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.     

Shadow attacks on users’ anonymity in pervasive computing environments

Privacy preserving technologies are likely to become an essential component of adaptive services in pervasive and mobile computing. Although privacy issues have been studied for a long time in computer science as well as in other fields, most studies are focused on the release of data from large repositories. Mobile and pervasive computing pose new challenges, requiring specific formal models for attacks and new privacy preserving techniques. This paper considers a specific pervasive computing scenario, and shows that the application of state-of-the-art techniques for the anonymization of service requests is insufficient to protect the privacy of users. A specific class of attacks, called shadow attacks, is formally defined and a defense technique is proposed. This defense is formally proved to be correct, and its effectiveness is validated by extensive experiments in a simulated environment.     

Querying and creating visualizations by analogy

While there have been advances in visualization systems, particularly in multi-view visualizations and visual exploration, the process of building visualizations remains a major bottleneck in data exploration. We show that provenance metadata collected during the creation of pipelines can be reused to suggest similar content in related visualizations and guide semi-automated changes. We introduce the idea of query-by-example in the context of an ensemble of visualizations, and the use of analogies as first-class operations in a system to guide scalable interactions. We describe an implementation of these techniques in VisTrails, a publicly-available, open-source system.     

Ambient occlusion and edge cueing to enhance real time molecular visualization

The paper presents a set of combined techniques to enhance the real-time visualization of simple or complex molecules (up to order of 106 atoms) space fill mode. The proposed approach includes an innovative technique for efficient computation and storage of ambient occlusion terms, a small set of GPU accelerated procedural impostors for space-fill and ball-and-stick rendering, and novel edge-cueing techniques. As a result, the user's understanding of the three-dimensional structure under inspection is strongly increased (even for still images), while the rendering still occurs in real time.     

Lower and upper bounds for the two-echelon capacitated location-routing problem

In this paper, we introduce two algorithms to address the two-echelon capacitated location-routing problem (2E-CLRP). We introduce a branch-and-cut algorithm based on the solution of a new two-index vehicle-flow formulation, which is strengthened with several families of valid inequalities. We also propose an adaptive large-neighbourhood search (ALNS) meta-heuristic with the objective of finding good-quality solutions quickly. The computational results on a large set of instances from the literature show that the ALNS outperforms existing heuristics. Furthermore, the branch-and-cut method provides tight lower bounds and is able to solve small- and medium-size instances to optimality within reasonable computing times.     

D-Index: Distance Searching Index for Metric Data Sets

In order to speedup retrieval in large collections of data, index structures partition the data into subsets so that query requests can be evaluated without examining the entire collection. As the complexity of modern data types grows, metric spaces have become a popular paradigm for similarity retrieval. We propose a new index structure, called D-Index, that combines a novel clustering technique and the pivot-based distance searching strategy to speed up execution of similarity range and nearest neighbor queries for large files with objects stored in disk memories. We have qualitatively analyzed D-Index and verified its properties on actual implementation. We have also compared D-Index with other index structures and demonstrated its superiority on several real-life data sets. Contrary to tree organizations, the D-Index structure is suitable for dynamic environments with a high rate of delete/insert operations.     

Memory for Visuospatial Location Following Selective Hippocampal Sclerosis: The Use of Different Coordinate Systems.

This study addressed the role of the medial temporal lobe regions and, more specifically, the contribution of the human hippocampus in memory for body-centered (egocentric) and environment-centered (allocentric) spatial location. Twenty-one patients with unilateral atrophy of the hippocampus secondary to long-standing epilepsy (left, n = 7; right, n = 14) and 15 normal control participants underwent 3 tasks measuring recall of egocentric or allocentric spatial location. Patients with left hippocampal sclerosis were consistently impaired in the allocentric conditions of all 3 tasks but not in the egocentric conditions. Patients with right hippocampal sclerosis were impaired to a lesser extent and in only 2 of the 3 tasks. It was concluded that hippocampal structures are crucial for allocentric, but not egocentric, spatial memory. (PsycINFO Database Record (c) 2010 APA, all rights reserved)