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Efficient representation of k-mer sets
Milyutina, Ekaterina ; Veselý, Pavel (advisor) ; Kolman, Petr (referee)
In this thesis we explore and compare various methods for efficient k-mer set representation. We evaluate traditional de Bruijn graph representation techniques against greedy approximation algorithms for the Shortest Superstring Problem. We describe the linear- time implementation of the well-known Greedy algorithm by Ukkonen [1990] and extend it to another related algorithm, called TGreedy. In addition, we test selected algorithms on a bacterial genome and pangenome to highlight the differences in the size of their output representation and the computational resources used, providing an insight into their respective efficiencies.
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Znalosti žáků vybrané střední odborné školy z oblasti první pomoci
Veselý, Pavel
The aim of this thesis is to gain the information about the first aid theoretical knowledge of the students of Secondary Technical and Secondary Vocational School of André Citroën in Boskovice within the context of the study programme Driving the Motor Vehicles. The thesis consists of theoretical and practical part. The theoretical part is compiled based on the literature using methods of compilation, description, analysis and synthesis. The practical part is focused on the research implemented in Secondary Technical and Secondary Vocational School of André Citroën in Boskovice. The research method applied is the didactic test designed for the 3rd year students. In the conclusion of this thesis, the students' knowledge in the first aid treatment is eva-luated and the recommendation for the future pedagogy is suggested.
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Study of the effect of migrastatics on the dynamics of tumour cell migration using a coherence-controlled holographic microscope
Muchová, Nikola ; Netíková,, Irena Štenglová (referee) ; Veselý, Pavel (advisor)
The thesis is focused on the exploitation of the coherence controlled holographic microscopy for the investigation of the influence of the supposed migrastatic drugs on the dynamics of cancer cell migration. The theoretical part briefly describes the history of holographic microscopy and the development of the holographic microscope at the Brno University of Technology in collaboration with Telight, Brno, including an insight into the design and principle of operation of the coherence-controlled holographic microscope. Next a brief description of current cancer treatments introduces new class of anti-cancer drug candidates designated migrastatics that should impair cancer cell migration and thus prevent late metastases formation. The main part of the thesis deals with the design of the experimental observation procedure and data processing using the holographic incoherent Quantitative Phase Imaging technique. The last part of the thesis is the subsequent analysis of the migrastatic effect of the selected drugs on cancer cells in vitro and the comparison of the obtained results with existing studies. Finally, the objectives with magnification 4x and 10x were evaluated and compared for starting “the Rapid Assessment of Cell Growth and Migration”.
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Identification of changes in the behaviour of tumour cells in low concentrations of migrastatics by coherence-controlled holographic microscope
Zábranská, Magdaléna ; Netíková,, Irena Štenglová (referee) ; Veselý, Pavel (advisor)
The subject of the diploma thesis was using of Coherence-Controlled Holographic Microscope in the research of the effect of migrastatics at different concentrations on tumor cells and the interpretation of quantitative phase imaging data. The theoretical introduction is divided into two parts. The first part is devoted to CCHM, which briefly describes the history of holographic microscopy, the principle and a detailed description of the main parts of the microscope. The second part is an introduction to the issue of cancer treatment and the introduction of migrastatic drugs. The experimental part of the work is the analysis of the influence of migrastatics on two tumor lines (H1299 and HT1080) from the measured time-lapse records taken by a holographic microscope. The effect of drugs was evaluated using characteristics describing morphological and dynamic cell changes in the SophiQ software. The data were then graphically and statistically processed to compare and evaluate the effect of migrastatics at low levels. In conclusion of the work, the findings were summarized and selected characteristics were proposed to analyze the impact of migrastatics.
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Analysis of changes in the phenotype of tumour cells induced by migrastatics in quantitative phase imaging
Kolínková, Veronika ; Netíková,, Irena Štenglová (referee) ; Veselý, Pavel (advisor)
This thesis focuses on the observation of living cells using the non-invasive methods of quantitative phase imaging (hiQPI). The imaging is enabled by a coherence-controlled holographic microscope (CCHM) developed in the Laboratory of Experimental Biophotonics at the VUT. Using this imaging technology, morphological changes of A549 and MCF7 after application of potential migrastatic drugs tumor cells are evaluated in the experimental part of the thesis. Migrastatics are defined as already approved drugs that could prevent the migration of cancer cells from the primary tumor and thus prevent metastasis. The RAC-GM (Rapid Assessment of Cell Growth and Migration in Vitro) method was chosen to assess their effect on tumor cells.
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Molecular basis of fluoropyrimidine toxic effect etiology with focus on palmar-plantar erythrodysesthesia and potential antidote use
Hartinger, Jan ; Veselý, Pavel (advisor) ; Květina, Jaroslav (referee) ; Brábek, Jan (referee)
(thesis): Palmar-plantar erythrodysesthesia (PPE) frequently accompanies the therapy with a continuous 5-FU infusion or peroral capecitabine (5-FU prodrug). In the most severe cases this adverse effect leads to discontinuation of a needful therapy. Local 10 % uridine ointment is used to prevent and treat the said adverse event. Nevertheless, this method is not generally accepted as an effective one because it has never been proved in a randomized controlled clinical trial. Most probably, a direct effect of a cytostatic compound on the skin of hands and foots causes PPE. The toxicity of 5-FU is mediated primarily by its incorporation into RNA and by thymidylate synthase (TS) inhibition and subsequent DNA synthesis disruption. The importance of particular 5-FU toxicity mechanisms varies in different cell types. For choosing the best PPE local antidote it is necessary to find out which molecular mechanism applies in keratinocytes. We have chosen pyrimidine nucleosides as the most suitable compounds for the local PPE therapy because the uridine ointment is already being used in several oncology centers in the Central Europe. In order to find out the 5-FU toxicity mechanism, we further tested the effect of calciumfolinate (CF) which strengthens the TS inhibition by 5-FU. We studied also uracil and...
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Artificial intelligence in abstract 2-player games
Veselý, Pavel ; Valla, Tomáš (advisor) ; Baudiš, Petr (referee)
In this thesis we focus on algorithms for searching for the best move in a given position in an abstract strategy 2-player game. We describe algorithms Alpha-beta and Proof-number Search with their enhancements and we come with new ideas for making them quicker. We also propose an algorithm for choosing randomly between moves not much worse than the best move and ideas how to play in lost positions. We apply the algorithms on the game Tzaar which is special for having a lot of possible moves which makes the game hard for a computer. Our goal is to create a robot for playing Tzaar as good as possible. We show that our artificial intelligence can play on the level of best human and computer players. We also examine experimentally how enhancements of the algorithms help making computations quicker in this game.
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Biological diversity of breast carcinoma cells in relation to the sensitivity on the antitumor treatment
Netíková, Irena ; Veselý, Pavel (advisor) ; Květina, Jaroslav (referee) ; Abrahámová, Jitka (referee)
Biological diversity of cancer cells isolated from breast carcinoma samples has been studied by in vitro exposure to cytotoxic agents. Primary cells from individual primary breast tumours and malignant effusions were in the first phase of the study used for experimental assessment of chemosensitivity/resistance using the standard MTT assay. Cytotoxic effects after short-term cultivation with antineoplastic drugs were evaluated. In several approachable cases relation to the clinical course of the disease was followed; in 4 out of 7 cases good correlation was found. The effect of combination of two cytotoxic drugs on cell viability was studied on EM-G3 cells, showing interesting results with some drug combinations (e.g. combination of paclitaxel and cisplatin resulted in a lower effect than cisplatin alone). Possibility of cell chemosensitisation by tamoxifen pretreatment was tested. Very low chemosensitisation effects of tamoxifen were observed. As a model cell population for diversification development study a new clonal cell line, EM-G3, was established. The EM-G3 line was derived from a primary lesion of human infiltrating ductal breast carcinoma. The EM-G3 represents a unique, spontaneously immortalized clonal cell line, evidently derived from premalignant progenitors of breast carcinoma. The cells are...
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