHONOUS AND AUTHOCHTHONOUS SURFACES FORMATIONS IN BASALTIC SUBSTRATUM

Este artigo apresenta a organização microscópica de colúvios encontrados no médio vale do rio Marrecas (Sudoeste do Estado do Paraná), visando auxiliar na diferenciação genética de formações superficiais lateríticas alóctones daquelas autóctones no Planalto Basáltico.  Os métodos incluem: i) o levantamento das propriedades sedimentológicas e a identificação de litofácies; e ii) a descrição micromorfológica de nove lâminas delgadas representantivas das unidades coluviais. A distribuição relativa dos constituintes e das microfeições por processos foram quantificadas nas lâminas, por meio da análise de imagem. As litofácies lama cascalhenta maciça com matriz suportada e cascalho lamoso maciço com matriz suportada foram identificadas. As propriedades microscópicas dos colúvios revelaram microfeições relacionadas a processos deposicionais, herdadas do material de origem e decorrentes de tranformações pós-deposicionais. As microfeições identificadas nas duas primeiras situações podem servir de marcadores da origem alóctone de formações superficiais ricas em oxihidróxidos de ferro, auxiliando na sua diferenciação genética.This article presents the microscopic organization of colluviums located in the valley of Marrecas River (South-west of Paraná State), aiding to help in the genetic differentiation of allochthonous from the authochthonous surfaces formations in basaltic substratum. It has been procceded as it follows: i) survey of the sedimentological properties and the identification of lithofacies; and ii) micromorphological description of nine thin sections representatives of the colluvial units. The relative distributions of constituents and microstructures by processes were quantified in the thin sections, through image analysis. It has been identified matrix support massive gravelly mud and matrix support massive muddy gravel lithofacies. Microscopic properties of the colluvium deposits showed microstructures related to depositional processes, which were inherited from the source material and are resulted from post-depositional transformations. The microstrutures identified in the two situations can work as markers of allochthonous origin of surface formations rich in iron oxyhydroxides, assisting in its genetic differentiation

Persistent pusher behavior after a stroke

Pusher behavior (PB) is a postural control disorder characterized by actively pushing away from the nonparetic side and resisting passive correction with a tendency to fall toward the paralyzed side.1 These patients have no awareness that their active pushing is counterproductive, which precludes the patients from standing without assistance. Several studies have already demonstrated that PB can occur in patients with lesions in both hemispheres, and PB is distinct from neglect and anosognosia.2-8 The high frequency of the association between PB and neurophysiological deficits might reflect an increased vulnerability of certain regions to stroke-induced injury rather than any direct involvement with the occurrence of PB.9,10 Traditionally, PB has only been reported in stroke patients; however, it has also been described under nonstroke conditions.8 Previous imaging studies have suggested the posterolateral thalamus as the brain structure that is typically damaged in pusher patients.4,11 Nevertheless, other cortical and subcortical areas, such as the insular cortex and post-central gyrus, have also been highlighted as structures that are potentially involved in the pathophysiology of PB.2,12-1

Análise de lineamentos na bacia do Rio Quatorze – Sudoeste do Paraná

O estudo buscou analisar lineamentos estabelecidos sobre rochas vulcânicas da Formação Serra Geral na Bacia do Rio Quatorze, integrante do sistema hidrográfico do Rio Marrecas, sudoeste do Paraná. A compreensão dos fatores condicionantes dos lineamentos é importante, pois pode revelar a influência da estrutura geológica na evolução da paisagem geomorfológica regional. Procedeu-se à identificação, distribuição espacial e mensuração da orientação (azimute) de lineamentos com auxílio de fotografias aéreas (1:25.000), carta topográfica (1:50.000) e software Corel Draw 10. Individualizaram-se falhamentos, em carta topográfica, e mensuraram-se fraturas, em campo. Identificou-se, na escala da bacia do Rio Marrecas, o padrão de drenagem, através da análise de mapa hidrográfico (1:50.000), e a disposição de sua superfície topográfica, a partir da análise de mosaico de imagens de satélite Landsat TM. Constata-se que os lineamentos observados na Bacia do Rio Quatorze têm gênese ligada a fraturamentos (direção predominante NW), falhamentos e planos de acamamento, articulados à zona de falha em escala regional

Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science