308 research outputs found
Supporting security-oriented, collaborative nanoCMOS electronics research
No full textGrid technologies support collaborative e-Research typified by multiple institutions and resources seamlessly shared to tackle common research problems. The rules for collaboration and resource sharing are commonly achieved through establishment and management of virtual organizations (VOs) where policies on access and usage of resources by collaborators are defined and enforced by sites involved in the collaboration. The expression and enforcement of these rules is made through access control systems where roles/privileges are defined and associated with individuals as digitally signed attribute certificates which collaborating sites then use to authorize access to resources. Key to this approach is that the roles are assigned to the right individuals in the VO; the attribute certificates are only presented to the appropriate resources in the VO; it is transparent to the end user researchers, and finally that it is manageable for resource providers and administrators in the collaboration. In this paper, we present a security model and implementation improving the overall usability and security of resources used in Grid-based e-Research collaborations through exploitation of the Internet2 Shibboleth technology. This is explored in the context of a major new security focused project at the National e-Science Centre (NeSC) at the University of Glasgow in the nanoCMOS electronics domain
A hybrid numerical techniques for the solution of a class of implicit matrix differential equation
No full texthis paper is concerned with the numerical solution of an implicit matrix differential system of the form (YY)-Y-T - F(t, Y) = 0, where Y(t) is a n x n real matrix which may converge to a singular matrix. We propose a hybrid numerical technique based on an implicit second order Runge Kutta scheme which derives a particular algebraic Riccati equation and via its solution approximates the solutions of the differential problem at hand. Numerical examples demonstrating the behavior of the proposed approach are also reported
Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission
No full textInferring disease transmission networks is important in epidemiology in order to understand and prevent the spread of infectious diseases. Reconstruction of the infection transmission networks requires insight into viral genome data as well as social interactions. For the HIV-1 epidemic, current research either uses genetic information of patients' virus to infer the past infection events or uses statistics of sexual interactions to model the network structure of viral spreading. Methods for a reliable reconstruction of HIV-1 transmission dynamics, taking into account both molecular and societal data are still lacking. The aim of this study is to combine information from both genetic and epidemiological scales to characterize and analyse a transmission network of the HIV-1 epidemic in central Italy.We introduce a novel filter-reduction method to build a network of HIV infected patients based on their social and treatment information. The network is then combined with a genetic network, to infer a hypothetical infection transmission network. We apply this method to a cohort study of HIV-1 infected patients in central Italy and find that patients who are highly connected in the network have longer untreated infection periods. We also find that the network structures for homosexual males and heterosexual populations are heterogeneous, consisting of a majority of 'peripheral nodes' that have only a few sexual interactions and a minority of 'hub nodes' that have many sexual interactions. Inferring HIV-1 transmission networks using this novel combined approach reveals remarkable correlations between high out-degree individuals and longer untreated infection periods. These findings signify the importance of early treatment and support the potential benefit of wide population screening, management of early diagnoses and anticipated antiretroviral treatment to prevent viral transmission and spread. The approach presented here for reconstructing HIV-1 transmission networks can have important repercussions in the design of intervention strategies for disease control
Runtime Verification of Scientific Codes Using Statistics
No full textAbstractRuntime verification of large-scale scientific codes is difficult because they often involve thousands of processes, and generate very large data structures. Further, the programs often embody complex algorithms making them difficult for non-experts to follow. Notably, typical scientific codes implement mathematical models that often possess predictable statistical features. Therefore, incorporating statistical analysis techniques in the verification process allows using program's state to reveal unusual details of the computation at runtime. In our earlier work, we proposed a statistical framework for debugging large-scale applications. In this paper, we argue that such framework can be useful in the runtime verification process of scientific codes. We demonstrate how two production simulation programs are verified using statistics. The system is evaluated on a 20,000-core Cray XE6
HIV Reservoirs and Immune Surveillance Evasion Cause the Failure of Structured Treatment Interruptions: A Computational Study
No full textContinuous antiretroviral therapy is currently the most effective way to treat HIV infection. Unstructured interruptions are quite common due to side effects and toxicity, among others, and cannot be prevented. Several attempts to structure these interruptions failed due to an increased morbidity compared to continuous treatment. The cause of this failure is poorly understood and often attributed to drug resistance. Here we show that structured treatment interruptions would fail regardless of the emergence of drug resistance. Our computational model of the HIV infection dynamics in lymphoid tissue inside lymph nodes, demonstrates that HIV reservoirs and evasion from immune surveillance themselves are sufficient to cause the failure of structured interruptions. We validate our model with data from a clinical trial and show that it is possible to optimize the schedule of interruptions to perform as well as the continuous treatment in the absence of drug resistance. Our methodology enables studying the problem of treatment optimization without having impact on human beings. We anticipate that it is feasible to steer new clinical trials using computational models
Using a (higher-order) Magnus method to solve the Sturm-Liouville problem
No full textThe main purpose of this paper is to describe techniques for the numerical solution of a Sturm-Liouville equation (in its Schrodinger form) by employing a Magnus expansion. With a suitable method to approximate the highly oscillatory integrals which appear in the Magnus series, high order schemes can be constructed. A method of order ten is presented. Even when the solution is highly-oscillatory, the scheme can accurately integrate the problem using stepsizes typically much larger than the solution "wavelength". This makes the method well suited to be applied in a shooting process to locate the eigenvalues of a boundary value problem
Automatic generation of virtual computer rooms on the Internet using X3D
No full text7th International Conference on Computational Science (ICCS 2007) -- MAY 27-30, 2007 -- Beijing, PEOPLES R CHINAIn this paper, some natural links between virtual reality and interactive 3D computer graphics are specified and Web3D technologies especially VRML and X3D are briefly introduced. Web-based tool which is called EasyLab3D was designed and implemented using X3D. This web-based tool is used to generate automatically 3D virtual computer rooms that can be navigated in. It is important for introduction of departments, companies and organizations which have computer laboratories and for planning new computer rooms. As a result, state-of-the art technologies and methods in development of automatic 3D scene and model generation tools are discussed.Chinese Acad Sci, Res Ctr Data Technol & Knowledge Econ, AMID, Springer, World Sci Publishing, Univ Nebraska, CAS, Grad Univ, Chinese Acad Sci, Inst Policy & Management, Univ Amsterda
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