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

Authors: Li, Sujiao | Zhang, Zhengxiang | Wang, Jue

Article Type: Research Article

Abstract: Prevention of pressure sores remains a significant problem confronting spinal cord injury patients and the elderly with limited mobility. One vital aspect of this subject concerns the development of cushions to decrease pressure ulcers for seated patients, particularly those bound by wheelchairs. Here, we present a novel cushion system that employs interface pressure distribution between the cushion and the buttocks to design custom contoured foam cushion. An optimized normalization algorithm was proposed, with which interface pressure distribution was transformed into the carving depth of foam cushions according to the biomechanical characteristics of the foam. The shape and pressure-relief performance of …the custom contoured foam cushions was investigated. The outcomes showed that the contoured shape of personalized cushion matched the buttock contour very well. Moreover, the custom contoured cushion could alleviate pressure under buttocks and increase subjective comfort and stability significantly. Furthermore, the fabricating method not only decreased the unit production cost but also simplified the procedure for manufacturing. All in all, this prototype seat cushion would be an effective and economical way to prevent pressure ulcers. Show more

Keywords: Prototype, manufacture system, custom-contoured cushion (CCC), pressure sores, optimized normalization algorithm

DOI: 10.3233/BME-141167

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3427-3438, 2014

Authors: Huan, Cheng | Qu, Yuanming | Ren, Zongming

Article Type: Research Article

Abstract: The purpose of this study was to assess gender-related distinction in the performance of Cushing's disease (CD) regarding clinical features, radiological findings, neurological and endocrine status, surgical outcome, and quality of life in Han Chinese. A retrospective study was conducted on 87 patients treated by trans-sphenoidal surgery, between 2006 and 2011, at a single treatment center in Shandong Provincial Hospital, China. Features of CD were compared and quality of life was analyzed between genders. The female-to-male ratio was 2.78: 1. Results showed that men have a younger age of diagnosis (P<0.001), a larger adenoma diameter (P<0.001), and a higher invasion …rate (P=0.032) and apoplexy rate (P=0.04) than women. To be specific, compared with women, men are more prone to suffering from osteoporosis, hypokalemia, sexual dysfunction, and hypertension (P<0.05), have significantly higher preoperative and postoperative (six months after surgery) cortisol levels (P<0.001, P=0.003) and a higher recurrence rate (30.43% vs. 7.81%; P=0.028). No significant differences were seen in the CushingQoL scores between genders. Therefore, male patients with CD need more careful and long-term follow-up than female patients. Show more

Keywords: Cushing's disease, gender differences, transsphenoidal surgery, CushingQoL scores

DOI: 10.3233/BME-141168

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3439-3446, 2014

Authors: Zhang, Bowen | Chai, Hua | Yang, Ziyi | Liang, Yong | Chu, Gejin | Liu, Xiaoying

Article Type: Research Article

Abstract: Heart disease has become the number one killer of human health, and its diagnosis depends on many features, such as age, blood pressure, heart rate and other dozens of physiological indicators. Although there are so many risk factors, doctors usually diagnose the disease depending on their intuition and experience, which requires a lot of knowledge and experience for correct determination. To find the hidden medical information in the existing clinical data is a noticeable and powerful approach in the study of heart disease diagnosis. In this paper, sparse logistic regression method is introduced to detect the key risk factors using …L1/2 regularization on the real heart disease data. Experimental results show that the sparse logistic L1/2 regularization method achieves fewer but informative key features than Lasso, SCAD, MCP and Elastic net regularization approaches. Simultaneously, the proposed method can cut down the computational complexity, save cost and time to undergo medical tests and checkups, reduce the number of attributes needed to be taken from patients. Show more

Keywords: Heart disease, feature selection, sparse logistic regression, L1/2 regularization

DOI: 10.3233/BME-141169

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3447-3454, 2014

Authors: Zhang, Liang | Liu, Peiguo | Dong, Xiuzhen | Zhou, Dongming | Shi, Xuetao

Article Type: Research Article

Abstract: In this paper, a convenient and noninvasive scanning imaging method using microwave frequency band for abnormal subepidermal tissues detection is proposed in the aim to improve diagnosis and prognosis in clinical environments. This method is based on the reflective detection technology with coaxial probe that is used to measure the dielectric properties of tissues. An improved equivalent circuit and simulated annealing algorithm (SA) were used in this work to analyze the dielectric properties of tissues. Computational simulations incorporating a simplified model of subcutaneous hemorrhage described in this work were used to evaluate this method. The dielectric properties data of tissues …in the model of simulation is derived from the literature. The simulation results demonstrated the potential of this method to detect abnormal subepidermal tissues conveniently and expose them in the image accurately. Show more

Keywords: Coaxial probe, dielectric properties, scanning imaging, simulated annealing, subepidermal tissues

DOI: 10.3233/BME-141170

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3455-3462, 2014

Authors: He, Ying | Jiang, Pengjun | Han, Shanshan | Wang, Rong | Li, Yue | Teng, Yichao | Gao, Tianxin

Article Type: Research Article

Abstract: Near-infrared spectroscopy (NIRS) was used to investigate the cerebral oxygenation of Moyamoya and healthy subjects. Continuous recordings of NIRS signals for 20 min (20 min signals) were obtained from 17 healthy subjects (age: 37.4±11.3) and 17 Moyamoya subjects (age: 40.1±11.2). Spectral analysis based on wavelet transformation identified five frequency intervals (I, 0.0095 Hz to 0.02 Hz; II, 0.02 Hz to 0.06 Hz; III, 0.06 Hz to 0.15 Hz; IV, 0.15 Hz to 0.40 Hz; and V, 0.40 Hz to 2.00 Hz) in the 20 min signals and three frequency intervals (III, 0.06 Hz to 0.15 Hz; IV, 0.15 Hz to …0.40 Hz; and V, 0.40 Hz to 2.00 Hz) in the 3 min signals (the first 3 min signals were continuously extracted from the 20 min signals). Significant differences (p < 0.05) were found in frequency intervals III and V. The former exhibited the myogenic activity of smooth muscle inside the blood vessels in both 20 min and 3 min signal analyses; the latter showed hemodynamic oscillation caused by heart pumping. This finding agrees with the vascular pathological changes in Moyamoya disease. As a potential screening method for Moyamoya disease, the simple threshold method exhibited 73.5% accuracy. Show more

Keywords: Moyamoya disease, near-infrared spectroscopy, cerebral oxygenation, wavelet transformation, screening

DOI: 10.3233/BME-141171

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3463-3469, 2014

Authors: Yang, Jian | Fu, Tianyu | Ai, Danni | Xing, Huijun | Li, Qin | Wang, Yongtian

Article Type: Research Article

Abstract: Shoulder instability is a major threat to people's daily life. Many patients suffer from shoulder instability such as the loss of the glenoid and humeral head. In clinical practice, an accurate 3D structure estimation of damaged joints is necessary to diagnose and treat bone defects. This study quantifies osteoarticular defects through the modeling and visualization of osteoarticular structures. An improved algorithm to extract the 3D structure of the bones is proposed. The bone contour is then automatically extracted using prior shape and gray scale intensity distribution of joint CT images. Joint structures with mirror symmetry are matched using the Iterative …Closest Point registration algorithm. Osteoarticular defects can be quantified on the basis of the symmetric information of the bones. Experimental results demonstrate that the proposed method can effectively segment the joint structures from the CT image. In addition, the proposed mirror symmetrical method can effectively estimate osteoarticular defects. Show more

Keywords: Joint bone, segmentation, modeling, quantitative analysis

DOI: 10.3233/BME-141172

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3471-3478, 2014

Authors: Zhou, Zhengdong | Chen, Yuanhua | Yu, Zili | Wang, Dongdong | Zhao, Chunsheng | Xu, Jun | Song, Wei | Li, Bing | Shen, Junshu | Zhu, Xixu

Article Type: Research Article

Abstract: Intensity-Modulated Radiation Therapy (IMRT) mathematically forms a large-scale optimization problem. The development of an IMRT plan is computationally expensive resulting in time-consuming, inefficient, and difficult to develop high-quality IMRT plans. By combining prior knowledge with proposed novel measures derived from both Overlap Volume Histogram (OVH) descriptors and Dose Volume Histograms (DVHs), a novel quality control method for IMRT planning is proposed to assure the high quality of IMRT plan. Clinical approved nasopharyngeal IMRT plans were employed for the experiments, where the reference plan is firstly retrieved from IMRT plan database for each query case by using measures derived from both …OVH descriptors and DVHs. Then the DVHs of the reference plan are served as additional goals for the IMRT plan re-optimization. The experimental results show that the proposed method can effectively pick out those IMRT plans, whose quality could be improved substantially (i.e. the doses of their Clinical Targets Volume (CTV) could be effectively increased) and the dose of their Organs at Risk (OARs) could be reduced after the IMRT plan has being re-optimized. In conclusion, the proposed methods can effectively guarantee the high quality of the IMRT planning. Show more

Keywords: Intensity-modulated radiation therapy (IMRT), quality control, overlap volume histogram (OVH), prior knowledge

DOI: 10.3233/BME-141173

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3479-3485, 2014

Authors: Wang, Chunxi | Cai, Xiangjun | Liang, Faqi | Chu, Futao | Chen, Gang | Duan, Zhiquan

Article Type: Research Article

Abstract: The celiomesenteric trunk is a rare anomaly characterized by a common origin of the celiac axis and superior mesenteric artery from the aorta, which accounts for less than 1% of all celiac artery anomalies, so the aneurysm occurred in such trunk is even rarer. There have been few reports on how to diagnose and deal with such malformed celiomesenteric trunk aneurysms till now. This paper tries to summarize the experience of how to expose and excise such kind of aneurysm according to the seven cases' data. The clinic data were collected retrospectively. There were seven cases with celiomesenteric trunk aneurysm …from February 2000 to February 2013, including 5 males and 2 females aged 35~62. The operations were done including aneurysm resection and vascular reconstruction under general anesthesia. The operated patients were followed-up at the sixth month and each year post operation. The vascular stomas were detected or examined by Color Doppler Sonography, spiral Computed Tomography angiography (SCTA). The seven operated patients were cured and discharged from hospital, and they were followed up for 3~10 years (mean time 5 years), with four patients being followed up longer than 5 years. No sign of intestinal ischemia or hepatic ischemia or splenic ischemia was found, and no image of anastomosis stricture or stenosis was found during the follow-up. Five patients are alive now while two patients were dead, with one dying of large area myocardial infarction unexpectedly at 6 years post operation and the other dying of cerebral infarction abruptly at 4 years post operation. It is an effective and safe method to treat the celiomesenteric trunk aneurysm by using by-pass operation with artificial blood vessels, originating from inferior kidney aorta to visceral arteries including hepatic artery, splenic artery and superior mesenteric artery. Its short-term and middle-term effects are relatively better. Show more

Keywords: Celiomesenteric trunk, superior mesenteric artery, celiac trunk, aneurysm, operation

DOI: 10.3233/BME-141174

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3487-3492, 2014

Authors: Eguiluz-Perez, Gonzalo | Garcia-Zapirain, Begonya

Article Type: Research Article

Abstract: People with Multiple Sclerosis (MS) need regular physical activities along with medical treatment despite their ability or disability level. However, poorly performed exercises could aggravate muscle imbalances and worsen their health. The goal of our work is to create a comprehensive system, encompassing a face-to-face sessions performed by MS patients one day a week at the medical center with exercises at home the rest of the week through a web platform in combination with a tracking tool to analyze the position of patients during exercise and correct them in real-time. The whole system is currently testing during six months with …ten participants, five persons with MS and 5 professionals related with MS. Two tests, the Functional Independence Measure and the Berg Balance Scale will be act as a barometer for measuring the degree of independence obtained by the people with MS and also the validity of the whole system as a rehabilitation tool. Preliminary results about the usability of the system using SUS scale, 72 and 76 points over 100 (patients and professionals respectively), demonstrate that our system is usable for both patients and professionals. Show more

Keywords: Multiple Sclerosis, telerehabilitation, web application, verticality analysis

DOI: 10.3233/BME-141175

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3493-3502, 2014

Authors: Tran, Thang Viet | Chung, Wan-Young

Article Type: Research Article

Abstract: This paper proposes the design and implementation of a low-voltage and low-power body sensor node based on the IEEE 802.15.4 standard to collect electrocardiography (ECG) and photoplethysmography (PPG) signals. To achieve compact size, low supply voltage, and low power consumption, the proposed platform is integrated into a ZigBee mote, which contains a DC-DC booster, a PPG sensor interface module, and an ECG front-end circuit that has ultra-low current consumption. The input voltage of the proposed node is very low and has a wide range, from 0.65 V to 3.3 V. An RF energy harvester is also designed to charge the …battery during the working mode or standby mode of the node. The power consumption of the proposed node reaches 14 mW in working mode to prolong the battery lifetime. The software is supported by the nesC language under the TinyOS environment, which enables the proposed node to be easily configured to function as an individual health monitoring node or a node in a wireless body sensor network (BSN). The proposed node is used to set up a wireless BSN that can simultaneously collect ECG and PPG signals and monitor the results on the personal computer. Show more

Keywords: Body sensor network, electrocardiography, photoplethysmography, low-power node, radio frequency energy harvester

DOI: 10.3233/BME-141176

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3503-3510, 2014

Authors: Viqueira Villarejo, María | Maeso García, Jose | García Zapirain, Begoña | Méndez Zorrilla, Amaia

Article Type: Research Article

Abstract: This paper describes a study dealing with a technological solution to measure gait quality in people suffering from multiple sclerosis (MS) by selecting objective parameters that focus on their step. Android mobile technology, online services and four wireless pressure sensors are used in concert for this purpose. The objective of this work is the early detection of deterioration of the patient so that a physician can quickly intervene. Tests were carried out on a group of 8 persons with MS, and these results were compared with a control a group of 6 healthy participants. The results indicated a statistical difference …in 7 of 40 general step features, with a minimum σ=0.013 and a maximum σ=0.029. These characteristics showed differences between first and fifth metatarsals for each group. It was concluded that these parameters can be used to evaluate gait degeneration in people with MS and that further information could be obtained from measurements with sensors to monitor activities such as bending and inertial sensors. Show more

Keywords: Gait analysis, objective parameterization, sensors

DOI: 10.3233/BME-141177

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3511-3522, 2014

Authors: Viqueira Villarejo, María | García Zapirain, Begoña | Méndez Zorrilla, Amaia

Article Type: Research Article

Abstract: This paper presents a shoe-integrated sensor device which collects objective information concerning the gait quality in patients' physical rehabilitation. It involves four pressure sensors, two bending sensors, an ultrasonic sensor and a 9dof IMU, an Inertial Measurement Unit with three accelerometers, three gyroscopes and three magnetometers. The device includes a SDRAMPS with the aim of storing the information for long periods of time. The collected data can be sent to the server for later visualization by the specialist and the patient on a web platform. An interface shows the data in real time, allowing it to verify the connections and …to check different movements. Show more

Keywords: Gait, sensor, wireless

DOI: 10.3233/BME-141178

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3523-3528, 2014

Authors: Tan, Yee-Yong | Chung, Wan-Young

Article Type: Research Article

Abstract: Promising development in the light emitting diode (LED) technology has spurred the interest to adapt LED for both illumination and data transmission. This has fostered the growth of interest in visible light communication (VLC), with on–going research to utilize VLC in various applications. This paper presents a mobile–health monitoring system, where healthcare information such as biomedical signals and patient information are transmitted via the LED lighting. A small and portable receiver module is designed and developed to be attached to the mobile device, providing a seamless monitoring environment. Three different healthcare information including ECG, PPG signals and HL7 text information …is transmitted simultaneously, using a single channel VLC. This allows for a more precise and accurate monitoring and diagnosis. The data packet size is carefully designed, to transmit information in a minimal packet error rate. A comprehensive monitoring application is designed and developed through the use of a tablet computer in our study. Monitoring and evaluation such as heart rate and arterial blood pressure measurement can be performed concurrently. Real–time monitoring is demonstrated through experiment, where non–hazardous transmission method can be implemented alongside a portable device for better and safer healthcare service. Show more

Keywords: Visible light communication, light emitting diode, mobile–health monitoring system, healthcare

DOI: 10.3233/BME-141179

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3529-3538, 2014

Authors: Moon, Yeon-Kwan | Lee, Jyung Hyun | Park, Hee-Joon | Cho, Jin-Ho | Choi, Hyun-Chul

Article Type: Research Article

Abstract: Recently, several medical devices that use wireless communication are under development. In this paper, the small size frequency shift keying (FSK) transmitter and a monofilar antenna for the capsule endoscope, enabling the medical device to transmit VGA-size images of the intestine. To verify the functionality of the proposed wireless communication system, computer simulations and animal experiments were performed with the implemented capsule endoscope that includes the proposed wireless communication system. Several fundamental experiments are carried out using the implemented transmitter and antenna, and animal in-vivo experiments were performed to verify VGA image transmission.

Keywords: Capsule endoscope, wireless communication, antenna

DOI: 10.3233/BME-141180

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3539-3547, 2014

Authors: Lopez-Samaniego, Leire | Garcia-Zapirain, Begonya | Mendez-Zorrilla, Amaia

Article Type: Research Article

Abstract: This paper presents the results of research that applies cognitive therapies associated with memory and mathematical problem-solving in elderly people. The exercises are programmed in an iPad and can be performed both from the Tablet and in an interactive format with a LEGO robot. The system has been tested with 2 men and 7 women over the age of 65 who have slight physical and cognitive impairment. Evaluation with the SUS resulted in a mean of 48.45 with a standard deviation of 5.82. The score of overall satisfaction was 84.37 with a standard deviation of 18.6. Interaction with the touch …screen caused some usability problems due to the elderly people's visual difficulties and clicking accuracy. Future versions will include visualization with more color contrast and less use of the keyboard. Show more

Keywords: iPad, cognitive rehabilitation, objective-C, system usability scale (SUS)

DOI: 10.3233/BME-141181

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3549-3556, 2014

Authors: Chang, Yen-Ching

Article Type: Research Article

Abstract: The discrete-time fractional Gaussian noise (DFGN) has been proven to be a regular process. Therefore, an autoregressive (AR) model of an infinite order can describe DFGN based on Wold and Kolmogorov theorems. A fast estimation algorithm on the Hurst exponent of DFGN or discrete-time fractional Brownian motion (DFBM) has been proposed, but the algorithm did not consider the order selection of AR model. Recently, a Hurst exponent estimator based on an AR model with six existing methods of order selection has been proposed to raise the accuracy of estimating the Hurst exponent. Although the estimation accuracy has been confirmed to …be better than the one without order selection, the estimator still requires computing all parameter sets through the Levinson algorithm. In order to lower computational cost, this paper proposes an efficient method of order selection, simply called data induction, which uses simulation data to induce an appropriate threshold of terminating the Levinson algorithm before computing all parameter sets. Experimental results show that the proposed data-induction method has a competitive advantage over six existing methods of order selection in terms of lowering computational cost and raising the accuracy. Show more

Keywords: Fractional Brownian motion, fractional Gaussian noise, Hurst exponent, autoregressive, order selection

DOI: 10.3233/BME-141182

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3557-3568, 2014

Authors: Ishaq, Rizwan | García Zapirain, Begoña

Article Type: Research Article

Abstract: This paper presents the single channel speech enhancement system using subband Kalman filtering by estimating optimal Autoregressive (AR) coefficients and variance for speech and noise, using Weighted Linear Prediction (WLP) and Noise Weighting Function (NWF). The system is applied for normal and Oesophageal speech signals. The method is evaluated by Perceptual Evaluation of Speech Quality (PESQ) score and Signal to Noise Ratio (SNR) improvement for normal speech and Harmonic to Noise Ratio (HNR) for Oesophageal Speech (OES). Compared with previous systems, the normal speech indicates 30% increase in PESQ score, 4 dB SNR improvement and OES shows 3 dB HNR …improvement. Show more

Keywords: Kalman filter, autoregressive, speech enhancement, weighted linear prediction

DOI: 10.3233/BME-141183

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3569-3578, 2014

Authors: Zhang, Ziyi | Liu, Peiguo | Zhou, Dongming | Zhang, Liang | Lei, Hengdong

Article Type: Research Article

Abstract: Biomedical magnetic induction measurement is a promising method for the detection of intracerebral hemorrhage (ICH), especially in China. Aiming at overcoming the problem of low sensitivity, a magnetic induction sensor is chosen to replace the conventional sensors. It uses a two-arm Archimedean spiral coil as the exciter and a circular coil as the receiver. In order to carry out high-fidelity simulations, the Chinese head model with real anatomical structure is introduced into this novel sensor for the first time. Simulations have been carried out upon early stage ICH measurements. By calculating the state sensitivity and time sensitivity of the perturbation …phase of two types of sensors using the electromagnetic software, we conclude that the primary signal received can be largely reduced using the novel sensor, which could effectively increase the time and state sensitivity simultaneously. Show more

Keywords: Intracerebral hemorrhage (ICH), magnetic induction measurement, sensor sensitivity, two-arm archimedean spiral coil (TAASC), Chinese head model

DOI: 10.3233/BME-141184

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3579-3587, 2014

Authors: Lin, Jium-Ming | Lu, Hung-Han | Lin, Cheng-Hung

Article Type: Research Article

Abstract: This paper proposes a bio-potential measurement apparatus including a wireless device for transmitting acupuncture bio-potential information to a remote control station for health conditions analysis and monitor. The key technology of this system is to make replaceable foam-rubber cushions, double-side conducting tapes, chip and antenna on the radio frequency identification (RFID) tag. The foam-rubber cushions can be wetted with salt-water and contact with the acupuncture points to reduce contact resistance. Besides, the double-side conducting tapes are applied to fix foam-rubber cushions. Thus, one can peel the used cushions or tapes away and supply new ones quickly. Since the tag is …a flexible plastic substrate, it is easy to deploy on the skin. Besides, the amplifier made by CMOS technology on RFID chip could amplify the signals to improve S/N ratio and impedance matching. Thus, cloud server can wirelessly monitor the health conditions. An example shows that the proposed system can be used as a wireless health condition monitor, the numerical method and the criteria are given to analyze eleven bio-potentials for the important acupunctures of eleven meridians on a person's hands and legs. Then a professional doctor can know the performance of an individual and the cross-linking effects of the organs. Show more

Keywords: RFID tag, bio-potential, flexible substrate, wireless health monitor, wetted replaceable foam-rubber cushion

DOI: 10.3233/BME-141185

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3589-3596, 2014

Authors: Tsai, Jang-Zern | Chen, Ching-Jung | Shie, Dung-Ting | Liu, Jen-Tsai

Article Type: Research Article

Abstract: The piezoelectric biosensor have been widely used in ultra-small mass detection of biomolecular, based on PZT piezoelectric material can create a variety of compositions geometrically; it could widely develop a high-frequency resonator and measure the change of the slightest mass while improve the limited detection simultaneously. Therefore, the piezoelectric biosensor of this study was fabricated by a spin-coating method and backside etching process for improving the characteristic of piezoelectric biosensor. The result exhibited that the 250 μm × 250 μm working size has the most favorable piezoelectric characteristic. The tunability was approximately 38.56 % and it showed that reducing the …substrate thickness could obtain a clear resonance signal in a range of 60 to 380 MHz. In theory calculated for gravimetric sensing, it could achieve 0.1 ng sensing sensitivity. In gravimetric sensing, the sensing range was between 50,000~100,000 CFU/ml. Sensing range was lower in clinical urinary tract infection (100,000 CFU/ml), thus demonstrating its usefulness for preventive medicine. It can understand the piezoelectric sensor of this study has potential application in the future for biomedical gravimetric sensing. Show more

Keywords: Lead zirconate titanate (PZT), piezoelectric, biosensor, resonance-frequency, escherichia coli (E. coli)

DOI: 10.3233/BME-141186

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3597-3604, 2014

Authors: Xu, Lisheng | Yao, Yang | Wang, Hao | He, Dianning | Wang, Lu | Jiang, Yongsheng

Article Type: Research Article

Abstract: Pulse wave contains much information on a cardiovascular system. Pulse wave variability during exercise is of great significance as it reflects more information combining with pulse wave under stationary state. This paper studied the morphology variability of radial pulse wave during exercise. Radial pulse waves were collected from 30 subjects with two pressure pulse sensors worn at the wrists of the right and left hands, respectively. Electrocardiography (ECG) was also detected synchronously. After data preprocessing and feature point extraction, the variability of several parameters of pulse wave and ECG were analyzed. It is notable that pulse rate (PR) and heart …rate (HR) change synchronously. During the exercise period, both systolic phase and diastolic phase of a radial pulse shorten but the latter is more obvious. The amplitude of the dicrotic notch decreases and even turns negative. Aligning the radial pulse waveforms together, the radial pulse waveforms prior to, during and after exercise coincide with each other except for some details like the tidal wave which fades away during exercise. Show more

Keywords: Pulse morphology, exercise, radial pulse wave

DOI: 10.3233/BME-141187

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3605-3611, 2014

Authors: Yoo, Ji Won | Lee, Dong Ryul | Sim, Yon Ju | You, Joshua H. | Kim, Cheol J.

Article Type: Research Article

Abstract: Sensorimotor control dysfunction or dyskinesia is a hallmark of neuromuscular impairment in children with cerebral palsy (CP), and is often implicated in reaching and grasping deficiencies due to a neuromuscular imbalance between the triceps and biceps. To mitigate such muscle imbalances, an innovative electromyography (EMG)-virtual reality (VR) biofeedback system were designed to provide accurate information about muscle activation and motivation. However, the clinical efficacy of this approach has not yet been determined in children with CP. The purpose of this study was to investigate the effectiveness of a combined EMG biofeedback and VR (EMG-VR biofeedback) intervention system to improve muscle …imbalance between triceps and biceps during reaching movements in children with spastic CP. Raw EMG signals were recorded at a sampling rate of 1,000 Hz, band-pass filtered between 20–450 Hz, and notch-filtered at 60 Hz during elbow flexion and extension movements. EMG data were then processed using MyoResearch Master Edition 1.08 XP software. All participants underwent both interventions consisting of the EMG-VR biofeedback combination and EMG biofeedback alone. EMG analysis resulted in improved muscle activation in the underactive triceps while decreasing overactive or hypertonic biceps in the EMG-VR biofeedback compared with EMG biofeedback. The muscle imbalance ratio between the triceps and biceps was consistently improved. The present study is the first clinical trial to provide evidence for the additive benefits of VR intervention for enhancing the upper limb function of children with spastic CP. Show more

Keywords: Virtual reality, EMG visual feedback, neuromotor control, muscle imbalance, cerebral palsy

DOI: 10.3233/BME-141188

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3613-3618, 2014

Authors: Chung, Soon-Cheol | Choi, Mi-Hyun | Park, Sung-Jun | Lee, Jung-Chul | Jeong, Ul-Ho | Baek, Ji-Hye | You, Ji-Hye | Choi, Young Chil | Lim, Dae-Woon | Yi, Jeong-Han | Kim, Hyung-Sik

Article Type: Research Article

Abstract: In this study, a tactile stimulator that could separately or simultaneously display the vibrotactile and pressure sense was developed. The developed system consisted of a control unit, a drive unit, and an actuator, and can be operated with PC or manually. This system quantitatively controls the stimulation parameters such as the stimulation intensity, duration, frequency, and stimulation type. A preliminary electroencephalogram (EEG) experiment for three types of stimulation (vibrotactile, pressure sense, vibrotactile + pressure sense) highlights that the system could be used in complex tactile cognitive studies. An event-related desynchronization (ERD) and synchronization (ERS) were measured at the area of …C3 and C4 for all three types of stimulation, and a clear response was identified in the contralateral somatosensory area from the brain topology. Therefore, it is expected that this system could be widely used in single and complex human tactile cognition and perception studies for vibrotactile and pressure sensation. Show more

Keywords: Tactile stimulator, vibration, pressure, simultaneous stimulation, electroencephalogram

DOI: 10.3233/BME-141189

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3619-3627, 2014

Authors: Zhang, Cheng | Zhang, Guanghao | Rong, Wei | Wang, Aihua | Wu, Changzhe | Huo, Xiaolin

Article Type: Research Article

Abstract: Demyelination is part of the cascading secondary injury after the primary insult and contributes to the loss of function after spinal cord injury (SCI). Oligodendrocyte precursor cells (OPCs) are the main remyelinating cells in the central nervous system (CNS). We explored whether oscillating field stimulation (OFS) could efficiently promote OPC differentiation and improve remyelination after SCI. SD rats with SCI induced by the Allen method were randomly divided into two groups, the SCI+OFS group and SCI group. The former group received active stimulator units and the latter group received sham (inoperative) stimulator units. Additionally, rats that only received laminectomy were …referred as the sham group. The electric field intensity was 600μV/mm, and the polarity was alternated every 15 minutes. The results showed that the SCI+OFS rats had significantly less demyelination and better locomotor function recovery after 12-weeks treatment. The OFS treatment significantly increased the number of Gal C-positive OPCs after 2-weeks treatment. Furthermore, these rats had higher protein expression of oligodendroglial transcription factors Olig2 and NKx2.2. These findings suggest OFS can promote locomotor recovery and remyelination in SCI rats and this effect may be related to the improved differentiation of OPCs in the spinal cord. Show more

Keywords: Oligodendrocyte precursor cells, remyelination, oscillating field stimulation, spinal cord injury, rat

DOI: 10.3233/BME-141190

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3629-3636, 2014

Authors: Xiong, Shi | Cheng, Chen | Wu, Xia | Guo, Xiaojuan | Yao, Li | Zhang, Jiacai

Article Type: Research Article

Abstract: Recent studies have shown that working memory (WM) performance can be improved by intensive and adaptive computerized training. Here, we explored the WM training effect using Electroencephalography (EEG) neurofeedback (NF) in normal young adults. In the first study, we identified the EEG features related to WM in normal young adults. The receiver operating characteristic (ROC) curve showed that the power ratio of the theta-to-alpha rhythms in the anterior-parietal region, accurately classified a high percentage of the EEG trials recorded during WM and fixation control (FC) tasks. Based on these results, a second study aimed to assess the training effects of …the theta-to-alpha ratio and tested the hypothesis that up-regulating the power ratio can improve working memory behavior. Our results demonstrated that these normal young adults succeeded in improving their WM performance with EEG NF, and the pre- and post-test evaluations also indicated that WM performance increase in experimental group was significantly greater than control groups. In summary, our findings provided preliminarily evidence that WM performance can be improved through learned regulation of the EEG power ratio using EEG NF. Show more

Keywords: Electroencephalography, neurofeedback, working memory, power spectrum, self-regulation

DOI: 10.3233/BME-141191

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3637-3644, 2014

Authors: Su, Jing | Zhu, Wenting | Liu, Jing | Yin, Jian | Qin, Wei | Jiang, Changbin

Article Type: Research Article

Abstract: The aim of the present study was to research the role of nitric oxide (NO) as a mediator of alpha (α)-asarone effect at the pentylenetetrazol (PTZ)-induced epileptiform discharge in rat. α-Asarone that was injected intraperitoneally twenty minutes before PTZ injection suppressed the clonic discharge effectively and the significant actions lasted for 30 min with no change of clonic amplitude. Administration of α-asarone did not influence interictal discharge. Four kinds of NO regulators were administered, including non-selective NG-nitro-L-arginine methyl ester (L-NAME), selective neuronal nitric oxide synthase (nNOS) inhibitor, 7-nitroindazole (7-NI), inducible nitric oxide synthase (iNOS) inhibitor, aminoguanidine (AG) and NO substrate, …L-arginine (ARG) and their influence on the actions of α-asarone were studied, and all of the regulators were administered fifteen minutes before α-asarone injection. L-NAME and 7-NI reversed the anticlonic activity of α-asarone, and a significant increase of clonic activity was induced by L-NAME later in L-NAME + .α-asarone + PTZ group. There were no significant differences between AG + α-asarone + PTZ and α-asarone + PTZ group. L-ARG played a dual role in this study. It aggravated clonic discharge in the early stage but relieved interictal discharge in the late stage compared with PTZ group alone, and the beneficial effect of α-asarone was also reversed. All the above results suggest that nNOS/NO pathway mediates the anticonvulsant effect of α-asarone, and NO played a biphasic role in PTZ modeling process, while iNOS was unrelated to the inhibition effect of α-asarone on PTZ induced epileptiform activity. Show more

Keywords: Alpha-asarone, epileptiform activity, nitric oxide synthase, pentylenetetrazol

DOI: 10.3233/BME-141192

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3645-3655, 2014

Authors: Zhang, Guanghao | Huo, Xiaolin | Wu, Changzhe | Zhang, Cheng | Duan, Zhongping

Article Type: Research Article

Abstract: Bioelectrical impedance phase angle has been recommended as a tool to assess nutrition state, but there are no measuring devices have been specially designed for hospital residents. In this study, a system was established for the measurement of bioelectrical impedance phase angle. The electrical composition, calculation method and measuring method of this system are presented in this paper. Experiments showed excellent performance of this system in measuring impedance made of resistors and capacitors. The designed system was also used to measure the bioelectrical impedance phase angle of both healthy subjects and patients with malnutrition, and the results demonstrated that the …phase angle of patients with malnutrition is lower than that of healthy subjects (P < 0.01 for male and P < 0.05 for female). These results suggest that phase angle has the potential to be a useful tool for the quantitative assessment of nutritional status. Show more

Keywords: Phase angle, bioelectrical impedance, nutritional status

DOI: 10.3233/BME-141193

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3657-3664, 2014

Authors: Yang, Banghua | Han, Zhijun | Zan, Peng | Wang, Qian

Article Type: Research Article

Abstract: Classification methods are a crucial direction in the current study of brain-computer interfaces (BCIs). To improve the classification accuracy for electroencephalogram (EEG) signals, a novel KF-PP-SVM (kernel fisher, posterior probability, and support vector machine) classification method is developed. Its detailed process entails the use of common spatial patterns to obtain features, based on which the within-class scatter is calculated. Then the scatter is added into the kernel function of a radial basis function to construct a new kernel function. This new kernel is integrated into the SVM to obtain a new classification model. Finally, the output of SVM is calculated …based on posterior probability and the final recognition result is obtained. To evaluate the effectiveness of the proposed KF-PP-SVM method, EEG data collected from laboratory are processed with four different classification schemes (KF-PP-SVM, KF-SVM, PP-SVM, and SVM). The results showed that the overall average improvements arising from the use of the KF-PP-SVM scheme as opposed to KF-SVM, PP-SVM and SVM schemes are 2.49%, 5.83 % and 6.49 % respectively. Show more

Keywords: Kernel fisher, posterior probability, support vector machine, brain computer interface, common spatial pattern

DOI: 10.3233/BME-141194

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3665-3673, 2014

Authors: Chen, Xiaoyan | Lv, Xinqiang | Du, Meng

Article Type: Research Article

Abstract: The electrode polarization effects on bioelectrical impedance measurement at low-frequency cannot be ignored. In this paper, the bioelectrical data of mice livers are measured to specify the polarization effects on the bio-impedance measurement data. We firstly introduce the measurement system and methodology. Using the depolarization method, the corrected results are obtained. Besides, the specific effects of electrode polarization on bio-impedance measurement results are investigated using comparative analysis of the previous and posterior correction results from dielectric spectroscopy, Cole-Cole plot, conductivity and spectroscopy of dissipation tangent. Experimental results show that electrode polarization has a significant influence on the characteristic parameters of …mouse liver tissues. To be specific, we see a low-frequency limit resistance R0 increase by 19.29%, a reactance peak XP increase by 8.50%, a low-frequency limit conductivity Kl decrease by 17.65% and a dissipation peak tangent decrease by 160%. Show more

Keywords: Electrode polarization, depolarization correction, impedance measurement, low-frequency

DOI: 10.3233/BME-141195

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3675-3683, 2014

Authors: Woo, Seong Tak | Lee, Gihyoun | Jung, Eui Sung | Lim, Hyung-Gyu | Seong, Ki Woong | Lee, Jyung Hyun | Kim, Myoung Nam | Cho, Jin-Ho

Article Type: Research Article

Abstract: The microphone in a fully implantable hearing device (FIHD) is generally implanted under the skin covering the temporal bone. However, the implanted microphone can be affected by the skin, which causes both sound attenuation and distortion, particularly at high frequencies. As the degree of attenuation and distortion through the skin is severe, speech quality evaluation parameters are needed for the received signal when designing an implantable microphone. However, the performance of most implantable microphones is only assessed based on the sensitivity and frequency response. Thus, practical indicators based on human auditory characteristics are needed for an objective evaluation of the …performance of implantable microphones. In this study, a subcutaneously implantable microphone was designed, and its frequency response investigated using an in vivo experiment. Plus, to evaluate the objective indicators, the speech quality of the signals measured by the implanted microphone was calculated using a MATLAB program, and the indicators compared before and after implantation. Show more

Keywords: Implantable microphone, in vivo experiment, speech quality score, fully implantable hearing devices

DOI: 10.3233/BME-141196

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3685-3691, 2014

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141197

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

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141198

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

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141199

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

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

Article Type: Research Article

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

Keywords: Transcriptional regulation, network, functional module

DOI: 10.3233/BME-141200

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

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141201

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

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

Article Type: Research Article

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

Keywords: Association network, correlation, microbiome, network deconvolution

DOI: 10.3233/BME-141202

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

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141203

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

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141204

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

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141205

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

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

Article Type: Research Article

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

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

DOI: 10.3233/BME-141206

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

Authors: Wu, Xiaohui | Zhao, Chuang | Su, Yaru

Article Type: Research Article

Abstract: Polyadenylation [poly(A)] of mRNA is a critical step during gene expression, which plays an important role in the termination of transcription. Prediction of poly(A) sites can help identify 3' ends of genes and improve genome annotation. Due to the limited knowledge of poly(A) signals in plants, predictive modeling of poly(A) sites in agricultural crops remains challenging. Recent studies have uncovered widespread occurrences of alternative poly(A) (APA) sites in intron and coding sequence (CDS), whereas the study on the prediction of these APA sites is scarce. In this study, four feature representation methods, involving a position weight matrix, the k-gram frequency, …core hexamers, and a transition matrix, were adopted to characterize poly(A) signals surrounding APA sites. The classification model was built to predict each group of APA sites. Experimental results showed that this model was effective in the identification of APA sites located in different genomic regions, with a compromise between sensitivity and specificity higher than 87%. Compared with previous model PASS rice, accuracies for the prediction of APA sites in 3'-UTR, intron and CDS were enhanced by 5%, 7%, and 27%, respectively. This model will contribute to genetic engineering by enabling researchers to control poly(A) site selection. Show more

Keywords: Rice, polyadenylation, alternative polyadenylation, prediction, classification model

DOI: 10.3233/BME-141207

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3779-3785, 2014

Authors: Wang, Gongming | Xu, Fan

Article Type: Research Article

Abstract: The output of icosahedral symmetry-adapted functions (ISAF) reconstruction algorithm is a virus capsid, where the density function of every outside point is theoretically zero. However, original ISAF algorithm takes reconstructed map as a solid sphere and density function of every point in the whole sphere is calculated. The density functions outside virus capsid may not be always zero, which may sometimes produce noise. In this study, Fourier shell correlation (FSC) is used for proving that density function calculation of original ISAF algorithm can reduce reconstruction precision. Subsequently, the range of virus capsid is determined with radial density function curve and …the original ISAF algorithm is improved by calculating density function inside virus capsid. The experimental results on Cryo-electron microscopy (Cryo-EM) data of cytoplasmic polyhedrosis virus (CPV) indicate that the improved ISAF algorithm can generate more details of virus capsid and achieve a higher resolution. Show more

Keywords: Single-particle reconstruction, icosahedral symmetry-adapted functions, virus capsid, density function, Fourier shell correlation

DOI: 10.3233/BME-141208

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3787-3795, 2014

Authors: Bao, Wenzheng | Chen, Yuehui | Wang, Dong

Article Type: Research Article

Abstract: Prediction of protein structural classes is of great significance to better understand protein folding patterns. An array of methods has been proposed to predict these structures based on sequences. However, the accuracy is strongly affected by the homology of sequences. In the present study, the features based on correlation coefficient of sequence and amino acid composition are extracted. Flexible neutral tree is employed as the classification model. To examine the performance of this method, four benchmark datasets are selected. Altogether, the results show that a higher prediction accuracy of alpha/beta can be achieved by the method compared to others.

Keywords: Protein structural classification, flexible neural tree, correlation coefficient

DOI: 10.3233/BME-141209

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3797-3806, 2014

Authors: Lee, Nung Kion | Fong, Pui Kwan | Abdullah, Mohd Tajuddin

Article Type: Research Article

Abstract: Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature …improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that tree-based features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features. Show more

Keywords: Genetic algorithm, tree-based feature, histone feature

DOI: 10.3233/BME-141210

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3807-3814, 2014

Authors: Zheng, Shichao | Ren, Zhenzhen | Zhang, Yanling | Qiao, Yanjiang

Article Type: Research Article

Abstract: Tanshinone IIA (Tan IIA) is one of the major fat-soluble ingredients in Salvia miltiorrhiza which has been widely used for various inflammatory conditions associated with cardiovascular and cerebrovascular disorders. However, the underlying anti-inflammatory mechanisms of Tan IIA are incompletely understood. The purpose of this study was to illuminate the anti-inflammatory mechanism of Tan IIA based on the protein interaction network (PIN) analysis. A PIN of Tan IIA was constructed with 281 nodes and 814 interactions and analyzed by gene ontology (GO) enrichment analysis based on Markov Cluster algorithm (MCL). Three modules were associated with anti-inflammatory actions. The most interesting finding …of this study was that the anti-inflammatory effect of Tan IIA may be partly attributable to the mediate activation of TRAF2, TRAF3 and TRAF6, to inhibit the toll-like receptor signaling pathway and combine with AGER. Therefore, the module-based network analysis approach will be a new method for better understanding the anti-inflammatory mechanism of Tan IIA. Show more

Keywords: Protein interaction network, module, anti-inflammatory actions, Tanshinone IIA, GO enrichment analysis

DOI: 10.3233/BME-141211

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3815-3824, 2014

Authors: Fernández-Granero, M.A. | Sánchez-Morillo, D. | León-Jiménez, A. | Crespo, L.F.

Article Type: Research Article

Abstract: Chronic Obstructive Pulmonary Disease (COPD) is a progressive disease of the lung with a great prevalence and a remarkable socio-economic impact on patients and health systems. Early detection of exacerbations could diminish the adverse effects on patients' health and cut down costs burdened on patients with COPD. A group of 16 patients were telemonitored at home using a novel electronic daily symptoms questionnaire during a 6-months field trial. Recorded data were used to train and validate a Probabilistic Neural Network (PNN) classifier in order to enable the automatic prediction of exacerbations. The proposed system was able to predict COPD exacerbations …early with a margin of 4.8±1.8 days (average ± SD). Detection accuracy was 80.5% (33 out of 41 exacerbations were early detected); 78.8% (26 out of 33) of theses detected events were reported exacerbation and 87.5% (7 out of 8) were unreported episodes. The proposed questionnaire and the designed automatic classifier could support the early detection of COPD exacerbations of benefit to both physicians and patients. Show more

Keywords: Chronic Obstructive Pulmonary Disease, exacerbation, telehealth, symptoms, questionnaire, early detection, Probabilistic Neural Network, telemonitoring

DOI: 10.3233/BME-141212

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3825-3832, 2014

Authors: Wang, Yong-Tang | Lu, Xiu-Min | Shu, Ya-Hai | Xiao, Lan | Chen, Kai-Ting

Article Type: Research Article

Abstract: To select tag single nucleotide polymorphisms (SNPs) within and around human p75 neurotrophin receptor (p75NTR) gene in Chinese Han population, the sequence involving p75NTR gene as well as the upstream and downstream of the gene was identified according to the data from National Center for Biotechnology Information (NCBI) GenBank database, and the SNP genotype data involving 63 SNPs in the regions were obtained from Chinese Han Beijing (CHB) population of HapMap database. Then, Haploview (version 4.2) was used to calculate linkage disequilibrium (LD) statistics for the selected 32 common SNPs with a minor allele frequence (MAF) more than 0.05. Haplotype …blocks were constructed throughout the p75NTR gene according to the upper and the lower 95% confidence bound of D' value, and the tag SNPs were selected based on the r2 and LOD values between SNPs as well as the results of bioinformatics analysis. The results indicated that five haplotype blocks were constructed within and around p75NTR gene and 12 tag SNPs including rs2537710, rs603769, rs614455, rs2537706, rs534561, rs2072445, rs2072446, rs7219709, rs734194, rs741071, rs741073 and rs2671641 were selected to represent the other 51 SNPs in p75NTR gene. Therefore, the 12 selected SNPs may act as tag SNPs for the entire p75NTR gene in Chinese Han population, which will provide an effective way to select tag SNPs in a whole gene, and its biological significance is to further guide the clinical association studies between the candidate gene and disease susceptibility. Show more

Keywords: p75NTR, haplotype block, tag SNP, haplotype, bioinformatics analysis

DOI: 10.3233/BME-141213

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3833-3839, 2014

Authors: Zhang, Jinping | Zhang, Leijia | Liu, Xuehong | Zhou, Fuqun

Article Type: Research Article

Abstract: To study the expression and roles of Connexin43 (Cx43) and Paired-box3 (Pax3) proteins in the human Chorionic villi and decidua during early pregnancy, Cx43 and Pax3 protein expression in the human placental villi and decidua at 5–7 weeks of early pregnancy was studied by immunohistochemistry (SABC). Integrated optical density (IOD) of Cx43 and Pax3 protein expression was obtained by using special image analysis software. Cx43 and Pax3 proteins were expressed in all trophoblastic cells, cells of villi central axis and decidual cells. IOD of Cx43 and Pax3 proteins expressed in the syncytiotrophoblast decreased from 5 to 7 weeks, while Cx43 …and Pax3 expressed in cytotrophoblast cells and decidual cells showed increased IOD during the same period. The differences between any two groups were statistically significant (P<0.05). Cx43 and Pax3 proteins were expressed during differentiation and development of placental villous cells in early phases of pregnancy. We propose that Cx43 and Pax3 may participate in endometrial decidualization and the regulation of trophoblastic invasion and differentiation. It is likely that Cx43 and Pax3 play critical roles in cell proliferation and differentiation during the processes of chorionic villi initiation/development and placental morphogenesis. Show more

Keywords: Connexin43, pax3, Chorionic villi, decidua, Immunohistochemistry

DOI: 10.3233/BME-141214

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3841-3847, 2014

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

Article Type: Research Article

Abstract: The purpose of this study is to predict human jejunal permeability (Peff ) and fraction absorbed in human (%Fa) for a group of antibacterial fluoroquinolones (FQs), by using a biophysical model based on measured Caco-2 permeability. The predicted Peff (in 10−4 cm·s−1 units) ranged from 0.7 (norfloxacin) to 4.5 (pefloxacin). The calculated %Fa for norfloxacin = 51% (lit. 35%) and for ciprofloxacin = 76% (lit. 81%). Most of the FQs showed calculated %Fa >90%, and are expected to be well-absorbed. Estimates of Peff can be predicted by the biophysical model. From these values, the human absorption may …be calculated. Where absorption comparisons were possible, the agreement was acceptably good. Show more

Keywords: permeability, fraction absorbed, fluoroquinolones, human intestine, Caco-2

DOI: 10.3233/BME-141215

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3849-3854, 2014

Authors: Xue, Dan | Na, Ri | Guo, Jiu Feng | Liu, Teng

Article Type: Research Article

Abstract: With a goal of obtaining the engineering probiotics that can produce both lactic acid and laccase, Pleurotus eryngii was selected as the test material. First, the laccase gene (Lacc1) was cloned by using RT-PCR (the length of which is 1596bp), and then, the gene was ligated to the food-grade vector pMG36e from Lactobacillus buchneri. The recombinant expression vector pMG36e-Lacc1 was constructed by transforming it into Lactobacillus buchneri via an electroporation method. The recombinant plasmid was constructed successfully as confirmed by gel electrophoresis. Then, the optimum conditions for electroporation were determined. The research revealed that when the electric field intensity is …1.75 kV with an SMRS medium recovery for 1.5 h, the electroporation translation efficiency reaches its maximum level. Show more

Keywords: Laccase, Lactobacillus buchneri, expression vector system

DOI: 10.3233/BME-141216

Citation: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3855-3861, 2014