WhatsBeenDone:Systems Biology, Organ and Body Physiology

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Contents 1 Books 2 Journal Articles 2.1 Renal and Circulatory Physiology 2.1.1 Models 2.1.2 Other Studies 2.2 Endocrine Physiology 2.2.1 Models 2.2.2 Other Studies 2.3 Immunology 2.3.1 Models 2.3.2 Other Studies 3 Conference Papers 4 Useful Links 5 Physiology Resources 6 Software 7 Miscellaneous

Books

• Akay, M. and A. Marsh (ed.s), 2001, Information Technologies in Medicine, Volume 1, Medical Simulation and Education, Wiley- IEEE Computer Society PR.

• Beuter, A., L. Glass, M.C. Mackey, M.S. Titcombe (ed.s), 2003, Nonlinear Dynamics in Physiology and Medicine (Interdisciplinary Applied Mathematics, V.25). Springer Verlag.

• Brown, J.H.U. and D. S. Gann, (ed.s), 1973, Engineering Principles in Physiology, Academic Press, New York and London.

• Cannon, W.B., 1932, The Wisdom of the Body, W. W. Norton, New York.

• Carson, E.R., C. Cobelli and L. Finkelstein, 1983, The Mathematical Modeling of Metabolic and Endocrine Systems: Model Formulation, Identification, and Validation, New York: Wiley.

• Carson, Ewart R. and C. Cobelli, 2000, Modeling Methodology for Physiology and Medicine (Academic Press Biomedical Engineering Series),Academic Press.

• Carson, Ewart R. and Derek G. Cramp (eds), 1985, Computers and Control in Clinical Medicine,Springer.

• Charlesworth, B., 1994, Evolution of Age-Structured Populations, Cambridge Studies in Mathematical Biology.

• Finkelstein, Ludwik and Ewart R. Carson, 1985, Mathematical Modeling of Dynamic Biological Systems,Research Studies Press.

• Ford, A., 1999, Modeling the Environment: An Introduction to System Dynamics Modeling of Environmental Systems, Island Press, Washington.

• Physiology exercises
• System dynamics applications to physiology

• Grossman, Stanley I. and James E. Turner, 1974,Mathematics for the Biological Sciences,Macmillan Publishing Co.

• Guyton, A.C. and J.E. Hall., 2000, Textbook of Medical Physiology, Philadelphia: W.B. Saunders Company.

• Hannon, B. and M. Ruth, 1997, Modeling Dynamic Biological Systems, ISBN 0-387-94850-3 Springer.

• Hargrove, J.L., 1998, Dynamic Modeling in the Health Sciences (Modeling Dynamic Systems), Springer Verlag.

• Downloadable Models

• Iyengar, S. Sitharama (eds.), 1992, Structuring Biological Systems: A Computer Modeling Approach,CRC Press.

• Keener, J., J. Sneyd, 1998, Mathematical Physiology, Springer-Verlag.

• Khoo, M.C.K., 1999, Physiological Control Systems: Analysis, Simulation, and Estimation. Wiley-IEEE Computer Society Pr.

• Kimko, Hui C., Stephen B. Duffull, K. Kimko, 2003, Simulation for Designing Clinical Trials, Marcel Dekker Inc.

• Koeppen, B., B. Stanton, 2001, Renal Physiology, The Mosby Physiology Monograph Series.

• Kreyszig, E., 2005, Advanced Engineering Mathematics, Wiley.

• Marmarelis, Vasilis Z., 2004, Nonlinear Dynamic Modeling of Physiological Systems, Wiley-IEEE Press.

• Mitchison, J. M., The Biology of the Cell Cycle, 1971, Cambridge University Press.

• Northrop, R. B., 2000, Endogenous and exogenous regulation and control of physiological systems, Chapman & Hall / CRC Press.

• Pollard, J. H., 1973, Mathematical models for the growth of human populations, Cambridge University Press.

• Reeve, E.B, and A.C. Guyton (eds.), 1967, Physical Bases of Circulatory Transport: Regulation and Exchange,Philadelphia: W.B. Saunders Company.

• Rideout, V.C, 1991, Mathematical and Computer Modeling of Physiological Systems, Englewood Cliffs, N.J.: Prentice Hall.

• Riggs, D.S, 1970, Control Theory and Physiological Feedback Mechanisms, Baltimore: Williams and Wilkins.

• Strogatz, Steven H., 2001, Nonlinear Dynamics and Chaos, Westview Press.

Journal Articles

• Abdel-Hamid, Tarek K., 2002, "Modeling the Dynamics of Human Energy Regulation and its Implications for Obesity Treatment", Syst. Dyn. Rev., Vol: 18, pp. 431-471.

• Bush, James W., Allan M. Schneider, L. Wachtel, John E. Brimm, "Fluid therapy in acute large area burns: a system dynamics model", Syst. Dyn. Rev., Vol: 1. Nr.1.

• Carson, Ewart R., 1998, "Decision support systems in diabetes: a systems perspective", Computer Methods and Programs in Biomedicine Vol:56, pp. 77–91.

• Dangerfield, B. and C. Roberts, 2001, "Model-based scenarios for the epidemiology of HIV/AIDS: The consequences of highly active antiretroviral therapy,Syst. Dyn. Rev., Vol:17, pp.119-150.

• Finkelstein, A. et al., 2004,"Computational Challenges of Systems Biology", IEEE Computer, Vol: 37, No:5, pp. 26-33.

• Gallaher, E. J., 1996, "Biological system dynamics: from personal discovery to universal application", Simulation, Vol: 66, pp. 243-257.

• Hansen, Jan E. and Peter Bie, 1987, "Distribution of body fluids, plasma protein, and sodium in dogs: a system dynamics model", Syst. Dyn. Rev., Vol: 3. Nr.2.

• Heydrich, J.G., 1999, "Using ‘off the shelf’, computer programs to mine additional insights from published data: diurnal variation in potency of ACTH stimulation of cortisol secretion revealed", Computer Methods and Programs in Biomedicine, Vol: 58, pp. 227–238.

• Homer, J.et. al, 2000, "Toward a Dynamic Theory of Antibiotic Resistance", Syst. Dyn. Rev. 16, 287–319.

• Kofráneka, J., 2001, "GOLEM - Multimedia Simulator for Medical Education", MEDINFO, Vol: 10, pp.1042-6.

• Kofráneka, J., S. Svacina, 2000, "From obesity to diabetes - a multimedia simulation guide", Diabetes Research and Clinical Practice, Vol:50, Suppl:1, pp.245.

Renal and Circulatory Physiology

Models

• Bigelow, J.H, J.C. DeHaven and M.L. Shapley, 1973, “Systems Analysis of the Renal Function”, Journal of Theoretical Biology, Vol: 41, pp. 287-322.

• Cameron, W. H., 1977, "A Model Framework for Computer Simulation of Overall Renal Function", Journal of Theoretical Biology, Vol: 66, pp. 551-572.

• Coleman, T.G. and J. E. Hall, 1992, "A Mathematical Model of Renal Hemodynamics and Excretory Function", in Structuring Biological Systems- A Computer Modeling Approach, edited by S. Sitharama Iyengar, CRC Press.

• DeHaven J.C., N.Z. Shapiro, 1967, "On the control of urine formation", Nephron, Vol: 4:Suppl 4, pp. 1-63.

• Dehaven, J. C. and N. Z. Shapiro, "Simulation of the renal effects of antidiuretic hormone (ADH) in man", Journal of Theoretical Biology, Vol: 28, pp. 261-286.

• Flood, R. L, 1985, Quantitative Modelling of the Fluid-Electrolyte, Acid-Base Balance for Clinical Application, Ph. D. Thesis , The City University, Department of Systems Science.

• Goldstein, L.J. and E.B. Rypins, 1992, "A Computer Model of the Kidney", Computer Methods and Programs in Biomedicine.

• Guyton, A.C., T.G. Coleman, 1967, “Long Term Regulation of the Circulation: Interrelationships with Body Fluid Volumes”. In: Physical Bases of Circulatory Transport: Regulation and Exchange, edited by E.B. Reeve, and A.C. Guyton. Philadelphia: W.B. Saunders Company.

• Guyton, A. C., T. G. Coleman, and H. J. Granger, 1972, "Circulation: overall regulation", Annu. Rev. Physiol.,Vol: 34, pp. 13-46.

• Gyenge, C.C., B.D. Bowen, R.K. Reed, J.L. Bert, 2003, "Mathematical model of renal elimination of fluid and small ions during hyper- and hypovolemic conditions", Acta Anaesthesiol. Scand. Vol: pp. 122-37.

• Ikeda N., Marumo F., Shirataka M., Sato T.,1979, "A model of overall regulation of body fluids", Annals of Biomedical Engineering, Vol: 7, pp. 135-66.

• Karaaslan, F., 2004, Modeling and Analysis of the Interaction Between Renal Symphathetic Nerve Activity, Arterial Pressure and Sodium Excretion, PhD Thesis, Bogazici University.

• Karanfil, Ö., 2005, A Dynamic Simulator for the Management of Disorders of the Body water Metabolism, MSc. Thesis, Bogazici University.

• Kofranek, J., L.D.Vu, H. Snaselova, R. Kerekes, T. Velan, 2001, “GOLEM—multimedia simulator for medical education”, Medinfo, Vol. 10, No: 2, pp. 1042-1046.

• Koushanpour, E. and Gordon K. Stipp, 1982, "Mathematical simulation of the body fluid regulating system in dog", Journal of Theoretical Biology, Vol:99, pp.203-235.

• Leaning M.S., R.L. Flood, D.G. Cramp, E.R. Carson, 1985, “A System of Models for Fluid-Electrolyte Dynamics”, IEEE Trans Biomed Eng., Vol: 32, No: 10, pp. 856-864.

• Reeve, E.B. and L. Kulhanek, 1967, "Regulation of Body Water Content: A Preliminary Analysis", in: Physical Bases of Circulatory Transport: Regulation and Exchange, edited by E.B. Reeve, and A.C. Guyton. Philadelphia: W.B. Saunders Company.

• Roman, R. J. and F. R. Sias, 1985, “Network Computer Analysis of the Human Kidney”, Mathematical Modelling, Vol: 7, pp. 1045-1069.

• Sagawa, K., 1975, "Critique of a large-scale organ system model: the Guytonian cardiovascular model", Annals of Biomedical Engineering.

• Toates, F.M. and K. Oatley, 1970, “Computer Simulation of Thirst and Water Balance”, Medical and Biological Engineering, Vol: 8, pp.71-87.

• Toates, F.M. and K. Qatley, 1977, “Control of Water Excretion by Antidiuretic Hormone: Some Aspects of Modelling the System”, Medical and Biological Engineering and Computing, Vol: 15, No: 6, pp.579-588.

• Uttamsingh, R. J., 1981, A Systems Approach to Renal Dialysis, PhD. Thesis, The City University, Department of Systems Science.

• Uttamsingh, R. J., M.S. Leaning, J.A. Bushman, E.R. Carson and L. Finkelstein, 1985, “Mathematical Model of the Human Renal System”, Medical and Biological Engineering and Computing, Vol: 23, pp. 525-536.

Other Studies

• Bagby, S.P. and W. M. Bennett, 1998, “Differentiating Disorders of ECF Volume/ Na Content Regulation versus Disorders of Total Body Fluid Osmolarity/ Water Regulation”, Advances in Physiology Education, Vol. 20, No: 1, pp. 169-184.

• Granger, Joey P., 1998, "Regulation of Extracellular Fluid Volume by Integrated Control of Sodium Excretion", Adv. Physiol. Educ., Vol: 275, pp. 157-168.

• Guyton, A. C., T.G. Coleman, D.B. Young, T.E.Lohmeier, and J. W. DeClue, 1980, "Salt Balance and Long-Term Blood Pressure Control", Ann. Rev. Med., Vol: 31, pp. 15-27.

• AC Guyton, 1987, "Renal function curve--a key to understanding the pathogenesis of hypertension", Hypertension, Vol: 10, pp.1-6.

• Halperin, M.L and D. Bohn, 2002, “Clinical Approach to Disorders of Salt and Water Balance; Emphasis on Integrative Physiology”, Critical Care Clinics, Vol: 18, No: 2, pp. 249-272.

• Halperin M.L., 2002, “Body Compartment Volumes and Composition After Giving a Vasopressin Antagonist”, Nephrol. Dial. Transplant, Vol: 17, No: 2, pp. 300-303.

• Verbalis, J.G., 1992, “Pathogenesis of Hyponatremia in an Experimental Model of the Syndrome of Inappropriate Antidiuresis”, American Journal of Physiology, Vol: 267, pp. 1617-1625.

• Verbalis, J.G., 2003, “Disorders of Body Water Homeostasis”, Best Practice & Research Clinical Endocrinology & Metabolism, Vol. 17, No. 4, pp. 471–503.

• Weir, M.R., V.J. Dzau, 1999, “The Renin-Angiotensin-Aldosterone System: a Specific Target for Hypertension Management”, American Journal of Hypertension, Vol: 12, pp. 205-213.

• Wong, L.L. and J.G. Verbalis, 2002, “Systemic Diseases Associated with Disorders of Water Homeostasis”, Endocrinology and Metabolism Clinics of North America, Vol: 31, No: 1, pp. 121-140.

Endocrine Physiology

Models

• Gonzalez-Heydrich J., Steingard R.J., and Kohane I.,"Hypothalamic-pituitary-adrenal Axis Modeling".

• Katzper, M., "Adrenal Dynamics and Corticosteroids", Proceedings of the 2003 International Symposium on Health Sciences Simulation, pp.93-96.

• Kyrylov, V., "A Model of the Hypothalamus-Pituitary-Adrenal Axis: A Java Applet".

• Otero, Jay Michael and Hans B. Sieburg, "Emergent Patterns of HPA Hormone Pulsatility and Diurnal Variability in silico".

• Stear, Edwin B., 1975, "Application of control theory to endocrine regulation and control", Journal Annals of Biomedical Engineering, Vol: 3, pp. 439-455.

Other Studies

• Northrop, R.B., 2000, "Hormonal Regulation of Sodium, Potassium, Calcium and Magnesium Ions", in: Endogeneous and Exogeneous Regulation and Control of Physiological Systems, Boca Raton, Fla.: Chapman & Hall/CRC, c2000.

• Sturis, J., Van Cauter E., Blackman J.D., Polonsky K.S., 1991 "Entrainment of pulsatile insulin secretion by oscillatory glucose infusion", J. Clin. Invest., Vol: 87, pp. 439-445.

Immunology

Models

• Bernard, S., L. Pujo-Menjouet and M. C. Mackey, 2003, “Analysis of Cell Kinetics Using a Cell Division Marker: Mathetical Modeling of Experimental Data”, Biophysical Journal, Vol: 84, pp. 3414-3424.

• Bonhoeffer, S., H. Mohri, D. Ho and A. Perelson, 2000, “Quantification of cell turnover kinetics using 5-Bromo-2-deoxyyuridine”, The Journal of Immunology, Vol: 164, pp. 5049-5054.

• DeBoer, R. J., V. V. Ganusov, D. Milutinovic, P. D. Hodgkin and A. Perelson, 2006, “Estimating lymphocyte division and death rates from CFSE data”, Bulletin of Mathematical Biology, Vol: 68, pp. 1011-31.

• DeBoer, R.J., A.A. Freitas and A. Perelson, “Resource Competition Determines Selection of B Cell Repertoires”, Journal of Theoretical Biology, Vol: 212, pp. 333-343.

• Haurie, C., D. C. Dale and M. C. Mackey, 1998, “Cyclical Neutropenia and Other Periodic Hematological Disorders: A Review of Mechanisms & Math. Models”, Blood, Vol: 92, pp. 2629-2640

• Kalet Leon et al, 2004, “A general mathematical framework to model generation structure in a population of asynchronously dividing cells”, Journal of Theoretical Biology, Vol: 229, pp. 455-476.

• Macallan et al., 2003, Measurement and modeling of human T cell kinetics”, European Journal of Immunology, Vol: 33, pp. 2316-2326.

• Mackey, M. C., 2000, “Cell kinetic status of haemotopoietic stem cells”, Cell Proliferation, Vol: 34, pp 71-83.

• Mackey, M.C., A.A. Aprikyan and D.C. Dale, 2003, “The rate of apoptosis in post mitotic neutrophil precursors of normal and neutropenic humans”, Cell Proliferation, Vol: 36, pp. 27-34.
• Mackey, M. C. and P. Dörmer, 1982, “Continuous maturation of proliferating erythroid precursors”, Cell Tissue Kinetics, Vol: 15, pp. 381-392.

• Mackey, M. C. and P. Dörmer, 1981, “Enigmatic Hemapoiesis”, Biomathematics and Cell Kinetics, pp. 87-103.

• McLean, A.R., M.M. Rosado, F. Agenes, R. Vasconcellos and A. A. Freitas, “Resource competition as a mechanism for B cell homeostasis”, Immunology, Vol: 94, pp. 5792-5797.

• Mehr, R., A. Perelson, M. Fridkis-Hareli and A. Globerson, 1996, “Feedback regulation of T cell development in the thymus”, Journal of Theoretical Biology, Vol: 181, pp. 157-167.

• Mehr, R., A. Perelson, M. Fridkis-Hareli and A. Globerson, 1997, “Regulatory feedback pathways in the thymus”, Immunology Today, Vol: 18, pp. 581-585.

• Mehr, R., A. Globerson and A. Perelson, 1995, “Modeling Positive and Negative Selection and Differentiation Processes in the Thymus”, Journal of Theoretical Biology, Vol: 175, pp. 103-126.

• Mehr, M., L. Abel, P. Ubezio, A. Globerson and Z. Agur, 1993, “A mathematical model of the effect of aging on bone marrow cells colonizing the thymus”, Mechanisms of Ageing and Development, Vol: 67, pp. 159-172.

• Mehr, R., G. Shahaf, A. Sah and M Cancro, 2003, “Asynchronus differentiation models explain BM labeling kinetics and predict reflux btw the pre-and immature B cell pools”, International Immunology, Vol: 15, pp. 301-312.

• Rubinow, S. I. and J. L. Lebowitz, 1975, “A mathematical model of neutrophil production and control in normal man”, Journal of Mathematical Biology, Vol: 1, pp. 187-225.

• Shahaf, G. D. Allman, M. P. Cancro and R. Mehr, 2004, “Screening of alternative models for transitional B cell maturation”, International Immunology, Vol: 16, pp. 1081-1090.

• Srivastava, B., R. C. Lindsley, N. Nikbakht and D. Allman, “Models for peripheral B cell development and homeostasis”, Seminars in Immunology, Vol: 17, pp. 175-182.

Other Studies

• Novak, J.P. and E. Necas, 1994, “Proliferation-differentiation pathways of murine haemopoiesis: correlation of lineage fluxes”, Cell Prolif., Vol: 27, pp. 597-633

• Tanchot, C. and B. Rocha, 1998, “The organization of mature T-cell pools”, Immunology Today, Vol: 19, pp. 575-579.

• Tanchot, C., M. M. Rosado, F. Agenes, A. A. Freitas and B. Rocha, 1997, “Lymphocyte homeostasis”, Seminars in Immunology, Vol: 9, pp. 331-337.

Conference Papers

• Asami, K. and T. Kitamura, "A Diagnostic Support System for a Circulatory Model based on Structural Modeling and Path Tracking", Proc. of the 2001 IEEE Systems, Man, and Cybernetics Conference.

• Fisher, Diana M. et al., "How Drugs Work in the Human Body, Analysis of a Modeling Unit Used in a Second Year Algebra Class", ISDC, 2002?

• George, A. and R. Taylor, "A Systems Theory of Small-Cell Lung Cancer", ISDC, 2006.

• Hirsch, G.B., "A Generic Model of Contagious Disease and Its Application to Human-to-Human Transmission of Avian Influenza", ISDC, 2006.

• Homer, J. et. al., "The CDC's Diabetes Systems Modeling Project: Developing a New Tool for Chronic Disease Prevention and Control", ISDC, 2004.

• Homer, J. and B. Milstein et. al., "Obesity Population Dynamics: Exploring Historical Growth and Plausible Futures in the U.S.", ISDC, 2006.

• Katzper, M., "Baroreceptor Dynamics", Health Sciences Conference, 2004.

• Karanfil, Ö., "A Dynamic Simulator for the Management of Disorders of the Body Water Metabolism", ISDC, 2006.

• McDonnell, G. and J. Dewdney, "Exploring the Political and Economic Dynamics of Health Policy", ISDC, 2006.

• Miller, R.L. et. al., "Recruiting clients to a community-based HIV-prevention program: A dynamic model", ISDC, 2006.

• Rees, D., "System Dynamics Modelling as a Tool in Healthcare Planning", ISDC, 2006.

• Toussaint, P. and G. McDonnell, "Modeling the Communications Dimension of Clinical Work and Medication Errors", ISDC, 2006.
• Azar, A, Mohamed, Abdalla S.A and Wahba, K., Analyzing the Dynamic Implications For Improving Hemodialysis Session Performance By System Dynamics Approach”, ISDC, 2006
• Wahba, K., F. Ahmed and A. Mohamed, "Modelling the Glucose Regulatory Feedback System -- Understand the Mechanism Underlying Ultradian Oscillations", ISDC, 2006.

Useful Links

• WHO | World Health Organization
• NSR Physiome Project
• Physiome Project Websites
• PhysioNet Simulation and Computation
• Medical Informatics Sites in US
• The Games for Health Project
• MITACS Project Website
• Medical Encyclopedia
• Medical Dictionaries
  • Free Medical Dictionary
  • Medline Plus
  • On-line medical dictionary
  • Essentials of Human Physiology Index
  • A Genetics Glossary
  • Dictionary of Cell and Molecular Biology
• Centers for Disease Control and Prevention
• National Center for Health Statistics

• Frequently Accessed Databases
  • Medline
  • Pubmed ['Open Access' version of Medline]
• Link to Canadian and American universities
• Book Sources

Physiology Resources

• Anatomy
• Essentials of Human Physiology]
  • Membrane Transport and Bioelectric Activity
  • Muscle Physiology
  • Cardiac and Circulatory Physiology
  • Respiratory Physiology
  • Intermediate/Advanced Respiratory Topics
    • Outline
    • Functional design of the respiratory system
    • Oxygen needs and ventilatory coupling
    • Mechanical aspects of breathing
    • Resting breathing pattern and its peripheral modulation
    • Appendix1, Appendix 2,Appendix 3
  • Endocrine Physiology
  • Gastrointestinal Physiology
  • Renal Physiology
  • Brain Function

Software

Opening Models
Models listed here can be opened by downloading and installing the appropriate player/viewer or demo version.

• Anylogic (*.ALP) Healthcare Demonstrations
• iThink (*.ITM) iSee Player,iThink Trial or Stella Trial
• Powersim Studio (*.SIP and *.SIM) Trial or Player (Player will only view models developed in * Powersim Studio Enterprise)
• Vensim (*.MDL) Vensim PLE

Miscellaneous

• Debunking third world myths about global health using statistics
• The inner life of the cell: probably a white blood cell:)

See also Systems Biology