A genetic algorithm for multiple molecular sequence alignment

MOTIVATION: Multiple molecular sequence alignment is among the most important and most challenging tasks in computational biology. The currently used alignment techniques are characterized by great computational complexity, which prevents their wider use. This research is aimed at developing a new technique for efficient multiple sequence alignment. APPROACH: The new method is based on genetic algorithms. Genetic algorithms are stochastic approaches for efficient and robust searching. By converting biomolecular sequence alignment into a problem of searching for optimal or near-optimal points in an 'alignment space', a genetic algorithm can be used to find good alignments very efficiently. RESULTS: Experiments on real data sets have shown that the average computing time of this technique may be two or three orders lower than that of a technique based on pairwise dynamic programming, while the alignment qualities are very similar. AVAILABILITY: A C program on UNIX has been written to implement the technique. It is available on request from the authors.     

Association of INAD with NORPA is essential for controlled activation and deactivation of Drosophila phototransduction in vivo

Visual transduction in Drosophila is a G protein-coupled phospholipase C-mediated process that leads to depolarization via activation of the transient receptor potential (TRP) calcium channel. Inactivation-no-afterpotential D (INAD) is an adaptor protein containing PDZ domains known to interact with TRP. Immunoprecipitation studies indicate that INAD also binds to eye-specific protein kinase C and the phospholipase C, no-receptor-potential A (NORPA). By overlay assay and site-directed mutagenesis we have defined the essential elements of the NORPA-INAD association and identified three critical residues in the C-terminal tail of NORPA that are required for the interaction. These residues, Phe-Cys-Ala, constitute a novel binding motif distinct from the sequences recognized by the PDZ domain in INAD. To evaluate the functional significance of the INAD-NORPA association in vivo, we generated transgenic flies expressing a modified NORPA, NORPAC1094S, that lacks the INAD interaction. The transgenic animals display a unique electroretinogram phenotype characterized by slow activation and prolonged deactivation. Double mutant analysis suggests a possible inaccessibility of eye-specific protein kinase C to NORPAC1094S, undermining the observed defective deactivation, and that delayed activation may similarly result from NORPAC1094S being unable to localize in close proximity to the TRP channel. We conclude that INAD acts as a scaffold protein that facilitates NORPA-TRP interactions required for gating of the TRP channel in photoreceptor cells.     

ACAT inhibitors derived from hetero-Diels-Alder cycloadducts of thioaldehydes

Acyl-CoA:cholesterol acyltransferase (ACAT) is the enzyme largely responsible for intracellular cholesterol esterification. A systemic inhibitor of ACAT is believed to be able to slow or even reverse the atherosclerotic process. Towards that goal, a series of cyclic sulfides, derived from the hetero-Diels-Alder reaction of thioaldehydes with 1,3-dienes, and bearing carboxamide substituents, were prepared and evaluated for in vitro (in several tissues and species) and ex vivo ACAT inhibition. Minor changes in subsequent structure were found to have a significant effect in optimization of the biological activity of this series of compounds.     

Design of optimum signals for the simultaneous estimation of timedelay and Doppler shift

The problem of joint estimation of time delay and Doppler shift is considered from the point of view of the Wigner distribution of the signal. A very efficient method of obtaining the optimum signal with minimum estimation error based on the convexity of the design region is developed. Practical applications, however, require the signal to satisfy other constraints which present complications in acquiring the optimum signal. A design approach based on the method of simulated annealing is suggested to solve for the optimum signal under constraints. The performance of the signals so obtained is evaluated and compared with that of signals obtained by synthesis     

能消除RGB差分视频传输线上共模噪声的放大器

5类网络电缆由四对双绞线组成,并有耐用的外套,这种电缆能为分量视频信号的传输提供一种通用而有良好性价比的选择。三个线对可以承载RGB视频信号,而第四对线可以承载音频信号、同步信号和其它传输信号。不幸的是,5类电缆缺乏屏蔽,因此容易遭受共模噪声耦合     

Data mining of resilience indicators

In recent years, the Asia-Pacific region has experienced several financial setbacks, including speculative attacks in 1998 and the SARS outbreak in 2003. Financial stresses of this nature are unanticipated, and not all of the dangers can be predicted by the examination of market information and macroeconomic indicators. The Early Warning System (EWS) that has been adopted by the International Monetary Fund may not be able to predict future financial crises for all possible scenarios, because shocks come in many different forms. To supplement the EWS, this paper proposes a data mining framework to measure the resilience of an economy. The resilience framework does not predict a crisis, but rather assesses the current state of health of an economy and its ability to withstand a financial shock should one occur. The framework is based on a feedback system consisting of two stages. The first stage assigns a resilience score to each economy based on a fuzzy logic scoring scheme that is built on the ambiguous reasoning of experts. The second stage uses the classification tree approach to estimate thresholds for each economic indicator, and examines the quality of the fuzzy score. The result from the second stage is then passed back to the first stage as feedback. The final result is obtained when the feedback system reaches its equilibrium state. The proposed resilience framework is applied to the external-sector and the public-sector economies of several countries to illustrate its applicability.