Covering arrays avoiding forbidden edges

Covering arrays (CAs) can be used to detect the existence of faulty pairwise interactions between parameters or components in a software system. The generalization considered here applies to the situation in which some input combinations are invalid, a requirement quite common in software testing. In this paper, we study covering arrays avoiding forbidden edges (CAFEs), where certain pairwise interactions are forbidden while all others must be covered, and we aim to minimize the number of tests. We establish a theoretical framework for this problem, by providing connections to the edge clique covering problem, lower and upper bounds, complexity results and a recursive construction. We also give an algorithm for the case of binary alphabets.     

Elastic Flow in an Application Specific Network-on-Chip

A Network-on-Chip (NoC) is increasingly needed to interconnect the large number and variety of Intellectual Property (IP) cells that make up a System-on-Chip (SoC). The network must be able to communicate between cells in di erent clock domains, and do so with minimal space, power, and latency overhead. In this paper, we describe an asynchronous NoC using an elastic-flow protocol, and methods of automatically generating a topology and router placement. We use the communication profile of the SoC design to drive the binary-tree topology creation and the physical placement of routers, and a force-directed approach to determine router locations. The nature of elastic-flow removes the need for large router bu ers, and thus we gain a significant power and space advantage compared to traditional NoCs. Additionally, our network is deadlock-free, and paths have bounded worst-case communication latencies.     

Introduction to building projection-based tiled display systems

This tutorial introduces the concepts and technologies needed to build projector-based display systems. Tiled displays offer scalability, high resolution, and large formats for various applications. Tiled displays are an emerging technology for constructing semi-immersive visualization environments capable of presenting high-resolution images from scientific simulation. The largest impact may well arise from using large-format tiled displays as one of possibly multiple displays in building information or active spaces that surround the user with diverse ways of interacting with data and multimedia information flows. These environments may prove the ultimate successor to the desktop metaphor for information technology work. Several fundamental technological problems must be addressed to make tiled displays practical. These include: the choice of screen materials and support structures; choice of projectors, projector supports, and optional fine positioners; techniques for integrating image tiles into a seamless whole; interface devices for interaction with applications; display generators and interfaces; and the display software environment     

The theoretical limits of DNA sequence discrimination by linked polyamides

Linked polyamides bind in the minor groove of double-stranded DNA in a partially sequence-specific manner. This report analyzes the theoretical limits of DNA sequence discrimination by linked polyamides composed of two to four different types of heterocyclic rings, determining (i) the optimal choice of base-binding specificity for each ring and (ii) the optimal design for a polyamide composed of these rings to target a given DNA sequence and designed to maximize the fraction of the total polyamide binding to the specified target sequence relative to all other sequences. The results show that, fortuitously, polyamides composed of pyrrole, a naturally occurring G-excluding element, and imidazole, a rationally designed G-favoring element, have features similar to the theoretical optimum design for polyamides composed of two different rings. The results also show that, in polyamides composed of two or three types of heterocyclic rings, choosing a nonspecific "placeholder" ring, which binds equally strongly to each of the four bases, along with one or two base-specific rings will often enhance sequence specificity over a polyamide composed entirely of base-specific rings.     

CD4+CD25+ T cells inhibit both the induction and effector function of autoreactive T cells and represent a unique lineage of immunoregulatory cells

Thymectomy of susceptible strains of mice on day 3 of life results in a spectrum of organ-specific autoimmunity that can be prevented by reconstitution of the thymectomized animals early in life with normal adult lymphocytes. The effectors and suppressors of autoimmunity in this model have been convincingly shown to be CD4+ T cells. It has been demonstrated recently that the regulatory CD4+ T cells that prevent disease coexpress CD25. We have further characterized the population of CD4+CD25+ immunoregulatory cells and demonstrated that they can suppress not only the induction of disease post-thymectomy, but can also efficiently suppress disease induced by cloned autoantigen-specific effector cells. Furthermore, the CD4+CD25+ T cells appear to be members of a unique lineage of regulatory T cells, as the induction of CD25 expression on a monospecific population of T cells derived from TCR transgenic SCID mice did not result in suppression of post-thymectomy autoimmunity. In addition, the TCR transgenic SCID mice were highly susceptible to autoimmune disease induced by the cloned line of autoantigen-specific effectors, while normal mice were relatively resistant. The capacity of the cloned line to transfer disease to nu/nu recipients could be inhibited by normal spleen cell populations containing CD4+CD25+ cells and by purified CD4+CD25+ cells. Although the target Ag(s) and mechanism of action of the CD4+CD25+ T cells remain to be determined, it is likely that they also play an important role in modulating other autoimmune diseases that are mediated by activation of "ignorant" self-reactive T cells present in the normal peripheral lymphocyte pool.     

Semantic influences on thematic role assignment: evidence from normals and aphasics

We report two studies that examine the role of semantic influences in the assignment of thematic roles. Semantic factors were manipulated by contrasting sentences in which one noun argument was a plausible filler of only one thematic role (e.g., the painting in The artist disliked the painting) with sentences in which both noun arguments were plausible fillers of both thematic roles (e.g., The robin ate the insect). Subjects were required to make plausibility judgments to sentences presented auditorily. Experiment 1 examined RTs of normal subjects on the plausibility judgment task. In Experiment 2, the same sentences were presented to aphasic patients identified as "asyntactic" comprehenders. In Experiment 1, RTs were speeded by semantic constraints on thematic assignment, particularly when the role-constrained NP occurred early in the sentence (as in The painting was disliked by the artist). The aphasic performance patterns in Experiment 2 paralleled those of normal subjects, but in greatly exaggerated fashion. The patients exhibited high error rates on sentences where semantic constraints conflicted with the syntactically based assignments, even on sentences with canonical (S-V-O) word order (e.g., #The deer shot the hunter).     

Gadolinia doped ceria/yttria stabilised zirconia electrolytes for solid oxide fuel cell applications

Solid oxide fuel cells are currently constructed using a yttria stabilised zirconia electrolyte membrane. However, zirconia has a number of disadvantages associated with its use, such as the high operational temperatures required for it to exhibit acceptable levels of ionic conductivity. Alternative ceramics such as doped cerium oxide show promise as electrolytes capable of operating at reduced temperatures, but introduce additional problems such as electronic conduction and inferior mechanical properties. This paper describes the manufacture and characterisation of a number of prototype electrolytes consisting of a mixture of yttria stabilised zirconia and gadolinium doped ceria. Traditional ceramic processing techniques were used to produce the samples, which were then examined using dilatometry, impedance spectroscopy and X-ray diffraction. Results show a lowering of the ionic conductivity of zirconia with the addition of doped ceria. X-ray diffraction patterns obtained from the samples suggested that this effect could be attributed to the formation of a solid solution of ceria in zirconia.     

Analysis of an anycast based overlay system for scalable service discovery and execution

Support for anycast in the IP network layer allows one source node to contact a single member out of a group of destination nodes configured with the same IP address. Due to the stateless nature of the IP protocol, subsequent packets from the same source node targeted at the same anycast group may arrive at different group members. Consequently, native IP anycast cannot be applied directly to support distributed session-based services. For this reason, an anycast overlay architecture combining the transparency offered by native anycast with support for stateful communications has been proposed. In this paper, we investigate the operational impact of deploying this overlay architecture. Performance evaluation of a data plane prototype implementation for an anycast overlay node shows that high throughput and small latency can be achieved. Additionally, we show how threshold-based update triggering, in combination with an appropriate inter-proxy update strategy, delivers control plane accuracy with minimal network overhead.     

Life sciences and cyberinfrastructure: Dual and interacting revolutions that will drive future science

Over the past quarter century, two revolutions, one in biomedicine, the other in computing and information technology leading to cyberinfrastructure, have made the largest advances and the most significant impacts on science, technology, and society. The interface between these areas is rich with opportunity for major advances. The Life Sciences Grid Research Group (LSG-RG) of the Global Grid Forum recognized the opportunities and needs to bring the communities together to ensure the cyberinfrastructure will be constructed for the benefit of science. This article gives an overview of the area, the activities of the LSG-RG, and the minisymposium organized by LSG-RG, and introduces the papers in this Special Issue of New Generation Computing. Peter Arzberger, Ph.D.: He is the Director of Life Sciences Initiatives, University of California San Diego; Director of the National Biomedical Computation Resource (http://nbcr.ucsd.edu), funded by the National Center of Research Resource of NIH; and the Chair of the Pacific Rim Application and Grid Middleware Assembly (http://www.pragma-grid.edu), an organization of 20 institutions around the pacific rim whose mission is to establish sustained collaborations and to advance the use of grid technologies in applications. He serves on the US National CODATA Committee and the National Advisory Board of the US Long Term Ecological Research. His hobby is working on Lloyds. Abbas Farazdel, Ph.D.: He is a Senior Scientist and an IT Solution Strategist in the Advanced Technologies unit at the IBM Life Sciences. Previously, Dr. Farazdel worked at several positions in IBM including Cluster System Strategist; Data Warehousing and Data Mining Solutions Implementation Manager; and High Performance Computing Consultant. Abbas is the co-chair of the Global Grid Forum (GGF) Life Sciences Grids Research Group. He serves on the Scientific Board of the European Health Grid and the Mid Hudson Technology Council of New York. Abbas received his Ph.D. in Quantum Chemistry and M.Sc. in Computational Physics from the University of Massachusetts concurrently. Akihiko Konagaya, Dr. Eng.: He is Project Director of Bioinformatics Group, RIKEN Genomic Sciences Center. He received his B.S. and M.S. from Tokyo Institute of Technology in 1978 and 1980 in Informatics Science, and joined NEC Corporation in 1980, Japan Advanced Institute of Science and Technology in 1997, RIKEN GSC in 2003. His research covers wide area from computer architectures to bioinformatics. He has been much involved into the Open Bioinformatics Grid project since 2002. Larry Ang: As the Project Director in the Bioinformatics Institute (BII), he is in charge of major international collaborative projects on biomedical grids between BII and other research organizations (http://web.bii.a-star.edu.sg/ larry/). In particular, he works actively with bodies such as Pragma where he serves on the Steering Committee. He is also the Secretary of the Life Sciences Grid Research Group of GGF (Global Grid Forum) He serves on the Gelato Federation; Gelato was started by HP Labs and pushes open source software on linux platforms. Shinji Shimojo, Ph.D.: He received his M.E. and Ph.D. degrees from Osaka University in 1983 and 1986, respectively. He was an Assistant Professor with the Department of Information and Computer Sciences, Faculty of Engineering Science at Osaka University from 1986, and an Associate Professor with Computation Center from 1991 to 1998. During the period, he also worked as a visiting researcher at the University of California, Irvine for a year. He has been a Professor with Cybermedia Center (then Computation Center) at Osaka University since 1998. His current research work is focusing on a wide variety of multimedia applications, peer-to-peer communication networks, ubiquitous network systems and Grid technologies. He is a member of ACM, IEEE and IEICE. Rick L. Stevens, Ph.D.: He is Professor, University of Chicago; director, Mathematics and Computer Science Division/Argonne National Laboratory; director, ANL/UC Computation Institute; project director for National Science Foundation supported TeraGrid project; head of the Argonne/Chicago Futures Lab. He is interested in the development of innovative tools and techniques that enable computational scientists to solve important large-scale problems effectively on advanced scientific computers. His research focuses on three principal areas: advanced collaboration and visualization environments, high-performance computer architectures (including Grids), and computational problems in life sciences and systems biology. He teaches courses on computer architecture, collaboration technology, virtual reality, parallel computing, and computational science.