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A Systems Biology Approach to Identify Affected Regulatory and Signaling Circuits in Protein Interaction Networks

A Systems Biology Approach to Identify Affected Regulatory a...

引用

International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS

作者： Ting Gong Jianhua Xuan Rebecca B. Reggins Robert Clarke Department of Electrical and Computer Engineering Virginia Polytechnic Institute and State University Arlington VA USA Department of Oncology and Physiology & Biophysics Georgetown University Medical Center Washington D.C. DC USA

Microarray technology and high-throughput proteomics have revolutionized cancer biology by generating vast amount of data for various cancers. To gain insights into the biological processes that drive breast cancer recurrence, we integrate gene expression profiles of breast cancer and protein interaction networks in search for affected regulatory and signaling networks statistically associated with endocrine resistance. To perform this integration systematically, we introduce a systems biology approach to screen related protein-protein interaction networks for active cliques, i.e., connected regions of the network that show significant changes in expression between recurrent and non-recurrent tumors. The experimental results from two breast cancer data sets show that the identified sub-networks can be effectively used to stratify patients treated with endocrine into groups with different outcomes. More importantly, the sub-networks can further help us gain mechanistic insights into estrogen action and endocrine resistance.

关键词： Systems biology Signal processing Circuits Proteins Breast cancer Endocrine system Immune system Proteomics Biological processes Gene expression

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Time-varying Control Laws with Guaranteed Persistence for a Class of Multi-Species Chemostats

Time-varying Control Laws with Guaranteed Persistence for a ...

引用

Joint 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference

作者： Frédéric Mazenc Zhong-Ping Jiang the EPI MERE INRIA-INRA UMR Analyse des Systèmes et Biométrie Department of Electrical and Computer Engineering Polytechnic Institute of New York UniversitySix Metrotech Center

We study classical families of chemostat models with an arbitrary number of species competing for a single limiting *** families of models, we present some obstructions to the existence of asymptotically stabilizable periodic *** other families of growth rates, we design a dilution rate and input substrate time-varying feedback controllers so that a positive trajectory of the chemostat model becomes globally asymptotically *** way, the control laws ensure persistence of all the species.A local version of this result is given in the case where only the substrate concentration is available by measurement.

关键词： Time-varying Control Laws with Guaranteed Persistence for a Class of Multi-Species Chemostats

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Multi-static synthetic aperture radar image formation

Multi-static synthetic aperture radar image formation

引用

IEEE International Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP)

作者： V. P. Krishnan J. Swoboda C. E. Yarman B. Yazici Department of Electrical Systems and Computer Engineering Rensselaer Polytechnic Institute Troy NY USA MITRE Corporation Bedford MA USA Houston Technology Center WesternGeco-Schlumberger Houston TX USA

ISBN: (纸本)9781424451791;9781424451807

In this paper, we consider a multi-static synthetic aperture radar (SAR) imaging scenario where a swarm of airborne antennas, some of which are transmitting, receiving or both, are traversing arbitrary flight trajectories and transmitting arbitrary waveforms without any form of multiplexing. The received signal at each receiving antenna may be interfered by the scattered signals from multiple transmitters and the additive thermal noise at the receiver. Standard bi-static SAR image reconstruction algorithms result in artifacts in reconstructed images due to these interferences. In this paper, we employ microlocal analysis in a statistical setting to develop a novel filtered-backprojection (FBP) type analytic image formation method that suppresses artifacts due to interference from multiple transmitters while preserving the location and orientation of edges of the scene in the reconstructed image.

关键词： Image reconstruction Receiving antennas Transmitting antennas Transmitters Additive noise Image analysis Synthetic aperture radar Aperture antennas Radar antennas Radar scattering

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Coverage tracking of a moving target by a group of mobile agents

Coverage tracking of a moving target by a group of mobile ag...

引用

Asian Control Conference

作者： Xiaoli Wang Yiguang Hong Zhong-Ping Jiang Key Laboratory of Systems and Control Institute of Systems Science Chinese Academy and Sciences Beijing China Department of Electrical and Computer Engineering Polytechnic Institute of New York University Brooklyn NY USA

In this paper, we consider finite-time tracking problems of a moving target by multiple mobile agents. The mobile agents with global sensing areas and limited actuation region are designed to track down a target with estimation error with the help of formation and coverage. In order to capture the target, its location and velocity are first estimated. With observer-based estimation and formation control, the group of agents can catch the target by a coverage tracking policy in finite time.

关键词： Target tracking Mobile agents Robot sensing systems Robot kinematics State estimation Estimation error Control systems Power system reliability Power system modeling Collaboration

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Shrinking Neighborhood Evolution--a novel stochastic algorithm for numerical optimization

Shrinking Neighborhood Evolution--a novel stochastic algorit...

引用

Congress on Evolutionary Computation

作者： Dongcai Su Junwei Dong Zuduo Zheng School of Communications Jilin University Changchun Jilin China Bradley Department of Electrical & Computer Engineering Virginia Polytechnic Institute and State University VA USA Department of Civil & Environmental Engineering Hohai University and Arizona State University Tempe AZ USA

In this paper we develop and test a novel stochastic algorithm SNE (Shrinking Neighborhood Evolution) based on the issue of bound constrained optimization problem. Its heuristic strategy is simple and direct-related to the search region of the solving problem based on the concept of ldquok-box-neighborhoodrdquo -defined in this paper. Our numerical experiments show that the optimization capability of SNE is competing to other congeneric algorithms such as Particle Swarm Optimizer (PSO), Evolution Strategy with Covariance Matrix Adaptation (CMA-ES) and Differential Evolution (DE). The new method requires few control parameters, easy to use, and has promising potentials to parallel computation.

关键词： Stochastic processes Ant colony optimization Evolution (biology) Particle swarm optimization Constraint optimization Testing Covariance matrix Genetic algorithms Genetic programming Genetic engineering

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Telemedicine applications of mobile ultrasound

Telemedicine applications of mobile ultrasound

引用

IEEE Workshop on Multimedia Signal Processing

作者： Peder C. Pedersen Brett W. Dickson Jacob Chakareski Department of Electrical and Computer Engineering Worcester Polytechnic Institute Worcester MA USA Signal Processing Laboratory-LTS4 Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland

This work evaluates the feasibility of real-time wireless video streaming of medical ultrasound signals over 802.11g ad-hoc and 3G cellular broadband networks for disaster relief, rescue, and medical transport applications. Scalable H.264 encoded echocardiographic ultrasound image sequences were transmitted in real-time at specified image resolutions (VGA and QVGA) and frame rates (10, 15, 20, and 30 frames per second). Relevant transmission parameters such as data rate, packet loss, delay jitter, and latency were measured. The 802.11g network permits high frame rate, VGA resolution, has low latency and jitter, but is suitable only for short communication ranges, while the 3G cellular broadband network allows medium to low frame rate streaming at QVGA image resolution with medium latency. However, video streaming can take place from any location with 3G service to any other site with Internet connectivity. Physicians with expertise in medical ultrasound subsequently rated the diagnostic content of the transmitted videos relative to the original ultrasound video signals. The physicians observed that the image quality in the case of both 802.11g and 3G wireless transmission was fully to adequately preserved, while missed frames could momentarily decrease the diagnostic value. This research demonstrates that sufficient wireless bandwidth and efficient video compression make diagnostically valuable wireless streaming of ultrasound video feasible.

关键词： Telemedicine Ultrasonic imaging Streaming media Delay Video compression Biomedical imaging Medical diagnostic imaging Image resolution Cellular networks Broadband communication

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A new model-based estimation of ellipses for object representation

A new model-based estimation of ellipses for object represen...

引用

Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Jun Kong Kim L. Boyer Joel H. Saltz Kun Huang Center of Comprehensive Informatics Emory University Atlanta GA USA Department of Electrical Computer and Systems Engineering Rensselaer Polytechnic Institute Troy NY USA Department of Biomedical Informatics Ohio State Uinversity Columbus OH USA

Fitting geometric models to objects of interest in images is one of the most classical problems studied in computer vision field. As a result of its strong representation power and flexibility, conic is one of the geometric primitives widely used in a large number of image analysis applications, in practice. As opposed to most existing conic fitting methods minimizing the fitting error with the use of the second order polynomial representation, in this paper, we propose a new method that formulates the geometric fitting problem as a process of seeking for the optimal mapping to a bivariate normal distribution model. As a result, some critical disadvantages tightly coupled with those methods following the routine polynomial representation can be well overcome. To demonstrate this, a set of carefully designed comparison experiments is conducted to show the superiority of the newly proposed method to a representative method using the polynomial representation. Additionally, the practical effectiveness of the proposed method is further manifested using a set of real image data with a promising accuracy.

关键词： Muscles Physiology Electromyography Microscopy Neuromuscular Low pass filters Musculoskeletal system Predictive models Filtering Joints

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System frequency monitoring in the Nigerian power system

System frequency monitoring in the Nigerian power system

引用

IEEE General Meeting Power& Energy Society

作者： Luigi Vanfretti Usman Aliyu Joe H. Chow James A. Momoh Department of Electrical Computer and Systems Engineering Rensselaer Polytechnic Institute Troy NY USA Abubakar Tafawa Balewa University Bauchi Nigeria Howard University College of Medicine Washington D.C. DC USA

Frequency is one of the most important measures of the state of a power system, especially for structurally weak and rapidly growing power systems. Thus, frequency monitoring is a desirable practice to ensure reliability and provide data for analysis. This paper reports the joint work between Abubakar Tafawa Balewa University (ATBU) and Rensselaer polytechnic Institute (RPI) to study frequency dynamics of a relative small power system. We describe the frequency disturbance recorder (FDR) implementation experience at ATBU, Bauchi, Nigeria, and present analysis on the digital recordings obtained by the FDR. A proposal for a university-based frequency monitoring network for the Nigerian power system is also presented. Such monitoring system will allow further investigations on the Nigerian system and ultimately enhance the understanding of the dynamics and control of structurally weak and rapidly growing power systems found in many developing countries.

关键词： Monitoring Power systems Power system dynamics Power system analysis computing Power system reliability Power system measurements Power measurement Frequency measurement Data analysis Economic indicators

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Reports of the AAAI 2009 spring symposia

Reports of the AAAI 2009 spring symposia

引用

作者： Bao, Jie Bojars, Uldis Choudhury, Tanzeem Ding, Li Greaves, Mark Kapoor, Ashish Louchart, Sandy Mehta, Manish Nebel, Bernhard Nirenburg, Sergei Oates, Tim Roberts, David L. Sanfilippo, Antonio Stojanovic, Nenad Stubbs, Kristen Thomaz, Andrea L. Tsui, Katherine Woelfl, Stefan Tetherless World Constellation Rensselaer Polytechnic Institute United States Social Software Unit of DERI Galway Ireland Computer Science Department Dartmouth College United States Knowledge Systems at Vulcan Inc United States Adaptive Systems and Interaction Group Microsoft Research Redmond United States School for Mathematics and Computer Sciences Heriot-Watt University United Kingdom School ot Interactive Computing Georgia Institute of Technology United States Department of Computer Science University of Freiburg Germany Computer Science and Electrical Engineering Department University of Maryland Baltimore County United States Pacific Northwest National Laboratory Richland WA United States University of Karlsruhe Germany IRobot Corporation United States University of Massachusetts Lowell United States

The Association for the Advancement of Artificial Intelligence, in cooperation with Stanford University's department of computer Science, was pleased to present the 2009 Spring Symposium Series, held Monday through Wednesday, March 23-25, 2009, at Stanford University. The titles of the nine symposia were Agents That Learn from Human Teachers, Benchmarking of Qualitative Spatial and Temporal Reasoning Systems, Experimental Design for Real- World Systems, Human Behavior Modeling, Intelligent Event Processing, Intelligent Narrative Technologies II, Learning by Reading and Learning to Read, Social Semantic Web: Where Web 2.0 Meets Web 3.0, and Technosocial Predictive Analytics. The goal of the Agents That Learn from Human Teachers symposium was to investigate how we can enable software and robotics agents to leam from real-time interaction with an everyday human partner. The aim of the Benchmarking of Qualitative Spatial and Temporal Reasoning Systems symposium was to initiate the development of a problem repository in the field of qualitative spatial and temporal reasoning and identify a graded set of challenges for future midterm and long-term research. The Experimental Design symposium discussed the challenges of evaluating AI systems. The Human Behavior Modeling symposium explored reasoning methods for understanding various aspects of human behavior, especially in the context of designing intelligent systems that interact with humans. The Intelligent Event Processing symposium discussed the need for more Al-based approaches in event pro-cessing and defined a kind of research agenda for the field, coined as intelligent complex event processing (iCEP). The Intelligent Narrative Technologies IIAAAI symposium discussed innovations, progress, and novel techniques in the research domain. The Learning by Reading and Learning to Read symposium explored two aspects of making natural language texts semantically accessible to, and processable by, machines. The Social Semantic

关键词： Benchmarking

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Further Results on Lyapunov-Krasovskii Functionals via Nonlinear Small-Gain Conditions for Interconnected Retarded iISS Systems

Further Results on Lyapunov-Krasovskii Functionals via Nonli...

引用

2009 American Control Conference (ACC 2009)

作者： Hiroshi Ito Pierdomenico Pepe Zhong-Ping Jiang Department of Systems Design and Informatics Kyushu Institute of Technology 680-4 Kawazu Iizuka Fukuoka 820-8502 Japan Department of Electrical and Information Engineering University of L'Aquila 67040 Poggio di Roio L'Aquila Italy Department of Electrical and Computer Engineering Polytechnic Institute of New York University Six Metrotech Center Brooklyn NY 11201 USA

ISBN: (纸本)9781424445233

This paper presents further results on the problem of establishing stability of retarded nonlinear interconnected systems comprising integral input-to-state stable subsystems. It is shown that the stability of the interconnected systems with respect to external signals can be verified by constructing Lyapunov-Krasovskii functionals explicitly whenever small-gain type conditions are satisfied. The primary result [12] is generalized in two aspects. One is to introduce a new flexibility in constructing Lyapunov-Krasovskii functionals to deal with distributed delays more effectively. The other is to cover systems involving time-varying delays in interconnecting channels.

关键词： Interconnected systems Stability Control systems Indium tin oxide Delay systems Nonlinear systems Nonlinear control systems Delay effects Time varying systems Networked control systems

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