An extensive review was made to study the wake characteristics of a backward-facing step. Experimental and numerical studies of the backward-facing step suggest that the wake of a separated shear layer to be dependent on parameters such as: expansion ratio, aspect ratio, free stream turbulence intensity, boundary layer state and thickness at separation. The individual and combined effects of these parameters on the reattachment length are investigated and discussed in detail in this thesis. A new scaling parameter, sum of step height and boundary layer thickness at separation is proposed, which yields significant collapse of the available data. Based on the literature review, an axisymmetric model is designed for further investigating the dynamics of the flow independent of aforementioned parameters. Additionally, porous suction strips are incorporated to study the step wake characteristics independent of Reynolds number. This model has been built and will be tested extensively at UTIAS.

This thesis is an examination of the traveler’s dilemma and its backward induction argument. I begin by explaining relevant terminology, the prisoner’s dilemma, and the iterated prisoner’s dilemma; the discussion of which aids my examination of the traveler’s dilemma and its backward induction argument. My evaluation of the traveler’s dilemma involves a dissection of the game into its different components, a presentation of the salient similarities and differences between the traveler’s dilemma and the prisoner’s dilemma, and the exploration of three possible solutions. The first two solutions are adapted from ones initially created to solve other backward induction argument problems. The third solution is original and its foundation rests on the unique structure of the traveler’s dilemma. I focus on this third solution and consider several objections to it. I end this thesis with some ancillary comments about the possibility of generalizing the third solution to other backward induction argument problems. / February 2008

A FORTRAN code was developed to numerically simulate the mixed convective flow over a three-dimensional horizontal backward-facing step. The momentum and energy equations under the assumption of the Boussinesq approximation were discretized by means of a finite volume technique. The SIMPLE algorithm scheme was applied to link the pressure and velocity fields inside the domain while an OpenMP parallel implementation was proposed to improve the numerical performance and to accelerate the numerical solution. The heating process corresponds to a channel heated from below at constant temperature keeping insulated all the other channel walls. In addition, the back-step was considered as a thermally conducting block and its influence in the heating process was explored by holding different solid to fluid thermal conductivity ratios. The effects over the velocity and temperature distribution of buoyancy forces, acting perpendicular to the mainstream flow, are studied for three different Richardson numbers Ri=3, 2, and 1 and the results are compared against those of pure forced convection Ri=0. In these simulations the Reynolds number is fixed at 200 while the bottom wall temperature is adjusted to fulfill the conditions for the different Ri. Under this assumption, as Ri increases the buoyancy effects are the dominant effects in the mixed convective process. The numerical results indicate that the velocity field and the temperature distribution for pure forced convection are highly distorted if compared with the mixed convective flow. If the Ri parameter is increased, then the primary re-circulation zone is reduced. Similarly, as the buoyancy forces become predominant in the flow, the convective rolls, in the form of spiral-flow structures, become curlier and then higher velocity components are found inside the domain. The temperature field distribution showed that as the Ri is increased a thicker layer of high temperature flow is located at the channel??s top wall as a result of the higher rates of low-density flow moving to the top wall. The flow is ascending by the channel sidewalls, while descending by the channel span-wise central plane. The parallel numerical strategy is presented and some results for the performance of the OpenMP implementation are included. In this sense, linear speedup was obtained when using 16 possessors in parallel.

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This thesis is an examination of the traveler’s dilemma and its backward induction argument. I begin by explaining relevant terminology, the prisoner’s dilemma, and the iterated prisoner’s dilemma; the discussion of which aids my examination of the traveler’s dilemma and its backward induction argument. My evaluation of the traveler’s dilemma involves a dissection of the game into its different components, a presentation of the salient similarities and differences between the traveler’s dilemma and the prisoner’s dilemma, and the exploration of three possible solutions. The first two solutions are adapted from ones initially created to solve other backward induction argument problems. The third solution is original and its foundation rests on the unique structure of the traveler’s dilemma. I focus on this third solution and consider several objections to it. I end this thesis with some ancillary comments about the possibility of generalizing the third solution to other backward induction argument problems.

This thesis is an examination of the traveler’s dilemma and its backward induction argument. I begin by explaining relevant terminology, the prisoner’s dilemma, and the iterated prisoner’s dilemma; the discussion of which aids my examination of the traveler’s dilemma and its backward induction argument. My evaluation of the traveler’s dilemma involves a dissection of the game into its different components, a presentation of the salient similarities and differences between the traveler’s dilemma and the prisoner’s dilemma, and the exploration of three possible solutions. The first two solutions are adapted from ones initially created to solve other backward induction argument problems. The third solution is original and its foundation rests on the unique structure of the traveler’s dilemma. I focus on this third solution and consider several objections to it. I end this thesis with some ancillary comments about the possibility of generalizing the third solution to other backward induction argument problems.

This thesis first investigates within-host HIV models for the acute stage. These models incorporate the immune responses and helper T cells produced from the activation of naive CD4 T cells. Because both naive CD4 T cells and helper T cells are susceptible classes, backward bifurcation and bistability may occur. We start with a simple model that ignores the CD8 T cell dynamics, then extend it to include this dynamics. We also extend our model to consider the latent infection of naive CD4 T cells. Backward bifurcation occurs in all these models. We numerically investigate the stability of viral equilibria, and show the bistability caused by backward bifurcation. Increasing the inflow of CTLs prevents the backward bifurcation. With a large homeostatic source of healthy naive CD4 T cells, the disease is easier to establish when the basic reproduction number is less than one. Reducing the reproduction number below one is not sufficient to control the infection of HIV. Secondly, this thesis investigates the development of AIDS caused by viral diversity, as proposed by Wodarz et al. using a model that does not include the details of immune responses. We extend their model to include density dependence, and show that the viral load increases with viral diversity. To study if this result still holds with more realistic HIV dynamics, we incorporate viral diversity into our first model. We conclude theoretically that the total viral load is positively correlated with the number of viral strains, and viral diversity can drive the development of AIDS. We also find that the total CD4 T cell count does not always decrease with viral diversity. Thus further investigation is needed to fully understand the development of AIDS. / Graduate

Bioconductor is the second largest R software package repository that is primarily used for the analysis of genomic and biological data. With downloads exceeding millions in recent years, the widespread growth of the repository's adoption can be attributed to it's diverse selection of community-created packages, written in the programming language R, that allow statistical methodologies for analysis and modelling of data. However, as these packages evolve, their APIs go through changes that can break existing user code. Fixing these API breaking changes whenever a package is updated can be frustrating and time-consuming, especially since a large fraction of the user community are researchers who do not necessarily have software engineering background. In that context, we first present a tool that can detect syntactic API breaking changes between two released versions of a library written in R through static analysis of the package source code. This tool can be of utility to R package developers, so that they can more comprehensively report or handle the breaking changes in their releases, and to R package users, who want to be aware of the API differences that may exist between two releases before upgrading the libraries in their code. Through the use of this tool and manual inspection, we also conducted an empirical study of the breaking changes and backward incompatibility in Bioconductor packages. We studied the 100 most downloaded packages in the repository and found that 28% of all packages releases are backward incompatible. We also found that 55% of these breaking changes go undocumented and developers don't maintain semantic versioning for 22% of the releases. Finally, we manually inspected 10 library releases that consisted of breaking changes and found 2% of the API-s to affect 31 client projects. / Master of Science / Bioconductor is a software repository that consists of over 2000 software libraries. These libraries can provide users with reusable functions, or APIs, to perform statistical and graphical data analysis. The developers of these libraries will generally make timely updates to the library source code and the functions for various maintainability purposes. However, when clients install these library updates in their existing code, their code might not compile, run or behave the same way it used to anymore due to the changes made in the APIs of the libraries. Such a library release that consists of changes that can potentially break older code is considered to be backward incompatible. Without proper documentation from the library developer's side, fixing these issues can be time consuming as the client might have to manually look at the changes made in the library's source code. In order to tackle this issue, we first present a tool that can analyse two versions of a library and identify a subset of the breaking changes in the API. This can be helpful for both the users and the developers of the libraries to be aware of any breaking changes that exist in a new release. Afterwards, we conduct a study on the Bioconductor ecosystem to see how serious the problem of backward incompatibility really is by studying the top 100 most downloaded packages from the repository. We see that 28% of the releases across these 100 packages are backward incompatible. Since clients are likely to be using multiple libraries at once, this figure can potentially cause frequent issues in client code. We then go on to check how often developers maintain the correct release protocols when updating their libraries. These include versioning the releases in correct ways, so as to let the users be aware of what releases may be backward incompatible and documenting any breaking changes that occur in a NEWS file that users have access to. In that aspect, we find that 22% of the releases are not versioned correctly and roughly 55% of the breaking changes in the API are not documented. Finally, we investigate how frequently these breaking changes can actually affect client code. Here, we manually inspect 10 releases with a high number of a subset of the breaking changes and find 31 projects that implement these APIs, which would break upon a library update.

Die bipolare Störung ist eine in depressiven und manischen Phasen verlaufende psychiatrische Erkrankung. Zwischen diesen Phasen kehren die Betroffenen zu einer ausgeglichenen Stimmungslage zurück. Dennoch verschlechtert sich der kognitive Allgemeinzustand der Patienten mit zunehmender Erkrankungsdauer und Anzahl der durchlittenen Episoden, was auch in euthymen Phasen erkennbar ist. Lithium ist das Medikament erster Wahl, das zur Behandlung der bipolaren Störung eingesetzt wird. Es zeichnet sich durch seine antimanische, antisuizidale und phasenprophylaktische Wirkung aus. In Zell- und Kleintierstudien konnte zudem gezeigt werden, dass Lithium sich positiv auf die Resilienz von Neuronen auswirkt und eine Zellen-erhaltende Wirkung hat. Im Rahmen dieser multizentrischen Querschnittstudie soll gezeigt werden, dass die neuroprotektiven Eigenschaften von Lithium sich bei einer Langzeitbehandlung auch schützend auf die kognitive Leistungsfähigkeit bipolarer Patienten auswirkt. Um diesen Effekt zu belegen, verglichen wir 3 Gruppen: Patienten mit einer bipolaren Störungvon einer minimalen Erkrankungsdauer von 10 Jahren und minimal 5 Erkrankungsepisoden mit (akut, seit mindestens 2 Jahren) und ohne (insgesamt maximal 3 Monate, vor mindesten 2 Jahren) Lithium-Langzeitbehandlung und gesunde Kontrollprobanden miteinander. Im Rahmen dieser Studie wurden folgende Daten erhoben: Hippokampusvolumen gemessen mit MRT, NAA-Konzentration im DLPFC gemessen mit MRS, Lebensqualität gemessen mit Quality of Well-Being Scale, allgemeine Intelligenz gemessen mit der HAWIE Testbatterie, verbales Lernen und Merkfähigkeit gemessen mit CVLT und frühe visuelle Informationsverarbeitung sowie Reaktionsgeschwindigkeit gemessen mit VBMT. Im Rahmen dieser Dissertation wurden die Ergebnisse der VBMT ausgewertet und interpretiert. Insgesamt wurden die Daten von 142 Studienteilnehmern ausgewertet, von denen 31 Patienten ohne Lithiumbehandlung, 58 mit Lithiumbehandlung und 53 gesunde Kontrollprobanden waren. Entgegengesetzt zur Studienhypothese, schnitten Patienten mit einer Lithiumbehandlung bezüglich Reaktionsgeschwindigkeit und Fehlerquote schlechter bei der VBMT ab, als gesunde Kontrollprobanden, aber auch als Patienten mit einer bipolaren Störung ohne Lithiumbehandlung. Bei der Untersuchung von allgemeiner Intelligenz und verbaler Lern- und Merkfähigkeit konnte kein signifikanter Unterschied zwischen den drei Gruppen gefunden werden. Dennoch wird bei Betrachtung der absoluten Zahlen deutlich, dass auch bei diesen Untersuchungen Patienten schlechter abschneiden als Gesunde und dass Lithiumpatienten tendenziell schlechter abschneiden als Patienten ohne Lithiumbehandlung. Andererseits ergaben die hirnphysiologischen Untersuchungen dieser Studie, dass sowohl die NAA-Konzentration, als neuronaler Marker, und auch das Volumen des Hippokampus bei Patienten mit Lithiumbehandlung größer war, als bei Patienten ohne Lithiumbehandlung. Zwischen den Volumina und den NAA-Levels der Lithiumpatienten und gesunder Probanden gab es keinen Unterschied. Aus diesen Ergebnissen lässt sich schlussfolgern, dass Lithium auch beim Menschen einen Zell-erhaltenden Effekt hat, der sich jedoch nur physiologisch messen lässt und sich nicht auf die neurokognitive Fähigkeit auswirkt. Patienten mit einer Lithiumbehandlung scheinen zwar eine bessere Resilienz ihrer neuronalen Zellen aufzuweisen, haben aber größere kognitive Defizite. Ob diese Defizite kausal mit der Lithiumbehandlung zusammenhängen, lässt sich bei einem einmaligen Messzeitpunkt nicht aussagen. Des Weiteren ist der kognitive Defizit deutlicher bei der Testung der frühen visuellen Informationsverarbeitung und Reaktionsgeschwindigkeit, gemessen mit der VBMT, als bei Merkfähigkeit und allgemeiner Intelligenzleistung zu erkennen. Dies deutet darauf hin, dass die Hirnregionen, welche bei der frühen visuellen Informationsverarbeitung und psychomotorischer Steuerung beteiligt sind, bei bipolaren Patienten stärker als bei Gesunden, und bei Lithiumpatienten stärker als bei Nicht-Lithiumpatienten beeinträchtigt sind.

International Telemetering Conference Proceedings / October 18-21, 2004 / Town & Country Resort, San Diego, California / This paper describes a new approach to object recognition by using ground-penetrating radar (GPR) imaging systems. The recognition procedure utilizes the spectral content instead of the object shape in traditional methods. To produce the identification feature of an object, the most common spectral component is obtained by singular value decomposition (SVD) of the training sets. The identification process is then integrated into the backward propagation image reconstruction algorithm, which is implemented on the FMCW GPR imaging systems.