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1. Knöchel, Jane. Model reduction of mechanism-based pharmacodynamic models and its link to classical drug effect models.

Degree: PhD, 2019, Universität Potsdam

Continuous insight into biological processes has led to the development of large-scale, mechanistic systems biology models of pharmacologically relevant networks. While these models are typically designed to study the impact of diverse stimuli or perturbations on multiple system variables, the focus in pharmacological research is often on a specific input, e.g., the dose of a drug, and a specific output related to the drug effect or response in terms of some surrogate marker. To study a chosen input-output pair, the complexity of the interactions as well as the size of the models hinders easy access and understanding of the details of the input-output relationship. The objective of this thesis is the development of a mathematical approach, in specific a model reduction technique, that allows (i) to quantify the importance of the different state variables for a given input-output relationship, and (ii) to reduce the dynamics to its essential features  – allowing for a physiological interpretation of state variables as well as parameter estimation in the statistical analysis of clinical data. We develop a model reduction technique using a control theoretic setting by first defining a novel type of time-limited controllability and observability gramians for nonlinear systems. We then show the superiority of the time-limited generalised gramians for nonlinear systems in the context of balanced truncation for a benchmark system from control theory. The concept of time-limited controllability and observability gramians is subsequently used to introduce a state and time-dependent quantity called the input-response (ir) index that quantifies the importance of state variables for a given input-response relationship at a particular time. We subsequently link our approach to sensitivity analysis, thus, enabling for the first time the use of sensitivity coefficients for state space reduction. The sensitivity based ir-indices are given as a product of two sensitivity coefficients. This allows not only for a computational more efficient calculation but also for a clear distinction of the extent to which the input impacts a state variable and the extent to which a state variable impacts the output. The ir-indices give insight into the coordinated action of specific state variables for a chosen input-response relationship. Our developed model reduction technique results in reduced models that still allow for a mechanistic interpretation in terms of the quantities/state variables of the original system, which is a key requirement in the field of systems pharmacology and systems biology and distinguished the reduced models from so-called empirical drug effect models. The ir-indices are explicitly defined with respect to a reference trajectory and thereby dependent on the initial state (this is an important feature of the measure). This is demonstrated for an example from the field of systems pharmacology, showing that the reduced models are very informative in their ability to detect (genetic) deficiencies in certain… Advisors/Committee Members: Huisinga, Wilhelm (advisor), Kloft, Charlotte (advisor), Huisinga, Wilhelm (referee), Hartmann, Carsten (referee), Lehr, Thorsten (referee).

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APA (6th Edition):

Knöchel, J. (2019). Model reduction of mechanism-based pharmacodynamic models and its link to classical drug effect models. (Doctoral Dissertation). Universität Potsdam. Retrieved from https://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/44059

Chicago Manual of Style (16th Edition):

Knöchel, Jane. “Model reduction of mechanism-based pharmacodynamic models and its link to classical drug effect models.” 2019. Doctoral Dissertation, Universität Potsdam. Accessed January 25, 2020. https://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/44059.

MLA Handbook (7th Edition):

Knöchel, Jane. “Model reduction of mechanism-based pharmacodynamic models and its link to classical drug effect models.” 2019. Web. 25 Jan 2020.

Vancouver:

Knöchel J. Model reduction of mechanism-based pharmacodynamic models and its link to classical drug effect models. [Internet] [Doctoral dissertation]. Universität Potsdam; 2019. [cited 2020 Jan 25]. Available from: https://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/44059.

Council of Science Editors:

Knöchel J. Model reduction of mechanism-based pharmacodynamic models and its link to classical drug effect models. [Doctoral Dissertation]. Universität Potsdam; 2019. Available from: https://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/44059

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