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Generalized autocalibrating partially parallel acquisition (GRAPPA) has been a widely used parallel MRI technique. However, noise deteriorates the reconstructed image when reduction factor increases or even at low reduction factor for some noisy datasets. Noise, initially generated from scanner, propagates noise-related errors during fitting and interpolation procedures of GRAPPA to distort the final reconstructed image quality. The basic idea we proposed to improve GRAPPA is to remove noise from a system identification perspective. In this paper, we first analyze the GRAPPA noise problem from a noisy input-output system perspective; then, a new framework based on errors-in-variables (EIV) model is developed for analyzing noise generation mechanism in GRAPPA and designing a concrete method—instrument variables (IV) GRAPPA to remove noise. The proposed EIV framework provides possibilities that noiseless GRAPPA reconstruction could be achieved by existing methods that solve EIV problem other than IV method. Experimental results show that the proposed reconstruction algorithm can better remove the noise compared to the conventional GRAPPA, as validated with both of phantom and in vivo brain data. [ABSTRACT FROM AUTHOR]

Tumors are a serious threat to human health. The oncolytic virus is a kind of tumor killer virus which can infect and lyse cancer cells and spread through the tumor, while leaving normal cells largely unharmed. Mathematical models can help us to understand the tumor-virus dynamics and find better treatment strategies. This paper gives a new mathematical model of tumor therapy with oncolytic virus and MEK inhibitor. Stable analysis was given. Because mitogen-activated protein kinase (MEK) can not only lead to greater oncolytic virus infection into cancer cells, but also limit the replication of the virus, in order to provide the best dosage of MEK inhibitors and balance the positive and negative effect of the inhibitors, we put forward an optimal control problem of the inhibitor. The optimal strategies are given by theory and simulation. [ABSTRACT FROM AUTHOR]

Although heart researches and acquirement of clinical and experimental data are progressively open to public use, cardiac biophysical functions are still not well understood. Due to the complex and fine structures of the heart, cardiac electrophysiological features of interest may be occluded when there is a necessity to demonstrate cardiac electrophysiological behaviors. To investigate cardiac abnormal electrophysiological features under the pathological condition, in this paper, we implement a human cardiac ischemic model and acquire the electrophysiological data of excitation propagation. A visualization framework is then proposed which integrates a novel depth weighted optic attenuation model into the pathological electrophysiological model. The hidden feature of interest in pathological tissue can be revealed from sophisticated overlapping biophysical information. Experiment results verify the effectiveness of the proposed method for intuitively exploring and inspecting cardiac electrophysiological activities, which is fundamental in analyzing and explaining biophysical mechanisms of cardiac functions for doctors and medical staff. [ABSTRACT FROM AUTHOR]

Constructing rooted phylogenetic networks from rooted phylogenetic trees has become an important problem in molecular evolution. So far, many methods have been presented in this area, in which most efficient methods are based on the incompatible graph, such as the CASS, the LNETWORK, and the BIMLR. This paper will research the commonness of the methods based on the incompatible graph, the relationship between incompatible graph and the phylogenetic network, and the topologies of incompatible graphs. We can find out all the simplest datasets for a topology G and construct a network for every dataset. For any one dataset C, we can compute a network from the network representing the simplest dataset which is isomorphic to C. This process will save more time for the algorithms when constructing networks. [ABSTRACT FROM AUTHOR]

This paper presents an ultrasound simulation model for pulsatile blood flow, modulated by the motion of a stenosed vessel wall. It aims at generating more realistic ultrasonic signals to provide an environment for evaluating ultrasound signal processing and imaging and a framework for investigating the behaviors of blood flow field modulated by wall motion. This model takes into account fluid-structure interaction, blood pulsatility, stenosis of the vessel, and arterial wall movement caused by surrounding tissue’s motion. The axial and radial velocity distributions of blood and the displacement of vessel wall are calculated by solving coupled Navier-Stokes and wall equations. With these obtained values, we made several different phantoms by treating blood and the vessel wall as a group of point scatterers. Then, ultrasound echoed signals from oscillating wall and blood in the axisymmetric stenotic-carotid arteries were computed by ultrasound simulation software, Field II. The results show better consistency with corresponding theoretical values and clinical data and reflect the influence of wall movement on the flow field. It can serve as an effective tool not only for investigating the behavior of blood flow field modulated by wall motion but also for quantitative or qualitative evaluation of new ultrasound imaging technology and estimation method of blood velocity. [ABSTRACT FROM AUTHOR]

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric, de-distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable. [ABSTRACT FROM AUTHOR]

Neurons are specialized, electrically excitable cells which use electrical to chemical signals to transmit and elaborate information. Understanding how the cooperation of a great many of neurons in a grid may modify and perhaps improve the information quality, in contrast to few neurons in isolation, is critical for the rational design of cell-materials interfaces for applications in regenerative medicine, tissue engineering, and personalized lab-on-a-chips. In the present paper, we couple an integrate-and-fire model with information theory variables to analyse the extent of information in a network of nerve cells. We provide an estimate of the information in the network in bits as a function of cell density and short-term depression time. In the model, neurons are connected through a Delaunay triangulation of not-intersecting edges; in doing so, the number of connecting synapses per neuron is approximately constant to reproduce the early time of network development in planar neural cell cultures. In simulations where the number of nodes is varied, we observe an optimal value of cell density for which information in the grid is maximized. In simulations in which the posttransmission latency time is varied, we observe that information increases as the latency time decreases and, for specific configurations of the grid, it is largely enhanced in a resonance effect. [ABSTRACT FROM AUTHOR]

Cancer is a class of diseases characterized by out-of-control cells’ growth which affect cells and make them damaged. Many treatment options for cancer exist. Chemotherapy as an important treatment option is the use of drugs to treat cancer. The anticancer drug travels to the tumor and then diffuses in it through capillaries. The diffusion of drugs in the solid tumor is limited by penetration depth which is different in case of different drugs and cancers. The computation of this depth is important as it helps physicians to investigate about treatment of infected tissue. Although many efforts have been made on studying and measuring drug penetration depth, less works have been done on computing this length from a mathematical point of view. In this paper, first we propose phase lagging model for diffusion of drug in the tumor. Then, using this model on one side and considering the classic diffusion on the other side, we compute the drug penetration depth in the solid tumor. This computed value of drug penetration depth is corroborated by comparison with the values measured by experiments. [ABSTRACT FROM AUTHOR]

Protein remote homology detection is one of the central problems in bioinformatics. Although some computational methods have been proposed, the problem is still far from being solved. In this paper, an ensemble classifier for protein remote homology detection, called SVM-Ensemble, was proposed with a weighted voting strategy. SVM-Ensemble combined three basic classifiers based on different feature spaces, including Kmer, ACC, and SC-PseAAC. These features consider the characteristics of proteins from various perspectives, incorporating both the sequence composition and the sequence-order information along the protein sequences. Experimental results on a widely used benchmark dataset showed that the proposed SVM-Ensemble can obviously improve the predictive performance for the protein remote homology detection. Moreover, it achieved the best performance and outperformed other state-of-the-art methods. [ABSTRACT FROM AUTHOR]

A comprehensive understanding of the integrative nature of the molecular network in thrombosis would be very helpful to develop multicomponent and multitarget antithrombosis drugs for use in traditional Chinese medicine (TCM). This paper attempts to comprehensively map the molecular network in thrombosis by combining platelet signaling, the coagulation cascade, and natural clot dissolution systems and to analyze the topological characteristics of the network, including the centralities of nodes, network modules, and network robustness. The results in this research advance understanding of functions of proteins in the thrombosis network and provide a reference for predicting potential therapeutic antithrombotic targets and evaluating their influence on the network. [ABSTRACT FROM AUTHOR]