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10th Pacific Symposium on Biocomputing, PSB 2005

作者： Li, Xiang Liang, Jie Graduate Program in Bioinformatics SEO University of Illinois 851 S. Morgan Street Chicago IL United States Department of Bioengineering SEO University of Illinois 851 S. Morgan Street Chicago IL United States

ISBN: (纸本)9812560467

Screening phage-displayed combinatorial peptide library is an effective approach for discovery of peptide modulators for protein-protein interactions. However, as peptide length increases, the chance of finding active peptides in a finite size library diminishes. To increase the likelihood of finding peptides that bind to a protein, we develop statistical potential for computational construction of biased combinatorial antibody-like peptide libraries. Based on the alpha shapes of antibody- antigen complexes, we developed an empirical pair potential for antigen-antibody interactions that depends on local packing. We validate this potential and show that it can successfully discriminate the native interface peptides from a simulated library of 10,000 random peptides for 34 antigen-antibody complexes. In addition, we show that it can successfully recognize the native binding surface patch among all possible surface patches taken from either the antibody or the antigen for seven antibody-antigen protein complexes contained in the CAPRI (Critical Assessment of Predicted Interactions) dataset. We then develop a Weighted Amino Acid Residue sequence Generator (WAARG) for design of biased peptide library. When compared with a random peptide library, WAARG libraries contain more native-like binding peptides at a significantly smaller size. Our method can be used to construct peptide library for screening of antibody variants with improved specificity and affinity to a target antigen. It can also be used for screening of antibody-like antagonist peptides modulating other protein-protein interactions.

关键词： Peptides

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Biomimetic in silico devices

Biomimetic in silico devices

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International Conference on Computational Methods in Systems Biology, CMSB 2004

作者： Hunt, C. Anthony Ropella, Glen E. P. Roberts, Michael S. Yan, Li Dept. of Biopharmaceutical Sciences Biosystems Group University of California San Francisco CA 94143-0446 United States Department of Medicine University of Queensland Princess Alexandra Hospital Woolloongabba Q 4102 Australia Joint UCSF UC Berkeley Bioengineering Graduate Program

ISBN: (纸本)3540253750

We introduce biomimetic in silico devices, and means for validation along with methods for testing and refining them. The devices are constructed from adaptable software components designed to map logically to biological components at multiple levels of resolution. In this report we focus on the liver;the goal is to validate components that mimic features of the lobule (the hepatic primary functional unit) and dynamic aspects of liver behavior, structure, and function. An assembly of lobule-mimetic devices represents an in silico liver. We validate against outflow profiles for sucrose administered as a bolus to isolated, perfused rat livers. Acceptable in silico profiles are experimentally indistinguishable from those of the in situ referent. This new technology is intended to provide powerful new tools for challenging our understanding of how biological functional units function in vivo. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Biomimetic materials

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Multi-electrode Arrays (MEAs) with guided network for cell-to-cell communication transduction

Multi-electrode Arrays (MEAs) with guided network for cell-t...

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IEEE International Electron Devices Meeting, 2005 IEDM

作者： Wang, Yijin Yeung, Chi-Kong Ingebrandt, Sven Offenhaeusser, Andreas Chan, Mansun Bioengineering Graduate Program Hong Kong University of Science and Technology Hong Kong Hong Kong Leo-Brandt Str. 52425 Juelich Germany Dept. of Electrical and Electronic Engineering Hong Kong University of Science and Technology Hong Kong Hong Kong

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ISBN: (纸本)078039268X

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Wireless hearing aid system simulations using advanced design system™: A behavioral modeling approach

Wireless hearing aid system simulations using advanced desig...

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2005 27th Annual International Conference of the Engineering in Medicine and Biology Society, IEEE-EMBS 2005

作者： Rana, Ram Singh Tang, Bin Zhang, Liang Krishna, Garg Hari Wang, Yun Institute of Microelectronics Singapore Science Park II 11 Science Park Road Singapore 117685 Singapore Graduate Program in Bioengineering National University of Singapore Singapore 117597 Singapore Department of Electrical and Computer Engineering National University of Singapore Singapore 119260 Singapore Department of Otolaryngology Faculty of Medicine National University of Singapore Singapore 119074 Singapore

ISBN: (纸本)0780387406

The stringent requirements on size and power consumption constrain the conventional hearing aid devices from providing the patients an economic and user friendly solution, specifically for better noise cancellation. With the advancements in technologies such as integrated circuits design, wireless communications and digital signal processing techniques, the wireless hearing aids having multi-microphones, analog, digital and mixed signals and radio frequency signals processing circuits, DSP and programmable units seem to be promising to provide enhanced performance. The focus of this paper is about the system simulation of a typical wireless hearing aid using Agilent Advanced Design System™. The behavioral modeling features are exploited to enable the whole system simulations including electro-acoustic transducers. A few system level simulation results are included. © 2005 IEEE.

关键词： Hearing aids

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Wireless Hearing Aids System Simulation

Wireless Hearing Aids System Simulation

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Asilomar Conference on Signals, Systems & Computers

作者： H.K. Garg Tang Bin Zhang Liang R.S. Rana Department of Electrical & Computer Engineering National University of Singapore Singapore 11 Science Park Road Institute of Microelectronics Singapore Graduate Program in Bioengineering National University of Singapore Singapore

Although wireless hearing aid systems have been proposed by several research groups, no viable whole-system simulation results have been reported so far for better evaluation of this advanced hearing device. In this paper, a system-level simulation using ADStrade is presented based on one of the typical wireless hearing aid architecture. The results show that the wireless hearing aid system function can be simulated and verified. And from these results, we can get a very promising performance which can be used for further design

关键词： Hearing aids Auditory system Circuit simulation Radio frequency Noise cancellation Mathematical model Costs RF signals Signal processing Computational modeling

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Large-scale parametric study of electroporation in cancer cells to construct phase diagrams using micro cellarray chips

Large-scale parametric study of electroporation in cancer ce...

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9th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2005

作者： He, Huiqi Chang, Donald C. Lee, Yi-Kuen Bioengineering Graduate Program Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Dept. of Biology Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Dept. of Mechanical Engineering Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong

ISBN: (纸本)0974361119

In this study, a new micro electroporation cell chip was fabricated by MEMS technology and tested by using cervical cancer (HeLa) cells. Large statistical data of the critical voltage and duration time were determined to construct the "phase diagram" which delineating the boundary for effective electroporation and electric cell lysis at the single-cell level. Copyright © 2005 by the Transducer Research Foundation, Inc.

关键词： Cancer cells

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A "bio-basics" short course: Bringing modern biology to an engineering faculty

A "bio-basics" short course: Bringing modern biology to an e...

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2005 ASEE Annual Conference and Exposition: The Changing Landscape of Engineering and Technology Education in a Global World

作者： Sweeney, James D. Joshi, Lokesh Panitch, Alyssa Hall, Edward Harrington Department of Bioengineering Arizona State University Tempe AZ United States Office of Engineering Research Services I.A. Fulton School of Engineering Arizona State University Tempe AZ United States Biodesign Institute Arizona State University Tempe AZ United States Flinn Foundation Multi- and Interdisciplinary Graduate Training Program in Bioengineering ASU United States Center for Protein and Peptide Therapeutics Biodesign Institute ASU United States Biodesign Institute's Center for Protein and Peptide Therapeutics United States

The objectives, design, implementation, as well as initial and ongoing assessment and evaluation of the Bio-Basics faculty short course are described. Course content was chosen on the assumption that participants would have little or no latest exposure to basic concepts and knowledge in modern biology. It was found that this short courses has been highly successful for those faculty members who dedicated themselves to regular participation. Long-term tracking of course participant productivity in biological or biomedical research areas and/or involving latest collaborations with life scientists has been initiated with the expectation that participants will in the long-term be better positioned for success in such efforts.

关键词： Curricula

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Cover Picture: Protein-Detecting Microarrays: Current Accomplishments and Requirements (ChemBioChem 5/2005)

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ChemBioChem 2005年第5期6卷 769-769页

作者： Kin-ya Tomizaki Dr. Kenji Usui Hisakazu Mihara Prof. Department of Bioengineering and The COE21 Program Graduate School of Bioscience and Biotechnology Tokyo Institute of Technology B-40 4259 Nagatsuta Midori Yokohama 226–8501 Japan Fax: (+81) 45-924-5833

The cover picture shows an emerging protein-detecting microarray technology that has the potential to uncover complex protein networks in a miniaturized and parallelized fashion. The microarray system comprises capture agents, such as antibodies, recombinant proteins, and peptides immobilized onto solid surfaces, and provides a large number of important parameters on molecular interactions in a single experiment. The system is supported by three independent but strongly correlated basic technologies that involve screening/production of capture agents, engineering of surface modification methodologies of solid supports, and development of detection methods. Although the system is currently in progress, it could be employed conveniently as a diagnostic/research tool in the near future. Further information on the current accomplishments and requirements of the technology can be found in the Review by Mihara and co-workers on p. 782 ff.

关键词： analytical methods arrays capture agents proteins surface chemistry

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Applicability of oxidation reduction potential response on a full-scale intermittently aerated suspended culture system

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Practice Periodical of Hazardous, Toxic, and Radioactive Waste Management 2004年第1期8卷 19-25页

作者： Shimabukuro, Melissa Yang, Ping-Yi Kim, Sun-Jip Graduate Program in Bioengineering Dept. of Molec. Biosciences/Bioeng. Univ. of Hawaii at Manoa Honolulu HI 96822 United States

On-line monitoring of oxidation reduction potential (ORP) was conducted at the full-scale aeration basin operated with intermittent aeration schedules and fed with the wastewater generated from fruit fly rearing facility owned by the California Department of Food and Agriculture, Waimanalo, Hawaii. The characteristics of the wastewater were fluctuated, severely. The 90 percentile level of total chemical oxygen demand, total Kjeldahl nitrogen, and total suspended solids for the wastewater are 5,200, 142, and 3,350 mg/L, respectively. Two aeration schedules of 4 h aeration/2 h nonaeration and 3 h aeration/3 h nonaeration were investigated in this study. Typical ORP curve with bending points of β (beginning of denitrification), X (disappearance of nitrate), and plateau (dORP/dt = 0) were observed for both aeration schedules. The α (end of nitrification) value couldn't detect in the aeration schedule of 3 h aeration/3 h nonaeration because of the ORP fluctuation at the onset of aeration. However, the α value detected without any difficulty for the aeration schedule of 4 h aeration/2 h nonaeration. This is due to the relatively lower gradient of the reduced substance concentration between supernatant and settled sludge layers during the air-off period. Through the ORP monitoring of the full-scale aeration basin treating fruit fly rearing facility wastewater, the aeration time can be reduced from 4 h to 3 h without deterioration of organic and nitrogen removal efficiencies. By reducing the aeration time, 25% of energy cost for aeration can be saved. From the result of real time monitoring of ORP response and water quality analysis of nitrogen, the behaviors of nitrogen forms are closely related to the ORP response. Therefore, the ORP monitoring is a practical and easy tool for the evaluation of the degree of nitrification and denitrification condition in biological wastewater-treatment systems.

关键词： Waste management

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Integrating entrapped mixed microbial cell (EMMC) technology for treatment of wastewater containing dimethyl sulfoxide (DMSO) for reuse in semiconductor industries

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Clean Technologies and Environmental Policy 2003年第1期6卷 43-50页

作者： Yang, P. Y. Myint, Tin Tin Graduate Program in Bioengineering Department of Molecular Biosciences and Bioengineering University of Hawaii at Manoa Honolulu USA

Solvents containing dimethyl sulfoxide (DMSO) are widely used in the rinse process of stripping photoresistors in semiconductor manufacturing industries. The disposal/reuse of wastewater containing DMSO is a serious problem because of its high concentration of organic carbon and the need to suppress the odor from its sulfur contents. An entrapped mixed microbial cell (EMMC) process was used to investigate the effectiveness of removing DMSO from a synthetic wastewater in a once-through up-flow fixed-bed bioreactor. Both cellulose triacetate and cellulose acetate were used to prepare the EMMC carriers. Various hydraulic retention times (HRTs) (based on the void volume) of 3, 4, 5, 6, and 12 h were investigated when the concentration of DMSO was 500 mg/l and 1,000 mg/l. It was found that the addition of 50 mg/l of sucrose was needed to serve as the carbon source for possible co-metabolism of DMSO. Based on the result of the impact of various dilution rates (1/HRT) on the TOC (total organic carbon) removal efficiency and TOC remaining, a dilute curve for this relationship was plotted. Thus, an optimal operational criterion was developed, i.e., it must be operated at a dilution rate of less than 0.15 h−1 or at an HRT of higher than 6.66 h, in order to achieve more than 95% of TOC (or more than 99% of DMSO) removal efficiency when using the cellulose triacetate as the EMMC carriers. This process performance was compared to the bio-contact filter (BCF) process conducted in Japan. It was found that the present study is capable of producing much less effluent nitrogen (including NH4-N and NO3-N) content than the BCF process under similar loading conditions. It is possible that integrating the unit process of EMMC as pretreatment with microfiltration (MF) and reversed osmosis (RO) processes is promising for the reuse and recycling of semiconductor wastewater. Thus, higher quality (less organic carbon and inorganic nitrogen content) pretreated wat

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