ics Institute of Computer Science
The Czech Academy of Sciences
Department of Computational Mathematics		 Rosenbrock

Ctirad Matonoha

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Publications

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--- Papers ---

Matonoha C., Papáček Š., Lynnyk V.
On an optimal setting of delays for the D-QSSA model reduction method applied to a class of chemical reaction networks
 • Applications of Mathematics, Vol. 67, No. 6, 2022, p. 831-857

Kalina J., Matonoha C.
A sparse pair-preserving centroid-based supervised learning method for high-dimensional biomedical data or images
 • Biocybernetics and Biomedical Engineering, Vol. 40, 2020, p. 774-786

Duintjer Tebbens J., Matonoha C., Matthios A., Papáček Š.
On parameter estimation in an in vitro compartmental model for drug-induced enzyme production in pharmacotherapy
 • Applications of Mathematics, Vol. 64, No. 2, 2019, p. 253-277

Papáček Š., Macdonald B., Matonoha C.
Closed-form formulas vs. PDE based numerical solution for the FRAP data processing: Theoretical and practical comparison
 • Computers & Mathematics With Applications, Vol. 73, No. 8, 2017, p. 1673-1683
 • In: L. Jódar, L. Acedo, J.C. Cortés, Instituto Universitario de Matemática Multidisciplinar (Eds.), Modelling for engineering and human behaviour, Valencia 2015, p. 359-364

Matonoha C., Papáček Š.
On the connection and equivalence of two methods for solving an ill-posed inverse problem based on FRAP data
 • Journal of Computational and Applied Mathematics, Vol. 290, 2015, p. 598-608
 • In: L. Jódar, L. Acedo, J.C. Cortés, J.R. Torregrosa, Instituto Universitario de Matemática Multidisciplinar (Ed.), Modelling for engineering and human behaviour, Valencia 2014, p. 102-105

Kaňa R., Kotabová E., Lukeš M., Papáček Š., Matonoha C., Liu L.N., Prášil O., Mullineaux C.W.
Phycobilisome Mobility and Its Role in the Regulation of Light Harvesting in Red Algae
 • Plant Physiology, Vol. 165, 2014, p. 1618-1631

Papáček Š., Kaňa R., Matonoha C.
Estimation of diffusivity of phycobilisomes on thylakoid membrane based on spatio-temporal FRAP images
 • Mathematical and Computer Modelling, Vol. 57, No. 7-8, 2013, p. 1907-1912
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'12", Liberec, 23.-27.1.2012, p. 146-148
 • In: L. Jódar, L. Acedo, J.C. Cortés, Instituto Universitario de Matemática Multidisciplinar (Ed.), Modelling for engineering and human behaviour, Valencia 2011, p. 248-251
 • Technical Report V-1123, ICS AS CR, Prague, 2011, 11 p.    download

Červinka M., Matonoha C., Outrata J.
On the computation of relaxed pessimistic solutions to MPECs
 • Optimization Methods and Software, Vol. 28, No. 1, 2013, p. 186-206
 • Technical Report V-1088 (revised version), ICS AS CR, Prague, 2010, 22 p.    download
 • Technical Report V-1057 (preliminary version), ICS AS CR, Prague, 2009, 15 p.    download

Finěk V., Matonoha C.
On the Problem of Variability of Interval Data
 • ACC Journal, Vol. 18, No. 4, 2012, p. 75-83

Papáček Š., Matonoha C., Štumbauer V., Štys D.
Modelling and Simulation of Photosynthetic Microorganism Growth: Random Walk vs. Finite Difference Method
 • Mathematics and Computers in Simulation, Vol. 82, 2012, p. 2022-2032
 • Abstracts of contributions "Modelling 2009", Rožnov pod Radhoštěm, 22.-26.6.2009, p.63
 • Technical Report V-1112, ICS AS CR, Prague, 2010, 17 p.    download

Papáček Š., Štumbauer V., Štys D., Petera K., Matonoha C.
Growth Impact of Hydrodynamic Dispersion in a Couette-Taylor Bioreactor
 • Mathematical and Computer Modelling, Vol. 54, No. 7-8, 2011, p. 1791-1795
 • In: L. Jódar, Instituto de Matemática Multidisciplinar (Ed.), Modelling for addictive behaviour, medicine and engineering, Valencia, 2010, p. 138-142
 • Technical Report V-1113, ICS AS CR, Prague, 2010, 9 p.    download

Lukšan L., Matonoha C., Vlček J.
Primal interior point method for minimization of generalized minimax functions
 • Kybernetika, Vol. 46, No. 4, 2010, p. 697-721
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 14", Dolní Maxov 1.-6.6.2008 (J. Chleboun, P. Přikryl, K. Segeth, T. Vejchodský, eds.), IM AS CR, Prague, 2008, p. 138-149
 • Technical report V-1017, ICS AS CR, Prague, 2007, 25 p.    download
 • Technical Report V-987 (Interior point methods for minimization of composite nonsmooth functions - preliminary version), ICS AS CR, Prague, 2006, 12 p.    download

Lukšan L., Matonoha C., Vlček J.
Primal interior-point method for large sparse minimax optimization
 • Kybernetika, Vol. 45, No. 5, 2009, p. 841-864
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'06", Monínec 16.-20.1.2006, p. 59-62
 • Technical Report V-941, ICS AS CR, Prague, 2005, 34 p.    download

Lukšan L., Matonoha C., Vlček J.
ALGORITHM 896: LSA: Algorithms for large-scale Optimization
 • ACM Transactions on Mathematical Software, Vol. 36, No. 3, 2009, p. 16:1-16:29
 • Technical report V-896, ICS AS CR, Prague, 2004, 41 p.    download

Lukšan L., Matonoha C., Vlček J.
Trust-region interior-point method for large sparse l1 optimization
 • Optimization Methods and Software, Vol. 22, No. 5, 2007, p. 737-753
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 13", Prague 28.-31.5.2006 (Chleboun J., Segeth K., Vejchodský T., eds.), MI AS CR, Prague, 2006, p. 190-195
 • Technical Report V-942, ICS AS CR, Prague, 2005, 22 p.    download

Lukšan L., Matonoha C., Vlček J.
On Lagrange Multipliers of trust region subproblems
 • BIT Numerical Mathematics, Vol. 48, No. 4, 2008, p. 763-768
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 14", Dolní Maxov 1.-6.6.2008 (J. Chleboun, P. Přikryl, K. Segeth, T. Vejchodský, eds.), IM AS CR, Prague, 2008, p. 130-137
 • Book af Abstracts "Applied Linear Algebra in honor of Ivo Marek", Novi Sad 28.-30.5.2008, p.47

Lukšan L., Matonoha C., Vlček J.
Interior point methods for large-scale nonlinear programming
 • Optimization Methods and Software, Vol. 20, No. 4-5, 2005, p. 569-582
 • Technical report V-917, ICS AS CR, Prague, 2004, 17 p.    download

Lukšan L., Matonoha C., Vlček J.
Interior point method for non-linear non-convex optimization
 • Numerical Linear Algebra with Applications, Vol. 11, No. 5-6, 2004, p. 431-453
 • Abstracts of contributions "Modelling 2009", Rožnov pod Radhoštěm, 22.-26.6.2009, p.62
 • Book of Abstracts "Applied and Numerical Linear Algebra", 8th GAMM Workshop, Hamburg, 11.-12.9.2008, p.20

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--- Monographies ---

Lukšan L., Matonoha C., Vlček J.
Numerical Solution of Generalized Minimax Problems
 • Numerical Nonsmooth Optimization. Cham: Springer (A. Bagirov, M. Gaudioso, N. Karmitsa, M. Mäkelä, S. Taheri), 2020, p. 363-414
 • Technical report V-1255, ICS AS CR, Prague, 2018, 49 p.    download

Matonoha C.
Lineární programování a geografické informační systémy
 • in "Metody umělé inteligence v geoinformatice", (V. Voženílek, J. Dvorský, D. Húsek, eds.), Univerzita Palackého, Olomouc, 2011, p. 105-115

Lukšan L., Matonoha C., Vlček J.
Nonsmooth equation method for nonlinear nonconvex optimization
 • in Conjugate Gradient Algorithms and Finite Element Methods, Springer-Verlag, Berlín, 2004, p. 131-145

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--- Proceedings ---

Duintjer Tebbens J., Lanzendörfer M., Matonoha C., Papáček Š.
Preconditioning for the integration of a spatiotemporal pharmacodynamic system
 • Proc. Appl. Math. Mech., Vol. 22, No. 1, 2023, e202200268

Papáček Š., Matonoha C., Duintjer Tebbens J.
Bohl-Marek decomposition applied to a class of biochemical networks with conservation properties
 • Proceedings of the seminar "Seminar on Numerical Analysis & Winter School SNA'23" (J. Starý, S. Sysala, D. Sysalová, eds.), IG CAS Ostrava, 2023, p. 56-59

Papáček Š., Matonoha C.
Testing the method of multiple scales and the averaging principle for model parameter estimation of quasiperiodic two time-scale models
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 21" (J. Chleboun, P. Kůs, J. Papež, M. Rozložník, K. Segeth, J. Šístek, eds.), IM CAS Prague, 2023, p. 163-172

Matonoha C., Moskovka A., Valdman Jan
Minimization of p-Laplacian via the Finite Element Method in MATLAB
 • LSSC 2021: International Conference on Large-Scale Scientific Computations /13./, Sozopol (BG), 7.6.-11.6.2021. Large-Scale Scientific Computing. Cham: Springer, 2022 (Lirkov, I., Margenov, S., eds), p. 533-540, Lecture Notes in Computer Science, 13127.

Kalina J., Matonoha C.
Robustness of Supervised Learning Based on Combined Centroids
 • In: Rutkowski L., Scherer R., Korytkowski M., Pedrycz W., Tadeusiewicz R., Zurada J.M. (eds), Artificial Intelligence and Soft Computing. ICAISC 2021, June 21–23. Lecture Notes in Computer Science, Vol. 12855, Springer, Cham, 2021, p. 171-182

Papáček Š., Matonoha C., Duintjer Tebbens J.
Mathematics and Optimal control theory meet Pharmacy: Towards application of special techniques in modeling, control and optimization of biochemical networks
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'21", Ostrava, 25.-29.1.2021, p. 60-63

Matonoha C., Papáček Š.
On the optimal initial conditions for an inverse problem of model parameter estimation - a complementarity principle
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'19", Ostrava, 21.-25.1.2019, p. 100-103

Matonoha C., Papáček Š., Kindermann S.
Disc vs. Annulus: On the Bleaching Pattern Optimization for FRAP Experiments
 • In: Kozubek T. et al. (Eds.), High Performance Computing in Science and Engineering (May 2017, Soláň), Lecture Notes in Computer Science, Vol. 11087, Springer, Cham, 2018, p. 160-173

Papáček Š., Matonoha C., Petera K.
Modeling and Simulation of Microalgae Growth in a Couette-Taylor Bioreactor
 • In: Kozubek T. et al. (Eds.), High Performance Computing in Science and Engineering (May 2017, Soláň), Lecture Notes in Computer Science, Vol. 11087, Springer, Cham, 2018, p. 174-187

Matonoha C., Papáček Š., Kindermann S.
On the optimization of initial conditions for a model parameter estimation
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 18", Janov nad Nisou 19.-24.6.2016 (J. Chleboun, P. Kůs, P. Přikryl, K. Segeth, J. Šístek, T. Vejchodský, eds.), IM AS CR, Prague, 2017, p. 73-80

Matonoha C., Papáček Š.
On the optimal initial conditions for an inverse problem of model parameter estimation
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'17", Ostrava, 30.1.-3.2.2017, p. 72-75

Matonoha C., Papáček Š.
Parameter identification problem based on FRAP images: From data processing to optimal design of photobleaching experiments
 • In: Kozubek T. et al. (Eds.), High Performance Computing in Science and Engineering (May 2015, Soláň), Lecture Notes in Computer Science, Vol. 9611, 2016, p. 186-195

Papáček Š., Jablonský J., Matonoha C., Kaňa R., Kindermann S.
FRAP & FLIP: Two Sides of the Same Coin?
 • In: F. Ortuno and I. Rojas (Eds.), IWBBIO 2015, Part II, p. 444-455

Matonoha C., Papáček Š.
Synergy between the parameter estimation and a design variable optimization for FRAP experiments
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'15", Ostrava, 19.-23.1.2015, p. 82-85

Papáček Š., Jablonský J., Matonoha C.
On two methods for the parameter estimation problem with spatio-temporal FRAP data
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 17", Dolní Maxov 8.-13.6.2014 (J. Chleboun, P. Přikryl, K. Segeth, J. Šístek, T. Vejchodský, eds.), IM AS CR, Prague, 2015, p. 163-168

Papáček Š., Jablonský J., Petera K., Rehák B., Matonoha C.
Modeling and optimization of microalgae growth in photobioreactors: A multidisciplinary problem
 • Emergence, Complexity and Computation ECC, Vol. 14, "ISCS 2014: Interdisciplinary symposium on complex systems" (Sanayei A., Rössler O.E., Zelinka I. eds.), Springer, 2014, p. 277-286

Matonoha C., Papáček Š.
On three equivalent methods for parameter estimation problem based on spatio-temporal FRAP data
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'14", Nymburk, 27.-31.1.2014, p. 78-82

Papáček Š., Matonoha C.
Error analysis of three methods for the parameter estimation problem based on spatio-temporal FRAP measurement
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'13", Rožnov pod Radhoštěm, 21.-25.1.2013, p. 93-96

Kaňa R., Matonoha C., Papáček Š., Soukup J.
On estimation of diffusion coefficient based on spatio-temporal FRAP images: An inverse ill-posed problem
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 16", Dolní Maxov 3.-8.6.2012 (J. Chleboun, K. Segeth, J. Šístek, T. Vejchodský, eds.), IM AS CR, Prague, 2013, p. 100-111

Matonoha C., Papáček Š.
Analysis of phycobilisomes mobility on thylakoid membrane: Part II. A single parameter estimation problem
 • Proceedings of seminar "Matematika na vysokých školách", Herbertov, 12.-14.9.2011, p. 67-70

Papáček Š., Matonoha C.
Analysis of phycobilisomes mobility on thylakoid membrane: Part I. Reconstruction of diffusion based on spatio-temporal FRAP images
 • Proceedings of seminar "Matematika na vysokých školách", Herbertov, 12.-14.9.2011, p. 63-66

Papáček Š., Štys D., Kaňa R., Matonoha C.
Parameter estimation of reaction-diffusion model based on spatio-temporal FRAP images of thylakoid membranes
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'11", Rožnov pod Radhoštěm, 24.-28.1.2011, p. 92-95

Lukšan L., Matonoha C., Vlček J.
Robust preconditioners for the matrix free truncated Newton method
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 15", Dolní Maxov 6.-11.6.2010 (T. Vejchodský, J. Chleboun, P. Přikryl, K. Segeth, J. Šístek, eds.), IM AS CR, Prague, 2010, p. 137-151

Papáček Š, Matonoha C.
Effect of hydrodynamic mixing on the photosynthetic microorganism growth: Revisited
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'10", Nové Hrady 18.-22.1.2010, p. 114-117

Papáček Š., Štys D., Matonoha C.
An analytical study of the effect of hydrodynamic mixing on the photosynthetic microorganism growth
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'09", Ostrava 2.-6.2.2009, p. 8-10 příloha

Lukšan L., Matonoha C., Vlček J.
Computational experience with modified conjugate gradient methods for unconstrained optimization
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'09", Ostrava 2.-6.2.2009, p. 5-7 příloha
 • Technical Report V-1038, ICS AS CR, Prague, 2008, 19 p.    download

Lukšan L., Matonoha C., Vlček J.
Metody vnitřních bodů pro nekonvexní úlohy nelineárního programování
 • 7. matematický workshop, Brno, 16.10.2008, p. 1-7

Lukšan L., Matonoha C., Vlček J.
Konvergence nelineární metody sdru.ených gradientů
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'08", TU Liberec 28.1.-1.2.2008, p. 94-97

Lukšan L., Matonoha C., Vlček J.
A shifted Steihaug-Toint method for computing a trust-region step
 • Proceedings of Seminar "Seminar on Numerical Analysis SNA'06", Monínec 16.-20.1.2006, p. 63-66
 • Abstracts of International Workshop "Numerical Linear Algebra in Signals and Systems", Monopoli (Bari), 11.-15.9.2006, p.37-41
 • Technical report V-914 ICS AS CR, Prague, 2004, 17 p.    download

Matonoha C.
Nonlinear optimization problem
 • Proceedings of Seminar "Programs and Algorithms of Numerical Mathematics 12", Dolní Maxov 6.-11.6.2004 (Chleboun J., Přikryl P., Segeth K., eds.), MI AS CR, Prague, 2004, p. 162-168

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--- Abstracts ---

Matonoha C., Papáček Š.
Bohl-Marek formulation of the nonlinear system of ODEs for a class of mathematical models with conservation laws
 • Book of abstracts International conference "Olomoucian Days of Applied Mathematics 2023", Olomouc 12.-14.6.2023, p. 51-52

Papáček Š., Matonoha C., Sanchez A.
On the D-QSSA method with optimal constant delays applied to a class of mathematical models
 • Book of abstracts International conference "Olomoucian Days of Applied Mathematics 2023", Olomouc 12.-14.6.2023, p. 58

Duintjer Tebbens J., Lanzendörfer M., Matonoha C., Papáček Š
On an ODE decomposition for biochemical networks due to Erich Bohl and Ivo Marek and its usage for preconditioning in PDE's
 • Abstract for "Seminar on Numerical Analysis & Winter School SNA'23", Ostrava 23.-27.1.2023, p. 9

Papáček Š., Matonoha C., Duintjer Tebbens J.
Computational costs related to Bohl-Marek decomposition applied to a class of biochemical networks
 • Abstract for "Seminar on Numerical Analysis SNA'23", Ostrava 23.-27.1.2023, p. 19

Papáček Š., Matonoha C.
An enhanced model parameter estimation by a slow-fast decomposition based on the first order two time-scale expansion
 • Book of abstracts "Programs and Algorithms of Numerical Mathematics 21", Jablonec n/N 19.-24.6.2022, p. 19

Matonoha C., Moskovka A., Valdman J.
Minimization of energy functionals via the finite element method in MATLAB
 • Book of abstracts 13th International Conference "Large-Scale Scientific Computations LSSC'21", Sozopol, June 7-11, 2021, p. 61-62

Duintjer Tebbens J., Lanzendörfer M., Matonoha C.
Extending a pharmacodynamic model for nuclear receptor-induced enzyme production with spatial resolution
 • Book of abstracts International conference on Mathematical Modelling and Computational Methods in Applied Sciences and Engineering "Modelling 2019", Olomouc, 16.-20.9.2019, p. 147

Lukšan L., Matonoha C., Vlček J.
Interior-point method for nonlinear programming with complementarity constraints
 • Abstracts "SIAM Conference on Optimization", Darmstadt, 16.-19.5.2011, p. 96
 • Abstracts of contributions "2nd IMA Conference on Numerical Linear Algebra and Optimisation", University of Birmingham, 13.-15.9.2010, p. 26
 • Abstracts of contributions "Modelling 2009", Rožnov pod Radhoštěm, 22.-26.6.2009, p. 59-60
 • Technical Report V-1039, ICS AS CR, Prague, 2008, 14 p.    download

Papácek Š., Aguilar J., Petera K., Matonoha C., Štumbauer V., Štys D.
Couette-Taylor photo-bioreactor: Growth impact of radial dispersion and shear stress
 • Abstract for "The 16th Couette-Taylor Workshop", Princeton University, 9.-11.9.2009

Lukšan L., Matonoha C., Vlček J.
Trust-region interior-point method for large sparse optimization
 • Book of Abstracts "13th Czech-French-German Conference on Optimization", Heidelberg, 17.-21.9.2007, p. 109-110
 • Book of Abstracts "Numerical Linear Algebra and Optimisation", Birmingham, 13.-15.9.2007
 • Book of Abstracts "Computational Linear Algebra with Applications", Harrachov, 19.-25.8.2007, p. 65

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--- Reports ---

Lukšan L., Matonoha C., Vlček J.
Hybrid methods for nonlinear least squares problems
 • Technical report V-1246, ICS AS CR, Prague, 2019, 52 p.    download

Lukšan L., Matonoha C., Vlček J.
Problems for Nonlinear Least Squares and Nonlinear Equations
 • Technical report V-1259, ICS AS CR, Prague, 2018, 36 p.    download

Lukšan L., Matonoha C., Vlček J.
Sparse Test Problems for Nonlinear Least Squares
 • Technical report V-1258, ICS AS CR, Prague, 2018, 20 p.    download

Lukšan L., Tůma M., Matonoha C., Vlček J., Ramešová N., Šiška M., Hartman J.
UFO 2017 - Interactive System for Universal Functional Optimization
 • Technical report V-1252, ICS AS CR, Prague, 2017, 395 p.    download

Matonoha C., Papáček Š., Štys D.
Model of Photosynthesis and Photoinhibition in Microalgae: A Singularly Perturbed Problem
 • Technical Report V-1114, ICS AS CR, Prague, 2010, 13 p.    download

Lukšan L., Matonoha C., Vlček J.
Modified CUTE Problems for Sparse Unconstrained Optimization
 • Technical Report V-1081, ICS AS CR, Prague, 2010, 15 p.    download

Lukšan L., Matonoha C., Vlček J.
Band preconditioners for the matrix free truncated Newton method
 • Technical Report V-1079, ICS AS CR, Prague, 2010, 23 p.    download

Lukšan L., Matonoha C., Vlček J.
Sparse Test Problems for Unconstrained Optimization
 • Technical Report V-1064, ICS AS CR, Prague, 2010, 25 p.    download

Lukšan L., Matonoha C., Vlček J.
Subroutines for large-scale nonlinear programming
 • Technical report V-1000, ICS AS CR, Prague, 2007, 12 p.    download

Lukšan L., Matonoha C., Vlček J.
New subroutines for large-scale optimization
 • Technical report V-999, ICS AS CR, Prague, 2007, 57 p.    download

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--- Others ---

Lukšan L., Matonoha C., Vlček J.
UFO 2022
 • software, 2022

Duintjer Tebbens J., Matonoha C.
Fiedler Anniversary Honored
 • Image 37, Fall 2006, p. 7

Matonoha C.
Konference k jubileu
 • Akademický bulletin 9/2006, p. 11

Matonoha C.
Numerická realizace metod s lokálně omezeným krokem
 • Ph.D. Thesis, MFF UK, Prague, 2004    cz download

Matonoha C.
Iterační metody pro obsáhlé řídké soustavy lineárních rovnic
 • Master Thesis, MFF UK, Prague, 1998    cz download

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