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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis (vol 69, pg 298, 2007)

CHEMICAL BIOLOGY & DRUG DESIGN 2007年第6期69卷 455-455页

作者： Chellappan, S. Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville MD 20850 USA Chemical Biology Program Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA Biological Engineering Division Department of Electrical Engineering & Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA

There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first prospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild‐type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors.

关键词： AIDS crystal drug design inhibitor protease

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Delivering Context-aware Learning Guidance in the Mobile Learning Environment based on Information Theory

Delivering Context-aware Learning Guidance in the Mobile Lea...

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International Conference on Advanced Learning Technologies (ICALT)

作者： Rita Kuo Min-Chang Wu Alex Chang Maiga Chang Jia-Sheng Heh Department of Electronic Engineer Chung Yuan Christian University Taiwan Department of Information and Computer Engineering Chung Yuan Christian University Taiwan Program Office of National Science and Technology Program for Learning in Taiwan Taiwan

Mobile Learning makes students get the advantages of both traditional learning and e-learning. How to give students learning sequence suggestions in the mobile learning environment is a big issue and is also the goal of this paper. This research uses knowledge map to store the characteristics of each learning object and designs a situated map to represent spatial knowledge in the mobile learning environment. By using these two knowledge structures, knowledge map and situated map, the system created by this research can generate various navigation sentences and ask students to observe the characteristics of learning objects. This research also takes information theory into consideration in order to decide which navigation sentence should deliver to the student first. The system calculates the entropy for each generated sentence and finds the most appropriate one to deliver to the student. At the end of this paper, an experiment system is implemented for the 5th year biology course, Plant Observation.

关键词： Information theory Navigation Electronic learning Mobile computing Knowledge representation Humans Cognition Personal digital assistants US Department of Transportation Sequences

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New Insights in the Modification of the Work Function of Cathode Materials due to Thin Surface Coatings using Ab-initio Modelling

New Insights in the Modification of the Work Function of Cat...

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International Conference on Vacuum Electronics

作者： Vasilios Vlahos Dane D. Morgan John H. Booske University of Wisconsin Madison Madison WI USA 1415 Engineering Dr. Madison WI Department of Materials Science and Engineering University of Wisconsin Madison Madison WI USA Department of Materials Science and Engineering Department of Electrical and Computer Engineering University of Wisconsin-Madison Madison USA Interdisciplinary Materials Science Program

The changes in the work function upon adsorption of coating layers on materials utilized in both field and thermionic emission applications have been investigated computationally within the framework of Density Functional Theory (DFT) [1] as implemented by the Vienna Ab-initio Simulation Package (VASP) [2]. This approach provides valuable information for understanding the origin of the improvement in the emitted current density by monitoring changes in the electronic structure of a material system upon adsorption of surface species. The presence of surface coatings induces changes in the charge density in the surface and sub-surface regions of the substrate, significantly influencing the value of the work function. The origin of the enhanced emission properties of Cesium-Iodide (Csl) coated Carbon-based field emission cathodes [3] as well as Barium-Oxide (Ba-O) Tungsten thermionic cathode systems has been investigated. The former is a promising cathode material system capable of operating under low global electric fields, demonstrating operation lifetimes in excess of one million pulses, and characterized by good shot-to-shot-reproducibility, low levels of outgassing, and no evident plasma formation upon appropriate conditioning.

关键词： Cathodes Coatings Thermionic emission Density functional theory Computational modeling Electronic packaging thermal management Current density Monitoring Tungsten Plasma applications

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Contributors to the Lab on a Chip cell and tissue engineering in microsystems special issue

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Lab on a Chip 2007年第6期7卷 667-671页

作者： Bhatia, Sangeeta N. Chen, Christoper Bashir, Rashid Beebe, David J. Desai, Tejal Gottwald, Eric Khademhosseini, Ali Langer, Robert S. Piel, Matthieu Takayama, Shuichi Thorsen, Todd Tien, Joe Voldman, Joel Vunjak-Novakovic, Gordana Wu, Mingming Yu, Hanry Massachusetts Institute of Technology Harvard-MIT Division of Health Sciences and Technology Department of Electrical Engineering and Computer Science United States Laboratory for Multiscale Regenerative Technologies United States Department of Innovation University of Pennsylvania Department of Bioengineering United States Cell Biology and Physiology Program Cell Growth and Cancer Program Tissue Microfabrication Laboratory Department of Electrical and Computer Engineering and Biomedical Engineering Purdue University United States Department of Electronics University of Glasgow United Kingdom Department of Physiology and Bioengineering University of California San Francisco CA United States California Institute for Quantitative Biomedical Research UCSF/UC Berkeley Graduate Group in Bioengineering United States Laboratory of Therapeutic Micro and Nanotechnology Institute for Biological Interfaces Germany 3D-Cell Culture Techniques Group Institute for Biological Interfaces Germany Department of Medicine and Health Sciences and Technology Massachusetts Institute of Technology (MIT) United States Institut Curie UMR 144 IC/CNRS France Biomedical Engineering Department University of Michigan United States Department of Biomedical Engineering Macromolecular Science and Engineering Program United States Sibley School of Mechanical and Aerospace Engineering School of Chemical and Molecular Engineering Cornell University United States National University of Singapore Singapore Institute of Bioengineering and Nanotechnology A STAR Singapore

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A Method to Realize Controlled Air/Liquid Interfaces and Interfacial Polymer Micro Membranes in Microfluidic Channels

A Method to Realize Controlled Air/Liquid Interfaces and Int...

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IEEE SENSORS

作者： Daming Cheng YoungJoon Paul Choe Hongrui Jiang Department of Electrical and Computer Engineering University of Wisconsin Madison Madison USA Department of Electrical and Computer Engineering University of Wisconsin Madison Madison WI USA Materials Science Program University of Wisconsin-Madison USA Department of Electrical and Computer Engineering University of Wisconsin-Madison Madison WI. Email: hongrui@engr.wisc.edu

In this study, stable air/liquid interfaces and high-aspect ratio polymer micro membranes with complex and controlled structures were formed within microfluidic channels. The air/liquid interfaces were formed at hydrophilic/hydrophobic boundaries defined by patterned and alkanethiols treated Cu surfaces. The two-phase interfaces were further utilized for interfacial polymerization with two immiscible liquid phases containing the reagents for polymer membrane in the microchannel, to generate polymer micro membranes with not only complex in-plane shapes but also z-direction configurations. To demonstrate this method, high quality and complex nylon membranes were fabricated in microchannels. Straight membranes as long as 15mm, 50 mum thick and 500 mum tall in a microfluidic channel were successfully fabricated, and membranes with different structures were realized.

关键词： Polymers Biomembranes Microfluidics Surface treatment Glass Microchannel Shape Materials science and technology Chemical processes Gold

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Evolving hypernetwork classifiers for microRNA expression profile analysis

Evolving hypernetwork classifiers for microRNA expression pr...

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Congress on Evolutionary Computation

作者： Sun Kim Soo-Jin Kim Byoung-Tak Zhang The Center for Bioinformatics Technology Graduate Program in Bioinformatics Seoul National University Seoul South Korea The School of Computer Science and Engineering Seoul National University Seoul South Korea

High-throughput microarrays inform us on different outlooks of the molecular mechanisms underlying the function of cells and organisms. While computational analysis for the microarrays show good performance, it is still difficult to infer modules of multiple co-regulated genes. Here, we present a novel classification method to identify the gene modules associated with cancers from microarray data. The proposed approach is based on 'hypernetworks', a hypergraph model consisting of vertices and weighted hyperedges. The hypernetwork model is inspired by biological networks and its learning process is suitable for identifying interacting gene modules. Applied to the analysis of microRNA (miRNA) expression profiles on multiple human cancers, the hypernetwork classifiers identified cancer-related miRNA modules. The results show that our method performs better than decision trees and naive Bayes. The biological meaning of the discovered miRNA modules has been examined by literature search.

关键词： Cancer Gene expression Biological system modeling Data analysis Support vector machines Support vector machine classification Evolutionary computation Humans Decision trees Diseases

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Non-Crosshybridizing Oligonucleotide Building Blocks for Accurate, Scalable Nanofabrication

Non-Crosshybridizing Oligonucleotide Building Blocks for Acc...

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IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS)

作者： Jin-woo Kim Ju Seok Lee Russell Deaton Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR USA IEEE Senior Member Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR 72701 USA. Department of Computer Science and Computer Engineering University of Arkansas Fayetteville AR 72701 USA.

The urgent need in the field of nanotechnology is functional, reliable, and scalable techniques for more complicated and controlled nanostructures in order to realize nanoscale materials and devices that have practical use and more capability than existing technologies. This paper addresses this need by presenting an in vitro protocol to select large non-crosshybridizing (NCH) libraries of oligonucleotides that provide a large address space of DNA sequences with which to increase both complexity and control in DNA-directed self-assembly processes. The selection protocol was experimentally verified and confirmed. The resultant large NCH libraries would allow self-assembling complex nanostructures with more precise control, leading to reliable, scaled-up, cost-effective manufacturing of nanoscale devices and systems.

关键词： Nanofabrication Nanostructures Nanostructured materials Nanoscale devices Space technology Protocols Libraries Self-assembly Nanotechnology Materials reliability

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DNA-Directed Self-Assembly of Microscopic 1-D Carbon Nanotube Wire

DNA-Directed Self-Assembly of Microscopic 1-D Carbon Nanotub...

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IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS)

作者： Jin-Woo Kim Nalinikanth Kotagiri Russell Deaton Steve Tung Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR USA IEEE Senior Member Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR 72701 USA. Department of Computer Science and Computer Engineering University of Arkansas Fayetteville AR 72701 USA. Department of Mechanical Engineering University of Arkansas Fayetteville AR USA

Molecular wire construction using DNA-directed self-assembly of multi-walled carbon nanotubes (MWNTs) has been attempted. MWNTs were selected owing to their exceptional electrical and structural properties. DNA, which possesses specific molecular recognition properties, served as the engine for the assembly. Non-crosshybridizing (NCH) sequences were designed to impart specificity and high throughput reaction. Stepwise manufacturing of the wire was accomplished by first functionalizing the NCH 20 base pair single-stranded sequences to the tips of MWNT using amide linkage. The adducts were then utilized to self-assemble 1D nanotube wire through DNA hybridization reactions between two complementary ssDNAs functionalized to the MWNT tips. TEM, epi-fluorescent microscopy and AFM analyses showed successful assemblies of micrometer-scale 1D MWNT-DNA wires, ranging from 2.7-20 mum. The results demonstrate great potentials of the DNA-guided self-assembly process, which would provide an uncomplicated, versatile and inexpensive way to manufacture micrometer-scale molecular wires.

关键词： Self-assembly Carbon nanotubes Wire Atomic force microscopy Transmission electron microscopy DNA Assembly Sequences Engines Throughput

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Using pitch, amplitude modulation, and spatial cues for separation of harmonic instruments from stereo music recordings

Eurasip Journal on Advances in Signal Processing

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Eurasip Journal on Advances in Signal Processing 2007年 2007卷

作者： Woodruff, John Pardo, Bryan Music Technology Program School of Music Northwestern University Evanston IL 60208 United States Department of Electrical Engineering and Computer Science Northwestern University Evanston IL 60208 United States

Recent work in blind source separation applied to anechoic mixtures of speech allows for improved reconstruction of sources that rarely overlap in a time-frequency representation. While the assumption that speech mixtures do not overlap significantly in time-frequency is reasonable, music mixtures rarely meet this constraint, requiring new approaches. We introduce a method that uses spatial cues from anechoic, stereo music recordings and assumptions regarding the structure of musical source signals to effectively separate mixtures of tonal music. We discuss existing techniques to create partial source signal estimates from regions of the mixture where source signals do not overlap significantly. We use these partial signals within a new demixing framework, in which we estimate harmonic masks for each source, allowing the determination of the number of active sources in important time-frequency frames of the mixture. We then propose a method for distributing energy from time-frequency frames of the mixture to multiple source signals. This allows dealing with mixtures that contain time-frequency frames in which multiple harmonic sources are active without requiring knowledge of source characteristics. Copyright © 2007 Hindawi Publishing Corporation. All rights reserved.

关键词： Harmonic generation

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A systematic approach to quantifying evolutionary functional trends across the universal tree of life

A systematic approach to quantifying evolutionary functional...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Alterovitz, Gil Muso, Taro Malalur, Paresh 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 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

ISBN: (纸本)1424415098

The accumulation of genomic and proteomic data of many organisms presents an opportunity to analyze entire phylogenetic trees in a systematic, quantified manner. The universal tree of life, constructed by genomic data, provides an evolutionary context for proteomic data of individual organisms. Using proteomic information mapped to biological functions, we survey the tree of life for evolutionary trends, where trends are low p-value linear regressions of relative protein diversity against an evolutionary timeline. These trends provide quantified perspectives across evolution that would be otherwise difficult to discern from the large amount of available bioinformatic data. We analyzed 22,762 functions across 167 proteomes for approximately 3.8 million information content calculations. Of particular interest is the rise of protein-protein interactions along the path of mammalian evolution. Of general interest are the numerous uncovered trends that open the door to future queries of focused scope. ©2007 IEEE.

关键词： Information theory

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