Bio-Medical Materials and Engineering - Volume 26, issue s1

Authors: Yan, Chun | Liu, Wei | Qiu, Yiwei | Sun, Haitang

Article Type: Research Article

Abstract: The problem of gene recognition based on the ratio of power spectrum, SNR, and Gabor transform and its implementation of the calculation were discussed. The optimal threshold could guarantee to identify the DNA sequences with the signal-to-noise ratio. It summarized three kinds of traditional ways to determine the threshold, and advanced the optimum entitled method showing the disparate degrees of highlight and the discrimination rate method of the exons or introns as far as possible to improve the rate of their accuracy. To evaluate different determination methods of threshold by using the calculation results of four kinds of DNA sequence. …In order to ensure the analysis of DNA sequence more accurate, it adopted and improved gene identification method of Fourier transformation in a short time which is based on Gabor transformation. By using of the ergodic theory, the fixed percentage of the sequence length of exons in DNA has been improved to be the dynamic percentages which focus on different gene types. The exons of the DNA sequence which have been already discovered were identified by using the improved algorithm. With comparison of the results and the actual endpoint of exons, it confirmed that the improved algorithm can figure out the endpoint of the exons more accurate. Show more

Keywords: The discrete Fourier transform, Gabor transform, gene identification, signal-to-noise ratio, threshold

DOI: 10.3233/BME-151492

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1891-S1901, 2015

Authors: Hua, Lin | Zheng, Weiying | Xia, Hong | Zhou, Ping | An, Li

Article Type: Research Article

Abstract: Currently, the mechanisms underlying chronic obstructive pulmonary disease (COPD) remain unclear. As potential biomarkers, microRNAs (miRNAs), which modulate the levels of specific genes and proteins, are important for enhancing our understanding of the mechanisms behind COPD. Although there have been a number of miRNA expression profiling analyses strategies used to document miRNA expression changes during physiological and pathological processes or used to identify differentially expressed miRNAs in disease or control samples, the study results have been inconsistently replicated using different datasets. For this reason, many findings cannot be well synthesized and interpreted. To address this issue, we used a multiple …co-inertia analysis (MCIA) method to extract potential COPD-related miRNAs using three COPD microarray datasets. The results showed that miR-223, miR-132, and miR-199a-5p are obviously associated with COPD, and these results are consistent with the highly significant differentially-expressed miRNAs that were observed across three microarray datasets. Moreover, when miR-223, miR-132, and miR-199a-5p are taken as predictors to classify the samples of three datasets, the pooled sensitivity and specificity is 0.96 and 0.75, respectively, thereby suggesting that these three miRNAs can effectively distinguish COPD patients and controls. Show more

Keywords: Chronic obstructive pulmonary disease, multiple co-inertia, miRNAs, differentially expressed

DOI: 10.3233/BME-151493

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1903-S1915, 2015

Authors: Lee, Kyung-Eun | Park, Hyun-Seok

Article Type: Research Article

Abstract: Epigenetic computational analyses based on Markov chains can integrate dependencies between regions in the genome that are directly adjacent. In this paper, the BED files of fifteen chromatin states of the Broad Histone Track of the ENCODE project are parsed, and comparative nucleotide frequencies of regional chromatin blocks are thoroughly analyzed to detect the Markov property in them. We perform various tests to examine the Markov property embedded in a frequency domain by checking for the presence of the Markov property in the various chromatin states. We apply these tests to each region of the fifteen chromatin states. The results …of our simulation indicate that some of the chromatin states possess a stronger Markov property than others. We discuss the significance of our findings in statistical models of nucleotide sequences that are necessary for the computational analysis of functional units in noncoding DNA. Show more

Keywords: Chromatin maps, nucleotide frequency patterns, Markov chain, noncoding DNA, computational epigenetics

DOI: 10.3233/BME-151494

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1917-S1927, 2015

Authors: Tian, Xue W. | Lim, Joon S.

Article Type: Research Article

Abstract: Naive Bayesian (NB) network classifier is a simple and well-known type of classifier, which can be easily induced from a DNA microarray data set. However, a strong conditional independence assumption of NB network sometimes can lead to weak classification performance. In this paper, we propose a new approach of interactive naive Bayesian (INB) network to weaken the conditional independence of NB network and classify cancers using DNA microarray data set. We selected the differently expressed genes (DEGs) to reduce the dimension of the microarray data set. Then, an interactive parent which has the biggest influence among all DEGs is searched …for each DEG. And then we calculate a weight to represent the interactive relationship between a DEG and its parent. Finally, the gene-gene interaction network is constructed. We experimentally test the INB network in terms of classification accuracy using leukemia and colon DNA microarray data sets, then we compare it with the NB network. The INB network can get higher classification accuracies than NB network. And INB network can show the gene-gene interactions visually. Show more

Keywords: Gene interaction, naive Bayesian, differently expressed genes (DEGs), leukemia, colon, DNA microarray

DOI: 10.3233/BME-151495

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1929-S1936, 2015

Authors: Belov, Oleg V. | Boyda, Denis L. | Plante, Ianik | Shirmovsky, Sergey Eh.

Article Type: Research Article

Abstract: A computer model to simulate the processes of charge injection and migration through DNA after irradiation by a heavy charged particle was developed. The most probable sites of charge injection were obtained by merging spatial models of short DNA sequence and a single 1 GeV/u iron particle track simulated by the code RITRACKS (Relativistic Ion Tracks). Charge migration was simulated by using a quantum-classical nonlinear model of the DNA–charge system. It was found that charge migration depends on the environmental conditions. The oxidative damage in DNA occurring during hole migration was simulated concurrently, which allowed the determination of probable locations …of radiation-induced DNA lesions. Show more

Keywords: DNA damage, charge migration, radiation

DOI: 10.3233/BME-151496

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1937-S1944, 2015

Authors: Assawinchaichote, Wudhichai

Article Type: Research Article

Abstract: The designing of H ∞ fuzzy controller for HIV/AIDS infected dynamic system has been considered in this paper. With TS fuzzy model and LMIs approach, the proposed controller is obtained for such a system. A set of sufficient conditions of the H ∞ controller is given to ensure the closed-loop system asymptotic stability and the prescribed …H ∞ performance level. Finally, the effectiveness of the fuzzy controller design approach is finally presented through the simulation results. Show more

Keywords: H∞ control, TS fuzzy model, robust control, linear matrix inequalities (LMIs), HIV/AIDS infection system, robust control

DOI: 10.3233/BME-151497

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1945-S1951, 2015

Authors: Xu, Jiucheng | Li, Tao | Sun, Lin

Article Type: Research Article

Abstract: In view of the characteristics of high dimension, small samples, nonlinearity and numeric type in the gene expression profile data, the logistic and the correlation information entropy are introduced into the feature gene selection. At first, the gene variable is screened preliminarily by logistic regression to obtain the genes that have a greater impact on the classification; then, the candidate features set is generated by deleting the unrelated features using Relief algorithm. On the basis of this, delete redundant features by using the correlation information entropy; finally, the feature gene subset is classified by using the classifier of support vector …machine (SVM). Experimental results show that the proposed method can obtain smaller subset of genes and achieve higher recognition rate. Show more

Keywords: Gene chips, logistic, correlation information entropy, feature selection

DOI: 10.3233/BME-151498

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1953-S1959, 2015

Authors: Chen, Tao | Xue, Huifeng | Hong, Zenglin | Cui, Man | Zhao, Hui

Article Type: Research Article

Abstract: Microarray data has small samples and high dimension, and it contains a significant amount of irrelevant and redundant genes. This paper proposes a hybrid ensemble method based on double disturbance to improve classification performance. Firstly, original genes are ranked through reliefF algorithm and part of the genes are selected from the original genes set, and then a new training set is generated from the original training set according to the previously selected genes. Secondly, D bootstrap training subsets are produced from the previously generated training set by bootstrap technology. Thirdly, an attribute reduction method based on neighborhood mutual information …with a different radius is used to reduce genes on each bootstrap training subset to produce new training subsets. Each new training subset is applied to train a base classifier. Finally, a part of the base classifiers are selected based on the teaching-learning-based optimization to build an ensemble by weighted voting. Experimental results on six benchmark cancer microarray datasets showed proposed method decreased ensemble size and obtained higher classification performance compared with Bagging, AdaBoost, and Random Forest. Show more

Keywords: Microarray data, bagging, reliefF, neighborhood mutual information, teaching-learning-based optimization

DOI: 10.3233/BME-151499

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1961-S1968, 2015

Authors: Liu, Xiaoli | Bao, Hang | Zhao, Dazhe | Cao, Peng

Article Type: Research Article

Abstract: Multi-label classification is useful in many bioinformatics tasks such as gene function prediction and protein site localization. This paper presents an improved neural network algorithm, Max Label Distance Back Propagation Algorithm for Multi-Label Classification. The method was formulated by modifying the total error function of the standard BP by adding a penalty term, which was realized by maximizing the distance between the positive and negative labels. Extensive experiments were conducted to compare this method against state-of-the-art multi-label methods on three popular bioinformatic benchmark datasets. The results illustrated that this proposed method is more effective for bioinformatic multi-label classification compared to …commonly used techniques. Show more

Keywords: Multi-label classification, neural networks, max label distance, self-adaptive learning rate

DOI: 10.3233/BME-151500

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1969-S1976, 2015

Authors: Zhang, Xuejuan | Zhao, Haiping | Zhang, Jietao | Han, Di | Zheng, Yu | Guo, Xiaozi | He, Dian | Guo, Jin | Wang, Yingcui

Article Type: Research Article

Abstract: In some GWAs studies, GALNT2 and APOE polymorphisms have been identified to be related to alterations of plasma or serum HDL-C and TG concentrations. The purpose of our study is to assess the contribution of GALNT2 rs4846914, APOE rs429358, rs7412, rs405509 variants, and several environmental factors to the development of hypertension disease in the China Han population. A hospital-based case-control study was conducted. Cases were hypertension (n =211) and controls were normal participants (n =434). The AA, AG, and GG genotype frequencies of GALNT2 rs4846914 were 22.8%, 43.1%, and 34.1% in hypertension subjects, and 35.3%, 44.2%, and 20.5% in controls …(P <0.05), respectively. The OR of the AG genotype adjusted for all risk factors compared to the AA genotype was 1.61 (95%CI: 1.02 to 2.56) and to the GG genotype 2.67 (95%CI: 1.59 to 4.488). There was no significant difference between the APOE rs429358, rs7412, and rs405509 genotype frequencies in hypertension and control subjects. The present work indicates that SNP rs4846914 in GALNT2 gene is related to an increased risk of hypertension in China Han population, but the APOE gene is not. Show more

Keywords: Gene polymorphisms, GALNT2, APOE, hypertension, China

DOI: 10.3233/BME-151501

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1977-S1983, 2015