A classificação de fungos microscópicos é limitada pela escassez de detalhes morfológicos e incertezas na caracterização bioquímica. Nesse trabalho desenvolvemos um método simples, baseado na amplificação de um segmento de cerca de 2.800 bares de bases seguida de digestão com DdeI e análise do padrão após eletroforese em agarose. Demonstramos que o método discrimina tão bem quanto a sequência de DNA do segmento após analisar mais de 400 amostras que foram classificadas em 33 espécies. Essa tecnologia facilita a busca por novos representantes da imensa diversidade existente, espécies que podem ser exploradas quanto ao seu valor potencial para a medicina e a indústria. Outras metodologias moleculares foram desenvolvidas para discriminar entre espécies próximas e na identificação de novas espécies. Em seguida, o trabalho esteve voltado para o desenvolvimento de um ensaio laboratorial que nos permitisse estudar a transição dimórfica em Candida albicans. Desenvolvemos dois novos ensaios, um biológico e outro sobre membrana artificial, para estudar a indução ou inibição da produção de hifas. A expressão de genes associados ao processo foi acompanhada de maneira quantitativa. Fracionando cromatograficamente o soro fetal bovino, obtivemos resultados indicativos de frações estimuladoras e inibidoras da transição morfológica. / Fungal identification is limited by few morphological details and uncertainty in the biochemical tests. In the present work we developed a simple procedure, based upon DNA amplification of a 2,800 base pairs region followed by the amplicon digestion with DdeI and electrophoretic analyzes in agarose gels. After analyzing more than 400 samples encompassing 33 species, we demonstrate that this method discriminates as well as DNA sequencing of the region. This technology simplifies the search for new representatives among the great diversity of fungi of medical and industrial interest. We devised also molecular methods to discriminate between closely related species and described a new putative species. Next our work was dedicated to develop an in vitro assay for the study of the dimorphic transition in Candida albicans. We devised two biological assays and one that used an artificial membrane to investigate the induction and inhibition of hyphal production. The expression of genes associated with the morphological transition was examined in a quantitative way. We fractionated bovine fetal serum by column chromatography and obtained results pointing to fractions that stimulate or inhibit hyphal production.

This thesis’ aim is to explore improvements to, and applications of, a fundamental quantum algorithm invented by Grover. Grover’s algorithm is a basic tool that can be applied to a large number of problems in computer science, creating quantum algorithms that are polynomially faster than fastest known and fastest possible classical algorithms that solve the same problems. Our goal in this thesis is to make these techniques readily accessible to those without a strong background in quantum physics: we achieve this by providing a set of tools, each of which makes use of Grover’s algorithm or similar techniques, that can be used as subroutines in many quantum algorithms. The tools we provide are carefully constructed: they are easy to use, and they are asymptotically faster than the best tools previously available. The tools that we supersede include algorithms by Boyer, Brassard, Hoyer and Tapp, Buhrman, Cleve, de Witt and Zalka and Durr and Hoyer. After creating our tools, we create several new quantum algorithms, each of which is faster than the fastest known classical algorithm that accomplishes the same aim, and some of which are faster than the fastest possible classical algorithm. These algorithms come from graph theory, computational geometry and dynamic programming. We discuss a breadth-first search that is faster than (edges) (the classical limit) in a dense graph, maximum-points-on-a-line in (N3/2 lgN) (faster than the fastest classical algorithm known), as well as several other algorithms that are similarly illustrative of solutions in some class of problem. Through these new algorithms we illustrate the use of our tools, working to encourage their use and the study of quantum algorithms in general.

This thesis aim is to explore improvements to, and applications of, a fundamental quantum algorithm invented by Grover. Grovers algorithm is a basic tool that can be applied to a large number of problems in computer science, creating quantum algorithms that are polynomially faster than fastest known and fastest possible classical algorithms that solve the same problems. Our goal in this thesis is to make these techniques readily accessible to those without a strong background in quantum physics: we achieve this by providing a set of tools, each of which makes use of Grovers algorithm or similar techniques, that can be used as subroutines in many quantum algorithms. The tools we provide are carefully constructed: they are easy to use, and they are asymptotically faster than the best tools previously available. The tools that we supersede include algorithms by Boyer, Brassard, Hoyer and Tapp, Buhrman, Cleve, de Witt and Zalka and Durr and Hoyer. After creating our tools, we create several new quantum algorithms, each of which is faster than the fastest known classical algorithm that accomplishes the same aim, and some of which are faster than the fastest possible classical algorithm. These algorithms come from graph theory, computational geometry and dynamic programming. We discuss a breadth-first search that is faster than (edges) (the classical limit) in a dense graph, maximum-points-on-a-line in (N3/2 lgN) (faster than the fastest classical algorithm known), as well as several other algorithms that are similarly illustrative of solutions in some class of problem. Through these new algorithms we illustrate the use of our tools, working to encourage their use and the study of quantum algorithms in general.

Current approaches integrating large scale data and information from a variety of sources to reveal molecular basis of cellular events do not adequately benefit from pathway information. Here, we portray a network structure based pathway enrichment system that fuses and exploits model and data: signalling pathways are taken as the biological models while microarray and ChIP-seq data are the sample input data sources among many other alternatives. Our model- and data-driven hybrid system allows to quantitatively assessing the biological activity of a cyclic pathway and simultaneous enrichment of the significant paths leading to the ultimate cellular response. Signal Transduction Score Flow (SiTSFlow) algorithm is the fundamental constituent of proposed network structure based pathway enrichment system. SiTSFlow algorithm converts each pathway into a cascaded graph and then gene scores are mapped onto the protein nodes. Gene scores are transferred to en route of the pathway to form a final activity score describing behaviour of a specific process in the pathway while enriching of the gene node scores. Because of cyclic pathways, the algorithm runs in an iterative manner and it terminates when the node scores converge. The converged final activity score provides a quantitative measure to assess the biological significance of a process under the given experimental conditions. The conversion of cyclic pathways into cascaded graphs is performed by using a linear time multiple source Breadth First Search Algorithm. Furthermore, proposed network structure based pathway enrichment system works in linear time in terms of nodes and edges of given pathways. In order to explore various biological responses of several processes in a global signalling network, the selected small pathways have been unified based on their common gene and process nodes. The merge algorithm for pathways also runs in linear time in terms of nodes and edges of given pathways. In the experiments, SiTSFlow algorithm proved the convergence behaviour of activity scores for several cyclic pathways and for a global signalling network. The biological results obtained by assessing of experimental data by described network structure based pathway enrichment system were in correlation with the expected cellular behaviour under the given experimental conditions.

A classificação de fungos microscópicos é limitada pela escassez de detalhes morfológicos e incertezas na caracterização bioquímica. Nesse trabalho desenvolvemos um método simples, baseado na amplificação de um segmento de cerca de 2.800 bares de bases seguida de digestão com DdeI e análise do padrão após eletroforese em agarose. Demonstramos que o método discrimina tão bem quanto a sequência de DNA do segmento após analisar mais de 400 amostras que foram classificadas em 33 espécies. Essa tecnologia facilita a busca por novos representantes da imensa diversidade existente, espécies que podem ser exploradas quanto ao seu valor potencial para a medicina e a indústria. Outras metodologias moleculares foram desenvolvidas para discriminar entre espécies próximas e na identificação de novas espécies. Em seguida, o trabalho esteve voltado para o desenvolvimento de um ensaio laboratorial que nos permitisse estudar a transição dimórfica em Candida albicans. Desenvolvemos dois novos ensaios, um biológico e outro sobre membrana artificial, para estudar a indução ou inibição da produção de hifas. A expressão de genes associados ao processo foi acompanhada de maneira quantitativa. Fracionando cromatograficamente o soro fetal bovino, obtivemos resultados indicativos de frações estimuladoras e inibidoras da transição morfológica. / Fungal identification is limited by few morphological details and uncertainty in the biochemical tests. In the present work we developed a simple procedure, based upon DNA amplification of a 2,800 base pairs region followed by the amplicon digestion with DdeI and electrophoretic analyzes in agarose gels. After analyzing more than 400 samples encompassing 33 species, we demonstrate that this method discriminates as well as DNA sequencing of the region. This technology simplifies the search for new representatives among the great diversity of fungi of medical and industrial interest. We devised also molecular methods to discriminate between closely related species and described a new putative species. Next our work was dedicated to develop an in vitro assay for the study of the dimorphic transition in Candida albicans. We devised two biological assays and one that used an artificial membrane to investigate the induction and inhibition of hyphal production. The expression of genes associated with the morphological transition was examined in a quantitative way. We fractionated bovine fetal serum by column chromatography and obtained results pointing to fractions that stimulate or inhibit hyphal production.

This master’s thesis is dedicated to user’s movement tracking in public transport, as well as to optimize route planning. In the first part, author presents information related to graph theory and graph theory algorithms, including Breadth-First Search, Djikstra’s algorithm and A*. In the second part of this thesis, author describes the design of server and mobile application including description of routing process and how individual parts works.

This work outlines ways of getting dynamic state into OMNeT++ model. SNMP as major technology was selected for reaching the goals. Protocols CDP and LLDP are participating in topology detection and in theoretical layer Breadth- first search is used. The output of this tool is file syntactically specied by NED language which is describing computer network.

Increasing awareness of sustainability in the concrete industry forces structural design and executionto focus on avoiding costly and unpredictable maintenance action, instead paying higher attention todamage prevention by direct actions on early stages of production. One of such approaches, whichdeals with the problem of freezing and thawing deterioration, is intentional air bubble introductionto the concrete mix. However, the mechanism of air entrainment in concrete can be negativelyaffected on different stages of production by many factors including cement type, admixture dosage,casting conditions or mixing procedure. Therefore, reliable tools for the end-product evaluationought to be considered. The experimental study, presented in this work, focuses on understandingthe blast furnace slag (BFS) influence as well as admixtures’ dosage effect on pore structure ofhardened concrete. Three types of cement were evaluated, including ordinary portland cement(OPC) and two types of CEM III cements with different BFS percentage. The optimal amountsof air entraining agent (AEA) and super plasticizer (SP) were chosen and later reduced in orderto evaluate their impact on total air content, spacing factor and specific surface of the air voids.The main method chosen for this evaluation was the use of an office flat-bed scanner to acquireimages and application of BubbleCounter software for the analysis of the air void structure. Thisapproach is based on linear traverse method and requires special surface treatment for contrastenhancement. Specimens for the analysis were cut from hardened concrete cubes and polishedto achieve a flat surface. The samples were later treated with black ink and zinc oxide paste toachieve a clear contrast between white voids and black paste/aggregate area. In order to estimatethe accuracy of this method, more conventional tools such as pressurised gauge method and air voidanalyser were applied for comparison. Resulted mixtures showed significant differences in air voidproperties between OPC and BFS containing concrete, with the latter being less affected by AEAdosage reduction. Changes in spacing factor and specific surface were also registered; however,their deterioration did not follow the same pattern as that of total air content. No significantdeviation between the two cements containing BFS was observed. An interesting effect of the usedpolycarboxylate ether SP on the AEA reactivity was registered, showing deterioration of air voidproperties with the decrease of plasticizer amount. Comparison of the results from different air voidanalysis methods, suggested an overall agreement on the measured air void system changes due tochanging the AEA content. However, the BubbleCounter software tended to slightly overestimatethe material’s resistance to freeze and thaw phenomenon, giving the most optimistic values inspacing factor and specific surface of air voids. / Betongindustrins ökande medvetenhet om hållbarhet leder till att man inom dimensionering ochutförande fokuserar mot att undvika kostnadskrävande och oförutsedda underhållsåtgärder ochistället lägga större vikt på att förebygga skador i produktionens tidiga skeden. En av dessaåtgärder, som hanterar problemet frostnedbrytning, är en medveten inblandning av luftbubblor ibetongen. Mekanismen för att skapa luftporssystemet kan emellertid bli negativt påverkad underolika skeden av produktionen av många faktorer såsom cementtyp, tillsatsmedelsdos, gjutvillkoroch blandningsordning. Därför behöver man reflektera över pålitliga verktyg för utvärderingenav slutprodukten. Den experimentella studien, som presenteras i detta arbete, fokuserar motförståelse hur slagg och tillsatsmedelsdos påverkar den hårdnade betongens luftporssystem. Tretyper av cement utvärderades, dels ett normalt portlandcement, dels två typer av CEM III-cementmed olika andelar av slagg. Optimala mängder av luftporbildare och flyttillsatsmedel valdesmen reducerades senare för att undersöka deras inverkan på totalt luftinnehåll samt luftporernasavståndsfaktor och specifika yta. Den huvudsakliga metoden som valdes för denna utvärderingvar en flatbäddsscanner (kontorsmodell) för att ta bilder och användningen av en programvaravid namn BubbleCounter för att analysera luftporssystemet. Detta tillvägagångssätt baseras påanalys av tvärgående linjer och kräver en speciell behandling av ytan för att åstadkomma kontraster.Provkroppar för analysen sågades ut ur hårdnade betongkuber och polerades för att erhålla en jämnyta. Provkropparna var senare behandlade med svart bläck och zinkoxidpasta för att åstadkomma entydlig kontrast mellan de vita porerna och den svarta ytan av cementpasta och ballast. För att studeranoggrannheten hos denna metod användes som jämförelse även mer konventionella metoder sommätningar med trycksatta givare och luftporsanalys. De framtagna blandningarna visade signifikantaskillnader i luftporernas egenskaper mellan betong med normalt portlandcement och betong medslaggcement, där den senare påverkades i mindre grad av reduktioner i dosen luftporbildare.Förändringar I avståndsfaktor och specifik yta noterades också men försämringen följde inte sammamönster som den för totala luftinnehållet. Ingen signifikant skillnad mellan de två cementeninnehållande slagg kunde observeras. En intressant inverkan av det använda polykarboxylateterbaseradeflyttillsatsmedlet på luftporbildarens reaktivitet noterades. Den visade en försämringav luftporernas egenskaper vid en reduktion av mängden flyttillsatsmedel. En jämförelse avresultaten från de olika metoderna för luftporsanalys indikerade en övergripande överensstämmelsegällande de uppmätta luftporssystemens förändring p.g.a. förändringar i mängden luftporbildare.Programvaran BubbleCounter tenderade emellertid att något överskatta materialets motstånd motfrostnedbrytning med de mest optimistiska värdena för luftporernas avståndsfaktor och specifikayta.

Die Auswirkungen des Braunkohlenbergbaus auf den Gebietswasserhaushalt bilden seit 1990 einen Schwerpunkt der regional- und fachplanerischen Auseinandersetzungen. Dabei fokussieren sich die Problemfelder aufgrund der Fläche, Dauer und Intensität der bergbaulichen Eingriffe auf den „Südraum Leipzig“.

This work is intended on identification with basic problems from the graphs theory area. There are the basic conceptions as well more complicated problems described. The one part of this work is specialized in working of individual types of graphs. It starts with single linked list through double linked list after as much as trees which represented the simplest graphs textures. The other part of this work devotes to the whole graph and describes more complicated problems and their resolution from the theory graphs area. Among these problems belongs to searching in graphs help by Depth First Search and Breadth First Search methods. Then searching the shortest way help by the specific algorithms as are: Dijkstra´s algorithm, Floyd-Warshall´s algorithm and Bellman-Ford´s algorithm. The last part is devoted to problems with searching minimal frames of graphs with usage Kruskal´s algorithm, Jarnik´s algorithm and Boruvka´s algorithm methods.