nSPARQL: A navigational language for RDF

Navigational features have been largely recognized as fundamental for graph database query languages. This fact has motivated several authors to propose RDF query languages with navigational capabilities. In this paper, we propose the query language nSPARQL that uses nested regular expressions to navigate RDF data. We study some of the fundamental properties of nSPARQL and nested regular expressions concerning expressiveness and complexity of evaluation. Regarding expressiveness, we show that nSPARQL is expressive enough to answer queries considering the semantics of the RDFS vocabulary by directly traversing the input graph. We also show that nesting is necessary in nSPARQL to obtain this last result, and we study the expressiveness of the combination of nested regular expressions and SPARQL operators. Regarding complexity of evaluation, we prove that given an RDF graph G and a nested regular expression E, this problem can be solved in time O(|G||E|).     

A spline framework for estimating the EEG surface laplacian using the Euclidean metric

This letter develops a framework for EEG analysis and similar applications based on polyharmonic splines. This development overcomes a basic problem with the method of splines in the Euclidean setting: that it does not work on low-degree algebraic surfaces such as spherical and ellipsoidal scalp models. The method's capability is illustrated through simulations on the three-sphere model and using empirical data.     

Shape-sensitive MLS deformation

This work presents methods for deforming meshes in a shape-sensitive way using Moving Least Squares (MLS) optimization. It extends an approach for deforming space (Cuno et al. in Proceedings of the 27th Computer Graphics International Conference, pp. 115–122, 2007) by showing how custom distance metrics may be used to achieve deformations which preserve the overall mesh shape. Several variant formulations are discussed and demonstrated, including the use of geodesic distances, distances constrained to paths contained in the mesh, the use of skeletons, and a reformulation of the MLS scheme which makes it possible to affect the bending behavior of the deformation. Finally, aspects of the implementation of these techniques in parallel architectures such as GPUs (graphics processing units) are described and compared with CPU-only implementations.     

New simple and efficient heuristics for the uncapacitated single allocation hub location problem

Hub-and-spoke networks are widely studied in the area of location theory. They arise in several contexts, including passenger airlines, postal and parcel delivery, and computer and telecommunication networks. Hub location problems usually involve three simultaneous decisions to be made: the optimal number of hub nodes, their locations and the allocation of the non-hub nodes to the hubs. In the uncapacitated single allocation hub location problem (USAHLP) hub nodes have no capacity constraints and non-hub nodes must be assigned to only one hub. In this paper, we propose three variants of a simple and efficient multi-start tabu search heuristic as well as a two-stage integrated tabu search heuristic to solve this problem. With multi-start heuristics, several different initial solutions are constructed and then improved by tabu search, while in the two-stage integrated heuristic tabu search is applied to improve both the locational and allocational part of the problem. Computational experiments using typical benchmark problems (Civil Aeronautics Board (CAB) and Australian Post (AP) data sets) as well as new and modified instances show that our approaches consistently return the optimal or best-known results in very short CPU times, thus allowing the possibility of efficiently solving larger instances of the USAHLP than those found in the literature. We also report the integer optimal solutions for all 80 CAB data set instances and the 12 AP instances up to 100 nodes, as well as for the corresponding new generated AP instances with reduced fixed costs.     

Parallel Lattice Boltzmann Method with Blocked Partitioning

This paper presents and discusses a blocked parallel implementation of bi- and three-dimensional versions of the Lattice Boltzmann Method. This method is used to represent and simulate fluid flows following a mesoscopic approach. Most traditional parallel implementations use simple data distribution strategies to parallelize the operations on the regular fluid data set. However, it is well known that block partitioning is usually better. Such a parallel implementation is discussed and its communication cost is established. Fluid flows simulations crossing a cavity have also been used as a real-world case study to evaluate our implementation. The presented results with our blocked implementation achieve a performance up to 31% better than non-blocked versions, for some data distributions. Thus, this work shows that blocked, parallel implementations can be efficiently used to reduce the parallel execution time of the method.     

Model-based testing approaches selection for software projects

Selecting software technologies for software projects represents a challenge to software engineers. It is known that software projects differ from each other by presenting different characteristics that can complicate the selection of such technologies. This is not different when considering model-based testing. There are many approaches with different characteristics described in the technical literature that can be used in software projects. However, there is no indication as to how they can fit a software project. Therefore, a strategy to select model-based testing approaches for software projects called Porantim is fully described in this paper. Porantim is based on a body of knowledge describing model-based testing approaches and their characterization attributes (identified by secondary and primary experimental studies), and a process to guide by adequacy and impact criteria regarding the use of this sort of software technology that can be used by software engineers to select model-based testing approaches for software projects.     

Template-based quadrilateral mesh generation from imaging data

This paper describes a novel template-based meshing approach for generating good quality quadrilateral meshes from 2D digital images. This approach builds upon an existing image-based mesh generation technique called Imeshp, which enables us to create a segmented triangle mesh from an image without the need for an image segmentation step. Our approach generates a quadrilateral mesh using an indirect scheme, which converts the segmented triangle mesh created by the initial steps of the Imesh technique into a quadrilateral one. The triangle-to-quadrilateral conversion makes use of template meshes of triangles. To ensure good element quality, the conversion step is followed by a smoothing step, which is based on a new optimization-based procedure. We show several examples of meshes generated by our approach, and present a thorough experimental evaluation of the quality of the meshes given as examples.     

Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations

Treatment of prostate cancer patients with antiandrogens is initially successful, though the therapy often becomes refractory over the time. This mechanism is not fully understood, but the presence of androgen receptor (AR) mutant forms which are activated by antiandrogens and other endogenous ligands, and overexpression of the receptor have been suggested. In an attempt to explain the molecular basis for agonicity and antagonicity in the androgen receptor, and the changes on biological activity of subtle modifications at the ligand and receptor (mutations) level, molecular dynamics simulations were performed on the androgen receptor wild type (WT), and T877A and W741 mutant forms, complexed with several non-steroidal androgens. The stabilizing role of residues from helices 3, 5, 11 and 12 was observed in non-steroidal androgens R-3, S-1, and R-bicalutamide and hydroxyflutamide in resistant mutations. In the AR WT antiandrogen R-bicalutamide complex, destabilization of M895 by both W741 and the sulfonyl linkage of the ligand may be responsible for reported antagonism. Changes in the ligand or mutations alleviating this effect were observed to stabilize the receptor in the active conformation, thus developing resistance to R-bicalutamide. The results presented provide a plausible explanation for the molecular basis of agonicity and antagonicity in the androgen receptor, and complement previous studies using static crystal structures, incorporating for the first time protein dynamics into the analysis. Thus, our results provide a valuable framework for the structure-based design of improved antiandrogens.