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

Authors: Liao, Mengjia | Guo, Yi | Qin, Yajie | Wang, Yuanyuan

Article Type: Research Article

Abstract: Activities recognition using a wearable device is a very popular research field. Among all wearable sensors, the accelerometer is one of the most common sensors due to its versatility and relative ease of use. This paper proposes a novel method for activity recognition based on a single accelerometer. To process the activity information from accelerometer data, two kinds of signal features are extracted. Firstly, five features including the mean, the standard deviation, the entropy, the energy and the correlation are calculated. Then a method called empirical mode decomposition (EMD) is used for the feature extraction since accelerometer data are non-linear …and non-stationary. Several time series named intrinsic mode functions (IMFs) can be obtained after the EMD. Additional features will be added by computing the mean and standard deviation of first three IMFs. A classifier called Adaboost is adopted for the final activities recognition. In the experiments, a single sensor is separately positioned in the waist, left thigh, right ankle and right arm. Results show that the classification accuracy is 94.69%, 86.53%, 91.84% and 92.65%, respectively. These relatively high performances demonstrate that activities can be detected irrespective of the position by reducing problems such as the movement constrain and discomfort. Show more

Keywords: Activity recognition, accelerometer, empirical mode decomposition (EMD), adaboost

DOI: 10.3233/BME-151452

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1533-S1539, 2015

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

Article Type: Research Article

Abstract: The false-positive reduction (FPR) is a crucial step in the computer aided detection system for the breast. The issues of imbalanced data distribution and the limitation of labeled samples complicate the classification procedure. To overcome these challenges, we propose oversampling and semi-supervised learning methods based on the restricted Boltzmann machines (RBMs) to solve the classification of imbalanced data with a few labeled samples. To evaluate the proposed method, we conducted a comprehensive performance study and compared its results with the commonly used techniques. Experiments on benchmark dataset of DDSM demonstrate the effectiveness of the RBMs based oversampling and semi-supervised learning …method in terms of geometric mean (G-mean) for false positive reduction in Breast CAD. Show more

Keywords: Breast computer aided detection, false-positive reduction, imbalanced data learning, semi-supervised learning, restricted Boltzmann machines

DOI: 10.3233/BME-151453

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1541-S1547, 2015

Authors: Yang, Jianli | Bai, Yang | Li, Guojun | Liu, Ming | Liu, Xiuling

Article Type: Research Article

Abstract: Premature ventricular contraction (PVC) is one of the most serious arrhythmias. Without early diagnosis and proper treatment, PVC can result in significant complications. In this paper, a novel feature extraction method based on a sparse auto-encoder (SAE) and softmax regression (SR) classifier was used to differentiate PVCs from other common Non-PVC rhythms, including normal sinus (N), left bundle branch block (LBBB), right bundle branch block (RBBB), atrial premature contraction (APC), and paced beat (PB) rhythms. The proposed method was analyzed using 40 ECG records obtained from the MIT-BIH Arrhythmia Database. The proposed method exhibited an overall accuracy of 99.4%, with …a PVC recognition sensitivity and positive predictability of 97.9% and 91.8%, respectively. Show more

Keywords: PVC diagnosis, sparse auto-encoder, softmax regression, feature extraction

DOI: 10.3233/BME-151454

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1549-S1558, 2015

Authors: Wei, Chang-An | Dai, Huhe

Article Type: Research Article

Abstract: P wave and T wave in human-body electrocardiogram (ECG) signals often fuse together when atrial premature contract (APC) occurs. P waves within the fused signals are valuable for the measurement of P wave parameters as well as diagnosis of supra-ventricular arrhythmias. However, the problem of extracting P wave from the fused signals is seldom addressed. In this study, a novel T wave cancellation method for P wave extraction based on maximum a posteriori (MAP) estimation is proposed. In order to accurately cancel the T wave within the fused signal, T wave and the timing point of T wave peak are …estimated simultaneously. The estimated timing point of T wave peak is used as alignment reference point for T wave subtraction. Simulation results show that the proposed method outperform the traditional T wave cancellation method in terms of both normalized mean square error and cross-correlation index. The results for real ECGs with APC demonstrate that the extracted P waves using the proposed method are more similar to the non-overlapping P waves in terms of morphology than the ones using the traditional T wave cancellation method. Show more

Keywords: Electrocardiogram, P wave extraction, atrial premature contract, maximum a posteriori

DOI: 10.3233/BME-151455

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1559-S1568, 2015

Authors: Sánchez-González, Alain | García-Zapirain, Begoña | Maestro Saiz, Iratxe | Yurrebaso Santamaría, Izaskun

Article Type: Research Article

Abstract: Periodic activity in electroencephalography (PA-EEG) is shown as comprising a series of repetitive wave patterns that may appear in different cerebral regions and are due to many different pathologies. The diagnosis based on PA-EEG is an arduous task for experts in Clinical Neurophysiology, being mainly based on other clinical features of patients. Considering this difficulty in the diagnosis it is also very complicated to establish the prognosis of patients who present PA-EEG. The goal of this paper is to propose a method capable of determining patient prognosis based on characteristics of the PA-EEG activity. The approach, based on a parallel …classification architecture and a majority vote system has proven successful by obtaining a success rate of 81.94% in the classification of patient prognosis of our database. Show more

Keywords: Medical classification, bioinformatics, feature selection, EEG periodic activity

DOI: 10.3233/BME-151456

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1569-S1578, 2015

Authors: Li, Xu | Yang, Jiali | Ding, Mingyue | Yuchi, Ming

Article Type: Research Article

Abstract: Ultrasound (US) has emerged as a non-invasive imaging modality that can provide anatomical structure information in real time. To enable the experimental analysis of new 2-D array ultrasound beamforming methods, a pre-beamformed parallel raw data acquisition system was developed for 3-D data capture of 2D array transducer. The transducer interconnection adopted the row-column addressing (RCA) scheme, where the columns and rows were active in sequential for transmit and receive events, respectively. The DAQ system captured the raw data in parallel and the digitized data were fed through the field programmable gate array (FPGA) to implement the pre-beamforming. Finally, 3-D images …were reconstructed through the devised platform in real-time. Show more

Keywords: 2-D array transducer, 3-D imaging system, row-column scheme, real-time

DOI: 10.3233/BME-151457

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1579-S1585, 2015

Authors: Choi, Hyun Ho | Lee, Ju Hwan | Kim, Sung Min | Park, Sung Yun

Article Type: Research Article

Abstract: Here, the speckle noise in ultrasonic images is removed using an image fusion-based denoising method. To optimize the denoising performance, each discrete wavelet transform (DWT) and filtering technique was analyzed and compared. In addition, the performances were compared in order to derive the optimal input conditions. To evaluate the speckle noise removal performance, an image fusion algorithm was applied to the ultrasound images, and comparatively analyzed with the original image without the algorithm. As a result, applying DWT and filtering techniques caused information loss and noise characteristics, and did not represent the most significant noise reduction performance. Conversely, an image …fusion method applying SRAD-original conditions preserved the key information in the original image, and the speckle noise was removed. Based on such characteristics, the input conditions of SRAD-original had the best denoising performance with the ultrasound images. From this study, the best denoising technique proposed based on the results was confirmed to have a high potential for clinical application. Show more

Keywords: Ultrasound imaging, speckle noise, image fusion, discrete wavelet transform, SRAD

DOI: 10.3233/BME-151458

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1587-S1597, 2015

Authors: Hwang, Yoo Na | Lee, Ju Hwan | Kim, Ga Young | Jiang, Yuan Yuan | Kim, Sung Min

Article Type: Research Article

Abstract: This paper focuses on the improvement of the diagnostic accuracy of focal liver lesions by quantifying the key features of cysts, hemangiomas, and malignant lesions on ultrasound images. The focal liver lesions were divided into 29 cysts, 37 hemangiomas, and 33 malignancies. A total of 42 hybrid textural features that composed of 5 first order statistics, 18 gray level co-occurrence matrices, 18 Law’s, and echogenicity were extracted. A total of 29 key features that were selected by principal component analysis were used as a set of inputs for a feed-forward neural network. For each lesion, the performance of the diagnosis …was evaluated by using the positive predictive value, negative predictive value, sensitivity, specificity, and accuracy. The results of the experiment indicate that the proposed method exhibits great performance, a high diagnosis accuracy of over 96% among all focal liver lesion groups (cyst vs. hemangioma, cyst vs. malignant, and hemangioma vs. malignant) on ultrasound images. The accuracy was slightly increased when echogenicity was included in the optimal feature set. These results indicate that it is possible for the proposed method to be applied clinically. Show more

Keywords: Ultrasound, focal liver lesions, classification, artificial neural network

DOI: 10.3233/BME-151459

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1599-S1611, 2015

Authors: Aliabadi, Saeid | Yu, Jinhua | Wang, Yuanyuan

Article Type: Research Article

Abstract: The contrast and resolution have trade-off in medical ultrasound imaging. Most of adaptive beamformer can enhance the imaging resolution significantly but not improve the contrast at the same time. The principal component analysis (PCA) based beamformers such as the eigenspace-based minimum variance (ESBMV) beamformer provide a good imaging resolution. Neighbors of the focal point include the common noise, interface and signal components. Echo signal of the neighbor points can be used to suppress the noise and extract the signal component of the focal point. Based on this idea, in order to improve the quality of PCA based beamformers both in …the imaging contrast and resolution, a novel beamforming method is proposed. This proposed beamformer utilizes a kernel to select neighbor points. The number of eigenvectors is estimated by using any PCA method. Then the number of selected eigenvectors for each focal point is compared with the number of selected eigenvectors of its neighbor points and is changed to a new value. The selected eigenvectors of the covariance matrix is used to construct the signal subspace. The estimated signal subspace is projected onto the minimum variance (MV) weight vector to calculate the desire weight vector. Results of experiments show that the proposed beamformer can improve the imaging contrast significantly while keeping the resolution quality similar to ESBMV beamformer. Show more

Keywords: Ultrasound imaging, beamforming, minimum variance, eigenvalue

DOI: 10.3233/BME-151460

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1613-S1621, 2015

Authors: He, Xiaonian | Liu, Weixiang | Chen, Siping | Qin, Zhengdi

Article Type: Research Article

Abstract: In the field of ultrasonic imaging technology, the problem of geometric distortion is often encountered, especially in the ultrasonic near-field. In this study, a new approach is proposed to compensate for geometric distortion in the synthetic aperture ultrasonic imaging system. This approach is based on the synthetic aperture ultrasonic holographic B-scan (UHB) imaging system, which is a combination of ultrasonic holography based on the backward propagation principle and the conventional B-scan technique. To solve the geometric distortion problem, the operation of the spatial compression and resampling in the frequency domain are introduced. The main advantage of the approach is that …the real holographic value can be calculated without distortion by using the spatial interpolation function after the spatial frequency compression. After the compensation for geometric distortion is performed, the synthetic aperture technique based on the backward propagation principle is then applied in the process of the two-dimensional numerical imaging reconstruction. Both the simulation and measurement experiment show that the approach is promising. The geometric distortion that is dependent on the wave front angle can be effectively compensated. The spatial resolution is practically uniform throughout the depth range and close to the theoretical limit in the experiments. Show more

Keywords: Synthetic aperture ultrasonic imaging, geometric distortion, spatial compression, re-sampling, numerical imaging reconstruction

DOI: 10.3233/BME-151461

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1623-S1632, 2015

Authors: Zhang, Yaonan | Sun, Tingting | Teng, Yueyang | Li, Hong | Kang, Yan

Article Type: Research Article

Abstract: Myocardial elastography (ME) is a strain imaging technique used to diagnose myocardial diseases. Axial and lateral displacement calculations are pre-conditions of strain image acquisition in ME. W.N. Lee et al. proposed a normalized cross-correlation (NCC) and recorrelation method to obtain both axial and lateral displacements in ME. However, this method is not noise-resistant and of high computational cost. This paper proposes a predicted fast NCC algorithm based on W.N. Lee’s method, with the additions of sum-table NCC and a displacement prediction algorithm, to obtain efficient and accurate axial and lateral displacements. Compared to experiments based on the NCC and recorrelation …methods, the results indicate that the proposed NCC method is much faster (predicted fast NCC method, 69.75s for a 520×260 image; NCC and recorrelation method, 1092.25s for a 520×260 image) and demonstrates better performance in eliminating decorrelation noise (SNR of the axial and lateral strain using the proposed method, 5.87 and 1.25, respectively; SNR of the axial and lateral strain using the NCC and recorrelation method, 1.48 and 1.09, respectively). Show more

Keywords: Myocardial elastography (ME), displacement estimation, normalized cross-correlation, recorrelation, prediction

DOI: 10.3233/BME-151462

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1633-S1639, 2015

Authors: Chiang, Hsien-Wen | Liu, Ya-Ling | Chen, Tou-Rong | Chen, Chun-Lon | Chiang, Hsien-Jen | Chao, Shin-Yu

Article Type: Research Article

Abstract: This work aimed to investigate the spatial distribution of scattered radiation doses induced by exposure to the portable X-ray, the C-arm machine, and to simulate the radiologist without a shield of lead clothing, radiation doses absorbed by medical staff at 2 m from the central exposure point. Material and method: With the adoption of the Rando Phantom, several frequently X-rayed body parts were exposed to X-ray radiation, and the scattered radiation doses were measured by ionization chamber dosimeters at various angles from the patient. Assuming that the central point of the X-ray was located at the belly button, five detection …points were distributed in the operation room at 1 m above the ground and 1-2 m from the central point horizontally. Results: The radiation dose measured at point B was the lowest, and the scattered radiation dose absorbed by the prosthesis from the X-ray’s vertical projection was 0.07 ±0.03 μ Gy, which was less than the background radiation levels. The Fluke biomedical model 660-5DE (400 cc) and 660-3DE (4 cc) ion chambers were used to detect air dose at a distance of approximately two meters from the central point. The AP projection radiation doses at point B was the lowest (0.07±0.03 μ Gy) and the radiation doses at point D was the highest (0.26±0.08 μ Gy) .Only taking the vertical projection into account, the radiation doses at point B was the lowest (0.52 μ Gy), and the radiation doses at point E was the highest (4 μ Gy).The PA projection radiation at point B was the lowest (0.36 μ Gy) and the radiation doses at point E was the highest(2.77 μ Gy), occupying 10-32% of the maximum doses. The maximum dose in five directions was nine times to the minimum dose. When the PX and the C-arm machine were used, the radiation doses at a distance of 2 m were attenuated to the background radiation level. The radiologist without a lead shield should stand at point B of patient’s feet. Accordingly, teaching materials on radiation safety for radiological interns and clinical technicians were formulated. Show more

Keywords: Portable X-ray machine, dose, exposure, ionization chamber dosimeter

DOI: 10.3233/BME-151463

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1641-S1650, 2015

Authors: Pan, Lung Fa | Erdene, Erdenetsetseg | Chen, Chun Chi | Pan, Lung Kwang

Article Type: Research Article

Abstract: In this study, the phantom imaging quality of 64-slice CT acquisition protocol was quantitatively evaluated using Taguchi. The phantom acrylic line group was designed and assembled with multiple layers of solid water plate in order to imitate the adult abdomen, and scanned with Philips brilliance CT in order to simulate a clinical examination. According to the Taguchi L8 (27 ) orthogonal array, four major factors of the acquisition protocol were optimized, including (A) CT slice thickness, (B) the image reconstruction filter type, (C) the spiral CT pitch, and (D) the matrix size. The reconstructed line group phantom image was counted …by four radiologists for three discrete rounds in order to obtain the averages and standard deviations of the line counts and the corresponding signal to noise ratios (S/N). The quantified S/N values were analyzed and the optimal combination of the four factor settings was determined to be comprised of (A) a 1-mm thickness, (B) a sharp filter type, (C) a 1.172 spiral CT pitch, and (D) a 1024×1024 matrix size. The dominant factors included the (A) filter type and the cross interaction between the filter type and CT slice thickness (A×B). The minor factors were determined to be (C) the spiral CT pitch and (D) the matrix size since neither was capable of yielding a 95% confidence level in the ANOVA test. Show more

Keywords: 64-slice CT, reconstructed imaging, optimization, ANOVA, line phantom

DOI: 10.3233/BME-151464

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1651-S1658, 2015

Authors: Liao, Xiongfei | Wang, Yunlai | Lang, Jinyi | Wang, Pei | Li, Jie | Ge, Ruigang | Yang, Jack

Article Type: Research Article

Abstract: To evaluate the Elekta kilovoltage CBCT doses and the associated technical protocols with patient dosimetry estimation. Image guidance technique with cone-beam CT (CBCT) in radiation oncology on a daily basis can deliver a significant dose to the patient. To evaluate the patient dose from LINAC-integrated kV cone beam CT imaging in image-guided radiotherapy. CT dose index (CTDI) were measured with PTW TM30009 CT ion chamber in air, in head phantom and body phantom, respectively; with different combinations of tube voltage, current, exposure time per frame, collimator and gantry rotation range. Dose length products (DLP) were subsequently calculated to account for …volume integration effects. The CTDI and DLP were also compared to AcQSim™ simulator CT for routine clinical protocols. Both CTDIair and CTDIw depended quadratically on the voltage, while linearly on milliampere x seconds (mAs) settings. It was shown that CTDIw and DLP had very close relationship with the collimator settings and the gantry rotation ranges. Normalized CTDIw for Elekta XVI™ CBCT was lower than that of ACQSim simulator CT owing to its pulsed radiation output characteristics. CTDIw can be used to assess the patient dose in CBCT due to its simplicity for measurement and reproducibility. Regular measurement should be performed in QA & QC program. Optimal image parameters should be chosen to reduce patient dose during CBCT. Show more

Keywords: Cone-beam CT, CT dose index, dose-length product, image-guided radiotherapy

DOI: 10.3233/BME-151465

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1659-S1667, 2015

Authors: Park, S.I. | Lee, J.H. | Ham, H.J. | Jung, Y.J. | Park, M.S. | Lee, J. | Maeng, L.S. | Chung, Y.A. | Jang, K.S.

Article Type: Research Article

Abstract: Liver cirrhosis is a predominant risk factor for hepatocellular carcinoma (HCC). However, the exact mechanism of the progression from cirrhosis to cancer remains unclear. The uptake of 2-[18 F]-fluoro-2-deoxy-D-glucose (18 F-FDG) is widely used as a marker of increased glucose metabolism to monitor the progression of cancer with positron emission tomography (PET)/computed tomography (CT). Here we investigated the feasibility of using 18 F-FDG PET/CT in the diethylnitrosamine (DEN) mediated experimental hepatocellular carcinoma model. Rats received weekly intraperitoneal injections of DEN for 16 weeks for induction of HCC. We recorded starting from 0 days or 0 weeks after the last DEN …injection. The weight and survival rate of rats were then measured. Also, an 18 F-FDG PET scan and serum analysis were performed at minus 2, 0, plus 2, and plus 4 weeks after the last DEN injection. The body weight of rats was maintained between 350 g and 370 g during 14 and 20 weeks, and the rats were euthanized at 35 days after the last DEN injection. The serum levels of alanine transaminase (ALT), aspartate transaminase (AST), and alkaline phosphate (ALP) were significantly higher at zero weeks after the last DEN injection. The 18 F-FDG uptake for the quantitative evaluation of HCC was done by measuring the region of interest (ROI). At minus two weeks after the last DEN injection, the ROI of rats had significantly increased compared to the normal group, in a time-dependent manner. These results suggest that FDG uptake serves as a good screening test to evaluate the feasibility of DEN-induced HCC. Show more

Keywords: Hepatocellular carcinoma, PET/CT, 18F-FDG

DOI: 10.3233/BME-151466

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1669-S1676, 2015

Authors: Tseng, Hsien-Chun | Pan, Lung-Kang | Chen, Hsin-Yu | Liu, Wen-Shan | Hsu, Chang-Chieh | Chen, Chien-Yi

Article Type: Research Article

Abstract: This study is the first to use 10- to 90-kg tissue-equivalent phantoms as patient surrogates to measure peripheral skin doses (Dskin ) in lung cancer treatment through Volumetric Modulated Arc Therapy of the Axesse linac. Five tissue-equivalent and Rando phantoms were used to simulate lung cancer patients using the thermoluminescent dosimetry (TLD-100H) approach. TLD-100H was calibrated using 6 MV photons coming from the Axesse linac. Then it was inserted into phantom positions that closely corresponded with the position of the represented organs and tissues. TLDs were measured using the Harshaw 3500 TLD reader. The ICRP 60 evaluated the mean Dskin …to the lung cancer for 1 fraction (7 Gy) undergoing VMAT. The Dskin of these phantoms ranged from 0.51±0.08 (10-kg) to 0.22±0.03 (90-kg) mSv/Gy. Each experiment examined the relationship between the Dskin and the distance from the treatment field. These revealed strong variations in positions close to the tumor center. The correlation between Dskin and body weight was Dskin (mSv) = -0.0034x + 0.5296, where x was phantom’s weight in kg. R2 is equal to 0.9788. This equation can be used to derive an equation for lung cancer in males. Finally, the results are compared to other published research. These findings are pertinent to patients, physicians, radiologists, and the public. Show more

Keywords: Axesse linac, skin dose, TLD, tissue-equivalent phantom, ICRP 60

DOI: 10.3233/BME-151467

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1677-S1683, 2015

Authors: Deng, Luzhen | Mi, Deling | He, Peng | Feng, Peng | Yu, Pengwei | Chen, Mianyi | Li, Zhichao | Wang, Jian | Wei, Biao

Article Type: Research Article

Abstract: For lack of directivity in Total Variation (TV) which only uses x-coordinate and y-coordinate gradient transform as its sparse representation approach during the iteration process, this paper brought in Adaptive-weighted Diagonal Total Variation (AwDTV) that uses the diagonal direction gradient to constraint reconstructed image and adds associated weights which are expressed as an exponential function and can be adaptively adjusted by the local image-intensity diagonal gradient for the purpose of preserving the edge details, then using the steepest descent method to solve the optimization problem. Finally, we did two sets of numerical simulation and the results show that the proposed …algorithm can reconstruct high-quality CT images from few-views projection, which has lower Root Mean Square Error (RMSE) and higher Universal Quality Index (UQI) than Algebraic Reconstruction Technique (ART) and TV-based reconstruction method. Show more

Keywords: Computed tomography (CT), sparse projection, adaptive-weighted diagonal total variation (AwDTV), compressive sensing (CS)

DOI: 10.3233/BME-151468

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1685-S1693, 2015

Authors: Ran, Peng | Xiao, Xiaoming | He, Wei | Li, Zhangyong

Article Type: Research Article

Abstract: Because of the need for rapid detection and location of diseases in clinical applications, this work proposes a composite measurement of magnetic induction tomography (MIT) and electrical impedance tomography (EIT). This paper is composed of the following aspects: portable and integral hardware design, stable dual constant-current sources, the composite detection method, cross-plane data acquirement, 3-dimensional image reconstruction and so on. A qualitative evaluation of conductivity, resolution and relative position error were taken by combining the EIT and MIT methods via the experiment model. The sensitivities of both methods were analyzed to improve the imaging results. The reconstruction results reveal that …the system is capable of obtaining better physiological measurements, which is very useful in clinical monitoring, quick medical diagnosing and preliminary screening of community health. Show more

Keywords: Bioelectrical impedance measurement, magnetic induction tomography, cross evaluation and imaging, 3-dimensional image

DOI: 10.3233/BME-151469

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1695-S1702, 2015

Authors: Avcı, Cafer | Akbaş, Ahmet

Article Type: Research Article

Abstract: In this study, an efficient and robust method classifying the minute based occurrence of sleep apnea is aimed. Three respiration signals obtained from abdominal, chest and nasal way extracted from polysomnography recordings. Wavelet transform based on feature extraction methods are applied on the 1 minute length respiration signals. Dimension reduction process is facilitated by using principal component analysis. The features obtained from 8 recordings are used for the classification sleep apnea by using three ensemble classifiers. According to the results, the classification accuracies have been obtained between 92.07-98.43%, 92.75-98.68% and 92.42-98.61% by using three different ensemble classifier based on abdominal, …chest and nasal based analysis, respectively for AdaBoost, Random Forest and Random Subspace. However the best result is obtained analyzing nasal based respiratory signal by using Random Forest method. In this case accuracy is 98.68%. Show more

Keywords: Sleep apnea, respiratory signals, wavelet, ensemble, boosting, bagging

DOI: 10.3233/BME-151470

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1703-S1710, 2015

Authors: Lu, Qibing | Wang, Pan | Guo, Sihai | Sheng, Buyun | Liu, Xingxing | Fan, Zhun

Article Type: Research Article

Abstract: This paper introduces an automatic bond graph design method based on genetic programming for the evolutionary design of micro-resonator. First, the system-level behavioral model is discussed, which based on genetic programming and bond graph. Then, the geometry parameters of components are automatically optimized, by using the genetic algorithm with constraints. To illustrate this approach, a typical device micro-resonator is designed as an example in biomedicine. This paper provides a new idea for the automatic optimization design of biomedical sensors by evolutionary calculation.

Keywords: Genetic programming (GP), bond graph (BG), micro-resonator, evolutionary computation

DOI: 10.3233/BME-151471

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1711-S1719, 2015

Authors: Shi, Yu | Yan, Guozheng | Zhu, Bingquan | Liu, Gang

Article Type: Research Article

Abstract: Wireless power transmission (WPT) technology can solve the energy shortage problem of the video capsule endoscope (VCE) powered by button batteries, but the fixed platform limited its clinical application. This paper presents a portable WPT system for VCE. Besides portability, power transfer efficiency and stability are considered as the main indexes of optimization design of the system, which consists of the transmitting coil structure, portable control box, operating frequency, magnetic core and winding of receiving coil. Upon the above principles, the correlation parameters are measured, compared and chosen. Finally, through experiments on the platform, the methods are tested and evaluated. …In the gastrointestinal tract of small pig, the VCE is supplied with sufficient energy by the WPT system, and the energy conversion efficiency is 2.8%. The video obtained is clear with a resolution of 320×240 and a frame rate of 30 frames per second. The experiments verify the feasibility of design scheme, and further improvement direction is discussed. Show more

Keywords: Portable wireless power transmission, video capsule endoscope, resonant circuit, frequency stability

DOI: 10.3233/BME-151472

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1721-S1730, 2015

Authors: Jia, Guifeng | Yang, Pan | Zhou, Jie | Zhang, Hengyi | Lin, Chengyu | Chen, Jin | Cai, Guolong | Yan, Jing | Ning, Gangmin

Article Type: Research Article

Abstract: Mobile health (mHealth) technology has been proposed to alleviate the lack of sufficient medical resources for personal healthcare. However, usage difficulties and compliance issues relating to this technology restrict the effect of mHealth system-supported self-management. In this study, an mHealth framework is introduced to overcome these drawbacks and improve the outcome of self-management. We implemented a set of ease of use principles in the mHealth design and employed the quantitative Fogg Behavior Model to enhance users’ execution ability. The framework was realized in a prototype design for the mHealth system, which consists of medical apparatuses, mobile applications and a health …management server. The system is able to monitor the physiological status in an unconstrained manner with simplified operations, while supervising the healthcare plan. The results suggest that the present framework design is accessible for ordinary users and effective in improving users’ execution ability in self-management. Show more

Keywords: Self-management, mobile health, execution ability, ease of use, persuasive technology

DOI: 10.3233/BME-151473

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1731-S1740, 2015

Authors: Lim, Hyung-Gyu | Kim, Jong Hoon | Shin, Dong Ho | Woo, Seong Tak | Seong, Ki Woong | Lee, Jyung Hyun | Kim, Myoung Nam | Wei, Qun | Cho, Jin-Ho

Article Type: Research Article

Abstract: Many types of fully implantable hearing aids have been developed. Most of these devices are implanted behind the ear. To maintain the implanted device for a long period of time, a rechargeable battery and wireless power transmission are used. Because inductive coupling is the most renowned method for wireless power transmission, many types of fully implantable hearing aids are transcutaneously powered using inductively coupled coils. Some patients with an implantable hearing aid require a method for conveniently charging their hearing aid while they are resting or sleeping. To address this need, a wireless charging pillow has been developed that employs …a circular array coil as one of its primary parts. In this device, all primary coils are simultaneously driven to maintain an effective charging area regardless of head motion. In this case, however, there may be a magnetic weak zone that cannot be charged at the specific secondary coil’s location on the array coil. In this study, assuming that a maximum charging distance is 4 cm, a circular array coil—serving as a primary part of the charging pillow—was designed using finite element analysis. Based on experimental results, the proposed device can charge an implantable hearing aid without a magnetic weak zone within 4 cm of the perpendicular distance between the primary and secondary coils. Show more

Keywords: Wireless charging pillow, fully implantable hearing aid, inductive coupling, circular array coil, magnetic weak zone

DOI: 10.3233/BME-151474

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1741-S1747, 2015

Authors: Nguyen, Tan Loc | Won, Yonggwan

Article Type: Research Article

Abstract: Snoring detection is important for diagnosing obstructive sleep apnea syndrome (OSAS) and other respiratory sleep disorders. In general, audio signal processing such as snoring sound analysis uses the frequency characteristics of the signal. Recently, a correlational filter Multilayer Perceptron neural network (f-MLP) has been proposed, which has the first hidden layer of correlational filter operations in frequency domain. It demonstrated a superior classification performance for the pattern sets; of these, frequency information is the dominant feature for classification. The first hidden layer is implemented with the correlational filter operation; its output is the power spectrum of the filter output, while …the other layers are the same as the ordinary multilayer Perceptron (o-MLP). By using the back-propagation learning algorithm for the correlational filter layer, f-MLP was able to self-adapt the filter coefficients to produce its output with more discrimination power for classification in the higher layer. In this research, this f-MLP was applied for sleep snoring signal detection. As a result, the f-MLP achieved an average detection rate of 96% for the test patterns, compared to the conventional multilayer neural network that demonstrates an 82% average detection rate. Show more

Keywords: Sleep snoring, Fourier transform, correlational filter, classification, multilayer perceptron neural network

DOI: 10.3233/BME-151475

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1749-S1755, 2015

Authors: Zhou, Xi Y. | Tian, Xue W. | Lim, Joon S.

Article Type: Research Article

Abstract: In the data mining field, classification is a very crucial technology, and the Bayesian classifier has been one of the hotspots in classification research area. However, assumptions of Naive Bayesian and Tree Augmented Naive Bayesian (TAN) are unfair to attribute relations. Therefore, this paper proposes a new algorithm named Fuzzy Naive Bayesian (FNB) using neural network with weighted membership function (NEWFM) to extract regulated relations and weights. Then, we can use regulated relations and weights to construct a regulated network. Finally, we will classify the heart and Haberman datasets by the FNB network to compare with experiments of Naive Bayesian …and TAN. The experiment results show that the FNB has a higher classification rate than Naive Bayesian and TAN. Show more

Keywords: Naive Bayesian, Tree Augmented Naive Bayesian, Fuzzy Naive Bayesian, fuzzy neural network, weights

DOI: 10.3233/BME-151476

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1757-S1762, 2015

Authors: Ha, Jihwan | Kim, Hyunjin | Yoon, Youngmi | Park, Sanghyun

Article Type: Research Article

Abstract: MicroRNAs (miRNA) are known to be involved in the development of various diseases. Hence various scientists in the field have been utilized computational analyses to determine the relationship between miRNA and diseases. However, the knowledge of miRNA and disease is still very limited. Therefore, we combined Environmental Factor (EF) data to a miRNA global network. Increasing research has shown that relationship between miRNAs and EFs play a significant role in classifying types of diseases. Environmental Factors consist of radiation, drugs, viruses, alcohol, cigarettes, and stress. Our global network considered all the interactions between every pair of miRNAs, which has led …to precise analyses in comparison to local networks. As a result, our approaches’ performance demonstrated its effectiveness in identifying disease-related miRNA and this is the area under the ROC curve (AUC) of 74.46%. Furthermore, comparative experiment has shown that our approach performs comparable to other existing methods with an accuracy of 94%, 90% and 96% for breast cancer, colonic cancer, and lung cancer respectively. In conclusion, these results support that our research has broadened new biological insights on identifying disease-related miRNAs. Show more

Keywords: miRNA, disease, environmental factor, network, propagation algorithm

DOI: 10.3233/BME-151477

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1763-S1772, 2015

Authors: Kim, Ji-Sun | Kim, A-Hee | Oh, Han-Byeol | Goh, Bong-Jun | Lee, Eun-Suk | Kim, Jun-Sik | Jung, Gu-In | Baek, Jin-Young | Jun, Jae-Hoon

Article Type: Research Article

Abstract: A spectrophotometer is the basic measuring equipment essential to most research activity fields requiring samples to be measured, such as physics, biotechnology and food engineering. This paper proposes a system that is able to detect sample concentration and color information by using LED and color sensor. Purity and wavelength information can be detected by CIE diagram, and the concentration can be estimated with purity information. This method is more economical and efficient than existing spectrophotometry, and can also be used by ordinary persons. This contribution is applicable to a number of fields because it can be used as a colorimeter …to detect the wavelength and purity of samples. Show more

Keywords: Color information, color space, light emitting diode, spectrophotometer

DOI: 10.3233/BME-151478

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1773-S1780, 2015

Authors: Manzoor, Umar | Shahid, Sarosh | Zafar, Bassam

Article Type: Research Article

Abstract: Multiple sequence alignment plays a key role in the computational analysis of biological data. Different programs are developed to analyze the sequence similarity. This paper highlights the algorithmic techniques of the most popular multiple sequence alignment programs. These programs are then evaluated on the basis of execution time and scalability. The overall performance of these programs is assessed to highlight their strengths and weaknesses with reference to their algorithmic techniques. In terms of overall alignment quality, T-Coffee and Mafft attain the highest average scores, whereas K-align has the minimum computation time.

Keywords: Multiple sequence alignment, clustalW, k-align, muscle, mafft, t-coffee, progressive alignment

DOI: 10.3233/BME-151479

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1781-S1789, 2015

Authors: Jo, Heeseung | Koh, Gunhwan

Article Type: Research Article

Abstract: Due to next-generation sequencing (NGS) technology, genome sequencing is able to process much more data at low cost. In NGS data analysis, the mapping of sequences into a reference genome takes the largest amount of time to process. Although the Burrows-Wheeler Aligner (BWA) tool is one of the most widely used open-source software tools to align read sequences, it is still limited in that it does not fully support multi-thread mechanisms during the alignment steps. In this paper, we propose a BWA-MT tool, evolved from BWA but supporting multi-thread computation, designed to fully utilize the underlying multi-core architecture of computing …resources. By using multi-thread computation, BWA-MT can significantly shorten the time needed to generate an alignment for single-end read sequences. Meanwhile, it generates an identical Sequence Alignment Map (SAM) result file as BWA. To evaluate BWA-MT, we use an evaluation system equipped with twelve cores and 32 GB memory. As a workload, we used the hg19 human genome reference sequence and various numbers of read sequences from 1M to 40M. In our evaluation, BWA-MT displays up to 3.7 times faster performance and generates an identical SAM result file to BWA. Although the increased speed might be dependent on computing resources, we confirm that BWA-MT is highly efficient and effective. Show more

Keywords: genome sequencing, next-generation sequencing (NGS), burrow-wheeler aligner (BWA) tool, multi-thread

DOI: 10.3233/BME-151480

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1791-S1796, 2015

Authors: Song, Dandan | Li, Ning | Liao, Lejian

Article Type: Research Article

Abstract: Due to the generation of enormous amounts of data at both lower costs as well as in shorter times, whole-exome sequencing technologies provide dramatic opportunities for identifying disease genes implicated in Mendelian disorders. Since upwards of thousands genomic variants can be sequenced in each exome, it is challenging to filter pathogenic variants in protein coding regions and reduce the number of missing true variants. Therefore, an automatic and efficient pipeline for finding disease variants in Mendelian disorders is designed by exploiting a combination of variants filtering steps to analyze the family-based exome sequencing approach. Recent studies on the Freeman-Sheldon disease …are revisited and show that the proposed method outperforms other existing candidate gene identification methods. Show more

Keywords: Mendelian disorders, disease gene identification, whole-exome sequencing

DOI: 10.3233/BME-151481

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1797-S1803, 2015

Authors: Feng, Yu | Cao, Hui | Zhang, Yanbin

Article Type: Research Article

Abstract: High order partial least squares (HOPLS) is a novel data processing method. It is highly suitable for building prediction model which has tensor input and output. The objective of this study is to build a prediction model of the relationship between sinoatrial node field potential and high glucose using HOPLS. The three sub-signals of the sinoatrial node field potential made up the model’s input. The concentration and the actuation duration of high glucose made up the model’s output. The results showed that on the premise of predicting two dimensional variables, HOPLS had the same predictive ability and a lower dispersion …degree compared with partial least squares (PLS). Show more

Keywords: High order partial least squares, sinoatrial node field potential, prediction model, signal decomposition

DOI: 10.3233/BME-151482

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1805-S1811, 2015

Authors: Ling, Ping | Gao, Dajin | Zhou, Xifeng | Huang, Zhining | Rong, Xiangsheng

Article Type: Research Article

Abstract: Computer-aided diagnosis (CAD) approaches succeed in detecting a number of diseases, however, they are not good at addressing atrial hypertrophy disease due to the lack of training data. Support Vector Machine (SVM) is very popular in few CAD solutions to atrial hypertrophy. Yet the performance of SVM is moderate in atrial hypertrophy detection compared to its success in other classification problems. In this paper we propose a novel CAD algorithm, Local Discriminative SVM (LDSVM), to overcome the above-mentioned difficulty. LDSVM consists of a global SVM that is trained on the training data, and a local kNN that is trained based …on the information of SVM and query. When a query arrives, SVM gives the initial decision. If the initial decision is less confident, local kNN begins to modify the initial decision. LDSVM improves the accuracy of SVM through some contributions: the risk tube, the discriminant information derived from SVM hyperplane, the new metric and the self-tuning size of neighborhood. Empirical evidence on real medical datasets show high performance of LDSVM over the peers in addressing atrial hypertrophy problems. Show more

Keywords: Computer-aided diagnosis, support vector machine, discriminative direction, derivative of hyperplane function

DOI: 10.3233/BME-151483

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1813-S1820, 2015

Authors: Garcia-Chimeno, Yolanda | Garcia-Zapirain, Begonya

Article Type: Research Article

Abstract: The classification of subjects’ pathologies enables a rigorousness to be applied to the treatment of certain pathologies, as doctors on occasions play with so many variables that they can end up confusing some illnesses with others. Thanks to Machine Learning techniques applied to a health-record database, it is possible to make using our algorithm. hClass contains a non-linear classification of either a supervised, non-supervised or semi-supervised type. The machine is configured using other techniques such as validation of the set to be classified (cross-validation), reduction in features (PCA) and committees for assessing the various classifiers. The tool is easy to …use, and the sample matrix and features that one wishes to classify, the number of iterations and the subjects who are going to be used to train the machine all need to be introduced as inputs. As a result, the success rate is shown either via a classifier or via a committee if one has been formed. A 90% success rate is obtained in the ADABoost classifier and 89.7% in the case of a committee (comprising three classifiers) when PCA is applied. This tool can be expanded to allow the user to totally characterise the classifiers by adjusting them to each classification use. Show more

Keywords: Classification, machine learning, PCA, cross-validation, committee

DOI: 10.3233/BME-151484

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1821-S1828, 2015

Authors: Nie, Guoping | Li, Yong | Wang, Feichi | Wang, Siwen | Hu, Xuehai

Article Type: Research Article

Abstract: G-protein-coupled receptors (GPCRs) are seven membrane-spanning proteins and regulate many important physiological processes, such as vision, neurotransmission, immune response and so on. GPCRs-related pathways are the targets of a large number of marketed drugs. Therefore, the design of a reliable computational model for predicting GPCRs from amino acid sequence has long been a significant biomedical problem. Chaos game representation (CGR) reveals the fractal patterns hidden in protein sequences, and then fractal dimension (FD) is an important feature of these highly irregular geometries with concise mathematical expression. Here, in order to extract important features from GPCR protein sequences, CGR algorithm, fractal …dimension and amino acid composition (AAC) are employed to formulate the numerical features of protein samples. Four groups of features are considered, and each group is evaluated by support vector machine (SVM) and 10-fold cross-validation test. To test the performance of the present method, a new non-redundant dataset was built based on latest GPCRDB database. Comparing the results of numerical experiments, the group of combined features with AAC and FD gets the best result, the accuracy is 99.22% and Matthew’s correlation coefficient (MCC) is 0.9845 for identifying GPCRs from non-GPCRs. Moreover, if it is classified as a GPCR, it will be further put into the second level, which will classify a GPCR into one of the five main subfamilies. At this level, the group of combined features with AAC and FD also gets best accuracy 85.73%. Finally, the proposed predictor is also compared with existing methods and shows better performances. Show more

Keywords: GPCR, chaos game representation, support vector machine, fractal dimension

DOI: 10.3233/BME-151485

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1829-S1836, 2015

Authors: Huang, Hai-Hui | Liu, Xiao-Ying | Liang, Yong | Chai, Hua | Xia, Liang-Yong

Article Type: Research Article

Abstract: Tuberculosis (TB), caused by infection with mycobacterium tuberculosis, is still a major threat to human health worldwide. Current diagnostic methods encounter some limitations, such as sample collection problem or unsatisfied sensitivity and specificity issue. Moreover, it is hard to identify TB from some of other lung diseases without invasive biopsy. In this paper, the logistic models with three representative regularization approaches including Lasso (the most popular regularization method), and L 1 / 2 (the method that inclines to achieve more sparse …solution than Lasso) and Elastic Net (the method that encourages a grouping effect of genes in the results) adopted together to select the common gene signatures in microarray data of peripheral blood cells. As the result, 13 common gene signatures were selected, and sequentially the classifier based on them is constructed by the SVM approach, which can accurately distinguish tuberculosis from other pulmonary diseases and healthy controls. In the test and validation datasets of the blood gene expression profiles, the generated classification model achieved 91.86% sensitivity and 93.48% specificity averagely. Its sensitivity is improved 6%, but only 26% gene signatures used compared to recent research results. These 13 gene signatures selected by our methods can be used as the basis of a blood-based test for the detection of TB from other pulmonary diseases and healthy controls. Show more

Keywords: Tuberculosis, feature selection, early diagnostic, regularization, biomarkers

DOI: 10.3233/BME-151486

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1837-S1843, 2015

Authors: Xia, Hong | Li, Ao | Yu, Zhenhua | Liu, Xiaocheng | Feng, Huanqing

Article Type: Research Article

Abstract: Application of the Next generation sequencing (NGS) technology has demonstrated that most tumor samples exhibit intra-tumor heterogeneity. Here we proposed SAPPH (Somatic Aberrations Prediction for Paired Heterogeneous tumor samples), as a new method for estimating tumor somatic copy number aberrations as well as inferring tumor subclone proportions from heterogeneous tumor sequencing data. This method is based on CBS and local proportion clustering strategy. When SAPPH is applied on simulated tumor samples, the agreement between the results analyzed by SAPPH and the sequencing signals suggests that SAPPH can find the solution to best fit the signal distributions. We benchmark the performance …of SAPPH and show that it outperforms existing method in estimating tumor copy number aberrations. Show more

Keywords: Intra-tumor heterogeneity, NGS, copy number aberration, tumor subclone, proportion

DOI: 10.3233/BME-151487

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1845-S1853, 2015

Authors: Cheng, Ke | Chen, Qingfang | Yang, Xibei | Gao, Shang | Yu, Hualong

Article Type: Research Article

Abstract: To address the imbalanced classification problem emerging in Bioinformatics, a boundary movement-based extreme learning machine (ELM) algorithm called BM-ELM was proposed. BM-ELM tries to firstly explore the prior information about data distribution by condensing all training instances into the one-dimensional feature space corresponding to the original output in ELM, and then on the transformed space, to find the optimal moving distance of the classification hyperplane by estimating the probability density distributions of the instances in different classes. Experimental results on four real imbalanced bioinformatics classification data sets indicated that the proposed BM-ELM algorithm outperforms some traditional bias correction algorithms due …to it can greatly improve the sensitivity of the classification results with small loss of specificity as possible. Also, BM-ELM algorithm has presented better performance than the widely used support vector machine (SVM) classifier. The algorithm can be widely popularized in various large-scale bioinformatics applications. Show more

Keywords: Bioinformatics, extreme learning machine, imbalanced classification, kernel density estimation

DOI: 10.3233/BME-151488

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1855-S1862, 2015

Authors: Sun, Lin | Xu, Jiucheng | Yin, Jiaojiao

Article Type: Research Article

Abstract: Fuzzy clustering is an important tool for analyzing microarray data. A major problem in applying fuzzy clustering method to microarray gene expression data is the choice of parameters with cluster number and centers. This paper proposes a new approach to fuzzy kernel clustering analysis (FKCA) that identifies desired cluster number and obtains more steady results for gene expression data. First of all, to optimize characteristic differences and estimate optimal cluster number, Gaussian kernel function is introduced to improve spectrum analysis method (SAM). By combining subtractive clustering with max-min distance mean, maximum distance method (MDM) is proposed to determine cluster centers. …Then, the corresponding steps of improved SAM (ISAM) and MDM are given respectively, whose superiority and stability are illustrated through performing experimental comparisons on gene expression data. Finally, by introducing ISAM and MDM into FKCA, an effective improved FKCA algorithm is proposed. Experimental results from public gene expression data and UCI database show that the proposed algorithms are feasible for cluster analysis, and the clustering accuracy is higher than the other related clustering algorithms. Show more

Keywords: Spectral analysis, maximum distance, fuzzy clustering, gene expression data

DOI: 10.3233/BME-151489

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1863-S1869, 2015

Authors: Zhang, Hui | Wang, Jing | Sun, Ling | Xu, Qiuqin | Hou, Miao | Ding, Yueyue | Huang, Jie | Chen, Ye | Cao, Lei | Zhang, Jianmin | Qian, Weiguo | Lv, Haitao

Article Type: Research Article

Abstract: Obesity has become an increasingly serious health problem and popular research topic. It is associated with many diseases, especially cardiovascular disease (CVD)-related endothelial dysfunction. This study analyzed genes related to endothelial dysfunction and obesity and then summarized their most significant signaling pathways. Genes related to vascular endothelial dysfunction and obesity were extracted from a PubMed database, and analyzed by STRING, DAVID, and Gene-Go Meta-Core software. 142 genes associated with obesity were found to play a role in endothelial dysfunction in PubMed. A significant pathway (Angiotensin system maturation in protein folding and maturation) associated with obesity and endothelial dysfunction was explored. …The genes and the pathway explored may play an important role in obesity. Further studies about preventing vascular endothelial dysfunction obesity should be conducted through targeting these loci and pathways. Show more

Keywords: Pathway, obesity, vascular endothelial function, system biology

DOI: 10.3233/BME-151490

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1871-S1881, 2015

Authors: Guan, Changge | Niu, Xiaohui | Shi, Feng | Yang, Kun | Li, Nana

Article Type: Research Article

Abstract: DNA-binding proteins are involved and play a crucial role in a lot of important biological processes. Hence, the identification of the DNA-binding proteins is a challenging and significant problem. In order to reveal the intrinsic information correlated to DNA-binding, nine classes of candidate features based on different mathematical fields are applied to construct the prediction model with random forest. They are fractal dimension, conjoint triad feature, Hilbert-Huang Transformation, amino acid composition, dipeptide composition, chaos game representation, and the corresponding information entropies. These mathematical expressions are evaluated with 5-fold cross validation test. The results of numerical simulations show that the mathematical …features consisted of amino acid composition, fractal dimension and information entropies of amino acid and chaos game representation achieve the best performance. Its accuracy is 0.8157, and Matthew’s correlation coefficient (MCC) achieves 0.5968 on the benchmark dataset from DNA-Prot. By analyzing the components of top combination of the nine candidate features, the concepts of fractal dimension and information entropy are the effective and vital features, which can provide complementary sequence-order information on the basis of amino acid composition. Show more

Keywords: DNA-binding proteins, random forest, information entropy, fractal dimension, Hilbert-Huang transformation

DOI: 10.3233/BME-151491

Citation: Bio-Medical Materials and Engineering, vol. 26, no. s1, pp. S1883-S1889, 2015

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