Master of Science / Department of Civil Engineering / Stacey E. Kulesza / Thousands of metallic drainage structures have been installed by the Kansas Department of Transportation (KDOT) to facilitate proper drainage of highway systems across the state. Several studies were conducted over the past 30 years by KDOT to determine the durability of different corrugated metal pipe (CMP) materials and estimate their performance against the deterioration that occurs due to the electrochemical process of corrosion. These past studies have influenced KDOT policy regarding pipe material, but a method to quickly determine the rate of deterioration, and accurately predict a service life, is still not well defined. With the last comprehensive study performed in 1990 by KDOT, there is now a need to perform a field evaluation to determine the performance of CMPs in Kansas. This research conducted a survey of observed CMP conditions for 80 sites across KDOT districts one and four using a quantitative observational rating system. The goal of the survey was to determine the performance of CMPs in the field. The findings of this study indicate that a 1975 change in KDOT pipe policy has increased the rapid deterioration of CMPs. An additional study was conducted to determine if accurate service life predictions could be made based on chemical and biological characteristics of soil taken near the CMP invert. A method to test the leachate water exposed to the soil sample was created. Laboratory results of four field samples indicated that the rate at which the invert deteriorated corresponded to the total amount of chloride anion mobilized in the leachate over a 72-hour period, along with the standard deviation of pH measured throughout the test. This contradicts most field corrosion tests that only measure field pH and resistivity. The developed method of measuring soil sample leachate may provide a more accurate estimate of the performance of CMP in the sample location.

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Sialyltransferases, CMP-sialic acid synthetases and CMP-sialic acid transport proteins play a crucial role in the construction of cell surface glycoconjugates. These proteins also have a pivotal role to play in a number of diseases, including cancer. The sialyltransferase enzymes are responsible for transfering sialic acids from the donor substrate (CMP-sialic acid) to growing cell surface glycoconjugate chains within the Golgi apparatus. The CMP-sialic acid synthetase enzymes are responsible for the synthesis of the CMP-sialic acid, the donor substrate of the sialyltransferases in the nucleus, while the CMP-sialic acid transport proteins are responsible for transporting CMP-sialic acid from the Cytosol to the Golgi apparatus. When these proteins function in an abnormal way, hypersialylation results, leading to an increased level of sialylation on the cell surface. This increased level of sialylation aids in the detachment of primary tumour cells due to an increase in the level of overall negative charge, causing repulsion between the cancer cells. Therefore, the sialyltransferase enzymes, CMP-sialic acid synthetases and CMP-sialic acid transport proteins are intimately involved in the metastatic cascade associated with cancer. Chapter 1 provides a general introduction of cancer metastasis, discussing the roles of three target proteins (CMP-sialic acid synthetases, CMP-sialic acid transport proteins and sialyltransferases), as well as discussing their substrate specificities, with an emphasis on their involvements in cancer metastasis. The Chapter concludes with an overview of the types of compounds intended to be utilised as probes or inhibitors of these proteins. Chapter 2 describes the general approach towards the synthesis of CMP-Neu5Ac mimetics with a sulfur linkage in the presence of a phosphate group in the general structure 38. The precursor phosphoramidite derivative 45 was prepared and isolated in a good yield using Py.TFA. Unfortunately, the target compound 38 could not be prepared. Chapter 3 describes an alternative strategy wherein S-linked sialylnucleoside mimetics, of the general structure 39, with a sulfur linkage, but no phosphate group, between the sialylmimetic and the ribose moiety in the base is targeted. A series of these S-linked sialylnucleoside mimetics were successfully prepared. Cytidine, uridine, adenosine and 5-fluorouridine nucleosides were used to create a library of different nucleosides and with structural variability also present in the sialylmimetic portion. This small 'library' of 15 compounds was designed to shed light on the interaction of these compounds with the binding sites of the sialyltranferase, CMP-sialic acid synthetase and/or CM-sialic acid transport protein. Approaches towards the synthesis of O-linked sialylnucleoside mimetics of the general structure 40 are described in Chapter 4. Several methodologies are reported, as well as protecting group manipulations, for successful preparation of these sialylnucleoside mimetics. Cytidine and uridine were employed as the nucleosides, thus allowing a direct comparison between the O- and S-linked sialylnucleoside mimetics in biological evaluation. It appears from these synthetic investigations that gaining access into the O-linked series is not as straightforward as for the S-linked series, with alternative protecting group strategies required for the different nucleosides. The biological evaluation of some of the compounds reported in Chapters 3 and 4 is detailed in Chapter 5. The sialylnucleoside mimetics were evaluated, by 1H NMR spectroscopy, for their ability to inhibit CMP-KDN synthetase. In addition, an initial 1H NMR spectroscopic-based assay was investigated for inhibition studies of α(2,6)sialyltranferase in the absence of potential inhibitors. The final chapter (Chapter 6) brings together full experimental details in support of the compounds described in the preceding Chapters.

When parallel applications do not fully utilize the cores that are available to them they are missing the opportunity to have better performance. Sometimes threads have to wait for other threads. I call the code segments that make other threads wait bottlenecks. Examples of these bottlenecks include contended critical sections, threads arriving late to barriers and the slowest stage of a pipelined program. Other times all threads are running but some of them, which I call lagging threads, are making less progress, setting the stage to become bottlenecks. My thesis proposes identifying the code segments that are more critical for performance and efficiently accelerating them using faster cores, by either migrating execution to large cores of an Asymmetric Chip Multi-Processor (ACMP) or executing locally on DVFS-accelerated cores. The key contribution of this dissertation is a Utility of Acceleration metric that combines a measure of the acceleration for each code segment with a measure of its criticality. This metric enables meaningful comparisons to decide which bottlenecks or lagging threads to accelerate with each of the available acceleration mechanisms. My evaluation shows significant performance improvement for single multithreaded applications and sets of multiple single- and multi-threaded applications, and also reduction in energy-delay product due to the efficient utilization of the available acceleration mechanisms. / text

Since first published in 1998, the Enterprise JavaBeans technology has become a popular choice for the development of middleware systems. Even though its popularity, the technology is considered quite complex and rather difficult to master. The main contribution to its complexity is the part of the EJB that deals with persistence. The most common and most popular way of implementing EJB persistence is called Container Managed Persistence (CMP). Today, developers consider the utilization of CASE tools for the EJB development process obvious. Despite this, available CASE tools have very limited support for the complete CMP development process. In this thesis we have isolated steps within the CMP development process that could benefit from CASE tool support. We have then identified possible solutions and remedies to address these steps. These solutions where then implemented in a full fledged CASE tool, called CMP Developer.

Since first published in 1998, the Enterprise JavaBeans technology has become a popular choice for the development of middleware systems. Even though its popularity, the technology is considered quite complex and rather difficult to master. The main contribution to its complexity is the part of the EJB that deals with persistence. The most common and most popular way of implementing EJB persistence is called Container Managed Persistence (CMP). Today, developers consider the utilization of CASE tools for the EJB development process obvious. Despite this, available CASE tools have very limited support for the complete CMP development process. In this thesis we have isolated steps within the CMP development process that could benefit from CASE tool support. We have then identified possible solutions and remedies to address these steps. These solutions where then implemented in a full fledged CASE tool, called CMP Developer.

The contribution to the global sea level change from the large ice sheet of Greenland and Antarctica if both ice sheet where to melt completely, is estimated to be approximately 70 meters. How much the actual contribution would be, is due to complex ice dynamics still unclear. It is crucial to gain knowledge about the spatial distribution of wet and frozen beds, in order to increase the understanding of ice-sheet flow. There are yet no complete models available that can fully explain and describe ice sheet motion and the feedback mechanisms that are involved, making this topic important for future predictions and modelling of the impact of a warming climate. Radar sounding can be used for distinguish the different reflectivity between wet and frozen beds, this is however limited by uncertainties caused by scattering and attenuation. To be able to map the spatial distribution of subglacial water, attenuation needs to be taken into account. Here, mapping of water under a smaller part of the Greenland ice sheet was performed, and three different methods for acquiring attenuation values was used to obtain a suitable value of the attenuation. A CMP analysis, an attenuation model based on temperature data and an attenuation estimation derived from common-offset radar data, the mean attenuation value from these methods was used for the determination of the reflectivity. Hydraulic potential calculations was also performed, analyzed and compared with the result from the mapping of the reflectivity. Higher reflectivity was observed closer to the front of the glacier, indicating wetter basal condition in that area. This area did also have more moulins and sinks which could lead water from the surface down to the base of the ice. / De båda istäckena Grönland och Antarktis uppskattas kunna bidra till den globala havsytehöjningen med ungefär 70 meter om de bägge istäckena skulle smälta helt och hållet. Hur mycket det faktiska bidraget skulle bli, är på grund av komplex isdynamik fortfarande oklart. Det är av yttersta vikt att öka kunskapen om den rumsliga fördelningen av frusna och icke-frusna bottnar under ett istäcke, för att öka förståelsen om isrörelse. Det finns i nuläget inga modeller som helt och fullt kan beskriva och förklara istäckens rörelse och de återkopplingsmekanismer som är involverade, vilket gör detta ämne viktigt för framtida förutsägelser och modellering av inverkan av ett allt varmare klimat.Radar kan användas för att särskilja den olika reflektivitet som uppvisas mellan frusna och icke-frusna bottnar, detta är dock begränsat på grund av dämpning och spridning av radarvågor genom isen. För att kunna kartera den rumsliga fördelningen av subglacialt vatten, behövs bland annat dämpningen i isen tas med i beräkningarna.Kartering av vatten under en mindre del av istäcket på Grönland har utförts i detta arbete, och för att erhålla ett bättre värde på dämpningen i isen användes tre olika metoder. En CMP-analys, en dämpningsmodell baserad på temperatur data och en dämpningsbedömning baserad på common-offset radardata, och medelvärdet på dämpningen från dessa tre metoder användes för fastställandet av reflektivitet i det undersökta området. Beräkningar av hydraulisk potential utfördes också, vilket analyserades och jämfördes med resultatet från karteringen av reflektivitet.Högre reflektivitet observerades närmre fronten av glaciären, vilket är en indikation på att vatten finns vid botten i det området. I detta område fanns också fler brunnar som skulle kunna leda ner vatten från ytan till botten av glaciären.

L'omniprésence du collagène dans le corps humain et les nombreuses pathologies qui sont associées à ses anomalies de structure en font un objet d'étude de premier plan. Le collagène possède dans sa séquence primaire de nombreux cycles pyrrolidines stabilisant une structure secondaire de type polyproline II (PPII) et une structure tertiaire en triple hélice correspondant à un superenroulement de trois chaines peptidiques. Lors de ce travail, nous nous sommes intéressés à la synthèse et la caractérisation structurale de peptides mimes de collagène (CMP), seuls ou en présence de collagène de type I. Pour appréhender les différents niveaux de structuration des CMP: conformation locale, structures secondaires, assemblages trimériques et supramoléculaires, nous avons privilégié une approche muti-échelle. Les études que nous avons menées par dichroïsme circulaire et RMN ont visé à analyser en détail les relations entre triples hélices et les différentes espèces monomériques présentes en solution. Grâce à l'utilisation de peptides modèles marqués, nous avons pu mesurer par RMN des paramètres structuraux locaux et les comparer à des simulations de dynamique moléculaire. La présence d'assemblages supramoléculaires a été mise en évidence et analysé d'un point de vue qualitatif, quantitatif et cinétique par des études de DLS, RMN et par différentes approches de microscopies. Enfin, l'ensemble de nos observations nous ont conduit à proposer de nouvelles molécules CMP. Nous avons ainsi entrepris la synthèse de peptidomimétiques fluorés en vue d'améliorer la cinétique de formation et la stabilité de la triple hélice et pour également favoriser des assemblages supramoléculaires ordonnés. / The collagen is omnipresent in the human body and many diseases are associated with its structural anomalies, these are the main reasons to study its stability. Collagen has in its primary sequence many pyrrolidine cycles, which stabilize a secondary structure such polyproline II (PPII), and a triple helix structure where three left-handed helical polypeptide chains are supercoiled. In this work, we focused on the synthesis and structural characterization of collagen model peptides (CMP), alone or in the presence of type I collagen. To understand the different levels of CMP structuration: local conformation, secondary structures, trimeric and supramolecular assemblies, we favoured a multi-scale approach. The studies we conducted by circular dichroism and NMR aimed to analyze the relationship between triple helices and the different monomeric species present in solution. Through the use of labeled peptides models, we were able to measure NMR local structural parameters and compare them to molecular dynamics simulations. The presence of supramolecular assemblies was demonstrated and analyzed from a qualitative, quantitative and kinectics point of view by DLS, NMR and different microscopies approaches. Finally, all of our observations have led us to propose new CMP molecules. We undertook the synthesis of fluorinated peptidomimetics to improve the kinetics formation and stability of the triple helix, and also promote ordered supramolecular assemblies.

Over the last two decades, functions of the embedded systems have evolved from simple real-time control and monitoring to more complicated services. Embedded systems equipped with powerful chips can provide the performance that computationally demanding information processing applications need. However, due to the power issue, the easy way to gain increasing performance by scaling up chip frequencies is no longer feasible. Recently, low-power architecture designs have been the main trend in embedded system designs. In this dissertation, we present our approaches to attack the energy-related issues in embedded system designs, such as thermal issues in the 3D chip multiprocessor (CMP), the endurance issue in the phase-change memory(PCM), the battery issue in the embedded system designs, the impact of inaccurate information in embedded system, and the cloud computing to move the workload to remote cloud computing facilities. We propose a real-time constrained task scheduling method to reduce peak temperature on a 3D CMP, including an online 3D CMP temperature prediction model and a set of algorithm for scheduling tasks to different cores in order to minimize the peak temperature on chip. To address the challenging issues in applying PCM in embedded systems, we propose a PCM main memory optimization mechanism through the utilization of the scratch pad memory (SPM). Furthermore, we propose an MLC/SLC configuration optimization algorithm to enhance the efficiency of the hybrid DRAM + PCM memory. We also propose an energy-aware task scheduling algorithm for parallel computing in mobile systems powered by batteries. When scheduling tasks in embedded systems, we make the scheduling decisions based on information, such as estimated execution time of tasks. Therefore, we design an evaluation method for impacts of inaccurate information on the resource allocation in embedded systems. Finally, in order to move workload from embedded systems to remote cloud computing facility, we present a resource optimization mechanism in heterogeneous federated multi-cloud systems. And we also propose two online dynamic algorithms for resource allocation and task scheduling. We consider the resource contention in the task scheduling.