This thesis deals with a design and implementation monitoring system of Starhill society computer network. Part of the design is development and realization hardware modules that provide restarting of remote network devices. Command transmission is realized through discretionary transceivers available, whose regulations can make such transmissions possible. A usage of 466~MHz frequency band is the main assumption. Both concept and implementation are described in the thesis. The designed system is integrated to the existing IS of the association.

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The progression of replication forks can be slowed down or paused by various external and internal factors during DNA replication. This phenomenon is referred to as replication stress and substantially contributes to genomic instability that is a hallmark of cancer. Transcription complex belongs to the internal replication-interfering factors and represents a barrier for progression of the replication complex. The replication forks are slowed down or paused while passing through the transcriptionally active regions of the genome that can lead to subsequent collapse of stalled forks and formation of DNA double-strand breaks, especially under conditions of increased replication stress. DNA helicase RECQ5 is significantly involved in maintenance of genomic stability during replication stress, but the mechanisms of its action are not clear. In this diploma theses, we have shown that RECQ5 helicase, in collaboration with BRCA1 protein, participates in the resolution of collisions between replication and transcription complexes. BRCA1 protein is a key factor in the homologous recombination process, which is essential for the restart of stalled replication forks. Furthermore, we have shown that RECQ5 helicase is involved in ubiquitination of PCNA protein at stalled replication forks. Key words DNA...

The thesis, Survey of the methods of costing of hospitalization, deals with the characteristics of the classification system DRG used for costing of hospitalization. The first half of the theoretical part of this work describes the Czech health care in general and specific ways of financing it. We focus on the costs related to the emergency care in hospitals which are classified by the DRG system. The second half of the theoretical part studies the actual principles of costing of hospitalization. The method chosen for this is called Activity Based Costing (ABC). It defines the procedures of costing which are being used in hospitals. At the end, we provide a description of the current and suggested procedures of costing of hospitalization and how they are utilized to set up parameters of the reimbursing mechanism. The practical part of this thesis maps the situation of hospitalization financing in Klatovska nemocnice, a. s. We suggest a new way of financing based on the methodology DRG Restart. Base on the data obtained in Klatovska nemocnice, a. s. we summarize and compare the results of the new method to the current one.

Double-stranded RNA fungal virus Helminthosporium victoriae virus 190S (genus Victorivirus, family Totiviridae) contains two large open reading frames (ORFs) that overlap in the tetranucleotide AUGA. Translation of the downstream ORF, which encodes the RNA-dependent RNA polymerase (RdRp), was previously proposed to depend on ribosomal reinitiation following termination of the upstream ORF, which encodes the capsid protein. In this study, I provided evidence to confirm that coupled termination-reinitiation (stop-restart) is indeed used. A dual-fluorescence method was established to define the RNA sequence determinants for RdRp translation. Stop-restart depends on a 32-nt stretch of RNA sequence immediately upstream of the AUGA motif, including a predicted pseudoknot structure. The presence of similar sequence motifs and predicted RNA structures in other victoriviruses suggest that they all share a related stop–restart strategy for RdRp translation. The close proximity of the secondary structure to the AUGA motif appears to be especially important for promoting translation of the downstream ORF. Normal strong preferences for AUG start codons and canonical sequence context for translation initiation of the downstream ORF appear somewhat relaxed. With dual-fluorescence system, reinitiation efficiency of the downstream ORF was determined to be ~3.9%. Pseudoknot swapping between the one in HvV190S and those predicted from other victoriviruses showed that reinitiation from the downstream ORF of HvV190S is quite tolerant to varying primary sequences of the various pseudoknots. Mutational analysis by introducing different combinations of nucleotide mutations into pseudoknot stems reproducibly confirmed the determinant role of pseudoknot on reinitiation using two different experimental systems. Together, these results provide the first example of coupled termination-reinitiation regulated by a simple pseudoknot stucture. These data expanded the understanding of coupled termination-reinitiation mechanism employed by RNA viruses and refined a new model for genus victorivirus, the largest genus in the family Totiviridae. The dual fluorescence system used in this study represented the first application of an efficient in vivo assay for recording low-frequency events in filamentous fungi.

Le passage de l'échelle des nouvelles plates-formes de calcul parallèle et distribué soulève de nombreux défis scientifiques. À terme, il est envisageable de voir apparaître des applications composées d'un milliard de processus exécutés sur des systèmes à un million de coeurs. Cette augmentation fulgurante du nombre de processeurs pose un défi de résilience incontournable, puisque ces applications devraient faire face à plusieurs pannes par jours. Pour assurer une bonne exécution dans ce contexte hautement perturbé par des interruptions, de nombreuses techniques de tolérance aux pannes telle que l'approche de sauvegarde et reprise (checkpoint) ont été imaginées et étudiées. Cependant, l'intégration de ces approches de tolérance aux pannes dans le couple formé par l'application et la plate-forme d'exécution soulève des problématiques d'optimisation pour déterminer le compromis entre le surcoût induit par le mécanisme de tolérance aux pannes d'un coté et l'impact des pannes sur l'exécution d'un autre coté. Dans la première partie de cette thèse nous concevons deux modèles de performance stochastique (minimisation de l'impact des pannes et du surcoût des points de sauvegarde sur l'espérance du temps de complétion de l'exécution en fonction de la distribution d'inter-arrivées des pannes). Dans la première variante l'objectif est la minimisation de l'espérance du temps de complétion en considérant que l'application est de nature préemptive. Nous exhibons dans ce cas de figure tout d'abord une expression analytique de la période de sauvegarde optimale quand le taux de panne et le surcoût des points de sauvegarde sont constants. Par contre dans le cas où le taux de panne ou les surcoûts des points de sauvegarde sont arbitraires nous présentons une approche numérique pour calculer l'ordonnancement optimal des points de sauvegarde. Dans la deuxième variante, l'objectif est la minimisation de l'espérance de la quantité totale de temps perdu avant la première panne en considérant les applications de nature non-préemptive. Dans ce cas de figure, nous démontrons tout d'abord que si les surcoûts des points sauvegarde sont arbitraires alors le problème du meilleur ordonnancement des points de sauvegarde est NP-complet. Ensuite, nous exhibons un schéma de programmation dynamique pour calculer un ordonnancement optimal. Dans la deuxième partie de cette thèse nous nous focalisons sur la conception des stratégies d'ordonnancement tolérant aux pannes qui optimisent à la fois le temps de complétion de la dernière tâche et la probabilité de succès de l'application. Nous mettons en évidence dans ce cas de figure qu'en fonction de la nature de la distribution de pannes, les deux objectifs à optimiser sont tantôt antagonistes, tantôt congruents. Ensuite en fonction de la nature de distribution de pannes nous donnons des approches d'ordonnancement avec des ratios de performance garantis par rapport aux deux objectifs. / The parallel computing platforms available today are increasingly larger. Typically the emerging parallel platforms will be composed of several millions of CPU cores running up to a billion of threads. This intensive growth of the number of parallel threads will make the application subject to more and more failures. Consequently it is necessary to develop efficient strategies providing safe and reliable completion for HPC parallel applications. Checkpointing is one of the most popular and efficient technique for developing fault-tolerant applications on such a context. However, checkpoint operations are costly in terms of time, computation and network communications. This will certainly affect the global performance of the application. In the first part of this thesis, we propose a performance model that expresses formally the checkpoint scheduling problem. Two variants of the problem have been considered. In the first variant, the objective is the minimization of the expected completion time. Under this model we prove that when the failure rate and the checkpoint cost are constant the optimal checkpoint strategy is necessarily periodic. For the general problem when the failure rate and the checkpoint cost are arbitrary we provide a numerical solution for the problem. In the second variant if the problem, we exhibit the tradeoff between the impact of the checkpoints operations and the lost computation due to failures. In particular, we prove that the checkpoint scheduling problem is NP-hard even in the simple case of uniform failure distribution. We also present a dynamic programming scheme for determining the optimal checkpointing times in all the variants of the problem. In the second part of this thesis, we design several fault tolerant scheduling algorithms that minimize the application makespan and in the same time maximize the application reliability. Mainly, in this part we point out that the growth rate of the failure distribution determines the relationship between both objectives. More precisely we show that when the failure rate is decreasing the two objectives are antagonist. In the second hand when the failure rate is increasing both objective are congruent. Finally, we provide approximation algorithms for both failure rate cases.

[pt] Além de uma crescente importância econômica da produço de petróleo contendo parafina dos recursos águas ultra-profundas, as preocupações coma deposição e gelificação de parafina desempenha uma funcão significativa nesta questão. óleos parafínicos gelificados frequentemente exibem comportamento reológico análoga para fuidos com tensão de cedência. Existe uma tensão crítica, abaixo do qual nenhum fluxo ocorre, mas acima doqual a viscosidade de uma sistema gelificada diminui drasticamente. Assim, para reinício de escoamento de óleo cru gelificado, uma pressão maior do que a pressão de funcionamento normal deve ser aplicada para exceder a tensão de cedência do fluido na parede, esta pressão mínima exegida deve ser determinada. Neste estudo para explorar o conceito de pressão mínima, fluidos com tensão de cedência foram investigados inteiramente. A investigação foi iniciada com o fluido de tensão de cedência simples e, em seguida, avanou com um tixotrpico usando reômetro e configuração experimental para escoamento de fluido em tubo. Em ambos, os casos a condio não deslizamento foi atingido, o comportamento de fluidos com tensão de cedência foi examinado em detalhe, os resultados de experimentos de reometria e transporte de fluido em tubos foram verificados. Com a colocação de todos juntos, a pressão mínima exigida ou em outra palavra a tensão crítica para partida de escoamento de fluidos com tensão de cedência foi descoberta. / [en] Besides an increasing economic importance of producing wax-containing crude oil from ultra deep water resources, concerns about wax deposition and gelation play a significant role in this area. Gelled waxy crude oils often exhibit rheological behavior analogous to yield stress fluids. There is a critical or range of stresses, below which no flow occurs, but above which the viscosity of a gelled system decreases drastically. Thus, in order to restart flow of a gelled crude, a pressure larger than the typical operating pressure should be applied to exceed the yield stress of the fluid at wall, this required minimum pressure should be determined. In this study to explore the minimum pressure notion, yield stress fluids were investigated comprehensively. The investigation was initiated with simpler yield stress fluid and then advanced with thixotropic one using rheometer and designed experimental setup for fluid flow into tube. In both cases no-slip condition was achieved, the behavior of yield stress fluids was screened in detail, the outcomes of fluid transport in tube and rheometric tests were combined and cross checked. Finally with putting all together, the required minimum pressure or in other words, the critical shear stress needed to startup the flow of yield stress fluids was discovered.

Le transport des bruts paraffiniques, et tout particulièrement leur remise en écoulement après un arrêt, dans de longues conduites sous-marines soumises à de basses températures, peut être difficile du fait de l'augmentation de leur viscosité. Le comportement rhéologique d´une huile paraffinique modèle, possédant des propriétés macroscopiques d'écoulement analogues à celles des bruts paraffiniques, est d'abord analysé en utilisant la vélocimétrie par imagerie par résonance magnétique associée à des mesures de contrainte de cisaillement au sein d'une géométrie Couette. Nous montrons que lors d'un écoulement forcé à température constante le matériau subit une déstructuration irréversible qui dépend de l'intensité du cisaillement. Ainsi la contrainte apparente critique permettant l'écoulement du matériau dépend de l'histoire thermique et d'écoulement subie par le matériau. Nous étudions ensuite le comportement rhéologique complet de deux bruts réels à partir de différents types de tests rhéométriques (fluages, redémarrage, régime permanent, changement brusque de vitesse) pour différentes histoires d'écoulement, notamment pendant la période de refroidissement. Le comportement détaillé du matériau en régime transitoire ainsi observé peut alors être modélisé. De plus les variations du seuil de contrainte en fonction de l'histoire thermique et de l'écoulement sont aussi décrites, ce qui nous donne le champ de contrainte seuil dans la conduite à l'état initial. Le modèle dans son ensemble est finalement implémenté dans un code de calcul pour simuler le redémarrage de l´écoulement d'un brut paraffinique dans une conduite réelle / Transporting waxy crude oils through long pipelines at low temperatures may be challenging, particularly its flow restart after a pipeline shut-in, due to its viscosity increase. The rheological behavior of a model waxy oil with macroscopic flow properties analogous to waxy crude oils is first analyzed using Magnetic Resonance Imaging velocimetry associated to stress measurements in a Couette geometry. While flowing at constant temperature, major irreversible structure break depending on shear intensity are observed. Thus, the critical apparent shear stress beyond which the material flows depends on the thermal and flow histories of the oil. Next, the rheological behavior of two waxy crude oils is studied using rheometrical tests (creep tests, flow restarts, abrupt changes of shear rate and steady flow) after different flow histories, notably during the cooling process. Then, those experimentally observed trends are modeled. Additionally, a comprehensive study of the yield stress in function of flow and temperature histories is presented. It provides an approach for describing the yield stress field inside the pipeline at the flow restart moment. Finally, the entire rheological model is implemented in the computational code for simulating waxy crude oils flow restart of a real scale pipeline

[pt] O petróleo é uma mistura complexa de hidrocarbonetos e pode conter em sua composição parafinas que, quando submetidas a baixas temperaturas, podem precipitar e gelificar, apresentando uma Tensão Limite de Escoamento. O estudo do comportamento do petróleo nesta condição é importante para a indústria porque, uma vez que o petróleo esteja gelificado, o reinício do escoamento pode demandar a adição de energia ao sistema, cujo dimensionamento para operação com altas pressões envolve custos elevados. Os valores de pressão de reinício de escoamento do petróleo gelificado encontrados no campo são frequentemente menores em relação aos valores calculados. O presente trabalho simulou o processo de reinício de escoamento através de uma bancada experimental que reproduz o resfriamento estático sofrido pelo petróleo parafínico em um duto submarino. Além disso, são apresentados dois métodos para cálculo da contração que resulta do resfriamentoe gelificação dos óleos parafínicos, objetivando verificar se existe uma relação entre a contração do fluido e a diferença entre a Tensão Limite de Escoamento e a tensão efetiva para iniciar o seu escoamento. O primeiro método proposto é o método da Pipeta, que consiste na utilização de uma pipeta, acoplada a um recipiente com controle de temperatura, para medição do volume de líquido. O segundo método proposto é o da célula PVT, que consiste na utilização de um sistema fechado de volume conhecido em que a medição da variação do volume de líquido é estimada pela variação do volume do gás à baixa pressão com a adoção da hipótese de gás ideal. Foram utilizados fluidos sintéticos, visando representar o petróleo parafínico, com diferentes concentrações de parafina, óleo mineral e querosene. A determinação da Tensão Limite de Escoamento foi feita a partir de testes de Creep. Os resultados mostraram que a contração do fluido é uma grandeza de difícil medição, com um alto grau de incerteza, mas que é possível estimar ordem de grandeza dessa contração para os fluidos estudados. / [en] Petroleum, as it is a complex mixture of hydrocarbons, may contain paraffinic compounds which, when subjected to low temperatures, can deposit and gel. The study of the behavior of petroleum in this condition is very important for the industry because, once the waxy crude oil gels, the restart process may demand extra energy addition to the system, whose dimensioning is expensive for high operation required pressures. Restart pressure values of the gelled oil found from laboratory tests often show a significant difference from the real values found in the field. In order to compare the yield stress and the effective stress, the present work simulated the flow restarting process through an experimental rig to reproduce the static cooling applied to a pipeline with waxy crude oil. In addition, two methods are presented for calculating the thermal shrinkage formed during the cooling and gelation of the waxy crude oils, in order to verify if there is a relationship between the shrinkage and the difference between the yield stress and the effective stress to start flowing. The first method proposed is the Pipette method, which consists of the use of a pipette, coupled to a container with temperature control, to measure the volume of liquid. The second method proposed is the PVT cell method, which consists of the use of a closed system of known volume in which the measurement of the liquid volume variation is estimated by the variation of the gas volume at low pressure with the adoption of the Ideal gas hypothesis. The fluids selected for the studies to represent paraffinic oil were laboratory-synthesized fluids with different concentrations of paraffin, mineral oil and kerosene, and they were characterized rheologically by stress ramp and creep tests for the determination of the yields stress. The results showed that thermal shrinkage is a difficult quantity to measure, which gives it a high degree of uncertainty, but it is possible to estimate the magnitude order of the thermal shrinkage for the fluids studied.

Le transport des bruts paraffiniques, et tout particulièrement leur remise en écoulement après un arrêt, dans de longues conduites sous-marines soumises à de basses températures, peut être difficile du fait de l'augmentation de leur viscosité. Le comportement rhéologique d´une huile paraffinique modèle, possédant des propriétés macroscopiques d'écoulement analogues à celles des bruts paraffiniques, est d'abord analysé en utilisant la vélocimétrie par imagerie par résonance magnétique associée à des mesures de contrainte de cisaillement au sein d'une géométrie Couette. Nous montrons que lors d'un écoulement forcé à température constante le matériau subit une déstructuration irréversible qui dépend de l'intensité du cisaillement. Ainsi la contrainte apparente critique permettant l'écoulement du matériau dépend de l'histoire thermique et d'écoulement subie par le matériau. Nous étudions ensuite le comportement rhéologique complet de deux bruts réels à partir de différents types de tests rhéométriques (fluages, redémarrage, régime permanent, changement brusque de vitesse) pour différentes histoires d'écoulement, notamment pendant la période de refroidissement. Le comportement détaillé du matériau en régime transitoire ainsi observé peut alors être modélisé. De plus les variations du seuil de contrainte en fonction de l'histoire thermique et de l'écoulement sont aussi décrites, ce qui nous donne le champ de contrainte seuil dans la conduite à l'état initial. Le modèle dans son ensemble est finalement implémenté dans un code de calcul pour simuler le redémarrage de l´écoulement d'un brut paraffinique dans une conduite réelle / Transporting waxy crude oils through long pipelines at low temperatures may be challenging, particularly its flow restart after a pipeline shut-in, due to its viscosity increase. The rheological behavior of a model waxy oil with macroscopic flow properties analogous to waxy crude oils is first analyzed using Magnetic Resonance Imaging velocimetry associated to stress measurements in a Couette geometry. While flowing at constant temperature, major irreversible structure break depending on shear intensity are observed. Thus, the critical apparent shear stress beyond which the material flows depends on the thermal and flow histories of the oil. Next, the rheological behavior of two waxy crude oils is studied using rheometrical tests (creep tests, flow restarts, abrupt changes of shear rate and steady flow) after different flow histories, notably during the cooling process. Then, those experimentally observed trends are modeled. Additionally, a comprehensive study of the yield stress in function of flow and temperature histories is presented. It provides an approach for describing the yield stress field inside the pipeline at the flow restart moment. Finally, the entire rheological model is implemented in the computational code for simulating waxy crude oils flow restart of a real scale pipeline