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Detection of Related Proteins with Modified Function
Hon, Jiří ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Protein engineering is a young dynamic discipline with great amount of potential practical applications. However, its success is primarily based on perfect knowledge and usage of all existing information about protein function and structure. To achieve that, protein engineering is supported by plenty of bioinformatic tools and analysis. The goal of this project is to create a new tool for protein engineering that would enable researchers to identificate related proteins with modified function in still growing biological databases. The tool is designed as an automated workflow of existing bioinformatic analyses that leads to identification of proteins with the same type of enzymatic function, but with slightly modified properties - primarily in terms of selectivity, reaction speed and stability.
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Computational Methods for Annotation Analysis of Genetic Variations
Fülöp, Tibor ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Analýza a interpretace variací DNA je důležité pro zkoumání genetického pozadí dědičnosti, nemocí a jiných fenotypových rysů. Tato práce stručně úvadí oblasti molekulární biologie a základních principů genetiky, popisuje metody pro anotační analýzy genetických variací, genomové asociační studie a metody pro analýzy obohacení s jejich implementací. V rámci této práce jsme představili nový webový nástroj Varanto, který může být použit k anotaci, vizualizaci a analýze genetických variací. Může být použit k analýze obohacení anotací pomocí hypergeometrického testu pro danou množinu variací. Varanto obsahuje uživatelské webové rozhraní vyvinuté pomocí frameworku Shiny jazyka R. Výkon a funkcionalita nástroje jsou testovány a demonstrovány podle výkonových benchmarků a na základě analýzy a interpretace dat z dříve publikovaných genomových asociačních studií.
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Finite element modelling of pathological changes in human vocal folds tissue and their influence on videokymograph
Martínek, Tomáš ; Matug, Michal (referee) ; Švancara, Pavel (advisor)
Master´s thesis deals with creating planar computational model of human folds, involving fluid-structure interaction. With this model, the influence of changes in vocal folds tissue layers (stiffness, thickness) and their effects on the videokymograph image are studied. Analysis of the results also deals with the evaluation of pressure at selected points below, between and above the vocal folds. The results indicate a possible similarity with the behavior of human vocal folds with pathology. Background research of vocal folds function, an overview of vocal folds pathology and summary of computational models are included.
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Sport car suspension
Martínek, Tomáš ; Beran, Martin (referee) ; Zháňal, Lubor (advisor)
This thesis deals with design of front and rear suspension of single-seater sports car. Design and optimization of geometrical parametres of axles is followed after theoretical introduction. Another section is concerned with calculation of the vehicle suspension and design of the steering. The construction of individual components is described in the final section.
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Proposal of a program for solving of problems of simple tension/compression of bars and strut frames
Martínek, Tomáš ; Kubík, Petr (referee) ; Polzer, Stanislav (advisor)
The aim of this work is a program that will solve problems from the simple tension /compression bars and strut frames in the range of bachelor. The work consists of two programs developed in the Borland Delphi development environment. The programs allow the user to define a bar (strut frames) on the basis of the geometrical parameters and constraints, determine the rate of statical indetermination, make the necessary calculations and, if necessary, indicate the condition of deformation (a program for solving bars). The written part of the work serves as a manual.
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Influence of euro on German economy
Martinek, Tomáš ; Pavlík, Zdeněk (advisor) ; Kopecký, Jan (referee)
Abstract Euro, as common currency is one of the biggest and the most ambitious projects in history of monetary integration. The aim of this thesis is to analyze an influence of euro on German economy. In the first part is analyzed history and formation of euro area. It describes the beginning of monetary integration from first thoughts until today. The second part of this thesis is dedicated to analysis. Objects of investigation are macroeconomics indicators. The goal of analysis is to find out if euro influenced German economy and if so, how. The main effort is to evaluate which parts of the economy influenced euro positively and which negatively.
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Podnikatelský plán startup jdinapiknik.cz
Martinek, Tomáš
This bachelor thesis is a suggestion of a business plan for a starting business project. The theoretical part describes all the different parts of the chosen business plan type. On this foundations, the practical part describes the business plan more specifically, defines potential risks of running such a business and gives some suggestions how to minimize the risks. Summing up, the presented business plan is assessed as feasible.
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Numerical simulation of videokymographic images from the results of the finite element model
Švancara, P. ; Horáček, Jaromír ; Martínek, T. ; Švec, J. G.
The study presents a two-dimensional (2D) finite element (FE) model of the fluid-structure-acoustic interaction during flow induced self-oscillation of the human vocal folds. The FE model combines the FE models of the vocal folds, the trachea and the simplified human vocal tract shaped for phonation of vowel [a:]. The fluid-structure interaction is solved using explicit coupling scheme with separated solvers for structure and fluid domain. The developed FE model comprises large deformations of the vocal-fold tissue, vocal-fold contact, fluid-structure interaction, morphing the fluid mesh according to the vocal-fold motion (Arbitrary Lagrangian-Eulerian approach), solution of unsteady viscous compressible airflow described by the Navier-Stokes equations and airflow separation during the glottis closure. The effect of lamina propria thickness and material properties on simulated videokymographic (VKG) images of vocal-fold vibrations are analyzed. Such variation of the lamina propria properties can be caused by certain vocal-fold pathologies such as Reinke's edema. The developed FE model can be used to study relations among pathological changes in vocal folds tissue, the resulting VKG images and the produced sound spectra.
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