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