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Antimicrobial peptides in infections with grammnegative bacteria.
Tocháčková, Petra ; Jílek, Petr (advisor) ; Andrýs, Ctirad (referee)
Bc. Petra Tocháčková Antimicrobial peptides in infections with grammnegative bacteria Diploma thesis - abstract Charles University in Prague, Faculty of Pharmacy in Hradec Králové Pharmacy Background: Aim of this thesis was a development of methods for detection of gene activation of antimicrobial peptides (beta defensins 1 and 2 - pBD1 and pBD2) in ileum during infection of gnotobiotic piglets with gramnegative bacteria. Salmonella enterica serovar Typhimurium strain LT2 and its R mutants (rfaG- and rfaL-) were selected as representants of gramnegative bacteria of different virulence. Methods: 1) Suggestion of systems for detection of pBD1 and pBD2 (software), 2) Purification of total RNA (commercial columns), quantification (spectrophotometry), and estimation of its purity (ratio A280/A260), 3) Reverse transcription (mixture of random n-mers and oligo d(T)m), 4) Quantification of cDNA (real time polymerase chain reaction - LNA probes), and 5) Normalization of gene transcription for pBD1 and pBD2 against beta actin, cyclophilin A or to both together. Results: We used a method reducing risk of contamination by genomic DNA and obtaining of false positive results for purification of total RNA. We suggested detection systems for estimation of pBD1 and pBD1 with efficiency approx. 100% (comparable with...
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Comparation of Software Process Maturity Level of Enterprises in Czech Republic
Borský, Miroslav ; Král, Josef (referee) ; Richta, Karel (advisor)
There are many software developing companies in the Czech republic. However the quality of their software processes is almost unknown. The thesis provides insight into the maturity level of the software processes and finds a relation between the maturity level and a size of the company. The survey of the maturity level was performed at fifteen companies developing the financial software. Additionally, a bank and a foreign company teams were chosen for a comparison. Collected data were represented in a graphical format and a description was provided. A correlation between a size of a company and the maturity level rating have been detected at five out of eighteen process areas and at two out of four process area groups. A possible explanation for those correlations was offered.
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Social Networks in Management - tools for analysis, application in management
Lucký, Jiří ; Jelínek, Jiří (advisor) ; Voráček, Jan (referee)
Social networks - a description of principles and theoretical background, dynamics and possibilities of their use, particularly in management and marketing; methods for detection of social networks and work with them, the available software tools, the practical application of theoretical knowledge - analysis of specific data structures and social networks subsequent processing with regard to potential applications in management
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Measuring efficiency of software projects
Tomšej, Radek ; Chocholatý, Drahomír (advisor) ; Gála, Libor (referee)
This thesis is aimed to possibilities of measuring of software projects efficiency. This efficiency is measurable by one-dimensional indexes, which are not capable to describe the complexity of software development, or multi-dimensional indexes. Multi-dimensionality gives you possibilities how to detect weak aspects of software project. The first part is dedicated to project characteristics, triple constraint and specifics of software development. The second part describes one-dimensional and multi-dimensional indexes, their advantages and disadvantages, and also work efficiency influences. The main contribution of this thesis is to show practical illustration of using multiple indexes of work efficency and to describe their influential factors.
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Behavior Composition in Component Systems
Adámek, Jiří ; Plášil, František (advisor) ; Černá, Ivana (referee) ; Madelaine, Erik (referee)
In order to formally verify a component application, it is suitable to structure the formal specification of its behavior according to the application architecture. Such an approach eases the maintenance of the specification and allows utilizing efficient verification algorithms that are based on decomposition of the application into several communicating parts. How those parts cooperate is formally described via an operation that is called behavior composition. In this thesis we claim that in current software component systems behavior composition has typically two drawbacks: (1) it lacks support for composition error detection and (2) it does not address the problem of unbounded parallelism specification. While detection of composition errors allows checking design inconsistencies at a design time, unbounded parallelism specification is necessary for precise formal description of reentrant components that are used in practice very often. Therefore we introduce two new concepts - the consent operator and the behavior templates - in order to address both the issues (1) and (2). Our solutions are demonstrated on the SOFA component model [35], behavior protocols [32] are used as a behavior specification language.
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Performance in Software Development Cycle: Regression Benchmarking
Kalibera, Tomáš ; Tůma, Petr (advisor) ; Hauswirth, Matthias (referee) ; Eeckhout, Lieven (referee)
The development cycle of large software is necessarily prone to introducing software errors that are hard to find and fix. Automated regular testing (regression testing) is a popular method used to reduce the cost of finding and fixing functionality errors, but it neglects software performance. The thesis focuses on performance errors, enabling automated detection of performance changes during software development (regression benchmarking). The key investigated problem is non-determinism in computer systems, which causes performance fluctuations. The problem is addressed by a novel benchmarking methodology based on statistical methods. The methodology is evaluated on a large open-source project Mono, detecting daily performance changes since August 2004, and on open-source CORBA implementations omniORB and TAO. The benchmark automation is a complex task in itself. As suggested by experience with compilation of weather forecast model Arpege/Aladin and implementation of component model SOFA, large systems place distinguishing demands on tasks such as automated compilation or execution. Complemented by experience from Mono benchmarking, the thesis proposes an architecture of a generic environment for automated regression benchmarking. The environment is being implemented by master students under supervision of...
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Analysis of oscillations in a traffic-flow problem
Hroch, Michal ; Dolejší, Vít (referee) ; Janovský, Vladimír (advisor)
A traffc model of a roundabout is considered. It can be classi ed as a follow-the-leader model. The solution may not be unique. Apart from a constant velocity solution there may exist particular oscillatory regimes called cycles. They are due to the Hopf bifurcation from the constant velocity solutions. The aim is to reproduce the numerical experiments of [5]: We used di erent continuation software. We observe that not all cycles detected are physical.
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Laboratory diagnostics of micrometastases in breast cancer patients
Mikulová, Veronika ; Zima, Tomáš (advisor) ; Svoboda, Marek (referee) ; Průša, Richard (referee)
Introduction: The presence of circulating tumor cells (CTC) in the peripheral blood has been associated with worse prognosis and early relapse in breast cancer patients. CTC determination in the peripheral blood has been considered as a liquid biopsy. The aim of this project was to analyze the presence of CTC followed by their molecular characterization with the potential use not only as a new biomarker for real-time monitoring of therapy efficacy but also as a suitable tool for patient's stratification and individualization of treatment for breast cancer. Methods: A total of 54 patients with diagnosed early breast cancer were enrolled into a prospective study. Ten millilitres of peripheral blood were sequentially collected to test for the presence and characterization of CTC during the follow-up of patients. CTC isolation and detection was performed by AdnaTest BreastCancer™ (AdnaGen AG, Germany), which is based on the detection of EpCAM, HER2 and MUC1 specific transcripts in enriched CTC- lysates. cDNA from isolated CTC has been further used for newly optimized qPCR assays for breast tumor and therapy resistance associated genes: TOP1, TOP2A, CSTD, ST6GAL, KRT19 and reference gene actin. qPCR results have been analyzed by Genex software (MultiD Analysis). Results: 195 blood samples have been...
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Effect of nutrients deficiencies on root architecture and growth of winter wheat
Rattanapichai, W. ; Klem, Karel
The study of the effects of N, P, K deficiencies on root architecture and growth was tested in phenotyping platform with winter wheat (Bohemia variety). The experiment was arranged with 4 treatments: Complete nutrient, Without N, Without P and Without K. The root were grown on the surface of vertically fixed black filter paper sheets (30x60cm), covered from both sides by black plastic sheets (PVC-P). The system was setup with a micro-irrigation channel in the top of sheets to ensure circulation of hydroponic medium as hydroponic system. Eighteen days after transplanting, we took the root images by the standard RGB digital camera. To evaluate the root architecture parameters the "SmartRoot" software was used. The results showed that nutrient deficiency had effect on root architecture of winter wheat. N deficiency increase in total seminal root and lateral root length and root/shoot ratio, while P deficiency resulted in increase of mean root diameter, total root area when compared to the control. N deficiency also decreased root and shoot dry weight and total leaf area. However, nutrient deficiency slightly decreased lateral density. There was a slight effect of K deficiency on root architecture when compared to the complete nutrient application. The increasing of leaf dry weight was related with the increased of root dry weight.
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