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Limitations of variant consequence predictors
Břicháčková, Kateřina ; Daněček, Petr (advisor) ; Kolář, Michal (referee)
Thanks to numerous large-scale sequencing projects, the number of discovered genomic variants is increasing. The key step in analyzing the variant data is the functional annotation, since it helps researchers and clinicians to categorize, filter and prioritize the variants for further research. This thesis discusses five commonly-used variant consequence predictors, offers advice on how to use them and briefly goes through the algorithms they employ. Moreover, various data formats as well as the human reference genome and different genome annotations are described in the thesis. The correctness of the reference is of great importance as all the predictors rely on it. This thesis highlights some situations in which the results given by different predictors can vary. All the tests were made using the Ensembl gene annotation (release 92) and the GRCh38 reference assembly.
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Hodnocení sběracího vozu STRAUTMANN GIGA VITESSE CFS 440
KOLÁŘ, Michal
This thesis is focused on the evaluation of the slip wagon Strautmann Giga Vitesse in the business of primary agricultural production. Measurements were made at harvest zavadlé forage, luskovinomixed grain and cereal straw. The literary part is focused on the historical development of pick-up cars, the agro-technical requirements, the main parts from which cars of the consist, information about the manufacturer of agricultural equipment company Strautmann and wagons Giga Vitesse. The practical part contains evaluation of the quality of work from the collection of plant matter from the lines after the flush, but also the calculation of individual performance and economic evaluation. The resulting information comes from the values measured at work pick up of the car, such as working times, the amount of unpicked vegetable matter or chop length. The necessary data for the economic evaluation of the car provided by the management of the enterprise Dražovický AGROPOL s.r.o the Resulting values are given in the form of tables or graphically.
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Visual tracking systém pro UAV
KOLÁŘ, Michal
This master thesis deals with the analysis of the current possibilities for object tracking in the image, based on which is designed a procedure for creating a system capable of tracking an object of interest. Part of this work is designing virtual reality for the needs of implementation of the tracking system, which is finally deployed and tested on a real prototype of unmanned vehicle.
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Does the Accrual Anomaly Persist? Evidence from the U.S. Stock Market
Kolář, Michal ; Kočenda, Evžen (advisor) ; Korbel, Václav (referee)
Understanding what drives stock returns is an essential question for investors, financial institutions, and economists. The question is important not only for individuals, but also for the overall economy, as forms of inefficiency such as bubbles can lead to stock market crashes that have a negative impact on the real economy itself. In contrast to the Efficient Markets Hypothesis, which posits that the stock market is efficient at correctly pricing stocks, the accrual anomaly is an example of one of the largest inefficiencies in the equity market. The aim of this thesis is to examine if the accrual anomaly has lessened in recent history. We analyze if the increasing trend of institutional funds trading on accrual mispricing, the increasing presence of cash flow forecasts, or earnings quality could be responsible for mitigating the accrual anomaly effect. A robust MM regression is used to assess the anomaly alleviation. The analysis focuses on the US stock market. We confirm the mitigation of accrual mispricing based on the increase in trading on the accrual anomaly and quality of earnings for the period from 1991 to 2015, but not the growing number of cash flow forecasts.
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Relationship between Stock Returns and Net Income: Evidence from U.S. Market
Kolář, Michal ; Kočenda, Evžen (advisor) ; Krištoufek, Ladislav (referee)
It is important to know if earnings variables influence stock returns. This is important not just for investors who want to know what drives stock returns, but also for the overall economy as stock returns and stock markets are also considered to be significant indicators of its performance. Many studies were conducted in the past but with inconclusive results. The aim of the thesis is to examine the relationship between net income and stock returns using two approaches, namely panel data model and multiple linear regression. We utilize a dataset of companies selected from the S&P500 Index. We also analyse possible heterogeneity in cross section and time. Moreover, we incorporate additional factors which have been proven to have significant explanation power for stock returns. Our findings from the panel data estimation suggest that there is no relationship between scaled net income and stock returns. We find there are random effects present between the companies and three structural breaks in time. Furthermore, we explore the significance of the consumer sentiment index and the percentage change in the book value per share variables in the panel estimation. We do not confirm the debt to equity ratio and the GDP growth news factors in the panel estimation as significant. Results concerning the...
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Molecular modelling in drug development
Kolář, Michal ; Hobza, Pavel (advisor) ; Vondrášek, Jiří (referee) ; Clark, Tim (referee)
Molecular modelling has become a well-established tool for studying biological mole- cules, moreover with the prospect of being useful for drug development. The thesis summarises research on the methodological advances in the treatment of molecular flexibility and intermolecular interactions. Altogether, seven original publications are accompanied by a text which aims to provide a general introduction to the topic as well as to emphasise some consequences of the computer-aided drug design. The molecular flexibility is tackled by a study of a drug-DNA interaction and also by an investigation of small drug molecules in the context of implicit solvent models. The approaches which neglect the conformational freedom are probed and compared with experiment in order to suggest later, how to cope with such a freedom if in- evitable. The noncovalent interactions involving halogen atoms and their importance for drug development are briefly introduced. Finally, a model for a faithful description of halogen bonds in the framework of molecular mechanics is developed and its per- formance and limits are tested by a comparison with benchmark ab initio calculations and experimental data. 1
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Úloha Londonových disperzních sil ve stabilitě struktury DNA: in silico experiment
Kolář, Michal
Author: Michal Kolář The Role of London Dispersion Forces in DNA structure stability: in silico experiment By means of computer simulations the role of the dispersion forces was elucidated. The free energy calculations obtained from the biased molecular dynamics and the simulations of the Dickerson's dodecamer of DNA suggested that the dispersion forces are important for the structure determination. While the overall aggregation of the DNA strands is attributed to the hydrophobic effect of the surrounding water, the particular conformation of the DNA, i.e. double helix, is claimed to be stabilised by London dispersion forces. These conclusions are with agreement with the previous theories. Keywords: dispersion force, DNA, molecular dynamics, hydrophobic effect, free energy Author: Michal Kolář Úloha Londonových disperzních sil ve stabilitě struktury DNA: in silico exper- iment Pomocí metod výpočetní chemie byla vyšetřována úloha disperzních sil ve stabilitě struk- tury DNA. Za účelem určení volné energie asociace bazí nukleových kyselin ve vodném prostředí byly provedeny molekulově dynamické simulace na pozměněné potenciálové hy- perploše a tyto výsledky byly porovnány se simulacemi Dickersonova dodecameru. Dis- perzní energie byla shledána jako důležitá komponenta...
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