MetaMol: high-quality visualization of molecular skin surface

Modeling and visualizing molecular surfaces is an important and challenging task in bioinformatics. Such surfaces play an essential role in better understanding the chemical and physical properties of molecules. However, constructing and displaying molecular surfaces requires complex algorithms. In this article we introduce MetaMol, a new program that generates high-quality images in interactive time. In contrast with existing software that discretizes the surface with triangles or grids, our program is based on a GPU accelerated ray-casting algorithm that directly uses the piecewise-defined algebraic equation of the molecular skin surface. As a result, both better performances and higher quality are obtained.     

Black-Box Correctness Tests for Basic Parallel Data Structures

Operations on basic data structures such as queues, priority queues, stacks, and counters can dominate the execution time of a parallel program due to both their frequency and their coordination and contention overheads. There are considerable performance payoffs in developing highly optimized, asynchronous, distributed, cache-conscious, parallel implementations of such data structures. Such implementations may employ a variety of tricks to reduce latencies and avoid serial bottlenecks, as long as the semantics of the data structure are preserved. The complexity of the implementation and the difficulty in reasoning about asynchronous systems increases concerns regarding possible bugs in the implementation. In this paper we consider postmortem, black-box procedures for testing whether a parallel data structure behaved correctly. We present the first systematic study of algorithms and hardness results for such testing procedures, focusing on queues, priority queues, stacks, and counters, under various important scenarios. Our results demonstrate the importance of selecting test data such that distinct values are inserted into the data structure (as appropriate). In such cases we present an O(n) time algorithm for testing linearizable queues, an O(n log n) time algorithm for testing linearizable priority queues, and an O( np ² ) time algorithm for testing sequentially consistent queues, where n is the number of data structure operations and p is the number of processors. In contrast, we show that testing such data structures for executions with arbitrary input values is NP-complete. Our results also help clarify the thresholds between scenarios that admit polynomial time solutions and those that are NP-complete. Our algorithms are the first nontrivial algorithms for these problems.     

Multimodal support to group dynamics

The complexity of group dynamics occurring in small group interactions often hinders the performance of teams. The availability of rich multimodal information about what is going on during the meeting makes it possible to explore the possibility of providing support to dysfunctional teams from facilitation to training sessions addressing both the individuals and the group as a whole. A necessary step in this direction is that of capturing and understanding group dynamics. In this paper, we discuss a particular scenario, in which meeting participants receive multimedia feedback on their relational behaviour, as a first step towards increasing self-awareness. We describe the background and the motivation for a coding scheme for annotating meeting recordings partially inspired by the Bales’ Interaction Process Analysis. This coding scheme was aimed at identifying suitable observable behavioural sequences. The study is complemented with an experimental investigation on the acceptability of such a service.

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Aero-structural optimization using adjoint coupled post-optimality sensitivities

A new subspace optimization method for performing aero-structural design is introduced. The method relies on a semi-analytic adjoint approach to the sensitivity analysis that includes post-optimality sensitivity information from the structural optimization subproblem. The resulting coupled post-optimality sensitivity approach is used to guide a gradient-based optimization algorithm. The new approach simplifies the system-level problem, thereby reducing the number of calls to a potentially costly aerodynamics solver. The aero-structural optimization of an aircraft wing is performed using linear aerodynamic and structural analyses, and a performance comparison is made between the new approach and the conventional multidisciplinary feasible method. The new asymmetric suboptimization method is found to be the more efficient approach when it adequately reduces the number of system evaluations or when there is a large enough discrepancy between disciplinary solution times.     

Dynamic voltage scaling under EDF revisited

Basic algorithms have been proposed in the field of low-power (Yao, F., et al. in Proceedings of lEEE annual foundations of computer science, pp. 374–382, 1995) which compute the minimum energy-schedule for a set of non-recurrent tasks (or jobs) scheduled under EDF on a dynamically variable voltage processor. In this study, we propose improvements upon existing algorithms with lower average and worst-case complexities. They are based on a new EDF feasibility test that helps to identify the “critical intervals”. The complexity of this feasibility test depends on structural characteristics of the set of jobs. More precisely, it depends on how tasks are included one in the other. The first step of the algorithm is to construct the Hasse diagram of the set of tasks where the partial order is defined by the inclusion relation on the tasks. Then, the algorithm constructs the shortest path in a geometrical representation at each level of the Hasse diagram. The optimal processor speed is chosen according to the maximal slope of each path.

QDENSITY—A Mathematica Quantum Computer simulation

This Mathematica 5.2 package¹ is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc. Selected examples of the basic commands are presented here and a tutorial notebook, Tutorial.nb is provided with the package (available on our website) that serves as a full guide to the package. Finally, application is made to a variety of relevant cases, including Teleportation, Quantum Fourier transform, Grover's search and Shor's algorithm, in separate notebooks: QFT.nb, Teleportation.nb, Grover.nb and Shor.nb where each algorithm is explained in detail. Finally, two examples of the construction and manipulation of cluster states, which are part of “one way computing” ideas, are included as an additional tool in the notebook Cluster.nb. A Mathematica palette containing most commands in QDENSITY is also included: QDENSpalette.nb.

Program summary

Title of program: QDENSITYCatalogue identifier: ADXH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_v1_0Program available from: CPC Program Library, Queen's University of Belfast, N. IrelandOperating systems: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4Programming language used: Mathematica 5.2No. of bytes in distributed program, including test data, etc.: 180 581No. of lines in distributed program, including test data, etc.: 19 382Distribution format: tar.gzMethod of solution: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed.     

Software assessment using metrics: A comparison across large C++ and Java systems

This paper presents an assessment method to evaluate the quality of object oriented software systems. The assessment method is based on source code abstraction, object–oriented metrics and graphical representation. The metrics used and the underlying model representing the software are presented. The assessment method experiment is part of an industrial research effort with the Bell Canada Quality Engineering and Research Group. It helps evaluators assess the quality and risks associated with software by identifying code fragments presenting unusual characteristics. The assessment method evaluates object–oriented software systems at three levels of granularity: system level, class level and method level. One large C++ and eight Java software systems, for a total of over one million lines of code, are presented as case studies. A critical analysis of the results is presented comparing the systems and the two languages.     

Histology, histochemistry and stereology of the adipose fin of Prochilodus lineatus

The adipose fin is small, nonpared, and usually located medially between the dorsal and caudal fin. Its taxonomic occurrence is very restrict; thus, it represents an important trace for taxon distinction. As it does not play a known vital physiological roll and it is easily removed, it is commonly used in marking and recapture studies. The present study characterizes the adipose fin of Prochilodus lineatus, as it is poorly explored by the literature. The adipose fin consists basically of a loose connective core, covered by a stratified epithelium supported by collagen fibers. At the epithelium, pigmented cells and alarm substance cells are found. Despite the name, adipocytes or lipid droplets are not observed on the structure of the fin.     

Hematopoietic progenitor constituents and adherent cell progenitor morphology isolated from black-rumped agouti (Dasyprocta prymnolopha, Wagler 1831) bone marrow

Stem cells are present in the adult tissues of most diverse species. Bone marrow is recognized to be the most exploited site to obtain stem cells and cell progenitors. The objective of the present study was to characterize hematopoietic progenitor (HP) morphology and analyze the performance of adherent cell progenitors (ACPs) cultivated in vitro from black‐rumped agouti bone marrow (Dasyprocta prymnolopha). Bone marrow aspirates were obtained from tibia crest and used to prepare histological slides and identify cell morphology. Cells were also scattered on culture plates for later isolation, expansion, and quantification. Smears obtained from bone marrow demonstrated HPs at different stages of maturity. In culture, these cells showed fibroblastoid morphology and a strong tendency to form colonies, demonstrated by the presence of cell aggregates, cytoplasmic elongations lying side by side. An 80% cell confluence was observed at 18 days in culture and progressive reduction in the percentage of nonadherent mononuclear cells. After eight passes, a mean cell viability of 96.07% was observed, from a pool of 1.6 × 10⁷ cells (ACP). Thirteen 25‐cm² culture bottles were trypsinized, resuspended in freezing medium, stored in 14 criotubes at a concentration of 1 × 10⁶ cells per milliliter, and placed in liquid nitrogen at ?196°C. Agouti bone marrow demonstrated high plasticity, moreover different HP lines, and a population of adherent cells demonstrated morphology similar to mesenchymal stem cells in culture. Microsc. Res. Tech. 2012. © 2012 Wiley Periodicals, Inc.     

Underwater Vehicle Localization with Complementary Filter: Performance Analysis in the Shallow Water Environment

Rapid development of underwater technology during the last two decades yielded more affordable sensors and underwater vehicles, and, as a result, expanded their use from exclusively offshore industry towards smaller interdisciplinary research groups. Regardless of application, knowing the location of the vehicle operating underwater is crucial. Relatively inexpensive solution is sensor fusion based on a dynamic model of the vehicle aided by a Doppler Velocity Log and a Ultra-Short Base Line position system. Raw data from the sensors are highly asynchronous and susceptible to outliers, especially in shallow water environment. This paper presents detailed sensor analysis based on experimental data gathered in shallow waters, identifies outliers, presents an intuitive and simple sensor fusion algorithm and finally, discusses outlier rejection. The approach has been experimentally verified on medium size remotely operated vehicle.