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Posttranslational modifications and structural alterations of protein synthesis elongation factor Tu in Actinomyces in relation to their life cycle
Holub, Martin
Posttranslational modifications and structural alterations of protein synthesis elongation factor Tu in Actinomyces in relation to their life cycle Protein synthesis elongation factor Tu represents a multifunctional protein with potential role in signaling and regulation of cell metabolism. The complex life cycle of Streptomycetes requires monitoring of changes in their environment and signaling pathways to control it. Here we present the results of analysis of membrane phosphoproteomes from individual morphological stages of Streptomyces coelicolor with the aim to follow developmentally dependent heterogeneity and phosphorylation of intrinsic and externally added Strepomyces aureofaciens EF-Tu in membrane proteomes. We used Mycobacterium smegmatis, fast growing non-pathogenic Mycobacterium, as a non-differentiating actinomycete comparative model. Phosphorylation of intrinsic M. smegmatis and externally added Streptomyces EF-Tu was followed in membrane proteomes from exponential and stationary phase of M. smegmatis liquid culture. We have found that Streptomycetes membrane fraction contains protein kinase(s) catalyzing phosphorylation of both, its own, and an externally added EF-Tu, whereas Mycobacterium membrane fraction contains protein kinase phosphorylating only its own EF-Tu. In vitro phosphorylation...
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Syntax in methods for information retrieval
Kravalová, Jana ; Holub, Martin (referee) ; Pecina, Pavel (advisor)
In the last years, application of language modeling in information retrieval has been studied quite extensively. Although language models of any type can be used with this approach, only traditional n-gram models based on surface word order have been employed and described in published experiments (often only unigram language models). The goal of this thesis is to design, implement, and evaluate (on Czech data) a method which would extend a language model with syntactic information, automatically obtained from documents and queries. We attempt to incorporate syntactic information into language models and experimentally compare this approach with unigram and bigram model based on surface word order. We also empirically compare methods for smoothing, stemming and lemmatization, effectiveness of using stopwords and pseudo relevance feedback. We perform a detailed analysis of these retrieval methods and describe their performance in detail.
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Universal Full-Text Index
Švantner, Marek ; Skopal, Tomáš (referee) ; Holub, Martin (advisor)
This diploma thesis deals with the design and implementation of a highly efficient universal index of textual documents. Universal stands for an opportunity to configure structures of index records and methods of the index data processing (without recompiling an application). Furthermore, it means that the index library can be used even for other purposes, for example to implement a thesaurus, to represent bibliographic relationships or even for generic representation of a specific class of functions in other areas than documentographic systems. The index is implemented using the dynamic inverted file which can be efficiently updated without need of the data structure rebuilding. Specific issue is on-line index compression and failure recovery via the transactional log. It is shown that the amortized complexity of the data structure is linear. This fact is afterwards experimentally verified. Other experiments address the compression methods and the impact of the data structure parameters on its efficiency. The diploma thesis contains the implementation of the universal index in C/C++. It has been tested in the Linux and Windows XP environments.
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Clusters of closely related documents
Diviš, Jiří ; Húsek, Dušan (referee) ; Holub, Martin (advisor)
This thesis focuses on automatic searching for clusters of topically similar texts in large text collection. We introduce an algorithm for nding the clusters and a method of optimizing its parameters using machine learning techniques. The algorithm is implemented and experimentaly evaluated. For evaluation we use a manually annotated collection of Czech documents, which contains a set of sample clusters chosen and tagged by a human annotator, and a huge collection of newspaper arcticles. Experiments show that the output of our algorithm ful ls our expectation and gives clusters of topically similar texts.
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Testing of Distance Protection
Holub, Martin ; Vaculík, Petr (referee) ; Orságová, Jaroslava (advisor)
Bachelor thesis Testing of Distance Protection introduces us to the issue of distance protection and its detailed principle. It deals with its individual elements and shows us different types of impedance characteristics of measuring elements. It describes a situation that occurs during a short circuit on a homogeneous line, then introduces us to a DC component compensation and discuss the effect of distance protection degrees. Among other things, it deals with the digital distance protections and settings of their characteristics. Finally the theoretical part evaluates advantages over other protections and advantages and disadvantages of distance protections themselves. Thesis will introduce the digital distance protection REL 511 from the company ABB and characterizes its settings, parameters and connection to the testing equipment OMICRON CMC 256plus, which is used to control the protection via personal computer. Description of the programs OMICRON Test Universe and CAP 540 and their settings follows. This section can serve as a manual for future operators of REL 511 protection. The work provides a suitable methodology for measuring the operating characteristics and uses this method in practice. Given the limited version of the OMICRON Test Universe, polygonal tripping characteristics are measured in the module "Distance" with the shot test. Evaluation of measurements is summarized at the end.
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Cavitation in microfluidics
Holub, Martin ; Kozák, Jiří (referee) ; Rudolf, Pavel (advisor)
Mikrofluidice byla v posledních letech věnována intenzivní pozornost výzkumnými týmy takřka po celém světě. Její možné aplikace jsou velmi početné, zejména pak v oblasti zdravotnictví, ukládání energie do baterií nebo chlazení vysoce výkonných počítačů. Bakalářská práce „Kavitace v mikrofluidice“ se zabývá kavitací na mikro-měřítku. Nedávný výzkum ukazuje, že mnohé charakteristiky kavitujícího proudění na takto malých rozměrech se podstatně liší oproti charakteristikám pozorovaným na konvenčních makro-rozměrech. Toto podtrhuje relevantnost této práce. Lepší pochopení tohoto jevu může být využito například k řešení jednoho ze značných úskalí mikrofluidiky a to sice mísení tekutin, nebo dále také k jejich pumpování. Mezi další možné aplikace se řadí mechanické namáhání a rozklad mikroorganismů a buněk, katalýza chemických reakcí a cílená doprava léčiv. První část této práce je věnována postupně základům z oblasti mechaniky tekutin a chemie kavitace. Tato část je následována stručným přehledem aplikací kavitace a to jak na měřítkách tradičních, tak na měřítkách v řádech mikrometrů. Poté je uveden popis numerického řešení kavitujícího proudění spolu s analýzou a ověřením získaných výsledků. Mezi výsledky je například popis rozložení fází, informace o tom, kde dochází k recirkulaci a také přehled vlivu změny kavitačního čísla na tvar a charakteristiky proudění. V závěrečné části práce je pak na základě získaných znalostí navržen experiment, který umožní dále studovat tuto problematiku a poslouží také k vyhodnocení vhodnosti laminárního modelu. Tato bakalářská práce slouží jako základní kámen pro další výzkum v této oblasti plánovaný na Vysokém učením technickém v Brně, a z tohoto důvodu jsou v textu uvedena doporučení pro další práci.
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Testing of Directional Earth Fault Protections Using The Experimentally Obtained Fault Records
Holub, Martin ; Topolánek, David (referee) ; Orságová, Jaroslava (advisor)
Master thesis Testing of Directional Earth Fault Protections Using the Experimentally Obtained Fault Records deals with the protective functions of earth fault protections during earth faults in compensated medium voltage distribution network and their testing options. At the beginning of the thesis we charakterize operation of medium voltage distribution system in general. We begin with definition and characteristics of earth fault and its compartmentalization by the type of the fault, size of the transition resistance and duration. We also mention grounding methods of node winding transformer on medium voltage distribution network and we describe the most common of them in detail, i.e. network grouded through the arc suppression coil and its operation with automatic switching auxiliary resistor. In this part of the thesis we discuss the localization of the earth fault using passive static methods in compensated systems, which include wattmetric, admittance and conductance method. In next section we deal with the fault records stored in COMTRADE file format, its structure and all elements of its configuration and data file. We create and describe an example of converting ADF file format, recorded by Yokogawa oscilloscope fault recorder, into COMTRADE file format using Microsoft Excel program and M-File created in the MATLAB program. In the practical part we introduce workspace devices and software, which includes secondary testing equipment OMICRON CMC 256plus and its software OMICRON Test Universe with Advance Transplay test module, we further describe multifunctional earth fault protection RYo from PROTECTION & CONSULTING, s. r. o. and machine terminal REM 543 from ABB and their protective functions. The last part describes the actual testing of parallel connected earth fault protection with COMTRADE fault records by Advance Transplay test module in the OMICRON Test Universe. In the conclusion we describe evaluation of the suitability of each protective functions of earth fault protection in a variety of sizes the transition resistance at the earth fault location.
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Data Standard of the Health Information Systems
Holub, Martin ; Dvořák, Miroslav (referee) ; Fedra, Petr (advisor)
The diploma thesis "Data Standard of the Health Information Systems" deals with the structure of data standard including XML language. Further the thesis is focusing on hospital information system CLINICOM with the inclusion of the access to data records from its database Caché company InterSystems. Description of the National registers of health is also included.The concept of web application is also one part of the thesis which enables to generate reports in the data standard of the Ministry of Healt of the Czech Republic for mandatory reporting by NHIS registers in the time interval from the Caché database. Found records from the database can be printed for archiving. The work also deals with security access to the HIS server and data communication between health organizations.
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Data standard of the Ministry of Health of the Czech Republic
Holub, Martin ; Roleček, Jiří (referee) ; Fedra, Petr (advisor)
Diploma thesis "Data standard of the Ministry of Health" deals with the structure of data standard including XML language. Further the thesis is focusing on hospital information system CLINICOM with the inclusion of the access to data records from its database Caché company InterSystems. The concept of web application is also one part of the thesis which enables to find out records with selective diagnosis from Caché database and their depictions in data standard of the Ministry of Health of the Czech Republic.
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