Bio-Medical Materials and Engineering - Volume 24, issue 6

Authors: Wang, Aihua | Zhang, Guanghao | Zhang, Cheng | Wu, Changzhe | Song, Tao | Huo, Xiaolin

Article Type: Research Article

Abstract: Injury potential, a significant index of spinal cord injury (SCI), is generated by the movement of extracellular ions. It can be compensated through applied direct current (DC) stimulation, which prevents the influx of the free calcium, and eventually reduces the development of secondary injury. Therefore, the compensation of injury potential is beneficial to the repairing of the function of spinal cord. The compensation effect can be evaluated by whether the magnitudes of longitudinal electric fields (EFs) are compensated to zero. However, there have been no established criteria to determine the distribution and shape of stimulating electrodes. In this study, in …order to optimize the stimulating electrodes, a finite element model (FEM) of rat spinal cord was developed, and the EFs changes induced by electrodes of different sizes, shapes and locations after SCI were calculated. All the designed configurations of electrodes were able to compensate injury potential, but the resultant compensation effects vary. Pin and disc electrodes produced uneven EFs, while ring electrodes produced uniformly distributed EFs. Moreover, large ring electrodes can compensate the longitudinal EFs almost to zero with relatively low current density (0.55 μA/mm2 ) applied. These results provide a basis for the determination of electrical stimulation parameters in the compensation of injury potential. Show more

Keywords: Direct current stimulation, finite element model, spinal cord injury, electric fields

DOI: 10.3233/BME-141197

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3693-3700, 2014

Authors: Kim, Jungyoon | Son, Jongsang | Kim, Youngho

Article Type: Research Article

Abstract: In this study, the bandwidth of the filter-based fatigue index was determined by the comparison of optimized cut-off frequencies in different inter-electrode distances. Sixty-one subjects participated in isometric knee extension, isotonic ankle dorsiflexion, and isotonic elbow extension exercises. Electromyography (EMG) signals were obtained from right rectus femoris, triceps brachii, and tibialis anterior muscles during exercises. The filter-based fatigue index was compared with mean root-mean-square values, median frequency, Dimitrov spectral index, and Gonzalez-Izal wavelet index. Optimized cut-off frequencies of the high-pass filter for three different exercises and three different inter-electrode distances were about 350 Hz. Results from this study support that …around 350 Hz high-pass filter could be useful to determine cut-off frequency for fatigue prediction in general purposes. Show more

Keywords: Electromyography, fatigue, filter, bandwidth optimization, inter-electrode distance

DOI: 10.3233/BME-141198

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3701-3708, 2014

Authors: Yi, Hui | Bo, Cuimei | Song, Xiaofeng | Yuan, Yuhao

Article Type: Research Article

Abstract: Clustering is considered one of the most powerful tools for analyzing gene expression data. Although clustering has been extensively studied, a problem remains significant: iterative techniques like k-means clustering are especially sensitive to initial starting conditions. An unreasonable selection of initial points leads to problems including local minima and massive computation. In this paper, a spatial contiguity analysis-based approach is proposed, aiming to solve this problem. It employs principal component analysis (PCA) to identify data points that are likely extracted from different clusters as initial points. This helps to avoid local minima, and accelerates the computation. The effectiveness of the …proposed approach was validated on several benchmark datasets. Show more

Keywords: Gene expression data, k-means, initial points, spatial contiguity analysis

DOI: 10.3233/BME-141199

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3709-3717, 2014

Authors: Zou, Qingyu | Liu, Fu | Hou, Tao | Jiang, Yihan | Mo, Reifeng

Article Type: Research Article

Abstract: The transcriptional regulation of cellular functions is carried out by the overlapping functional modules of a complex network. In this paper, a statistical approach for detecting functional modules in the transcriptional regulatory networks (TRNs) is studied. The proposed method defines modules as groups of links rather than nodes since nodes naturally belong to more than one module. Furthermore, the proposed algorithm is evaluated on the Escherichia coli TRN. The experimental results demonstrate that it detected a suitable number of overlapping modules that were biologically meaningful without any prior knowledge about the modules.

Keywords: Transcriptional regulation, network, functional module

DOI: 10.3233/BME-141200

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3719-3727, 2014

Authors: Cui, Haibo | Wei, Xiaomei | Huang, Yu | Hu, Bin | Fang, Yaping | Wang, Jia

Article Type: Research Article

Abstract: Among human influenza viruses, strain A/H3N2 accounts for over a quarter of a million deaths annually. Antigenic variants of these viruses often render current vaccinations ineffective and lead to repeated infections. In this study, a computational model was developed to predict antigenic variants of the A/H3N2 strain. First, 18 critical antigenic amino acids in the hemagglutinin (HA) protein were recognized using a scoring method combining phi (ϕ) coefficient and information entropy. Next, a prediction model was developed by integrating multiple linear regression method with eight types of physicochemical changes in critical amino acid positions. When compared to other three known …models, our prediction model achieved the best performance not only on the training dataset but also on the commonly-used testing dataset composed of 31878 antigenic relationships of the H3N2 influenza virus. Show more

Keywords: Influenza A virus, H3N2, antigenic variant, multiple linear regression, physicochemical properties

DOI: 10.3233/BME-141201

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3729-3735, 2014

Authors: Lee, Min Su | Oh, Sangyoon | Tang, Haixu

Article Type: Research Article

Abstract: Microorganisms interact with each other within a community. Within the same community, some microorganisms tend to co-exist, whereas some others tend to avoid each other. The association among microorganisms can be revealed by computing the correlation between their abundance patterns that are measured through metagenomic sequencing across multiple communities. In this paper, we built an association network among microorganisms from the human oral microbiome. To improve its accuracy, we adopted a network deconvolution algorithm to filter out indirect associations, and we used an ensemble of three correlation measures to filter out the false-positive associations. When applying on the metagenomic data …from human oral samples, experimental results showed that phylogenetically close microorganisms formed highly correlated network clusters. Additionally, most of the identified mutually exclusive associations were related to the order Lactobacillales. Show more

Keywords: Association network, correlation, microbiome, network deconvolution

DOI: 10.3233/BME-141202

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3737-3744, 2014

Authors: Zhang, Wen | Wang, Chenyin | Tam, Kin Y.

Article Type: Research Article

Abstract: The objective of this study is to evaluate whether the accumulation model developed by Zarfl et al. (2008) could be used to predict the minimal inhibitory concentration (MIC) of a group of antibacterial fluoroquinolones (FQs) for Escherichia coli (E. coli). Our model, which is based on the “Fick-Nernst-Planck” equation and the permeability of the neutral and charged species as well as the physicochemical parameters of the FQs, could predict 1/MIC9 0 using a linear function. It is envisaged that in the drug development projects of new FQs, the accumulation model described in this study could be utilized as an effective …tool to enable early assessment of MIC value using physiochemical parameters. Show more

Keywords: Fluoroquinolones, minimal inhibitory concentration, Escherichia coli, physicochemical parameters

DOI: 10.3233/BME-141203

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3745-3751, 2014

Authors: Wu, Jingli | Chen, Xixi | Li, Xianchen

Article Type: Research Article

Abstract: The minimum error correction model is an important combinatorial model for haplotyping a single individual. In this article, triploid individual haplotype reconstruction problem is studied by using the model. A genetic algorithm based method GTIHR is presented for reconstructing the triploid individual haplotype. A novel coding method and an effectual hill-climbing operator are introduced for the GTIHR algorithm. This relatively short chromosome code can lead to a smaller solution space, which plays a positive role in speeding up the convergence process. The hill-climbing operator ensures algorithm GTIHR converge at a good solution quickly, and prevents premature convergence simultaneously. The experimental …results prove that algorithm GTIHR can be implemented efficiently, and can get higher reconstruction rate than previous algorithms. Show more

Keywords: Triploid, haplotype, Single nucleotide polymorphism (SNP), the minimum error correction, genetic algorithm

DOI: 10.3233/BME-141204

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3753-3762, 2014

Authors: Lu, Yaosheng | Li, Xiaodong | Wei, Shouyi | Liu, Xiaolei

Article Type: Research Article

Abstract: In order to assign appropriate baseline estimation algorithms to different fetal heart rate tracing, a method to evaluate the fetal heart rate (FHR) baseline combining with the fetal movement information was proposed. Fetal actography and tocography were used to extract the fetal movement information. The results showed that the combined method, where the fetal movement detection result was the union of results of actography and tocography, achieved a better performance with the highest sensitivity and an acceptable positive predictive value (PPV). Furthermore, the mean absolute errors (MAEs) of basal FHR values between the two algorithms and the expert were calculated …with respect to the duration coefficient of fetal movement. The results showed that the algorithm using empirical mode decomposition (EMD) and Kohonen neural network (KNN) had lower MAEs than a traditional linear baseline estimation algorithm as the duration coefficient increased. However, if the duration coefficient is below 0.2, the errors may be tolerant for the FHR baseline estimation by a linear baseline estimation algorithm, which indicates that different algorithms may be selected for FHR baseline estimation based on different duration coefficients of fetal movement. Show more

Keywords: Fetal heart rate, baseline estimation, fetal movement, Ostu method

DOI: 10.3233/BME-141205

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3763-3769, 2014

Authors: Sun, Xin | Dong, Junyu | Xu, Mantao | Wang, Shengke | Xie, Cui

Article Type: Research Article

Abstract: Microarray technologies offer practical diagnostic tools for cancer detection. One great challenge is to identify salient genes from the high dimensionality of microarray data that can directly contribute to the symptom of cancer. Interactions among genes have been recognized to be fundamentally important for understanding biological function. This paper proposes an interacting gene selection method for cancer classification by identifying useful interacting genes. The method firstly evaluates the interactivity degree of each gene according to the intricate interrelation among genes by cooperative game analysis. Then genes are selected in a forward way by considering both interactivity and relevance characters. Experimental …comparisons are carried out on four publicly available microarray data sets with three outstanding gene selection methods. Moreover a gene set enrichment analysis is also performed on the selected gene subset. The results show that the proposed method achieves better classification performance and enrichment score than other gene selection methods. Show more

Keywords: Medical diagnosis, cancer classification, gene selection, information theory, cooperative game analysis

DOI: 10.3233/BME-141206

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3771-3778, 2014