Faculty Profiles - Shimayoshi Takao

Papers - Shimayoshi Takao

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Application of the Kalman Filter for Faster Strong Coupling of Cardiovascular Simulations Reviewed International journal

Yuki Hasegawa, Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

IEEE Journal of Biomedical and Health Informatics 20 ( 4 ) 1100 - 1106 2016.7

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Institute of Electrical and Electronics Engineers ({IEEE})

In this paper, we propose a method for reducing the computational cost of strong coupling for multiscale cardiovascular simulation models. In such a model, individual model modules of myocardial cell, left ventricular structural dynamics, and circulatory hemodynamics are coupled. The strong coupling method enables stable and accurate calculation, but requires iterative calculations which are computationally expensive. The iterative calculations can be reduced, if accurate initial approximations are made available by predictors. The proposed method uses the Kalman filter to estimate accurate predictions by filtering out noise included in past values. The performance of the proposed method was assessed with an application to a previously published multiscale cardiovascular model. The proposed method reduced the number of iterations by 90% and 62% compared with no prediction and Lagrange extrapolation, respectively. Even when the parameters were varied and number of elements of the left ventricular finite-element model increased, the number of iterations required by the proposed method was significantly lower than that without prediction. These results indicate the robustness, scalability, and validity of the proposed method.

DOI： 10.1109/JBHI.2015.2436212

左心室拍動シミュレーションにおけるメッシュ分割の影響 Reviewed

嶋吉隆夫, 小川貴史, 松田哲也

J99-D ( 5 ) 571 - 578 2016.5

Authorship：Lead author,　Corresponding author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：(一社)電子情報通信学会

心壁の拍動現象のシミュレーションでは一般的に、有限要素法による構造力学解析が用いられる。構造力学解析では一般にメッシュ分割が計算結果に影響を与えることが知られている。本論文では、通常の構造力学解析では扱われない、心筋線維方向に生じる心筋細胞の自発的収縮力を考慮した左心室拍動連成シミュレーションにおいて、メッシュ分割の差異が計算結果に与える影響について報告する。本研究では、厚肉回転だ円体の上部を切除した左心室を表現する形状に対して、経緯線に沿って分割したメッシュモデルと、半正多面体である斜方二十・十二面体を細分化して生成したメッシュモデルを比較した。シミュレーション結果の応力分布では心尖部付近に顕著な差が認められたが、ひずみに応じて生じる受動応力成分には大きな差は見られず、心筋線維方向と細胞の自発的収縮力とにおけるメッシュモデル間の差異が主に応力分布の相違を生じていることが明らかとなった。(著者抄録)

Modeling analysis of inositol 1,4,5-trisphosphate receptor-mediated ca²⁺ mobilization under the control of glucagon-like peptide-1 in mouse pancreatic β-cells Reviewed International journal

Yukari Takeda, Takao Shimayoshi, George G. Holz, Akinori Noma

American Journal of Physiology - Cell Physiology 310 ( 5 ) C337 - C347 2016.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER PHYSIOLOGICAL SOC

Glucagon-like peptide-1 (GLP-1) is an intestinally derived blood glucose-lowering hormone that potentiates glucose-stimulated insulin secretion from pancreatic β-cells. The secretagogue action of GLP-1 is explained, at least in part, by its ability to stimulate cAMP production so that cAMP may facilitate the release of Ca from inositol trisphosphate receptor (IP R)-regulated Ca stores. However, a quantitative model has yet to be provided that explains the molecular mechanisms and dynamic processes linking GLP-1-stimulated cAMP production to Ca mobilization. Here, we performed simulation studies to investigate how GLP-1 alters the abilities of Ca and IP to act as coagonists at IP R Ca release channels. A new dynamic model was constructed based on the Kaftan model, which demonstrates dual steady-state allosteric regulation of the IP R by Ca and IP . Data obtained from β-cells were then analyzed to understand how GLP-1 facilitates IP R-mediated Ca mobilization when UV flash photolysis is used to uncage Ca and IP intracellularly. When the dynamic model for IP R activation was incorporated into a minimal cell model, the Ca transients and oscillations induced by GLP-1 were successfully reconstructed. Simulation studies indicated that transient and oscillatory responses to GLP-1 were produced by sequential positive and negative feedback regulation due to fast activation and slow inhibition of the IP R by Ca . The slow rate of Ca -dependent inhibition was revealed to provide a remarkable contribution to the time course of the decay of cytosolic Ca transients. It also served to drive and pace Ca oscillations that are significant when evaluating how GLP-1 stimulates insulin secretion. 2+ 2+ 2+ 2+ 2+ 2+ 2+ 2+ 2+ 2+ 2+ 2+ 2+ 3 3 3 3 3 3 3 3 3

DOI： 10.1152/ajpcell.00234.2015

Simulation system for multiscale biological function models that require complex calculation scheme Reviewed

Akira Amano, Florencio Punzalan Rusty, Takao Shimayoshi, Yoshitoshi Kunieda

Transactions of Japanese Society for Medical and Biological Engineering 53 ( 3 ) 115 - 122 2015.10

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japanese Society for Medical and Biological Engineering

Many biological findings are continuously reported in the life science area. Most of them are reports on the correlations between some proteins, or correlations between some proteins and macroscopic phenomena such as whole body hemodynamics. In order to understand the underlying mechanisms of the biological systems, simulation and analysis of multiscale biological function models are considered useful. Since the complex calculation schemes are necessary to calculate these models efficiently, it is useful to represent both the biological function models and the calculation schemes in descriptive languages which are readable by the computer programs. In this report, we introduce our simulation system which generates simulation programs from biological function models and calculation schemes both described by description languages. Using our system, we were able to generate simulation programs for a hemodynamic simulation model coupling a ventricular myocyte model and a whole body circulation model, a simulation model that evaluates the changes in action potential of a ventricular myocyte model after drug administration, and a program that calculates the changes in action potential of ventricular myocytes by changing specific parameters.

DOI： 10.11239/jsmbe.53.115

Quantitative decomposition of dynamics of mathematical cell models: Method and application to ventricular myocyte models Reviewed International journal

Takao Shimayoshi, Chae Young Cha, Akira Amano

PLoS ONE 10 ( 6 ) e0124970 2015.6

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：PUBLIC LIBRARY SCIENCE

Mathematical cell models are effective tools to understand cellular physiological functions precisely. For detailed analysis of model dynamics in order to investigate how much each component affects cellular behaviour, mathematical approaches are essential. This article presents a numerical analysis technique, which is applicable to any complicated cell model formulated as a system of ordinary differential equations, to quantitatively evaluate contributions of respective model components to the model dynamics in the intact situation. The present technique employs a novel mathematical index for decomposed dynamics with respect to each differential variable, along with a concept named instantaneous equilibrium point, which represents the trend of a model variable at some instant. This article also illustrates applications of the method to comprehensive myocardial cell models for analysing insights into the mechanisms of action potential generation and calcium transient. The analysis results exhibit quantitative contributions of individual channel gating mechanisms and ion exchanger activities to membrane repolarization and of calcium fluxes and buffers to raising and descending of the cytosolic calcium level. These analyses quantitatively explicate principle of the model, which leads to a better understanding of cellular dynamics.

DOI： 10.1371/journal.pone.0124970

Efficient Algorithm for Extracting the Multiple Loop Structure of the Corresponding Calculation Program from the Complex Recurrence Relation Equation

KOMIYAMA SHIGERU, TATARA TAIKI, PUNZALAN FLORENCIO RUSTY, SHIMAYOSHI TAKAO, KUNIEDA YOSHITOSHI, AMANO AKIRA

電子情報通信学会技術研究報告 114 ( 514(MBE2014 116-179) ) 111 - 116 2015.3

Nonlinear multiscale circulation model reproducable linear end-systolic pressure-volume relationship Reviewed International journal

Takao Shimayoshi, Mitsuharu Mishima, Akira Amano, Tetsuya Matsuda

2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014 2014 6778 - 6781 2014.11

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (international conference proceedings) Publisher：IEEE

As a well-known property of the heart, many studies has reported that the left ventricular end-systolic pressure-volume relationship (ESPVR) is linear. However, the reason of the linearity is poorly understood. This article presents a multiscale circulation model to be a tool for theoretical analyses on the mechanism of the linearity of ESPVR. The model is composed of three sub-models; a detailed closed-loop lumped-parameter model for cardiovascular system, geometric left ventricle model, a comprehensive ventricular myocyte model. Although the present model integrates nonlinear sub-models, the model can successfully reproduce highly linear ESPVR without any arbitrary modifications.

DOI： 10.1109/EMBC.2014.6945184

Other Link： https://dblp.uni-trier.de/conf/embc/2014

A study on the relationship between electrical transmural heterogeneity and ventricular energetics Reviewed

Yuki Hasegawa, Mitsuharu Mishima, Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

Transactions of Japanese Society for Medical and Biological Engineering 52 ( 3 ) 129 - 135 2014.9

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japanese Society for Medical and Biological Engineering

Although there are numerous reports on the electrical heterogeneity of the myocardium, little has been given attention to its relation to cardiovascular mechanics, because of difficulties of simultaneously observing multiple effects in vivo. In this research, a multi-scale cardiovascular simulation model, which describes the myocyte physiology, left ventricular structural dynamics, and hemodynamics, was used to theoretically investigate the relationshipbetween the electrical transmural heterogeneity of myocytes and ventricular energetics. The parameters which describe the characteristics of ion channels of an existing myocyte model were changed to create endo-, mid-, and epi-cardium myocyte models. Simulations were performed with electrically heterogeneous and homogeneous models. As a result, the heterogeneous model had lower contractility and higher total mechanical energy generation per ATP consumption. These findings indicate that electrical heterogeneity contribute to cardiac efficiency.

DOI： 10.11239/jsmbe.52.129

An effect of meshing on coupling simulation of left ventricular wall motion Reviewed

Takafumi Ogawa, Takao Shimayoshi, Naoki Kida, Taiji Adachi, Tetsuya Matsuda

Transactions of Japanese Society for Medical and Biological Engineering 52 ( Supplement ) O-186 - O-187 2014.8

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japanese Society for Medical and Biological Engineering

In standard finite element analysis in structural dynamics, meshing can affect computation results. However, there have been no detailed report about effects of meshing on results of coupling simulation of left ventricular wall motion which involves myocardial spontaneous contractile force and fiber orientation. In this study, we examined an effect of meshing on simulation of left ventricular wall motion, which couples precise ventricular myocyte model and myocardial fiber orientation. We compared two shape models; spheroid mesh divided along graticule and spheroid mesh subdivided from a semi-regular polyhedron. The comparison results show significant differences between two models around the ventricular apex, which are mainly caused by the contractile force and the fiber orientation.

DOI： 10.11239/jsmbe.52.O-186

A simulation model of myocardial microcirculation for local distribution of oxygen consumption Reviewed

Takao Shimayoshi, Yuuta Kubota, Akira Amano, Tetsuya Matsuda

Transactions of Japanese Society for Medical and Biological Engineering 51 ( 4 ) 248 - 253 2013.8

Authorship：Lead author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japanese Society for Medical and Biological Engineering

Detailed analysis of oxygen consumption within the myocardial microcirculation is of importance to understand conditions under ischemic heart disease. However, there are currently difficulties in microscopically precise measurements of local oxygen consumptions in myocardial tissue. In this paper, a simulation model of myocardial microcirculation is proposed for analysis of local distribution of oxygen consumption. The proposed model is composed by integrating a theoretical spatially-distributed model of myocardial tissue and a detailed lumped-parameter model of normal cardiac myocyte. The proposed model was validated for an animal research in reproduction of a linear correlation between myocardial oxygen consumption and myocardial contractility. A simulation result of the model shows that local oxygen consumptions under low myocardial blood flow are spatially partitioned into an arteriolar-side normal area and a venular-side low area. Myocytes in the venular-side area lose normal activity under extremely low oxygen concentration. This result indicates the possibility that cardiac tissue is locally damaged under extreme hypoxia in the venular-side area even in case of a slight reduction of mean oxygen consumption of the myocadial tissue caused by decreased myocardial blood flow.

DOI： 10.11239/jsmbe.51.248

A study on the relationship between electrical transmural heterogeneity and ventricular energetics Reviewed International journal

Yuki Hasegawa, Mitsuharu Mishima, Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2013 6854 - 6857 2013.7

Language：English Publishing type：Research paper (international conference proceedings) Publisher：IEEE

In this study, we use cardiovascular simulation to gain new insights on the correlation between electrical heterogeneity and ventricular energetics. Although there are numerous in vivo and in vitro studies on the electrical heterogeneity within the ventricular myocardium, not much attention has been directed to its correlation to cardiovascular mechanics, because of difficulties in simultaneously observing and analyzing multiple spatial scales(the cell, the organ, and the system). We performed simulations with two cardiovascular simulation models, one which uses different myocardial cell models for the epicardial, endocardial, and mid-myocardial cells, and another which uses a homogeneous model throughout the entire myocardium. The epicardial, endocardial, and midmyocardial cell models were created by parametrically tuning a homogenous cell model. From the cardiovascular simulation we obtained pressure-volume loops which were used to calculate cardiovascular energetic efficiency and myocardial contractility. We found that energetic efficiency is higher in the electrically heterogeneous model. © 2013 IEEE.

DOI： 10.1109/EMBC.2013.6611132

Other Link： https://dblp.uni-trier.de/conf/embc/2013

Code generator for distributed parameter biological model simulation with PDE numerical schemes Reviewed International journal

Florencio Rusty Punzalan, Yoshiharu Yamashita, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, Akira Amano

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2013 1494 - 1497 2013.7

Language：English Publishing type：Research paper (international conference proceedings) Publisher：IEEE

The physiological simulation at the tissue and organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and in cases like pharmacokinetics, distributed parameters add to the complexity of the PDE solution. These factors make most PDE solutions and their corresponding program codes tailored for specific problems. We propose a general approach for handling PDEs in computational models using a replacement scheme for discretization. This method allows for the handling of the different PDE types. The replacement scheme involves substituting all the partial differential terms with the numerical solution equations. Once the model equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to determine the simulation loop structure and generate the program code. © 2013 IEEE.

DOI： 10.1109/EMBC.2013.6609795

Other Link： https://dblp.uni-trier.de/conf/embc/2013

Theoretical analysis on the relationship between left ventricular energetic efficiency and acute infarct size Reviewed International journal

Takao Shimayoshi, Yuki Hasegawa, Mitsuharu Mishima, Tetsuya Matsuda

IET Systems Biology 7 ( 3 ) 74 - 78 2013.6

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：INST ENGINEERING TECHNOLOGY-IET

Energetic efficiency is an important indicator of cardiac function in acute myocardial infarction. However, the relationship between cardiac energetic efficiency and infarct size is not perfectly elucidated. In this study, the relationship is analysed by means of simulation using a theoretical model of the guinea pig left ventricle. In simulation with varied ratios of infarct area, pressure-volume area (PVA), which is an index of total mechanical energy by ventricular contraction, and myocardial oxygen consumption (MVO ) are calculated for each infarct ratio. Then, change of PVA when MVO alters (PVA/MVO ) as a well-known index of energy conversion efficiency is evaluated. In addition, PVA/VO , which represents a ratio of PVA change to alteration of mean oxygen consumption of myocytes except for infarct myocytes, is introduced as an index for real energetic efficiency. In simulation results, PVA/MVO increases but PVA/VO decreases as infarct area expands, because with expansion of infarct area PVA decreases but VO remains almost unchanged because of larger shortening of myocytes. This implies that the enlargement of shortening of noninfarcted myocyte to compensate for depression of cardiac output is a potential cause of myocardial remodelling. © The Institution of engineering and technology 2013. 2 2 2 2 2 2 2

DOI： 10.1049/iet-syb.2011.0080

形式的記述された組織・臓器モデルのための汎用シミュレーションシステム

AMANO AKIRA, SHIMAYOSHI TAKAO, KUNIEDA YOSHITOSHI

心電図 33 ( Supplement 2 ) 59 2013.5

Implementation of a Ventricular Cell Model to a Cardiovascular Model Regulated by the Autonomic Nervous System

Yukiko Himeno, Takao Shimayoshi, Akinori Noma, Akira Amano

JOURNAL OF PHYSIOLOGICAL SCIENCES 63 ( Suppl 1 ) S234 - S234 2013.1

Distributed Parameter Biological Function Model Simulation with User-Provided PDE Numerical Solution Scheme Reviewed

Rusty Punzalan Florencio, YAMASHITA Yoshiharu, KAWABATA Masanari, SHIMAYOSHI Takao, KUWABARA Hiroaki, KUNIEDA Yoshitoshi, AMANO Akira

Transactions of Japanese Society for Medical and Biological Engineering 50 ( 6 ) 666 - 674 2012.12

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japanese Society for Medical and Biological Engineering

The coupling of cellular processes at the tissue and organ level usually involves the handling of partial differential equations (PDEs). Since physiological computational models using PDEs have varied greatly in terms of complexity, most solutions are tailored for specific problems. Space-time discretization schemes like FTCS (Forward-Time Centered-Space), BTCS (Backward-Time Centered-Space), Dufort-Frankel, Crank-Nicolson and Lax-Friedrichs exist. We propose a general approach for handling PDEs in computational models using a replacement scheme for discretization. The replacement scheme involves substituting all the partial differential terms with the numerical solution equations. During the replacement algorithm, the time and spatial indices are also appended to the model variables. This method allows for handling of different forms of equation. Once the derivatives are replaced with the discretized terms, the resulting equations are then written in a recurrence relation form. Finally, the equations for solving the unknown variables are generated. The solution to the linear system of equations uses iterative methods like Gauss-Jacobi and Gauss-Seidel algorithm. If the system is explicit, corresponding loop structure is generated as program code to solve the system. We could successfully generate an excitation propagation simulation program for FTCS scheme with a complex cell model.

DOI： 10.11239/jsmbe.50.666

Other Link： http://search.jamas.or.jp/link/ui/2013307326

A CellML simulation compiler and code generator using ODE solving schemes Reviewed International journal

Punzalan, F.R., Yamashita, Y., Soejima, N., Kawabata, M., Shimayoshi, T., Kuwabara, H., Kunieda, Y., Amano, A.

Source Code for Biology and Medicine 7 ( 1 ) 11 - 11 2012.10

Language：English Publishing type：Research paper (scientific journal)

Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. The CellML Compiler source code is available for download at http://sourceforge.net/projects/cellmlcompiler. © 2012 Punzalan et al.; licensee BioMed Central Ltd.

DOI： 10.1186/1751-0473-7-11

A coupling method for a cardiovascular simulation model which includes the Kalman Filter Reviewed International journal

Yuki Hasegawa, Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2012 1222 - 1225 2012.8

Language：English Publishing type：Research paper (international conference proceedings) Publisher：IEEE

Multi-scale models of the cardiovascular system provide new insight that was unavailable with in vivo and in vitro experiments. For the cardiovascular system, multi-scale simulations provide a valuable perspective in analyzing the interaction of three phenomenons occurring at different spatial scales: circulatory hemodynamics, ventricular structural dynamics, and myocardial excitation-contraction. In order to simulate these interactions, multiscale cardiovascular simulation systems couple models that simulate different phenomena. However, coupling methods require a significant amount of calculation, since a system of non-linear equations must be solved for each timestep. Therefore, we proposed a coupling method which decreases the amount of calculation by using the Kalman filter. In our method, the Kalman filter calculates approximations for the solution to the system of non-linear equations at each timestep. The approximations are then used as initial values for solving the system of non-linear equations. The proposed method decreases the number of iterations required by 94.0% compared to the conventional strong coupling method. When compared with a smoothing spline predictor, the proposed method required 49.4% fewer iterations. © 2012 IEEE.

DOI： 10.1109/EMBC.2012.6346157

A program code generator for multiphysics biological simulation using markup languages Reviewed International journal

Akira Amano, Masanari Kawabata, Yoshiharu Yamashita, Florencio Rusty Punzalan, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2012 6624 - 6627 2012.8

Language：English Publishing type：Research paper (international conference proceedings) Publisher：IEEE

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown. © 2012 IEEE.

DOI： 10.1109/EMBC.2012.6347513

連成循環動態シミュレーションモデルにおける数値法

長谷川雄基, 嶋吉隆夫, 天野晃, 松田哲也

第51回生体医工学会大会 2012.5

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