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Geometric optimization methods for the analysis of gene expression data

Geometric optimization methods for the analysis of gene expr...

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作者： Journée, Michel Teschendorff, Andrew E. Absil, Pierre-Antoine Tavaré, Simon Sepulchre, Rodolphe Department of Electrical Engineering and Computer Science University of Liège Belgium Breast Cancer Functional Genomics Program Cancer Research UK Cambridge Research Institute University of Cambridge Robinson Way Cambridge CB2 0RE United Kingdom Department of Mathematical Engineering Université catholique de Louvain Belgium

ISBN: (纸本)9783540737490

DNA microarrays provide such a huge amount of data that unsupervised methods are required to reduce the dimension of the data set and to extract meaningful biological information. This work shows that Independent Component Analysis (ICA) is a promising approach for the analysis of genome-wide transcriptomic data. The paper first presents an overview of the most popular algorithms to perform ICA. These algorithms are then applied on a microarray breast-cancer data set. Some issues about the application of ICA and the evaluation of biological relevance of the results are discussed. This study indicates that ICA significantly outperforms Principal Component Analysis (PCA).

关键词： Independent component analysis

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Label free detection of PCR amplification

Label free detection of PCR amplification

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2008 IEEE Sensors, SENSORS 2008

作者： Liu, Yi-Shao Banada, Padmapriya P. Bhunia, Arun K. Bashir, Rashid Micro and Nanotechnology Laboratory United States Department of Electrical and Computer Engineering Department of Bioengineering University of Illinois at Urbana-Champaign Urbana IL 61801 United States Molecular Microbiology Laboratory and Department of Food Science Purdue University West Lafayette IN 47907 United States Center for infectious diseases Department of Medicine New Jersey Medical school Newark NJ 07130 United States

ISBN: (纸本)9781424425808

In this paper, we present a method for the label-free detection of PCR products using impedance spectroscopy. Instead of using conventional optical detection instruments, our method provides a direct detection of amplified target genes in PCR. As a proof of concept, identification of a target bacterium in a mixture of microorganisms is demonstrated. © 2008 IEEE.

关键词： Polymerase chain reaction

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Accelerating advanced MRI reconstructions on GPUs 08

Accelerating advanced MRI reconstructions on GPUs

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2008 Conference on Computing Frontiers, CF'08

作者： Stone, Sam S. Haldar, Justin P. Tsao, Stephanie C. Hwu, Wen-Mei W. Liang, Zhi-Pei Sutton, Bradley P. Center for Reliable and High-Performance Computing University of Illinois at Urbana-Champaign Urbana IL United States Department of Electrical and Computer Engineering University of Illinois at Urbana-Champaign Urbana IL United States Bioengineering Department Biomedical Imaging Center Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana IL United States

ISBN: (纸本)9781605580777

Computational acceleration on graphics processing units (GPUs) can make advanced magnetic resonance imaging (MRI) reconstruction algorithms attractive in clinical settings, thereby improving the quality of MR images across a broad spectrum of applications. At present, MR imaging is often limited by high noise levels, significant imaging artifacts, and/or long data acquisition (scan) times. Advanced image reconstruction algorithms can mitigate these limitations and improve image quality by simultaneously operating on scan data acquired with arbitrary trajectories and incorporating additional information such as anatomical constraints. However, the improvements in image quality come at the expense of a considerable increase in computation. This paper describes the acceleration of an advanced reconstruction algorithm on NVIDIA's Quadro FX 5600. Optimizations such as register allocating the voxel data, tiling the scan data, and storing the scan data in the Quadro's constant memory dramatically reduce the reconstruction's required bandwidth to off-chip memory. The Quadro's special functional units provide substantial acceleration of the trigonometric computations in the algorithm's inner loops, and experimentally-tuned code transformations increase the reconstruction's performance by an additional 20%. The reconstruction of a 3D image with 1283 voxels ultimately achieves 150 GFLOPS and requires less than two minutes on the Quadro, while reconstruction on a quadcore CPU is thirteen times slower. Furthermore, relative to the true image, the error exhibited by the advanced reconstruction is only 12%, while conventional reconstruction techniques incur error of 42%. In short, the acceleration afforded by the GPU greatly increases the appeal of the advanced reconstruction for clinical MRI applications. Copyright 2008 ACM.

关键词： Magnetic resonance imaging

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The Third International Conference on human-robot interaction

The Third International Conference on human-robot interactio...

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作者： Fong, Terry Dautenhahn, Kerstin Scheutz, Matthias Demiris, Yiannis Intelligent Robotics Group NASA Ames Research Center Department of Artificial Intelligence School of Computer Science University of Herfordshire Herfordshire United Kingdom Adaptive Systems Research Group University of Herfordshire Herfordshire United Kingdom Department of Cognitive Science Computer Science and Informatics Cognitive Science Program Indiana University Bloomington IN United States Intelligent Robotics Team Department of Electrical Engineering Imperial College London London United Kingdom

The third international conference on Human-Robot Interaction (HRI-2008) was held in Amsterdam, The Netherlands, March 12-15, 2008. The theme of HRI-2008, "living with robots," highlights the importance of the technical and social issues underlying human-robot interaction with companion and assistive robots for long-term use in everyday life and work activities. More than 250 researchers, practitioners, and exhibitors attended the conference, and many more contributed to the conference as authors or reviewers. HRI-2009 will be held in San Diego, California, from March 11-13, 2009. Copyright © 2008, Association for the Advancement of Artificial Intelligence. All rights reserved.

关键词： Human robot interaction

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Gate-length and drain-bias dependence of band-to-band tunneling-induced drain leakage in irradiated fully depleted SOI devices

Gate-length and drain-bias dependence of band-to-band tunnel...

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作者： Mamouni, Farah E. Dixit, Sriram K. Schrimpf, Ronald D. Adell, Philippe C. Esqueda, Ivan S. McLain, Michael L. Barnaby, Hugh J. Cristoloveanu, Sorin Xiong, Weize Electrical Engineering and Computer Science Department Vanderbilt University Nashville TN 37232 United States Interdisciplinary Materials Science Program Vanderbilt University Nashville TN 37235 United States Jet Propulsion Laboratory Pasadena CA 91109 United States Department of Electrical Engineering Arizona State University Tempe AZ 85287 United States IMEP-INP Grenoble MINATEC 38016 Grenoble France Texas Instruments Inc. Dallas TX 75808 United States

The effects of gate length and drain bias on the off-state drain leakage current of irradiated fully-depleted SOI $n$-channel MOSFETs are reported. The experimental results are interpreted using a model based on the combined effects of band-to-band tunneling (BBT) and the trapped charge in the buried oxide. For negative gate-source voltages, the drain leakage current increases with the drain voltage because the electric field in the gate-to-drain overlap region is increasing. The off-state current in these devices increases with total ionizing dose due to oxide trapped charge build up in the buried oxide, enhanced by the BBT mechanism. The experimental data show that these effects are more significant for devices with shorter gate-lengths. Simulation results suggest that the BBT-generated holes are more likely to drift all the way from the drain to the source in shorter devices, enhancing the drain leakage current, while they tend to tunnel across the gate oxide in longer devices. © 2006 IEEE.

关键词： MOSFET devices

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Spike-based acoustic signal processing chips for detection and localization

Spike-based acoustic signal processing chips for detection a...

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IEEE Biomedical Circuits and Systems (BIOCAS)

作者： Hisham Abdalla Timothy K. Horiuchi Electrical and Computer Engineering Department Institute for Systems Research University of Maryland College Park MD USA Electrical and Computer Engineering Department Institute for Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

Voltage spikes are ubiquitous in biological nervous systems. How spikes can be used to encode signals, facilitate communication, and implement important computations is an important question of contemporary neuroscience. Acoustic processing tasks provide a rich range of applications for this encoding scheme. As a summary of the Ph.D. research of the first author, we present two analog VLSI spike-based example systems that process acoustic information using spikes: a model of the neural signal processing involved in bat echolocation, and a low-power, time-domain acoustic periodicity detector.

关键词： Acoustic signal processing Acoustic signal detection Voltage Biological information theory Nervous system Biology computing Pervasive computing Neuroscience Acoustic applications Encoding

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K-space and image space combination for motion artifact correction in multicoil multishot diffusion weighted imaging

K-space and image space combination for motion artifact corr...

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

作者： Anh T. Van Dimitrios C. Karampinos John G. Georgiadis Bradley P. Sutton Electrical and Computer Engineering Department University of Illinois Urbana-Champaign Urbana IL USA Department of Mechanical Science and Engineering and the Beckman Institute University of Illinois Urbana-Champaign IL USA Bioengineering Department the Electrical Engineering Department and the Beckman Institute University of Illinois Urbana IL USA

Motion during diffusion encodings leads to phase errors in different shots of a multishot acquisition. Phase differences in k-space data among shots result in phase cancellation artifacts in the reconstructed image. Due to aliasing of the phase from under-sampled regions of the shot, correction of the phase error using direct low-resolution phase subtraction is incomplete. We introduce a new k-space and image-space combination (KICT) method for motion artifacts cancellation that avoids incomplete phase error correction. Further, the method preserves the phase of the object, which is important for parallel imaging applications.

关键词： Image reconstruction Motion artifacts Imaging Trajectory Image resolution Image coding Encoding

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Novel Mems-based technology for measuring the mechanical properties of a live biological cell

Novel Mems-based technology for measuring the mechanical pro...

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11th International Congress and Exhibition on Experimental and Applied Mechanics 2008

作者： Gneriich, Markus Zhang, Wenyue Donahue, Henry Voloshin, Arkady Tatic-Lucic, Svetlana Sherman Fairchild Center Department of Electrical and Computer Engineering Lehigh University Bethlehem PA 18015 United States Pennsylvania State University College of Medicine Hershey PA United States Bioengineering Program Lehigh University Bethlehem PA 18015 United States Department of Mechanical Engineering and Mechanics Lehigh University 16A Memorial Drive East Bethlehem PA 18015 United States Lehigh University Bethlehem PA 10815 United States

ISBN: (纸本)9781605604152

This paper presents an experimental platform for measuring the mechanical properties of live biological cells. The polymer-based MEMS device integrates a V-shaped electrothermal actuator (ETA) array, a force sensor, a displacement sensor, a thermal sensor, and a cell-positioning system in a single chip. The integrated cell-positioning system based on dielectrophoresis precisely places a cell to a designed spot, the MEMS ETA array provides a predefined deformation to the cell, the force and displacement sensors measure the magnitude of the force applied to the cell and the corresponding cell deformation, and the thermal sensor monitors temperature in the liquid cell medium environment during the experiment. This MEMS device was able to compress a NIH3T3 fibroblast cell and cause 25% mechanical strain. © 2008 Society for Experimental Mechanics Inc.

关键词： Electrophoresis

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Nanoscale porous silicon waveguides for biosensing applications

Nanoscale porous silicon waveguides for biosensing applicati...

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21st Annual Meeting of the IEEE Lasers and Electro-Optics Society, LEOS 2008

作者： Rong, G. Wei, X. Kang, C. Liscidini, M. Sipe, J.E. Mernaugh, R.L. Weiss, S.M. Department of Electrical Engineering and Computer Science Vanderbilt University Nashville TN 37235 United States Interdisciplinary Graduate Program in Materials Science Vanderbilt University Nashville TN 37235 United States Department of Physics Institute for Optical Sciences University of Toronto Toronto ON M5S 1A7 Canada Department of Biochemistry Vanderbilt University Nashville TN 37235 United States

Nanoscale porous silicon waveguides, both on silicon substrates and free-standing membranes, are explored for biosensing applications. Measured detection limits in the nanomolar range are reported for DNA sensing. ... 详细信息

ISBN: (纸本)9781424419326

关键词： Porous silicon

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Binaural Spectral Cues for Ultrasonic Localization

Binaural Spectral Cues for Ultrasonic Localization

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2008 IEEE International Symposium on Circuits and Systems (ISCAS 2008), vol.6

作者： Hisham Abdalla Timothy K Horiuchi Electrical and Computer Engineering Department Institute for systems research University of Maryland College Park MD USA Electrical and Computer Engineering dept Insitute for Systems Research Neuroscience and Cognitive Science Program University of Maryland College Park MD USA

To support our ongoing work in modeling bat echolocation, an artificial bat head was designed and fabricated using a 3D printer, an ultrasonic cochlea-like filter bank with 16 channels was designed with moderate quality (Q) factor, and 128 spiking neurons convert these signals to spike trains. A two-dimensional address-event arbiter is used to transmit these spikes off of the chip. We demonstrate that the population of spiking neurons can be decoded to estimate azimuth and elevation of ultrasonic chirps. This chip was fabricated in a commercially-available 0.5(mu)m CMOS process and consumes approximately 36(mu)W.

关键词： Hafnium

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