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ECG Wave Delineation
Trnová, Kateřina ; Provazník, Ivo (referee) ; Kozumplík, Jiří (advisor)
This thesis deals with the detailed measurement one cycle of the ECG signal from the known beginning and end of each major wave of this cycle of the values listed in the database TESPRO. Another objective of this work is to find a representative cycle. The text describes the basic types of measurement intervals, principles of multiple methods of measurement and description of the program, which was implemented. Algorithm for Measurement of function-al units cycle of ECG signal, which was designed based on the detection of trend growth in the field of signal using first differences. Functionality was tested on a standard database CSE.
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Determination of genetic differences of biological DNA sequences
Sliž, Ladislav ; Škutková, Helena (referee) ; Provazník, Ivo (advisor)
Work on determining the genetic diversity of biological signal aligning DNA sequences, will address a brief description of the composition of DNA. Following is basic information on the bioinformatics analysis. Then the work will describe the possibility of aligning DNA sequences. Work will focus primarily on global Needleman-Wunsch algorithm and local Smit - Watermanovův algorithm. Furthermore, this work will focus on aligning DNA sequences using methods CGR and FCGR. At the end of the work will describe the practical application of identifying genetic differences by aligning the sequences.
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Transcriptomic Characterization Using RNA-Seq Data Analysis
Abo Khayal, Layal ; Babula, Petr (referee) ; Lexa,, Matej (referee) ; Provazník, Ivo (advisor)
Vysoce výkonné sekvenční technologie produkují obrovské množství dat, která mohou odhalit nové geny, identifikovat splice varianty a kvantifikovat genovou expresi v celém genomu. Objem a složitost dat z RNA-seq experimentů vyžadují škálovatelné metody matematické analýzy založené na robustníchstatistických modelech. Je náročné navrhnout integrované pracovní postupy, které zahrnují různé postupy analýzy. Konkrétně jsou to srovnávací testy transkriptů, které jsou komplikovány několika zdroji variability měření a představují řadu statistických problémů. V tomto výzkumu byla sestavena integrovaná transkripční profilová pipeline k produkci nových reprodukovatelných kódů pro získání biologicky interpretovovatelných výsledků. Počínaje anotací údajů RNA-seq a hodnocení kvality je navržen soubor kódů, který slouží pro vizualizaci hodnocení kvality, potřebné pro zajištění RNA-Seq experimentu s analýzou dat. Dále je provedena komplexní diferenciální analýza genových expresí, která poskytuje popisné metody pro testované RNA-Seq data. Pro implementaci analýzy alternativního sestřihu a diferenciálních exonů jsme zlepšili výkon DEXSeq definováním otevřeného čtecího rámce exonového regionu, který se používá alternativně. Dále je popsána nová metodologie pro analýzu diferenciálně exprimované dlouhé nekódující RNA nalezením funkční korelace této RNA se sousedícími diferenciálně exprimovanými geny kódujícími proteiny. Takto je získán jasnější pohled na regulační mechanismus a poskytnuta hypotéza o úloze dlouhé nekódující RNA v regulaci genové exprese.
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3D Printing of Ceramic Bone Grafts with Different Internal Architecture
Novotná, Lenka ; Sekora, Jiří (referee) ; Provazník, Ivo (advisor)
Bioceramics in the form of scaffolds hold great promise in bone tissue regeneration. While the scaffold composition is important for biocompatibility, the internal architecture plays a key role in allowing proper cell penetration, nutrient diffusion, bone ingrowth, vascularization as well as mechanical properties. A solid freeform fabrication is a promising processing technique, allowing to study structural parameters independently. This bachelor thesis is focused on ceramic bone replacements with different internal structure. The thesis is divided into 8 chapters. The first four chapters briefly summarize the current state of the art in the following fields: bone structure, requirements for synthetic bone replacements, scaffold architecture, and fabrication methods with an emphasis on 3D printing. The next chapters deal with experimental part. The image analysis of mouse skeleton was performed. On the basis of the measured pore size (50 200 m) and according to the literature search, 16 structures with various shape, curvature and pore size were designed. The CAD models were printed by a stereolithography from a tricalcium phosphate dispersion. Sintered ceramic scaffolds exhibited an ideal structure for application in bone tissue engineering. Scaffolds contained both interconnected macro- and micropores of optimal sizes up to 500 m and about 3 m, respectively. The results confirm that stereolithography is suitable, and compared to others, precise method for preparing scaffolds having different internal structures. The individual structural characteristics influencing the scaffold behaviour will be possible to study independently to each other. And thus improve the scientific knowledge in the field of treatment of large segmental bone defects.
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Bipartite graphs for microbiome analysis
Šafárová, Marcela ; Provazník, Ivo (referee) ; Sedlář, Karel (advisor)
Microorganisms are all around us. Some of them even live in our body and are essential for our healthy being. Study of microbial communities based on their genetic content has become very popular with the development of new technologies, which enable easy reading of DNA or RNA. The key role of these studies is usually to characterize significant microbial patterns of an environment. However, currently used visualization tools have many drawbacks for such analyses. The subject of this thesis is to design a R/Bioconductor package for simple creation of bipartite graphs from microbial data. This type of visualization brings many advantages for microbiome analysis. Benefits of bipartite graphs are further demonstrated by analysis of main parameters affecting computer processing of microbial data.
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Security of Biometric Systems
Lodrová, Dana ; Busch, Christoph (referee) ; Provazník, Ivo (referee) ; Drahanský, Martin (advisor)
Hlavním přínosem této práce jsou dva nové přístupy pro zvýšení bezpečnosti biometrických systémů založených na rozpoznávání podle otisků prstů. První přístup je z oblasti testování živosti a znemožňuje použití různých typů falešných otisků prstů a jiných metod oklamání senzoru v průběhu procesu snímání otisků. Tento patentovaný přístup je založen na změně barvy a šířky papilárních linií vlivem přitlačení prstu na skleněný podklad. Výsledná jednotka pro testování živosti může být integrována do optických senzorů. Druhý přístup je z oblasti standardizace a zvyšuje bezpečnost a interoperabilitu procesů extrakce markantů a porovnání. Pro tyto účely jsem vytvořila metodologii, která stanovuje míry sémantické shody pro extraktory markantů otisků prstů. Markanty nalezené testovanými extraktory jsou porovnávány oproti Ground-Truth markantům získaným pomocí shlukování dat poskytnutých daktyloskopickými experty. Tato navrhovaná metodologie je zahrnuta v navrhovaném dodatku k normě ISO/IEC 29109-2 (Amd. 2 WD4).
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Optical Measurement of Electromechanical Characteristics of Heart Cells
Čmiel, Vratislav ; Križanová,, Olga (referee) ; Babula, Petr (referee) ; Provazník, Ivo (advisor)
Dissertation is focused on the application of optical measurement methods using techniques of optical microscopy and fluorescence microscopy in measurements of electromechanical characteristics of isolated cardiac cells and clusters of differentiated cardiomyocytes. The first proposed method uses a practical combination of fluorescence microscopy equipped with fluorescent fast and high-resolution camera and atomic force microscopy for simultaneous measurement of calcium transients and contraction of cardiomyocyte clusters. The signals obtained undergoes filtration, processing and analysis. Result function parameters obtained by analyzing signals after application of caffeine are evaluated by comparison with functional parameters obtained during the control measurement. The second proposed method is applied to the cardiomyocyte clusters for the purpose of cardiomyocyte contraction signals measurement. The signals obtained by optical methods are analyzed and compared with the reference signal obtained using atomic force microscopy. Optical measurement method of cell contractins based on detection of cell ends using adjusting of microscopy images by re-sharpening and fluorescence method for cardiomyocyte contractions measurements were designed to increase realiability in simultaneous measurement of cell contractions simultaneously with calcium transients in isolated cardiomyocytes experiments.
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Comparative study of body temperature measurement using various technologies
Vaněk, Ondřej ; Sekora, Jiří (referee) ; Provazník, Ivo (advisor)
The aim of this work is to compare the body temperature measurement with different contact thermometers. The theoretical part includes studying the topic, familiarization with the situation at the Faculty Hospital Brno, Bohunice and suggestion of method for comparison. The practical part includes thermometers measurement in the laboratory to verify the accuracy, clinical measurement on patients in different parts of the body and under various conditions and statistical evaluation of results.
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Effects of trypsin to HEK293 cell membrane
Lipnická, Soňa ; Provazník, Ivo (referee) ; Čmiel, Vratislav (advisor)
This Bachelor’s thesis examines the effect of trypsin on the membranes of cell cultures. HEK293 cell lines nontransfected and cell lines stably transfected through the CaV3.1 membrane channels were selected for the optimization. They were gradually exposed to 0.25, 0.375 and 0.5 % trypsin. The concentration of trypsin influences the separation of the adherent cells on structure, as well as the degradation of cell membranes, which influences the cell cultures viability. Part of this thesis is an attempt to establish a methodology for the research of the effect of trypsin on membranes of HEK293 cell lines.
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Accuracy of body temperature measurement using infrared technologies
Mezera, Jiří ; Chmelař, Milan (referee) ; Provazník, Ivo (advisor)
This thesis deals with the measurement of body temperature using the infrared thermometers. The literature research is devoted to the description of the human body temperature, methods of its measurement and types of thermometers. The theoretical part further examines the infrared radiation, the principles of measurement, physical quantities, laws of infrared radiation, types of detectors and measurement uncertainties. The practical part focuses on experimental measurements with selected kinds of thermometers and verifying their accuracy. Finally, an experimental procedure has been designed which has then been used for the clinical measurements of body temperature under various conditions and their subsequent statistical evaluation.
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