Module-based multiscale simulation of angiogenesis in skeletal muscle

<p>Abstract</p> <p>Background</p> <p>Mathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem.</p> <p>Results</p> <p>We present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis.</p> <p>Conclusions</p> <p>This systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions.</p

Research in the Language, Information and Computation Laboratory of the University of Pennsylvania

This report takes its name from the Computational Linguistics Feedback Forum (CLiFF), an informal discussion group for students and faculty. However the scope of the research covered in this report is broader than the title might suggest; this is the yearly report of the LINC Lab, the Language, Information and Computation Laboratory of the University of Pennsylvania. It may at first be hard to see the threads that bind together the work presented here, work by faculty, graduate students and postdocs in the Computer Science and Linguistics Departments, and the Institute for Research in Cognitive Science. It includes prototypical Natural Language fields such as: Combinatorial Categorial Grammars, Tree Adjoining Grammars, syntactic parsing and the syntax-semantics interface; but it extends to statistical methods, plan inference, instruction understanding, intonation, causal reasoning, free word order languages, geometric reasoning, medical informatics, connectionism, and language acquisition. Naturally, this introduction cannot spell out all the connections between these abstracts; we invite you to explore them on your own. In fact, with this issue it’s easier than ever to do so: this document is accessible on the “information superhighway”. Just call up http://www.cis.upenn.edu/~cliff-group/94/cliffnotes.html In addition, you can find many of the papers referenced in the CLiFF Notes on the net. Most can be obtained by following links from the authors’ abstracts in the web version of this report. The abstracts describe the researchers’ many areas of investigation, explain their shared concerns, and present some interesting work in Cognitive Science. We hope its new online format makes the CLiFF Notes a more useful and interesting guide to Computational Linguistics activity at Penn

Cooperative agents for enhancing learner practice

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal

Proceedings of the 2004 ONR Decision-Support Workshop Series: Interoperability

In August of 1998 the Collaborative Agent Design Research Center (CADRC) of the California Polytechnic State University in San Luis Obispo (Cal Poly), approached Dr. Phillip Abraham of the Office of Naval Research (ONR) with the proposal for an annual workshop focusing on emerging concepts in decision-support systems for military applications. The proposal was considered timely by the ONR Logistics Program Office for at least two reasons. First, rapid advances in information systems technology over the past decade had produced distributed collaborative computer-assistance capabilities with profound potential for providing meaningful support to military decision makers. Indeed, some systems based on these new capabilities such as the Integrated Marine Multi-Agent Command and Control System (IMMACCS) and the Integrated Computerized Deployment System (ICODES) had already reached the field-testing and final product stages, respectively. Second, over the past two decades the US Navy and Marine Corps had been increasingly challenged by missions demanding the rapid deployment of forces into hostile or devastate dterritories with minimum or non-existent indigenous support capabilities. Under these conditions Marine Corps forces had to rely mostly, if not entirely, on sea-based support and sustainment operations. Particularly today, operational strategies such as Operational Maneuver From The Sea (OMFTS) and Sea To Objective Maneuver (STOM) are very much in need of intelligent, near real-time and adaptive decision-support tools to assist military commanders and their staff under conditions of rapid change and overwhelming data loads. In the light of these developments the Logistics Program Office of ONR considered it timely to provide an annual forum for the interchange of ideas, needs and concepts that would address the decision-support requirements and opportunities in combined Navy and Marine Corps sea-based warfare and humanitarian relief operations. The first ONR Workshop was held April 20-22, 1999 at the Embassy Suites Hotel in San Luis Obispo, California. It focused on advances in technology with particular emphasis on an emerging family of powerful computer-based tools, and concluded that the most able members of this family of tools appear to be computer-based agents that are capable of communicating within a virtual environment of the real world. From 2001 onward the venue of the Workshop moved from the West Coast to Washington, and in 2003 the sponsorship was taken over by ONR’s Littoral Combat/Power Projection (FNC) Program Office (Program Manager: Mr. Barry Blumenthal). Themes and keynote speakers of past Workshops have included: 1999: ‘Collaborative Decision Making Tools’ Vadm Jerry Tuttle (USN Ret.); LtGen Paul Van Riper (USMC Ret.);Radm Leland Kollmorgen (USN Ret.); and, Dr. Gary Klein (KleinAssociates) 2000: ‘The Human-Computer Partnership in Decision-Support’ Dr. Ronald DeMarco (Associate Technical Director, ONR); Radm CharlesMunns; Col Robert Schmidle; and, Col Ray Cole (USMC Ret.) 2001: ‘Continuing the Revolution in Military Affairs’ Mr. Andrew Marshall (Director, Office of Net Assessment, OSD); and,Radm Jay M. Cohen (Chief of Naval Research, ONR) 2002: ‘Transformation ... ’ Vadm Jerry Tuttle (USN Ret.); and, Steve Cooper (CIO, Office ofHomeland Security) 2003: ‘Developing the New Infostructure’ Richard P. Lee (Assistant Deputy Under Secretary, OSD); and, MichaelO’Neil (Boeing) 2004: ‘Interoperability’ MajGen Bradley M. Lott (USMC), Deputy Commanding General, Marine Corps Combat Development Command; Donald Diggs, Director, C2 Policy, OASD (NII

Personalized Service Creation and Provision for the Mobile Web

The convergence of telecom networks and the Internet is fostering the emergence of environments where Web services are available to mobile users. The variability in computing resources, display terminal, and communication channel require intelligent support on personalized delivery of relevant data and services to mobile users. Personalized service provisioning presents several research challenges on context information management, service creation, and inherent limitations of mobile devices. In this chapter, we describe a novel framework that supports weaving context information and services for personalized service creation and execution. By leveraging technologies on Web services, agents, and publish/subscribe systems, our framework enables an effective, user-centric access of integrated services over the mobile Web environments. This chapter overviews the design, architecture, and implementation of the framework

Abstract Representation of Music: A Type-Based Knowledge Representation Framework

The wholesale efficacy of computer-based music research is contingent on the sharing and reuse of information and analysis methods amongst researchers across the constituent disciplines. However, computer systems for the analysis and manipulation of musical data are generally not interoperable. Knowledge representation has been extensively used in the domain of music to harness the benefits of formal conceptual modelling combined with logic based automated inference. However, the available knowledge representation languages lack sufficient logical expressivity to support sophisticated musicological concepts. In this thesis we present a type-based framework for abstract representation of musical knowledge. The core of the framework is a multiple-hierarchical information model called a constituent structure, which accommodates diverse kinds of musical information. The framework includes a specification logic for expressing formal descriptions of the components of the representation. We give a formal specification for the framework in the Calculus of Inductive Constructions, an expressive logical language which lends itself to the abstract specification of data types and information structures. We give an implementation of our framework using Semantic Web ontologies and JavaScript. The ontologies capture the core structural aspects of the representation, while the JavaScript tools implement the functionality of the abstract specification. We describe how our framework supports three music analysis tasks: pattern search and discovery, paradigmatic analysis and hierarchical set-class analysis, detailing how constituent structures are used to represent both the input and output of these analyses including sophisticated structural annotations. We present a simple demonstrator application, built with the JavaScript tools, which performs simple analysis and visualisation of linked data documents structured by the ontologies. We conclude with a summary of the contributions of the thesis and a discussion of the type-based approach to knowledge representation, as well as a number of avenues for future work in this area