Faculty Profiles - Shimayoshi Takao

Papers - Shimayoshi Takao

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A Simulation Method of Cell Physiological Experiments with a Novel Description Language for Experimental Protocols Reviewed

SHIMAYOSHI Takao, AMANO Akira, MATSUDA Tetsuya

Transactions of Japanese Society for Medical and Biological Engineering 46 ( 1 ) 77 - 84 2008.2

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

For computer simulations of physiological experiments by physiological models, a machine-readable description of experimental protocols is useful. Although description formats for cell physiological models are already available, there is no specialized representation format for experimental protocols. Here, we propose an XML-based language, PEPML (Physiological Experimental Protocol Markup Language), and a simulation method of experimental protocols in PEPML. In the PEPML, conditions and procedures of an experimental protocol are procedurally described as a list of events, each of which consists of a condition for execution and an action to be executed. By specifying the references of variables in a protocol using an ontology, the protocol can be applied to various models without editing tasks. The proposed simulation method allows unambiguous numerical calculation of a procedural experimental protocol, which is applied to a declaratively represented model by interpretation of the protocol as a set of boundary conditions for the model variables. PEPML and the proposed method allow applying both multiple protocols to a single model and a single protocol to multiple models. This feature facilitates the efficient simulation for verification, comparison and utilization of physiological models.

DOI： 10.11239/jsmbe.46.77

Other Link： http://search.jamas.or.jp/link/ui/2008208214

The Influence of Activation Time on Left Ventricular Wall Motion : Simulation Study of Ring Shape Left Ventricular Model Reviewed

TAKADA Yasuhiro, AMANO Akira, SONG Inhwan, LU Jianyin, SHIMAYOSHI Takao, ISHIKAWA Satoshi, KOTERA Hidetoshi, MATSUDA Tetsuya

Transactions of Japanese Society for Medical and Biological Engineering 46 ( 1 ) 85 - 92 2008.2

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

The heart is an organ with highly complex structure and its pump function is affected by various factors. Many reports showed the strong relation between the excitation-propagation phenomenon in the heart and its pump function. But the experimental studies often failed to provide the mechanistic insights due to the complex cross-talks built in these processes. In this study, we focus on the relation between the activation time and the contraction of the tissue. The contraction simulation coupled with the excitation propagation simulation was performed using the finite element model of the ventricular ring. We performed the simulation with 7 types of stimulation with various pacing sites in the tissue, and compared the pump functions by the area ejection fraction. The results showed that when the activation time became long, the area ejection fraction became nonlinearly small. The results of this study showed the excitation propagation is one of the important parameter of the left ventricular wall motion.

DOI： 10.11239/jsmbe.46.85

Other Link： http://search.jamas.or.jp/link/ui/2008208215

DynaBioS : A Platform for Cell/Biodynamics Simulators Reviewed

SHIMAYOSHI Takao, HORI Kenta, LU Jianyin, AMANO Akira, MATSUDA Tetsuya, NOMA Akinori

IEEJ Transactions on Electronics, Information and Systems 127 ( 11 ) 1928 - 1936 2007.11

Authorship：Lead author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Institute of Electrical Engineers of Japan

Biological simulation has become an important technology for biological research. Though multi-domain simulation technique is required for analysis of complicated biological activities, multi-domain biosimuator system tends to be very complicated and so requires a high developing cost. To improve this situation, we propose a biosimulator development platform, DynaBioS, which can handle complex interactions between phenomena in different domains, such as electrophysiology and mechanics. A biosimulator system is composed of components, each of which is a sub-simulator of a phenomenon, and exchanges event messages to each others as the interaction of the phenomena. This design allows easy replacement of a model for a phenomena by interchanging a corresponding component. This platform reduces costs to develop simulators, by implementation of components by wrapping existing software products, and by reuse of components. Examples of developed simulators are given to show that this platform facilitates the development of biosimulators.

DOI： 10.1541/ieejeiss.127.1928

The cross-bridae dynamics during ventricular contraction predicted by coupling the cardiac cell model with a circulation model Reviewed

Eun Bo Shim, Akira Amano, Takayuki Takahata, Takao Shimayoshi, Akinori Noma

JOURNAL OF PHYSIOLOGICAL SCIENCES 57 ( 5 ) 275 - 285 2007.10

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

The force-velocity (F-V) relationship of filament sliding is traditionally used to define the inotropic condition of striated muscles. A simple circulation model combined with the Laplace heart was developed to get a deeper insight into the relationship between the F-V characteristics and the cardiac ventricular inotropy. The circulation model consists of a preload and an afterload compartments. The linear F-V relationship for filament sliding in the NL model (Negroni and Lascano 1996) was replaced by the exponential F-V relation observed by Piazzesi et al. (2002). We also modified the NL model to a hybrid model to benefit from the Ca2+ cooperativity described by the Robinson model (Robinson et al. 2002). The model was validated by determining the diastolic ventricular pressure-volume relationship of the Laplace heart and the F-V relation of the new hybrid model. The computed parameters of the cardiac cycle agreed well with the physiological data. Computational results showed that the cross-bridge elongation (h in the NL model) temporally undershot the equilibrium h(c) during the ejection period and overshot it during the rapid refilling phase. Thereby the time course of ejection and refilling was retarded. In a simulation where the velocity of the mobile myosin head (dX/dt) was varied, the systolic peak pressure of the ventricle varied from a minimum value at dX/dt = 0 to a saturating value obtained with a constant h, providing in silico evidence for a functional impact of the cross-bridge sliding rate on the ventricular inotropy.

DOI： 10.2170/physiolsci.RP006007

Other Link： http://search.jamas.or.jp/link/ui/2008155020

A generic representation format of physiological experimental protocols for computer simulation using ontology Reviewed

Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings 2007 382 - 385 2007.8

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

For computer simulations of physiological experiments using physiological models, a machine-readable format of experimental protocols is effective. Here, we propose an XML-based language, PEPML (Physiological Experimental Protocol Markup Language). In the PEPML, conditions and procedures of an experimental protocol are procedurally described as a list of events, each of which consists of a condition for execution and an action to be executed. Since variables used in a protocol can be specified using an ontology, the protocol can be applied to various models without editing tasks. The PEPML allows both application of multiple protocols to a single model and application of a single protocol to multiple models. This feature facilitates the efficient simulation for verifications, comparisons and utilizations of physiological models. © 2007 IEEE.

DOI： 10.1109/IEMBS.2007.4352304

Infant circulation model based on the electrophysiological cell model Reviewed

Yutaka Nobuaki, Akira Amano, Takao Shimayoshi, Jianyin Lu, Eun B. Shim, Tetsuya Matsuda

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings 2007 1010 - 1013 2007.8

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

It is important to use a myocardial cell model to evaluate the effects of the drugs to the hemodynamic parameters. We developed an infant circulation model which incorporates an accurate myocardial cell model including a beta adrenergic system. The beta adrenergic system is essential mechanism for reproducing the response of baroreflex control system. The parameters of the published adult human circulation model were modified to fit the infant hemodynamic values. The guinea pig myocardial cell model was introduced to the circulation model whose baseline heart rate is close to that of an infant. The presented model is in good agreement with results obtained in physiological experiments. ©2007 IEEE.

DOI： 10.1109/IEMBS.2007.4352465

A model for simulation of infant cardiovascular response to orthostatic stress Reviewed

Yutaka Nobuaki, Akira Amano, Takao Shimayoshi, Jianyin Lu, Eun B. Shim, Tetsuya Matsuda

FUNCTIONAL IMAGING AND MODELING OF THE HEART, PROCEEDINGS 4466 190 - 199 2007.6

Language：English Publishing type：Research paper (international conference proceedings) Publisher：SPRINGER-VERLAG BERLIN

We developed an infant circulation model which incorporates an accurate myocardial cell model including a beta adrenergic system. The beta adrenergic system is essential for the response reproduction of the baroreflex control system. The proposed model was constructed by modifying the parameters of a human adult circulation model with the aid of a guinea pig myocardial cell model, whose baseline heart rate is close to that of an infant. The presented model is in good agreement with results obtained in physiological experiments.

DOI： 10.1007/978-3-540-72907-5_20

Other Link： https://dblp.uni-trier.de/db/conf/fimh/fimh2007.html#NobuakiASLSM07

Stress Distribution in a Cylinder and a Measurement-based Left Ventricular Shape Model Reviewed

TAKADA Yasuhiro, LU Jianyin, SHIMAYOSHI Takao, ISHIKAWA Satoshi, AMANO Akira, KOTERA Hidetoshi, MATSUDA Tetsuya

Transactions of Japanese Society for Medical and Biological Engineering 44 ( 4 ) 613 - 620 2006.12

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

We evaluated the stress distribution in a cylindrical model and a shape model obtained from human heart using two different fiber orientations. For both orientation models, the results showed large differences between the stress distribution in the cylindrical model and the measurement-based shape model. These results suggest that stress distribution is highly dependent on the model geometry, and the usage of a measurement-based shape model is important for evaluating left ventricular (LV) wall stress distribution. This fact may have some influence on the reported homogeneity of stress distribution in an anatomical fiber orientation model that uses a mathematical symmetric shape model.

DOI： 10.11239/jsmbe.44.613

Other Link： http://search.jamas.or.jp/link/ui/2007253872

A Method to Support Cell Physiological Modelling Using Description Language and Ontology Reviewed

Shimayoshi Takao, Komurasaki Kazuhiro, Amano Akira, Iwashita Takeshi, Matsuda Tetsuya, Kanazawa Masanori

IPSJ Digital Courier 2 ( 2 ) 726 - 735 2006.11

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Information Processing Society of Japan

The development of physiological cell models to support the understanding of biological mechanisms gains increasingly importance. Due to the complexity of biological systems, whole cell models, which are composed of many imported component models of functional elements, get quite complex, making modifications difficult. Here, we propose a method to enhance structural changes of cell models, employing the markup languages of CellML and our original PMSML (Physiological Model Structure Markup Language), in addition to a new ontology for cell physiological modelling, the Cell Model Ontology. In particular, a method to make references from CellML files to the ontology and a method to assist with manipulation of model structures using PMSML together with the Cell Model Ontology are reported. Using these methods two software utilities, an interactive ontology ID assigner, the CellML Ontologizer, and a graphical cell model editor, the Cell Structure Editor, are implemented. Experimental results proved that the proposed method and the implemented software are useful for the modification of physiological models.

DOI： 10.2197/ipsjdc.2.726

実心臓に基づく形状及びリング形状を用いた左心室拍動シミュレーションにおける収縮末期応力分布の比較

高田康弘, 陸建銀, 嶋吉隆夫, 石川覚志, 天野晃, 小寺秀俊, 松田哲也

生体医工学シンポジウム2006予稿集 222 2006.9

Mechanism of the Frank-Starling law - A simulation study with a novel cardiac muscle contraction model that includes titin and troponin I Reviewed International journal

Natalie S. Schneider, Takao Shimayoshi, Akira Amano, Tetsuya Matsuda

JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY 41 ( 3 ) 522 - 536 2006.9

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCI LTD

A stretch-induced increase of active tension is one of the most important properties of the heart, known as the Frank-Starling law. Although a variation of myofilament Ca2+ sensitivity with sarcomere length (SL) change was found to be involved, the underlying molecular mechanisms are not fully clarified. Some recent experimental studies indicate that a reduction of the lattice spacing between thin and thick filaments, through the increase of passive tension caused by the sarcomeric protein titin with an increase in SL within the physiological range, promotes formation of force-generating crossbridges (Xbs). However, the mechanism by which the Xb concentration determines the degree of cooperativity for a given SL has so far evaded experimental elucidation. In this simulation study, a novel, rather simple molecular-based cardiac contraction model, appropriate for integration into a ventricular cell model, was designed, being the first model to introduce experimental data on titin-based radial tension to account for the SL-dependent modulation of the interfilament lattice spacing and to include a conformational change of troponin I (TnI). Simulation results for the isometric twitch contraction time course, the length-tension and the force-[Ca2+] relationships are comparable to experimental data. A complete potential Frank-Starling mechanism was analyzed by this simulation study. The SL-dependent modulation of the myosin binding rate through titin's passive tension determines the Xb concentration which then alters the degree of positive cooperativity affecting the rate of the TnI conformation change and causing the Hill coefficient to be SL-dependent. (c) 2006 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.yjmcc.2006.06.003

Computer Support for Physiological Cell Modelling using an Ontology on Cell Physiology Reviewed

Shimayoshi Takao, Komurasaki Kazuhiro, Amano Akira, Iwashita Takeshi, Kanazawa Masanori, Matsuda Tetsuya

2006 International Conference of the IEEE Engineering in Medicine and Biology Society 4171 - 4174 2006.8

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

The development of electrophyslological whole cell models to support the understanding of biological mechanisms Is Increasing rapidly. Due to the complexity of biological systems, comprehensive cell models, which are composed of many Imported sub-models of functional elements, can get quite complicated as well, making computer modification difficult. Here, we propose a computer support to enhance structural changes of cell models, employing the markup languages CellML and our original PMSML (Physiological Model Structure Markup Language), In addition to a new ontology for cell physiological modelling. In particular, a method to make references from CellML files to the ontology and a method to assist manipulation of model structures using markup languages together with the ontology are reported. Using these methods three software utilities, Including a graphical model editor, are Implemented. Experimental results proved that these methods are effective for the modification of electrophyslological models. © 2006 IEEE.

DOI： 10.1109/iembs.2006.260282

Reproducing nonlinear force velocity relation of myocardial tissue by a nonlinear parallel elastic component Reviewed

Yutaka Nobuaki, Yu Kamei, Jianyin Lu, Takao Shimayoshi, Satoshi Ishikawa, Akira Amano, Hidetoshi Kotera, Tetsuya Matsuda

2006 28TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-15 1 612 - 615 2006.8

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

To realize precise simulation of the left ventricular motion, it is important to utilize an accurate myocardial tissue model which can reproduce various characteristics of myocardial tissue contraction. In this study, we show that the nonlinear characteristics of the passive myocardial tissue property is the essential nature of the nonlinear force-velocity relation and present a formulation for hyperelastic physiological tissue property. Experimental results of our myocardial tissue simulation with the hyperelastic material property proposed are in good agreement with the reported force-velocity relation of real tissue.

DOI： 10.1109/IEMBS.2006.259852

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

Stress distribution in a rotationally symmetric and a measurement based left ventricular shape model Reviewed

Yasuhiro Takada, Akira Amano, Jianyin Lu, Takao Shimayoshi, Satoshi Ishikawa, Tetsuya Matsuda, Hidetoshi Kotera

2006 28TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY 1 624 - 627 2006.8

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

We evaluated the stress distribution in a geometrical shape model and a shape model obtained from human heart using two different fiber orientations. For both orientation models, the results showed large differences of the stress distributions between the mathematical shape model and the maesurement based shape model. These results suggest that stress distribution is highly dependent on the model geometry and the usage of a maesurement based shape model is important for the evaluation of the left ventricular (LV) wall stress distribution. This fact may have some influences on the reported homogeneity of stress distribution with anatomical fiber orientation model that uses mathematical shape model.

DOI： 10.1109/IEMBS.2006.259854

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

心筋組織における非線形張力速度関係再現のための非線形並列弾性要素モデル

信秋裕, 瓶井悠, 陸建銀, 嶋吉隆夫, 石川覚志, 天野晃, 小寺秀俊, 松田哲也

複合医工学シンポジウム予稿集, pp.172-175, 京都府京都市, 複合医工学インスティテュート 2006.5

Design of DynaBioS Architecture for Distributed Biodynamics Simulator Reviewed

Hori Kenta, Lu Jianyin, Shimayoshi Takao, Nishi Toshifumi, Ashihara Takashi, Terashima Keisuke, Amano Akira, Matsuda Tetsuya

Proceedings of the Annual Conference of the Institute of Systems, Control and Information Engineers 5 237 - 238 2005.5

A software environment for simulators suitable for complex biological analysis Reviewed

T. Shimayoshi, K. Hori, J.Y. Lu, A. Amano, T. Matsuda

The 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 26 3047 - 3050 2004.9

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

In order to understand the function of biological elements and their interactions, computer analysis and simulation is an essential technique. For higher research efficiency, it is important to provide a system framework for constructing biological simulation systems that handle multiple phenomena. This paper proposes "DynaBioS", a comprehensive system framework for complex biological simulations. This framework consists of three main features, a component-based architecture, a customizable system operation, and an exchangeable model set. The system based on DynaBioS consists of a Simulation Core and System Components. The System Components are sub-simulators for individual functional factors and utility modules corresponding to specific information technologies. The Simulation Core manages and controls all components, in accordance with a Simulation Scenario and a Simulation Model. The DynaBioS makes it possible to implement different simulation systems by combining individual functional components, specific interactions and different simulation models. The versatility of DynaBioS is shown by two examples, a heart pumping simulator and a parameter optimization system for physiological models.

DOI： 10.1109/iembs.2004.1403862

マルチフィジックス細胞・生体機能シミュレーションのための統合シミュレーション環境

嶋吉隆夫, 堀謙太, 陸建銀, 皿井伸明, 天野晃, 松岡達, 松田哲也

生体医工学 42 ( 特別号 ) 437 - 437 2004.5

A software environment for simulators suitable for complex biological analysis

T. Shimayoshi, K. Hori, J. Y. Lu, A. Amano, T. Matsuda

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings 26 IV 3047 - 3050 2004

Publishing type：Research paper (international conference proceedings)

In order to understand the function of biological elements and their interactions, computer analysis and simulation is an essential technique. For higher research efficiency, it is important to provide a system framework for constructing biological simulation systems that handle multiple phenomena. This paper proposes "DynaBioS", a comprehensive system framework for complex biological simulations. This framework consists of three main features, a component-based architecture, a customizable system operation, and an exchangeable model set. The system based on DynaBioS consists of a Simulation Core and System Components. The System Components are sub-simulators for individual functional factors and utility modules corresponding to specific information technologies. The Simulation Core manages and controls all components, in accordance with a Simulation Scenario and a Simulation Model. The DynaBioS makes it possible to implement different simulation systems by combining individual functional components, specific interactions and different simulation models. The versatility of DynaBioS is shown by two examples, a heart pumping simulator and a parameter optimization system for physiological models.

階層符号化を用いた受信能力の異なる複数の受信者に対応できるマルチキャスト ATM上での階層符号化によるQoS選択可能な資源予約方法 (文部省S)

SHIMAYOSHI TAKAO, FUJIKAWA KENJI, IKEDA KATSUO

ATM網におけるインターネット技術を基盤とした多地点・多品質同時伝送方式平成9-11年度 No.09305027 97 - 98 2000

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