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Process Control with Dynamic Resource Scheduling
Šinkora, Jan ; Kočí, Radek (referee) ; Janoušek, Vladimír (advisor)
This project pursues issues on the border of information technologies and process optimization. Previously published concepts of~modeling projects and shared resources with object-oriented Petri nets are presented and further expanded. The possibilites of~the use of~genetic algorithms for dynamic realtime optimization of the resource schedules are explored. The resource constrained project sheduling problem is presented and it is shown, how instances of the problem can be implemented. A more complex model that is inspired by real production systems is then created. Next, a control agent, which monitors a running production system and allows for it's dynamic optimization is designed. The whole system is implemented in the Squeak Smalltalk environment with the use of the tool PNtalk, which is an experimental implementation of the object oriented Petri nets paradigm.
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Attributes Calculation for Prediction of Mutation Effect on Protein Function
Šinkora, Jan ; Filák, Jakub (referee) ; Jaša, Petr (advisor)
This thesis deals with issues of bioinformatics, machine learning, algorithms and data structures. The thesis is based on existing applications, Caver and Deleterious, developed by students from the Faculty of Informatics, Masaryk University and the Faculty of Information Technology, Brno University of Technology. The Deleterious framework calculates protein attributes that are important for the prediction of the effect of protein mutations on its function. Caver is a tool that finds tunnels in the 3-dimensional model of a protein. The goal of the thesis is to extend these applications by adding more attributes to the prediction process that could lead to improved prediction. The added attributes are related to detection and measurement of protein pockets.
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Modern mathematical methods in the research of immune reconstitutions and immunodeficiencies
Stuchlý, Jan ; Kalina, Tomáš (advisor) ; Šinkora, Jiří (referee) ; Štěpánek, Ondřej (referee)
In this thesis we present new analytical and integrative approaches for broad spectrum of applications of flow cytometry. CVID Large (88 individuals) cohort of CVID patients was immunopheno- typed by flow cytometry. The "probability binning" algorithm was used to au- tomatically assess the immunophenotype which presented unprecedented stabi- lity. We were able to define sub-group of CVID patients with highly activated immunophenotype showing hallmarks of immunosenescence and common clinical characteristics (thrombocytopenia, lung fibrosis and bronchiectasis). The severity of clinical complications correlated quantitatively with the immunophenotype. Analysis of cellular proteome We have designed technics which allow for highly multiplexed (>1000 of antibodies) analysis of human proteome using af- finity proteomics. We analyzed the changes of proteome of human cell lines and characterized the proteome of acute leukemias. The yet undescribed stability of proteome with respect the sub-cellular localization is shown and theoretical and practical background for antibody standardization and validation for the use in a nity proteomics is presented. Topological analysis of cytometry data Multiparametric flow cytometry allows for description of complex topological relationships of the cells in di erent stages of...
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Attributes Calculation for Prediction of Mutation Effect on Protein Function
Šinkora, Jan ; Filák, Jakub (referee) ; Jaša, Petr (advisor)
This thesis deals with issues of bioinformatics, machine learning, algorithms and data structures. The thesis is based on existing applications, Caver and Deleterious, developed by students from the Faculty of Informatics, Masaryk University and the Faculty of Information Technology, Brno University of Technology. The Deleterious framework calculates protein attributes that are important for the prediction of the effect of protein mutations on its function. Caver is a tool that finds tunnels in the 3-dimensional model of a protein. The goal of the thesis is to extend these applications by adding more attributes to the prediction process that could lead to improved prediction. The added attributes are related to detection and measurement of protein pockets.
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Process Control with Dynamic Resource Scheduling
Šinkora, Jan ; Kočí, Radek (referee) ; Janoušek, Vladimír (advisor)
This project pursues issues on the border of information technologies and process optimization. Previously published concepts of~modeling projects and shared resources with object-oriented Petri nets are presented and further expanded. The possibilites of~the use of~genetic algorithms for dynamic realtime optimization of the resource schedules are explored. The resource constrained project sheduling problem is presented and it is shown, how instances of the problem can be implemented. A more complex model that is inspired by real production systems is then created. Next, a control agent, which monitors a running production system and allows for it's dynamic optimization is designed. The whole system is implemented in the Squeak Smalltalk environment with the use of the tool PNtalk, which is an experimental implementation of the object oriented Petri nets paradigm.
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Prenatal deverlopment of the intestinal and extraintestinal T cell receptor repertoire: identical, dominant TCRDV3 transcripts are present in different fetal piglets
Holrmeier, W. ; Geisel, W. ; Bernert, K. ; Butler, J. ; Šinkora, Marek ; Šinkora, Jiří ; Caspary, W. F.
Specimens from the small andf large intestine, spleen, thymus, liver, bone marrow and PBMC were obtained from fetal piglets between 38 and 114 days of gestation.
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