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Gawthrop PJ, Pan M. Network thermodynamics of biological systems: A bond graph approach. Math Biosci 2022; 352:108899. [PMID: 36057321 DOI: 10.1016/j.mbs.2022.108899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Edmund Crampin (1973-2021) was at the forefront of Systems Biology research and his work will influence the field for years to come. This paper brings together and summarises the seminal work of his group in applying energy-based bond graph methods to biological systems. In particular, this paper: (a) motivates the need to consider energy in modelling biology; (b) introduces bond graphs as a methodology for achieving this; (c) describes extensions to modelling electrochemical transduction; (d) outlines how bond graph models can be constructed in a modular manner and (e) describes stoichiometric approaches to deriving fundamental properties of reaction networks. These concepts are illustrated using a new bond graph model of photosynthesis in chloroplasts.
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Affiliation(s)
- Peter J Gawthrop
- Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Victoria 3010, Australia.
| | - Michael Pan
- Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Victoria 3010, Australia; School of Mathematics and Statistics, University of Melbourne, Victoria 3010, Australia
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2
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De Lazzari B, Badagliacca R, Filomena D, Papa S, Vizza CD, Capoccia M, De Lazzari C. CARDIOSIM©: The First Italian Software Platform for Simulation of the Cardiovascular System and Mechanical Circulatory and Ventilatory Support. Bioengineering (Basel) 2022; 9:bioengineering9080383. [PMID: 36004908 PMCID: PMC9404951 DOI: 10.3390/bioengineering9080383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
This review is devoted to presenting the history of the CARDIOSIM© software simulator platform, which was developed in Italy to simulate the human cardiovascular and respiratory systems. The first version of CARDIOSIM© was developed at the Institute of Biomedical Technologies of the National Research Council in Rome. The first platform version published in 1991 ran on a PC with a disk operating system (MS-DOS) and was developed using the Turbo Basic language. The latest version runs on PC with Microsoft Windows 10 operating system; it is implemented in Visual Basic and C++ languages. The platform has a modular structure consisting of seven different general sections, which can be assembled to reproduce the most important pathophysiological conditions. One or more zero-dimensional (0-D) modules have been implemented in the platform for each section. The different modules can be assembled to reproduce part or the whole circulation according to Starling’s law of the heart. Different mechanical ventilatory and circulatory devices have been implemented in the platform, including thoracic artificial lungs, ECMO, IABPs, pulsatile and continuous right and left ventricular assist devices, biventricular pacemakers and biventricular assist devices. CARDIOSIM© is used in clinical and educational environments.
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Affiliation(s)
- Beatrice De Lazzari
- Department of Human Movement and Sport Sciences, “Foro Italico” 4th University of Rome, 00135 Rome, Italy
- Correspondence:
| | - Roberto Badagliacca
- Department of Clinical, Internal Anesthesiology and Cardiovascular Sciences, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Domenico Filomena
- Department of Clinical, Internal Anesthesiology and Cardiovascular Sciences, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Silvia Papa
- Department of Clinical, Internal Anesthesiology and Cardiovascular Sciences, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Carmine Dario Vizza
- Department of Clinical, Internal Anesthesiology and Cardiovascular Sciences, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Massimo Capoccia
- Department of Cardiac Surgery, Leeds General Infirmary, Leeds Teaching Hospitals NHS Trust, Leeds LS1 3EX, UK
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G4 0NW, UK
| | - Claudio De Lazzari
- National Research Council, Institute of Clinical Physiology (IFC-CNR), 00185 Rome, Italy
- Faculty of Medicine, Teaching University Geomedi, Tbilisi 0114, Georgia
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3
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Yang B, Jiang Q, He S, Li T, Ou X, Chen T, Fan X, Jiang F, Zeng X, Huang CLH, Lei M, Tan X. Ventricular SK2 upregulation following angiotensin II challenge: Modulation by p21-activated kinase-1. J Mol Cell Cardiol 2022; 164:110-125. [PMID: 34774547 DOI: 10.1016/j.yjmcc.2021.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/15/2021] [Accepted: 11/03/2021] [Indexed: 12/11/2022]
Abstract
Effects of hypertrophic challenge on small-conductance, Ca2+-activated K+(SK2) channel expression were explored in intact murine hearts, isolated ventricular myocytes and neonatal rat cardiomyocytes (NRCMs). An established experimental platform applied angiotensin II (Ang II) challenge in the presence and absence of reduced p21-activated kinase (PAK1) (PAK1cko vs. PAK1f/f, or shRNA-PAK1 interference) expression. SK2 current contributions were detected through their sensitivity to apamin block. Ang II treatment increased such SK2 contributions to optically mapped action potential durations (APD80) and their heterogeneity, and to patch-clamp currents. Such changes were accentuated in PAK1cko compared to PAK1f/f, intact hearts and isolated cardiomyocytes. They paralleled increased histological and echocardiographic hypertrophic indices, reduced cardiac contractility, and increased SK2 protein expression, changes similarly greater with PAK1cko than PAK1f/f. In NRCMs, Ang II challenge replicated such increases in apamin-sensitive SK patch clamp currents as well as in real-time PCR and western blot measures of SK2 mRNA and protein expression and cell hypertrophy. Furthermore, the latter were enhanced by shRNA-PAK1 interference and mitigated by the PAK1 agonist FTY720. Increased CaMKII and CREB phosphorylation accompanied these effects. These were rescued by both FTY720 as well as the CaMKII inhibitor KN93, but not its inactive analogue KN92. Such CREB then specifically bound to the KCNN2 promoter sequence in luciferase assays. These findings associate Ang II induced hypertrophy with increased SK2 expression brought about by a CaMKII/CREB signaling convergent with the PAK1 pathway thence upregulating the KCNN2 promoter activity. SK2 may then influence cardiac electrophysiology under conditions of cardiac hypertrophy and failure.
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Affiliation(s)
- Binbin Yang
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China; Oral & Maxillofacial Reconstruction and Regeneration Laboratory, The Affiliated Stomatology Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Qin Jiang
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Shicheng He
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Tao Li
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xianhong Ou
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Tangting Chen
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xuehui Fan
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Feng Jiang
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiaorong Zeng
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Christopher L-H Huang
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China; Physiological Laboratory and Department of Biochemistry, University of Cambridge, Cambridge CB2 3EG, UK
| | - Ming Lei
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
| | - Xiaoqiu Tan
- Key Laboratory of Medical Electrophysiology of the Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
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4
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Sermesant M, Delingette H, Cochet H, Jaïs P, Ayache N. Applications of artificial intelligence in cardiovascular imaging. Nat Rev Cardiol 2021; 18:600-609. [PMID: 33712806 DOI: 10.1038/s41569-021-00527-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 01/31/2023]
Abstract
Research into artificial intelligence (AI) has made tremendous progress over the past decade. In particular, the AI-powered analysis of images and signals has reached human-level performance in many applications owing to the efficiency of modern machine learning methods, in particular deep learning using convolutional neural networks. Research into the application of AI to medical imaging is now very active, especially in the field of cardiovascular imaging because of the challenges associated with acquiring and analysing images of this dynamic organ. In this Review, we discuss the clinical questions in cardiovascular imaging that AI can be used to address and the principal methodological AI approaches that have been developed to solve the related image analysis problems. Some approaches are purely data-driven and rely mainly on statistical associations, whereas others integrate anatomical and physiological information through additional statistical, geometric and biophysical models of the human heart. In a structured manner, we provide representative examples of each of these approaches, with particular attention to the underlying computational imaging challenges. Finally, we discuss the remaining limitations of AI approaches in cardiovascular imaging (such as generalizability and explainability) and how they can be overcome.
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Affiliation(s)
| | | | - Hubert Cochet
- IHU Liryc, CHU Bordeaux, Université Bordeaux, Inserm 1045, Pessac, France
| | - Pierre Jaïs
- IHU Liryc, CHU Bordeaux, Université Bordeaux, Inserm 1045, Pessac, France
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Lei CL, Ghosh S, Whittaker DG, Aboelkassem Y, Beattie KA, Cantwell CD, Delhaas T, Houston C, Novaes GM, Panfilov AV, Pathmanathan P, Riabiz M, dos Santos RW, Walmsley J, Worden K, Mirams GR, Wilkinson RD. Considering discrepancy when calibrating a mechanistic electrophysiology model. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190349. [PMID: 32448065 PMCID: PMC7287333 DOI: 10.1098/rsta.2019.0349] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 05/21/2023]
Abstract
Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterize uncertainty in model inputs and how that propagates through to outputs or predictions; examples of this can be seen in the papers of this issue. In this review and perspective piece, we draw attention to an important and under-addressed source of uncertainty in our predictions-that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here, we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes and autoregressive-moving-average models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. This article is part of the theme issue 'Uncertainty quantification in cardiac and cardiovascular modelling and simulation'.
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Affiliation(s)
- Chon Lok Lei
- Computational Biology and Health Informatics, Department of Computer Science, University of Oxford, Oxford, UK
| | - Sanmitra Ghosh
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Dominic G. Whittaker
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Yasser Aboelkassem
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Kylie A. Beattie
- Systems Modeling and Translational Biology, GlaxoSmithKline R&D, Stevenage, UK
| | - Chris D. Cantwell
- ElectroCardioMaths Programme, Centre for Cardiac Engineering, Imperial College London, London, UK
| | - Tammo Delhaas
- CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Charles Houston
- ElectroCardioMaths Programme, Centre for Cardiac Engineering, Imperial College London, London, UK
| | - Gustavo Montes Novaes
- Graduate Program in Computational Modeling, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Alexander V. Panfilov
- Department of Physics and Astronomy, Ghent University, Ghent, Belgium
- Laboratory of Computational Biology and Medicine, Ural Federal University, Ekaterinburg, Russia
| | - Pras Pathmanathan
- US Food and Drug Administration, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Silver Spring, MD, USA
| | - Marina Riabiz
- Department of Biomedical Engineering King’s College London and Alan Turing Institute, London, UK
| | - Rodrigo Weber dos Santos
- Graduate Program in Computational Modeling, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - John Walmsley
- James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Keith Worden
- Dynamics Research Group, Department of Mechanical Engineering, University of Sheffield, Sheffield, UK
| | - Gary R. Mirams
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
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Clayton RH, Aboelkassem Y, Cantwell CD, Corrado C, Delhaas T, Huberts W, Lei CL, Ni H, Panfilov AV, Roney C, dos Santos RW. An audit of uncertainty in multi-scale cardiac electrophysiology models. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190335. [PMID: 32448070 PMCID: PMC7287340 DOI: 10.1098/rsta.2019.0335] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
Abstract
Models of electrical activation and recovery in cardiac cells and tissue have become valuable research tools, and are beginning to be used in safety-critical applications including guidance for clinical procedures and for drug safety assessment. As a consequence, there is an urgent need for a more detailed and quantitative understanding of the ways that uncertainty and variability influence model predictions. In this paper, we review the sources of uncertainty in these models at different spatial scales, discuss how uncertainties are communicated across scales, and begin to assess their relative importance. We conclude by highlighting important challenges that continue to face the cardiac modelling community, identifying open questions, and making recommendations for future studies. This article is part of the theme issue 'Uncertainty quantification in cardiac and cardiovascular modelling and simulation'.
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Affiliation(s)
- Richard H. Clayton
- Insigneo institute for in-silico Medicine and Department of Computer Science, University of Sheffield, Sheffield, UK
- e-mail:
| | - Yasser Aboelkassem
- Department of Bioengineering, University of California, San Diego, CA, USA
| | | | - Cesare Corrado
- Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, UK
| | - Tammo Delhaas
- School of Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Wouter Huberts
- School of Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Chon Lok Lei
- Computational Biology and Health Informatics, Department of Computer Science, University of Oxford, Oxford, UK
| | - Haibo Ni
- Department of Pharmacology, University of California, Davis, CA, USA
| | - Alexander V. Panfilov
- Department of Physics and Astronomy, University of Gent, Gent, Belgium
- Laboratory of Computational Biology and Medicine, Ural Federal University, Ekaterinburg, Russia
| | - Caroline Roney
- Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, UK
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7
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Takeuchi A, Matsuoka S. Integration of mitochondrial energetics in heart with mathematical modelling. J Physiol 2020; 598:1443-1457. [DOI: 10.1113/jp276817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/23/2020] [Indexed: 11/08/2022] Open
Affiliation(s)
- Ayako Takeuchi
- Department of Integrative and Systems PhysiologyFaculty of Medical Sciencesand Life Science Innovation CenterUniversity of Fukui Fukui 910‐1193 Japan
| | - Satoshi Matsuoka
- Department of Integrative and Systems PhysiologyFaculty of Medical Sciencesand Life Science Innovation CenterUniversity of Fukui Fukui 910‐1193 Japan
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Capoccia M, Marconi S, Singh SA, Pisanelli DM, De Lazzari C. Simulation as a preoperative planning approach in advanced heart failure patients. A retrospective clinical analysis. Biomed Eng Online 2018; 17:52. [PMID: 29720187 PMCID: PMC5930731 DOI: 10.1186/s12938-018-0491-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Modelling and simulation may become clinically applicable tools for detailed evaluation of the cardiovascular system and clinical decision-making to guide therapeutic intervention. Models based on pressure-volume relationship and zero-dimensional representation of the cardiovascular system may be a suitable choice given their simplicity and versatility. This approach has great potential for application in heart failure where the impact of left ventricular assist devices has played a significant role as a bridge to transplant and more recently as a long-term solution for non eligible candidates. RESULTS We sought to investigate the value of simulation in the context of three heart failure patients with a view to predict or guide further management. CARDIOSIM© was the software used for this purpose. The study was based on retrospective analysis of haemodynamic data previously discussed at a multidisciplinary meeting. The outcome of the simulations addressed the value of a more quantitative approach in the clinical decision process. CONCLUSIONS Although previous experience, co-morbidities and the risk of potentially fatal complications play a role in clinical decision-making, patient-specific modelling may become a daily approach for selection and optimisation of device-based treatment for heart failure patients. Willingness to adopt this integrated approach may be the key to further progress.
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Affiliation(s)
- Massimo Capoccia
- Department of Cardiac Surgery, University Hospitals of Leicester NHS Trust, Leicester, UK.,Department of Biomedical Engineering, University of Strathclyde, Glasgow, UK
| | - Silvia Marconi
- National Research Council, Institute of Clinical Physiology, Rome, Italy
| | | | - Domenico M Pisanelli
- National Research Council, Institute of Cognitive Sciences and Technologies, Rome, Italy
| | - Claudio De Lazzari
- National Research Council, Institute of Clinical Physiology, Rome, Italy. .,National Institute for Cardiovascular Research (I.N.R.C.), Bologna, Italy.
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Chase JG, Preiser JC, Dickson JL, Pironet A, Chiew YS, Pretty CG, Shaw GM, Benyo B, Moeller K, Safaei S, Tawhai M, Hunter P, Desaive T. Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them. Biomed Eng Online 2018; 17:24. [PMID: 29463246 PMCID: PMC5819676 DOI: 10.1186/s12938-018-0455-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/12/2018] [Indexed: 01/17/2023] Open
Abstract
Critical care, like many healthcare areas, is under a dual assault from significantly increasing demographic and economic pressures. Intensive care unit (ICU) patients are highly variable in response to treatment, and increasingly aging populations mean ICUs are under increasing demand and their cohorts are increasingly ill. Equally, patient expectations are growing, while the economic ability to deliver care to all is declining. Better, more productive care is thus the big challenge. One means to that end is personalised care designed to manage the significant inter- and intra-patient variability that makes the ICU patient difficult. Thus, moving from current "one size fits all" protocolised care to adaptive, model-based "one method fits all" personalised care could deliver the required step change in the quality, and simultaneously the productivity and cost, of care. Computer models of human physiology are a unique tool to personalise care, as they can couple clinical data with mathematical methods to create subject-specific models and virtual patients to design new, personalised and more optimal protocols, as well as to guide care in real-time. They rely on identifying time varying patient-specific parameters in the model that capture inter- and intra-patient variability, the difference between patients and the evolution of patient condition. Properly validated, virtual patients represent the real patients, and can be used in silico to test different protocols or interventions, or in real-time to guide care. Hence, the underlying models and methods create the foundation for next generation care, as well as a tool for safely and rapidly developing personalised treatment protocols over large virtual cohorts using virtual trials. This review examines the models and methods used to create virtual patients. Specifically, it presents the models types and structures used and the data required. It then covers how to validate the resulting virtual patients and trials, and how these virtual trials can help design and optimise clinical trial. Links between these models and higher order, more complex physiome models are also discussed. In each section, it explores the progress reported up to date, especially on core ICU therapies in glycemic, circulatory and mechanical ventilation management, where high cost and frequency of occurrence provide a significant opportunity for model-based methods to have measurable clinical and economic impact. The outcomes are readily generalised to other areas of medical care.
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Affiliation(s)
- J. Geoffrey Chase
- Department of Mechanical Engineering, Centre for Bio-Engineering, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Jean-Charles Preiser
- Department of Intensive Care, Erasme University of Hospital, 1070 Brussels, Belgium
| | - Jennifer L. Dickson
- Department of Mechanical Engineering, Centre for Bio-Engineering, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Antoine Pironet
- GIGA In Silico Medicine, University of Liege, 4000 Liege, Belgium
| | - Yeong Shiong Chiew
- Department of Mechanical Engineering, School of Engineering, Monash University Malaysia, 47500 Selangor, Malaysia
| | - Christopher G. Pretty
- Department of Mechanical Engineering, Centre for Bio-Engineering, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Geoffrey M. Shaw
- Department of Intensive Care, Christchurch Hospital, Christchurch, New Zealand
| | - Balazs Benyo
- Department of Control Engineering and Information Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Knut Moeller
- Department of Biomedical Engineering, Institute of Technical Medicine, Furtwangen University, Villingen-Schwenningen, Germany
| | - Soroush Safaei
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Merryn Tawhai
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Peter Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Thomas Desaive
- GIGA In Silico Medicine, University of Liege, 4000 Liege, Belgium
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Berlin R, Gruen R, Best J. Systems Medicine-Complexity Within, Simplicity Without. JOURNAL OF HEALTHCARE INFORMATICS RESEARCH 2017; 1:119-137. [PMID: 28713872 PMCID: PMC5491616 DOI: 10.1007/s41666-017-0002-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 04/12/2017] [Accepted: 04/25/2017] [Indexed: 12/14/2022]
Abstract
This paper presents a brief history of Systems Theory, progresses to Systems Biology, and its relation to the more traditional investigative method of reductionism. The emergence of Systems Medicine represents the application of Systems Biology to disease and clinical issues. The challenges faced by this transition from Systems Biology to Systems Medicine are explained; the requirements of physicians at the bedside, caring for patients, as well as the place of human-human interaction and the needs of the patients are addressed. An organ-focused transition to Systems Medicine, rather than a genomic-, molecular-, or cell-based effort is emphasized. Organ focus represents a middle-out approach to ease this transition and to maximize the benefits of scientific discovery and clinical application. This method manages the perceptions of time and space, the massive amounts of human- and patient-related data, and the ensuing complexity of information.
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Affiliation(s)
- Richard Berlin
- Department of Computer Science, University of Illinois, Urbana, IL USA
| | - Russell Gruen
- Nanyang Institute of Technology in Health and Medicine, Department of Surgery, Lee Kong Chian School of Medicine, Singapore, Singapore
| | - James Best
- Lee Kong Chian School of Medicine, Singapore, Singapore
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Green S, Batterman R. Biology meets physics: Reductionism and multi-scale modeling of morphogenesis. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2017; 61:20-34. [PMID: 28024174 DOI: 10.1016/j.shpsc.2016.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 06/06/2023]
Abstract
A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the "tyranny of scales" problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanical modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent.
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Affiliation(s)
- Sara Green
- Department of Science Education, University of Copenhagen, Øster Voldgade 3, 1350 Copenhagen, Denmark.
| | - Robert Batterman
- Department of Philosophy, University of Pittsburgh, 1028-A Cathedral of Learning, Pittsburgh, PA 15260, USA
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12
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Abstract
Mathematical modeling has been used for over half a century to advance our understanding of cardiac electrophysiology and arrhythmia mechanisms. Notably, computational studies using mathematical models of the cardiac action potential (AP) have provided important insight into the fundamental nature of cell excitability, mechanisms underlying both acquired and inherited arrhythmia, and potential therapies. Ultimately, an approach that tightly integrates mathematical modeling and experimental techniques has great potential to accelerate discovery. Despite the increasing acceptance of mathematical modeling as a powerful tool in cardiac electrophysiology research, there remain significant barriers to its more widespread use in the field, due in part to the increasing complexity of models and growing need for specialization. To help bridge the gap between experimental and theoretical worlds that stands as a barrier to transformational breakthroughs, we present LongQt, which has the following key features: Cross-platform, threaded application with accessible graphical user interface. Facilitates advanced computational cardiac electrophysiology and arrhythmia studies. Does not require advanced programming skills.
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Affiliation(s)
- Birce Onal
- The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH, USA
| | - Daniel Gratz
- The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Thomas Hund
- The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH, USA; Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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13
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Mirams GR, Pathmanathan P, Gray RA, Challenor P, Clayton RH. Uncertainty and variability in computational and mathematical models of cardiac physiology. J Physiol 2016; 594:6833-6847. [PMID: 26990229 PMCID: PMC5134370 DOI: 10.1113/jp271671] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/28/2016] [Indexed: 12/22/2022] Open
Abstract
KEY POINTS Mathematical and computational models of cardiac physiology have been an integral component of cardiac electrophysiology since its inception, and are collectively known as the Cardiac Physiome. We identify and classify the numerous sources of variability and uncertainty in model formulation, parameters and other inputs that arise from both natural variation in experimental data and lack of knowledge. The impact of uncertainty on the outputs of Cardiac Physiome models is not well understood, and this limits their utility as clinical tools. We argue that incorporating variability and uncertainty should be a high priority for the future of the Cardiac Physiome. We suggest investigating the adoption of approaches developed in other areas of science and engineering while recognising unique challenges for the Cardiac Physiome; it is likely that novel methods will be necessary that require engagement with the mathematics and statistics community. ABSTRACT The Cardiac Physiome effort is one of the most mature and successful applications of mathematical and computational modelling for describing and advancing the understanding of physiology. After five decades of development, physiological cardiac models are poised to realise the promise of translational research via clinical applications such as drug development and patient-specific approaches as well as ablation, cardiac resynchronisation and contractility modulation therapies. For models to be included as a vital component of the decision process in safety-critical applications, rigorous assessment of model credibility will be required. This White Paper describes one aspect of this process by identifying and classifying sources of variability and uncertainty in models as well as their implications for the application and development of cardiac models. We stress the need to understand and quantify the sources of variability and uncertainty in model inputs, and the impact of model structure and complexity and their consequences for predictive model outputs. We propose that the future of the Cardiac Physiome should include a probabilistic approach to quantify the relationship of variability and uncertainty of model inputs and outputs.
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Affiliation(s)
- Gary R Mirams
- Computational Biology, Department of Computer Science, University of Oxford, Oxford, OX1 3QD, UK
| | - Pras Pathmanathan
- US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Richard A Gray
- US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Peter Challenor
- College of Engineering, Mathematics and Physical Science, University of Exeter, Exeter, EX4 4QF, UK
| | - Richard H Clayton
- Insigneo institute for in-silico medicine and Department of Computer Science, University of Sheffield, Regent Court, Sheffield, S1 4DP, UK
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14
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van Beek JHGM, Kirkwood TBL, Bassingthwaighte JB. Understanding the physiology of the ageing individual: computational modelling of changes in metabolism and endurance. Interface Focus 2016; 6:20150079. [PMID: 27051508 DOI: 10.1098/rsfs.2015.0079] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ageing and lifespan are strongly affected by metabolism. The maximal possible uptake of oxygen is not only a good predictor of performance in endurance sports, but also of life expectancy. Figuratively speaking, healthy ageing is a competitive sport. Although the root cause of ageing is damage to macromolecules, it is the balance with repair processes that is decisive. Reduced or intermittent nutrition, hormones and intracellular signalling pathways that regulate metabolism have strong effects on ageing. Homeostatic regulatory processes tend to keep the environment of the cells within relatively narrow bounds. On the other hand, the body is constantly adapting to physical activity and food consumption. Spontaneous fluctuations in heart rate and other processes indicate youth and health. A (homeo)dynamic aspect of homeostasis deteriorates with age. We are now in a position to develop computational models of human metabolism and the dynamics of heart rhythm and oxygen transport that will advance our understanding of ageing. Computational modelling of the connections between dietary restriction, metabolism and protein turnover may increase insight into homeostasis of the proteins in our body. In this way, the computational reconstruction of human physiological processes, the Physiome, can help prevent frailty and age-related disease.
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Affiliation(s)
- Johannes H G M van Beek
- Section Functional Genomics, Department of Clinical Genetics , VU University medical centre , Amsterdam , The Netherlands
| | - Thomas B L Kirkwood
- Newcastle University Institute for Ageing , Newcastle upon Tyne NE4 5PL , UK
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15
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Nim HT, Furtado MB, Costa MW, Kitano H, Rosenthal NA, Boyd SE. CARFMAP: A Curated Pathway Map of Cardiac Fibroblasts. PLoS One 2015; 10:e0143274. [PMID: 26673252 PMCID: PMC4684407 DOI: 10.1371/journal.pone.0143274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/02/2015] [Indexed: 11/18/2022] Open
Abstract
The adult mammalian heart contains multiple cell types that work in unison under tightly regulated conditions to maintain homeostasis. Cardiac fibroblasts are a significant and unique population of non-muscle cells in the heart that have recently gained substantial interest in the cardiac biology community. To better understand this renaissance cell, it is essential to systematically survey what has been known in the literature about the cellular and molecular processes involved. We have built CARFMAP (http://visionet.erc.monash.edu.au/CARFMAP), an interactive cardiac fibroblast pathway map derived from the biomedical literature using a software-assisted manual data collection approach. CARFMAP is an information-rich interactive tool that enables cardiac biologists to explore the large body of literature in various creative ways. There is surprisingly little overlap between the cardiac fibroblast pathway map, a foreskin fibroblast pathway map, and a whole mouse organism signalling pathway map from the REACTOME database. Among the use cases of CARFMAP is a common task in our cardiac biology laboratory of identifying new genes that are (1) relevant to cardiac literature, and (2) differentially regulated in high-throughput assays. From the expression profiles of mouse cardiac and tail fibroblasts, we employed CARFMAP to characterise cardiac fibroblast pathways. Using CARFMAP in conjunction with transcriptomic data, we generated a stringent list of six genes that would not have been singled out using bioinformatics analyses alone. Experimental validation showed that five genes (Mmp3, Il6, Edn1, Pdgfc and Fgf10) are differentially regulated in the cardiac fibroblast. CARFMAP is a powerful tool for systems analyses of cardiac fibroblasts, facilitating systems-level cardiovascular research.
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Affiliation(s)
- Hieu T. Nim
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
- Faculty of Information Technology, Monash University, Clayton, VIC, 3800, Australia
- * E-mail: (HTN); (SEB)
| | - Milena B. Furtado
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Mauro W. Costa
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hiroaki Kitano
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
- Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Okinawa Institute of Science and Technology, Onna, Onna-son, Kunigami, Okinawa, Japan
| | - Nadia A. Rosenthal
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
- National Heart and Lung Institute, Imperial College London, White City, W12 0NN, United Kingdom
- The Jackson Laboratory, Bar Harbor, ME, 04609, United States of America
| | - Sarah E. Boyd
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
- Faculty of Information Technology, Monash University, Clayton, VIC, 3800, Australia
- * E-mail: (HTN); (SEB)
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16
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Trenor B, Gomis-Tena J, Cardona K, Romero L, Rajamani S, Belardinelli L, Giles WR, Saiz J. In silico assessment of drug safety in human heart applied to late sodium current blockers. Channels (Austin) 2015; 7:249-62. [PMID: 23696033 DOI: 10.4161/chan.24905] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Drug-induced action potential (AP) prolongation leading to Torsade de Pointes is a major concern for the development of anti-arrhythmic drugs. Nevertheless the development of improved anti-arrhythmic agents, some of which may block different channels, remains an important opportunity. Partial block of the late sodium current (I(NaL)) has emerged as a novel anti-arrhythmic mechanism. It can be effective in the settings of free radical challenge or hypoxia. In addition, this approach can attenuate pro-arrhythmic effects of blocking the rapid delayed rectifying K(+) current (I(Kr)). The main goal of our computational work was to develop an in-silico tool for preclinical anti-arrhythmic drug safety assessment, by illustrating the impact of I(Kr)/I(NaL) ratio of steady-state block of drug candidates on "torsadogenic" biomarkers. The O'Hara et al. AP model for human ventricular myocytes was used. Biomarkers for arrhythmic risk, i.e., AP duration, triangulation, reverse rate-dependence, transmural dispersion of repolarization and electrocardiogram QT intervals, were calculated using single myocyte and one-dimensional strand simulations. Predetermined amounts of block of I(NaL) and I(Kr) were evaluated. "Safety plots" were developed to illustrate the value of the specific biomarker for selected combinations of IC(50)s for I(Kr) and I(NaL) of potential drugs. The reference biomarkers at baseline changed depending on the "drug" specificity for these two ion channel targets. Ranolazine and GS967 (a novel potent inhibitor of I(NaL)) yielded a biomarker data set that is considered safe by standard regulatory criteria. This novel in-silico approach is useful for evaluating pro-arrhythmic potential of drugs and drug candidates in the human ventricle.
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17
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Nim HT, Boyd SE, Rosenthal NA. Systems approaches in integrative cardiac biology: illustrations from cardiac heterocellular signalling studies. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 117:69-77. [PMID: 25499442 DOI: 10.1016/j.pbiomolbio.2014.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/26/2014] [Accepted: 11/28/2014] [Indexed: 12/27/2022]
Abstract
Understanding the complexity of cardiac physiology requires system-level studies of multiple cardiac cell types. Frequently, however, the end result of published research lacks the detail of the collaborative and integrative experimental design process, and the underlying conceptual framework. We review the recent progress in systems modelling and omics analysis of the heterocellular heart environment through complementary forward and inverse approaches, illustrating these conceptual and experimental frameworks with case studies from our own research program. The forward approach begins by collecting curated information from the niche cardiac biology literature, and connecting the dots to form mechanistic network models that generate testable system-level predictions. The inverse approach starts from the vast pool of public omics data in recent cardiac biological research, and applies bioinformatics analysis to produce novel candidates for further investigation. We also discuss the possibility of combining these two approaches into a hybrid framework, together with the benefits and challenges. These interdisciplinary research frameworks illustrate the interplay between computational models, omics analysis, and wet lab experiments, which holds the key to making real progress in improving human cardiac wellbeing.
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Affiliation(s)
- Hieu T Nim
- Systems Biology Institute (SBI) Australia, Level 1, Building 75, Monash University, VIC 3800, Australia; Australian Regenerative Medicine Institute, Level 1, Building 75, Monash University, VIC 3800, Australia.
| | - Sarah E Boyd
- Systems Biology Institute (SBI) Australia, Level 1, Building 75, Monash University, VIC 3800, Australia; Australian Regenerative Medicine Institute, Level 1, Building 75, Monash University, VIC 3800, Australia
| | - Nadia A Rosenthal
- Australian Regenerative Medicine Institute, Level 1, Building 75, Monash University, VIC 3800, Australia
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18
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Wierling C. Bridging the gap between metabolic liver processes and functional tissue structure by integrated spatiotemporal modeling applied to hepatic ammonia detoxification. Hepatology 2014; 60:1823-5. [PMID: 25130974 DOI: 10.1002/hep.27364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/07/2014] [Indexed: 12/07/2022]
Affiliation(s)
- Christoph Wierling
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics / Systems Biology Group, Berlin, Germany
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19
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Tong WC, Ghouri I, Taggart MJ. Computational modeling of inhibition of voltage-gated Ca channels: identification of different effects on uterine and cardiac action potentials. Front Physiol 2014; 5:399. [PMID: 25360118 PMCID: PMC4199256 DOI: 10.3389/fphys.2014.00399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/26/2014] [Indexed: 11/13/2022] Open
Abstract
The uterus and heart share the important physiological feature whereby contractile activation of the muscle tissue is regulated by the generation of periodic, spontaneous electrical action potentials (APs). Preterm birth arising from premature uterine contractions is a major complication of pregnancy and there remains a need to pursue avenues of research that facilitate the use of drugs, tocolytics, to limit these inappropriate contractions without deleterious actions on cardiac electrical excitation. A novel approach is to make use of mathematical models of uterine and cardiac APs, which incorporate many ionic currents contributing to the AP forms, and test the cell-specific responses to interventions. We have used three such models-of uterine smooth muscle cells (USMC), cardiac sinoatrial node cells (SAN), and ventricular cells-to investigate the relative effects of reducing two important voltage-gated Ca currents-the L-type (ICaL) and T-type (ICaT) Ca currents. Reduction of ICaL (10%) alone, or ICaT (40%) alone, blunted USMC APs with little effect on ventricular APs and only mild effects on SAN activity. Larger reductions in either current further attenuated the USMC APs but with also greater effects on SAN APs. Encouragingly, a combination of ICaL and ICaT reduction did blunt USMC APs as intended with little detriment to APs of either cardiac cell type. Subsequent overlapping maps of ICaL and ICaT inhibition profiles from each model revealed a range of combined reductions of ICaL and ICaT over which an appreciable diminution of USMC APs could be achieved with no deleterious action on cardiac SAN or ventricular APs. This novel approach illustrates the potential for computational biology to inform us of possible uterine and cardiac cell-specific mechanisms. Incorporating such computational approaches in future studies directed at designing new, or repurposing existing, tocolytics will be beneficial for establishing a desired uterine specificity of action.
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Affiliation(s)
- Wing-Chiu Tong
- Institute of Cellular Medicine, Newcastle UniversityNewcastle upon Tyne, UK
| | | | - Michael J. Taggart
- Institute of Cellular Medicine, Newcastle UniversityNewcastle upon Tyne, UK
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20
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Tøndel K, Martens H. Analyzing complex mathematical model behavior by partial least squares regression‐based multivariate metamodeling. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/wics.1325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Kristin Tøndel
- Simula Research Laboratory AS Fornebu Norway
- Department of Biomedical Engineering King's College London, St. Thomas' Hospital London UK
| | - Harald Martens
- Department of Engineering Cybernetics Norwegian University of Science and Technology Trondheim Norway
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21
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Lekadir K, Pashaei A, Hoogendoorn C, Pereanez M, Albà X, Frangi AF. Effect of statistically derived fiber models on the estimation of cardiac electrical activation. IEEE Trans Biomed Eng 2014; 61:2740-8. [PMID: 24893365 DOI: 10.1109/tbme.2014.2327025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Myocardial fiber orientation plays a critical role in the electrical activation and subsequent contraction of the heart. To increase the clinical potential of electrophysiological (EP) simulation for the study of cardiac phenomena and the planning of interventions, accurate personalization of the fibers is a necessary yet challenging task. Due to the difficulties associated with the in vivo imaging of cardiac fiber structure, researchers have developed alternative techniques to personalize fibers. Thus far, cardiac simulation was performed mainly based on rule-based fiber models. More recently, there has been a significant interest in data-driven and statistically derived fiber models. In particular, our predictive method in [1] allows us to estimate the unknown subject-specific fiber orientation based on the more easily available shape information. The aim of this work is to estimate the effect of using such statistical predictive models for the estimation of cardiac electrical activation times and patterns. To this end, we perform EP simulations based on a database of ten canine ex vivo diffusion tensor imaging (DTI) datasets that include normal and failing cases. To assess the strength of the fiber models under varying conditions, we consider both sinus rhythm and biventricular pacing simulations. The results show that 1) the statistically derived fibers improve the estimation of the local activation times by an average of 53.7% over traditional rule-based models, and that 2) the obtained electrical activations are consistently similar to those of the DTI-based fibers.
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22
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Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JAH, Zecchina R, Jirstrand M. Bridging the gaps in systems biology. Mol Genet Genomics 2014; 289:727-34. [DOI: 10.1007/s00438-014-0843-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/21/2014] [Indexed: 12/17/2022]
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23
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Lekadir K, Hoogendoorn C, Pereanez M, Albà X, Pashaei A, Frangi AF. Statistical personalization of ventricular fiber orientation using shape predictors. IEEE TRANSACTIONS ON MEDICAL IMAGING 2014; 33:882-890. [PMID: 24710157 DOI: 10.1109/tmi.2013.2297333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper presents a predictive framework for the statistical personalization of ventricular fibers. To this end, the relationship between subject-specific geometry of the left (LV) and right ventricles (RV) and fiber orientation is learned statistically from a training sample of ex vivo diffusion tensor imaging datasets. More specifically, the axes in the shape space which correlate most with the myocardial fiber orientations are extracted and used for prediction in new subjects. With this approach and unlike existing fiber models, inter-subject variability is taken into account to generate latent shape predictors that are statistically optimal to estimate fiber orientation at each individual myocardial location. The proposed predictive model was applied to the task of personalizing fibers in 10 canine subjects. The results indicate that the ventricular shapes are good predictors of fiber orientation, with an improvement of 11.4% in accuracy over the average fiber model.
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24
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Abstract
The adult mammalian heart predominantly comprises myocytes, fibroblasts, endothelial cells, smooth muscle cells, and epicardial cells arranged in a precise three-dimensional framework. Following cardiac injury, the spatial arrangement of cells is disrupted as different populations of cells are recruited to the heart in a temporally regulated manner. The alteration of the cellular composition of the heart after cardiac injury thus enables different phenotypes of cells to interact with each other in a spatio-temporal-dependent manner. It can be argued that the integrated study of such cellular interactions rather than the examination of single populations of cells can provide more insights into the biology of cardiac repair especially at an organ-wide level. Many signalling systems undoubtedly mediate such cross talk between cells after cardiac injury. The Wnt/β-catenin system plays an important role during cardiac development and disease. Here, we describe how cell populations in the heart after cardiac injury mediate their interactions via the Wnt/β-catenin pathway, determine how such interactions can affect a cardiac repair response and finally suggest an integrated approach to study cardiac cellular interactions.
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Affiliation(s)
- Arjun Deb
- Division of Cardiology, Department of Medicine, Cardiovascular Research Laboratory, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Programs in Molecular Cellular and Integrative Physiology and Cell and Developmental Biology, David Geffen School of Medicine, University of California, Los Angeles, 675 Charles E Young Drive S, MRL 3609, Los Angeles, CA 90095, USA
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25
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Butterworth E, Jardine BE, Raymond GM, Neal ML, Bassingthwaighte JB. JSim, an open-source modeling system for data analysis. F1000Res 2013; 2:288. [PMID: 24555116 PMCID: PMC3901508 DOI: 10.12688/f1000research.2-288.v1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/17/2013] [Indexed: 11/28/2022] Open
Abstract
JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research. For high throughput applications, JSim can be run as a batch job. JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.
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Affiliation(s)
- Erik Butterworth
- Dept. of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | | | - Gary M. Raymond
- Dept. of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Maxwell L. Neal
- Dept. of Bioengineering, University of Washington, Seattle, WA 98195, USA
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26
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Shublaq N, Sansom C, Coveney PV. Patient-specific modelling in drug design, development and selection including its role in clinical decision-making. Chem Biol Drug Des 2013; 81:5-12. [PMID: 22765044 DOI: 10.1111/j.1747-0285.2012.01444.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomics has made enormous progress in the twelve years since the publication of the first draft human genome sequence, but it has not yet been translated into the clinic. Despite spiralling development costs, the number of new drug registrations is not increasing. One reason for this lies in the genetic complexity of disease. Most diseases involve dysregulation in pathways that involve many genes, and many (including most cancers) are themselves genetically heterogeneous. Systems biology involves the multi-level simulation of physiology, cell biology and biochemistry using complex computational techniques. We show here using case studies in cancer and HIV how such computational models, and particularly models based on individual patient data, can be used for drug design and development, and in the selection of the appropriate treatment for a given patient in the face of resistance mutations. If these techniques are to be adopted in routine clinical practice, clinicians will need better training in modern approaches to the integrated analysis of large-scale heterogeneous data and multi-scale models, while developers will need to provide much more usable tools. Investment in computational infrastructure is needed so that results can be returned on clinically relevant timescales and data warehouses designed with data protection as well as accessibility in mind.
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Affiliation(s)
- Nour Shublaq
- Centre for Computational Science & Computational Life & Medical Sciences Network, University College London, London, UK
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27
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Coveney PV, Diaz-Zuccarini V, Graf N, Hunter P, Kohl P, Tegner J, Viceconti M. Integrative approaches to computational biomedicine. Interface Focus 2013. [DOI: 10.1098/rsfs.2013.0003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The new discipline of computational biomedicine is concerned with the application of computer-based techniques and particularly modelling and simulation to human health. Since 2007, this discipline has been synonymous, in Europe, with the name given to the European Union's ambitious investment in integrating these techniques with the eventual aim of modelling the human body as a whole: the virtual physiological human. This programme and its successors are expected, over the next decades, to transform the study and practice of healthcare, moving it towards the priorities known as ‘4P's’: predictive, preventative, personalized and participatory medicine.
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Affiliation(s)
- Peter V. Coveney
- Centre for Computational Science, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Vanessa Diaz-Zuccarini
- Department of Mechanical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Norbert Graf
- Clinic for Paediatric Haematology and Oncology, University of the Saarland, 66123 Saarbrücken, Germany
| | - Peter Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland 1142, New Zealand
| | - Peter Kohl
- National Heart and Lung Institute, Imperial College, Harefield Hospital, Hill End Road, Harefield UB9 6JH, UK
| | - Jesper Tegner
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska University Hospital, 17176 Solna, Sweden
| | - Marco Viceconti
- INSIGNEO Institute for In Silico Medicine, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
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28
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Gould RA, Aboulmouna LM, Varner JD, Butcher JT. Hierarchical approaches for systems modeling in cardiac development. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:289-305. [PMID: 23463736 DOI: 10.1002/wsbm.1217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ordered cardiac morphogenesis and function are essential for all vertebrate life. The heart begins as a simple contractile tube, but quickly grows and morphs into a multichambered pumping organ complete with valves, while maintaining regulation of blood flow and nutrient distribution. Though not identical, cardiac morphogenesis shares many molecular and morphological processes across vertebrate species. Quantitative data across multiple time and length scales have been gathered through decades of reductionist single variable analyses. These range from detailed molecular signaling pathways at the cellular levels to cardiac function at the tissue/organ levels. However, none of these components act in true isolation from others, and each, in turn, exhibits short- and long-range effects in both time and space. With the absence of a gene, entire signaling cascades and genetic profiles may be shifted, resulting in complex feedback mechanisms. Also taking into account local microenvironmental changes throughout development, it is apparent that a systems level approach is an essential resource to accelerate information generation concerning the functional relationships across multiple length scales (molecular data vs physiological function) and structural development. In this review, we discuss relevant in vivo and in vitro experimental approaches, compare different computational frameworks for systems modeling, and the latest information about systems modeling of cardiac development. Finally, we conclude with some important future directions for cardiac systems modeling.
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Affiliation(s)
- Russell A Gould
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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Ludewig B, Stein JV, Sharpe J, Cervantes-Barragan L, Thiel V, Bocharov G. A global "imaging'' view on systems approaches in immunology. Eur J Immunol 2013; 42:3116-25. [PMID: 23255008 DOI: 10.1002/eji.201242508] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 06/02/2012] [Accepted: 10/27/2012] [Indexed: 12/30/2022]
Abstract
The immune system exhibits an enormous complexity. High throughput methods such as the "-omic'' technologies generate vast amounts of data that facilitate dissection of immunological processes at ever finer resolution. Using high-resolution data-driven systems analysis, causal relationships between complex molecular processes and particular immunological phenotypes can be constructed. However, processes in tissues, organs, and the organism itself (so-called higher level processes) also control and regulate the molecular (lower level) processes. Reverse systems engineering approaches, which focus on the examination of the structure, dynamics and control of the immune system, can help to understand the construction principles of the immune system. Such integrative mechanistic models can properly describe, explain, and predict the behavior of the immune system in health and disease by combining both higher and lower level processes. Moving from molecular and cellular levels to a multiscale systems understanding requires the development of methodologies that integrate data from different biological levels into multiscale mechanistic models. In particular, 3D imaging techniques and 4D modeling of the spatiotemporal dynamics of immune processes within lymphoid tissues are central for such integrative approaches. Both dynamic and global organ imaging technologies will be instrumental in facilitating comprehensive multiscale systems immunology analyses as discussed in this review.
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Affiliation(s)
- Burkhard Ludewig
- Institute of Immunobiology, Kantonal Hospital St Gallen, St Gallen, Switzerland.
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Abstract
Adverse drug events (ADEs) remain a universal problem in drug development, regulatory review, and clinical practice with a substantial financial burden on the global health-care system. Recent advances in molecular and "omics" technologies, along with online databases and bioinformatics, have enabled a more integrative approach to understanding drug-target (protein) interactions, both desirable and undesirable, within a biological system. This has led to the development of systems approaches to risk assessment in an attempt to complement and improve on contemporary observational and predictive strategies for assessing risk. Although still in an evolutionary phase, systems approaches have the potential to markedly advance our understanding of ADEs and ability to predict them. Systems approaches will also move personalized medicine forward by enabling better identification of individual and subgroup risk factors.
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Abstract
This unique overview of systems toxicology methods and techniques begins with a brief account of systems thinking in biology over the last century. We discuss how systems biology and toxicology continue to leverage advances in computational modeling, informatics, large-scale computing, and biotechnology. Next, we chart the genesis of systems toxicology from previous work in physiologically based models, models of early development, and more recently, molecular systems biology. For readers interested in further details this background provides useful linkages to the relevant literature. It also lays the foundations for new ideas in systems toxicology that could translate laboratory measurements of molecular responses from xenobiotic perturbations to adverse organ level effects in humans. By providing innovative solutions across disciplinary boundaries and highlighting key scientific gaps, we believe this chapter provides useful information about the current state, and valuable insight about future directions in systems toxicity.
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Abstract
A new generation of technologies commonly named omics permits assessment of the entirety of the components of biological systems and produces an explosion of data and a major shift in our concepts of disease. These technologies will likely shape the future of health care. One aspect of these advances is that the data generated document the uniqueness of each human being in regard to disease risk and treatment response. These developments have reemphasized the concept of personalized medicine. Here we review the impact of omics technologies on one key aspect of personalized medicine: the individual drug response. We describe how knowledge of different omics may affect treatment decisions, namely drug choice and drug dose, and how it can be used to improve clinical outcomes.
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Affiliation(s)
- Urs A Meyer
- Division of Pharmacology and Neurobiology, Biozentrum of the University of Basel, CH-4056 Basel, Switzerland.
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Erson EZ, Cavuşoğlu MC. Design of a framework for modeling, integration and simulation of physiological models. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2012; 107:524-537. [PMID: 22309809 DOI: 10.1016/j.cmpb.2011.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 10/11/2011] [Accepted: 11/30/2011] [Indexed: 05/31/2023]
Abstract
Multiscale modeling and integration of physiological models carry challenges due to the complex nature of physiological processes. High coupling within and among scales present a significant challenge in constructing and integrating multiscale physiological models. In order to deal with such challenges in a systematic way, there is a significant need for an information technology framework together with related analytical and computational tools that will facilitate integration of models and simulations of complex biological systems. Physiological Model Simulation, Integration and Modeling Framework (Phy-SIM) is an information technology framework providing the tools to facilitate development, integration and simulation of integrated models of human physiology. Phy-SIM brings software level solutions to the challenges raised by the complex nature of physiological systems. The aim of Phy-SIM, and this paper is to lay some foundation with the new approaches such as information flow and modular representation of the physiological models. The ultimate goal is to enhance the development of both the models and the integration approaches of multiscale physiological processes and thus this paper focuses on the design approaches that would achieve such a goal.
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Affiliation(s)
- E Zeynep Erson
- Case Western Reserve University, Electrical Engineering and Computer Science Department, 10900 Euclid Ave.,Cleveland, OH 44106, USA.
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Modeling to link regional myocardial work, metabolism and blood flows. Ann Biomed Eng 2012; 40:2379-98. [PMID: 22915334 DOI: 10.1007/s10439-012-0613-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 06/21/2012] [Indexed: 12/13/2022]
Abstract
Given the mono-functional, highly coordinated processes of cardiac excitation and contraction, the observations that regional myocardial blood flows, rMBF, are broadly heterogeneous has provoked much attention, but a clear explanation has not emerged. In isolated and in vivo heart studies the total coronary flow is found to be proportional to the rate-pressure product (systolic mean blood pressure times heart rate), a measure of external cardiac work. The same relationship might be expected on a local basis: more work requires more flow. The validity of this expectation has never been demonstrated experimentally. In this article we review the concepts linking cellular excitation and contractile work to cellular energetics and ATP demand, substrate utilization, oxygen demand, vasoregulation, and local blood flow. Mathematical models of these processes are now rather well developed. We propose that the construction of an integrated model encompassing the biophysics, biochemistry and physiology of cardiomyocyte contraction, then combined with a detailed three-dimensional structuring of the fiber bundle and sheet arrangements of the heart as a whole will frame an hypothesis that can be quantitatively evaluated to settle the prime issue: Does local work drive local flow in a predictable fashion that explains the heterogeneity? While in one sense one can feel content that work drives flow is irrefutable, the are no cardiac contractile models that demonstrate the required heterogeneity in local strain-stress-work; quite the contrary, cardiac contraction models have tended toward trying to show that work should be uniform. The object of this review is to argue that uniformity of work does not occur, and is impossible in any case, and that further experimentation and analysis are necessary to test the hypothesis.
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Cerutti S. In the spotlight: biomedical signal processing--a well established discipline or a paradigm to promising integrated visions? IEEE Rev Biomed Eng 2012; 2:9-11. [PMID: 22275038 DOI: 10.1109/rbme.2009.2034698] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Biomedical signals carry fundamental information about the nature and the status of the living systems under study. A proper processing of these signals obtains useful physiological and clinical information. A closer integration between signal processing and modeling of the relevant biological systems is capable to directly attribute pathophysiological meaning to the parameters obtained from the processing and vice versa. Another issue of great interest in which BSP plays an important role is the Brain-Computer Interface (BCI) or Brain-Machine Interface (BMI) where fast and reliable signal processing approaches are fundamental for a practical implementation. The physiological mechanisms underlying these heart rate variability findings are supposed to be related to stochastic processes at the cellular level, to influence of respiration on the heart rate, and to the interactions of the multiple feedback loops regulating the cardiovascular system. Another important area in which BSP plays a pivotal role is the "computational genomics and proteomics." It is true that "traditional" biomedical engineering studies biomedical signals which are obtained at the level of the major physiological systems.
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Affiliation(s)
- Sergio Cerutti
- Department of Biomedical Engineering, Politecnico University, Milano 20133, Italy.
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Abstract
In contrast to the current state of knowledge of cardiac and of gastrointestinal electrophysiology, our current knowledge of the physiology of the uterus during pregnancy is still very rudimentary. Despite seminal work performed in the past decades, there are still significant areas that we know little about. In this review, some of these areas are explored. For example, although many studies have tried to find the site of the uterus pacemaker, such a site has not yet been found and its mechanism and location remain, to date, a mystery. Similarly, there is much confusion as to the mechanism of propagation of the electrical impulse. Although the existence of gap junctions, connecting neighboring myometrial cells to each other, have been known since 1977, alternative or additional mechanisms are being suggested such as the potential existence of a network of interstitial cells, similar to the one that is functioning in the gut, or the involvement of stretch receptors to synchronize activity and contraction. In recent years, high-resolution studies have been introduced enabling detailed analysis of the location and spatial patterns of propagation. This work is being developed at the in-vitro level in isolated tissues, in the whole organ and in several animal species. Most recently, a surge in new technology enabling high fidelity and high resolution recording from the human uterus through the abdominal wall are being explored which could ultimately lead to new diagnostic tools and a clearer understanding of the physiology of pregnancies and (premature) labor.
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Affiliation(s)
- Wim J E P Lammers
- Department of Physiology, Faculty of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates.
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Corley RA, Kabilan S, Kuprat AP, Carson JP, Minard KR, Jacob RE, Timchalk C, Glenny R, Pipavath S, Cox T, Wallis CD, Larson RF, Fanucchi MV, Postlethwait EM, Einstein DR. Comparative computational modeling of airflows and vapor dosimetry in the respiratory tracts of rat, monkey, and human. Toxicol Sci 2012; 128:500-16. [PMID: 22584687 DOI: 10.1093/toxsci/kfs168] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Computational fluid dynamics (CFD) models are useful for predicting site-specific dosimetry of airborne materials in the respiratory tract and elucidating the importance of species differences in anatomy, physiology, and breathing patterns. We improved the imaging and model development methods to the point where CFD models for the rat, monkey, and human now encompass airways from the nose or mouth to the lung. A total of 1272, 2172, and 135 pulmonary airways representing 17±7, 19±9, or 9±2 airway generations were included in the rat, monkey and human models, respectively. A CFD/physiologically based pharmacokinetic model previously developed for acrolein was adapted for these anatomically correct extended airway models. Model parameters were obtained from the literature or measured directly. Airflow and acrolein uptake patterns were determined under steady-state inhalation conditions to provide direct comparisons with prior data and nasal-only simulations. Results confirmed that regional uptake was sensitive to airway geometry, airflow rates, acrolein concentrations, air:tissue partition coefficients, tissue thickness, and the maximum rate of metabolism. Nasal extraction efficiencies were predicted to be greatest in the rat, followed by the monkey, and then the human. For both nasal and oral breathing modes in humans, higher uptake rates were predicted for lower tracheobronchial tissues than either the rat or monkey. These extended airway models provide a unique foundation for comparing material transport and site-specific tissue uptake across a significantly greater range of conducting airways in the rat, monkey, and human than prior CFD models.
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Affiliation(s)
- Richard A Corley
- Systems Toxicology, Pacific Northwest National Laboratory Richland, Washington 99352, USA.
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Noble D. A theory of biological relativity: no privileged level of causation. Interface Focus 2012; 2:55-64. [PMID: 23386960 PMCID: PMC3262309 DOI: 10.1098/rsfs.2011.0067] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 10/17/2011] [Indexed: 12/29/2022] Open
Abstract
Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of 'biological relativity' and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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Holzhütter HG, Drasdo D, Preusser T, Lippert J, Henney AM. The virtual liver: a multidisciplinary, multilevel challenge for systems biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:221-35. [PMID: 22246674 DOI: 10.1002/wsbm.1158] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The liver is the central metabolic organ in human physiology, with functions that are fundamentally important to the detoxification of xenobiotics (drugs), the maintenance of homeostasis of numerous blood metabolites, and the production of mediators of the acute phase response. Liver toxicity, whether actual or implied is the reason for the failure of a significant proportion of many promising novel medicines that consequently never reach the market, and diseases such as atherosclerosis, diabetes, and fatty liver diseases, that are a major burden on current health resources, are directly linked to functional and structural disorders of the liver. This article presents the concepts and approaches underpinning one of the most exciting and ambitious modeling projects in the field of systems biology and systems medicine. This major multidisciplinary research program is aimed at developing a whole-organ model of the human liver, representing its central physiological functions under normal and pathological conditions The model will be composed of a larger battery of interconnected submodels representing liver anatomy and physiology, integrating processes across hierarchical levels in space, time, and structural organization. In this article, we outline the general architecture of the liver model and present first step taken to reach this ambitious goal.
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An accurate, fast and robust method to generate patient-specific cubic Hermite meshes. Med Image Anal 2011; 15:801-13. [PMID: 21788150 DOI: 10.1016/j.media.2011.06.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 06/19/2011] [Accepted: 06/28/2011] [Indexed: 12/20/2022]
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Abstract
PURPOSE OF REVIEW Heart failure remains a leading cause of morbidity and mortality in developed nations. Our current understanding of molecular pathways involved in heart failure reveals little of the multiscale biological systems at work. Here we consider recent advances in understanding the integrative multiscale biology, or systems biology, of heart failure and present a framework for future work in the area. RECENT FINDINGS Multiplexed assays of gene expression and the complex dynamics of protein-protein interactions in heart failure have illuminated key pathways important to myocardial adaptation. Modeling of complex systems has advanced to incorporate these dynamic data sources into networks that capture fundamental interactions on different biological scales. The complex syndrome of heart failure, like other complex disease syndromes, can be viewed as an emergent property of these multiscale systems. SUMMARY A comprehensive understanding of adaptive mechanisms in heart failure requires integration of multiple data sources on several biological scales. A combination of holistic systems biology approaches and traditional reductionist experimentation will be required for a nuanced understanding of this multifaceted disease process.
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Viceconti M. A tentative taxonomy for predictive models in relation to their falsifiability. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2011; 369:4149-4161. [PMID: 21969670 DOI: 10.1098/rsta.2011.0227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The growing importance of predictive models in biomedical research raises some concerns on the correct methodological approach to the falsification of such models, as they are developed in interdisciplinary research contexts between physics, biology and medicine. In each of these research sectors, there are established methods to develop cause-effect explanations for observed phenomena, which can be used to predict: epidemiological models, biochemical models, biophysical models, Bayesian models, neural networks, etc. Each research sector has accepted processes to verify how correct these models are (falsification). But interdisciplinary research imposes a broader perspective, which encompasses all possible models in a general methodological framework of falsification. The present paper proposes a general definition of 'scientific model' that makes it possible to categorize predictive models into broad categories. For each of these categories, generic falsification strategies are proposed, except for the so-called 'abductive' models. For this category, which includes artificial neural networks, Bayesian models and integrative models, the definition of a generic falsification strategy requires further investigation by researchers and philosophers of science.
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Affiliation(s)
- Marco Viceconti
- Laboratorio di Tecnologia Medica, Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy.
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Silvester NC, George CH. Searching for new cardiovascular drugs: towards improved systems for drug screening? Expert Opin Drug Discov 2011; 6:1155-70. [PMID: 22646984 DOI: 10.1517/17460441.2011.625652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The pharmaceutical industry urgently needs new ways of profiling the safety and efficacy of new cardiovascular (CV) drugs and more effectively transitioning these compounds through the stages of CV drug screening. This article reviews new technologies and methodological innovations and assesses whether these frameworks offer improved solutions to the problems facing the contemporary CV drug development. AREAS COVERED The article comprises literature derived from a systematic search (from 2000 onwards) using the US patent office and ESP@CENET search engines as well as through multiple Boolean terms. The article focuses on patents relating to technologies and resources and categorises the patents according to their niche in the CV drug screening landscape. EXPERT OPINION The CV drug pipeline is stalling due to the inability of many contemporary drug screening frameworks to discriminate between safe, efficacious therapy and hazardous off-target effect. Given the current limitations of drug screening frameworks, there is little scope for expanding the CV drug portfolio with newer, safer drugs with improved mechanisms of action. New screening modalities are urgently needed. Searches reveal that there are few examples of truly new technologies and systems in the patent literature. This apparent failure to revamp facets of the CV drug screening process can only perpetuate the inability of current platforms to improve the CV drug pipeline. Consequently, with few exceptions, there is stagnation in pre-clinical assay design that limits the pharmaceutical industry's ability to search for new drugs in new and more effective ways.
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Affiliation(s)
- Nicole C Silvester
- Cardiff University, Wales Heart Research Institute , School of Medicine, Heath Park, Cardiff, CF14 4XN , UK
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Quinn TA, Granite S, Allessie MA, Antzelevitch C, Bollensdorff C, Bub G, Burton RAB, Cerbai E, Chen PS, Delmar M, Difrancesco D, Earm YE, Efimov IR, Egger M, Entcheva E, Fink M, Fischmeister R, Franz MR, Garny A, Giles WR, Hannes T, Harding SE, Hunter PJ, Iribe G, Jalife J, Johnson CR, Kass RS, Kodama I, Koren G, Lord P, Markhasin VS, Matsuoka S, McCulloch AD, Mirams GR, Morley GE, Nattel S, Noble D, Olesen SP, Panfilov AV, Trayanova NA, Ravens U, Richard S, Rosenbaum DS, Rudy Y, Sachs F, Sachse FB, Saint DA, Schotten U, Solovyova O, Taggart P, Tung L, Varró A, Volders PG, Wang K, Weiss JN, Wettwer E, White E, Wilders R, Winslow RL, Kohl P. Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 107:4-10. [PMID: 21745496 PMCID: PMC3190048 DOI: 10.1016/j.pbiomolbio.2011.07.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 07/01/2011] [Indexed: 11/21/2022]
Abstract
Cardiac experimental electrophysiology is in need of a well-defined Minimum Information Standard for recording, annotating, and reporting experimental data. As a step towards establishing this, we present a draft standard, called Minimum Information about a Cardiac Electrophysiology Experiment (MICEE). The ultimate goal is to develop a useful tool for cardiac electrophysiologists which facilitates and improves dissemination of the minimum information necessary for reproduction of cardiac electrophysiology research, allowing for easier comparison and utilisation of findings by others. It is hoped that this will enhance the integration of individual results into experimental, computational, and conceptual models. In its present form, this draft is intended for assessment and development by the research community. We invite the reader to join this effort, and, if deemed productive, implement the Minimum Information about a Cardiac Electrophysiology Experiment standard in their own work.
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Affiliation(s)
- T A Quinn
- National Heart and Lung Institute, Imperial College London, London, UK.
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Di Martino ES, Bellini C, Schwartzman DS. In vivo porcine left atrial wall stress: Computational model. J Biomech 2011; 44:2589-94. [PMID: 21907340 DOI: 10.1016/j.jbiomech.2011.08.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/20/2011] [Accepted: 08/29/2011] [Indexed: 11/25/2022]
Abstract
Most computational models of the heart have so far concentrated on the study of the left ventricle, mainly using simplified geometries. The same approach cannot be adopted to model the left atrium, whose irregular shape does not allow morphological simplifications. In addition, the deformation of the left atrium during the cardiac cycle strongly depends on the interaction with its surrounding structures. We present a procedure to generate a comprehensive computational model of the left atrium, including physiological loads (blood pressure), boundary conditions (pericardium, pulmonary veins and mitral valve annulus movement) and mechanical properties based on planar biaxial experiments. The model was able to accurately reproduce the in vivo dynamics of the left atrium during the passive portion of the cardiac cycle. A shift in time between the peak pressure and the maximum displacement of the mitral valve annulus allows the appendage to inflate and bend towards the ventricle before the pulling effect associated with the ventricle contraction takes place. The ventricular systole creates room for further expansion of the appendage, which gets in close contact with the pericardium. The temporal evolution of the volume in the atrial cavity as predicted by the finite element simulation matches the volume changes obtained from CT scans. The stress field computed at each time point shows remarkable spatial heterogeneity. In particular, high stress concentration occurs along the appendage rim and in the region surrounding the pulmonary veins.
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Affiliation(s)
- Elena S Di Martino
- Department of Civil Engineering and Centre for Bioengineering Research and Education, The University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N1N4.
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Graphical approach to model reduction for nonlinear biochemical networks. PLoS One 2011; 6:e23795. [PMID: 21901136 PMCID: PMC3162006 DOI: 10.1371/journal.pone.0023795] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 07/27/2011] [Indexed: 01/08/2023] Open
Abstract
Model reduction is a central challenge to the development and analysis of multiscale physiology models. Advances in model reduction are needed not only for computational feasibility but also for obtaining conceptual insights from complex systems. Here, we introduce an intuitive graphical approach to model reduction based on phase plane analysis. Timescale separation is identified by the degree of hysteresis observed in phase-loops, which guides a “concentration-clamp” procedure for estimating explicit algebraic relationships between species equilibrating on fast timescales. The primary advantages of this approach over Jacobian-based timescale decomposition are that: 1) it incorporates nonlinear system dynamics, and 2) it can be easily visualized, even directly from experimental data. We tested this graphical model reduction approach using a 25-variable model of cardiac β1-adrenergic signaling, obtaining 6- and 4-variable reduced models that retain good predictive capabilities even in response to new perturbations. These 6 signaling species appear to be optimal “kinetic biomarkers” of the overall β1-adrenergic pathway. The 6-variable reduced model is well suited for integration into multiscale models of heart function, and more generally, this graphical model reduction approach is readily applicable to a variety of other complex biological systems.
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Buckland GL. Harnessing opportunities in non-animal asthma research for a 21st-century science. Drug Discov Today 2011; 16:914-27. [PMID: 21875684 DOI: 10.1016/j.drudis.2011.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 06/29/2011] [Accepted: 08/02/2011] [Indexed: 10/17/2022]
Abstract
The incidence of asthma is on the increase and calls for research are growing, yet asthma is a disease that scientists are still trying to come to grips with. Asthma research has relied heavily on animal use; however, in light of increasingly robust in vitro and computational models and the need to more fully incorporate the 'Three Rs' principles of Replacement, Reduction and Refinement, is it time to reassess the asthma research paradigm? Progress in non-animal research techniques is reaching a level where commitment and integration are necessary. Many scientists believe that progress in this field rests on linking disciplines to make research directly translatable from the bench to the clinic; a '21st-century' scientific approach to address age-old questions.
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Noble D. Could there be a Synthesis between Western and Oriental Medicine, and with Sasang Constitutional Medicine in Particular? EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2011; 6 Suppl 1:5-10. [PMID: 19745006 PMCID: PMC2741627 DOI: 10.1093/ecam/nep101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Attitudes towards oriental medicine are changing for two major reasons. The first is that many patients, even in the West, are choosing to use its practitioners and methods. The second is that the rise of Systems Biology may offer a better basis for dialogue, and even for synthesis, between the oriental and Western traditions. However, a lot of work is needed to clear the way for such dialogue and synthesis. Much of this work should be devoted to clarifying the meanings of the terms used, and the framework of theory and practice within which oriental methods operate. But it is also necessary for Systems Biology itself to mature as a discipline, particularly at the higher levels of biological organization since it is at these levels that oriental medicine derives its ideas and practice. Higher level Systems Biology could be a basis for interpretation of the Korean version of oriental medicine: Sasang constitutional medicine since it seeks patient specific analysis and treatment, and the mathematical methods of systems biology could be used to analyze the central concept of balance in Sasang.
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Affiliation(s)
- Denis Noble
- CBE, FRS, Department of Physiology, Anatomy and Genetics Parks Road, Oxford OX1 3PT, UK.
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Christ GJ, Chen AF. The grand challenge for integrative and regenerative pharmacology. Front Pharmacol 2011; 2:5. [PMID: 21687500 PMCID: PMC3108500 DOI: 10.3389/fphar.2011.00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 02/03/2011] [Indexed: 12/28/2022] Open
Affiliation(s)
- George J Christ
- Institute for Regenerative Medicine, Wake Forest University Health Sciences Winston-Salem, NC, USA
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50
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Noble D. Successes and failures in modeling heart cell electrophysiology. Heart Rhythm 2011; 8:1798-803. [PMID: 21699872 DOI: 10.1016/j.hrthm.2011.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/09/2011] [Indexed: 11/15/2022]
Abstract
Mathematical models of the electrical activity of the heart using equations for protein ion channels and other transporters began with the Noble 1962 model. These models then developed over a period of about 50 years. Cell types in all regions have been modeled and now are available for download from the CellML website (www.cellml.org). Simulation is a necessary tool of analysis in attempting to understand biological complexity. We often learn as much from the failures as from the successes of mathematical models. It is the iterative interaction between experiment and simulation that is important.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, UK.
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