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Test benches for microcontroller kits
Žaludek, Ivo ; Arm, Jakub ; Bradáč, Zdeněk
This paper deals with the design of a test bench for modules used in educational labs. The first section outlines the requirements for the tester, followed by a description of the printed circuit board design process. Implementation details of the software are then examined, including a graphical user interface based on Model-View-Controller (MVC) architecture that allows for easy result printing. The obtained results are presented, and further work is discussed.
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Comparison of similarities of mass spectra and structures of small molecules
Malíčková, Viktorie ; Galgonek, Jakub (advisor) ; Škrhák, Vít (referee)
Methods for measuring the similarity of mass spectra and the structures of small molecules are crucial for advancements in medicinal chemistry, pharmacology, and metabolomics. One commonly used method for comparing the mass spectra of molecules is cosine similarity. This measures the similarity between two non-zero vectors by calculating the cosine of the angle between them. Comparing the mass spectra of molecules enables searching in molecular databases, clustering of spectra, and exploration of spectral libraries. Structural similarity is measured based on various molecular fingerprints, such as Daylight, RDKit, Atom-Pair, Topological Torsion, Extended-Connectivity fingerprints, and others. These fingerprints are compared using similarity coefficients. The methods for comparing structures and mass spectra of molecules mentioned can be applied using bioinformatic libraries such as RDKit and CDK for generating and analyzing structural fingerprints, and the MatchMS library for comparing mass spectra. The work provides a theoretical overview of molecular descriptors, including various types of molecular fingerprints and techniques for measuring structural similarity, as well as the principles of mass spectrometry and approaches to comparing mass spectra. The practical part of the work focuses on...
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Investigation of changes in epigenetic modofications in rat brain induced by morphine treatment
Hronová, Anna ; Novotný, Jiří (advisor) ; Roubalová, Lenka (referee)
This study addressed the impact of varying lengths of abstinence periods on the epitranscriptomic modification of m6 A and the enzymes involved in this modification as well as on transcription factors in the brains of morphine-dependent rats. The methods used included a colorimetric kit to determine m6 A levels and Western blotting to quantify the levels of enzymes and transcription factors. The results showed that different lengths of morphine abstinence did not have a significant effect on m6 A modification, suggesting that this pathway was likely not influenced by morphine abstinence. However, significant changes were observed in the levels of enzymes involved in the regulation of m6 A, which were localized and time-specific, without a clear trend. Examination of transcriptional regulators ∆FosB and MeCP2 also revealed significant changes only in certain parts of the brain and at specific times, but without a clear trend in changes in levels. The outcome of this study is that the dynamics of transcriptional regulators, N6 -methyl-adenosine, and enzymes involved in m6 A modification are localized and time-specific, opening new questions regarding the mechanisms that govern neurobiological processes during the abstinence period.
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Laboratory diagnosis of microRNA in different diagnostic groups
Hrachovcová, Eliška ; Urbánková Rathouská, Jana (advisor) ; Tripská, Katarína (referee)
Charles University, Faculty of Pharmacy in Hradec Králové Department of Biological and Medical Sciences Student: Bc. Eliška Hrachovcová Supervisor: PharmDr. Jana Rathouská, Ph.D. Consultant: doc. RNDr. Pavlína Kušnierová, Ph.D. Title of diploma thesis: Laboratory diagnostics of microRNAs in different diagnostic groups Background: Identification of potential miRNA targets for differential diagnosis of patients with atherosclerosis and dementia. Comparison of miRNA expression and uptake in serum samples with cerebrospinal fluid samples. Selection of appropriate miRNAs for differential diagnosis in patients with atherosclerosis and dementia. Furthermore, the selection of miRNA targets with the most significant fold-change and also the lowest p-value for subsequent validation studiues. Methods: To identify potential miRNAs, the received samples were centrifuged, aliquoted and stored at - 80C. miRNAs were isolated using the iCatcher Circulating cfRNA 1000 kit and the CatchGene isolator. Reverse transcription and amplification with detection were then performed. Data were processed in Excel and then statistically processed in GenEx using Mann-Whitney test. Results: The results were evaluated for 2 groups of patients: group A (samples of patients with Parkinson's disease and dementia) and group B (with...
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Complex molecular diagnostics of gastrointestinal stromal tumors
Kalfusová, Alena ; Kodet, Roman (advisor) ; Mandys, Václav (referee) ; Vaněček, Tomáš (referee)
Complex molecular diagnostics of gastrointestinal stromal tumors ABSTRACT Most of gastrointestinal stromal tumors (GISTs) are characterized by activating mutations in the KIT and PDGFRA genes (80 - 85 %). Mutations in the BRAF, KRAS, defects in the SDH complex or FGFR1::TACC1, ETV6::NTRK3 fusions were detected in the group of KIT/PDGFRA non-mutated GISTs (10 - 15 %). Targeted therapy with Imatinib mesylate (IM) marked a significant breakthrough in treating GISTs. A significant problem with targeted therapy is the formation of primary or secondary resistance. The biological behavior of the GIST is unpredictable. Determining the activity of selected markers for cell proliferation and senescence will enable the objectification risk of tumor behavior's aggressivness. The aim of the first part of our work was the mutational analysis of the KIT and PDGFRA genes and the detection of secondary mutations in patients with disease progression. We detected primary mutations in KIT and PDGFRA genes in 83.5 % of samples. We also demonstrated the presence of secondary mutations in 16 patients with progression of disease (in 29 progressive lesions - 69 %). We confirmed significant intratumor and also intertumor heterogeneity of secondary mutations. The aim of the second part of the thesis was the analysis of alterations in...
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Thrombin generation in pathophysiological conditions
Malíková, Ivana
Introduction: Thrombophilic conditions may be accompanied by increased thrombin generation (TG), especially during pregnancy when the increase in thrombin generation results from a series of changes in the haemostatic system. During administration of anticoagulant treatment, it is desirable to reduce the increase in thrombin generation. Aims of the study: The first aim of our study was to compare TG in individuals with a proven factor V Leiden mutation and individuals with elevated levels of factor VIII. Another aim was to compare patients with VTE and also with or without proven FV Leiden mutation that are taking different anticoagulation treatments. The final aim was to assess thrombin generation in pregnant women and their response to LMWH administration during severe thrombophilic conditions. Group of patients and methods: There were included 170 healthy blood donors in the control group, the congenital and acquired thrombophilia group included 44 individuals with FV Leiden mutation and 38 individuals with factor VIII level >150 % without other proven thrombophilia. 347 subjects with VTE taking direct coagulation inhibitors were included in the anticoagulation group. Sixty women with a prophylactic dose of LMWH were included in the group of pregnant women. Kit Technothrombin® TGA RC Low and RC...
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Mobilní kamera realizovaná prostředky ROS2
Onderka, Daniel ; Peringer, Petr (referee) ; Janoušek, Vladimír (advisor)
This thesis focuses on the middleware Robot Operating System 2. Specifically, it aims to explore and demonstrate its capabilities. It utilizes an Adeept AWR 4WD robot as the foundational hardware platform, onto which the ROS2 system is deployed. The system offers both manual control and a wandering mode equipped with obstacle avoidance functionality. In addition to its primary goal, the thesis explores various related subjects. One of them is the integration of the developed system with the Gazebo simulator. All functionality implemented on the real physical robot has been duplicated in the simulation environment. Furthermore, the original Adeept AWR kit was extended with additional hardware. This extension allowed for the use of slam_toolbox and Nav2 libraries for mapping and navigation purposes. The final extension involves the use of ros2_control for controlling robot motion.
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Sensor for bars of mallet percussion instruments
Pribol, Sebastián ; Balík, Miroslav (referee) ; Jirásek, Ondřej (advisor)
This thesis addresses the issue of capturing melodic percussion instruments using dynamic sensors that can be attached to a musical instrument. It includes theoretical knowledge, analysis, and selection of appropriate sensing methods, and the actual implementation, which consists of testing, integration with MIDI, manufacturing of the device itself, and final calibration and adjustments for proper functionality. The device uses an ESP32-S3 Dev Kit N8R8 microcontroller, which was programmed in the Arduino IDE for proper operation. The device consists of twelve piezoelectric sensors that capture the dynamics of playing the musical instrument and send MIDI information to a DAW via a Bluetooth module.
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Soil application of hydrogels containing rhizobacteria
Hlaváčková, Barbora ; Černayová, Diana (referee) ; Kalina, Michal (advisor)
Plant growth-promoting rhizobacteria (PGPR) are a group of bacteria that can influence plant growth by their mechanisms. In recent years, there has been an increase in the use of these soil-supporting products in the form of biofertilizers to increase yields and improve crop growth in adverse conditions in an environmentally friendly way. The aim of this bachelor thesis was to assess the effect of the external addition of different application forms of PGPR on soil physico-chemical characteristics and on the growth of model plants of lactuca sativa without irrigation restriction in the first case and in the second case under irrigation restricted conditions. A particular strain of Azotobacter vinelandii CCM 289 was selected for the preparation of four forms of PGPR treatments, namely bacterial biomass suspended in PBS, alginate gel without bacterial culture, gel with bacterial culture and lyophilized gel with bacterial culture. The effect of the different treatments was compared with the negative control without the addition of PGPR, as different forms of treatments may achieve different efficiencies of rhizosphere colonization, which in consequence may have different effect on plant growth. To assess the effect of PGPR addition, soil physico-chemical characteristics (moisture content, pH) and growth characteristics of lactuca sativa such as number of leaves, height and width of aerial parts of these model plants were measured during the cultivation experiments. After the termination of the cultivation experiments, the basic growth parameters of the model plants from each treatment such as total plant length, length of aerial parts and roots of the model plants, as well as total weight of each plant and weight of their aerial parts and roots were determined. After drying, the total dry weight of individual plants and the dry weight of the aerial parts and roots were characterized. After drying, root density was analyzed by performing root scans and compared between treatments. Soil extracts from individual treatments after the cultivation experiments were analyzed to assess the effect of PGPR addition on the microbial activity of the soil used in the experiments by plate cultivation using Petri dishes with agar medium, and the average well colour development (AWCD) value determined using the BIOLOG EcoPlate kit. The obtained results were compared between the individual treatments and also between cultivation experiments conducted with different irrigation conditions. Physico-chemical characterization (pH, conductivity) was performed on soil extracts from the drained soils after the cultivation experiments. The amount of organic and inorganic fractions was analyzed on the dried soils of each treatment by TGA. The results were compared with each other and the effect of different forms of external addition of PGPR on the physico-chemical characteristics of the selected soil under conditions without irrigation limitation and under conditions with irrigation limitation during the experiments was assessed.
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Demonstration kit for fiber optic sensing system
Beránek, Karel ; Klíčník, Ondřej (referee) ; Dejdar, Petr (advisor)
This bachelor thesis focuses on the design and implementation of a~demonstration kit for a~fiber optic sensing system. The thesis includes a~theoretical analysis of optical phenomena such as polarization, dispersion, and interference, which are crucial to understanding the principles of fiber optic sensors. The designed sensing system comprises a~Mach-Zehnder interferometer, a~UP-Board development kit, an external 24-bit sound card, and a~touch display. The practical part of the thesis is focused on the construction of the enclosure using 3D printing, the integration of individual components, the design of a~custom application, and the testing of the system. The results of this work contribute to the development of knowledge in the field of fiber optic sensors and can be utilized in both academic and industrial settings.
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