DNA damage or replication stress during S-phase can activate the S-phase checkpoint which executes a variety of responses, such as the inhibition of origin firing and replication fork stabilisation. Deregulation of the S-phase checkpoint leads to genomic instability, which has been implicated in diseases such as cancer. In this thesis, I aimed to address whether the S-phase checkpoint is regulated outside of S-phase, and how the S-phase checkpoint targets its substrates in budding yeast. Although this checkpoint has thus far been associated exclusively with S-phase, it remains unknown whether its responses such as inhibition of origin firing can also occur in other phases of the cell cycle. To investigate this, the targets of the S-phase checkpoint for the inhibition of origin firing were analysed outside of S-phase upon DNA damage. Interestingly, I showed that the S-phase checkpoint effector kinase Rad53 phosphorylates its targets to inhibit origin firing outside of S-phase upon DNA damage when there is no replication. I then set out to test whether inhibition of origin firing by Rad53 outside of S-phase might be important for faithful DNA replication. Having shown that the checkpoint response is not specific for any cell cycle phases, I then tested how the specificity of Rad53 for its substrates might be determined. After demonstrating that the essential replication protein Cdc45 is required for Rad53 to phosphorylate the initiation factor Sld3, the key residues of Cdc45 necessary for Rad53 interaction were identified. A Cdc45 allele was produced by mutating the identified residues. This allele of Cdc45 is a separation-of-function mutant which prevents Sld3 phosphorylation upon DNA damage, but retains its function in DNA replication. Because Cdc45 travels with the replication fork, it is possible that Cdc45 also targets Rad53 to the replication fork to stabilise it upon replication stress. Overall, this thesis provides evidence that the S-phase checkpoint can function throughout the cell cycle and that Cdc45 targets Rad53 to some of its substrates, and possibly plays a role in replication fork stabilisation.

Esta Dissertação de Mestrado propõe dois novos algoritmos para tornar mais eficiente o escalonamento on-line de tarefas com dependências estritas em agregados de computadores que usam como middleware para troca de mensagens alguma implementação da MPI (até a versão 2.1). Esses algoritmos foram projetados tendo-se em vista programas construídos no modelo de programação fork/join, onde a operação de fork é usada sobre uma chamada recursiva da função. São eles: 1. O algoritmo RatMD, implementado através de uma biblioteca de primitivas do tipo map-reduce, que funciona para qualquer implementação MPI, com qualquer versão da norma. Utilizado para minimizar o tempo de execução de uma computação paralela; e 2. O algoritmo RtMPD, implementado através de um sistema distribuído sobre daemons gerenciadores de processos criados dinamicamente com a implementação MPICH2 (que implementa a MPI-2). Utilizado para permitir execuções de instâncias maiores de programas paralelos dinâmicos. Ambos se baseiam em roubo de tarefas, que é a estratégia de balanceamento de carga mais difundida na literatura. Para ambos os algoritmos apresenta-se modelagem téorica de custos. Resultados experimentais obtidos ficam dentro dos limites teóricos calculados. RatMD provê uma redução no tempo de execução de até 80% em relação ao algoritmo usual (baseado em round-robin), com manutenção do speedup próximo ao linear e complexidade espacial idêntica à popular implementação com round-robin. RtMPD mantém, no mínimo, o mesmo desempenho que a implementação canônica do escalonamento em MPICH2, dobrando-se o limite físico de processos executados simultaneamente por cada nó. / This Master’s Dissertation proposes two new algorithms for improvement on on-line scheduling of dynamic-created tasks with strict dependencies on clusters of computers using MPI (up to version 2.1) as its middleware for message-passing communication. These algorithms were built targeting programs written on the fork-join model, where the fork operation is always called over an recursive function call. They are: 1. RatMD, implemented as a map-reduce library working for any MPI implementation, on whatever norm’s version. Used for performance gain; and 2. RtMPD, implemented as a distributed system over dynamic-generated processes manager daemons with MPICH2 implentation of MPI. Used for executing larger instances of dynamic parallel programs. Both algorithms are based on the (literature consolidated) work stealing technique and have formal guarantees on its execution time and load balancing. Experimental results are within theoretical bounds. RatMD shows an improvement on the performance up to 80% when paired with more usual algorithms (based on round-robin strategy). It also provides near-linear speedup and just about the same space-complexity on similar implementations. RtMPD keeps, at minimum, the very same performance of the canonical MPICH2 implementation, near doubling the physical limit of simultaneous program execution per cluster node.

abstract: The accurate and fast determination of organic air pollutants for many applications and studies is critical. Exposure to volatile organic compounds (VOCs) has become an important public health concern, which may induce a lot of health effects such as respiratory irritation, headaches and dizziness. In order to monitor the personal VOCs exposure level at point-of-care, a wearable real time monitor for VOCs detection is necessary. For it to be useful in real world application, it requires low cost, small size and weight, low power consumption, high sensitivity and selectivity. To meet these requirements, a novel mobile device for personal VOCs exposure monitor has been developed. The key sensing element is a disposable molecularly imprinted polymer based quartz tuning fork resonator. The sensor and fabrication protocol are low cost, reproducible and stable. Characterization on the sensing material and device has been done. Comparisons with gold standards in the field such as GC-MS have been conducted. And the device’s functionality and capability have been validated in field tests, proving that it’s a great tool for VOCs monitoring under different scenarios. / Dissertation/Thesis / Doctoral Dissertation Chemical Engineering 2017

Parallel processing is prevalent in many manufacturing and service systems. Many manufactured products are built and assembled from several components fabricated in parallel lines. An example of this manufacturing system configuration is observed at a manufacturing facility equipped to assemble and test web servers. Characteristics of a typical web server assembly line are: multiple products, job circulation, and paralleling processing. The primary objective of this research was to develop analytical approximations to predict performance measures of manufacturing systems with job failures and parallel processing. The analytical formulations extend previous queueing models used in assembly manufacturing systems in that they can handle serial and different configurations of paralleling processing with multiple product classes, and job circulation due to random part failures. In addition, appropriate correction terms via regression analysis were added to the approximations in order to minimize the gap in the error between the analytical approximation and the simulation models. Markovian and general type manufacturing systems, with multiple product classes, job circulation due to failures, and fork and join systems to model parallel processing were studied. In the Markovian and general case, the approximations without correction terms performed quite well for one and two product problem instances. However, it was observed that the flow time error increased as the number of products and net traffic intensity increased. Therefore, correction terms for single and fork-join stations were developed via regression analysis to deal with more than two products. The numerical comparisons showed that the approximations perform remarkably well when the corrections factors were used in the approximations. In general, the average flow time error was reduced from 38.19% to 5.59% in the Markovian case, and from 26.39% to 7.23% in the general case. All the equations stated in the analytical formulations were implemented as a set of Matlab scripts. By using this set, operations managers of web server assembly lines, manufacturing or other service systems with similar characteristics can estimate different system performance measures, and make judicious decisions - especially setting delivery due dates, capacity planning, and bottleneck mitigation, among others.

In order to monitor the T7 replisome fate upon encountering abasic lesion, I optimized a single molecule flow stretching assay where the replisome encounters either abasic site or undamaged site inserted at 3.5 kilobases from the replication fork. The obtained events were categorized into three groups; bypass, restart and permanent stop. The results showed 52% bypass, 39% pause and 9% stop upon encountering the abasic lesion. The pause duration in the restart events was found to be ten times longer than the undamaged one. Moreover, an ensemble experiment was performed, and the results were slightly consistent with regard to the bypass percentage (70%) but the stoppage percentage was significantly higher in the ensemble replication reaction (30%). Further investigations were made and it was found that the rate of the T7 replisome increases after bypassing the abasic lesion. To inquire more about this rate switch and the difference between the single molecule and ensemble results, another unwinding experiment was performed where only gp4 (helicase) was used from the replisome. Interestingly, the rate of DNA unwinding by gp4 was similar to the rate observed after the replisome bypasses the lesion. We hypothesize that the polymerase is stalled at the abasic site and its interaction with the helicase is lost. Consequently, the helicase and the polymerase will uncouple where the helicase continues unwinding the DNA to result in a higher observed rate after bypassing the abasic site. Additional studies will be performed in the future to directly observe the helicase and polymerase uncoupling upon encountering the lesion.

The aim of this thesis is to investigate the force loading of the front telescopic fork girder of the motorcycle and its impact on the structure of the girders. The force effect in fork storage is solved by a mathematical model in Adams View based on calculated and experimentally determined parameters. Managed to gather a series of data and parameters of the Triumph Daytona 955i. The created model achieves high accuracy in terms of motorcycle kinematics. The benefit of this work is to get an overview of the forces acting in the suspension of the front wheel of the motorcycle.

Purpose of this master´s thesis is the construction proposal of azimuth fork mount with load capacity to 20kg including both axes drives. The solution contains design options of azimuth fork mount, calculations, design proposal of the mount and drawings of the shaft, fork and the assembly.

The cell division cycles of differentiating cells are coordinated so as to generate sufficient numbers of mature cells. The cell cycle may also regulate the process of differentiation, in ways that are not well understood. We previously discovered that during erythropoiesis, the cell cycle is synchronized with a specific developmental switch, where erythroid progenitors known as colony-forming-unit-erythroid (CFU-e) transition from a self-renewal state to a state of erythroid terminal differentiation (ETD). This switch takes place during a single cell cycle S phase and is dependent on S-phase progression. My work shows that this S phase is unusual, in that it is shorter than S phase in preceding cycles, as a result of a global increase in replication fork speed. I found that the CDK inhibitor, p57KIP2, negatively regulates replication fork speed in self-renewing CFU-e, and its down-regulation at the switch to ETD results in S-phase shortening. p57KIP2-mediated inhibition of CDK2 is essential for CFU-e self-renewal. It exerts this effect by reducing replication stress and also reducing the probability of transition from CFU-e to ETD, promoting CFU-e self-renewal instead. CDK2 inhibiting drugs that mimic the action of p57KIP2 stimulate erythropoiesis both in vitro and in vivo, through expansion of the CFU-e pool. In addition to p57KIP2, E2f4 also regulates S-phase shortening and the efficiency of the CFU-e to ETD transition. Overall, my work shows that S-phase speed regulates a key erythroid cell fate decision, and suggests a possible translational application of CDK2 inhibiting drugs in the stimulation of erythropoiesis.

The mathematical characterization of the sound of a musical instrument still follows Schumann’s laws [1]. According to this theory, the resonances of the instrument body, “the formants”, filter the oscillations of the sound generator (e.g., strings) and produce the characteristic “timbre” of an instrument. This is a strong simplification of the actual situation. It applies to a point source and does not distinguish between a loudspeaker and a three-dimensional instrument. In this work we investigate Finite-Element-based numerical simulations of eigenfrequencies and eigenmodes of a tuning fork in order to capture the oscillation behavior of its eigenfrequencies. We model the tuning fork as an elastic solid body and solve an eigenvalue equation derived from a system of coupled equations from linear elasticity theory on an unstructured three-dimensional grid. The eigenvalue problem is solved using the preconditioned inverse iteration (PINVIT) method with an efficient geometric multigrid (GMG) preconditioner. The latter allows us to resolve the tuning fork with a high resolution grid, which is required to capture fine modes of the simulated eigenfrequencies. To verify our results, we compare them with measurement data obtained from an experimental modal analyses of a real reference tuning fork. It turns out that our model is sufficient to capture the first eight eigenmodes of a reference tuning fork, whose identification and reproduction by simulation is novel to the knowledge of the author.

Exponential rates of digestion are described for brown trout and whitefish for July, October, December (1969), and April (1970). The slope of the line fitted to the digestion data from each month was defined as the instantaneous rate of digestion and applied to an exponential growth model to determine the instantaneous consumption rate. The digestion and consumption rates were applied to field measurements of percent fullness to determine the amount of food material ingested during a 24 hour period. Brown trout consumed 127, 24, 19, and 84 mean percent of their stomach capacity in the July, October, December, and April studies. Whitefish consumed 74, 21, 46, and 51 mean percent of their stomach capacity in the same respective study periods. Mean daily ration from four major collection periods was calculated on fish in the 50 gram to BOO gram size range. Brown trout daily ration varied between 1.35 percent and 2.59 percent. Whitefish daily ration varied between 0.44 percent and 0.83 percent. Brown trout diets were quite variable with 44 percent of their caloric intake comprised of terrestrial invertebrates in October, 55 percent of the December calories comprised of fish eggs, and 39 percent of the April calories made up of Leptoceridae larvae. Emerging imagoes were important items in the brown trout diets, contributing as much as 62 percent and not less than 11 percent of the numeric intake for one collection period. Whitefish did not rely upon emerging imagoes as a significant food source. Their stomachs consistently contained mayflies, chironomids, and caddis larvae. Both fish species occasionally consumed substantial amounts of the large stonefly, Pteronarcys.