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Studying lymphocyte development using mass cytometry
Novák, David ; Stuchlý, Jan (advisor) ; Špidlen, Josef (referee)
Studying lymphocyte development using mass cytometry Abstract Development of mature lymphocytes, a white blood cell subtype, is crucial for the correct function of the human immune system. Currently, developmental pathways of lymphocytes can be studied using high-throughput single-cell measurements. In particular, mass cytometry enables the study of immunologically relevant pheno- typic and functional markers on a vast scale. In this work I present my individual contribution to tviblindi, a powerful software tool for analysis of cytometric data aimed at uncovering developmental trajectories. tviblindi is a package written in R, Python and C++. It provides a means to integrate prior knowledge with data analyses grounded in graph theory and algebraic topology. tviblindi is accessible to biological researchers without background in computer science or mathematics. It is an addition to the expanding field of trajectory inference in single-cell data. Furthermore, I review current knowledge of T-cell development and conduct a tviblindi analysis thereof using human thymus and peripheral blood datasets and evaluate the results. 1
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The Elements of Liability for Damage under Civil Law
Novák, David ; Dvořák, Jan (advisor) ; Doležal, Tomáš (referee) ; Frinta, Ondřej (referee)
1 Abstract The objective of this thesis is to analyse the liability in civil law, mainly from the prospective of individual preconditions that together result in such liability for inflicted harm. The text is divided into nine parts including introduction and conclusion. The first part comprises the analysis of the legal term of liability from the prospective of existing theoretical concepts, then the approach as set forth under Act no. 89/2012 Sb, Civil Code, as amended (hereinafter referred to as "Civil Code") and the author's own approach is presented at the end of this part. The next part discusses in details the preconditions of liability for harm and then the sets of preconditions that together result in such liability are analysed. The author calls these sets as liability systems, as they are actually a variant of the objective and subjective liability. A separate chapter is dedicated to the objective liability. A separate chapter is also dedicated to the division of types of liabilities such as for defects, harm, default, etc., as this is crucial for the discussed topic. Next parts focus on individual preconditions for liability for harm, namely on violating legal obligations and relevant damage, harm, causality and fault as on the precondition typical for subjective liability, i.e. liability for...
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Raytracing for GPUEngine
Novák, David ; Milet, Tomáš (referee) ; Starka, Tomáš (advisor)
The main goal of this thesis is ray tracing optimization, especially with the use of acceleration data structure. It'll be focused on discretion about various structure build strategies and their traversal. Different algorithms on the CPU and on the GPU will be implemented and compared in the thesis, specifically will be compared the speed of build and final structure quality, which have a direct influence on ray tracing performance. A ray tracing application will be implemented for the purpose of the acceleration structure quality test. A part with acceleration structure building will be added to GPUEngine library.
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Design of a Lean Manufacturing Process with the Realization of the Production Layout
Novák, David ; Zíma, Jakub (referee) ; Jurová, Marie (advisor)
This thesis deals with the design of a lean manufacturing process with the main focus on the modification of the production layout of the heat pump production line, at Daikin Device Czech Republic s.r.o. In the introductory part of the thesis, the theoretical background is elaborated and then the company is introduced briefly. The next part analyzes the currently produced models, production processes, the line in terms of current layout and finally the process times. Based on these analyzes, a new layout of the production line and storage space is presented. In the next part of the thesis, the conditions of implementation are defined. The final part evaluates the benefits of this work based on the real results that the new layout resulted in.
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Computer applications in archaeology 17/2018. Kouty, 28.-30. 5. 2018. Abstract book
Novák, David
The bilingual proceedings summarise the contributions presented at the international conference Computer Applications in Archaeology 2018, in the form of extended abstracts. The main topic of the conference was “big data” in archaeology, among others the collection of archaeological data using modern methods, archaeological remote sensing and 3D modeling and visualization in archaeology. The key-note lecture was given by a foreign expert (Christopher Green, University of Oxford). The conference included a workshop by L. Šmejda focused on working with Google Earth Engine.
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Implementation of 10 Gb Ethernet Interface for Arria 10 SoC
Novák, David ; Košař, Vlastimil (referee) ; Kořenek, Jan (advisor)
This thesis addresses design, implementation and testing of 10 Gb Ethernet interface for chip Arria 10 SoC (combination of FPGA and ARM Cortex-A9). Composition of the interface, its parts and communication between them is described with main focus being on MAC layer, which was designed and implemented in the course of this work. Secondary aspect of this thesis is increasing CPU performance demands for processing of packets and problems it brings. The performance of common CPUs is seriously lacking with network speeds over 10 Gb/s and alternative solutions has to be considered - namely acceleration of some tasks using FPGA and utilization of new ways of packet processing. Therefore, the description of DPDK (library for fast packet processing) as well as implementation of DPDK interface for newly created MAC module, are part of this thesis.
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Human lymphopoiesis and its examination via single-cell analysis
Novák, David ; Kalina, Tomáš (advisor) ; Drbal, Karel (referee)
Development of human B-lymphocytes is a convoluted process. A self-renewing stem cell progenitor in a primary lymphoid tissue commits to the lymphoid lineage. Subsequent B-lineage commitment entails somatic gene recombination processes which lead to the eventual expression of a surface antigen receptor. Functionality of the B-cell receptor, as well as successful testing for autoreactivity by the cell, are preconditions for the differenti- ation of a mature B-lymphocyte. Processes within this development are often investigated using single-cell analysis via flow cytometry, fluorescence-activated cell sorting and mass cytometry. Coupling these high-throughput methods with modern approaches to data analysis carries enormous potential in revealing rare cell populations and aberrant events in haematopoiesis. Keywords: B-lymphocyte, lymphopoiesis, flow cytometry, FACS, mass cytometry, clus- ter analysis, FlowSOM, PCA, t-SNE, Wanderlust.
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Combined heat and biogas production using a bioreactor
Novák, David ; Radil, Lukáš (referee) ; Baxant, Petr (advisor)
This diploma thesis deals with the bioreactor system and its use for the production of heat and biogas. The bioreactor uses the composting and metanogation process of fermentation that humanity has known for hundreds of years, but the combination of these processes is a relatively unexplored area. The theoretical part of the thesis analyzes the existing possibilities of utilization of the heat generated in the compost, and also describes the used technology of small biogas stations and other small systems for biogas production. It follows the practical part of the work, when it was the task to design a bioreactor working at low temperatures during the winter. Part of the solution is the initial design and testing of the basic test structure of the bioreactor, followed by the implementation of a more advanced and more complex system, including a control and measuring center realized by a microcontroller.
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