Challenges and rewards on the road to translational systems biology in acute illness: four case reports from interdisciplinary teams

Journal of Critical Care

Volumn 22, Issue 2, 2007, Pages 169-175

  An, Gary ^a   Hunt, C Anthony ^b   Clermont, Gilles ^c,f   Neugebauer, Edmund ^d   Vodovotz, Yoram ^c,e,f  

^a NORTHWESTERN UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF WITTEN HERDECKE   (Germany)

^e UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

^f UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Complexity; Computer simulation; Education programs; Glossary; Inflammation; Interactive model; Mathematical modeling; Sepsis; Transdisciplinary approaches; Trauma

Indexed keywords

ACUTE DISEASE; ARTICLE; HEALTH CARE PERSONNEL; INFLAMMATION; INTERDISCIPLINARY EDUCATION; LANGUAGE; MATHEMATICAL MODEL; MEDICAL EDUCATION; MEDICAL RESEARCH; MEDICAL SOCIETY; MULTIPLE ORGAN FAILURE;

BIOMEDICAL RESEARCH; COMPUTER SIMULATION; GERMANY; HUMANS; INFLAMMATION; INTERDISCIPLINARY COMMUNICATION; INTERPROFESSIONAL RELATIONS; MODELS, THEORETICAL; ORGANIZATIONAL CASE STUDIES; SYSTEMIC INFLAMMATORY RESPONSE SYNDROME; SYSTEMS BIOLOGY; UNITED STATES;

EID: 34249826054     PISSN: 08839441     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jcrc.2006.12.011     Document Type: Article

References (41)

1. NIH Roadmap for Medical Research: Research Teams. Available at:. http://nihroadmap.nih.gov/researchteams/ [Accessed June 15, 2006]
2. US Food and Drug Administration report: innovation or stagnation: challenge and opportunity in the critical path to new medical products. Available at:. http://www.fda.gov/oc/initiatives/criticalpath/whitepaper.html [Accessed June 15, 2006]
3. Buchman T.G. Physiologic stability and physiologic state. J Trauma 41 (1996) 599-605
4. Neugebauer E.A., Willy C., and Sauerland S. Complexity and non-linearity in shock research: reductionism or synthesis?. Shock 16 4 (2001) 252-258
5. Ropella G.E.P., Hunt C.A., and Sheikh-Bahaei S. Methodological considerations of heuristic modeling of biological systems. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics, July 10-13, Orlando, Florida (2005). http://biosystems.ucsf.edu/Researc/ Available at:
6. Neugebauer E.A., Tjardes T., and Multidisciplinary Working Group on Complexity. New approaches to shock and trauma research: learning from multidisciplinary exchange. J Trauma 56 5 (2004) 1156-1165
7. Committee on Facilitating Interdisciplinary Research and Engineering and Public Policy Committee on Science. Facilitating interdisciplinary research (2005), National Academy Press, Washington (DC). http://www.nationalacademies.org/cosepup
8. An G. Agent-based computer simulation and SIRS: building a bridge between basic science and clinical trials. Shock 16 4 (2001) 266-273
9. An G. In-silico experiments of existing and hypothetical cytokine-directed clinical trials using agent based modeling. Crit Care Med 32 10 (2004) 2050-2060
10. Northwestern University Center for Connected Learning: Netlogo Homepage. Available at:. http://ccl.northwestern.edu/netlogo/ [Accessed June 10, 2006]
11. An G, Lee I. Complexity, emergence and pathophysiology: using agent based computer simulation to characterize the non-adaptive inflammatory response. InterJournal Complex Systems: http://www.interjournal.org/. Manuscript # [344]. May, 2000.
12. An G., and Lee I. Agent-Based Computer simulation (ABCS) and the inflammatory response: building a tool to study Systemic Inflammatory Response Syndrome (SIRS). Simul Gaming 32 3 (2001) 344-361
13. An G. Synthetic microanalysis, agent based computer simulation and Systemic Inflammatory Response Syndrome: capturing the complexity of the inflammatory response. Crit Care Med 28 12S (2000) A64 (Supp)(abstr)
14. An G., and Delude R. Agent based model of cell culture epithelial barrier function: using computer simulation in conjunction with a basic science model. Shock 21S2 (2004) s13 (Supp)(abstr)
15. An G., Feinman R., Xu D.-Z., and Deitch E. In-silico unification of different basic science models of gut epithelial barrier function using agent based modeling. Crit Care Med 32 12s (2004) A95 (Supp)(abstr)
16. An G. Agent based models of pulmonary epithelial barrier function. Advance Program from the 102nd Annual International Conference of the American Thoracic Society (2006) (Supp)(abstr)
17. An G. Computer simulations of multiple organ failure secondary to shock and sepsis with a multi-tissue, endothelial level agent based model. Shock 21S2 (2004) s66 (Supp)(abstr)
18. An G. Concepts for developing a collaborative in-silico model of the acute inflammatory response using agent based modeling. J Crit Care 21 1 (2006) 105-110
19. An G. A synthetic framework for investigating multiple intracellular signaling pathways using agent based modeling. Shock 25 S1 (2006) 83 (Supp)(abstr)
20. An G. Integrative modeling of inflammation and organ function using agent based modeling. Shock 26 S1 (2006) 2 (Supp)(abstr)
21. Tjardes T., and Neugebauer E.A. Sepsis research in the next millennium: concentrate on the software rather than the hardware. Shock 17 1 (2002) 1-8
22. In: Neugebauer E.A., and Holaday J.W. (Eds). Handbook of mediators in septic shock (1993), CRC Press, Boca Raton (Fla)
23. Neugebauer E.A.M., Willy C., and Sauerland S. Complexity and non-linearity in shock research: reductionism or synthesis. Shock 16 (2001) 252-258
24. Willy C., Neugebauer E.A.M., and Gerngroß H. The concept of nonlinearity in complex systems. Eur J Trauma 29 (2003) 11-22
25. Bouillon B., Lefering R., Vorweg M., Tiling T., Neugebauer E., and Troidl H. Trauma score systems: Cologne Validation Study. J Trauma 42 4 (1997) 652-658
26. AG Polytrauma (DGU), Neugebauer E.A.M., et al. Das Traumaregister der deutschen Gesellschaft für Unfallchirurgie als Grundlage des interklinischen Qualitätsmanagements in der Schwerverletztenversorgung-Eine Multicenterstudie der DGU. Unfallchirurgie 103 (2000) 30-37
27. Rixen D., Raum M., Bouillon B., Lefering R., Neugebauer E.A.M., and AG Polytrauma (DGU). Base deficit development and its prognostic significance in posttrauma critical illness: an analysis by the trauma registry of the Deutsche Gesellschaft für Unfallchirurgie. Shock 15 (2001) 83-89
28. Hunt C.A., Ropella G.E.P., Yan L., Hung D.Y., and Roberts M.S. Physiologically based synthetic models of hepatic disposition. J Pharmacokinet Pharmacodyn (2006) doi: 10.1007/s10928-006-9031-3
29. Sheikh-Bahaei S., Ropella G.E.P., and Hunt C.A. In silico hepatocyte: agent-based modeling of the biliary excretion of drugs in vitro. In: Yilmaz L., et al. (Ed). Proc 2006 Agent-Direc Simul Symp (Huntsville, AL, Apr 3-9) (ADS '06) (2006), SCS Press, San Diego (Calif) 157-163
30. Hunt C.A., Ropella G.E., Yan L., Hung D.Y., and Roberts M.S. Physiologically based synthetic models of hepatic disposition. J Pharmokinetic Pharmacody 33 6 (2006) 737-772
31. Grant M.R., Kim S.H., and Hunt C.A. Simulating in vitro epithelial morphogenesis in multiple environments. Comput Syst Bioinformatics Conf (2006) 381-384
32. Grant M.R., Mostov K.E., Tlsty T.D., and Hunt C.A. Simulating properties of in vitro epithelial cell morphogenesis. PLoS Comput Biol 2 9 (2006) e129 doi: 10.1371/journal.pcbi.0020129
33. Clermont G., Bartels J., Kumar R., Constantine G., Vodovotz Y., and Chow C. In silico design of clinical trials: a method coming of age. Crit Care Med 32 (2004) 2061-2070
34. Chow C.C., Clermont G., Kumar R., Lagoa C., Tawadrous Z., Gallo D., et al. The acute inflammatory response in diverse shock states. Shock 24 (2005) 74-84
35. Lagoa C.E., Bartels J., Baratt A., Tseng G., Clermont G., Fink M.P., Billiar T.R., and Vodovotz Y. The role of initial trauma in the host's response to injury and hemorrhage: insights from a comparison of mathematical simulations and hepatic transcriptomic analysis. Shock 26 6 (2006) 592-600
36. Prince J.M., Levy R.M., Bartels J., Baratt A., Kane III J.M., Lagoa C., et al. In silico and in vivo approach to elucidate the inflammatory complexity of CD14-deficient mice. Mol Med 12 (2006) 88-96
37. Kumar R., Clermont G., Vodovotz Y., and Chow C.C. The dynamics of acute inflammation. J Theor Biol 230 (2004) 145-155
38. Reynolds A., Rubin J., Clermont G., Day J., Vodovotz Y., and Ermentrout G.B. A reduced mathematical model of the acute inflammatory response: I. Derivation of model and analysis of anti-inflammation. J Theor Biol 242 (2006) 220-236
39. Day J., Rubin J., Vodovotz Y., Chow C.C., Reynolds A., and Clermont G. A reduced mathematical model of the acute inflammatory response: II. Capturing scenarios of repeated endotoxin administration. J Theor Biol 242 (2006) 237-256
40. Constantine G., Bartels J., Buliga M., Clermont G., and Vodovotz Y. A linear code parameter search algorithm with applications to immunology. Computational Optimization and Applications (2007) [in press]
41. Chang S., Baratt A., Clermont G., Planquois J.-M., Yan S.B., Williams M., et al. Mathematical model predicting outcomes of sepsis patients treated with Xigris(R): ENHANCE trial. Shock 25 (2006) 70-71 (Supp)(abstr)