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OPTIMIZATION OF ALGORITHMS AND DATA STRUCTURES FOR REGULAR EXPRESSION MATCHING USING FPGA TECHNOLOGY
Kaštil, Jan ; Plíva, Zdeněk (referee) ; Vlček, Karel (referee) ; Kotásek, Zdeněk (advisor)
Disertační práce se zabývá rychlým vyhledáváním regulárních výrazů v síťovém provozu s použitím technologie FPGA. Vyhledávání regulárních výrazů v síťovém provozu je výpočetně náročnou operací využívanou převážně v oblasti síťové bezpečnosti a v oblasti monitorování provozu vysokorychlostních počítačových sítí. Současná řešení neumožňují dosáhnout požadovaných multigigabitových propustností při dodržení všech požadavků, které jsou na vyhledávací jednotky kladeny. Nejvyšších propustností dosahují implementace založené na využití inovativních hardwarových architektur implementovaných v FPGA případně v ASIC. Tato disertační práce popisuje nové architektury vyhledávací jednotky, které jsou vhodné pro implementaci jak v FPGA tak v ASIC. Základní myšlenkou navržených architektur je využití perfektní hashovací funkce pro implementaci přechodové tabulky konečného automatu. Dále byla navržena architektura, která umožňuje uživateli zanést malou pravděpodobnost chyby při vyhledávání a tím snížit paměťové nároky vyhledávací jednotky. Disertační práce analyzuje vliv pravděpodobnosti této chyby na celkovou spolehlivost systému a srovnává ji s řešením používaným v současnosti. V rámci disertační práce byla provedena měření vlastností regulárních výrazů používaných při analýze provozu moderních počítačových sítí. Z provedené analýzy vyplývá, že velká část regulárních výrazů je vhodná pro implementaci pomocí navržených architektur. Pro dosažení vysoké propustnosti vyhledávací jednotky práce navrhuje nový algoritmus transformace abecedy, který umožňuje, aby vyhledávací jednotka zpracovala více znaků v jednom kroku. Na rozdíl od současných metod, navržený algoritmus umožňuje konstrukci automatu zpracovávajícího libovolný počet symbolů v jednom taktu. Implementované architektury dosahují v porovnání se současnými metodami úspory paměti zlepšení až 200MB.
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Methods for class prediction with high-dimensional gene expression data
Šilhavá, Jana ; Matula, Petr (referee) ; Železný, Filip (referee) ; Smrž, Pavel (advisor)
Dizertační práce se zabývá predikcí vysokodimenzionálních dat genových expresí. Množství dostupných genomických dat významně vzrostlo v průběhu posledního desetiletí. Kombinování dat genových expresí s dalšími daty nachází uplatnění v mnoha oblastech. Například v klinickém řízení rakoviny (clinical cancer management) může přispět k přesnějšímu určení prognózy nemocí. Hlavní část této dizertační práce je zaměřena na kombinování dat genových expresí a klinických dat. Používáme logistické regresní modely vytvořené prostřednictvím různých regularizačních technik. Generalizované lineární modely umožňují kombinování modelů s různou strukturou dat. V dizertační práci je ukázáno, že kombinování modelu dat genových expresí a klinických dat může vést ke zpřesnění výsledku predikce oproti vytvoření modelu pouze z dat genových expresí nebo klinických dat. Navrhované postupy přitom nejsou výpočetně náročné. Testování je provedeno nejprve se simulovanými datovými sadami v různých nastaveních a následně s~reálnými srovnávacími daty. Také se zde zabýváme určením přídavné hodnoty microarray dat. Dizertační práce obsahuje porovnání příznaků vybraných pomocí klasifikátoru genových expresí na pěti různých sadách dat týkajících se rakoviny prsu. Navrhujeme také postup výběru příznaků, který kombinuje data genových expresí a znalosti z genových ontologií.
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Optimization of network flow monitoring
Žádník, Martin ; Lhotka,, Ladislav (referee) ; Matoušek, Radomil (referee) ; Sekanina, Lukáš (advisor)
The thesis deals with optimization of network flow monitoring. Flow-based network traffic processing, that is, processing packets based on some state information associated to the flows which the packets belong to, is a key enabler for a variety of network services and applications. The number of simultaneous flows increases with the growing number of new services and applications. It has become a challenge to keep a state per each flow in a network device processing high speed traffic. A flow table, a structure with flow states, must be stored in a memory hierarchy. The memory closest to the processing is known as a flow cache. Flow cache management plays an important role in terms of its effective utilization, which affects the performance of the whole system. This thesis focuses on an automated design of cache replacement policy optimized to a deployment on particular networks. A genetic algorithm is proposed to automate this process. The genetic algorithm generates and evaluates evolved replacement policies by a simulation on obtained traffic traces. The proposed algorithm is evaluated by designing replacement policies for two variations of the cache management problem. The first variation is an evolution of the replacement policy with an overall low number of state evictions from the flow cache. The second variation represents an evolution of the replacement policy with a low number of evictions belonging to large flows only. Optimized replacement policies for both variations are found while experimenting with various encoding of the replacement policy and genetic operators. The newly evolved replacement policies achieve better results than other tested policies. The evolved replacement policy lowers the overall amount of evictions by ten percent in comparison with the best compared policy. The evolved replacement policy focusing on large flows lowers the amount of their evictions two times. Moreover, no eviction occurs for most of the large flows (over 90%). The evolved replacement policy offers better resilience against flooding the flow cache with large amount of short flows which are typical side effects of scanning or distributed denial of service activities. An extension of the replacement policy is also proposed. The extension complements the replacement policy with an additional information extracted from packet headers. The results show further decrease in the number of evictions when the extension is used.
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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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(Arbo)viruses in high European Arctic
ELSTEROVÁ, Jana
Since an ongoing climate change covers strongly the polar areas. Higher temperatures and related climate parameters bring the emergence of new parasites and their pathogens to higher latitudes. This may influence zoonotic diseases including arthropod-transmitted diseases. The tick species Ixodes uriae, parasitizing seabirds in the Arctic, may transmit many pathogens including various arboviruses, Borrelia spirochetes and Babesia apicomplexans. In the study we diagnosed 89 individuals of seabird tick Ixodes uriae and searched for arthropod-borne viruses from the genera Flavivirus, Alphavirus, Orthobunyavirus, Phlebovirus and Orbivirus using genus-specific primers. Moreover we searched for presence of Borrelia spp. and Babesia spp. DNA in the ticks. All samples were negative after PCR amplification for all tested pathogens. The result signalizes that tested pathogens might not be present in such high latitudes of European Arctic. Though, the possibility of introduction of these pathogens may be observable in near future due to quick changing of the Arctic ecosystem with the rising of migration of vertebrate hosts including humans to the polar areas. It is though important to continue to study potential presence of pathogens in polar areas. We are working on increase of the number of tick samples to confirm the presence or absence of the tick-borne pathogens in the European Arctic.
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Právní a zdravotně sociální aspekty činnosti OSPOD jako ustanovených opatrovníků v zámu nezletilých dětí
BORSKÁ, Jana
The Czech Republic as a signatory of the Convention on the Rights of the Child has vested the practice of state administration in the field of care for minor children to municipalities with extended powers, where the protection of the rights and legitimate interests of minor children is safeguarded by state authorities of social and legal protection of children (ASLPC hereinafter). These authorities are incorporated to the extent laid down by the Act on Social and Legal Protection of Children (Act No 359/1999 Coll., as amended). The position and roles of ASLPC and their competence and jurisdiction are also regulated by the same act. The position of workers of these authorities and its legal embodiment is equally important. Regarding professionality, there are high demands on these workers. In the Czech Republic, significant changes in legislature have been made over the past three years. These amendments have led to the strengthening of the rights of minor children and to the establishing of new tools for their protection. In connection with the adoption of new substantive regulation of family law, which is now exhaustively dealt with by the Act No 89/2012 Coll., the Civil Code, new procedural rules have been established regarding protection of rights of minor children. Such procedural legislation includes (apart from the long-existent Act No. 99/1963, the Code of Civil Procedure) the Act No 292/2013 Coll., on Special Civil Proceedings. The decision-making regarding minor children has been vested mainly by the state into the competence of courts. The courts appoint the locally relevant ASLPC as a guardian who then represents the interests of minor children. The purpose, interwoven with and derived from the first one, was to explore the opinions of selected social workers of ASLPC and of district court judges regarding the defined problems occurring during the work of ASLPCs and courts while protecting the interests of minor children. These particularly include: the use of the tool of precautionary measure; problems of different territorial jurisdiction of courts and ASLPCs; processing of complaints regarding bias in various phases of the proceedings; professional training of workers of ASLPC It is evident from the proposals of both judges and ASLPC workers that it is necessary to unify territorial jurisdiction. The courts are suggesting the priority criterion of the address where the child mainly resides. ASLPC workers suggest the official permanent residence as the prime criterion. Bias causes problems in all phases of proceedings. It is obvious that courts take differing approaches towards the solution of this problem (some courts solve the problem of bias complaints filed by the parties while other courts do not) and for ASLPC workers it is difficult to assess how to act when such complaint is raised against them. The training of ASLPC workers - workers are obliged to educate themselves and their employer is obliged to finance such training. Not all ASLPCs are able to provide training in the required extent - due to financial reasons (the average costs of education of one employee pose from 9,169 to 13,400 CZK annually and they cover approximately 6 days of training). The heavy work-load caused by insufficient numbers of ASLPC employees prevents them from completing such compulsory training. As part of the examination of the "participation of a collision guardian in court proceedings" it has been found out that irregular participation of the worker in the proceedings (absence from participation in appeals proceedings); incomplete reports (directed to courts) from surveys in families. Based on comprehensive examination of the problems of territorial jurisdiction, it was recommended that requests are independently recorded and financial compensation is provided for ASLPCs who are requested to represent minors in front of courts, to draft proposals for precautionary measures.
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Is genetic diversity congruent with morphological diversity across the distributional range of the Melampyrum subalpinum group (Orobanchaceae)?
CHLUMSKÝ, Jan
Allozymes were used to assess the genetic structure of 27 populations of Melampyrum subalpinum group and an artificial pollination experiment was carried out to examine the possibility of autogamy. Genetic variation was generally congruent with the known morphological variation of the group. The results corresponded with the central-marginal concept. Allelic enrichment due to hybridization with M. nemorosum was observed in some Austrian populations. Czech and Slovak populations do not differ from Austrian populations. The high inbreeding coefficient and the pollination experiment do not contradict the possibility of autogamy.
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Measuring phonological awareness – blend phoneme test in the beginning of schooling: an comparison of classical test theory and item response theory
Gorčíková, M. ; Šafr, Jiří
The main purpose of this paper is to show dis/advantages of two approaches classical test theory (CTT) and item response theory (IRT) to assess the level of diagnostic tools for evaluating phonemic awareness among first-grade students using longitudinal survey of children during the first grade of primary school (25 schools in Prague and Central Bohemia, 439 pupils). Phonemic awareness (FA) was measured by the task blend phonemes into syllables and words. The advantage of IRT compared to CTT is primarily a concept of independence of the test items. The probability of a response is dependent on the level of latent ability and characteristics of items. So if we know the characteristic of items parameter (difficulty) it could be estimated from the pupil´s responses the level of language skill for diagnostics. The results showed the need for blend phoneme test modifications (in particular for the end of the first grade) so as to adequately measure the high growth of FA ability levels during the first grade.
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Adolescent overweight and obesity
JINDROVÁ, Kateřina
My bachelor´s thesis deal with obesity of adolescents and problems with overweight. These problems are described in details, and after that divided into specific parts. The main goal of my bachelor´s thesis is to chart problems with obesity and overweight in age group from 15 to 18 (adolescents) and primary describe their eating habits and physical activity. Theoretical part is focused on occurrence of overweight and obesity in the Czech Republic and in the world, causes of its origin, risk factors, classification and diagnosis, types, therapy and prevention. This bachelor´s work dealing with rational diet, describing basic principles of healthy catering and explaining right or wrong foodstuffs. I point mainly on prevention of overweight and obesity by healthy eating and physical activity. Methodical part is processed thanks to quantitative research. Data were gained by questionnaires, which were given to high school students (1st - 3rd grade). The research group contains 150 respondents from different schools in České Budějovice and close neighborhood. Final results are written down primary in graphs with commentary and data charts. In case of right use of qualitative research, there were determined two hypotheses. First hypothesis: Overweight and obesity is more occurred at adolescents with wrong eating habits. Second hypothesis: Overweight and obesity is more occurred at adolescents with low physical activity. For developing exploratory part, there was used quantitative research, which was provided by questionnaires given to students of age from 15 to 18. Entire data were processed by the use of program Microsoft Excel, and its calculations and functions. The answers of respondents were registered into database, and, by using specific excel functions, I was able to report data in determined categories. The research was mainly concentrated on physical activity and eating habits. Final results are put into well-arranged graphs, which are always enriched by comments, eventually completed by data tables, and, subsequently, statistically evaluated. In results, there might be seen two main differences between adolescents with standard weight and adolescents with overweight or obesity problems. One of those is irregularity in eating and wrong eating habits; big difference is also proved in physical activity. Adolescents with obesity or overweight have often irregular food intake, they drink a lot of high caloric beverages such as Coca-Cola, Sprite, Fanta etc., deficient income of fruit, vegetables, legumes, fish, or low physical activity. Only few of obese adolescents is different, because their problem is caused genetically. Adolescents with standard weight eat more regularly, but there are also some special cases, who have similarly wrong eating habits as obese people; however, all of these adolescents have one typical quality regular physical activity. Both hypotheses are confirmed. The results show that obesity is mainly caused by genetic predispositions, but these factors can be positively affected by periodic physical activity or appropriate eating habits. At the end of the thesis, it should be mentioned that it is necessary to be focused on right eating habits and regular physical from the very young age, when the basic customs and habits are assumed. That should include parents' action around their children, as they are usually the first example and they have the biggest influence.It is important to develop knowledge about all kinds of prevention, which are in most cases major in defending against formation of overweight and obesity.
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