title: A SERIES OF STUDIES ON USING SOCIAL NETWORKS TO INFORM AND SUPPORT EVIDENCE-INFORMED PUBLIC HEALTH PRACTICE IN CANADA: INVESTIGATING ORGANIZATIONAL SOCIAL NETWORKS

contributor: Clinical Epidemiology/Clinical Epidemiology & Biostatistics

subject:
Social Network Analysis
Knowledge Translation
Implementation
Public Health
Mixed methods study

abstract:
Introduction: In a mixed-methods study I assessed the role of social networks as predictors and outcomes of the implementation of an intervention to promote evidence-informed decision-making (EIDM) in three public health departments in Ontario, Canada. The quantitative strand included the analysis of the role of staff’s position in networks on the adoption of EIDM, the longitudinal evolution of networks, and the association between the name generators’ position in surveys and respondents’ motivation to answer survey questions. The qualitative strand aimed to explain and contextualize the quantitative findings.
Methods: A tailored intervention was implemented in the public health departments, including the mentoring of staff through the EIDM process by a knowledge broker. The staff participated in three online surveys before and after the 22-month intervention, providing the names of peers to whom they turned to seek information, whom they considered as experts, and their friends. I assessed the dynamic evolution of social networks, and the role of local opinion leaders (OL) in promoting the adoption of EIDM. I interviewed key network actors about their interpretation and experience regarding the quantitative findings.
Results: Overall, there was no statistically significant impact on EIDM behavior and skill in health departments. However, the analysis of the role of OLs in behaviour change showed that non-engaged staff who were connected to highly engaged OLs, and those OLs who communicated with each other improved their EIDM behavior. Social networks became more centralized around already popular staff due to selective training of recognized experts. Highly engaged staff tended to connect to each other, and to limit their connections within organizational divisions over time. In the department where multiple activities were being implemented to support EIDM, the highly engaged staff became more popular due to department-wise presentations and informal information spread. I also found that when name generator questions are asked later in surveys then respondents are more likely to refuse, indicate they do not know anyone, or provide fewer names than when these questions are asked earlier Conclusion: Social network analysis showed the structure of information-seeking relations, the impact of opinion leaders on the EIDM behavior of their peers, and underlying social changes through implementing an EIDM intervention. These findings can inform the design and tailoring of EIDM interventions in public health organizations.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: In three public health departments in Ontario, where we offered an intervention to a group of staff on how to use more research evidence in practice, I studied how the pattern of communication among staff influenced their use of evidence, how those communications changed over time, and how the staff themselves viewed those changes.  In the department that largely promoted staff engagement in the intervention, the staff who were engaged became more popular over time. In all departments, already popular staff became more popular. The staff who sought information from popular people engaged in the intervention, and those popular people who communicated with each other used more research evidence over time. Network analysis helped reveal the social structure and identify popular staff and could be used to inform similar interventions. It also showed how selecting and training a group of staff can change the way people communicate in health departments.


title: Difference Engines: Technology and Gender in Eighteenth-Century Britain

contributor:
Walmsley, Peter
English

subject: restoration, eighteenth century, long eighteenth century, technology, gender, embodiment, selfhood, subjectivity, sexuality

abstract:
In this dissertation, I argue that modern understandings of both technology and gendered selfhood were mutually fashioned across the long eighteenth century. This argument makes a number of interventions in current scholarly narratives by contending, first, that interiorized subjectivity was conceptualized in the eighteenth century as constructed from (and perceptible through) a series of technological objects; second, that as gender difference was increasingly inscribed on bodies thought to be characterized by intrinsic biological variance, the importance of technological supplements to defining bodily capacities meant that this variance was often realized through artificial objects; and third, that the mechanization of the British textile manufacture, which has been identified as the industrial revolution’s catalyst, was premised not on machines’ inherent efficacy, but on the identification of technological ingenuity with a new kind of British masculinity, and a concurrent devaluation of supposedly primitive Indian and British female labourers.

In my first chapter, I explore the relationship between optical technologies and stage machinery through a reading of Aphra Behn’s The Emperor of the Moon, arguing that Behn’s play enacts a radical revision of technological empiricism by privileging experiences of feminized spectacular materiality as sites of knowledge. My second chapter traces the afterlife of Restoration mechanical philosophy in Samuel Richardson’s Clarissa, and explores how Clarissa’s interiority is conceptualized by both Lovelace and Richardson as fundamentally technological. In my third chapter I turn to John Cleland’s pornographic Memoirs of a Woman of Pleasure, showing how the text’s representations of the technologies of textual production are intimately linked with its eroticism and violence. In my final chapter, I analyse a collection of political pamphlets and popular treatises to show how the industrialization of the British cotton manufacture erected a technological nationalism through the mechanical appropriation of women’s labour.

By attending to the material, textual, and conceptual operations of eighteenth-century technologies through readings of a wide range of literary and popular works, this project ultimately demonstrates how the boundaries of modern gender difference were constructed along with and out of the body’s most artificial parts.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: New Polygeneration Processes for Power Generation and Liquid Fuel Production with Zero CO2 Emissions

contributor:
Adams II, Thomas
Chemical Engineering

subject:
Polygeneration
Process optimization
CO2 emissions
Petroleum coke
Shale gas
Chemical looping

abstract:
The price and accessibility of fossil fuels, especially crude oil, are subject to considerable fluctuations due to growing demand on energy, limited resources, and energy security concerns. In addition, climate change caused by burning of fossil fuels is a challenge that energy sector is currently facing. These challenges incentivize development of alternative processes with no greenhouse gas emissions that can meet transportation fuels, chemical liquids, and electricity demands. Coal-based processes are of particular interest because coal price is both low and stable. However, these processes have a large environmental impact and are also less economically attractive than natural gas based plants due to the recent significant drop in natural gas price. However, even for natural gas plants, attempts to reduce CO2 emissions by using traditional CO2 capture and sequestration technologies not only decrease the thermal efficiency and profitability of the plant significantly but still release some CO2 to the atmosphere.
The aim of this thesis is to develop, simulate and optimize an integrated polygeneration plant that uses multiple feedstocks and produces multiple products with low to zero CO2 emissions. Several process alternatives are investigated in this work to show the effect of each feedstock and product on the performance of the proposed plant. A comprehensive study is performed in each section, including process simulation in Aspen Plus software, development of custom models required for some units, as well as cost analysis by using Aspen Icarus software and empirical cost estimations from literature.
Moreover, derivative free optimization techniques such as particle swarm optimization (PSO), genetic algorithm (GA) and simulated annealing (SA) are implemented to drive the design to economically optimum conditions as a function of the market price and carbon taxes. The final model will also introduce emerging technologies that can achieve higher efficiency and lower CO2 emissions compared to commercial systems, such as chemical looping gasification, chemical looping combustion, nuclear heat reforming, etc. By integrating multiple feedstocks and processes, the model can exploit certain synergies which are unavailable to traditional plants, resulting in significant efficiency improvements. In addition to power and liquid fuels, this polygeneration process offers benefits for petrochemical plants. Despite limited worldwide crude oil reserves, the demand for petrochemical products is still growing fast and it is highly important for petrochemical industry to find new resources as feedstock and diversify their supply chain network. By integration of the polygeneration plant in the same facility with novel processes that produce olefins (petrochemical feedstock) not from oil, but from syngas, it is possible to supply the required feed at lower cost than commercial steam cracking plants.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Quaternary and Quintenary Semicontinuous Distillation

subject:
Semicontinuous distillation
Process design
Alkanes
BTEX
Butanol
Process control
Quaternary
Quintenary

abstract:
The separation of four or more components traditionally requires the use of three or more distillation columns. Due to the associated high costs, process intensification techniques have been studied. Semicontinuous separation is one method that allows multiple separations using one column integrated with middle vessels.

This thesis aims to develop a new semicontinuous separation process that can separate a mixture with four or more components into high purity products with one column and two or more middle vessels. It is an extension of the conventional ternary semicontinuous process, which has been repeatedly shown to be profitable at intermediate throughputs when compared to continuous systems. The semicontinuous process operates in a forced cycle, with three operating modes that ensure separation objectives are met.

The performance of the proposed quaternary semicontinuous separation is analyzed through rigorous dynamic simulations over a range of production capacities. To determine the feasibility, operability, and applicability to non-ideal mixtures, three case studies were considered:
1.	Equimolar mixture of alkanes (n-hexane; n-heptane; n-octane; n-nonane).
2.	Equimolar mixture of aromatics (benzene; toluene; ethyl-benzene; and o-xylene).
3.	Non-ideal mixture of mixed-alcohols (methanol, ethanol, and water; propanol; isobutanol; pentanol and hexanol)

The extendibility of the quaternary semicontinuous separation process, referred to as quintenary semicontinuous separation, is then evaluated on a five-component alkane mixture (n-hexane; n-heptane; n-octane; n-nonane; n-decane), via three case studies:
1.	Equimolar mixture
2.	Non-equimolar mixture, rich in light and heavy components.
3.	Non-equimolar mixture, rich in intermediate components.

The results for both the quaternary and quintenary semicontinuous processes indicate that this new technique is successful at achieving separation objectives while staying within safe operating limits. Comparison of both equimolar mixtures of alkanes for quaternary and quintenary semicontinuous processes with continuous systems indicates that the proposed system is profitable for intermediate flow rates.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Traditionally, several large distillation columns (that can be hundreds of feet tall) are required to split a mixture of liquid chemicals into its individual components. Distillation is the separation of mixtures due to differences in boiling points. When the mixture is heated, the vapour phase will contain the components with lower boiling points, which can be separated once the vapour phase is cooled and condensed. The main goal of this research is to create a new system that can carry out the same separation, but using complex techniques that require only one column and a few extra storage tanks that are much cheaper and smaller than a distillation column. Different liquid mixtures were used to show how well the new process is able to separate the liquid into its individual components, while remaining in safe operating limits.


title: THE EXPERIMENTAL CHARACTERIZATION AND NUMERICAL MODELLING OF FROST HEAVE

contributor:
Guo, Peijun
Civil Engineering

subject:
Frost Heave
Thermal Conductivity
Finite Element Method

abstract:
Frost heave is the expansion of soil upon freezing due to the formation and growth of segregated ice lenses. Because of the large stresses and displacements associated with frost heave, it is an import design consideration for geotechnical structures such as roads, foundations, and buried pipelines, particularly in cold regions. The objective of this research was to characterize frost heave expansion within the context of design and analysis applications.
A series of laboratory-scale frost heave experiments were conducted to examine frost heave under one-dimensional freezing. The previously established segregation potential concept (SP) was utilized to characterize both the intrinsic frost heave behavior of two reference soils. A novel modification was proposed to account for the observed variation of SP with freezing rate; it was noted that ignoring this influence would lead under-predictions the heave expansion.
The thermal properties of frozen soils were explored. A method for characterizing the anisotropic thermal conductivity was proposed utilizing existing composite models in a multi-level homogenization. Ultimately it was determined that for ice lens-rich soils, a simpler and isotropic expression may provide similar performance, namely the geometric mean approximation. Additionally, a method was proposed to characterize the thermal conductivity of composite materials containing discrete particle phases using numerical simulations of complex phase geometries. This method was used to develop a specified characterization of discrete particle composites.
iv
A two-dimensional, fully coupled thermal-mechanical and implicitly coupled hydraulic frost heave model was formulated from thermodynamic principles. The model included the proposed form of SP to characterize the mass transport process. The finite element method was used to implement the model and its performance was validated in one-dimension through comparative analysis with the laboratory frost heave tests. Finally, the model was applied to a two-dimensional, full-scale problem involving the frost heave- induced displacement of a chilled natural gas problem.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: An experimental investigation was conducted and a numerical model was developed to predict the effects of frost heave in freezing soils. Frost heave is the expansion of soils caused by the formation of a specific type of ice, called ice lenses. This expansion can cause damage and lead to failure in roads, foundations, buried pipelines and other infrastructure exposed to heaving soils. The research developed a model capable of providing engineers with the information necessary to account for, and possibly avoid, these effects when designing such infrastructure. A series of experiments were conducted to produce frost heave in soils in a laboratory. The information gained from these tests was used to both develop and confirm the performance of a frost heave model using established numerical techniques. Finally, the model was used to simulate the upward movement of a buried natural gas pipeline exposed to frost heave in a cold region.


title: Assessing Decision Rules For Stopped Cricket Games

contributor:
Bolker, Ben
Statistics

subject: Duckworth-Lewis; cricket; resource table

abstract:
In interrupted limited overs cricket games, teams do not always get a chance to  finish the full game. In such cases, different methods can be used to establish which team wins. The method currently in use is called the Duckworth-Lewis method; it was introduced at the international level in 1998. The purpose of this project is to investigate and check the accuracy of Duckworth-Lewis method and make statistical comparisons with other proposed methods. The accuracy is checked via bias estimation, Cohen's Kappa and root mean square
error methods; cross-validation is used to assess out-of-sample accuracy. The resource table, a summary of the expected fraction of total runs scored by a given point in the game, has missing values and monotonicity flaws. To improve the resource table, different statistical methods such as isotonic regression and Gibbs sampling, are used to construct different resource surfaces. The accuracy results show that the Duckworth-Lewis displays the lowest accuracy out of all the methods; whereas, the improved Duckworth-Lewis is more accurate at predicting the new target or results of stopped games. Thus, the accuracy of the Duckworth-
Lewis can be improved by ignoring the old games and constructing the resource surface using the modern data.

abstract: Thesis

abstract: Master of Science (MSc)


title: Fluidelastic Instability of Tube Arrays Subjected to Axisymmetric Jet Flow

contributor:
Weaver, David
Mechanical Engineering

subject:
Fluidelastic Instability
Partial Admission
Submerged Axisymmetric Turbulent Jet
Equivalent Velocity

abstract:
An experimental scale model study was conducted to investigate the onset of fluidelastic instability in a tube array subjected to axisymmetric jet flow.  A tube array was constructed using aluminum tubes with 44.45 mm outer diameter, $D$, which were arranged in a square pattern with 88 mm pitch, $P$.  The pitch to diameter ratio, $P/D$, was approximately 2.0.  The tubes were flexibly mounted using threaded rod and tuned to a first mode natural frequency, $f_n$, of 9 Hz.  Auxiliary damping devices were added to each tube, and tuned, to achieve a damping ratio, $\zeta$, of 1 % of critical.  The mass damping parameter, $m(2 \pi \zeta)/(\rho D^{2})$, of the tube array was 27.9.  The tube array was tested under uniform flow conditions in McMaster University's 2 ft wind tunnel to establish the critical reduced velocity, $V_{cr}/(f_n D)$, of 30.0 at the onset of fluidelastic instability.  The uniform flow test established a basis for comparing the results with the existing literature and evaluating the validity of the proposed partial admission calculation.  The tube array was also tested in open air using an axisymmetric jet, with two different physical arrangements, the first with the jet aimed between tubes and perpendicular to the tube spans and the second with the jet aimed at a tube face and perpendicular to the tube spans.  In each case the jet flow velocity was incrementally increased to characterize the onset of fluidelastic instability.  To characterize the flow dispersion through the tube array a series of velocity profile measurements were also collected.

The measured velocity profiles were used to estimate the spanwise function of transverse average gap velocity, $\bar{V}(x)$, which was used to predict the equivalent critical uniform gap flow velocity, $V_{cr}$, using the concept of partial admission.  The predicted $V_{cr}$ values showed reasonable agreement with the experimental results.  However, the prediction method did indicate instabilities in tube rows where instability was not actually observed.

A simplified prediction approach was developed which was based on using a predicted three dimensional velocity profile, $V(x,y)$, at the $z$ location of the first row tube gap, under the assumption of free field conditions, to calculate an estimate of the spanwise function of transverse average gap velocity, $\bar{V}(x)$.  Although the predictions of $V_{cr}$ agreed reasonably well with the experimental results, first row instabilities were not observed in any of axisymmetric jet flow experiments.  Therefore, this method can be used to estimate the the critical uniform gap velocity, $V_{cr}$, but not the spatial location of the instability.

Based on the results of the experiments and calculations, adoption of the modified partial admission formula is recommended and possible avenues for further investigation and verification are suggested.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: THE SURFACE AND SUBSURFACE CHARACTERIZATION OF RETRIEVED METAL-ON-POLYETHYLENE HIP PROSTHESES USING ELECTRON MICROSCOPY

contributor:
Grandfield, Kathryn
Materials Science and Engineering

subject:
Electron microscopy
Hip Implant Retrievals
Metal-on-Polyethylene Hip Implants
Total Hip Arthroplasty

abstract: First devised over half a century ago, metal-on-polyethylene (MoP) hip prostheses have become the gold standard for total hip arthroplasty (THA), a surgical intervention for degenerative hip joint conditions. The accumulation of polyethylene wear debris after long-term, in vivo articulations, can induce adverse cellular reactions, osteolysis and aseptic loosening of the implant – ultimately resulting in the failure of the THA. Despite the distinct differences between the biotribology of MoP and MoM prostheses, there is a lack of congruent high resolution research investigating the biotribological interactions and surface structures of MoP hip prosthesis components. This study characterized the surface and subsurface microstructural changes in failed MoP hip prosthesis retrievals using advanced electron microscopy techniques. The samples were comprised of retrieved metallic cobalt-chromium-molybdenum (CoCrMo) alloy femoral head components, one ultra-high molecular weight polyethylene (UHMWPE) acetabular cup component, and unused CoCrMo reference samples. The surface of the reference samples contained linear, parallel, uniform scratches as a result of the manufacturing process; whereas the surface of the retrieval samples were covered in an abundance of scratches and a layer of residual deposits, attributable to in vivo articulation of the implant. Characteristic hard phases were observed and examined on the surface and from the cross-sectional preparation of the cast CoCrMo samples. The multiphasic hard phases on the cast samples can strengthen the material but also be sites of crack propagation and material detachment, contributing to the generation of wear particles. Lastly, a nanocrystalline layer, 20 to 400 nm in thickness was observed in the subsurface microstructure of all samples (including references). Previous MoM studies suggest that the nanocrystalline layer is a result of dynamic crystallization in response to multidirectional, chronic loading in vivo, however, the presence of the layer in the unimplanted references suggest that the nanocrystalline layer can be formed during the production of the prosthesis component and therefore, pre-exists implantation. The imperfections on new, unused implants can have protective effects (e.g. troughs from scratches can be a reservoir for wear debris) but may influence in vivo wear processes after implantation (e.g. scratches may be a source of wear debris). Higher resolution analyses on more retrieval and reference samples are required to pinpoint the exact mechanism of failure in MoP hip prostheses and extend the longevity and efficacy of THA.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: FUNCTIONAL CHARACTERIZATION AND CELLULAR PHYSIOLOGY OF RAT CAROTID BODY TYPE II CELLS

contributor:
Nurse, Colin A.
Biology

subject:
carotid body
angiotensin II
ATP
5-HT
glia
tripartite synapse
pannexin-1

abstract: Carotid body (CB) receptor type I cells transduce blood-borne chemical stimuli into electrical signals and release the excitatory neurotransmitter ATP onto afferent terminals that project to the breathing centre located in the brainstem. Within the CB, type I cells are ensheathed by glial-like processes of type II cells. Recently, it was hypothesized that type II cells have a paracrine function in CB chemotransduction by acting as an ATP amplifier and enhancing chemoexcitation (Zhang et al. 2012). Given this recent development, the primary goal of this thesis was to further elucidate the paracrine function of type II cells and characterize the signalling mechanisms involved in type I and type II cell interactions. Ratiometric calcium imaging was used to investigate type II cell sensitivity to two prominent CB neuromodulators, angiotensin II (ANG II) and 5-HT, in rat CB cultures. Both ANG II and 5-HT elicited large rises in intracellular Ca2+ that were present in the absence of extracellular Ca2+ and were inhibited by intracellular store depletion agents. ANG II and 5-HT acted on their respective G-protein coupled receptors, AT1 receptor and 5-HT2A receptor, to initiate these Ca2+ responses presumably via a PLC-IP3 mediated mechanism. Interestingly, these Ca2+ responses were required to activate pannexin-1 channels (Panx-1), a channel that has been previously shown to be a conduit for ATP in type II cells (Zhang et al. 2012). We were also interested in determining whether type II cells were capable of indirectly responding to a chemostimulus such that the stimulus would elicit neurosecretion from type I cells and result in a secondary Ca2+ responses in type II cells. Isohydric hypercapnia and a depolarizing stimulus (30 mM KCl saline) were capable of eliciting indirect Ca2+ responses in type II cells. These secondary Ca2+ responses in type II cells were partially inhibited by suramin, a purinergic P2Y2 receptor antagonist, suggesting that ATP was the predominant neurotransmitter responsible for type I to type II crosstalk. Similarly, a selective agonist for type II cells, UTP, evoked indirect Ca2+ responses in nearby type I cells. Type II to type I cell communication was dependent on Panx-1 channels since the secondary Ca2+ responses in type I cells were inhibited by the Panx-1 blocker, carbenoxolone (5 µM). UTP-evoked indirect Ca2+ in type I cells were partially inhibited by adenosine A2 receptor antagonists suggesting that the neuromodulator, adenosine, governs cross-talk between type II and type I cells. This study elucidates the importance of purinergic signalling in the bi-directional cross-talk between receptor type I cells and glial-like type II cells.

abstract: Thesis

abstract: Master of Science (MSc)


title: MECHANISMS AND APPLICATIONS OF THE ELECTROCHEMICAL FORMATION OF NANOPATTERNS

contributor:
Kruse, Peter
Chemistry and Chemical Biology

abstract:
Surface nanofabrication is the art of making novel materials with surface features or patterns smaller than 100 nm. To this end, various techniques have been proposed, e.g. optical/ electron lithography, Langmuir Blodgett films, Dip-pen lithography, block co-polymer templates, and ion irradiation. However, each technique has its own inborn limitation, whether time-consuming or expensive or lack of resolution.
In this thesis, the author describes a cheap and time-efficient alternative to generate nanopatterns on several transition metals, alloy, and silicon via electrochemical methods and provides more insight into the mechanism that leads to the formation of these patterns.
Self-organized nanopatterns discovered on electropolished vanadium include dots (called pimples), labyrinths (interconnected elongated pimples), and valleys (called dimples). The window for these patterns to occur is extremely small. A little (0.1%) variance of the electrolyte composition can lead to pattern transition. A time evolution of patterns, from a flat surface to pimple pattern to labyrinth pattern to dimple pattern, has been observed as well.
The author also found out that dimple pattern can be achieved on tantalum via electropolishing and nanotubes can be fabricated by anodization. The relative amount of HF and water in the electrolyte is the key that controls the switch between these two patterns.
The author has extended the formation of dimples from pure metals to a biomedical alloy (Ti-6Al-4V). Since the size of the dimple pattern is on the same scale as cell features, this dimpled alloy has great potential in biomedical implantation.
Last but not least, this thesis explores the pattern formation on silicon, a semiconductor, via electropolishing, which is thus proven to be a universal nanopatterning technique.
This thesis opens a route to nanopatterning metals, alloys, and semiconductors via electropolishing, while making a contribution to a deeper understanding of the mechanisms behind the formation of these patterns.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Atlas Selection for Automated Segmentation of Pelvic CT for Prostate Radiotherapy

contributor:
Wierzbicki, Marcin
Medical Physics

abstract:
Radiotherapy has become a standard modality for treating prostate cancer. Typically, intensity modulated radiotherapy (IMRT) is employed. Accurate delineation is important to ensure that the clinical target volume (prostate) is sufficiently irradiated and that the organs at risk (OARs) are appropriately spared. A recent technological development in radiotherapy treatment planning is the employment of atlas-based segmentation to automate target volume and OAR delineation. Atlas based-segmentation utilizes the spatial relationship between a pre-contoured atlas subject and a new patient image to derive the segmentation result. The typical approach has three steps: many atlas subject images are globally registered to the target image, an atlas subject image that is the most similar to the target is selected, and the chosen atlas image and contours are aligned with the target image space using deformable registration.  The purpose of this work was to design an atlas selection strategy and evaluate its impact on the final atlas-based segmentation outcome.  Segmentation accuracy was mainly quantified using the Dice Similarity Coefficient (DSC), which was used to score the overlap between automatic and manual contours on a 0 to 1 scale.

An alternative atlas selection approach was proposed that identified the most similar atlas subject based on several anatomical measurements that were chosen to indicate the overall prostate and body shape.  A brute force procedure was first performed for a training dataset of 20 patients using image registration to pair subjects with similar contours based on DSC.  For the identified best matches, anatomical measurements were compared.  An atlas selection procedure was designed; relying on the computation of a similarity score defined as a weighted sum of differences between the target and atlas subject anatomical measurements.  Finally, an optimization procedure was performed to obtain the weights that gave the highest DSC between automatic and manual contours for the training set.  The mean DSCs obtained using brute force were 0.78±0.07 and 0.90±0.02 for the prostate and either femoral head.  The proposed atlas selection method achieved 0.72±0.11 and 0.87±0.03 for the prostate and either femoral head.  Clearly, the algorithm was able to identify the best matching atlas subject for any target subject in the training set of data.

 	The key point of this work was to also validate the atlas selection strategy.  Thus, the optimized atlas selection procedure was tested on images of 10 additional subjects. Again, the algorithm’s ability to predict the most similar atlas subject was excellent.  A brute force search for the set of 10 images achieved mean DSCs of 0.76±0.03 and 0.88±0.03 for the prostate and either femoral head.  The proposed method yielded DSCs of 0.64±0.09 and 0.86±0.04 for the prostate and either femoral head.    The difference in mean DSCs between the proposed method and the brute force was statically significant (p < 0.05). Overall, the brute force results demonstrated that atlas-based segmentation can reproduce a similar level of accuracy as manual recontouring (Granberg et al., 2011).  More importantly, the same level of accuracy was achieved with the proposed atlas selection method as with more computationally intensive techniques.  These results indicate that atlas-based segmentation is a promising technique for prostate radiation therapy.

abstract: Thesis

abstract: Master of Science (MSc)


title: Approximations of the lattice dynamics

contributor:
Pelinovsky, Dmitry
Mathematics and Statistics

subject: Lattice Dynamics, Generalized Korteweg-de Vries (gKDV) equation

abstract:
This investigation is devoted to the study of the Fermi-Pasta-Ulam (FPU) lattice dynamics.
Approximations of the FPU lattice dynamics have been an old subject, it is believed that
the stability of the FPU traveling waves depends on the stability of the KDV solitary waves.
The key question is: Are the traveling waves of the FPU lattice stable if the traveling waves
of KDV type equation are stable?.
We consider the FPU lattice with the nonlinear potential which leads to the generalized
Korteweg-de Vries (gKDV) equation, which is known to have orbitally stable traveling waves
in a subcritical case and orbitally unstable traveling waves in critical and supercritical cases.
In order to pursue the question asked above, we use the energy method.
We establish that the H^s(R) norm of the solution of the gKDV equation is bounded by
a time-independent constant in the subcritical case, whereas the H^s(R) norm grows at most
exponentially in the critical and supercritical cases. With the help of these results,
we extend the time scale for the approximation of the traveling waves of the FPU lattice
by the traveling waves of the gKDV equation logarithmically in the subcritical case. In the
critical and supercritical cases, we extend the time scale by a double-logarithmic factor.
Our results show that the traveling waves of the FPU lattice are stable if the solitary
waves of the gKDV equation are stable in the subcritical case. On the other hand, in the
critical and supercritical cases, our results are restricted to small-norm initial data, which
exclude solitary waves.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Water Use Dynamics of Temperate Pine Forest Plantations and their Response to Thinning and Climate Variability

contributor:
Arain, M. Altaf
Earth and Environmental Sciences

subject:
Temperate Forest
Climate variability
Water Use
Eddy Covariance
Forest Management
Micrometeorology

abstract:
Forest plantations have been long-employed to reverse land degradation and support biodiversity, and are now recognized to both take in atmospheric carbon dioxide, reducing the intensity of the greenhouse effect, and moderate local weather. It is important to consider the impact forest aging and management will have on provisioning of these services under climate change and extreme weather events, such as drought. This study encompasses a chronosequence of three Eastern White Pine stands planted in 1939, 1974 and 2002, situated in Turkey Point, Ontario, Canada. The oldest forest received two selective thinning treatments, removing 30% of trees, in 1983 and 2012.

Forest water use efficiency (WUE), which represents the amount of gross ecosystem productivity (GEP) per unit of water released through evapotranspiration (E), was compared among the three sites over 2008-2013. The youngest forest’s annual WUE increased over the study period, surpassing that of the older sites by 2013. When bulk surface conductance (Gs), representing gas exchange, was compared across the sites for the same years, the youngest site had the lowest Gs, particularly during drought. Gs at the oldest forest was highest and the most variable. Statistical analysis showed that across all the sites, E was more responsive to air temperature than atmospheric demand, soil moisture, and incident radiation. This study indicated that younger plantations may be more water-conservative during drought, and that air temperature is important to consider in projections of temperate coniferous forests’ carbon and water exchange.

To assess the impact of the 2012 selective thinning on tree-level and ecosystem-level water use at the oldest forest, sapflow velocity (Js), transpiration (Et) and E were compared between the two stands planted in 1939 and 1974, from 2011 to 2013. A relatively severe drought over the 2012 growing season led to a decline in Et at the unthinned site for that year, however the Et decline was more pronounced at the older, thinned site. From 2011 to 2012, Js increased at the thinned site, converse to the unthinned site – wherein Js was low as expected during drought. Hydraulic redistribution and lag time from sapflow at 1.3 m height to canopy evapotranspiration were seemingly unaffected by the thinning, indicating that low-level selective harvesting was not detrimental to the hydrological functionality of the stand, and may have been beneficial in allowing more soil moisture access per tree. As such, the stand may be better positioned to withstand recurrent dry spells resulting from precipitation variability, as predicted with climate change.

abstract: Thesis

abstract: Master of Science (MSc)


title: Perceptual Quality Model for Enhancing Telemedical Video Under Restricted Communication Channels

contributor:
Doyle, Thomas E.
Musson, David M.
Electrical and Computer Engineering

abstract:
Telemedicine has the potential to provide greatly increased access to medical training, consultation and care for individuals and populations located in remote regions of the Earth. In order for this to happen, telemedicine relies on delivery of high quality video over bandwidth limited internet connections. Methods of video encoding to accommodate these connections reduce the perceptual quality of telemedical video, reducing its clinical or educational impact.
This thesis aims to understand how changes in bitrate, frame rate and frame size affect the perceptual quality of telemedical video through studies of objective and perceptual quality of two types of medical simulation video. H.264/AVC encoding was used to encode two medical simulation videos with varying bitrates, frame rates and frame sizes. Objective frame image quality tests and subjective video quality tests were performed on the resulting videos.
It was observed that the objective frame image quality, as measured by the Structural Similarity (SSIM), is linearly related to the number of pixels per bit of the encoded video. It was also determined that perceptual quality of these videos was dependent primarily on the frame rate and frame image quality of the encoded video.
Models are proposed from the results of each type of video showing how perceptual quality can be determined by the parameters chosen to encode a video (maximum bitrate, frame rate and frame size).  The models proposed are unique for the type and purpose of video under investigation as well as the encoding method used. The models created will be useful to encode video for transmission over limited bandwidth networks while maintaining diagnostic and education quality.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Analysis of Postulated Pool Draining Accidents in the MNR

contributor:
Luxat, John
Engineering Physics

subject:
Natural Convection
Research Reactor

abstract:
A safety analysis for the McMaster Nuclear Reactor has been carried out for
postulated scenarios of loss or termination of forced flow in the reactor core in a
state of shutdown, with loss of pool inventory of different magnitudes including core
uncovery. Models were developed to evaluate the natural convection flow through the
core assemblies for the different conditions within the aforementioned envelope. The
flow rate was used to get the temperature or enthalpy rise along the heated channel in
order to estimate the corresponding clad temperatures in the given scenarios.
The models were constructed from first principles using the one-dimensional momentum conservation law, incorporating the Boussinesq approximation for the single-phase
case and the Homogeneous Equilibrium Model assumptions when a two-phase mixture
was present. In order to obtain the flow rate and enthalpy rise along the channel,
knowledge of the assembly power and inlet temperature is required. The power was
calculated using a well known decay power correlation. The pool temperature which
was used as the assembly inlet temperature was calculated via a lumped parameter
model using a simple energy balance between the core output (again by using the
decay-heat profile) and the pool heatup. Heat losses from the pool were neglected and
the model allowed for reaching saturation temperature in the pool. In this case, water
vaporization was calculated using the latent heat to assess pool inventory loss rate.
For all scenarios before core uncovery, the models predict that clad and fuel
temperatures remained well below limits associated with clad blistering or melting.
Consequently, it is asserted natural convection and acceptable temperatures will be
sustained in the McMaster Nuclear Reactor while the core remains covered. In the
most severe draining before uncovery, in which the pool drains to just before exposing
the core, it takes approximately a week (180 hours) after shutdown for boiling to start
in the core’s hottest channel. For core uncovery, the models predict that the clad
remains below the blistering temperature for pool height at 9.4% of the heated channel’s
height (corresponding to exposing about 61.7 cm of the assembly), and below melting
temperature for pool height at 8.1% of the heated channel’s height (corresponding to
exposing about 62.5 cm of the assembly). Both heights are below the height of the
bottom of the lowest beam tube, at which the worst draining case will end.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The ontogeny and mechanisms of branchial and cutaneous ammonia excretion in freshwater rainbow trout, Oncorhynchus mykiss

contributor:
Wood, Chris
Biology

abstract: The mechanism by which freshwater fish excrete ammonia, the primary nitrogenous waste, has been a focus of comparative physiologists for nearly a century. The majority of ammonia in typical adult fish is excreted across the gill and is loosely coupled Na+/NH4+ exchange. However, few studies have addressed the mechanisms by which larval fish, lacking a functional gill, excrete ammonia. In the work presented in this thesis, cutaneous surfaces of post-hatch larval rainbow trout accounted for the majority of ammonia excretion (Jamm) and Na+ uptake (JNain), and both processes shifted to the gills at the exact same time over development (15 days post-hatch; dph), prior to the skin-to-gill shift in oxygen uptake (26 dph). Moreover, branchial Jamm and JNain¬ were tightly correlated over development (R2=0.95), while no such relationship existed at the skin. Moreover, experimental manipulation of Jamm and JNain demonstrated a lack of coupling of these processes by the yolk sac and body skin while branchial Jamm and JNain were functionally coupled to one another. Thus, Jamm by the gill of trout is a Na+-coupled process, while Jamm by the skin of larval trout is Na+-independent. Perhaps the most important finding of this thesis was that ammonia may play a role in driving the ontogeny of branchial ionoregulation. A new “ammonia hypothesis” was proposed, which is a refinement upon the current theory of gill development (the “ionoregulatory hypothesis”) and posits that Jamm, coordinated by Na+/NH4+ exchange, is the earliest function of the developing gill. Moreover, the demand for ammonia excretion may represent the primary driving force for the transition from cutaneous to branchial ionoregulation. Overall, this thesis extends the current knowledge of several aspects of ammonia excretion by freshwater fish, some of which had previously never been explored, and presents a number of new and exciting avenues for future research.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Dynamic Myocardial SPECT Imaging Using Single-Pinhole Collimator Detectors: Distance-Driven Forward and Back-Projection, and KDE-Based Image Reconstruction Methods

contributor:
Farncombe, Troy
Computational Engineering and Science

subject: dynamic emission tomography imaging

subject: kernel density estimation-based image reconstruction

subject: distance-driven projection for single-pinhole collimators

subject: sampling criteria for single-pinhole collimator imaging systems

abstract:
SPECT (Single Photon Emission Computed Tomography) is the modality of choice for myocardial perfusion imaging due to the high sensitivity and specificity, and the lower cost of equipment and radiotracers compared to PET. Dynamic SPECT imaging provides new possibilities for myocardial perfusion imaging by encoding more information in the reconstructed images in the form of time-activity functions. The recent introduction of small solid-state SPECT cameras using multiple pinhole collimators, such as the GE Discovery NM 530c, offers the ability to obtain accurate myocardial perfusion information with markedly decreased acquisition times and offers the possibility to obtain quantitative dynamic perfusion information.

This research targets two aspects of dynamic SPECT imaging with the intent of contributing to the improvement of projection and reconstruction methods. First, we propose an adaptation of distance-driven projection to SPECT imaging systems using single-pinhole collimator detectors. The proposed distance-driven projection approach accounts for the finite size of the pinhole, the possibly coarse discretization of the detector and object spaces, and the tilt of the detector surface. We evaluate the projection method in terms of resolution and signal to noise ratio (SNR).

We also propose two maximum a posteriori (MAP) iterative image reconstruction methods employing kernel density estimators. The proposed reconstruction methods cluster time-activity functions  (or intensity values) by their spatial proximity and similarity, each of which is determined by spatial and range scaling parameters respectively. The results of our experiments support our belief that the proposed reconstruction methods are especially effective when performing reconstructions from low-count measurements.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Load-following heat, hot water and power distributed generation using an integrated solid oxide fuel cell, compressed air energy storage and solar panel array system.

subject:
SOFC
Distributed Generation
CAES

abstract: Distributed generation (defined as the production of power in small quantities at the point of use) has recently gained significant interest due to its benefits over a centralized approach. This thesis investigates the integration of a natural gas fed solid-oxide fuel cell (SOFC) and compressed air energy storage (CAES) technologies for distributed generation at the building-level scale. The SOFC/CAES system is also integrated with multiple vital sub-systems (including on-site solar panels) for the building to provide the heat, through an in-floor heating system, hot water, and power demanded by the building. This thesis investigates the models for the SOFC/CAES system, and implements them in a generic analysis tool providing a means for rapid analysis of a wide variety of case studies. The analysis tool determines the ability of the SOFC/CAES system to follow the power and heat loads demanded by the building, and evaluates its performance with an assortment of metrics, including efficiencies, CO2 emissions and grid-independence. The SOFC/CAES system was investigated for the new ExCEL building at McMaster University. It was found that the system was able to produce upwards 75% of the heat and hot water demand, and upwards of 94% of the power demand of the building. When compared to the current state-of-the-art natural gas based power producing technology and high efficiency furnace, the SOFC/CAES system reduces the CO2 emissions associated with the building by a minimum of 8.7% and a maximum of 26.95%. The cost of electricity for the system is significantly (21% to 150%) more costly than current market prices; however the SOFC/CAES system is the least costly of all other distributed generation technologies investigated for the case of the ExCEL building.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Simultaneously Isolating Multiple Biosensors for Multiple Targets from a Single SELEX Procedure

contributor:
Li, Yingfu
Chemistry and Chemical Biology

subject: aptamers, aptazymes, biosensors, SELEX

abstract: SELEX is a selective amplification technique based on the assumption that functional nucleic acids (FNAs) can be found in a pool of chemically synthesized random nucleic acid sequences.  These FNAs can either bind to a target of interest  (aptamers) or catalyze a chemical reaction (DNAzymes and ribozymes) or both (aptazyme).  The aptazymes discussed herein, are RNA-cleaving DNAzymes that become catalytically active upon target recognition at the aptamer domain.  In chapter 2, two SELEX experiments were performed in parallel to determine whether it was possible to obtain multiple aptazymes from a single SELEX procedure.  Two different crude intercellular mixtures (CIM) each containing 35 unique overexpressed ASKA clone gene products were used.  After 10 rounds of SELEX, the sequence pool was analyzed using Illumina Genome Analyzer.  The sequences tested appeared to bind to a protein other than the 35 gene products of interest.  To redirect these SELEX experiments towards the gene products of interest, 12 gene products from each parallel selection was purified and incubated with sequences from round 6 of the CIM SELEX.   A total of 13 rounds of selection were performed using these purified proteins.  The sequences were analyzed and found to either not cleave at all or self-cleave.  In chapter 3 a similar SELEX approach was explored using 36 purified proteins, from the CIM SELEX to isolate protein-binding DNA aptamers.  This SELEX approach served as another means to explore isolating multiple aptamers against multiple targets.  However both the RNA-cleaving aptazyme and protein-binding DNA aptamer SELEX experiments both experienced challenges in non-specific binding. Although negative selection steps were taken in order to avoid non-specific binding species, such sequences were still isolated.  In order for these approaches to be successful, negative selection steps are required to remove any self-cleaving and non-specific FNAs.  Although these studies did not conclusively give rise to the desired FNAs, it has produced some insight to the potential setbacks associated with developing a screen for multiple targets.

abstract: Thesis

abstract: Master of Science (MSc)


title: Assortative Configuration Random Graphs

contributor:
Hurd, Thomas R.
Mathematics

abstract: A random graph model is introduced, which is supposed to capture the assortativity effect in various real-world networks. An effect that appears when different types of vertices have non-uniform tendencies to connect to each other. Therefore, given the node- and edge-type distributions P, Q a discrete matching method is developed, so that the empirical distributions asymptotically passes to their given limits P, Q. Applications of martingale convergence methods are exploited to prove the large n limits of the discrete Markov setup. Finally, the relation between inhomogeneous random graph model as another recently studied topic and our model is investigated.

abstract: Dissertation

abstract: Master of Science (MSc)


title: Chemical Interrogation Of Sporulation And Cell Division In Streptomyces

contributor:
Nodwell, Justin
Biochemistry and Biomedical Sciences

subject: Cell division, bacteria, Strepomyces, Small-molecule, sporulation, DNA-damage, SOS response

abstract:
Cell division is essential for spore formation but not for viability in the filamentous
streptomycetes bacteria. Failure to complete cell division instead blocks spore formation,
a phenotype that can be visualized by the absence of gray (in Streptomyces coelicolor)
and green (in Streptomyces venezuelae) spore-associated pigmentation. The
streptomycetes divisome is however, similar to that of other prokaryotes.
We hypothesized chemical inhibitors of sporulation in model streptomycetes might
interfere with cell division in rod shaped bacteria. To test this, we investigated 196
compounds that inhibit sporulation in Streptomyces coelicolor. We show that 19 of these
compounds cause filamentous growth in Bacillus subtilis, consistent with impaired cell
division. One of the compounds is a DNA damaging agent and inhibits cell division by
activating the SOS response. The remaining 18 act independently of known stress
responses and may therefore act on the divisome or on divisome positioning and stability.
Three of the compounds (Fil-1, 2 and 3) confer distinct cell division defects on B.
subtilis. They also block B. subtilis sporulation, which is mechanistically unrelated to the
sporulation pathway of streptomycetes but which is also dependent on the divisome. We
discuss ways in which these differing phenotypes can be used in screens for cell division
inhibitors.
In addition to the molecules affecting the divisome, DNA and cell wall damage also
affects the process indirectly by temporarily halting the cell division. To further explore
the cell division regulation in stressful conditions, we carried the complete transcriptomic analysis of S. venezuelae after the DNA damage. The observed changes in the gene
expression as a result of the DNA damage paves the way for identification of the DNAdamage
induced cell division inhibitor in streptomycetes.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: OVEREXPRESSION OF THE TRANSCRIPTION FACTOR KAISO IN MURINE INTESTINES INDUCES INFLAMMATION

title: THE BELLY DANCE OF KAISO IN MURINE INTESTINES

contributor:
Daniel, Juliet
Biology

subject:
Mouse intestine
Inflamamtion
Kaiso
Transgenics

abstract: Since the discovery of the p120ctn binding partner, Kaiso, a BTB/POZ transcription factor, several studies have implicated the protein in both development and tumourigenesis. Most information about Kaiso’s function in vertebrate development has been gleaned from studies in Xenopus laevis embryos where Kaiso negatively regulates the Wnt signalling pathway. Since the Wnt signalling pathway is crucial in intestinal development, intestinal-specific Kaiso overexpressing mice were generated and characterized to elucidate Kaiso’s role in a mammalian context. Kaiso transgenic (KaisoTg/+) mice were viable and fertile but developed gross histopathological changes in the small intestine. The KaisoTg/+ mice exhibited enlarged crypts accompanied by increased secretory cell differentiation reminiscent of inhibition of the Notch pathway. Indeed, the Notch effector protein, HES1, is decreased in KaisoTg/+ mice. Additionally, KaisoTg/+ mice display a neutrophil-specific intestinal inflammation reminiscent of the knockdown of p120ctn. Interestingly, the KaisoTg/+ mice display decreased p120ctn localization at the membranes and an increase in the neutrophil adhesion molecule, ICAM-1, both of which induce neutrophilia. Notably, the KaisoTg/+ mice developed multiple crypt abscesses over time due to massive neutrophil infiltration of the epithelial cell layers. This is the first study to examine the in vivo roles of Kaiso in a mammalian context and our findings suggest a regulatory role for Kaiso in the inflammatory and Notch signalling pathways.

abstract: Thesis

abstract: Candidate in Philosophy


title: Mammalian Cell Surface Display of Functional Alpha 1-Protease Inhibitor: Building "Designer" Serpins

contributor: Medical Sciences (Blood and Cardiovascular)

subject: Serpins, Mammalian display

abstract:
Human serpins belong to a superfamily of serine protease inhibitors involved in the regulation of essential physiological processes, including coagulation via thrombin inhibition by AT.  Inhibitory serpins undergo a remarkable folding mechanism to a thermodynamically unstable (i.e. metastable) conformation, highlighted by a long and flexible RCL, prior to secretion as soluble proteins into circulation.  The serpin alpha-1-proteinase inhibitor (API) normally protects tissues from proteases released from inflammatory cells (e.g., neutrophil elastase).  Importantly, a variant of API (i.e. API-Pittsburgh or API-M358R) was reported to be the cause of a fatal bleeding disorder in a young patient in the late 1970`s; the point mutation M358R at P1 of the RCL resulted in a dramatic shift in function toward thrombin inhibition.

This dissertation summarizes the results from experiments performed with serpins expressed as membrane proteins tethered to the surface of mammalian cells.  Serpins API-M358R, AT, HCII, and the non-inhibitory double mutant API-M358R/T345R were anchored to 293 and COS cell plasma membranes with N-terminal non-cleavable protein sequences derived from either the human asialoglycoprotein (AR) or transferrin (TF) receptors.  Sub-cellular fractionation (with or without monolayer exposure to thrombin) immunoblots confirmed serpin localization to the integral membrane fraction using either anchoring approach or cell type.  The blots also revealed that tethered API-Pittsburgh in particular, and AT to a lesser extent formed serpin-enzyme complex (SEC) with thrombin, while HCII and API-M358R/T345R (as expected) did not.  While tethered API-M358R maintained inhibitory function, kinetic studies revealed that the rate of SEC formation was less rapid compared to its soluble counterpart.  Additional testing by immunofluorescence microscopy, and flow cytometry confirmed the status of tethered API-M358R as a robust inhibitor of thrombin.

That tethered serpins maintained the ability to inhibit thrombin provided the underlying rationale for the thesis hypotheses:  surface displayed serpins can be used in gene therapy to temper thrombogenicity associated with certain diseased tissues (i.e. cancer), and tethered serpins can be used as a platform for screening RCL mutant libraries to identify “better” protease (i.e. thrombin) inhibitors.

The potential gene therapy scheme was tested by expressing tethered API-Pittsburgh on the surface of T24/83 cancer cells constitutively co-expressing tissue factor (TF), and then measuring endogenous thrombin generation in the presence of re-calcified, and defibrinated human plasma by either discontinuous or continuous fluorescence-based thrombin generation assays (TGA).  Unexpectedly, the displayed API-Pittsburgh did not appear to reduce discontinuous TGA thrombin suggesting that the difference may have been too low for accurate measurement by this method.  Moreover, the results were identical when the same reaction was continuously monitored by fluorescence-based TGA, indicating that the levels of API-Pittsburgh expression were simply insufficient to effectively counter thrombin generation.  The high levels were confirmed when up to 1 µM of hirudin variant 3, or soluble API-M358R, were required to completely abolish the thrombin profile.  With this in mind, a measureable reduction in TGA was achieved when 293 cells were co-transfected with DNA ratios of API-M358R: TF adjusted to 9:1.

Mammalian cell display, in combination with FACS/flow cytometry, has previously been employed to successfully develop improved monoclonal antibodies.  However, there was never any certainty that the technique was applicable to the screening of displayed serpin mutant RCL libraries.  The method was tested with a modest library degenerate only at P1; the rationale was that successful sorting would generate the expected wild-type (WT) P1 Arg (i.e. API-Pittsburgh).  Unfortunately, repeated attempts did not result in enrichment, and flow cytometry was abandoned.

An alternate protocol based on bacterial expression, and previously developed in our lab, was implemented in order to perform the library screens.  This technique involved incubating lysates, containing soluble serpin RCL mutant candidates, with immobilized thrombin.  Encouragingly, the P1 library screen identified the WT candidate at the expected frequency (5 in 150 lysates) as well as the more rare P1 mutant Lys (1 in 150 lysates).  A kinetic comparison between mutant proteins containing the three basic residues revealed that P1 Arg  (k2 ~ 105 M-1sec-1) was approximately two orders of magnitude more efficient than either Lys or His (both with k2 ~ 103 M-1sec-1) at inhibiting thrombin.

The bacterial expression technique was then enhanced through kinetic optimization in order to facilitate the screening of more complex libraries.  Analysis of the P7 to P1 (always Arg) library returned a selection of anticipated non-polar residues (5 in 100 lysates; 2 x Pro, 2 x Leu and Met) at P2.

Extensive screening (~ 1300 colonies) of a second expanded library with the repeated VNN nucleotide sequence (i.e. no stop codons to eliminate truncated proteins) at P7 to P2 and P1 Arg, identified 7 x Pro mutants at P2 further confirming the results from the original library screen.  Importantly, the assay also identified the novel mutant TLSATPR which registered the largest kinetic response (k2 ~ 5 x 105 M-1sec-1), and even exceeding API- M358R by a factor of ~ 3 (k2 ~ 1.5 x 105 M-1 sec-1).

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Microbe-Contaminant Linkages in the Upper Waters of Lakes

contributor:
Warren, Lesley A.
Earth Sciences

subject:
aquatic
freshwater
neuston
bacteria
iron
floc
antibiotic resistance

abstract: The upper water column (<1 m depth) of freshwater lakes, which includes the surface microlayer (SML; <1 mm depth), is an important microbial habitat as well as an accumulation and dissemination site for chemical and microbial contaminants. This doctoral thesis reports novel insights into how the physical structure and functional capabilities of microbial communities can influence the presence of trace metals and health-relevant bacteria in the upper waters (SML and 0.5 m depth) of freshwater lakes. Two physically and geochemically contrasting lake environments, a remote sheltered boreal lake and a higher energy urban beach on Lake Ontario, were investigated to identify system-dependent physical and biogeochemical factors controlling contaminant-relevant microbial characteristics. The SML was identified as a major site for generation of contaminant-sequestering suspended flocs from a distinct biofilm-forming microbial community over diurnal timeframes via wind and sunlight exposure, with this process being enhanced at the higher energy beach site. More generally, upper waters including the SML were demonstrated to be inhabited by a diverse group of atypical facultative Fe(III)-reducing bacteria (IRB) that exhibited a SML- and lake-specific capacity for solid Fe(III) reduction directly related to floc and Fe(III) availability. Although IRB were hypothesized to be highly resistant to metals and antibiotics relative to other bacteria due to their ability to dissolve metal-rich Fe(III) minerals, this was not found to be the case. Nevertheless, IRB enriched from the SML demonstrated higher antibiotic resistance compared to those from 0.5 m depth and enriched Fe(III)-reducing communities from both depths harboured resistance-mobilizing genetic elements and included potentially pathogenic bacteria. Results of this thesis represent new knowledge concerning how microbial communities regulate the presence of contaminants in the upper waters of lakes. This has important implications for assessing the ecological and human health impacts of contaminants in freshwater systems.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A GFRP Bar Bond Stress and Strength: Comparison of Beam-bond and Pullout Tests Results

contributor:
Razaqpur, A. Ghani
Civil Engineering

subject: GFRP bond stress distribution

subject: GFRP bond

subject: GFRP embedment/development length

subject: Beam bond and pullout test method for a GFRP bar

abstract:
Four beam-bond test specimens, two in accordance with RILEM TC-RC5 recommendation, labelled as RILEM and two based on a modified form of the ACI 208 beam-bond test method, labelled as Notched, were tested in four-point bending to investigate the bond stress distribution and values along the bar embedment length of a 15 𝑚𝑚 nominal diameter GFRP rebar. The beams experienced failure through the rupturing of the longitudinal GFRP tensile reinforcement. In addition, two Modified and ten Standard pullout specimens were tested using the same bar. The beam-bond and the Modified pullout specimens had embedment length of 600 𝑚𝑚 while the Standard pullout specimens had, in accordance with CSA S806, 60 𝑚𝑚 embedment, or four times the bar nominal diameter. The first Modified pullout specimen experienced concrete splitting failure and as a result, the second was lightly confined and failed by GFRP bar rupture. All ten Standard pullout specimens failed due to bar pullout.
It was determined that the actual bond stress distribution as a function of the embedment length is practically parabolic and can be described by the derivative of a modified form of the logistic growth function used to approximate the strain distribution along the embedment length. Furthermore, the maximum bond stress location progressively moves from the loaded-end towards the unloaded-end as the bond continues to deteriorate with increasing GFRP stress levels. The development length recommendations by ACI 440.1 and to a lesser degree, CSA S806 and CSA S6 are quite conservative compared to that which is required. It is observed that pullout tests alone cannot provide sufficient knowledge regarding the bond behaviour of FRP reinforcement; consequently, the results of beam-bond testing are more appropriate. Standard pullout tests may be incorporated into quality assurance programs with the understanding that they cannot provide valuable information regarding bond stress distribution and required development length in real structural elements with large embedment lengths. In terms of the beam-bond test method, the RILEM TC-RC5 design recommendation appears to be superior since it eschews severe stress perturbation caused by incidence of flexural cracks at beam midspan. As a result, it produces stability in the terms of the data gathered from the strain gauges placed on the GFRP bar. This benefit outweighs the ease of constructability of the Notched beams as well as their resemblance to real beams.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: The force that bonds a reinforcing rod to concrete is determined using three test methods. Each method is recommended by some design standards, but it is unclear how the results of these tests compare to each other. To shed light on the issue, a 15 𝑚𝑚 fibre glass rod was tested using three well-known test methods. It was discovered that two of the methods give results that are reasonably close while the third gives variable results that generally do not agree with the results of the other two. It was also discovered that the required embedment length recommended for such a bar by design codes and standards are relatively excessive because they underestimate the actual bond strength of the rod. Since sometimes it may be difficult to provide such long length in practice, it is recommended that the code requirements be revisited.


title: NANO-MECHANICAL CHARACTERISTICS OF WEAR RESISTANT PVD COATINGS IN RELATION TO WEAR PERFORMANCE OF CUTTING TOOLS DURING HARD END MILLING OF H13 TOOL STEEL

contributor:
Veldhuis, Stephen C.
Mechanical Engineering

subject:
PVD
loading support
nanoindentation
nano-scaled scratch

abstract: Two families of PVD hard coatings were successfully used for high performance end milling of hardened H13 tool steel. The first family of coatings are AlCrN-based, they are used for wet machining and the other family is based on TiAlCrSiYN coating and are used for dry machining of H13. It was shown that there is a strong potential for further advancement in the wear performance of the coatings by improving the coating architecture as well as by varying the deposition parameters used during their synthesis. A number of deposition parameters of the coatings show a strong impact on wear performance of the cutting tools. Wear performance was related to the structure and a number of nano-mechanical characteristics of the coating layer assessed using the NanoTest system produced by Micro Materials. It was shown that critical characteristics like nano-hardness, loading support factor and nano-scaled scratch resistance can be used to predict the wear performance of a cutting tool.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: MAMMALIAN CELL SURFACE DISPLAY OF FUNCTIONAL ALPHA 1-PROTEASE INHIBITOR: BUILDING “DESIGNER” SERPINS

subject: Serpins, Mammalian display

abstract: Thesis

abstract: Doctor of Philosophy (Medical Science)


title: RAMAN SPECTROSCOPY CHARACTERIZATION OF PULSED LASER DEPOSITION GROWN ZNTE THIN FILMS ON SAPPHIRE SUBSTRATE

title: RAMAN CHARACTERIZATION OF PLD GROWN ZNTE FILMS ON SAPPHIRE

contributor:
Preston, John S
Engineering Physics

subject:
Raman Spectroscopy
Epitaxy
Thin Films
Pulsed Laser Deposition
ZnTe
Crystal Structure
Vibrational modes
Semiconductor growth

abstract: Compound semiconductors are the foundation of many electronic and optoelectronic devices. As a result semiconductor epitaxy can be viewed as the first significant step in device engineering. Accurate and reliable characterization methods are needed to measure semiconductor properties including optical, electrical, vibrational and crystal structure. In this thesis, the epitaxy of ZnTe thin films on sapphire substrate by Pulsed Laser Deposition system at different growth temperatures is studied. The texture analysis is inspected by Two Dimensional X-Ray Diffraction. The lattice constant of the films and strain studies are investigated by High Resolution X-Ray Diffraction. UV-Vis spectroscopy is applied to find absorption edge in ZnTe thin film in order to estimate optical bandgap. These common characterization methods reveal the great effect of growth temperature on crystalline and optical properties of ZnTe thin films. In addition, Raman spectroscopy is used for the first time in the Preston's group to examine vibrational modes in ZnTe thin films. This new characterization method, which is the main focus of this thesis, uncovers some new features of ZnTe thin films not accessible through other techniques. In this thesis, optimum experimental conditions, instrumentation and data analysis of Raman observations in thin films are studied in detail. The final results are in good agreement with other characterization methods and they can justify crystalline and optical observations. These results demonstrate that Raman spectroscopy is a non-destructive characterization method applicable to thin film analysis.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Accelerator Based Radiation Measurements of In Vivo Total Body Nitrogen

contributor:
Chettle, David R
Medical Physics

abstract: Accurate measurement of protein in the human body is essential to the management and maintenance of health in individuals when correct balance cannot be achieved without intervention.  It can be measured in a number of ways but the least invasive method is by neutron activation analysis, in this case using the 14N(n,γ)15N reaction and measuring the prompt γ-rays in the region of 9 – 11 MeV, the single most prominent γ-ray being at 10.83 MeV.  During the course of investigations, using phantoms containing different ratios of nitrogen to water, flux suppression was observed as the nitrogen content increased.  This was attributed primarily to the 14N(n,p)14C reaction, which cannot be measured directly by the methods used in these investigations.  The suppression of flux at 2.6% nitrogen content, typical of human body composition content, was found to be 7.0+/-1.0%, which should be taken into account when using hydrogen as an internal standard to quantify nitrogen.  The optimum proton beam energy and current from the KN accelerator used to liberate neutrons from a thick lithium target was determined to be 2.5 MeV and 0.3 μA respectively.  Over the course of the experiments, an overall improvement in precision was achieved by the addition of a fast pile-up rejector and pulsing of the proton beam.  High energy γ-rays were observed, which can interfere with the counts in the nitrogen region via Compton scattering.  The origin of these γ-rays was identified and then reduced by the effective use of beam pulsing.  Investigations to achieve this reduction included shielding, filtering, and optimization of the pulsing parameters using a purpose-built multi-scalar unit, specifically designed to identify the timing of the arrival of the thermal neutrons.

abstract: Thesis

abstract: Doctor of Science  (PhD)


title: The Process of Creative Resilience: Experiences of Medical Students with Disabilities and Accessibility

contributor:
Jung, Bonny
Dore, Kelly
Health Science Education

subject:
Disability
Accessibility
Resilience
Medical Students
Medical Education

abstract:
In light of Accessibility for Ontarians with Disabilities Act, 2005, medical schools witnessed increased number of students with disabilities matriculating in their program. However, the administrators face challenges because ensuring accessibility in dynamic clinical settings may not always be feasible or ideal while considering the resource implication and patient safety. There is little consensus and established guidance on how to provide responsible accommodations for otherwise-qualified medical students with disabilities.
To understand the development of resilience in medical students with disabilities as they confront potential institutional barriers and social or self-imposed stigma, we asked: how do medical students with disabilities identify and communicate their learning needs to negotiate necessary accommodations with the Student Accessibility Services and/or the MD program?
The Constructivist Grounded Theory approach by Charmaz (2006) served as the methodological guide. In-depth individual interviews were conducted capturing the students’ perspective on accommodations arranged by the program, inclusion challenges in medical education and their recommendations on how to enhance program accessibility.
Three major themes emerged: 1) creating a dialogue to devise learner-centered accommodation strategies, 2) recognizing available extrinsic and intrinsic resources, and 3) optimizing available extrinsic and intrinsic resources. Self-reflection was the key underlying ingredient driving students’ resilience development in partnership with inclusive learning environment and supportive faculty.
Student diversity present in the medical schools merits further research. Diminishing stigma towards health professionals with disabilities is imperative. Endorsement of cross-departmental and institutional collaboration that enables dissemination of cost-effective and comprehensive accommodation strategies is recommended.

abstract: Thesis

abstract: Master of Science (MSc)


title: Inference for Birnbaum-Saunders, Laplace and Some Related Distributions under Censored Data

contributor:
Balakrishnan, Narayanaswamy
Mathematics and Statistics

subject:
BS distribution
BVBS distribution
Cumulative hazard
GBS distribution
Hazard function
Kaplan-Meier curve
Kolmogorov-Smirnov test
Laplace distribution
LBS distribution
Mixture distribution
P-P plot
Q-Q plot

abstract:
The Birnbaum-Saunders (BS) distribution is a positively skewed distribution and is a popular model for analyzing lifetime data. In this thesis, we first develop an improved method of estimation for the BS distribution and the corresponding inference. Compared to the maximum likelihood estimators (MLEs) and the modified moment estimators (MMEs), the proposed method results in estimators with smaller bias, but having the same mean squared errors (MSEs) as these two estimators. Next, the existence and uniqueness of the MLEs of the parameters of BS distribution are discussed based on Type-I, Type-II and hybrid censored samples. In the case of five-parameter bivariate Birnbaum-Saunders (BVBS) distribution, we use the distributional relationship between the bivariate normal and BVBS distributions to propose a simple and efficient method of estimation based on Type-II censored samples. Regression analysis is commonly used in the analysis of life-test data when
some covariates are involved. For this reason, we consider the regression problem based on BS and BVBS distributions and develop the associated inferential methods.
One may generalize the BS distribution by using Laplace kernel in place of the normal kernel, referred to as the Laplace BS (LBS) distribution, and it is one of the generalized Birnbaum-Saunders (GBS) distributions. Since the LBS distribution has a close relationship with the Laplace distribution, it becomes necessary to first carry out a detailed study of inference for the Laplace distribution before studying the LBS distribution. Several inferential results have been developed in the literature for the Laplace distribution based on complete samples. However, research on Type-II censored samples is somewhat scarce and in fact there is no work on Type-I censoring. For this reason, we first start with MLEs of the location and scale parameters of Laplace distribution based on Type-II and Type-I censored samples. In the case of Type-II censoring, we derive the exact joint and marginal moment generating functions (MGF) of the MLEs. Then, using these expressions, we derive the exact conditional marginal and joint density functions of the MLEs and utilize them to develop exact confidence intervals (CIs) for some life parameters of interest. In the case of Type-I censoring, we first derive explicit expressions for the MLEs of the parameters, and then derive the exact conditional joint and marginal MGFs and use them to derive the exact conditional marginal and joint density functions of the MLEs. These densities are used in turn to develop marginal and joint CIs for some quantities of interest.
Finally, we consider the LBS distribution and formally show the different kinds of shapes of the probability density function (PDF) and the hazard function. We then derive the MLEs of the parameters and prove that they always exist and are unique. Next, we propose the MMEs, which can be used as initial values in the numerical computation of the MLEs. We also discuss the interval estimation of parameters.

abstract: Thesis

abstract: Doctor of Science  (PhD)


title: Essential residues in IMC recruitment of PfGAP45 in the malaria parasite

contributor:
Gilberger, Tim
Biochemistry and Biomedical Sciences

abstract: The Plasmodium falciparum merozoite utilizes an actin-myosin motor to invade into erythrocytes, which is a part of the protein complex termed the glideosome. The glideosome provides the parasite with substrate dependent gliding motility, and is connected to the unique organelle named the inner membrane complex (IMC). The glideosome associated protein 45 (GAP45) is a crucial member of the glideosome. Here, we investigate the differential role of two post-translational modifications, specifically palmitoylation and phosphorylation, for recruitment of the protein to the IMC as well as glideosome association. Through comprehensive mutational analysis, it was shown that in addition to the N-terminal dual acylation motif, the C-terminal residues C189 and C192 must be present to mediate GAP45 recruitment to the IMC. Despite the abundant in vivo phosphorylation sites in GAP45, a phosphorylation null mutant does not affect the protein’s IMC localization. Therefore this modification may be involved in glideosome complex formation, which will be further investigated through co-immunoprecipitation and gaining structural insight of GAP45.

abstract: Thesis

abstract: Master of Science (MSc)


title: Structural and functional characterization of Pseudomonas aeruginosa major and minor pilins

contributor:
Burrows, Lori
Biochemistry and Biomedical Sciences

subject:
type IV pili
pilin
Pseudomonas

abstract: Type IV pili (T4P) are long, fibrous surface appendages involved in attachment, motility, biofilm formation and DNA uptake that are expressed by bacteria and archaea. They are an important virulence factor for a number of bacteria, including Pseudomonas aeruginosa, an opportunistic pathogen that is a common cause of nosocomial infections. T4P are composed mainly of monomers of the major pilin subunit, PilA, although several low abundance proteins called minor pilins are also present. These surface-exposed proteins are potential vaccine candidates, although a more complete understanding of their diversity and function is required for the rational development of a pilus-based vaccine. There are five distinct groups of P. aeruginosa major pilins, which vary based on their sequence and their associated accessory proteins, and two distinct sets of minor pilins, although the roles of the latter in pilus biology are poorly understood. This study focuses on the structural characterization of major and minor pilins and functional implications for pilus assembly and disassembly dynamics. The structural analysis of major pilins from groups III and V revealed specific differences in pilin structure that may affect subunit interactions within the pilus fibre and interactions with their specific accessory proteins and minor pilins. The minor pilins PilVWX were shown to form a putative subcomplex with the adhesin and anti-retraction protein PilY1, which is proposed to prime pilus assembly and thus traffic PilY1 to the bacterial surface. High resolution X-ray crystal structures of the minor pilins FimU and PilE were solved and functional characterization suggested that FimU and PilE are necessary for efficient pilus assembly to stably connect the priming subcomplex to the major pilin subunits. Together, this work has increased our understanding of pilin diversity and defined a concrete role for the minor pilins in pilus assembly.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Pseudomonas aeruginosa is a bacterium that can take advantage of a weakened immune system to cause lethal infections. The first step of infection involves attachment to the host using long sticky fibres called type IV pili. Each fibre is composed primarily of a single protein, the major pilin, but also contains low abundance proteins called minor pilins. Without these proteins, the bacteria can’t attach and cause infections, making pilins excellent vaccine candidates. This study focused on the characterization of major and minor pilins to understand the diversity of these proteins and how these differences might affect pilus assembly. We show that the molecular structure of the major pilin differs between strains although the core architecture is the same, and that the minor pilins are required for initiation of pilus assembly. This work furthers our understanding of the structures and functions of pilin proteins, and provides information helpful for the development of vaccines.


title: Rhetoric, Spatiality, and the First-Century Synagogue: The Description and Narrative Use of Jewish Institutions in the Works of Flavius Josephus

contributor:
Runesson, Anders
Religious Studies

subject:
Ancient Synagogues
Flavius Josephus
Hellenistic Judaism
Graeco-Roman Associations
Critical Spatial Theory

abstract:
The information about the first-century synagogue provided by Flavius Josephus must be handled with care when used in historical reconstructions. Josephus was a skilled rhetorician who was ideologically invested in the presentation of this institution. Due care must therefore be placed on understanding the context of his various mentions of synagogues within the overall rhetorical context of his works if we are interested in historical reconstruction of this Jewish institution. However, the tendentious nature of Josephus’ writings does not preclude historical study, not least because the assumptions and ideologies inherent in this tendenz are themselves historical. Especially in his later works (Antiquitates judaicae, Vita, and Contra Apionem), we find a deliberate presentation of the synagogue as a viable, supra-local rallying point for the Jews throughout the known world, as this institution represents an assembly in which the customs and Law of Judaism may be practiced and disseminated following the loss of the Temple and the Land. Even in the earliest work of Josephus, Bellum judaicum, we find a tendentious presentation of the synagogue as a ‘holy place’ whose precincts were breached due to the impiety of the Jewish insurgents and certain non-Jewish troublemakers.
	Due to the rhetorical nature of Josephus’ writings and the many hermeneutical issues that arise when we deal with space, the language of Edward Soja’s spatial theory is utilized, where heuristically profitable, in order to distinguish between the ‘spaces themselves’ (firstspace), the ideals held by the author regarding the institution (secondspace), and the combination of the two in the experience represented in the passages (thirdspace). It is precisely the rhetoric with which Josephus presents the synagogue that will lead us to a better understanding of the ideological importance that synagogues had in the lives of the communities and individuals inhabiting these spaces during the period in question.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: A Mechanisation of Internal Galois Connections In Order Theory Formalised Without Meets

contributor:
Kahl, Wolfram
Computing and Software

subject: relation algebra, ordered category, converse, order, galois connection

abstract:
Using the the dependently-typed programming language Agda,
we formalise orders, with attention to the theory of Galois Connections,
and showcase it by formalising a few results of the category of algebraic
contexts with relational homomorphisms presented by Jipsen (2012) and Moshier (2013).

We aim to exhibit an internal theory of Galois Connections and Closure operators
where the ambient space need not have a notion of meets (intersections), which
are the usual medium in presenting antisymmetry of partial orders.
Instead we consider `symmetric quotients' as being the relational counterpart of
propositional calculus' primitive connective: equivalence. We argue that it as a more
natural primitive than meet --- especially its connection with certain proof heuristics
regarding posets. Moreover, not only do we constrain ourselves to an unconventional
set of primitive operators, but in fact we discard the familiar setting of relations
and sets in favour of the more general setting of ordered categories with converse
(OCCs) --- in fact, a large portion does not require identities and so semigroupoids
may be used instead.

abstract: Thesis

abstract: Master of Science (MSc)


title: Synthesis and Characterization of Novel Silicone-Boronic Acid Materials

title: Silicone-Boronic Acids

contributor:
Brook, Michael A.
Chemistry

subject:
poly(dimethylsiloxane)
boronic acid
interface
thermoplastic
stimuli-responsive
selective sensing
saccharide binding
elastomer
Lewis acid/base
reversible crosslinking
silicone
thermoresponsive

abstract:
Silicone polymers and network-materials have proven extremely useful in a variety of applications owing to their superb properties when compared to carbon-based polymers. Polysiloxanes containing functional groups other than simple alkyl moieties have allowed for further manipulations of pendant groups along the polymer backbone leading to a greater range of possible chemical transformations, as well as changes in physical/interfacial properties. One aspect of functional polymers that has yet to be explored with respect to primarily silicone-based systems is that of stimuli-responsive materials. In order for this unique application to work, silicones must be functionalized with a group or groups that can influence the polymer’s properties based on that group’s response to specific external stimuli.  Boronic acids represent one such group, wherein the most common stimuli used to affect changes in ionization state and solubility are pH and diol-binding. Boronic acids are also capable of forming weak hydrogen-bonded dimers with other boronic acids, and dynamic covalent bonds with Lewis bases. It is proposed that the covalent attachment of boronic acids and their derivatives onto silicones could lead to stimuli-responsive silicone materials.
Herein, the synthesis of silicone-boronic acids and their protected boronic esters is described. The simple two-step method involving boronic acid protection followed by hydrosilylation has led to a variety of molecules differing in molecular weight and three-dimensional geometry through the use of commercially available hydride-functional silicones. Initial results regarding saccharide binding selectivity and the impacts on silicone solubility are provided.
The unique interfacial behaviour of silicone-boronic esters and their propensity to form self-assembled, crosslinked films at an air/water interface are also reported. Using several different diol protecting groups and a variety of aqueous sub-phases, the mechanism for changes in physical properties as well as crosslinking were revealed.
Finally, the production of new thermoplastic silicone elastomers from silicone-boronic esters and amine-containing molecules is discussed. The Lewis acid/Lewis base complexation that occurs between nitrogen and boron can provide enough strength to produce robust, yet recyclable, silicone elastomers without the use of catalyst or solvent. Elastomers can be easily dissolved and reformed through the introduction and removal of a mono-functional Lewis base. The impact of crosslink density, controlled by the quantities and molecular weights of each polymer component used, on physical characteristics is reported.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A Tabular Expression to Event-B Language Transformation Tool

contributor:
Maibaum, Tom
Computing and Software

abstract: Tabular expressions have been proved in practice to be an excellent way to check the completeness (all possibilities are considered) and disjointness (no overlap among conditions) of software requirements described as functions. However, just these two properties alone are not sufficient for justifying the safety and efficacy of safety critical systems. Formal specification languages like Z, CSP and Event-B can also support mathematical reasoning required for these kinds of systems and have more effective tool support available. This thesis reports on a new transformation tool TX2EB (Tabular Expressions to Event-B) which combines the completeness and disjointness checks and mathematical reasoning needed for verification and classification of the documented requirements. Moreover, the proposed tool can generate formal specifications from the tabular expressions automatically and support subsequent refinement and analysis of the specifications. Therefore, it can liberate researchers from tedious and time-consuming manual application of the transformation.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Aspects of Crystallization History in Spanish Peaks, Colorado

contributor:
Clifford, P.M.
Geology

subject: Rio Grande rift, Colorado, igneous, Spanish, peaks, crystallization,

abstract:
 The opening of the Rio Grande Rift of Southern Colorado
resulted in a wide variety of igneous features including the
Spanish Peaks dual stocks, their surrounding radial dyke
system and several proximal enigmatic plugs.

 Aspects of the crystallization history of two magmas have been studied by using petrographic observations and Crystal Size Distribution (CSD). These were used to examine opaques and feldspars from a rhyolitic dyke in the Spanish
Peaks swarm and augite, olivine, and opaques from a gabbroic
dyke within Huerfano Butte.

 Augite and opaques from Huerfano Butte reveal a history of no crystal fractionation during emplacement, no size
dependent growth, and constant, continuous nucleation and
growth.

 Huerfano Butte olivine and Spanish Peaks opaques have
been subjected to resorption and depletion of nucleii. The
resorbed olivine material was probably redeposited as
augite. This could explain why Huerfano Butte augite has a
much higher nucleation density than the other minerals.

 The phenocrystic feldspars from Spanish Peaks also have a deficit of nucleii, but they lack resorption features. Xenocrystic skeletal feldspars throughout the dyke lack a fines population and show resorption. The absence of fines
is probably due to sorting of grains by density during magma
convection before eruption.

abstract: Thesis

abstract: Master of Science (MSc)


title: Evolutionary Aspects of Huerfano Butte Colorado

contributor:
Clifford, Paul
Geology

subject: evolutionary, Huerfano, Butte, Colorado, dyke, specimens

abstract: Gabbroic dyke and syenitic plug intrusives have been sampled and studied across Huerfano Butte. Petrography and geochemical analyses were performed on selected specimens; from these analyses chemical variation diagrams have been prepared. Crystal Size Distribution analyses have been done on magnetites and olivines to determine crystal nucleation and growth rate in the dyke. These data have been used to infer aspects of the evolution of Huerfano Butte.

abstract: Thesis

abstract: Bachelor of Science (BSc)


title: Some Ordination and Classification Methods in Plant Ecology

contributor:
Macdonald, Peter D.M.
Statistics

subject: ordination, methods, ecological, classification, plant

abstract:
 This project studies the applicability of two
ordination methods, principle component analysis and
correspondence analysis, and one classification method,
mode analysis, for a specific ecological data set. The
differences between techniques are discussed and the
results are compared.

abstract: Thesis

abstract: Master of Science (MSc)


title: Developing An Ecclesiology Based Upon Kaleidoscope Atonement Theory

contributor:
Studebaker, Steven
Christian Studies

subject: kaleidoscope, sin, atonement, church,

abstract: Kaleidoscope theory inspires the beliefs and practices of the church in a variety of ways. The atonement is God's action on behalf of humanity to remove the barrier and repercussions of sin. The works of Joel Green and Mark Baker have been instrumental in advancing the kaleidoscopic perspective. These works have called into question the current articulation and practices of the atonement within the western church. Kaleidoscope theory inspires a church that encourages a diversity of views on the atonement. Furthermore, the church continues the work of interpreting the scriptural account of the atonement in a culturally sensitive manner. Yet, every interpretation of the atonement must account for the creative purpose of God, Jesus' life and death, and the propulsion towards community. The church embraces the tensions within competing reflections upon the atonement. Kaleidoscope theory encourages the church towards atonement-filled teaching and practice.

abstract: Thesis

abstract: Master of Arts (MA)


title: Contrasting Canons: A Comparative Analysis of Malachi 2:10-16 in the Traditions of the Hebrew Leningradensis and the Greek Sinaiticus

contributor:
Boda, Mark J.
Christian Studies

subject: canons, Malachi 2:10-16, Hebrew, Greek Sinaiticus,

abstract: The textual corruption found in Malachi 2:10-16 while providing frustration for the modem scholar also presents a unique opportunity to observe how ancient interpreters chose to deal with such difficulties. The Hebrew Leningradensis (L) and the Greek Sinaiticus (N) manuscripts diverge, at least to some degree, in their rendition and subsequent interpretation of Mal 2:10-16. The following thesis examines and compares this difficult corpus within these two manuscript traditions, in their similarities and differences, through an analysis of their various grammatical, syntactical and semantic features. This analysis shows that these two traditions present two variant versions of Mal 2:10-16 but yet still functioned as Scripture within their respective communities of faith. The findings of this analysis are brought into the discussion regarding concepts of biblical canonicity as presented by Brevard S. Childs and James A. Sanders.

abstract: Thesis

abstract: Master of Arts (MA)