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PCA for predicting quaternary structure of protein
WANG Tong, SHEN Hongbin, YAO Lixiu, YANG Jie, CHOU Kuochen
Front. Electr. Electron. Eng.. 2008, 3 (4): 376-380.
https://doi.org/10.1007/s11460-008-0084-5
The number and arrangement of subunits that form a protein are referred to as quaternary structure. Knowing the quaternary structure of an uncharacterized protein provides clues to finding its biological function and interaction process with other molecules in a biological system. With the explosion of protein sequences generated in the Post-Genomic Age, it is vital to develop an automated method to deal with such a challenge. To explore this problem, we adopted an approach based on the pseudo position-specific score matrix (Pse-PSSM) descriptor, proposed by Chou and Shen, representing a protein sample. The Pse-PSSM descriptor is advantageous in that it can combine the evolution information and sequence-correlated information. However, incorporating all these effects into a descriptor may cause ‘high dimension disaster’. To overcome such a problem, the fusion approach was adopted by Chou and Shen. A completely different approach, linear dimensionality reduction algorithm principal component analysis (PCA) is introduced to extract key features from the high-dimensional Pse-PSSM space. The obtained dimension-reduced descriptor vector is a compact representation of the original high dimensional vector. The jackknife test results indicate that the dimensionality reduction approach is efficient in coping with complicated problems in biological systems, such as predicting the quaternary structure of proteins.
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Integrative decomposition procedure and Kappa
statistics set up ATF2 ion binding module in malignant pleural mesothelioma
(MPM)
SUN Ying, WANG Lin, LIU Lei
Front. Electr. Electron. Eng.. 2008, 3 (4): 381-387.
https://doi.org/10.1007/s11460-008-0086-3
Activating transcription factor 2 (ATF2) is a member of the ATF/cyclic AMP-responsive element binding protein family of transcription factors. However, the information concerning ATF2 ion-mediated DNA binding module and function of ATF2 in malignant pleural mesothelioma (MPM) has never been addressed. In this study, by using GRNInfer and GVedit based on linear programming and a decomposition procedure, with integrated analysis of the function cluster using Kappa statistics and fuzzy heuristic clustering in MPM, we identified one ATF2 ion-mediated DNA binding module involved in invasive function including ATF2 inhibition to target genes FALZ, C20orf31, NME2, PLOD2, RNF10, and RNASEH1, upstream RNF10 and PLOD2 activation to ATF2, upstream RNASEH1 and FALZ inhibition to ATF2 from 40 MPM tumors and 5 normal pleural tissues. Remarkably, our results showed that the predominant effect of ATF2 occupancy is to suppress the activation of target genes on MPM. Importantly, the ATF2 ion-mediated DNA binding module reflects ‘mutual’ positive and negative feedback regulation mechanism of ATF2 with up-and down-stream genes. It may be useful for developing novel prognostic markers and therapeutic targets in MPM.
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Research on food-chain algorithm and its parameters
YU Haifei, WANG Dingwei
Front. Electr. Electron. Eng.. 2008, 3 (4): 394-398.
https://doi.org/10.1007/s11460-008-0078-3
Based on the characteristics of colony emergence of artificial organisms, their dynamic interaction with the environment, and the food-chain crucial to the life system, the rules of local activities of artificial organisms at different levels are defined. The article proposes an artificial life-based algorithm, which is referred to as the food-chain algorithm. This algorithm optimizes computation by simulating the evolution of natural ecosystems and the information processing mechanism of natural organisms. The definition, idea and flow of the algorithm are introduced, and relevant rules on metabolic energy and change in the surroundings where artificial-life individuals live are depicted. Furthermore, key parameters of the algorithm are systematically analyzed. Test results show that the algorithm has quasi-life traits that include being autonomous, evolutionary, and self-adaptive. These traits are highly fit for optimization problems of life-like systems such as the location-allocation problem of a distribution network system.
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Indoor and outdoor people detection and shadow
suppression by exploiting HSV color information
CHEN Baisheng
Front. Electr. Electron. Eng.. 2008, 3 (4): 406-410.
https://doi.org/10.1007/s11460-008-0083-6
An adaptive background model based on maximum statistical probability and a shadow suppression scheme for indoor and outdoor people detection by exploiting hue saturation value (HSV) color information is proposed. To obtain the initial background scene, the frequency of R, G, and B component values for each pixel at the same position in the learning sequence are respectively calculated; the R, G, and B component values with the biggest ratios are incorporated to model the initial background. The background maintenance, or the so-called background re-initiation, is also proposed to adapt to scene changes such as illumination changes and scene geometry changes. Moving cast shadows generally exhibit a challenge for accurate moving target detection. Based on the observation that a shadow cast on a background region lowers its brightness but does not change its chromaticity significantly, we address this problem in the article by exploiting HSV color information. In addition, quantitative metrics is introduced to evaluate the algorithm on a benchmark suite of indoor and outdoor video sequences. The experimental results are given to show the performance of the algorithm.
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Analysis of maximal-ratio of transmitting/receiving
antenna selection with perfect and partial channel information
XIAO Xiao, ZHU Guangxi, ZHOU Lin, WANG Desheng, LI Li
Front. Electr. Electron. Eng.. 2008, 3 (4): 411-417.
https://doi.org/10.1007/s11460-008-0060-0
To improve system performance and reduce the complexity and cost of receiver hardware, we investigated a new multiple-input multiple-output (MIMO) scheme combining maximal-ratio transmitting and receiver antenna selection (MRT/RAS). In this scheme, a single receiving antenna, which maximizes the signal-to-noise ratio (SNR) at the receiver, is selected for demodulation. The closed-form outage probability and the bit error rate (BER) of the MRT/RAS system are both presented. The simulation demonstrates that the MRT/RAS scheme can achieve a full diversity order as if all the receiving antennas were used. It is shown that the MRT/RAS scheme outperforms some more complex space-time codes of the same spectral efficiency. The analytical results are verified by simulation. In the end, we also analyze the MRT/RAS system based on partial channel information.
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Rearrangeability of 7-stage 16 × 16 shuffle
exchange networks
DAI Hao, SHEN Xiaojun
Front. Electr. Electron. Eng.. 2008, 3 (4): 440-458.
https://doi.org/10.1007/s11460-008-0071-x
It has long been an outstanding conjecture that any (2 n - 1)-stage shuffle exchange network (Omega network) is rearrangeable for 2 n × 2 n. Many researchers have failed to prove this conjecture, including a recent one established by Hasan. However, nobody has pointed out its fallacy. Therefore, as one of the objectives, this paper shall clarify this fact. Since the case of n = 3 has been proven by many researchers 12, this paper uses a constructive approach to prove that when n = 4, the 7-stage 16 × 16 shuffle exchange network is also rearrangeable. The paper also presents the model of a balanced tree to avoid internal conflict, the representation of permutations using a connection graph and loop graph, and the concepts of symmetry graph and identical transform. Based on graphic composition and bipartition, the permutations 16 × 16 are divided into five classes, with five assignment algorithms proposed. These algorithms are simpler, clearer and easier to program. The techniques used for n = 4 may provide hints for the general case of n > 4.
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17 articles
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