Computational and Mathematical Methods in Medicine

Publications in this journal

• Article: patGPCR: A Multitemplate Approach for Improving 3D Structure Prediction of Transmembrane Helices of G-Protein-Coupled Receptors.

  Hongjie Wu, Qiang Lü, Lijun Quan, Peide Qian, Xiaoyan Xia
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  ABSTRACT: The structures of the seven transmembrane helices of G-protein-coupled receptors are critically involved in many aspects of these receptors, such as receptor stability, ligand docking, and molecular function. Most of the previous multitemplate approaches have built a "super" template with very little merging of aligned fragments from different templates. Here, we present a parallelized multitemplate approach, patGPCR, to predict the 3D structures of transmembrane helices of G-protein-coupled receptors. patGPCR, which employs a bundle-packing related energy function that extends on the RosettaMem energy, parallelizes eight pipelines for transmembrane helix refinement and exchanges the optimized helix structures from multiple templates. We have investigated the performance of patGPCR on a test set containing eight determined G-protein-coupled receptors. The results indicate that patGPCR improves the TM RMSD of the predicted models by 33.64% on average against a single-template method. Compared with other homology approaches, the best models for five of the eight targets built by patGPCR had a lower TM RMSD than that obtained from SWISS-MODEL; patGPCR also showed lower average TM RMSD than single-template and multiple-template MODELLER.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:486125.
• Article: Piecewise-Constant-Model-Based Interior Tomography Applied to Dentin Tubules.

  Peng He, Biao Wei, Steve Wang, Stuart R Stock, Hengyong Yu, Ge Wang
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  ABSTRACT: Dentin is a hierarchically structured biomineralized composite material, and dentin's tubules are difficult to study in situ. Nano-CT provides the requisite resolution, but the field of view typically contains only a few tubules. Using a plate-like specimen allows reconstruction of a volume containing specific tubules from a number of truncated projections typically collected over an angular range of about 140°, which is practically accessible. Classical computed tomography (CT) theory cannot exactly reconstruct an object only from truncated projections, needless to say a limited angular range. Recently, interior tomography was developed to reconstruct a region-of-interest (ROI) from truncated data in a theoretically exact fashion via the total variation (TV) minimization under the condition that the ROI is piecewise constant. In this paper, we employ a TV minimization interior tomography algorithm to reconstruct interior microstructures in dentin from truncated projections over a limited angular range. Compared to the filtered backprojection (FBP) reconstruction, our reconstruction method reduces noise and suppresses artifacts. Volume rendering confirms the merits of our method in terms of preserving the interior microstructure of the dentin specimen.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:892451.
• Article: Current Density Imaging Using Directly Measured Harmonic B z Data in MREIT.

  Chunjae Park, Oh In Kwon
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  ABSTRACT: Magnetic resonance electrical impedance tomography (MREIT) measures magnetic flux density signals through the use of a magnetic resonance imaging (MRI) in order to visualize the internal conductivity and/or current density. Understanding the reconstruction procedure for the internal current density, we directly measure the second derivative of B z data from the measured k-space data, from which we can avoid a tedious phase unwrapping to obtain the phase signal of B z . We determine optimal weighting factors to combine the derivatives of magnetic flux density data, ∇(2) B z , measured using the multi-echo train. The proposed method reconstructs the internal current density using the relationships between the induced internal current and the measured ∇(2) B z data. Results from a phantom experiment demonstrate that the proposed method reduces the scanning time and provides the internal current density, while suppressing the background field inhomogeneity. To implement the real experiment, we use a phantom with a saline solution including a balloon, which excludes other artifacts by any concentration gradient in the phantom.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:381507.
• Article: Knee joint vibration signal analysis with matching pursuit decomposition and dynamic weighted classifier fusion.

  Suxian Cai, Shanshan Yang, Fang Zheng, Meng Lu, Yunfeng Wu, Sridhar Krishnan
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  ABSTRACT: Analysis of knee joint vibration (VAG) signals can provide quantitative indices for detection of knee joint pathology at an early stage. In addition to the statistical features developed in the related previous studies, we extracted two separable features, that is, the number of atoms derived from the wavelet matching pursuit decomposition and the number of significant signal turns detected with the fixed threshold in the time domain. To perform a better classification over the data set of 89 VAG signals, we applied a novel classifier fusion system based on the dynamic weighted fusion (DWF) method to ameliorate the classification performance. For comparison, a single leastsquares support vector machine (LS-SVM) and the Bagging ensemble were used for the classification task as well. The results in terms of overall accuracy in percentage and area under the receiver operating characteristic curve obtained with the DWF-based classifier fusion method reached 88.76% and 0.9515, respectively, which demonstrated the effectiveness and superiority of the DWF method with two distinct features for the VAG signal analysis.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:904267.
• Article: Optimization of Contrast-to-Tissue Ratio by Adaptation of Transmitted Ternary Signal in Ultrasound Pulse Inversion Imaging.

  Sébastien Ménigot, Jean-Marc Girault
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  ABSTRACT: Ultrasound contrast imaging has provided more accurate medical diagnoses thanks to the development of innovating modalities like the pulse inversion imaging. However, this latter modality that improves the contrast-to-tissue ratio (CTR) is not optimal, since the frequency is manually chosen jointly with the probe. However, an optimal choice of this command is possible, but it requires precise information about the transducer and the medium which can be experimentally difficult to obtain, even inaccessible. It turns out that the optimization can become more complex by taking into account the kind of generators, since the generators of electrical signals in a conventional ultrasound scanner can be unipolar, bipolar, or tripolar. Our aim was to seek the ternary command which maximized the CTR. By combining a genetic algorithm and a closed loop, the system automatically proposed the optimal ternary command. In simulation, the gain compared with the usual ternary signal could reach about 3.9 dB. Another interesting finding was that, in contrast to what is generally accepted, the optimal command was not a fixed-frequency signal but had harmonic components.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:297463.
• Article: Applications of machine learning in genomics and systems biology.

  Chunmei Liu, Dongsheng Che, Xumin Liu, Yinglei Song
  Computational and Mathematical Methods in Medicine 01/2013; 2013:587492.
• Article: White blood cell segmentation by circle detection using electromagnetism-like optimization.

  Erik Cuevas, Diego Oliva, Margarita Díaz, Daniel Zaldivar, Marco Pérez-Cisneros, Gonzalo Pajares
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  ABSTRACT: Medical imaging is a relevant field of application of image processing algorithms. In particular, the analysis of white blood cell (WBC) images has engaged researchers from fields of medicine and computer vision alike. Since WBCs can be approximated by a quasicircular form, a circular detector algorithm may be successfully applied. This paper presents an algorithm for the automatic detection of white blood cells embedded into complicated and cluttered smear images that considers the complete process as a circle detection problem. The approach is based on a nature-inspired technique called the electromagnetism-like optimization (EMO) algorithm which is a heuristic method that follows electromagnetism principles for solving complex optimization problems. The proposed approach uses an objective function which measures the resemblance of a candidate circle to an actual WBC. Guided by the values of such objective function, the set of encoded candidate circles are evolved by using EMO, so that they can fit into the actual blood cells contained in the edge map of the image. Experimental results from blood cell images with a varying range of complexity are included to validate the efficiency of the proposed technique regarding detection, robustness, and stability.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:395071.
• Article: A General Framework for Modeling Sub- and Ultraharmonics of Ultrasound Contrast Agent Signals with MISO Volterra Series.

  Fatima Sbeity, Sébastien Ménigot, Jamal Charara, Jean-Marc Girault
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  ABSTRACT: Sub- and ultraharmonics generation by ultrasound contrast agents makes possible sub- and ultraharmonics imaging to enhance the contrast of ultrasound images and overcome the limitations of harmonic imaging. In order to separate different frequency components of ultrasound contrast agents signals, nonlinear models like single-input single-output (SISO) Volterra model are used. One important limitation of this model is its incapacity to model sub- and ultraharmonic components. Many attempts are made to model sub- and ultraharmonics using Volterra model. It led to the design of mutiple-input singe-output (MISO) Volterra model instead of SISO Volterra model. The key idea of MISO modeling was to decompose the input signal of the nonlinear system into periodic subsignals at the subharmonic frequency. In this paper, sub- and ultraharmonics modeling with MISO Volterra model is presented in a general framework that details and explains the required conditions to optimally model sub- and ultraharmonics. A new decomposition of the input signal in periodic orthogonal basis functions is presented. Results of application of different MISO Volterra methods to model simulated ultrasound contrast agents signals show its efficiency in sub- and ultraharmonics imaging.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:934538.
• Article: Robust Myocardial Motion Tracking for Echocardiography: Variational Framework Integrating Local-to-Global Deformation.

  Chi Young Ahn
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  ABSTRACT: This paper proposes a robust real-time myocardial border tracking algorithm for echocardiography. Commonly, after an initial contour of LV border is traced at one or two frames from the entire cardiac cycle, LV contour tracking is performed over the remaining frames. Among a variety of tracking techniques, optical flow method is the most widely used for motion estimation of moving objects. However, when echocardiography data is heavily corrupted in some local regions, the errors bring the tracking point out of the endocardial border, resulting in distorted LV contours. This shape distortion often occurs in practice since the data acquisition is affected by ultrasound artifacts, dropouts, or shadowing phenomena of cardiac walls. The proposed method is designed to deal with this shape distortion problem by integrating local optical flow motion and global deformation into a variational framework. The proposed descent method controls the individual tracking points to follow the local motions of a specific speckle pattern, while their overall motions are confined to the global motion constraint being approximately an affine transform of the initial tracking points. Many real experiments show that the proposed method achieves better overall performance than conventional methods.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:974027.
• Article: Computational approach to seasonal changes of living leaves.

  Ying Tang, Dong-Yan Wu, Jing Fan
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  ABSTRACT: This paper proposes a computational approach to seasonal changes of living leaves by combining the geometric deformations and textural color changes. The geometric model of a leaf is generated by triangulating the scanned image of a leaf using an optimized mesh. The triangular mesh of the leaf is deformed by the improved mass-spring model, while the deformation is controlled by setting different mass values for the vertices on the leaf model. In order to adaptively control the deformation of different regions in the leaf, the mass values of vertices are set to be in proportion to the pixels' intensities of the corresponding user-specified grayscale mask map. The geometric deformations as well as the textural color changes of a leaf are used to simulate the seasonal changing process of leaves based on Markov chain model with different environmental parameters including temperature, humidness, and time. Experimental results show that the method successfully simulates the seasonal changes of leaves.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:619385.
• Article: Continuous- and discrete-time stimulus sequences for high stimulus rate paradigm in evoked potential studies.

  Tao Wang, Jiang-Hua Huang, Lin Lin, Chang'an A Zhan
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  ABSTRACT: To obtain reliable transient auditory evoked potentials (AEPs) from EEGs recorded using high stimulus rate (HSR) paradigm, it is critical to design the stimulus sequences of appropriate frequency properties. Traditionally, the individual stimulus events in a stimulus sequence occur only at discrete time points dependent on the sampling frequency of the recording system and the duration of stimulus sequence. This dependency likely causes the implementation of suboptimal stimulus sequences, sacrificing the reliability of resulting AEPs. In this paper, we explicate the use of continuous-time stimulus sequence for HSR paradigm, which is independent of the discrete electroencephalogram (EEG) recording system. We employ simulation studies to examine the applicability of the continuous-time stimulus sequences and the impacts of sampling frequency on AEPs in traditional studies using discrete-time design. Results from these studies show that the continuous-time sequences can offer better frequency properties and improve the reliability of recovered AEPs. Furthermore, we find that the errors in the recovered AEPs depend critically on the sampling frequencies of experimental systems, and their relationship can be fitted using a reciprocal function. As such, our study contributes to the literature by demonstrating the applicability and advantages of continuous-time stimulus sequences for HSR paradigm and by revealing the relationship between the reliability of AEPs and sampling frequencies of the experimental systems when discrete-time stimulus sequences are used in traditional manner for the HSR paradigm.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:396034.
• Article: The Analysis of the Artifacts due to the Simultaneous Use of Two Ultrasound Probes with Different/Similar Operating Frequencies.

  Samreen Amir, B S Chowdhry, Manzoor Hashmani, Musarrat Hasan
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  ABSTRACT: The ultrasound imaging has the potential to become a dominant technique for noninvasive therapies and least invasive surgeries. Few cases may require using multiple probes of different units with different modes of ultrasound on the same patient. It generates imaging artifacts, which makes it complicated to gather information from the acquired image. This study was to identify and analyse the artifacts which are produced by simultaneous use of two probes with different/same operating frequencies. Six imaging studies were performed. First of all, the imaging artifacts of the 3.5 MHz and 6 MHz center frequencies with similar (longitudinal) positions of the probes. Secondly, with similar operating frequencies the 6 MHz probe changed from longitudinal to transverse placement to analyse the resulting artifacts. The third study was done with transverse placement of 3.5 MHz probe. The rest of the three cases were just the repetition with common pulse frequencies. Such artifacts in 3D ultrasound images are more obscure than the other artifacts associated and reported.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:890170.
• Article: Numerical study of magnetoacoustic signal generation with magnetic induction based on inhomogeneous conductivity anisotropy.

  Xun Li, Sanqing Hu, Lihua Li, Shanan Zhu
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  ABSTRACT: Magnetoacoustic tomography with magnetic induction (MAT-MI) is a noninvasive imaging modality for generating electrical conductivity images of biological tissues with high spatial resolution. In this paper, we create a numerical model, including a permanent magnet, a coil, and a two-layer coaxial cylinder with anisotropic electrical conductivities, for the MAT-MI forward problem. We analyze the MAT-MI sources in two cases, on a thin conductive boundary layer and in a homogeneous medium, and then develop a feasible numerical approach to solve the MAT-MI sound source densities in the anisotropic conductive model based on finite element analysis of electromagnetic field. Using the numerical finite element method, we then investigate the magnetoacoustic effect of anisotropic conductivity under the inhomogeneous static magnetic field and inhomogeneous magnetic field, quantitatively compute the boundary source densities in the conductive model, and calculate the sound pressure. The anisotropic conductivity contributes to the distribution of the eddy current density, Lorentz force density, and acoustic signal. The proposed models and approaches provide a more realistic simulation environment for MAT-MI.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:161357.
• Article: Improving Spatial Adaptivity of Nonlocal Means in Low-Dosed CT Imaging Using Pointwise Fractal Dimension.

  Xiuqing Zheng, Zhiwu Liao, Shaoxiang Hu, Ming Li, Jiliu Zhou
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  ABSTRACT: NLMs is a state-of-art image denoising method; however, it sometimes oversmoothes anatomical features in low-dose CT (LDCT) imaging. In this paper, we propose a simple way to improve the spatial adaptivity (SA) of NLMs using pointwise fractal dimension (PWFD). Unlike existing fractal image dimensions that are computed on the whole images or blocks of images, the new PWFD, named pointwise box-counting dimension (PWBCD), is computed for each image pixel. PWBCD uses a fixed size local window centered at the considered image pixel to fit the different local structures of images. Then based on PWBCD, a new method that uses PWBCD to improve SA of NLMs directly is proposed. That is, PWBCD is combined with the weight of the difference between local comparison windows for NLMs. Smoothing results for test images and real sinograms show that PWBCD-NLMs with well-chosen parameters can preserve anatomical features better while suppressing the noises efficiently. In addition, PWBCD-NLMs also has better performance both in visual quality and peak signal to noise ratio (PSNR) than NLMs in LDCT imaging.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:902143.
• Article: The Prevalence of Asthma and Declared Asthma in Poland on the Basis of ECAP Survey Using Correspondence Analysis.

  M Zalewska, K Furmańczyk, S Jaworski, W Niemiro, B Samoliński
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  ABSTRACT: Results of epidemiological and public health surveys are often presented in the form of cross-classification tables. It is sometimes difficult to analyze data described in this way and to understand relations between variables. Graphical methods such as correspondence analysis are more convenient and useful. Our paper describes an application of correspondence analysis to epidemiological research. We apply the basic concepts of correspondence analysis like profiles, chi-square distance to medical data concerning prevalence of asthma. We aim at describing the relationship between asthma, region, and age. The data presented in this paper come from Epidemiology of Allergy in Poland (ECAP) survey in years 2006-2008. Correspondence analysis shows that there is a fundamental difference in the structure of age groups for people with symptoms compared to those who have declared asthma (regardless of the level of symptoms of asthma and the level of declaration). The variable which best differentiates declared asthma in all regions is "wheezing and whistling." Correspondence analysis also shows significant differences between locations. Our analyses are performed in the R package "ca".
  Computational and Mathematical Methods in Medicine 01/2013; 2013:597845.
• Article: Modelling tumour oxygenation, reoxygenation and implications on treatment outcome.

  Iuliana Toma-Dasu, Alexandru Dasu
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  ABSTRACT: Oxygenation is an important component of the tumour microenvironment, having a significant impact on the progression and management of cancer. Theoretical determination of tissue oxygenation through simulations of the oxygen transport process is a powerful tool to characterise the spatial distribution of oxygen on the microscopic scale and its dynamics and to study its impact on the response to radiation. Accurate modelling of tumour oxygenation must take into account important aspects that are specific to tumours, making the quantitative characterisation of oxygenation rather difficult. This paper aims to discuss the important aspects of modelling tumour oxygenation, reoxygenation, and implications for treatment.
  Computational and Mathematical Methods in Medicine 01/2013; 2013:141087.