yes / River morphological dynamics are complex phenomena in natural and environmental flows. In particular, the sediment transport around braid mid-channel bars has not gained enough understanding from previous research. The effect of submergence ratio on the turbulence behavior in the proximity of the bar has been investigated in this study. The spatial distribution of turbulent flow in the proximity of bar has been studied by plotting the depth-averaged two-dimensional contours of turbulent kinetic energy. The high value of TKE has been observed in regions just downstream from the bar. It is due to the vortex shedding occurring in that region. The interaction of sweep and ejection events have been analyzed using the parameter Dominance Function obtained from the ratio of occurrence probability of ejection events to the occurrence probability of sweep events. This outcome indicates that the depth averaged parameter Dominance Function has successfully predicted the high scouring region which makes it an ideal parameter for analyzing the scour phenomena in real-world water management projects. The high scouring zone lies in the close proximity of the bar. This shows that the scouring effect from the bar is limited to its close region. The magnitude of scouring occurring at the upstream region of the bar also increases with the increment of submergence ratio. The relationship of quadrant event inclination angles with the sediment transport occurring in the proximity of bar has been also studied, where an Angle Ratio parameter has been utilized for linking the bed elevation change with the inclination angle. The results indicate that the AR parameter has been successfully tested in this study to show its competence to represent the turbulent burst-induced bed sedimentation and scouring. / The author has confirmed that no changes were made to the content of this proof on publication, although the paper is watermarked uncorrected proof.

Les oscillateurs paramétriques optiques (OPO) continus sont des sources de lumière cohérente largement accordables reposant sur l'interaction paramétrique de trois champs dans un cristal non-linéaire. Leur utilité est aussi bien liée à cette accordabilité (spectroscopie) qu'aux propriétés quantiques propres au système (génération d'états comprimés, photons jumeaux). D'autre part, en tant que systèmes non-linéaires, les OPO sont susceptibles de présenter une grande richesse de phénomènes dynamiques temporels et spatio-temporels. Nous présentons une étude expérimentale, théorique et numérique de différentes instabilités temporelles présentées par les intensités des champs à la sortie de la cavité de notre OPO. Nous caractérisons des oscillations de fréquence de 1 à 300MHz dont nous montrons expérimentalement qu'elles ont pour origine l'interaction entre plusieurs modes transverses. Ces oscillations rapides peuvent être couplées à des oscillations plus lentes d'origine thermique, menant à l'apparition d'instabilités du type oscillations en rafales. Un développement perturbatif multi-échelle permet d'obtenir des solutions analytiques pour les champs une fois les oscillations rapides moyennées. Nous avons d'autre part observé ce qui est à notre connaissance la première observation expérimentale de chaos déterministe dans ce système. Enfin nos travaux expérimentaux et théoriques ont permis d'améliorer notre compréhension de la sélection de modes dans les OPO.

The methods that fueled the microscale revolution (top-down design/fabrication, combined with application of forces large enough to overpower stochasticity) constitute an approach that will not scale down to nanoscale systems. In contrast, in nanotechnology, we strive to embrace nature’s quite different paradigms to create functional systems, such as self-assembly to create structures, exploiting stochasticity, rather than overwhelming it, in order to create deterministic, yet highly adaptable, behavior. Nature’s approach, through billions of years of evolutionary development, has achieved self-assembling, self-duplicating, self-healing, adaptive systems. Compared to microprocessors, nature’s approach has achieved eight orders of magnitude higher memory density and three orders of magnitude higher computing capacity while utilizing eight orders of magnitude less power. Perhaps the most complex of functions, homeostatis by a biological cell – i.e., the regulation of its internal environment to maintain stability and function – in a fluctuating and unpredictable environment, emerges from the interactions between perhaps 50M molecules of a few thousand different types. Many of these molecules (e.g. proteins, RNA) are produced in the stochastic processes of gene expression, and the resulting populations of these molecules are distributed across a range of values. So although homeostasis is maintained at the system (i.e. cell) level, there are considerable and unavoidable fluctuations at the component (protein, RNA) level. While on at least some level, we understand the variability in individual components, we have no understanding of how to integrate these fluctuating components together to achieve complex function at the system level. This thesis will explore the regulation and control of stochasticity in cells. In particular, the focus will be on (1) how genetic circuits use noise to generate more function in less space; (2) how stochastic and deterministic responses are co-regulated to enhance function at a system level; and (3) the development of high-throughput analytical techniques that enable a comprehensive view of the structure and distribution of noise on a whole organism level.

Polymer pipes, typically high density polyethylene (HDPE), can be pulled-into-place, avoiding traditional cut-and-cover construction, using pipe bursting and horizontal directional drilling (HDD) pipe installation techniques. Of particular interest, are the ground displacements, induced by cavity expansion, associated with these techniques and the strains that develop in existing pipes in response to these displacements. Further, the axial stress-strain response of the new HDPE pipe during and after the cyclic pulling force history required to pull the pipe into place is of interest. Surface displacements and strains in an adjacent polyvinyl chloride (PVC) pipe induced by static pipe bursting were measured during the replacement of a new unreinforced concrete pipe. For the pipe bursting geometry tested, the maximum vertical surface displacement measured at the ground surface was 6 mm, while the distribution of vertical surface displacements extended no more than 2 m on either side of the centreline. The maximum longitudinal strain measured in the PVC pipe was less than 0.1% and its vertical diameter decreased by only 0.5%, suggesting that pipe bursting did not jeopardize the long-term performance of the water pipe tested. In addition, results from identical stress relaxation and creep tests performed on whole pipe samples and coupons trimmed from a pipe wall were compared, and these demonstrated that the coupons exhibited higher modulus than the pipe samples. Therefore, isolated pipe samples, as opposed to coupons, were tested to quantify the stress-strain response of HDPE pipe during the simulated installation, strain recovery, and axial restraint stages of HDD. Axial strains were found to progressively accumulate when an HDPE pipe sample was subjected to the cyclic stress history used to simulate an HDD installation. It was shown that existing linear and nonlinear viscoelastic models can serve as predictive design tools for estimating the cyclic strain history of HDPE pipe during installation. For the specific conditions examined, the tensile axial stresses redeveloped in the pipe samples, once restrained, were not large enough to lead to long-term stress conditions conducive to slow crack growth even when the short-term performance limits were exceeded by a factor of 1.5. / Thesis (Ph.D, Civil Engineering) -- Queen's University, 2009-04-01 18:19:24.434

The brain processes information sensed from the environment and guides behaviour. A fundamental component in this process is the storage and retrieval of past experiences as memories, which relies on the hippocampal formation. Although there has been a great progress in understanding the underlying neural code by which neurons communicate information, there are still open questions. Neural activity can be measured extracellularly as either spikes or field potentials. Isolated spikes and bursts of high-frequency spikes followed by silent periods can transmit messages to distant networks. The local field potential (LFP) reflects synaptic activity within a local network. The interplay between the two has been linked to cognitive functions, such as memory, attention and decision making. However, the code by which this neural communication is achieved is not well understood. We investigated a mechanism by which local network information contained in LFP rhythms can be transmitted to distant networks in the formof spike patterns fired by bursting neurons. Since rhythms within different frequency bands are prevalent during behavioural states, we studied this encoding during different states within the hippocampal formation. In the first paper, using a computational model we show that bursts of different size preferentially lock to the phase of the dominant rhythm within the LFP.We also present examples showing that bursting activity in the subiculum of an anaesthetised rat was phase-locked to delta or theta rhythms as predicted by the model. In the second paper, we explored possible neural codes by which bursting neurons can encode features of the LFP.We used the computational model reported in the first paper and analysed recordings from the subiculum of anaesthetised rats and the medial entorhinal cortex of an awake behaving rat. We show that bursting neurons encoded information about the instantaneous voltage, phase, slope and/or amplitude of the dominant LFP rhythm (delta or theta) in their firing rate. In addition, some neurons encoded about 10-15% of this information in intra-burst spike counts. We subsequently studied how the interactions between delta or theta rhythms can transfer information between different areas within the hippocampal formation. In the third paper, we show that delta and theta rhythms can act as separate routes for simultaneously transferring segregate information between the hippocampus and the subiculum of anaesthetised mice. We found that the phase of the rhythms conveyed more information than amplitude. We next investigated whether neurodegenerative pathology affects this information exchange. We compared information transfer within the hippocampal formation of young transgenic mice exhibiting Alzheimer’s disease-like pathology and healthy aged-matched control mice and show that at early stages of the disease the information transmission by LFP rhythm interactions appears to be intact but with some differences. The outcome of this project supports a burst code for relaying information about local network activity to downstream neurons and underscores the importance of LFP phase, which provides a reference time frame for coordinating neural activity, in information exchange between neural networks.

A administração intraperitoneal de 5-fluorouracil (5-FU) no pós-operatório imediato reduz a recorrência local e prolonga a sobrevida dos pacientes com câncer colônico. Contudo, esse tratamento também pode prejudicar a cicatrização das anastomoses intestinais. O objetivo deste estudo foi determinar os efeitos da quimioterapia (QT) intraperitoneal (IP) pós-operatória (PO) precoce com o 5-FU e da selagem anastomótica com o TachoSil sobre o processo de cicatrização de anastomoses colônicas. Quarenta ratos foram divididos em quatro grupos (I - IV, com dez ratos em cada) e submetidos à secção do cólon esquerdo seguida por anastomose. As anastomoses dos ratos dos grupos II e IV foram cobertas com o TachoSil. Solução salina (2 ml/dia grupos I e II) ou 5-FU (20 mg/kg/dia grupos III e IV) foi administrado por via IP uma vez ao dia, desde do procedimento cirúrgico até a morte programada dos animais no quarto dia pós-operatório. Foram realizadas medidas da pressão de ruptura e análise histopatológica das anastomoses. A perda relativa de peso foi significativamente maior nos animais do grupo III comparado a todos os demais grupos (p=0,0004). Não houve diferença significativa entre os grupos no que se refere à presença de fístulas, coleções perianastomóticas, sinais de dilatação intestinal pré-anastomótica ou aderências pós-operatórias. A pressão de ruptura foi significativamente menor no grupo III comparada a todos os demais grupos (p=0,001). A neoangiogênese foi significativamente menor no grupo III comparada aos grupos I e II (p=0,05). A infiltração fibroblástica foi significativamente maior no grupo I e em comparação ao grupo III (p=0,035). Não ocorreu diferença significativa entre os grupos no que concerne à presença de infiltração de células inflamatórias e deposição de colágeno. Os dados obtidos permitem concluir que a QT IP precoce com 5-FU afetou negativamente a fase inicial da cicatrização de anastomoses colônicas. Contudo, a selagem com o TachoSil foi capaz de reverter alguns dos efeitos adversos decorrentes da QT. / The administration of 5-fluorouracil (5-FU) during the early postoperative period can decrease local cancer recurrence but may also cause impairment of the anastomotic healing. This study examined the effects of the use of this therapy and of the anastomotic sealing with a fibrin-collagen patch (TachoSil) on the healing of colon anastomoses. Forty male rats were divided into four groups (I to IV, 10 rats each) that underwent transection and anastomosis of the left colon. The anastomoses were covered with TachoSil in groups II and IV. Saline solution (2 ml/day groups I and II) or 5-FU (20 mg/kg/day; groups III and IV) was administered intraperitoneally (IP) once daily for three days. Bursting pressure (BP) was recorded and the anastomoses were examined macroscopically and graded histologically. The relative weight loss was significantly higher in group III than in the other groups (p=0.0004). Anastomotic dehiscense, postoperative adhesion formation, perianastomotic collections, and preanastomotic dilatation did not differ significantly among groups. BP was significantly lower in group III compared to all other groups (p=0.001). Neoangiogenesis was significantly lower in group III compared to groups I and II (p=0.05). Fibroblastic activity was significantly higher in group I compared to group III (p=0.035). Inflammatory cell infiltration and collagen deposition did not differ significantly among groups. Our results shown that the early postoperative IP chemotherapy with 5-FU impaired the healing of colon anastomoses. However, anastomotic sealing with TachoSil reversed some of the negative effects of this therapy.

Doctor of Philosophy / Civil Engineering / Kyle Riding / Air voids are purposefully entrained in concrete to provide freeze-thaw durability of prestressed concrete railroad ties. Durability assurance requires consistent provision of an air void system comprised of small, well-distributed bubbles in sufficient quantity for durability and a quality control method for testing tie freeze-thaw durability. Manufacturing processes at three concrete manufacturing plants were investigated in order to determine the effects of process variability on resulting concrete air void system variability. Variation in the concrete air void system and other rheological properties occurred as results of the manufacturing process and vibration. Freezing and thawing durability testing of prestressed concrete ties is currently performed by applying ASTM C666 on 3 x 4 x 11 to 16 in. specimens cut from the shoulders of concrete ties. However, excising these specimens from prestressed concrete could lead to stress changes in the sample and cracking, potentially causing false interpretations of results. Therefore, testing was undertaken to understand the effects of prestressing and sample extraction on freeze-thaw durability measured by ASTM C666. In order to assess the effects of sampling and testing procedures on freeze-thaw quality control testing results of prestressed concrete railroad ties, full ties, half ties, and 3 x 4 x 11 in. excised samples were tested. Freeze-thaw testing included determination of the optimal method to measure freeze-thaw deterioration in large sections, the effects of saw-cutting, and the presence of reinforcement. Results indicated that the Ultrasonic Pulse Velocity accurately represented deterioration in large sections. The presence of reinforcement in excised samples led to faster deterioration compared to cast ASTM C666 samples, while saw-cutting without reinforcement did not significantly affect freeze-thaw durability.

A administração intraperitoneal de 5-fluorouracil (5-FU) no pós-operatório imediato reduz a recorrência local e prolonga a sobrevida dos pacientes com câncer colônico. Contudo, esse tratamento também pode prejudicar a cicatrização das anastomoses intestinais. O objetivo deste estudo foi determinar os efeitos da quimioterapia (QT) intraperitoneal (IP) pós-operatória (PO) precoce com o 5-FU e da selagem anastomótica com o TachoSil sobre o processo de cicatrização de anastomoses colônicas. Quarenta ratos foram divididos em quatro grupos (I - IV, com dez ratos em cada) e submetidos à secção do cólon esquerdo seguida por anastomose. As anastomoses dos ratos dos grupos II e IV foram cobertas com o TachoSil. Solução salina (2 ml/dia grupos I e II) ou 5-FU (20 mg/kg/dia grupos III e IV) foi administrado por via IP uma vez ao dia, desde do procedimento cirúrgico até a morte programada dos animais no quarto dia pós-operatório. Foram realizadas medidas da pressão de ruptura e análise histopatológica das anastomoses. A perda relativa de peso foi significativamente maior nos animais do grupo III comparado a todos os demais grupos (p=0,0004). Não houve diferença significativa entre os grupos no que se refere à presença de fístulas, coleções perianastomóticas, sinais de dilatação intestinal pré-anastomótica ou aderências pós-operatórias. A pressão de ruptura foi significativamente menor no grupo III comparada a todos os demais grupos (p=0,001). A neoangiogênese foi significativamente menor no grupo III comparada aos grupos I e II (p=0,05). A infiltração fibroblástica foi significativamente maior no grupo I e em comparação ao grupo III (p=0,035). Não ocorreu diferença significativa entre os grupos no que concerne à presença de infiltração de células inflamatórias e deposição de colágeno. Os dados obtidos permitem concluir que a QT IP precoce com 5-FU afetou negativamente a fase inicial da cicatrização de anastomoses colônicas. Contudo, a selagem com o TachoSil foi capaz de reverter alguns dos efeitos adversos decorrentes da QT. / The administration of 5-fluorouracil (5-FU) during the early postoperative period can decrease local cancer recurrence but may also cause impairment of the anastomotic healing. This study examined the effects of the use of this therapy and of the anastomotic sealing with a fibrin-collagen patch (TachoSil) on the healing of colon anastomoses. Forty male rats were divided into four groups (I to IV, 10 rats each) that underwent transection and anastomosis of the left colon. The anastomoses were covered with TachoSil in groups II and IV. Saline solution (2 ml/day groups I and II) or 5-FU (20 mg/kg/day; groups III and IV) was administered intraperitoneally (IP) once daily for three days. Bursting pressure (BP) was recorded and the anastomoses were examined macroscopically and graded histologically. The relative weight loss was significantly higher in group III than in the other groups (p=0.0004). Anastomotic dehiscense, postoperative adhesion formation, perianastomotic collections, and preanastomotic dilatation did not differ significantly among groups. BP was significantly lower in group III compared to all other groups (p=0.001). Neoangiogenesis was significantly lower in group III compared to groups I and II (p=0.05). Fibroblastic activity was significantly higher in group I compared to group III (p=0.035). Inflammatory cell infiltration and collagen deposition did not differ significantly among groups. Our results shown that the early postoperative IP chemotherapy with 5-FU impaired the healing of colon anastomoses. However, anastomotic sealing with TachoSil reversed some of the negative effects of this therapy.

La régulation de la transcription est l‟un des processus cellulaires des plus fondamentaux et constitue la première étape menant à l‟expression protéique. Son altération a des effets sur l‟homéostasie cellulaire et est associée au développement de maladies telles que le cancer. Il est donc crucial de comprendre les règles fondamentales de la fonction cellulaire afin de mieux cibler les traitements pour les maladies. La transcription d‟un gène peut se produire selon l‟un des deux modes fondamentaux de transcription : en continu ou en burst. Le premier est décrit comme un processus aléatoire et stochastique qui suit une distribution de Poisson. À chaque initiation de la transcription, indépendante de la précédente, un seul transcrit est produit. L‟expression en burst se produit lorsque le promoteur est activé pour une courte période de temps pendant laquelle plusieurs transcrits naissants sont produits. Apportant la plus grande variabilité au sein d‟une population isogénique, il est représenté par une distribution bimodale, où une sous-population n‟exprime pas le gène en question, alors que le reste de la population l‟exprime fortement. Les gènes des eucaryotes inférieurs sont pour la plupart exprimés de manière continuelle, alors que les gènes des eucaryotes supérieurs le sont plutôt en burst. Le but de ce projet est d‟étudier comment l‟expression des gènes a évolué et si la transcription aléatoire, ou de Poisson, est une propriété des eucaryotes inférieurs et si ces patrons ont changé avec la complexité des organismes et des génomes. Par la technique de smFISH, nous avons étudié de manière systématique quatre gènes évolutivement conservés (mdn1+, PRP8/spp42+, pol1+ et cdc13+) qui sont continuellement transcrits dans la levure S. cerevisiae. Nous avons observé que le mode d‟expression est gène-et-organisme spécifique puisque prp8 est exprimé de manière continuelle dans la levure S. pombe, alors que les autres gènes seraient plutôt exprimés en légers burst. / Regulating transcription is one of the most fundamental cellular processes and the first step of a long cascade of processes leading to protein expression. Altering transcriptional output often has major effects on cellular homeostasis and is associated with many disease phenotypes, such as cancer. Understanding the fundamental rules governing transcription regulation is therefore instrumental in understanding cellular function as well as in finding disease treatments. Transcription of a gene can occur through two fundamental different modes: “continuous” or “bursting”. Continuous transcription is defined as stochastic process where a promoter is always in its “on” state and each initiation event is independent of the previous. Bursting transcription occurs when a promoter is activated for a short time and multiple mRNAs are produced during the “on” state, followed by long periods of transcription inactivity. It leads to greater variability in an isogenic population, as expression is often bimodal as a sub-population does not express a given gene. Bursting expression is frequently observed in higher eukaryotes, while a continuous pattern seems to be common in lower eukaryotes. The goal of this project is to study how gene expression patterns evolved. We investigate whether Poisson-like transcription is a property of lower eukaryotes and whether transcription patterns have changed when organisms and genomes evolved into more complex systems. Using smFISH, we have systematically determined expression patterns of four evolutionarily conserved genes; mdn1+, PRP8/spp42+, pol1+ and cdc13+, previously shown to be continuously expressed in the yeast S. cerevisiae. Expression was studied in the yeast S. pombe, as an example for another lower eukaryote as well as in human cell-lines. We observe that expression patterns are organism-and-gene specific suggesting that expression patterns have evolved to fulfill gene specific functions.

An experimental program was conducted at the Ferguson Structural Engineering Laboratory of The University of Texas at Austin, under the auspices of Texas Department of Transportation (TxDOT) Research Project 5831, to investigate the tensile stresses that develop in the end regions of pretensioned concrete U-beams at transfer of prestress. Understanding the effect of these “bursting” and “spalling” stresses is essential in order to design standard details that might lead to reliably-serviceable end regions. Two full-scale beam specimens, designed to be worst-case scenarios for bursting and spalling, were fabricated. Each beam had one square and one highly skewed end. Extensive instrumentation, including strain gages on transverse and lateral reinforcing bars, was employed in the end regions of these U-beams. Experimentally determined bursting and spalling stresses in these bars were compared to results of past projects (from the literature) investigating I-beams and inverted T-beams. Preliminary recommendations are made for changes in the standard reinforcing details for U-beam end regions. Such recommended details will be tested in the upcoming phase of Research Project 5831. / text