Relative blocking in posets

Poset-theoretic generalizations of set-theoretic committee constructions are presented. The structure of the corresponding subposets is described. Sequences of irreducible fractions associated to the principal order ideals of finite bounded posets are considered and those related to the Boolean lattices are explored; it is shown that such sequences inherit all the familiar properties of the Farey sequences.Comment: 29 pages. Corrected version of original publication which is available at http://www.springerlink.com, see Corrigendu

Testing Nelder-Mead based repulsion algorithms for multiple roots of nonlinear systems via a two-level factorial design of experiments

This paper addresses the challenging task of computing multiple roots of a system of nonlinear equations. A repulsion algorithm that invokes the Nelder-Mead (N-M) local search method and uses a penalty-type merit function based on the error function, known as 'erf', is presented. In the N-M algorithm context, different strategies are proposed to enhance the quality of the solutions and improve the overall efficiency. The main goal of this paper is to use a two-level factorial design of experiments to analyze the statistical significance of the observed differences in selected performance criteria produced when testing different strategies in the N-M based repulsion algorithm. The main goal of this paper is to use a two-level factorial design of experiments to analyze the statistical significance of the observed differences in selected performance criteria produced when testing different strategies in the N-M based repulsion algorithm.Fundação para a Ciência e Tecnologia (FCT

CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation

<p>Abstract</p> <p>Background</p> <p>The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been developed to predict protein function, but these methods need to be improved further, such as, enhancing the accuracy, sensitivity, and the computational speed. Here, an accurate algorithm, the CMASA (Contact MAtrix based local Structural Alignment algorithm), has been developed to predict unknown functions of proteins based on the local protein structural similarity. This algorithm has been evaluated by building a test set including 164 enzyme families, and also been compared to other methods.</p> <p>Results</p> <p>The evaluation of CMASA shows that the CMASA is highly accurate (0.96), sensitive (0.86), and fast enough to be used in the large-scale functional annotation. Comparing to both sequence-based and global structure-based methods, not only the CMASA can find remote homologous proteins, but also can find the active site convergence. Comparing to other local structure comparison-based methods, the CMASA can obtain the better performance than both FFF (a method using geometry to predict protein function) and SPASM (a local structure alignment method); and the CMASA is more sensitive than PINTS and is more accurate than JESS (both are local structure alignment methods). The CMASA was applied to annotate the enzyme catalytic sites of the non-redundant PDB, and at least 166 putative catalytic sites have been suggested, these sites can not be observed by the Catalytic Site Atlas (CSA).</p> <p>Conclusions</p> <p>The CMASA is an accurate algorithm for detecting local protein structural similarity, and it holds several advantages in predicting enzyme active sites. The CMASA can be used in large-scale enzyme active site annotation. The CMASA can be available by the mail-based server (<url>http://159.226.149.45/other1/CMASA/CMASA.htm</url>).</p

3D Constitutive model of the rat large intestine: estimation of the material parameters of the single layers

Several functions of the large intestine depend on its morphology and biomechanical properties. Since some classes of soft tissues have non-linear mechanical behavior, they may be modeled as hyperelastic materials applying the strain energy function. Moreover, as the arterial walls, the colonic walls are composed by collagen fibers characterized by an anisotropic behavior. It is known a mechanical model of artery that considered its walls composed of two cylindrical layers reinforced with fibers of collagen suitably oriented. Afterwards, it has been proposed a structure-based mathematical model for mechanical passive behavior of the rat colon, fitted to data obtained from inflation/extension tests that doesn’t subdivide the walls into layers. However, the wall of the rat large intestine is composed by four distinct layers, i.e. mucosa, submucosa, muscle layer and serosa. Thus, the aim of this paper is to identify a method for estimating the parameters of a computational model that considers each layer of the colonic walls. We use the Nelder-Mead nonlinear regression technique for minimizing the residual sum of squares between experimental data reported in literature and the outcomes of the proposed model. The estimated material parameters (k1,k2,c) are used to develop a 3D finite element model. Furthermore, we computed the components of the Cauchy stress over the colonic wall across each layer for different values of internal pressure and axial stretch

Recent advances in the theory of nonlinear pseudorandom number generators

Abstract. We pr esent a sur vey of recent developments in the t heory of nonlinear generators for uni form pseud orandom nu mb ers. The emphasis is on discrepan cybased tests for inversive generators where most of t he progress has taken place.