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System-wide peripheral biomarker discovery using information theory

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13th Pacific Symposium on Biocomputing, PSB 2008

作者： Alterovitz, Gil Xiang, Michael Liu, Jonathan Chang, Amelia Ramoni, Marco F. Division of Health Sciences and Technology Harvard University Massachusetts Institute of Technology Cambridge MA United States Childrens Hospital Informatics Program Boston MA 02115 United States Department of Electrical Engineering and Computer Science Cambridge MA 02139 United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston 02115 United States Department of Biology Massachusetts Institute of Technology Cambridge MA 02139 United States

ISBN: (纸本)9812776087

The identification of reliable peripheral biomarkers for clinical diagnosis, patient prognosis, and biological functional studies would allow for access to biological information currently available only through invasive methods. Traditional approaches have so far considered aspects of tissues and biofluid markers independently. Here we introduce an information theoretic framework for biomarker discovery, integrating biofluid and tissue information. This allows us to identify tissue information in peripheral biofluids. We treat tissue-biofluid interactions as an information channel through functional space using 26 proteomes from 45 different sources to determine quantitatively the correspondence of each biofluid for specific tissues via relative entropy calculation of proteomes mapped onto phenotype, function, and drug space. Next, we identify candidate biofluids and biomarkers responsible for functional information transfer (p

关键词： Tissue

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Using a literature-based NMF model for discovering gene functional relationships

Using a literature-based NMF model for discovering gene func...

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IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

作者： Elina Tjioe Michael Berry Ramin Homayouni Genome Science and Technology Graduate School University of Tennessee Knoxville TN USA Department of Electrical Engineering and Computer Science University of Tennessee Knoxville TN USA Bioinformatics Program Department of Biology University of Memphis Memphis TN USA

The rapid growth of the biomedical literature and genomic information presents a major challenge for determining the functional relationships among genes. In this study, we develop a Web-based bioinformatics software environment called FAUN or feature annotation using nonnegative matrix factorization (NMF) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity and parameterization of NMF for processing gene sets are discussed. We tested FAUN on three manually constructed gene document collections, and then used it to analyze several microarray-derived gene sets obtained from studies of the developing cerebellum in normal and mutant mice. FAUN provides utilities for collaborative knowledge discovery and identification of new gene relationships from text streams and repositories (e.g., MEDLINE). It is particularly useful for the validation and analysis of gene associations suggested by microarray experimentation.

关键词： Bioinformatics Genomics Data mining Matrix decomposition Large scale integration Feature extraction Iterative methods Biological system modeling computer science Computational biology

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An information theoretic framework for genomic data analysis

An information theoretic framework for genomic data analysis

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： Aaron McKenna Gil Alterovitz Bioinformatics Program Boston University Boston MA USA Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA Children's Hospital Informatics Program Boston MA

The breadth of biological data collected in the last decade has far outstripped the methods available to process it. To effectively investigate and explore this abundance of data, novel automated collection and analysis approaches must be devised. We have developed a new open software framework, the Open Genomic Analysis Platform (OGAP), to aid in the analysis of genomic data. It is capable of analyzing a variety of data source, and focuses on using information theory to characterize data. The frameworks has is capable of import a variety of genome tied data, and provides custom analysis and visualization of results. We then demonstrate the use of this framework analyzing the Prochlorococcus Marinus organism. We show a strong correlation between the information content of sequence data and up regulation of gene expression during lytic infection.

关键词： Genomics Bioinformatics Data analysis Biological information theory Open source software Information analysis Information theory Data visualization Organisms Gene expression

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Moisture Absorption Phenomena in Green Composite Printed Circuit Board Prototypes

Moisture Absorption Phenomena in Green Composite Printed Cir...

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Pulsed Power Conference, 2005 IEEE;San Francisco,CA,USA

作者： John D. Lincoln Andrew A. Shapiro Jean-Daniel M. Saphores Oladele A. Ogunseitan Department of Chemical Engineering and Materials Science University of California Irvine CA USA Department of Electrical Engineering and Computer Science University of California Irvine CA USA Departments of Civil and Environmental Engineering Economics and Planning Policy and Design University of California Irvine CA USA Public Health Program College of Health Sciences and the Program in Industrial Ecology Department of Environmental Health Science and Policy University of California Irvine CA USA

ISBN: (纸本)9781424422722

This research developed the moisture-resistance of printed circuit board (PCB) laminate prototypes based on the non-toxic composite materials made from epoxidized linseed oil, melamine polyphosphate, and flax fibers. One of the key issues associated with using renewable base materials in composites is their sensitivity to moisture. A characterization of the properties of the 'green' printed circuit boards developed in the present study showed that moisture absorption for untreated fiber laminates (4.87% vs. established limit <0.8% for FR4 boards over a 24 hour submersion period) compromised electrical resistance and decreased dielectric breakdown to an unacceptable level. A theoretical model was used to target methods for reducing moisture absorption. Based on this model, we found that reductions in fiber diffusivity and fiber volume fraction substantially reduce composite diffusivity. Through the use of chemical treatment, moisture absorption over a 24 hour time period was reduced from 4.87% to 1.15%, which improved electrical properties. At the end of this study, 15 of 18 PCB property requirements were met, while 3 moisture-critical property targets were narrowly missed.

关键词： Printed Circuit Board Design for Environment Green Composite Moisture Absorption Natural Fiber

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Multi-bit functional NOR type SONOS memories

Multi-bit functional NOR type SONOS memories

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Device Research Conference

作者： Moonkyung Kim Chung Woo Kim Jo-won Lee S. Tiwari Department of Electrical and Computer Engineering Cornell University Ithaca NY USA Semiconductor R&D Center Memory BusinessSamsung Electronics Co. Ltd. Korea National Program for Tera-level Nano Devices Korea

We show that nearly 90 electrons can be stored at 30 nm dimensions of memory nodes, sufficient for reproducibility with having multi-bit memory windows, and that a minimum of tunneling oxide thickness is required to assure reliable retention characteristics. This work has achieved ultra-low number of electron storage while achieving high threshold shifts and demonstrates predictability through self-consistent modeling of programming and erasure characteristics.

关键词： SONOS devices Voltage MONOS devices Nonvolatile memory Carrier confinement Hafnium oxide High K dielectric materials High-K gate dielectrics Network address translation Temperature

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Nanoscale porous silicon waveguides for biosensing applications

Nanoscale porous silicon waveguides for biosensing applicati...

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IEEE Photonics Conference (IPC)

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

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.

关键词： Silicon Biosensors Optical waveguides Gratings Biomembranes Resonance DNA Biological materials Optical materials Optical surface waves

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Characterization of device degradation of poly-Si TFTS under dynamic operation with drain biased

Characterization of device degradation of poly-Si TFTS under...

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Annual International Symposium on Reliability Physics

作者： Ya-Hsiang Tai Shih-Che Huang Chang-Lung Chan Department of Photonics & Display Institute National Chiao Tung University Hsinchu Taiwan Department of Photonics & Institute of Electro-Optical Engineering National Chiao Tung University Hsinchu Taiwan College of Electrical and Computer Engineering Industrial Technology R & D Master Program on Photonics and Display Technologies National Chiao Tung University Hsinchu Taiwan

Poly-Si TFTs, which have the similar structures to the MOSFETs, are now having extensive studies for the applications in display system. The high device mobility of these devices enables the possibility to form both the in-pixel switches and integrated circuits with the poly-Si technology, which may greatly reduce the process complexity and fabrication cost. [1] Though recently several kinds of products formed with poly-Si technology had hit the market, the degradation mechanisms of the devices under dynamic operation with the drain biased are still not so clear. Y. Uraoka previously reported that the degradation behavior of the devices under gate AC operation with source/drain grounded is as a result of the swept carriers as the device is about to be turned off. [2] We have also reported that the degradation for the device operated in the off region as the source/drain grounded is because of the discharge behavior in the channel as the gate voltage toggling in the off region. [3] But these stress conditions are still far from the real operation conditions in applications. In this work, the degradation of the poly-Si TFTs under gate dynamic operation with drain biased, which would be much similar to the conditions operated in real applications, is carefully investigated.

关键词： Degradation Integrated circuit technology MOSFETs Displays Switching circuits Switches Fabrication Costs Fault location Voltage

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On a combined electrical engineering and computer Science department

On a combined electrical engineering and Computer Science De...

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114th Annual ASEE Conference and Exposition, 2007

作者： Blandford, Dick Hwang, Deborah University of Evansville United States Electrical Engineering and Computer Science Department University of Evansville United States Computer Science Program University of Evansville United States

In the United States, more than 10% of traditional electrical engineering programs have combined with computer science into a single department \Historically computer science programs emerged from mathematics or electrical engineering departments in the mid to late 1960's. Since mathematics is not typically in the engineering college many computer science programs developed independently from engineering programs. In the 1970's and early 1980's, with the advent of the microprocessor and embedded computer systems, computer engineering evolved mostly out of existing electrical engineering programs and has since become a separate discipline distinct from electrical engineering with its own accreditation process. It is common to see electrical engineering and computer engineering in the same department. computer engineering course work complements courses in computer science and in many cases there is considerable duplication. Thus, it makes sense to consider a combined electrical engineering and computer science department. At the authors' university, electrical engineering and computer science have been combined into a single department since 1990, with computer science, computer engineering, and the more traditional electrical engineering as ABET accredited programs within that department. A combined department offers the obvious advantages of administrative efficiency and elimination of duplication. There are many not-so-obvious advantages as well in the areas of program assessment, shared resources, team projects, and the new ideas and opportunities that are generated when programs are mixed. Disadvantages of a combined department have arisen as well. This paper presents the advantages and disadvantages of a combined department, details the methods used to accomplish the successful combination, and provides advice for those contemplating such a change. © American Society for engineering Education, 2007.

关键词： electrical engineering

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Interoperability frameworks for electronic governance panel discussion

Interoperability frameworks for electronic governance panel ...

引用

2nd International Conference on Theory and Practice of Electronic Governance, ICEGOV'08

作者： Cechich, Alejandra Gibbons, Jeremy Madrid, Lorenzo Kesan, Jay Departamento Cs. Computación Universidad Nacional del Comahue Buenos Aires 1400 8300 Neuquen Argentina Computing Laboratory Oxford University Wolfson Building Parks Road Oxford OX1 3QD United Kingdom Government Interoperability Engagement Program Microsoft Corporation One Microsoft Way Redmond WA 98052 United States College of Law Department of Electrical and Computer Engineering University of Illinois 504 East Pennsylvania Avenue Champaign IL 61820 United States

ISBN: (纸本)9781605583860

Today, there is a growing awareness that the interoperability of national public information and communication technology (ICT) infrastructures is a precondition for a more service-oriented and competitive public sector. Interoperability means the ability of ICT systems and of business processes they support to exchange data and to enable the sharing of information and knowledge. To help achieve interoperability, both within and across different policy areas, many countries have developed their own interoperability frameworks. However, in spite of the recommendations and guidelines provided by these frameworks, issues such as socio-economic disparities between regions challenge their effective and successful use. This panel will explore several key questions concerning success factors for an interoperability program from various perspectives, including: 1) When are organizations ready to think of running an interoperability initiative? 2) The actions the organization must take to ensure that the process is established and will endure. 3) Preconditions that must exist in the organization to implement interoperability (eventually through a framework). 4) Roles and procedures necessary to implement an interoperability program. 5) Is it possible to start an interoperability program in under-resourced administrations? Opportunities and challenges in less-developed countries. Copyright 2008 ACM.

关键词： Interoperability

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Flagellar swimming for medical micro robots: Theory, experiments and application

Flagellar swimming for medical micro robots: Theory, experim...

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IEEE/RAS-EMBS International Conference on Biomedical Robotics and Biomechatronics (BioRob)

作者： Gabor Kosa Peter Jakab Nobuhiko Hata Ferenc Jolesz Zipi Neubach Moshe Shoham Menashe Zaaroor Gabor Szekely Computer Vision Laboratory Department of Information Technology and Electrical Engineering ETH Zurich Switzerland Harvard Medical School Boston MA USA Division of MRI and Image Guided Therapy Program at Department of Radiology Brigham and Women's Hospital Boston MA USA Faculty of Mechanical Engineering Technion-Israel Institute of Technology Haifa Israel Department of Neurosurgery Rambam Medical Center Haifa Israel

Flagellar swimming is one of the swimming methods used by micro-organisms to advance in aquatic environment. The undulating motion of the flagella was successfully imitated to create propulsion for a medical swimming micro robot. The influence of a head section on the performance of such a robot is shown analytically. Swimming experiments demonstrate forward and backward swimming of a novel magnetically driven swimming tail. We intend to use the flagellar swimming tail in a three tail configuration for neurosurgical intervention in the ventricular system.

关键词： Medical robotics Tail Medical diagnostic imaging Propulsion Magnetosphere Neurosurgery Intestines computer vision Laboratories Information technology

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