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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Alterovitz, Gil Lyashenko, Eugenia Xiang, Michael Ramoni, Marco F. Division of Health Sciences and Technology Harvard Medical School Massachusetts Institute of Technology Boston MA United States Children's Hospital Informatics Program at Health Sciences and Technology Harvard Medical School Boston MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA United States Department of Biomedical Informatics Columbia University New York NY United States

ISBN: (纸本)1424415098

With the human genome sequenced, attention has been shifting to proteins and their function. Several technologies including mass spectrometry and gel electrophoresis have traditionally been used to study proteins. These technologies rely on proteins' masses to characterize and/or identify them. Once identified, the discovered proteins' are often analyzed for their functional relevance. In this paper, we present an alternative approach to studying protein function directly, based on protein mass. By analyzing proteins with similar mass ranges (bins), we discovered that certain biological functions are associated with specific mass bins more frequently than would be expected by chance. Biological functional classes found in this manner could be seen across the three examined organisms: human, worm and fly. We found no sequence-based homology across significant mass-function proteins in the three different organisms. This investigation leads to useful property that the mass-based biological functional classes are preserved across the organisms. Thus, this paper describes a potential constraint for evolution of similar function based on mass constraints. Finally, this work yields a roadmap for experimental design for functional exploration of proteomes in mass-based technologies such as gel electrophoresis and mass spectrometry. ©2007 IEEE.

关键词： Proteins

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Abstracts for the 6th Congress of Asian Sleep Research Society

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Sleep and Biological Rhythms 2009年第4期7卷 A1-A49页

作者： Seog Ju Kim In Kyoon Lyoo Yu-Jin Lee Do-Un Jeong Hirohiko Kanai Masanori Ookubo Atsushi Yoshimura Masako Okawa Noto Yamada Takeshi Munezawa Yoshitaka Kaneita Yoneatsu Osaki Hideyuki Kanda Tadahiro Ohtsu Masumi Minowa Kenji Suzuki Susumu Hijuchi Hiroyuki Suzuki Takashi Ohida Takashi Abe Yoko Komada Shoichi Asaoka Yuichi Inoue Jin-Seong Lee Sang-Yong Cho Deependra Kumar Hruda N. Mallick Velayudhan M. Kumar Mahesh K. Kaushik Akihiro Karashima Noiihiro Katayama Mitsuyuki Nakao Ravindra P. Nagendra Sathiamma Sulekha Sathyaprabha T. Narasappa Pradhan Nityanadan Bindu M. Kutty M. Nirmala P. N. Ravindra Basavaraj Ramappa Tubaki T. N. Sathyaprabha D. Sudhakar G. S. Lavekar C. R. Chandrashekar Kazuyoshi Kitaoka Mika Shimizu Sachiko Chikahisa Kazuo Yoshizaki Hiroyoshi Sei Jong-Won Kim Misa Takegami Shin Yamazaki Yasuaki Hayashino Rei Ono Koji Otani Miho Sekiguchi Shinichi Konno Shunichi Fukuhara Antonia J. Jakobson Paul Fitzgerald Russell Conduit Xin Shirley Li Siu Ping Joyce Lam Wai Man Mandy Yu Yun Kwok Wing Kazue Okamoto-Mizuno Koh Mizuno Mituaki Yamamoto Shuichiro Shirakawa Hirokazu Doi Mikako Kato Kazuyuki Shinohara Masako Tamaki Shiori Matsuda Katsuo Yamazaki Tadao Hori Keiko Ogawa Kazumi Takahashi Kunio Kitahama Katuo Yamazaki Yoshimasa Koyama Kohei Shioda Yugo Ueda Yukiko Nakamura Clara Inoue Kazushige Goto Sunao Uchida Yuko Morita Yoshiko Honda Tohru Kodama Mari Hagihara Toru Nakajima Masato Saito Yoshihiko Koga Shinichiro Tanaka Hiroshi Yamadera Madoka Takahara Sachiko Suwa Minoru Onozuka Sadao Sato Fumiharu Togo Taiki Komatsu Takeshi Mitani Jongbae Choi Bin Zhang Taeko Sasai Hiromi Mitsubayashi Mitsuhiro Ohtsu Isao Hasegawa Tatsuya Ishii Akira Komori Asami Suzuki Yue Nakahara Mitsuyasu Hiroki Mariko Nakauma Nobuo Someya Tomomasa Ochiai Shouhei Komori Rayleigh Ping-Ying Chiang Zai-Ting Yeh Seong T. Kim Seung H. Yoon Jeong S. Kwon Jong H. Choi Hyung J. Ahn Youngsoo Kim Bolortuya Yunren Lichao Chen Radhika Basheer Robert W. Mccarley Robert E. Strecker Makoto Honda Tetsuaki Arai Miyuki Fukazawa Yutaka Honda Kuniaki T Department of Psychiatry Gachon University of Medicine and Science Incheon Republic of Korea Department of Psychiatry Seoul National University Seoul Republic of Korea Department of Neuropsychiatry and Center for Sleep and Chronobiology Seoul National University Hospital Seoul Republic of Korea Department of Neuropsychiatry Seoul National University Hospital Seoul Republic of Korea Seoul National University Hospital Seoul Republic of Korea Department of Psychiatry Shiga University of Medical Science Otsu Japan Division of Public Health Department of Social Medicine Nihon University School of Medicine Tokyo Japan Department of Public Health Nihon University School of Medicine Tokyo Japan Division of Environmental and Preventive Medicine Department of Social Medicine Faculty of Medicine Tottori University Yonago Japan Department of Hygiene and Preventive Medicine Fukushima Medical University Fukushima Japan Department of Public Health Showa University School of Medicine Tokyo Japan Faculty of Humanities Seitoku University Matsudo Japan Section on Behavioral Science Division of Clinical Research National Hospital Organization Kurihama Alcoholism Center Yokosuka Japan Department of Otolaryngology Second Hospital Fujita Health University Nagoya Japan National Hospital Organization Kurihama Alcoholism Center Kanagawa Japan Metropolitan Police Department Criminal Investigation Laboratory Tokyo Japan Japan Somnology Center Neuropsychiatrie Research Institute Tokyo Japan Department of Somnology Tokyo Medical University Tokyo Japan Japan Somnology Center Neuropsychiatric Research Institute Tokyo Japan Department of Somnology Tokyo Medical and Dental University Tokyo Japan Center for Sleep and Chronobiology Department of Psychiatry and Behavioral Science Seoul National University College of Medicine Seoul Republic of Korea Department of Psychiatry and Behavioral Science Center for Sleep and Chronobiology Seoul Republic of Korea Department of Physiology Al

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Decision Fusion of Circulating Markers for Breast Cancer Detection in Premenopausal Women

Decision Fusion of Circulating Markers for Breast Cancer Det...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： Jonathan L. Jesneck Sayan Mukherjee Loren W. Nolte Anna E. Lokshin Jeffrey R. Marks Joseph Lo Duke Advanced Imaging Labs Institute for Genome Sciences and Policy Department of Computer Science Duke University USA Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh PA USA Division of Hematology/Oncology University of Pittsburgh Cancer Institute Pittsburgh PA USA Division of Hematology/Oncology University of Pittsburgh Cancer Institute Pittsburgh PA Institute for Genome Sciences and Policy Department of Experimental Surgery Medical Center Duke University USA Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC USA

Current mammographic screening for breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions.

关键词： Breast cancer Cancer detection Lesions Proteins Support vector machines Support vector machine classification Mammography Testing Blood Linear regression

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An Information Theoretic Framework for Ontology-based Bioinformatics

An Information Theoretic Framework for Ontology-based Bioinf...

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Information Theory and Applications Workshop, ITA

作者： Gil Alterovitz Michael Xiang Marco F. Ramoni Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Biology Massachusetts Institute of Technology Cambridge MA USA Division of Health Sciences and Technology Harvard Medical School and Massachusetts Institute of Technology Boston MA Children's Hospital Informatics Program Boston MA Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA.

With myriad information being generated from high-throughput experiments such as microarrays and sequencing technologies, an ever-increasing amount of data is being recorded and analyzed with the help of hierarchical ontologies, such as the gene ontology (GO). We have developed a novel framework- based on the well established foundations of information theory- that allows for the evaluation of new types of hypotheses. The framework, encapsulated in open biomedical ontology-based exploration and search (OBOES), has already been applied in the investigation of different kinds of questions. The resulting framework enables the new field of information theoretic ontology-based analysis. We have applied this framework to create methods to re-engineer ontologies, explore fundamental questions on the evolution of biological complexity, determine optimal ontology terms for bioinformatics analysis, and quantify the usefulness of biofluids as proxies for tissues/diseases. In each case, we found that our methods provide novel, significant findings. An open source Java implementation of OBOES is available at: http://***.

关键词： Ontologies Bioinformatics Genomics Information analysis Biological information theory Information theory Genetic communication Humans Biochemistry Frequency

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Workshop on imaging science development for cancer prevention and preemption

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Cancer Biomarkers 2007年第1期3卷 1-33页

作者： Kelloff, Gary J. Sullivan, Daniel C. Baker, Houston Clarke, Lawrence P. Nordstrom, Robert Tatum, James L. Dorfman, Gary S. Jacobs, Paula Berg, Christine D. Pomper, Martin G. Birrer, Michael J. Tempero, Margaret Higley, Howard R. Petty, Brenda Gumbs Sigman, Caroline C. Maley, Carlo Sharma, Prateek Wax, Adam Ginsberg, Gregory G. Dannenberg, Andrew J. Hawk, Ernest T. Messing, Edward M. Grossman, H. Barton Harisinghani, Mukesh Bigio, Irving J. Griebel, Donna Henson, Donald E. Fabian, Carol J. Ferrara, Katherine Fantini, Sergio Schnall, Mitchell D. Zujewski, Jo Anne Hayes, Wendy Klein, Eric A. DeMarzo, Angelo Ocak, Iclal Ketterling, Jeffrey A. Tempany, Clare Shtern, Faina Parnes, Howard L. Gomez, Jorge Srivastava, Sudhir Szabo, Eva Lam, Stephen Seibel, Eric J. Massion, Pierre McLennan, Geoffrey Cleary, Kevin Suh, Robert Burt, Randall W. Pfeiffer, Ruth M. Hoffman, John M. Roy, Hemant K. Wang, Thomas Limburg, Paul J. El-Deiry, Wafik S. Papadimitrakopoulou, Vali Hittelman, Walter N. MacAulay, Calum Veltri, Robert W. Solomonzz, Diane Jeronimo, Jose Richards-Kortum, Rebecca Johnson, Karen A. Viner, Jaye L. Stratton, Steven P. Rajadhyaksha, Milind Dhawan, Atam NIH/NCI/DCTD Cancer Imaging Program Bethesda MD United States NIH/NCI/DCTD Cancer Imaging Program NCI-Frederick Frederick MD United States NIH/NCI/DCP Early Detection Research Group Bethesda MD United States The Johns Hopkins University School of Medicine Departments of Radiology Pharmacology and Oncology Division of Neuroradiology Baltimore MD United States NIH/NCI/CCR Cell and Cancer Biology Branch Bethesda MD United States University of California San Francisco Department of Medicine Division of Medical Oncology San Francisco CA United States CCS Associates Inc. Mountain View CA United States Wistar Institute Molecular and Cellular Oncogenesis Program Philadelphia PA United States University of Kansas School of Medicine VA Hospital Kansas City MO United States Duke University Department of Biomedical Engineering Medical Physics Program Durham NC United States University of Pennsylvania School of Medicine Department of Gastroenterology Philadelphia PA United States New York Presbyterian Hospital Weill Medical College of Cornell University New York NY United States NIH/NCI/OD Office of Centers for Training and Resources Bethesda MD United States University of Rochester Medical Center Department of Urology Rochester NY United States University of Texas MD Anderson Cancer Center Department of Urology Houston TX United States Massachusetts General Hospital Abdominal Imaging/Interventional Radiology Boston MA United States Boston University Biomedical Engineering Electrical and Computer Engineering and Physics Boston MA United States NIH/NCI/DCP Gastrointestinal and Other Cancers Research Group Bethesda MD United States The George Washington University Cancer Institute Office of Cancer Prevention and Control Washington DC United States University of Kansas Cancer Center Clinical Oncology Kansas City KS United States University of California Davis Department of Biomedical Engineering Davis CA United States Tufts University De

The article provides information on a workshop on the development of imaging systems for cancer prevention and preemption convened by the U.S. National Cancer Institute (NCI) Cancer Imaging program held in Gaithersburg, Maryland. Doctor Katherine Ferrara of the University of California discussed the function of ultrasound in breast tumor imaging. Ways to close the gap between development and application of imaging approaches were tackled in a roundtable discussion on cervix and skin cancer.

关键词： FORUMS (Discussion & debate) IMAGING systems in medicine CANCER prevention

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Good Stability of Protocrystalline Silicon Multilayer Solar Cells Against Light Irradiation Originating from Vertically Regular Distribution of Isolated Nano-Sized Silicon Grains

Good Stability of Protocrystalline Silicon Multilayer Solar ...

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World Conference on Photovoltaic Energy Conversion

作者： Seung Yeop Myong Seong Won Kwon Joong Hwan Kwak Koeng Su Lim Joshua M. Pearce Makoto Konagai Division of Electrical Engineering Department of Electrical Engineering & Computer Science KAIST Daejeon South Korea Physics Department Clarion University of Pennsylvania Clarion PA USA Department of Physical Electronics TIT Tokyo Japan

ISBN: (纸本)1424400163

Photoluminescence and Fourier transform infrared spectra measured at room temperature, and transmission electron microscopy micrographs produce strong evidence that nano-sized silicon grains are embedded in alternately hydrogen-diluted protocrystalline silicon multilayers. We suggest that the vertically regular distribution of isolated nano-sized silicon grains caused by the repeatedly layered structure, as well as the improved structural order in the a-Si:H matrix reduces "slow" metastable defects, resulting in a fast light-induced stabilization with a low degradation

关键词： Silicon Stability Nonhomogeneous media Photovoltaic cells Temperature measurement Photoluminescence Fourier transforms Infrared spectra Transmission electron microscopy Metastasis

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Disorder induced bands in first order Raman spectra of carbon nanowalls

Disorder induced bands in first order Raman spectra of carbo...

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2006 6th IEEE Conference on Nanotechnology, IEEE-NANO 2006

作者： Wang, Haomin Wu, Yihong Choong, Catherine Kai Shin Zhang, Jun Teo, Kie Leong Ni, Zhenhua Shen, Zexiang Department of Electrical and Computer Engineering National University of Singapore 4 Engineering Drive 3 Singapore 117576 Singapore Data Storage Institute 5 Engineering Drive 1 Singapore 117608 Singapore Department of Physics National University of Singapore 2 Science Drive 3 Singapore 117542 Singapore Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University 1 Nanyang Walk Block 5 Singapore 637616 Singapore

ISBN: (纸本)1424400783

Raman spectra of carbon nanowalls grown by microwave plasma enhanced chemical vapor deposition were analyzed. A typical Raman spectrum of carbon nanowalls exhibits three main bands, i.e., the G, D and D' bands centered at about 1580, 1350 and 1620 cm-1, respectively. The peak intensity ratio of D to G band (ID/IG) was found to be strongly influenced by edge length density of carbon nanowalls, suggesting that the strong D band is originated from the defects at the edges. The addition of water during the growth process increased the defects formed by water assisted oxidization which in turn, resulted in the increase of the D band's relative intensity. © 2006 IEEE.

关键词： Walls (structural partitions)

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ISHM implementation for Constellation Systems

ISHM implementation for Constellation Systems

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AIAA/ASME/SAE/ASEE 42nd Joint Propulsion Conference

作者： Figueroa, Fernando Holland, Randy Schmalzel, John Duncavage, Dan Crocker, Alan Alena, Rick NASA Stennis Space Center Stennis Space Center MS 39529 Rowan University Dept. of Electrical and Computer Engineering Glassboro NJ 08028 NASA Johnson Space Center Houston TX 77058 NASA Ames Research Center Moffett Field CA 94035 Science and Technology Division EA41 Stennis Space Center MS 39529 AIAA Department of Electrical and Computer Engineering Rowan University Glassboro NJ 08028 International Space Station Program OD NASA Johnson Space Center Houston TX 77058 Systems Division Mission Operations Directorate DF NASA Johnson Space Center Houston TX 77058 Intelligent Systems Division MS 269-4 Moffett Field CA 94035

ISBN: (纸本)1563478188

This paper addresses methodic implementation of a credible ISHM capability for elements of Constellation Systems. ISHM capability must be implemented by a combination of on-board and ground elements, each contributing to determining the health of systems in the most effective manner. Implementation of ISHM capability must evolve continuously to reach higher and higher levels of functional capability. The implication is that a sustainable approach must be defined in order to accomplish a believable capability. This paper describes the methodology, the elements, and the technology to implement ISHM capability throughout the life cycle of elements of Constellation Systems, reaching beyond individual elements that might have a limited life while the constellation moves on.

关键词： Spacecraft propulsion

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Biological network epitomes via topological compression

Biological network epitomes via topological compression

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IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Gil Alterovitz Marco F. Ramon Health Science and Technology/Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology / Harvard Medical School- Partners Center for Genetics and Genomics Boston 02115 USA.

High-throughput generation of new types of relational biological datasets is creating a demand for network-based signal processing and pattern recognition to provide new insights. Such networks are often too large to interpret visually and too complicated to be explained solely based on local topological properties. Just as signal processing and statistical techniques have been used in traditional, sequential-based biological datasets, so too are methodologies needed to automatically discern patterns in the huge, emerging networks. One way to do this is by transforming these very large networks into discernable epitomes, or abstracts, of the original networks. This work presents an approach for doing this via topological compression. Through capturing nodes' global topologies and subsequent compression, a new network epitome can be derived. Here, this is done with an E. Coli gene regulation network, resulting in biological findings that could not be derived from the local topology of the original network.

关键词： Biological information theory Network topology Genomics Bioinformatics Biomedical signal processing Compression algorithms Visualization Biology Gas insulated transmission lines Computer science

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Gene lethality detection across biological network domains: Hubs versus stochastic global topological analysis

Gene lethality detection across biological network domains: ...

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IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Gil Alterovitz Vinayak Muralidhar Marco F. Ramoni Health Science and Technology/Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA Harvard Medical School-Partners Center for Genetics and Genomics Boston USA Harvard-MIT Division of Health Sciences and Technology Children's Hospital Informatics Program Boston USA

In this paper, we investigate the properties of lethal genes in E. coli, our model organism. Topological analysis of networks of functional interactions among genes has shown that lethal genes share common local connectivity properties. In this paper, we analyze cellular networks across three domains. We show that a stochastic global topological analysis, via random walks, is more effective at predicting gene lethality than simply looking at local topology using the standard hub-based method. We also introduce the possibility of using metabolic pathways to understand lethal genes, as regulating these pathways is among one of the most important functions of the gene-encoded proteins. Additionally, we analyze lethal genes in terms of the Gene Ontology (GO) and find that the graph forms two highly connected clusters that are each GO enriched for specific terms. We also find that lethal metabolic regulators are extremely enriched. Finally, we provide applications of the work and avenues for future research.

关键词： Stochastic processes Proteins Organisms Humans Genomics Bioinformatics Databases Genetics Network topology Production

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