Faculty Profiles - Shimayoshi Takao

J-GLOBAL

A Computational Model of Infantile Cardiovascular Dynamics for Cardiac Function Assessment Reviewed

WANG Yuwen, SHIMAYOSHI Takao, AMANO Akira, MATSUDA Tetsuya

The IEICE transactions on information and systems (Japanese edetion) 95 ( 2 ) 331 - 338 2012.2

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Institute of Electronics, Information and Communication Engineers

臨床試験を代替する一手段,あるいは,臨床教育の教材として,特に,臨床試験や臨床教育が困難な乳児について,精密に生体機能を再現する計算機シミュレーションの実現が望まれている.生命維持に欠かせない心臓血管系は生体機能シミュレーションにおいて非常に重要な対象であり,その中で中心的な役割を果たす心臓の機能を評価することは重要である.本論文では,ヒト乳児を対象に血圧変化などの循環動態を再現するような,心機能評価が可能なシミュレーションモデルを提案する.提案モデルは,既存の生理特性を詳細に再現した心室筋細胞モデル,及び,全身の血圧変化を表現する血管系モデルを利用し,更に,計測結果に基づき左心室の圧と容積の関係を表現する左心室物理モデルを導入して構築したモデルである.シミュレーション実験により,提案モデルは生現状態のヒト乳児の主要な循環動態パラメータを再現し,心機能の評価に重要な左心室の収縮末期圧容積関係(ESPVR),及び,収縮期圧容積面積と心筋酸素消費量との高い相関(PVA-MVO_2)が再現されていることを確認した.

Efficient Configuration of Solvable Calculation Condition for Differential Algebraic Equations in Cell Models Reviewed

Other Link： http://search.jamas.or.jp/link/ui/2012185963

A general CellML simulation code generator using ODE solving scheme description. Reviewed International journal

Amano, A., Soejima, N., Shimayoshi, T., Kuwabara, H., Kunieda, Y.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2011 940 - 944 2011.8

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 target computation resources or numerical calculation methods or simulation conditions. Typical biological function simulation software consists of 1) model equation, 2) boundary conditions and 3) ODE solving scheme. Introducing the description model file such as CellML is useful for generalizing the first point and partly second point, however, third point is difficult to handle. We introduce a simulation software generation system which use markup language based description of ODE solving scheme together with cell model description file. By using this software, we can easily generate biological simulation program code with different ODE solving schemes. To show the efficiency of our system, experimental results of several simulation models with different ODE scheme and different computation resources are shown.

DOI： 10.1109/IEMBS.2011.6090212

A study on prediction methods for a cardiovascular strong-coupling simulation. Reviewed International journal

Hasegawa, Y., Shimayoshi, T., Amano, A., Matsuda, T.

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

We investigated numerical methods for predictors in a multiscale cardiovascular simulation model. The proposed method predicts initial approximations for the iterative convergence calculations of the strong coupling method using the smoothing spline to remove errors from values of past timesteps and using the linear and second-order extrapolation. The new coupling algorithm was used for coupling a left ventricular finite element model to a myocardial excitation-contraction model. We performed experiments with different values for the smoothing parameter lambda and with linear and second-order extrapolations. lambda = 1 with the linear extrapolation gave the best results. It reduced computation time by 91% compared to the strong coupling method. With the use of the smoothing spline, distance between the initial approximation and converged solution reduced by 62%, while the average number of iterations reduced by 32%. The smoothing spline can be used to improve the accuracy of predictors and reduce the number of iterations needed for the computation of the convergence procedure.

DOI： 10.1109/IEMBS.2011.6089913

嶋吉隆夫, 天野晃, 松田哲也

情報処理学会論文誌 52 ( 8 ) 2412 - 2421 2011.8

Authorship：Lead author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：情報処理学会

A model of cellular physiological functions is generally defined as a set of ordinary differential equations and algebraic equations. Some models form semi-explicit differential algebraic equations. Numerical simulation of a declaratively defined model requires a calculation condition by selecting parameter constants, the values of which are extrinsically provided. However, manual configuration of consistent calculation conditions for large-scale complicated models is a difficult task. In this paper, we propose a method for efficient configuration of consistent calculation conditions for declaratively defined models. The present method progressively eliminates invalid calculation conditions from candidates in order to assist interactive configuration of a calculation condition, by applying a method based on graph theory for structural solvability of simultaneous equations.

イオンチャンネルやトランスポーターの膜電位変化への定量的寄与度;リードポテンシャル解析法 Invited

Other Link： http://id.nii.ac.jp/1001/00075767/

Time-dependent changes in membrane excitability during glucose-induced bursting activity in pancreatic beta cells Reviewed International journal

Chae Young Cha, Enrique Santos, Akira Amano, Takao Shimayoshi, Akinori Noma

JOURNAL OF GENERAL PHYSIOLOGY 138 ( 1 ) 39 - 47 2011.7

Language：English Publishing type：Research paper (scientific journal) Publisher：ROCKEFELLER UNIV PRESS

In our companion paper, the physiological functions of pancreatic. cells were analyzed with a new beta-cell model by time-based integration of a set of differential equations that describe individual reaction steps or functional components based on experimental studies. In this study, we calculate steady-state solutions of these differential equations to obtain the limit cycles (LCs) as well as the equilibrium points (EPs) to make all of the time derivatives equal to zero. The sequential transitions from quiescence to burst-interburst oscillations and then to continuous firing with an increasing glucose concentration were defined objectively by the EPs or LCs for the whole set of equations. We also demonstrated that membrane excitability changed between the extremes of a single action potential mode and a stable firing mode during one cycle of bursting rhythm. Membrane excitability was determined by the EPs or LCs of the membrane subsystem, with the slow variables fixed at each time point. Details of the mode changes were expressed as functions of slowly changing variables, such as intracellular [ATP], [Ca2+], and [Na+]. In conclusion, using our model, we could suggest quantitatively the mutual interactions among multiple membrane and cytosolic factors occurring in pancreatic. cells.

DOI： 10.1085/jgp.201110612

車采映, 姫野友紀子, 嶋吉隆夫, 天野晃, 野間昭典

日本生理学雑誌 72 ( 5 ) 146 2010.5

Construction of Myocardial Cell Model Including Glycolysis Model for Reproducing Hypoxic Reaction Reviewed

AMANO Akira, TOMITA Sachiko, MATSUOKA Satoshi, SHIMAYOSHI Takao, LU Jianyin, MATSUDA Tetsuya

The IEICE transactions on information and systems 93 ( 3 ) 398 - 408 2010.3

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Institute of Electronics, Information and Communication Engineers

心臓は非常に多くのエネルギーを消費して血液を拍出しており,心筋細胞におけるエネルギー代謝と,心筋細胞の興奮収縮連関の関連性の解明は,病態解明等のために重要なテーマである.特に虚血性心疾患は,細胞への酸素供給低下により,細胞に異常を来す疾病であり,このような疾病における心機能の低下は,第1に酸素濃度の低下によって生じるエネルギーバランスの不均衡が原因と考えられている.虚血時の心機能の低下の主たる原因である低酸素に対する心筋細胞の応答を再現するためには,低酸素状態で活性化される解糖系が重要である.しかしながら,現在提案されている心筋細胞モデルは,解糖系が導入されていないために,低酸素状態の再現性に問題がある.本研究では,低酸素に対する心筋細胞の応答を再現するために,モルモットの心筋細胞モデルであるKyoto modelに解糖系を導入した新たな心筋細胞モデルを構築した.構築したモデルを用いて,動物実験の実験条件に従ったシミュレーションを行い,非ペーシング状態の心筋細胞における低酸素に対する応答の再現を試みた.再現結果は,対応する動物実験結果の傾向と高い類似性を示した.

Analysis of the underlying mechanism of frank-starling law of a constructive hemodynamics model Reviewed

Other Link： http://search.jamas.or.jp/link/ui/2010156108

A Novel Method to Quantify Contribution of Channels and Transporters to Membrane Potential Dynamics Reviewed International journal

Chae Young Cha, Yukiko Himeno, Takao Shimayoshi, Akira Amano, Akinori Noma

BIOPHYSICAL JOURNAL 97 ( 12 ) 3086 - 3094 2009.12

Language：English Publishing type：Research paper (scientific journal) Publisher：CELL PRESS

The action potential, once triggered in ventricular or atrial myocytes, automatically proceeds on its time course or is generated spontaneously in sinoatrial node pacemaker cells. It is induced by complex interactions among such cellular components as ion channels, transporters, intracellular ion concentrations, and signaling molecules. We have developed what is, to our knowledge, a new method using a mathematical model to quantify the contribution of each cellular component to the automatic time courses of the action potential. In this method, an equilibrium value, which the membrane potential is approaching at a given moment, is calculated along the time course of the membrane potential. The calculation itself is based on the time-varying conductance and the reversal potentials of individual ion channels and electrogenic ion transporters. Since the equilibrium potential moves in advance of the membrane potential change, we refer to it as the lead potential, V-L. The contribution of an individual current was successfully quantified by comparing dV(L)/dt before and after fixing the time-dependent change of a component of interest, such as the variations in the open probability of a channel or the turnover rate of an ion transporter. In addition to the action potential, the lead-potential analysis should also be applicable in all types of membrane excitation in many different kinds of cells.

DOI： 10.1016/j.bpj.2009.08.060

Mitsuharu Mishima, Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

Asia Simulation Conference 2009, JSST 2009 2009.10

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

Frank-Starling law, which describes a relation between cardiac contraction energy and end-diastolic volume, is of importance, but the detailed mechanism is not quantitatively understood yet. In this paper, the mechanism of a linear relation between end-diastolic volume and end-systolic pressure as a part of Frank-Starling law is analyzed by means of computer simulation. A hemodynamics model, which is constructed by composing a vascular system model, a left ventricular dynamics model and a myocardial cell model, reproduced a linear relation between end-diastolic volume and end-systolic pressure successfully. In this paper, the simulation results and the detailed analysis are reported.

Scopus

膵β細胞シミュレーションモデルによる膜電位オシレーション機構の解析

Other Link： http://orcid.org/0000-0001-8187-9915

中村靖彦, 藤本新平, WANG Jian‐Wu, 姫野友紀子, CHA Chae Young, 嶋吉隆夫, 野間昭典, 稲垣暢也

生化学 ROMBUNNO.4T6A-13 2009.9

Evaluation of Cardiac Oxygen Consumption under Hypoxia with Tissue Model integrating Microcirculation Model and Cell Model Reviewed International journal

Akira Amano, Yuuta Kubota, Takao Shimayoshi, Tetsuya Matsuda

2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20 2009 3885 - 3888 2009.9

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

Analyzing the microscopic energy balance of cardiac tissue is very important for understanding heart diseases. However, such analysis is difficult with animal experiments. Therefore, the accurate simulation model is expected to be an important tool for such research. We propose a cardiac tissue model which can reproduce accurate distribution of oxygen consumption under hypoxia. The model includes blood tissue exchange model of capillary and oxygen consumption model of cells. The capillary model is based on the model proposed by Dash et al. 2006, and the cell model is based on the model proposed by Kuzumoto et al. 2007. By analyzing the oxygen consumption of the proposed model, the relation between the oxygen consumption and the arterial oxygen concentration was found to be largely different from that of single cell model. This implies that the animal experimental data should be carefully used for constructing a biological simulation model, depending on whether the experiment is performed within a cell or a tissue.

DOI： 10.1109/IEMBS.2009.5332645

A Method for Analysis of Simultaneous Equations in Cell Models Reviewed International journal

Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20 2009 2343 - 2346 2009.9

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

Some models of cellular physiological functions are formulated as ordinary differential equations that contain multiple systems of simultaneous nonlinear equations. Simulation of such a model described in a declarative representation format requires determination of equations to be simultaneously solved with specification of independent and parameter variables in the model. In this report, a method for extracting systems of simultaneous equations in a cell model is presented. The present method analyzes a graph representation of a model and extracts the subgraphs that represent equation systems to be simultaneously solved, by efficiently interactive selection of independent variables of the model.

DOI： 10.1109/IEMBS.2009.5335041

Estimating Contribution Of Individual Ionic Components To The Cardiac Pacemaker Potential

Yukiko Himeno, Chae Young Cha, Takao Shimayoshi, Yasuhiko Nakamura, Jian-Wu Wang, Akinori Noma, Nobuya Inagaki

BIOPHYSICAL JOURNAL 96 ( 3 ) 259A - 259A 2009.2

EVALUATION OF CELL AND TISSUE HYPOXIC REACTION - MODEL STUDY Reviewed

Akira Amano, Yuuta Kubota, Takao Shimayoshi, Tetsuya Matsuda

JOURNAL OF PHYSIOLOGICAL SCIENCES 59 261 - 261 2009.1

COMPARING CONTRIBUTIONS OF EACH IONIC COMPONENT TO CARDIAC PACEMAKER POTENTIAL BETWEEN DIFFERENT MODELS USING THE LEAD POTENTIAL ANALYSIS Reviewed

Yukiko Himeno, Chae Young Cha, Takao Shimayoshi, Akinori Noma, Nobuya Inagaki

JOURNAL OF PHYSIOLOGICAL SCIENCES 59 259 - 259 2009.1

A NOVEL METHOD TO QUANTIFY CONTRIBUTION OF CELLULAR COMPONENTS TO AUTOMATIC CHANGES OF MEMBRANE POTENTIAL IN MATHEMATICAL MODELS Reviewed

Chae Young Cha, Yukiko Himeno, Takao Shimayoshi, Akinori Noma

JOURNAL OF PHYSIOLOGICAL SCIENCES 59 260 - 260 2009.1

An Approximation Model of Myocardial Crossbridge for Weak Coupling Calculation of Left Ventricle Model and Circulation Model Reviewed International journal

Akira Amano, Yasuhiro Takada, Jianyin Lu, Takao Shimayoshi, Tetsuya Matsuda

2008 30TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-8 2008 957 - 960 2008.8

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

It is necessary to use complicated myocardial cell model and heart model to evaluate the regional energy production and consumption which leads to the unrealistic computational time. In this research, a left ventricle (LV) simulation model was constructed which includes accurate myocardial cell model. In order to simulate the model in realistic time, we introduced an approximation model of the crossbridge model which can be calculated with weak coupling calculation. The LV model was combined with a circulation model to validate the proposed model by calculating the hemodynamics parameters and ventricular energetics indices. The ESPVR (End Systolic Pressure Volume Relation) showed linear relation, and also the PVA - ATP consumption relation showed linear relation which are widely known as the physiological characteristics of mammalian hearts. From these results, we can say that the model can be used as a model for physiological simulation experiments which are related to the ventricular energetics.

DOI： 10.1109/IEMBS.2008.4649313

A Model for Simulation of Infant Cardiovascular Response to Orthostatic Stress Reviewed

AMANO Akira, NOBUAKI Yutaka, SHIMAYOSHI Takao, LU Jianyin, SHIM Eun B., MATSUDA Tetsuya

The IEICE transactions on information and systems (Japanese edition) 91 ( 8 ) 2177 - 2187 2008.8

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Institute of Electronics, Information and Communication Engineers

循環系を構成する様々な要素の血圧変化に対する反応を再現可能な循環動態シミュレーションモデルは,左心室の圧容積関係を表現する左心室モデルと,血管系の圧容積関係を表現する血管系モデル,更に循環動態の変化に対しフィードバック制御を行う制御系モデルを用いて実現される.本論文では,カテコールアミンβ刺激系モデルを含むモルモットの心筋細胞モデルであるKyoto modelを導入した左心室モデルと,ヒト成人の循環系モデルであるHeldtらの循環系モデルを組み合わせ,パラメータの変更と制御モデルの変更を行うことによりヒト乳児循環動態シミュレーションモデルを実現した.生理学シミュレーション実験により,シミュレーションモデルの妥当性を確認した.安静時循環動態シミュレーション実験により,左心室拡張末期圧,左心室収縮末期圧,心拍出量,最高・最低動脈圧及び中心静脈圧に関して,生理学的な範囲にあることが確認された.また,圧受容体反射機能を確認する起立負荷(HUT)試験についてのシミュレーション実験を行った.HUT開始前と開始後安定状態における,動脈圧パルス幅の変化率は29%の減少,心拍数は13%の増加であった.これは,生理学実験における23%の減少及び14%の増加と同様の傾向であった.