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Jayathungage Don TD, Safaei S, Maso Talou GD, Russell PS, Phillips ARJ, Reynolds HM. Computational fluid dynamic modeling of the lymphatic system: a review of existing models and future directions. Biomech Model Mechanobiol 2024; 23:3-22. [PMID: 37902894 PMCID: PMC10901951 DOI: 10.1007/s10237-023-01780-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/02/2023] [Indexed: 11/01/2023]
Abstract
Historically, research into the lymphatic system has been overlooked due to both a lack of knowledge and limited recognition of its importance. In the last decade however, lymphatic research has gained substantial momentum and has included the development of a variety of computational models to aid understanding of this complex system. This article reviews existing computational fluid dynamic models of the lymphatics covering each structural component including the initial lymphatics, pre-collecting and collecting vessels, and lymph nodes. This is followed by a summary of limitations and gaps in existing computational models and reasons that development in this field has been hindered to date. Over the next decade, efforts to further characterize lymphatic anatomy and physiology are anticipated to provide key data to further inform and validate lymphatic fluid dynamic models. Development of more comprehensive multiscale- and multi-physics computational models has the potential to significantly enhance the understanding of lymphatic function in both health and disease.
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Affiliation(s)
| | - Soroush Safaei
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Gonzalo D Maso Talou
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Peter S Russell
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Surgical and Translational Research Centre, Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Anthony R J Phillips
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Surgical and Translational Research Centre, Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Hayley M Reynolds
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand.
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2
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Li X, Liang H. Project, toolkit, and database of neuroinformatics ecosystem: A summary of previous studies on "Frontiers in Neuroinformatics". Front Neuroinform 2022; 16:902452. [PMID: 36225654 PMCID: PMC9549929 DOI: 10.3389/fninf.2022.902452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
In the field of neuroscience, the core of the cohort study project consists of collection, analysis, and sharing of multi-modal data. Recent years have witnessed a host of efficient and high-quality toolkits published and employed to improve the quality of multi-modal data in the cohort study. In turn, gleaning answers to relevant questions from such a conglomeration of studies is a time-consuming task for cohort researchers. As part of our efforts to tackle this problem, we propose a hierarchical neuroscience knowledge base that consists of projects/organizations, multi-modal databases, and toolkits, so as to facilitate researchers' answer searching process. We first classified studies conducted for the topic "Frontiers in Neuroinformatics" according to the multi-modal data life cycle, and from these studies, information objects as projects/organizations, multi-modal databases, and toolkits have been extracted. Then, we map these information objects into our proposed knowledge base framework. A Python-based query tool has also been developed in tandem for quicker access to the knowledge base, (accessible at https://github.com/Romantic-Pumpkin/PDT_fninf). Finally, based on the constructed knowledge base, we discussed some key research issues and underlying trends in different stages of the multi-modal data life cycle.
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Affiliation(s)
- Xin Li
- School of Information Science and Technology, University of Science and Technology of China, Hefei, China
| | - Huadong Liang
- AI Research Institute, iFLYTEK Co., LTD, Hefei, China
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3
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Surles-Zeigler MC, Sincomb T, Gillespie TH, de Bono B, Bresnahan J, Mawe GM, Grethe JS, Tappan S, Heal M, Martone ME. Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. Front Neuroinform 2022; 16:819198. [PMID: 36090663 PMCID: PMC9449460 DOI: 10.3389/fninf.2022.819198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
The stimulating peripheral activity to relieve conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system (ANS) in support of bioelectronic medicine. As part of this effort, the SPARC project is generating multi-species, multimodal data, models, simulations, and anatomical maps supported by a comprehensive knowledge base of autonomic circuitry. To facilitate the organization of and integration across multi-faceted SPARC data and models, SPARC is implementing the findable, accessible, interoperable, and reusable (FAIR) data principles to ensure that all SPARC products are findable, accessible, interoperable, and reusable. We are therefore annotating and describing all products with a common FAIR vocabulary. The SPARC Vocabulary is built from a set of community ontologies covering major domains relevant to SPARC, including anatomy, physiology, experimental techniques, and molecules. The SPARC Vocabulary is incorporated into tools researchers use to segment and annotate their data, facilitating the application of these ontologies for annotation of research data. However, since investigators perform deep annotations on experimental data, not all terms and relationships are available in community ontologies. We therefore implemented a term management and vocabulary extension pipeline where SPARC researchers may extend the SPARC Vocabulary using InterLex, an online vocabulary management system. To ensure the quality of contributed terms, we have set up a curated term request and review pipeline specifically for anatomical terms involving expert review. Accepted terms are added to the SPARC Vocabulary and, when appropriate, contributed back to community ontologies to enhance ANS coverage. Here, we provide an overview of the SPARC Vocabulary, the infrastructure and process for implementing the term management and review pipeline. In an analysis of >300 anatomical contributed terms, the majority represented composite terms that necessitated combining terms within and across existing ontologies. Although these terms are not good candidates for community ontologies, they can be linked to structures contained within these ontologies. We conclude that the term request pipeline serves as a useful adjunct to community ontologies for annotating experimental data and increases the FAIRness of SPARC data.
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Affiliation(s)
- Monique C. Surles-Zeigler
- Department of Neuroscience, University of California, San Diego, La Jolla, CA, United States
- *Correspondence: Monique C. Surles-Zeigler,
| | - Troy Sincomb
- Department of Neuroscience, University of California, San Diego, La Jolla, CA, United States
| | - Thomas H. Gillespie
- Department of Neuroscience, University of California, San Diego, La Jolla, CA, United States
| | - Bernard de Bono
- Whitby et al., Inc., Indianapolis, IN, United States
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Jacqueline Bresnahan
- Brain and Spinal Injury Center, University of California, San Francisco, San Francisco, CA, United States
| | - Gary M. Mawe
- Department of Neurological Sciences, University of Vermont, Burlington, VT, United States
| | - Jeffrey S. Grethe
- Department of Neuroscience, University of California, San Diego, La Jolla, CA, United States
| | | | - Maci Heal
- MBF Bioscience, Williston, VT, United States
| | - Maryann E. Martone
- Department of Neuroscience, University of California, San Diego, La Jolla, CA, United States
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4
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Maggioli F, Mancini T, Tronci E. SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems. Bioinformatics 2020; 36:2165-2172. [PMID: 31738386 DOI: 10.1093/bioinformatics/btz860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/15/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g. enable in silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models. Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems. RESULTS In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2-compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialized SBML simulators. AVAILABILITY AND IMPLEMENTATION SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica.
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Affiliation(s)
- F Maggioli
- Computer Science Department, Sapienza University of Rome, Rome, Italy
| | - T Mancini
- Computer Science Department, Sapienza University of Rome, Rome, Italy
| | - E Tronci
- Computer Science Department, Sapienza University of Rome, Rome, Italy
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5
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Zhang X, Yang J, Chen N, Zhang S, Xu Y, Tan L. Modeling and simulation of an anatomy teaching system. Vis Comput Ind Biomed Art 2019; 2:8. [PMID: 32240405 PMCID: PMC7099570 DOI: 10.1186/s42492-019-0019-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/14/2019] [Indexed: 11/16/2022] Open
Abstract
Specimen observation and dissection have been regarded as the best approach to teach anatomy, but due to the severe lack of anatomical specimens in recent years, the quality of anatomy teaching has been seriously affected. In order to disseminate anatomical knowledge effectively under such circumstances, this study discusses three key factors (modeling, perception, and interaction) involved in constructing virtual anatomy teaching systems in detail. To ensure the authenticity, integrity, and accuracy of modeling, detailed three-dimensional (3D) digital anatomical models are constructed using multi-scale data, such as the Chinese Visible Human dataset, clinical imaging data, tissue sections, and other sources. The anatomical knowledge ontology is built according to the needs of the particular teaching purposes. Various kinds of anatomical knowledge and 3D digital anatomical models are organically combined to construct virtual anatomy teaching system by means of virtual reality equipment and technology. The perception of knowledge is realized by the Yi Chuang Digital Human Anatomy Teaching System that we have created. The virtual interaction mode, which is similar to actual anatomical specimen observation and dissection, can enhance the transmissibility of anatomical knowledge. This virtual anatomy teaching system captures the three key factors. It can provide realistic and reusable teaching resources, expand the new medical education model, and effectively improve the quality of anatomy teaching.
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Affiliation(s)
- Xiaoqin Zhang
- Institute of Digital Medicine, School of Biomedical Engineering and Medical Imaging, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Jingyi Yang
- Institute of Digital Medicine, School of Biomedical Engineering and Medical Imaging, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Na Chen
- Institute of Digital Medicine, School of Biomedical Engineering and Medical Imaging, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Shaoxiang Zhang
- Institute of Digital Medicine, School of Biomedical Engineering and Medical Imaging, Army Medical University (Third Military Medical University), Chongqing, 400038, China
| | - Yifa Xu
- Shandong Digihuman Technology Co., Inc, Jinan, 250101, China
| | - Liwen Tan
- Institute of Digital Medicine, School of Biomedical Engineering and Medical Imaging, Army Medical University (Third Military Medical University), Chongqing, 400038, China.
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6
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Sarma GP, Lee CW, Portegys T, Ghayoomie V, Jacobs T, Alicea B, Cantarelli M, Currie M, Gerkin RC, Gingell S, Gleeson P, Gordon R, Hasani RM, Idili G, Khayrulin S, Lung D, Palyanov A, Watts M, Larson SD. OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0382. [PMID: 30201845 PMCID: PMC6158220 DOI: 10.1098/rstb.2017.0382] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2018] [Indexed: 01/02/2023] Open
Abstract
The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization working towards an integrative simulation of the nematode Caenorhabditis elegans, with the aim of providing a powerful new tool to understand how the organism's behaviour arises from its fundamental biology. In this perspective, we give an overview of the history and philosophy of OpenWorm, descriptions of the constituent sub-projects and corresponding open-science management practices, and discuss current achievements of the project and future directions.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.
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Affiliation(s)
- Gopal P Sarma
- School of Medicine, Emory University, Atlanta, GA, USA
| | | | | | - Vahid Ghayoomie
- Laboratory of Systems Biology and Bioinformatics, University of Tehran, Tehran, Iran
| | | | | | | | - Michael Currie
- Fling Inc., Bangkok, Thailand.,Raytheon Company, Waltham, MA, USA
| | - Richard C Gerkin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Richard Gordon
- Embryogenesis Center, Gulf Specimen Marine Laboratory, Panacea, FL, USA.,C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Ramin M Hasani
- Cyber-Physical Systems, Technische Universität Wien, Wien, Austria
| | | | - Sergey Khayrulin
- The OpenWorm Foundation, New York, NY, USA.,Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems, Novosibirsk, Russia.,Laboratory of Structural Bioinformatics and Molecular Modeling, Novosibirsk State University, Novosibirsk, Russia
| | - David Lung
- Cyber-Physical Systems, Technische Universität Wien, Wien, Austria
| | - Andrey Palyanov
- Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems, Novosibirsk, Russia.,Laboratory of Structural Bioinformatics and Molecular Modeling, Novosibirsk State University, Novosibirsk, Russia
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7
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Vinnakota KC, Cha CY, Rorsman P, Balaban RS, La Gerche A, Wade-Martins R, Beard DA, Jeneson JAL. Improving the physiological realism of experimental models. Interface Focus 2016; 6:20150076. [PMID: 27051507 PMCID: PMC4759746 DOI: 10.1098/rsfs.2015.0076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Virtual Physiological Human (VPH) project aims to develop integrative, explanatory and predictive computational models (C-Models) as numerical investigational tools to study disease, identify and design effective therapies and provide an in silico platform for drug screening. Ultimately, these models rely on the analysis and integration of experimental data. As such, the success of VPH depends on the availability of physiologically realistic experimental models (E-Models) of human organ function that can be parametrized to test the numerical models. Here, the current state of suitable E-models, ranging from in vitro non-human cell organelles to in vivo human organ systems, is discussed. Specifically, challenges and recent progress in improving the physiological realism of E-models that may benefit the VPH project are highlighted and discussed using examples from the field of research on cardiovascular disease, musculoskeletal disorders, diabetes and Parkinson's disease.
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Affiliation(s)
- Kalyan C. Vinnakota
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Chae Y. Cha
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Robert S. Balaban
- Laboratory of Cardiac Energetics, National Heart Lung Blood Institute, Bethesda, MD, USA
| | - Andre La Gerche
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Daniel A. Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Jeroen A. L. Jeneson
- Neuroimaging Centre, Division of Neuroscience, University Medical Center Groningen, Groningen, The Netherlands
- Department of Radiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
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8
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Lee S. Systems Biology - A Pivotal Research Methodology for Understanding the Mechanisms of Traditional Medicine. J Pharmacopuncture 2015; 18:11-8. [PMID: 26388998 PMCID: PMC4573803 DOI: 10.3831/kpi.2015.18.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 08/31/2015] [Indexed: 12/14/2022] Open
Abstract
Objectives: Systems biology is a novel subject in the field of life science that aims at a systems’ level understanding of biological systems. Because of the significant progress in high-throughput technologies and molecular biology, systems biology occupies an important place in research during the post-genome era. Methods: The characteristics of systems biology and its applicability to traditional medicine research have been discussed from three points of view: data and databases, network analysis and inference, and modeling and systems prediction. Results: The existing databases are mostly associated with medicinal herbs and their activities, but new databases reflecting clinical situations and platforms to extract, visualize and analyze data easily need to be constructed. Network pharmacology is a key element of systems biology, so addressing the multi-component, multi-target aspect of pharmacology is important. Studies of network pharmacology highlight the drug target network and network target. Mathematical modeling and simulation are just in their infancy, but mathematical modeling of dynamic biological processes is a central aspect of systems biology. Computational simulations allow structured systems and their functional properties to be understood and the effects of herbal medicines in clinical situations to be predicted. Conclusion: Systems biology based on a holistic approach is a pivotal research methodology for understanding the mechanisms of traditional medicine. If systems biology is to be incorporated into traditional medicine, computational technologies and holistic insights need to be integrated.
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Affiliation(s)
- Soojin Lee
- Department of Physiology, College of Korean Medicine, Sangji University, Wonju, Korea
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9
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D'Alessandro LA, Hoehme S, Henney A, Drasdo D, Klingmüller U. Unraveling liver complexity from molecular to organ level: challenges and perspectives. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 117:78-86. [PMID: 25433231 DOI: 10.1016/j.pbiomolbio.2014.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/28/2014] [Accepted: 11/19/2014] [Indexed: 12/13/2022]
Abstract
Biological responses are determined by information processing at multiple and highly interconnected scales. Within a tissue the individual cells respond to extracellular stimuli by regulating intracellular signaling pathways that in turn determine cell fate decisions and influence the behavior of neighboring cells. As a consequence the cellular responses critically impact tissue composition and architecture. Understanding the regulation of these mechanisms at different scales is key to unravel the emergent properties of biological systems. In this perspective, a multidisciplinary approach combining experimental data with mathematical modeling is introduced. We report the approach applied within the Virtual Liver Network to analyze processes that regulate liver functions from single cell responses to the organ level using a number of examples. By facilitating interdisciplinary collaborations, the Virtual Liver Network studies liver regeneration and inflammatory processes as well as liver metabolic functions at multiple scales, and thus provides a suitable example to identify challenges and point out potential future application of multi-scale systems biology.
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Affiliation(s)
- L A D'Alessandro
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - S Hoehme
- Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Germany
| | - A Henney
- Obsidian Biomedical Consulting Ltd., Macclesfield, UK; The German Virtual Liver Network, University of Heidelberg, 69120 Heidelberg, Germany
| | - D Drasdo
- Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig, Germany; Institut National de Recherche en Informatique et en Automatique (INRIA), Domaine de Voluceau, 78150 Rocquencourt, France; University Pierre and Marie Curie and CNRS UMR 7598, LJLL, F-75005 Paris, France; CNRS, 7598 Paris, France
| | - U Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany.
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10
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Bhattacharya-Ghosh B, Bozkurt S, Rutten MCM, van de Vosse FN, Díaz-Zuccarini V. An in silico case study of idiopathic dilated cardiomyopathy via a multi-scale model of the cardiovascular system. Comput Biol Med 2014; 53:141-53. [PMID: 25147131 DOI: 10.1016/j.compbiomed.2014.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/27/2014] [Accepted: 06/21/2014] [Indexed: 10/25/2022]
Abstract
Mathematical modelling has been used to comprehend the pathology and the assessment of different treatment techniques such as heart failure and left ventricular assist device therapy in the cardiovascular field. In this study, an in-silico model of the heart is developed to understand the effects of idiopathic dilated cardiomyopathy (IDC) as a pathological scenario, with mechanisms described at the cellular, protein and organ levels. This model includes the right and left atria and ventricles, as well as the systemic and pulmonary arteries and veins. First, a multi-scale model of the whole heart is simulated for healthy conditions. Subsequently, the model is modified at its microscopic and macroscopic spatial scale to obtain the characteristics of IDC. The extracellular calcium concentration, the binding affinity of calcium binding proteins and the maximum and minimum elastances have been identified as key parameters across all relevant scales. The modified parameters cause a change in (a) intracellular calcium concentration characterising cellular properties, such as calcium channel currents or the action potential, (b) the proteins being involved in the sliding filament mechanism and the proportion of the attached crossbridges at the protein level, as well as (c) the pressure and volume values at the organ level. This model allows to obtain insight and understanding of the effects of the treatment techniques, from a physiological and biological point of view.
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Affiliation(s)
| | - Selim Bozkurt
- Eindhoven University of Technology, Biomedical Engineering, Materials Technology, PO Box 513, GEM-Z 4.18, 5600 MB, Eindhoven, The Netherlands.
| | - Marcel C M Rutten
- Eindhoven University of Technology, Biomedical Engineering, Materials Technology, PO Box 513, GEM-Z 4.18, 5600 MB, Eindhoven, The Netherlands.
| | - Frans N van de Vosse
- Eindhoven University of Technology, Biomedical Engineering, Materials Technology, PO Box 513, GEM-Z 4.18, 5600 MB, Eindhoven, The Netherlands.
| | - Vanessa Díaz-Zuccarini
- University College London, Mechanical Engineering Department, Torrington Place, WC1E 7JE London, UK.
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11
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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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12
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Yang A. On the Common Conceptual and Computational Frameworks for Multiscale Modeling. Ind Eng Chem Res 2013. [DOI: 10.1021/ie303123s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Aidong Yang
- Department of Chemical and Process
Engineering, Faculty
of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, U.K
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13
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Abstract
This special issue on "Systems biology and personalized medicine" includes five complementary articles that highlight how functional genomics and computational physiology can contribute to the development of predictive, preventive, personalized and participatory (P4) medicine. Edited by Prof. Leroy Hood and Prof. Charles Auffray.
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14
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Nickerson DP, Garny A, Nielsen PMF, Hunter PJ. Standards and tools supporting collaborative development of the virtual physiological human. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:5541-5544. [PMID: 24110992 DOI: 10.1109/embc.2013.6610805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The development of a virtual physiological human has an ambitious goal that requires the participation of a large and diverse community of scientists. To be successful in achieving this goal, members of this community must be able to share their work and easily collaborate on new developments and novel applications of existing work. To aid in this, various standardization projects have evolved as part of the Physiome community, as well as supporting computational tools and infrastructure. We present here an overview of the current state of these standardization efforts and key tools that support the collaborative development, integration, and exchange of computational physiology models under the Physiome umbrella.
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15
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Cerutti S. In the Spotlight: Biomedical Signal Processing. IEEE Rev Biomed Eng 2013; 6:17-8. [DOI: 10.1109/rbme.2012.2228313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Tasaki KM. Circular causality in integrative multi-scale systems biology and its interaction with traditional medicine. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 111:144-6. [PMID: 23085071 DOI: 10.1016/j.pbiomolbio.2012.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
Abstract
This paper discusses the concept of circular causality in "biological relativity" (Noble, Interface Focus. 2, 56-64, 2012) in the context of integrative and multi-scale systems approaches to biology. It also discusses the relationship between systems biology and traditional medicine (sometimes called scholarly medical traditions) mainly from East Asia and India. Systems biology helps illuminate circular processes identified in traditional medicine, while the systems concept of attractors in complex systems will also be important in analysing dynamic balance in the body processes that traditional medicine is concerned with. Ways of nudging disordered processes towards good attractors through the use of traditional medicines can lead to the development of new ways not only of curing disease but also of its prevention. Examples are given of cost-effective multi-component remedies that use integrative ideas derived from traditional medicine.
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Affiliation(s)
- Kazuyo Maria Tasaki
- University of Oxford, Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK.
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