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Updating XML data
Mikuš, Tomáš ; Pokorný, Jaroslav (advisor) ; Holubová, Irena (referee)
Updating XML data is very wide area, which must solve a number of difficult problems. From designing language with sufficient expressive power to the XML data repository able to apply the changes. Ways to deal with them are few. From this perspective, is this work very closely dedicated only to the language XQuery. Thus, its extension for updates, for which the candidate recommendation by the W3C were published only recently. Another specialization of this work is to focus only on the XML data stored in the objectrelational database with that repository will enforce the validity of documents to the scheme described in XML Schema. This requirement, combined with the possibility of updating of data in the repository is on the contradictory requirements. In this thesis is designed language based on XQuery language, designed and implemented evaluating of the update queries of the language on the store and a description and implementation of the store in objectrelational database.
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Abilities and importance long-term cultivation embryonic cells from different species of animals
Houdek, Zbyněk ; Vožeh, František (advisor) ; Bártová, Eva (referee) ; Pokorný, Jaroslav (referee)
Embryonic cells inside the blastocyst, which divide and differentiate into cells of all tissues of organism, are called embryonic stem (ES) cells. Using the ES cells for transplantations is one the potential ways in regenerative medicine. The present study deals with two different lines of mouse pluripotent cells: embryonic carcinoma (EC) cells line P19 and ES cells line D3. The in vitro cultivation was performed in basal cultivation medium with fetal bovine serum (FBS) and in addition of leukemia inhibitory factor (LIF) in case of ES cells. The neurodifferentiation was induced by medium without FBS and without LIF in case of ES cells and supported by retinoic acid in case of P19 cells and embryoid bodies cultivation in case of ES cells. Pluripotency and neurodifferentiation of the cells were confirmed by presence of molecular markers of pluripotency and neurodifferentiation in both lines in nondifferentiated and differentiated states. Mouse EC P19 cells were transfected by gene for green fluorescent protein (GFP) and used for transplantation in cerebellum of wild type (WT) and Lurcher (Lc) mutant mice. Nondifferentiated cells (P19) and neuroprogenitors (NPG) derived from these cells were used. The study followed the survival, morphology and localization of the grafts. The survival of both types of GFP...
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Fuzzy database based on an E-R schema
Plachý, Milan ; Pokorný, Jaroslav (advisor) ; Kopecký, Michal (referee)
This text is especialy intended to those who are interested into fuzzy logic and its application in relational databases. It is mainly focused on concept of fuzzyfied relational database and implementation of such database. This text consists of two parts: theoretical aspects of fuzzyfication and implementation part. Selected extension is based on fuzzy E-R model so the requirements of the real world can be better met. This paper also describes existing solutions on different level of fuzzyfication. Part of the work is design and implementation of a simple software for querying over fuzzyfied relational database. This work shoud also serve as a guide for design and implementation of fuzzy database.
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Robot Localization
Obdržálek, David ; Pokorný, Jaroslav (advisor) ; Borovac, Branislav A. (referee) ; Gottscheber, Achim (referee)
Title: Robot Localization Author: RNDr. David Obdržálek Department: Department of Software Engineering Supervisor: Prof. RNDr. Jaroslav Pokorný, CSc., Department of Software Engi- neering Abstract: Localization is one of the most important areas in low-level support for successful robot operations. This work presents several localization methods which have been also used for practical implementation on real robots. Among others, Monte Carlo Localization (MCL) was selected for implementation. It represents very successful method of probability localization in situations when data acquired from the sensors does not fully correspond to the reality. The resulting localization technique was successfully used for localization of several robots. The work also shows how a cheap low-end GPS receiver module can be used for localization on a graph-based map. Keywords: robotics, localization, GPS, Monte Carlo Localization
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Top-k querying over a relational databases: analysis and problems
Čech, Martin ; Pokorný, Jaroslav (advisor) ; Eckhardt, Alan (referee)
Due to increasing capacity of storage devices and speed of computer networks during last years, it is still more required to sort and search data effectively. Query result containing thousands of rows is usually useless and unreadable. In that situation, users may prefer to define constraints and sorting priorities in the query, and see only several top rows from the result. This thesis deals with top-k queries problems, extension of relational algebra by new operators and their implementation in database system. It focuses on optimization of operations join and sort. The thesis includes implementation and comparison of some algorithms in standalone .NET library NRank.
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Methods for effective querying of RDF data
Dokulil, Jiří ; Pokorný, Jaroslav (advisor) ; Svátek, Vojtěch (referee) ; Benczúr, András (referee)
The RDF is one of the basic building blocks of the Semantic Web. It is a low-level data format intended to be used by software developers to create semantic-enabled applications. The ability to place and efficiently evaluate queries is key in this scenario. In this thesis, we approach the problem of RDF querying from three different angles. First, we present an RDF visualization tool, that the developer can use to get an idea about the structure and contents of the data. Second, we have designed extensions of the XQuery language that allow us to give it RDF handling capabilities. The main contribution is introduction of records into the language. Third, to cover query evaluation, we have designed the Bobox parallel framework, which can be used to simplify development of parallel data processing applications. It provides both task and data parallelism.
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Improvements of multistream compression
Unger, Lukáš ; Žemlička, Michal (advisor) ; Pokorný, Jaroslav (referee)
Multistream compression is based on a transformation significantly different from the ones commonly used for data compression. This Master thesis concerns with the use of said method for the compression of text files written in natural language. The main goal of the thesis is to find suitable preprocessing methods for text transformation, which would enable the Multistream compression to achieve better compression ratios, together with searching for the best methods for coding of individual streams. The practical part of the thesis deals with the implementation of several transformation algorithms into the XBW project.
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Conceptual Modeling for XML
Nečaský, Martin ; Pokorný, Jaroslav (advisor) ; Krátký, Michal (referee) ; Thalheim, Bernhardt (referee)
XML is a popular format for data representation. As the amount of data represented in XML grows, it is necessary to concentrate on the process of modeling XML schemes of the XML representations. However, modeling the XML schemes on the level f XML schema languages, such as XML Schema, has some drawbacks. A natural idea to improve this situation is to model the XML schemes rst on the conceptual level. It is motivated by the world of relational databases where we also start modeling the data fi rst on the conceptual level. In this thesis we focus on conceptual modeling for XML. We start with a motivating example to point out to several problems that can arise when using only XML schema languages for modeling XML schemes. We discuss how modeling the data rst on the conceptual level can help. We also show that conceptual modeling for XML has some speci cs that should be taken into account by a conceptual model for XML. Mainly, we show that it is necessary to separate the conceptual modeling process to two parts. First, we need to model the data independently of its representation in XML. Second, we need to model how the data is represented in di erent types of XML documents. In the next step, we analyze in detail existing approaches to conceptual modeling for XML and show their limitations. In the main part of...
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Retinoid regulation of target gene transcription and antitumor activity of retinoid related molecules
Raška, Ivan ; Broulík, Petr (advisor) ; Kostrouch, Zdeněk (referee) ; Pokorný, Jaroslav (referee)
Nuclear Retinoic Acid (RA) Receptors (RARs) activate gene expression through dynamic interactions with coregulators in coordination with the ligand and phosphorylation processes. In the first part of this work, we showed that during RA-dependent activation of the RARq isotype, the pi 60 coactivator pCIP/ACTR/AIВ-1 /RAC-3/TRAM-1 /SRC-3 was phosphorylated by p38MAPK. SRC-3 phosphorylation was correlated to an initial facilitation of RARa-target genes activation, via the control of the dynamics of the interactions of the coactivator with RARa. Then phosphorylation inhibited transcription via promoting the degradation of SRC-3. In line with this, inhibition of p38MAPK markedly enhanced RARa-mediated transcription and RA-dependent induction of cell differentiation. SRC-3 phosphorylation and degradation occurred only within the context of RARa complexes, suggesting that the RAR isotype defined a phosphorylation code through dictating the accessibility of the coactivator to p38MAPK. We proposed a model in which RARa transcriptional activity was regulated by SRC-3 through coordinated events that are fine- tuned by RA and p38MAPK. The retinoid related molecules (RRMs), ST1926 and CD437, are promising anti-cancer agents. In the second part of this work, we compared the RAR trans-activating properties of the two RRMs...
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Cendelín, Jan ; Vožeh, František (advisor) ; Mareš, Jan (referee) ; Pokorný, Jaroslav (referee)
Lurcher mutant mice represent a model of olivocerebellar degeneration. They are heterozygots carrying a mutation in the glutamate receptor 52-subunit gene. The receptor malfunction causes excitotoxic apoptosis of Purkinje cells, extinction of which leads to secondary degeneration of cerebellar granule cells and inferior olive neurons. Lurcher mutants suffer from ataxia and deterioration of spatial learning and orientation ability. The aim of the work was to assess the effect of embryonic cerebellar tissue transplantation and enforced physical activity as well as the effect of their combination on spatial orientation ability in Lurcher mutant mice and to observe cerebellar graft survival in adult and young Lurcher and adult wild type mice. For the graft survival analysis adult wild type mice and young and adult Lurcher B6CBA mice were used. To study the effect of the transplantation and enforced activity on spatial orientation adult and young Lurchers of the same strain were used. The graft obtained from mouse embryos without the Lurcher mutation was applied into the cerebellar area of the host as solid pieces. Control mice were treated only with vehicle. Enforced activity was represented with repeated rotarod training. Spatial orientation was tested in the Morris maze 9 weeks after the surgery. Histological...
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