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Holistic view on cell survival and dna damage: how model-based data analysis supports exploration of dynamics in biological systems

  • Weyland, Mathias S. Zurich University of Applied Sciences Winterthur, Switzerland - Bio, Nanomaterials Group, Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
  • Thumser-Henner, Pauline Division of Radiation Oncology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland - Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Zurich, Switzerland - Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Switzerland
  • Nytko, Katarzyna J. Division of Radiation Oncology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland - Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Zurich, Switzerland - Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Switzerland
  • Rohrer Bley, Carla Division of Radiation Oncology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland - Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Zurich, Switzerland
  • Ulzega, Simone Zurich University of Applied Sciences Winterthur, Switzerland
  • Petri-Fink, Alke Bio, Nanomaterials Group, Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland - Department of Chemistry, University of Fribourg, Fribourg, Switzerland
  • Lattuada, Marco Department of Chemistry, University of Fribourg, Fribourg, Switzerland
  • Füchslin, Rudolf M. Zurich University of Applied Sciences Winterthur, Switzerland
  • Scheidegger, Stephan Zurich University of Applied Sciences Winterthur, Switzerland
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    06.07.2020
Published in:
  • Computational and Mathematical Methods in Medicine. - 2020, vol. 2020, p. 1–11
English In this work, a method is established to calibrate a model that describes the basic dynamics of DNA damage and repair. The model can be used to extend planning for radiotherapy and hyperthermia in order to include the biological effects. In contrast to “syntactic” models (e.g., describing molecular kinetics), the model used here describes radiobiological semantics, resulting in a more powerful model but also in a far more challenging calibration. Model calibration is attempted from clonogenic assay data (doses of 0–6 Gy) and from time-resolved comet assay data obtained within 6 h after irradiation with 6 Gy. It is demonstrated that either of those two sources of information alone is insufficient for successful model calibration, and that both sources of information combined in a holistic approach are necessary to find viable model parameters. Approximate Bayesian computation (ABC) with simulated annealing is used for parameter search, revealing two aspects that are beneficial to resolving the calibration problem: (1) assessing posterior parameter distributions instead of point- estimates and (2) combining calibration runs from different assays by joining posterior distributions instead of running a single calibration run with a combined, computationally very expensive objective function.
Faculty
Faculté des sciences et de médecine
Department
Département de Chimie
Language
  • English
Classification
Biology
License
License undefined
Identifiers
Persistent URL
https://folia.unifr.ch/unifr/documents/308742
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