Bio-Medical Materials and Engineering - Volume 24, issue 1

Authors: Jia, Xibin | Huang, Haiyong | Wang, Runyuan

Article Type: Research Article

Abstract: Edge detection has been widely used in medical image processing, automatic diagnosis, et al. A novel edge detection algorithm, based on the fusion model, is proposed by combination with the two proposed models as follows: the matrix of most probable distribution of edge point and the matrix of the difference weight of each point. The most probable distribution of edge point can be obtained by analyzing the variance among 4-connected neighborhood points around each pixel under estimation in the image to label the all candidate edge points in the image. The difference weight of each point can be gotten by …analyzing the brightness difference between the neighborhood point and the under-estimating pixel to represent the probability of being edge. The two matrices gotten from the different descriptions of spatial structure are fused together and derive from the final edge image with thresholding method on the fusion matrix. The experiments are performed based on the public diabetic retinopathy database DRIVE. According to the edge images obtained, the proposed method is subjectively analyzed to be complete and close to the Ground Truth image with very low noise in comparison with the Sobel, Canny and LOG edge detectors. The F1 measure, ROC measure and PFOM measure are separately adopted to make quantitative evaluation of the proposed edge detection algorithm. Experimental results show that the proposed method is able to improve the effect of edge detection on medical images. Show more

Keywords: Edge detection, retinal image analysis, most probable distribution, fusion, spatial structure clues

DOI: 10.3233/BME-130931

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1289-1298, 2014

Authors: George, Uduak Z. | Wang, Jun | Yu, Zeyun

Article Type: Research Article

Abstract: Intracellular calcium (Ca2+ ) signaling in cardiac myocytes is vital for proper functioning of the heart. Understanding the intracellular Ca2+ dynamics would give an insight into the functions of normal and diseased hearts. In the current study, spatiotemporal Ca2+ dynamics is investigated in ventricular myocytes by considering Ca2+ release and re-uptake via sarcolemma and transverse tubules (T-tubules), Ca2+ diffusion and buffering in the cytosol, and the blockade of Ca2+ activities associated with the sarcoplasmic reticulum. This study is carried out using a three dimensional (3D) geometric model of a branch of T-tubule extracted from the …electron microscopy (EM) images of a partial ventricular myocyte. Mathematical modeling is done by using a system of partial differential equations involving Ca2+ , buffers, and membrane channels. Numerical simulation results suggest that a lack of T-tubule structure at the vicinity of the cell surface could increase the peak time of Ca2+ concentration in myocytes. The results also show that T-tubules and mobile buffers play an important role in the regulation of Ca2+ transient in ventricular myocytes. Show more

Keywords: Cardiac myocytes, calcium dynamics, reaction-diffusion equations, numerical analysis, finite element method

DOI: 10.3233/BME-130932

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1299-1306, 2014

Authors: Sun, Lin | Xu, Jiucheng

Article Type: Research Article

Abstract: Gene selection is a key step in performing cancer classification with DNA microarrays. The challenges from high dimension and small sample size of microarray dataset still exist. On rough set theory applied to gene selection, many algorithms have been presented, but most are time-consuming. In this paper, a granular computing-based gene selection as a new method is proposed. First, some granular computing-based concepts are introduced and then some of their important properties are derived. The relationship between positive region-based reduct and granular space-based reduct is discussed. Then, a significance measure of feature is proposed to improve the efficiency and decrease …the complexity of classical algorithm. By using Hashtable and input sequence techniques, a fast heuristic algorithm is constructed for the better computational efficiency of gene selection for cancer classification. Extensive experiments are conducted on five public gene expression data sets and seven data sets from UCI respectively. The experimental results confirm the efficiency and effectiveness of the proposed algorithm. Show more

Keywords: Feature selection, rough set theory, granular computing, granular space

DOI: 10.3233/BME-130933

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1307-1314, 2014

Authors: Wang, Xing | Ren, Zhenzhen | He, Yusu | Xiang, Yuhong | Zhang, Yanling | Qiao, Yanjiang

Article Type: Research Article

Abstract: Inducible Nitric Oxide Synthase (iNOS) has been involved in a variety of diseases, and thus it is interesting to discover new iNOS inhibitors. This study was performed to identify natural iNOS inhibitors from traditional Chinese herbs through a combination of pharmacophore modeling, molecular docking and virtual screening. First, the pharmacophore models were generated though six known iNOS inhibitors and validated by a test database. The pharmacophore model_017 showed good performance in external validation and was employed to screen Traditional Chinese Medicine Database (Version 2009), which resulting in a hit list of 498 compounds with matching score (QFIT) above 40. Then, …the hits were subjected to molecular docking for further refinement. An empirical scoring function was used to evaluate the affinity of the compounds and the target protein. Parts of compounds with high docking scores have been reported to have the related pharmacological activity from the literatures. The results provide a set of useful guidelines for the rational discovery of natural iNOS inhibitors from Chinese herbs. Show more

Keywords: Inducible Nitric Oxide Synthase, Virtual screening, pharmacophore, Traditional Chinese Medicine, active natural ingredients identification

DOI: 10.3233/BME-130934

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1315-1322, 2014

Authors: Chen, Yifei | Hou, Ping | Manderick, Bernard

Article Type: Research Article

Abstract: Protein-protein interaction (PPI) is essential to understand the fundamental processes governing cell biology. The mining and curation of PPI knowledge are critical for analyzing proteomics data. Hence it is desired to classify articles PPI-related or not automatically. In order to build interaction article classification systems, an annotated corpus is needed. However, it is usually the case that only a small number of labeled articles can be obtained manually. Meanwhile, a large number of unlabeled articles are available. By combining ensemble learning and semi-supervised self-training, an ensemble self-training interaction classifier called EST_IACer is designed to classify PPI-related articles based on a …small number of labeled articles and a large number of unlabeled articles. A biological background based feature weighting strategy is extended using the category information from both labeled and unlabeled data. Moreover, a heuristic constraint is put forward to select optimal instances from unlabeled data to improve the performance further. Experiment results show that the EST_IACer can classify the PPI related articles effectively and efficiently. Show more

Keywords: Interaction article classification, ensemble semi-supervised learning, instance selection, feature weighting

DOI: 10.3233/BME-130935

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1323-1332, 2014

Authors: Ren, Zhenzhen | Wang, Xing | Wang, Shifeng | Zhai, Chenxi | He, Yusu | Zhang, Yanling | Qiao, Yanjiang

Article Type: Research Article

Abstract: Salvianolic Acid B (Sal B) is one of the main medicinal ingredients of Radix Salvia miltiorrhiza (Danshen) and possesses a variety of pharmacological effects. The purpose of this study was to discover the new mechanism of action of Sal B based on the protein interaction network (PIN) analysis. A PIN of Sal B was constructed with 852 nodes and 8,626 interactions. By fast agglomerate algorithm based on the edge clustering coefficients (FAG-EC), 11 modules were detected from the network. Gene ontology (GO) enrichment analysis of the modules demonstrated that the roles of Sal B played in cardiovascular disease were related …to multiple biological processes, which could represent the characteristics of Chinese Material Medica (CMM) as a whole to regulate the disease. The most interesting finding of this work was that the anti-inflammatory effect of Sal B was due to the immune response of T lymphocytes by regulating IL-2 family, CD3E, CD79A, MAP3K7 and PRKCQ. Therefore, the module-based network analysis will be an effective method for better understanding CMM. Show more

Keywords: Protein interaction network, module, mechanism of action, Salvianolic Acid B, GO enrichment analysis

DOI: 10.3233/BME-130936

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1333-1340, 2014

Authors: Xu, Lijun | Zhang, Andi | Du, Guohao | Xie, Honglan | Chen, Ying

Article Type: Research Article

Abstract: Purpose: To establish a method for mouse coronary angiography in vivo using synchrotron radiation, which is essential for physiological and pathological research on coronary diseases. Methods: 1) The imaging parameters (e.g., photon energy, spatial resolution of the detector, and injection rate of contrast agent) optimal for the quality of acquired images in a simulation were determined. 2) Through animal experiments, the effectiveness of these optimal parameters and the repeatability of in vivo coronary angiography were verified. 3) An algorithm for background subtraction and contrast enhancement was designed and employed to compensate for the effects of interference and the effective …information extracted used for diagnosing coronary disease. Results and conclusions: An optimal set of the imaging parameters was finally determined: photon energy of 33–34 keV, detector's spatial resolution of 30 μm or higher, image capture rate of 20 f/s or more, concentration of lopamidol solution of 75% as contrast agent and a pulse injection of contrast agent at a high rate. Show more

Keywords: Coronary angiography, Synchrotron radiation, In vivo, Optimization, Background subtraction

DOI: 10.3233/BME-130937

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1341-1349, 2014

Authors: Hong, Qingqi | Wang, Beizhan | Li, Qingde | Li, Yan | Wu, Qingqiang

Article Type: Research Article

Abstract: With the flooding datasets of medical Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), implicit modeling techniques are increasingly applied to reconstruct the human organs, especially the vasculature. However, displaying implicitly represented geometric objects arises heavy computational burden. In this study, a Graphics Processing Unit (GPU) accelerating technique was developed for high performance rendering of implicitly represented objects, especially the vasculatures. The experimental results suggested that the rendering performance was greatly enhanced via exploiting the advantages of modern GPUs.

Keywords: GPU accelerating techniques, implicit surfaces, rendering, vascular structures

DOI: 10.3233/BME-130938

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1351-1357, 2014

Authors: Chen, Songjing | Luo, Senlin | Pan, Limin | Zhang, Tiemei | Han, Longfei | Zhao, Haixiu

Article Type: Research Article

Abstract: The aim of this study is to quantitatively analyze the influence of risk factors on the blood glucose level, and to provide theory basis for understanding the characteristics of blood glucose change and confirming the intervention index for type 2 diabetes. The quantitative method is proposed to analyze the influence of risk factors on blood glucose using back propagation (BP) neural network. Ten risk factors are screened first. Then the cohort is divided into nine groups by gender and age. According to the minimum error principle, nine BP models are trained respectively. The quantitative values of the influence of different …risk factors on the blood glucose change can be obtained by sensitivity calculation. The experiment results indicate that weight is the leading cause of blood glucose change (0.2449). The second factors are cholesterol, age and triglyceride. The total ratio of these four factors reaches to 77% of the nine screened risk factors. And the sensitivity sequences can provide judgment method for individual intervention. This method can be applied to risk factors quantitative analysis of other diseases and potentially used for clinical practitioners to identify high risk populations for type 2 diabetes as well as other disease. Show more

Keywords: sensitivity, risk factors, blood glucose, BP neural network

DOI: 10.3233/BME-130939

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1359-1366, 2014

Authors: Jiang, Jiehui | Lin, Xiaoman | Wen, Junlin | Huang, Zhemin | Yan, Zhuangzhi

Article Type: Research Article

Abstract: Alzheimer's disease (AD) is a common health problem for elderly populations. Positron emission tomography-computed tomography (PET-CT)11 C-PiB for beta-P (amyloid-β peptide, β-AP) imaging is an advanced method to diagnose AD in early stage. However, in practice radiologists lack a standardized value to semi-quantify β-AP. This paper proposes such a standardized value: SVβ−AP . This standardized value measures the mean ratio between the dimension of β-AP areas in PET and CT images. A computer aided diagnosis approach is also proposed to achieve SVβ−AP . A simulation experiment was carried out to pre-test the technical feasibility of the CAD approach and SVβ−AP …. The experiment results showed that it is technically feasible. Show more

Keywords: Beta-Amyloid Peptide, Positron Emission Tomography (PET), 11C-PiB, Standardized Uptake Values (SUVs), Alzheimer's Disease (AD)

DOI: 10.3233/BME-130940

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1367-1373, 2014

Authors: Wan, Chao | Hao, Zhi-Xiu | Wen, Shi-Zhu

Article Type: Research Article

Abstract: It is known that the anterior cruciate ligament (ACL) plays a role in providing joint stabilities under tibial varus/valgus torques and the material behavior of the ACL has changed with ageing. However, the effect of this variation of the ACL material property on joint kinematics and biomechanics under tibial varus/valgus torques has still not been clarified. In this paper, three finite element (FE) models of an intact tibiofemoral joint were reconstructed with different ACL material properties, corresponding to the ACL on the younger, middle and older ages, respectively. The joint kinematics, the stress distribution and resultant force of the …ACL were obtained under a tibial varus or valgus torque load. It was found that the variation in the ACL material property would result in great changes in some joint displacements (i.e., the tibial anterior translation and external rotation). The maximal stress value in the ACL had also altered while the stress distribution did not varied obviously. The great change in the tibial anterior translation illustrated that ACL played an important role against varus/valgus torques by controlling the coupled tibial anterior translation//external rotation rather than the corresponding varus/valgus rotation. Show more

Keywords: material property change, ageing, anterior cruciate ligament, tibiofemoral joint, finite element

DOI: 10.3233/BME-130941

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1375-1382, 2014

Authors: Chen, Wen-Pei | Hung, Che-Lun | Tsai, Suh-Jen Jane | Lin, Yaw-Ling

Article Type: Research Article

Abstract: SNPs are the most abundant forms of genetic variations amongst species; the association studies between complex diseases and SNPs or haplotypes have received great attention. However, these studies are restricted by the cost of genotyping all SNPs; thus, it is necessary to find smaller subsets, or tag SNPs, representing the rest of the SNPs. In fact, the existing tag SNP selection algorithms are notoriously time-consuming. An efficient algorithm for tag SNP selection was presented, which was applied to analyze the HapMap YRI data. The experimental results show that the proposed algorithm can achieve better performance than the existing tag SNP …selection algorithms; in most cases, this proposed algorithm is at least ten times faster than the existing methods. In many cases, when the redundant ratio of the block is high, the proposed algorithm can even be thousands times faster than the previously known methods. Tools and web services for haplotype block analysis integrated by hadoop MapReduce framework are also developed using the proposed algorithm as computation kernels. Show more

Keywords: SNP, haplotype block, tag SNP selection, hadoop, non-redundant site, redundant ratio

DOI: 10.3233/BME-130942

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1383-1389, 2014

Authors: Geng, D.Y. | Li, C.H. | Wan, X.W. | Xu, G.Z.

Article Type: Research Article

Abstract: To study the mechanism of cells subjected to external electromagnetic fields, the expression of cyclin kinase inhibitor p27 is analyzed in the four cell cycle phases. The regulatory functions are investigated in gap phase1 to synthesis, gap phase 2 to mitotic phase and post mitotic phase transition in the mammalian cell cycle processes. A mathematical model is developed to meet the general cell cycle regulatory network based on the molecular dynamics method. Phase plane analysis results show that the p27 over-expression can lead to the hysteresis effect of cell cycle processes and phase transition delay. It is an universal approach …to predict the key regulatory gene in signal transduction pathway. Show more

Keywords: Electromagnetic fields, Mathematical model, Molecular dynamics method, Cell cycle, Phase plane analysis

DOI: 10.3233/BME-130943

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1391-1397, 2014

Authors: Wang, Huiya | Zhang, Shanwen

Article Type: Research Article

Abstract: Gene expression profiles have great potential for accurate tumor diagnosis. It is expected to enable us to diagnose tumors precisely and systematically, and also bring the researchers of machine learning two challenges, the curse of dimensionality and the small sample size problems. We propose a manifold learning based dimensional reduction algorithm named orthogonal local discriminant embedding (O-LDE) and apply it to tumor classification. Comparing with the classical local discriminant embedding (LDE), O-LDE aims to obtain an orthogonal linear projection matrix by solving an optimization problem. After being projected into a low-dimensional subspace by O-LDE, the data points of the same …class maintain their intrinsic neighbor relations, whereas the neighboring points of the different classes are far from each other. Experimental results on a public tumor dataset validate the effectiveness and feasibility of the proposed algorithm. Show more

Keywords: Tumor classification, local discriminant embedding (LDE), orthogonal local discriminant embedding (O-LDE)

DOI: 10.3233/BME-130944

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1399-1405, 2014

Authors: Huang, You-Min | Chou, I-Chiang | Jiang, Cho-Pei | Wu, Yi-Syun | Lee, Shyh-Yuan

Article Type: Research Article

Abstract: The purpose of this study is to investigate the effect of implant neck design and cortical bone thickness by means of 3-D linearly elastic finite element analysis and to analyze primary and secondary stability of clinical evidence based on micromotion and principal stress. Four commercial dental implants, comparable in size, for a type IV bone and mandibular segments were created. Various parameters were considered, including the osseointegration condition (non- and full bonded), force direction (vertical and horizontal) and cortical bone thickness (0.3, 0.5 and 1mm). The force was considered a static load applied at the top of the platform. The …magnitudes of the vertical and horizontal loading direction were 500 N and 250 N. Micromotion and principal stresses were employed to evaluate the failure of osseointegration and bone overloading, respectively. The results show that Maximum stress of the peri-implant bone decreased as cortical bone thickness increased. The stress concentration regions were located at the implant neck between the cortical bone and cancellous bone. The micromotion level in full osseointegration is less than that in non-osseointegration and it also decreases as a increasing of cortical bone thickness. Consequently, cortical bone thickness is a key factor for primary stability. Show more

Keywords: Dental, Neck, Osseointegration, Mandible

DOI: 10.3233/BME-130945

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1407-1415, 2014

Authors: Liu, Ke | Yao, Guangming | Yu, Zeyun

Article Type: Research Article

Abstract: Spatial-temporal calcium dynamics due to calcium release, buffering, and re-uptaking plays a central role in studying excitation-contraction (E-C) coupling in both healthy and defected cardiac myocytes. In our previous work, partial differential equations (PDEs) had been used to simulate calcium dynamics with realistic geometries extracted from electron microscopic imaging data. However, the computational costs of such simulations are very high on a single processor. To alleviate this problem, we have accelerated the numerical simulations of calcium dynamics by using graphics processing units (GPUs). Computational performance and simulation accuracy are compared with those based on a single CPU and another popular …parallel computing technique, OpenMP. Show more

Keywords: calcium dynamics, PDEs, parallel, OpenMP, CUDA, GPU

DOI: 10.3233/BME-130946

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 1, pp. 1417-1424, 2014