948 resultados para local sequence alignment problem


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The Team Formation problem (TFP) has become a well-known problem in the OR literature over the last few years. In this problem, the allocation of multiple individuals that match a required set of skills as a group must be chosen to maximise one or several social positive attributes. Speci�cally, the aim of the current research is two-fold. First, two new dimensions of the TFP are added by considering multiple projects and fractions of people's dedication. This new problem is named the Multiple Team Formation Problem (MTFP). Second, an optimization model consisting in a quadratic objective function, linear constraints and integer variables is proposed for the problem. The optimization model is solved by three algorithms: a Constraint Programming approach provided by a commercial solver, a Local Search heuristic and a Variable Neighbourhood Search metaheuristic. These three algorithms constitute the first attempt to solve the MTFP, being a variable neighbourhood local search metaheuristic the most effi�cient in almost all cases. Applications of this problem commonly appear in real-life situations, particularly with the current and ongoing development of social network analysis. Therefore, this work opens multiple paths for future research.

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Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm, clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas. (c) 2007 Elsevier Inc. All rights reserved.

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In this paper, we consider an initial value problem for a class of generalized ODEs, also known as Kurzweil equations, and we prove the existence of a local semidynamical system there. Under certain perturbation conditions, we also show that this class of generalized ODEs admits a discontinuous semiflow which we shall refer to as an impulsive semidynamical system. As a consequence, we obtain LaSalle`s invariance principle for such a class of generalized ODEs. Due to the importance of LaSalle`s invariance principle in studying stability of differential systems, we include an application to autonomous ordinary differential systems with impulse action at variable times. (C) 2011 Elsevier Inc. All rights reserved.

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Let M be a compact, connected non-orientable surface without boundary and of genus g >= 3. We investigate the pure braid groups P,(M) of M, and in particular the possible splitting of the Fadell-Neuwirth short exact sequence 1 -> P(m)(M \ {x(1), ..., x(n)}) hooked right arrow P(n+m)(M) (P*) under right arrow P(n)(M) -> 1, where m, n >= 1, and p* is the homomorphism which corresponds geometrically to forgetting the last m strings. This problem is equivalent to that of the existence of a section for the associated fibration p: F(n+m)(M) -> F(n)(M) of configuration spaces, defined by p((x(1), ..., x(n), x(n+1), ..., x(n+m))) = (x(1), ..., x(n)). We show that p and p* admit a section if and only if n = 1. Together with previous results, this completes the resolution of the splitting problem for surface pure braid groups. (C) 2009 Elsevier B.V. All rights reserved.

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In this paper we obtain asymptotic expansions up to order n(-1/2) for the nonnull distribution functions of the likelihood ratio, Wald, score and gradient test statistics in exponential family nonlinear models (Cordeiro and Paula, 1989), under a sequence of Pitman alternatives. The asymptotic distributions of all four statistics are obtained for testing a subset of regression parameters and for testing the dispersion parameter, thus generalising the results given in Cordeiro et al. (1994) and Ferrari et al. (1997). We also present Monte Carlo simulations in order to compare the finite-sample performance of these tests. (C) 2010 Elsevier B.V. All rights reserved.

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Glycine-rich proteins (GRP), serve a variety of biological functions. Acanthoscurrin is an antimicrobial GRP isolated front hemocytes-of the Brazilian spider Acanthoscurria gomesiana. Aiming to contribute to the knowledge of the secondary structure and stepwise solid-phase synthesis of GRPs` glycine-rich domains, we attempted to prepare G(101)GGLGGGRGGGYG(113) GGGGYGGGYG(123)GGy(126)GGGKYK(132)-NH(2), acanthoscurrin C-terminal amidated fragment. Although a theoretical prediction did not indicate high aggregation potential for this peptide, repetitive incomplete aminoacylations were observed after incorporating Tyr(126) to the growing peptide-MBHA resin (Boc chemistry) at 60 degrees C. The problem was not solved by varying the coupling reagents or solvents, adding chaotropic salts to the reaction media or changing the resin/chemistry (Rink amide resin/Fmoc chemistry). Some improvement was mode when CLEAR amide resin (Fmoc chemistry) was 32 used, as it allowed for obtaining fragment (G(113)-K(132) NIR-FT-Raman spectra collected for samples of the growing peptide-MBHA, -Rink amide resin and -CLEAR amide resin revealed the presence of beta-sheet structures. Only the combination of CLEAR-amide resin, 60 degrees C, Fmoc-(Fmoc-Hmb)Gly-OH and LiCl (the last two used alternately) was able to inhibit the phenomenon, as proven by NIR-FT-Raman analysis of the growing peptide-resin, allowing the total synthesis of desired 132 fragment Gly(101)-K(132). In summary, this work describes a new difficult sequence, contributes to understanding stepwise solid-phase synthesis of this type of peptide and shows that, at least while protected and linked to a resin, this GRPs glycine-rich motif presents all early tendency to assume beta-sheet structures. (c) 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 65-75, 2009.

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BACKGROUND: Facilitation of local women's groups may reportedly reduce neonatal mortality. It is not known whether facilitation of groups composed of local health care staff and politicians can improve perinatal outcomes. We hypothesised that facilitation of local stakeholder groups would reduce neonatal mortality (primary outcome) and improve maternal, delivery, and newborn care indicators (secondary outcomes) in Quang Ninh province, Vietnam. METHODS AND FINDINGS: In a cluster-randomized design 44 communes were allocated to intervention and 46 to control. Laywomen facilitated monthly meetings during 3 years in groups composed of health care staff and key persons in the communes. A problem-solving approach was employed. Births and neonatal deaths were monitored, and interviews were performed in households of neonatal deaths and of randomly selected surviving infants. A latent period before effect is expected in this type of intervention, but this timeframe was not pre-specified. Neonatal mortality rate (NMR) from July 2008 to June 2011 was 16.5/1,000 (195 deaths per 11,818 live births) in the intervention communes and 18.4/1,000 (194 per 10,559 live births) in control communes (adjusted odds ratio [OR] 0.96 [95% CI 0.73-1.25]). There was a significant downward time trend of NMR in intervention communes (p = 0.003) but not in control communes (p = 0.184). No significant difference in NMR was observed during the first two years (July 2008 to June 2010) while the third year (July 2010 to June 2011) had significantly lower NMR in intervention arm: adjusted OR 0.51 (95% CI 0.30-0.89). Women in intervention communes more frequently attended antenatal care (adjusted OR 2.27 [95% CI 1.07-4.8]). CONCLUSIONS: A randomized facilitation intervention with local stakeholder groups composed of primary care staff and local politicians working for three years with a perinatal problem-solving approach resulted in increased attendance to antenatal care and reduced neonatal mortality after a latent period. TRIAL REGISTRATION: Current Controlled Trials ISRCTN44599712. Please see later in the article for the Editors' Summary.

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Este trabalho discute a racionalidade econômica para o desenvolvimento de um sistema de metas sociais como forma de o governo federal aumentar a eficiência na utilização dos recursos sociais transferidos para os municípios. O trabalho desenvolve algumas extensões do modelo de agente-principal incluindo abordagens estáticas com e sem informação imperfeita e abordagens dinâmicas com contratos perfeitos e imperfeitos. Os resultados dos modelos estáticos indicam que o uso de critérios usuais de focalização onde localidades mais pobres recebem mais recursos pode levar a incentivos adversos para a erradicação da pobreza. Nós também mostramos que transferências incondicionais do governo federal deslocam gastos sociais locais. O trabalho argumenta em favor do uso de contratos onde quanto maior for a melhora no indicador social escolhido, mais recursos o município receberia. A introdução de informação imperfeita neste modelo basicamente gera uma penalidade aos segmentos pobres de áreas onde os governos demonstram ser menos avessos a pobreza. O trabalho também aborda o problema de favoritismo político onde determinados grupos sociais têm maior, ou menor, atenção por parte de governos locais. O resultado é que as políticas sociais acabam privilegiando determinados setores em detrimento de outros. Com o estabelecimento de metas sociais é possível, se não eliminar o problema, ao menos criar incentivos corretos para que os gastos sociais sejam distribuídos de forma mais equânime. Também desenvolvemos modelos dinâmicos com diferentes possibilidades de renegociação ao longo do tempo. Demonstramos que a melhor forma de aumentar a eficiência alocativa dos fundos seria criar mecanismos institucionais garantindo a impossibilidade de renegociações bilaterais. Esse contrato ótimo reproduz a seqüência de metas e transferências de vários períodos encontrada na solução do modelo estático. Entretanto, esse resultado- desaparece quando incorporamos contratos incompletos. Nesse caso, as ineficiências ex-ante criadas pela possibilidade de renegociação devem ser comparadas com as ineficiências ex-post criadas por não se usar a informação nova revelada ao longo do processo. Finalmente, introduzimos a possibilidade do resultado social observado depender não só do investimento realizado, mas também da presença de choques. Nesse caso, tanto o governo quanto o município aumentam as suas metas de investimento na área social. Contratos lineares na presença de choques negativos fazem com que os municípios recebem menos recursos justamente em situações adversas. Para contornar esse problema, mostramos a importância da utilização de contratos com comparação de performance.

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Partindo de uma avaliação sobre o contexto mundial de descentralização fiscal e de democratização em que o Brasil se encontrava no final do século XX, essa tese apresenta na primeira parte uma análise empírica para países em desenvolvimento evidenciando o condicionamento do tipo de regime de governo na relação entre descentralização fiscal e tamanho de governo. Estimações por system-GMM para países em desenvolvimento mostram que existe um nível de descentralização fiscal, entre 20% e 30%, que uma vez superado, resulta em democracias com tamanhos de governos menores do que as ditaduras. Esses resultado, que chama a atenção tanto para os governos locais, como para a influência da democracia no gasto público, estimulou a continuação da pesquisa na avaliação da eficiência dos gastos municipais no Brasil e sua relação com o voto. Assim, no segundo ensaio, são calculados indicadores de evolução da eficiência e da produtividade do gasto municipal (fatores de Malmquist) entre 2004 e 2008, para as áreas da saúde e educação. Os resultados da análise por fronteira estocástica mostram que tanto na educação, como na saúde, houve avanços na fronteira de produção (TFPC, em média, de 18.7%, na educação e de 14.2% na saúde) por avanços de mudança técnica (Technical Change - TC), ao invés de elevação da eficiência (Technical Efficiency Change – TEC). No último ensaio, os indicadores de eficiência e de produtividade são usados para testar a hipótese de que o eleitor municipal premia com o voto os prefeitos que melhoraram a eficiência do gasto da educação e/ou saúde em sua gestão. Os resultados não rejeitam a hipótese para a educação, mas rejeitam para a saúde. A fim de tratar prováveis erros de medida das variáveis de produtividade, as estimações são instrumentalizadas em regressões por dois estágios.

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How can managers successfully access political rents by way of corporate political strategies (CPA)? Existing research has suggested several endogenous factors that correlate with CPA outcomes. I offer a more robust solution to this problem. Drawing on insights from the perspective of CPA as exchanges between firms and political decision-makers, and from the special interest politics of political economy, I develop and test a causal mechanism that links local elections, legislative bargaining and access to political rents at the national level. I conducted a natural experiment using regression discontinuity design and propensity score matching in municipal elections in Brazil to show that firms enjoy superior access to subsidized financing from the state-owned national development bank (BNDES) when they decide to invest in municipalities whose winning mayoral candidate is coalition-aligned with the national ruler. This effect fades away fades away as the level of competition in the local election decreases. The evidence implies that when managers bet on national coalition-aligned winners in close local elections, they positively affect CPA outcomes. I extend the exchange-based typology of corporate political strategies by offering a novel possibility of targeting voters with financial inducements, which I call a private local development strategy. Finally, these results show that firms exchange their project-execution capabilities for superior access to subsidized financing.

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This work proposes a computational methodology to solve problems of optimization in structural design. The application develops, implements and integrates methods for structural analysis, geometric modeling, design sensitivity analysis and optimization. So, the optimum design problem is particularized for plane stress case, with the objective to minimize the structural mass subject to a stress criterion. Notice that, these constraints must be evaluated at a series of discrete points, whose distribution should be dense enough in order to minimize the chance of any significant constraint violation between specified points. Therefore, the local stress constraints are transformed into a global stress measure reducing the computational cost in deriving the optimal shape design. The problem is approximated by Finite Element Method using Lagrangian triangular elements with six nodes, and use a automatic mesh generation with a mesh quality criterion of geometric element. The geometric modeling, i.e., the contour is defined by parametric curves of type B-splines, these curves hold suitable characteristics to implement the Shape Optimization Method, that uses the key points like design variables to determine the solution of minimum problem. A reliable tool for design sensitivity analysis is a prerequisite for performing interactive structural design, synthesis and optimization. General expressions for design sensitivity analysis are derived with respect to key points of B-splines. The method of design sensitivity analysis used is the adjoin approach and the analytical method. The formulation of the optimization problem applies the Augmented Lagrangian Method, which convert an optimization problem constrained problem in an unconstrained. The solution of the Augmented Lagrangian function is achieved by determining the analysis of sensitivity. Therefore, the optimization problem reduces to the solution of a sequence of problems with lateral limits constraints, which is solved by the Memoryless Quasi-Newton Method It is demonstrated by several examples that this new approach of analytical design sensitivity analysis of integrated shape design optimization with a global stress criterion purpose is computationally efficient

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The topology optimization problem characterize and determine the optimum distribution of material into the domain. In other words, after the definition of the boundary conditions in a pre-established domain, the problem is how to distribute the material to solve the minimization problem. The objective of this work is to propose a competitive formulation for optimum structural topologies determination in 3D problems and able to provide high-resolution layouts. The procedure combines the Galerkin Finite Elements Method with the optimization method, looking for the best material distribution along the fixed domain of project. The layout topology optimization method is based on the material approach, proposed by Bendsoe & Kikuchi (1988), and considers a homogenized constitutive equation that depends only on the relative density of the material. The finite element used for the approach is a four nodes tetrahedron with a selective integration scheme, which interpolate not only the components of the displacement field but also the relative density field. The proposed procedure consists in the solution of a sequence of layout optimization problems applied to compliance minimization problems and mass minimization problems under local stress constraint. The microstructure used in this procedure was the SIMP (Solid Isotropic Material with Penalty). The approach reduces considerably the computational cost, showing to be efficient and robust. The results provided a well defined structural layout, with a sharpness distribution of the material and a boundary condition definition. The layout quality was proporcional to the medium size of the element and a considerable reduction of the project variables was observed due to the tetrahedrycal element

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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

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The Capacitated Centered Clustering Problem (CCCP) consists of defining a set of p groups with minimum dissimilarity on a network with n points. Demand values are associated with each point and each group has a demand capacity. The problem is well known to be NP-hard and has many practical applications. In this paper, the hybrid method Clustering Search (CS) is implemented to solve the CCCP. This method identifies promising regions of the search space by generating solutions with a metaheuristic, such as Genetic Algorithm, and clustering them into clusters that are then explored further with local search heuristics. Computational results considering instances available in the literature are presented to demonstrate the efficacy of CS. (C) 2010 Elsevier Ltd. All rights reserved.

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This work presents the application of a multiobjective evolutionary algorithm (MOEA) for optimal power flow (OPF) solution. The OPF is modeled as a constrained nonlinear optimization problem, non-convex of large-scale, with continuous and discrete variables. The violated inequality constraints are treated as objective function of the problem. This strategy allows attending the physical and operational restrictions without compromise the quality of the found solutions. The developed MOEA is based on the theory of Pareto and employs a diversity-preserving mechanism to overcome the premature convergence of algorithm and local optimal solutions. Fuzzy set theory is employed to extract the best compromises of the Pareto set. Results for the IEEE-30, RTS-96 and IEEE-354 test systems are presents to validate the efficiency of proposed model and solution technique.