contributor:
Pritchard, R.M.
Psychology

abstract: Title: Neural Representation of Simple Visual Stimuli, Author: Thomas Hoeppner, Location: Thode

abstract:
Activity of individual cells in the
visual cortex of the cat was observed during patterned
stimulation of the retina. Orientation
and illumination of a simple light-dark stimulus
were varied. Cells gave the same response to different
stimuli, suggesting that 'place' theories
of pattern recognition, theories based solely on
'which' cells are responding, are inadequate. It
is suggested that stimuli are represented by the
relative activity across several neurons.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Comparative Safety Evaluation of Thorium Fuel to Natural Uranium Fuel in a CANDU 6 Reactor

contributor: Engineering Physics and Nuclear Engineering

subject:
Thorium
CANDU
transient
comparison
point kinetic model
protactinium
Uranium
Safety
Analysis
Evaluation

abstract:
Fuel comprised of thorium has been explored since the early development of nuclear energy in the 1960s. In the last decade, there has been a renewed interest in thorium fuel and it has now become a primary focus in studies and proposed in next-generation nuclear reactors. This has been prompted by a limited supply of uranium in the foreseeable future and an abundance of thorium resources. Additionally, when compared to natural uranium (NU), thoria (ThO$_2$) produces substantially less long-lived radioactive waste and the fissile content can be reprocessed for additional fuel cycles. The CANDU 6 reactor has a unique ability to harvest thorium fuels because of its superior neutron economy. Thorium requires a driving isotope to sustain neutron fission until the long absorption chain produces viable amounts of U-233. Previous studies have investigated many different practical fissile isotopes and core modeling techniques that would make thorium feasible in a CANDU 6 reactor. This thesis focuses on a safety evaluation of thorium fuel compared to NU fuel in a lattice cell and full core configuration. \\

DRAGON 3.06 and SERPENT 2 are used to examine the infinite lattice cell containing NU and homogeneous thorium fuel enriched with 2.0\% U-235, emphasizing the relationship between multiple nuclear libraries. This configuration is used to determine the enrichment concentration, temperature coefficient, coolant void reactivity, and the power relationship. Thorium fuel exhibits a higher negative temperature coefficient, a lower coolant void reactivity, and a greater reactivity change when simulated at different powers. If the lattice cell is simulated at 75\% nominal power there is an 11 mk adjustment for thorium fuel, whereas the adjustment is only three mk for NU fuel. This is related to the extensive cross section of Th-232 and the long fertile absorption chain results in a sizeable inventory of the intermediate isotope Pa-233. The fissile content of the fuel bundle after exiting the reactor will continue to accumulate U-233 and should be monitored and properly stored.  \\

A full core evaluation in a CANDU 6 reactor is performed in DONJON 4. Thorium fuel has an inferior reactivity worth for the control mechanism than does NU fuel in an operating CANDU 6 reactor. The reactivity worth of leakage and absorption in the reactor is estimated to be slightly lower for the thorium fuel. \\

This thesis presents a new computational model for analyzing full core power transients built upon previous results. The approximation model utilizes many assumptions to develop an expeditious code for analyzing the infinite square lattice retaining the isotopic densities. This model has demonstrated the ability to accurately emulate the reactivity of a lattice cell at different powers and power transients formed in DRAGON. The model is coupled with a point kinetic code to perform power transients in a CANDU 6 reactor. \\

Load following operations are performed in cycles of 24 hours examined at 80\%, 60\%, and 40\% full power. Power adjustments are performed in increments of 10 minutes, two hour, or four hour periods with a constant reactivity input. The power adjustment time has minimal effect on the reactivity perturbations and only influences the rate of reactivity. Thorium fuel has enhanced load following capabilities compared to conventional NU fuel.\\

The long-lasting effects of Pa-233 introduces safety concern when reducing power or reactor shutdown scenarios. Reactivity transformation within the first two days of immediate power reduction will yield similar results for both fuels. Excess reactivity in the thorium fuel will continue to accumulate and eventually double the reactivity peak of NU fuel in the following 90 to 120 days. A shutdown simulation is performed in incremental power reduction steps of 20\% for a range of different days. It is found that NU fuel can adequately control the additional reactivity in this simulation. Thorium fuel maintains a disconcerting amount of excess reactivity that will need to be addressed accordingly. The protactinium transient highlights the need to adequately monitor the buildup of Pa-233 for thorium-based fuels in a reactor.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Tailoring Material Properties by Filler Particle Arrangements

contributor:
Puri, Ishwar
Mechanical Engineering

abstract: The bulk properties of a material are governed by the internal particle arrangements. Nature has the luxury of arranging atoms into different morphologies that produce distinct properties among materials. The manipulation of atoms using human technology is both very expensive and inefficient. Fortunately, nanoparticles can be used to alter bulk material properties by varying their configuration inside materials. The self-assembly of nanoparticles is an effective method for organizing nanoparticles into designated arrangements, providing rapid and remote assembly with minimum human interference. Nanoparticles can either be preprogrammed to communicate with each other to form certain patterns under an external excitation, or be guided by external fields to assemble. The latter approach is relevant to the emerging development of additive manufacturing, broadening possibilities for material design. To fully utilize this facet of advanced additive manufacturing, a comprehensive understanding of material structure-property relationships is essential. However, precise control over particle arrangements using field-assisted assembly is still impractical. In this dissertation, a numerical approach using finite element analysis that explores the relationship between chainlike particle structures and material properties of elastomeric composites, specifically mechanical stiffness, electrical permittivity and thermal conductivity, is reported. With particles aligning into linear chains parallel to the mechanical loading direction, the bulk stiffness enhances 100-fold compared to the same composite with randomly distributed particles. Similar trends are observed for electrical permittivity and thermal conductivity. In contrast, when chains are aligned perpendicular to the direction of mechanical loading, applied voltage, or the heat transfer path, the influence of particle chains on these material properties is negligible. The introduction of zigzag chains provides intermediate results, offering granular modulation over the bulk properties. The mechanical stiffness, electric permittivity, and axial thermal conductivity decrease gradually with increasing zigzag angle, while the transverse thermal conductivity increases as this angle is increased. The electric permittivity also increases with interchain spacing, but decreases as interparticle spacing increases. When the filler volume fraction is lower than 9%, smaller particles contribute towards higher permittivity, while when the volume fraction is larger than 9%, the sample containing larger particles has a higher permittivity. To predict the anisotropic thermal conductivity of a composite consisting of particle chains, a modified empirical model that accounts for the effects of interparticle spacing and zigzag angle is proposed. Prospective research directions are discussed in the last chapter.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Characterization of the Activation Mechanism of Bax

contributor:
Andrews, David
Biochemistry and Biomedical Sciences

subject:
Bax
Apoptosis
Bcl-2 proteins
Bcl-XL
Biochemistry
Biophysics
FRET
Fluorescence Spectroscopy
Cancer
AKT

abstract: Mitochondrial outer membrane permeabilization (MOMP) is regulated by protein-protein and protein-membrane interactions between Bcl-2 family proteins. These interactions are governed by the concentrations and relative binding affinities of the proteins for each other. These affinities are altered by conformation changes of Bcl-2 family proteins resulting from interactions with each other and with membranes. How Bcl-2 proteins transition into and out of the conformations that controls their functions, and ultimately the fate of the cell, is not well understood. Here, kinetic analysis of the pore-forming Bcl-2 family member, Bax, revealed that Bax undergoes a conformational rearrangement through at least one structurally distinct intermediate that is a necessary precursor to pore formation. We discover that four cancer-associated Bax point mutants are trapped in the intermediate state, suggesting that transitions into and out of this intermediate can be modulated independently with consequences for the execution of apoptosis.  Furthermore we report that the conformation changes Bax undergoes can be regulated by phosphorylation of Bax on residue S184 by the pro-survival kinase, Akt. Phosphorylation converts Bax into an anti-apoptotic protein that functions in a dominant-negative fashion. Bioinformatics revealed that in human cancers, higher levels of Bax are positively associated with high levels of PI3K/AKT pathway genes representing an added mechanism for cancer cells to evade apoptosis. Additionally we studied the interactions between Bax, the anti-apoptotic protein Bcl-XL, the sensitizer BH3 protein Bad and the BH3 activator protein Bid. We uncover a new mechanism of apoptosis regulation whereby Bad binds to one monomer of a Bcl-XL dimer eliciting an activating conformation change in a tBid bound to the other monomer of the Bcl-XL dimer. This allows Bad to function as a non-competitive inhibitor of Bcl-XL, and represents a novel mechanism that significantly enhances the potency of Bad to elicit apoptosis.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Every day the human body creates billions of cells replacing damaged or unwanted cells. The death of these cells is tightly controlled and can result in disease when misregulated. Cancers arise when there is too little cell death and neurodegenerative diseases, such as Alzheimer’s, arise from too much cell death. Much research, including this thesis, is focused on understanding how cells die because once understood, cell death can be manipulated to treat disease. Cell death ironically occurs at the mitochondria, a cellular organ normally responsible for creating the energy required for the cell to live. When cell death is initiated, the mitochondria get holes poked into them, releasing pro-death factors that irreversibly commit the cell to dying. The work presented here uncovers new information about the regulation of the hole poking process, how it is blocked in breast cancer and how the process may be modulated to treat cancers.


contributor:
Viveros-Aguilera, Roman
Statistics

abstract: Title: Statistical Analysis of Electrocardiogram Data, Author: Zhiyong Tang, Location: Thode

abstract:
In this thesis we focus on statistical analysis of electrocardiogram data. These data
record the electrical activity of the heart muscle. The data used in this thesis were
provided by Dr. Raimond Wong from Hamilton Regional Cancer Centre (HRCC). The
number of independent cases is small (6 cases), but each electrocardiogram contains over
400000 plotting points. Three electrocardiograms came from cancer patients while the
other 3 came from healthy volunteers. We conduct statistical analysis in two stages: extraction of feature vectors and clustering
analysis of feature vectors. During the first stage, we define 7 statistics that
capture important features of the electrocardiogram data. Then these 7 features are
separately used in a univariate way to classify the electrocardiogram data into two
groups as patients and volunteers. Results show that some of the features can separate
the electrocardiogram data well, but others can not do the job well. During the stage of clustering analysis using the 7 features in a multivariate way,
we employ three methods of clustering analysis: hierarchical clustering analysis, K-means
clustering analysis, and Andrews plot clustering analysis. Results show that
hierarchical clustering analysis and K-means clustering analysis misclassify one of the
subjects. Andrews plot clustering analysis however successfully classify all the subjects.
The first two methods are more objective while the latter requires more judgement.
Note that the limited number of independent cases available does not support general
conclusions, but our study suggest some potential for the methods discussed.

abstract: Thesis

abstract: Master of Science (MS)


title: Program for the Identification of Actionable Atrial Fibrillation – Analysis of Professional Pharmacy Services (PIAAF-PPS): An Analysis of Service Recipients Following Community Pharmacy Screening

contributor:
Dolovich, Lisa
Health Research Methodology

subject: Community pharmacy, opportunistic screening, pharmacy services

abstract:
Background and Objectives: Community pharmacy screening for chronic disease risk factors can promote early detection. Little is known about how pharmacy services are used post-screening. The PIAAF Pharmacy study screened elderly participants for hypertension, diabetes, and atrial fibrillation (AF) in 26 pharmacies in Ontario and Alberta. The primary objective was to determine whether patients screening at risk for AF, hypertension and diabetes had increased odds and rates of pharmacy service receipt than those at lower risk.
Methods: Participants’ pharmacy data were extracted. A conceptual framework of potentially influential factors was constructed. Measurable factors were used as variables in regression analyses. Generalized estimating equations (GEE) were created to model 1) receipt of all pharmacy services, 2) receipt of medication review, and 3) receipt of influenza vaccination.
Results: 165 of 535 patients received 229 pharmacy services. 64% were medication reviews and 25% were influenza vaccinations. Screening at high risk for diabetes, hypertension, and AF was not associated with increased receipt of pharmacy services, except for influenza vaccine, which was associated with screening as high risk for diabetes (OR = 1.69 [95% CI 1.09, 2.64]). Screening in October (IRR = 2.85 [95% CI 1.67, 4.84]), eligibility for annual-only medication reviews (IRR = 2.15 [95% CI 1.53, 3.01]), number of medications (IRR = 1.92 [95% CI 1.07, 3.46]), new medications (IRR = 2.00 [95% CI 1.37, 2.93]), and living in Alberta (IRR = 1.46 [95% CI 1.07, 2.01]) were associated with increased rates of receiving pharmacy services.
Discussion and Conclusions: Screening results were not associated with increased receipt of pharmacy services, with the exception of influenza vaccine and high risk of diabetes. A gap exists between screening and pharmacy service receipt. Pharmacists can use screening interventions and individual screening results as an opportunity to provide pharmacy services to those with chronic disease risk factors.

abstract: Thesis

abstract: Master of Health Sciences (MSc)

abstract: Community pharmacies may be ideal locations for screening of chronic diseases such as diabetes, high blood pressure, and abnormal heart rhythms. It is not well understood how pharmacy services are used in people after screening for these risk factors. This project aims to see if people screening at higher risk levels were more likely to receive pharmacy services than those at lower risk. We used patients’ pharmacy data to see what services they had received after screening, and then created statistical models to determine which patient-, pharmacy-, community-, and screening-related factors were associated with a greater chance of receiving pharmacy services. Being at risk of diabetes, high blood pressure, and irregular heart rhythms were not associated with a greater likelihood of receiving pharmacy services, except in those at high risk for diabetes—these patients were found be associated with a higher chance of receiving flu shots.


abstract: Title: McMaster Grid Scheduling Testing Environment, Author: Majd Kokaly, Location: Thode

abstract:
With the phenomenal growth of the Internet and the advancement of computing hardware,
grid architectures have been developed to exploit idle cycles in large networks of
computational resources. One key aim of resource management (scheduling) schemes
is to find mappings of incoming workload to machines within the grid to maximize
the output. The first contribution of this thesis is the construction of a tool to aid
researchers in testing and improving scheduling schemes, namely the McMaster Grid
Scheduling Testing Environment (MGST). The Linear Programming Based Affinity Scheduling Scheme (LPAS_DG) was introduced
by researchers at McMaster, and simulation results have been promising
in suggesting that this scheduling scheme outperforms other schemes when there is
high system heterogeneity and is competitive under lower levels of heterogeneity. The
second contribution of this research is providing suggestions to improve this scheme,
based on the results of experiments where the LPAS_DG scheme was actually deployed
on the MGST test bed.

abstract: Thesis

abstract: Master of Applied Science (MASc)


contributor:
Canty, Angelo
Statistics

abstract: Title: Comparison Between Affymetrix and Illumina Gene Expression Microarray Platforms, Author: Yiqiang Luo, Location: Thode

abstract:
DNA microarray technology is an exploratory tool that can be used to measure thousands of gene expression values simultaneously. Many different microarray platforms have been developed. Various studies have shown that the same experiment performed in different laboratories using the same or different microarray platforms sometimes produce very different results. The lack of reproducibility is becoming a major challenge when comparing the microarray experiments across different labs and different platforms.

Our study is focused on the cross-platform reproducibility between the Affymetrix GeneChip and Illumina BeadChip using two rodent experimental models for Type-1 diabetes. Within-platform reproducibility is also checked for the Illumina platform. Comparisons are carried between the two platforms in terms of the physical array features, the data quality and the chip effects, and finally the SAM analysis. Our study suggested that the overall comparability between these two platforms is fairly poor, however some findings are promising and the results show some agreement with the conclusions found in Barnes et al. (2005).

abstract: Thesis

abstract: Master of Science (MS)


title: Divide and Conquer: How Conquering Multiple Niches Influenced the Evolution of the Divided Bacterial Genome

contributor:
Finan, Turlough
Biology

subject:
Multipartite genome
Divided genome
Chromosome
Chromid
Megaplasmid
Genome evolution
Sinorhizobium meliloti
Symbiotic nitrogen fixation
Bacterial genetics
Systems biology
Metabolic modelling
Genome engineering

abstract: Approximately 10% of sequenced bacterial genomes are multipartite, consisting of two or more large chromosome-sized replicons.  This genome organization can be found in many plant, animal, and human pathogens and symbionts.  However, the advantage of harbouring multiple replicons remains unclear.  One species with a multipartite genome is Sinorhizobium meliloti, a model rhizobium that enters into N2-fixing symbioses with various legume crops.  In this work, S. meliloti derivatives lacking one or both of the secondary replicons (termed pSymA and pSymB) were constructed.  Phenotypic characterization of these strains, including growth rate, metabolic capacity, and competitive fitness, provided some of the first experimental evidence that secondary replicons evolved to provide a niche specific advantage, improving fitness in a newly colonized environment.  These results were further supported by characterizing the symbiotic phenotypes of 36 large-scale pSymA and pSymB deletion mutants.  To further this analysis, an in silico S. meliloti genome-scale metabolic network reconstruction was developed and flux balance analysis used to examine the contribution of each replicon to fitness in three niches.  These simulations were consistent with the hypothesis that metabolic pathways encoded by pSymB improve fitness specifically during growth in the plant-associated rhizosphere.  Phylogenetic analysis of a pSymB region containing two essential genes provided a clean example of how a translocation from the primary chromosome to a secondary replicon can render the secondary replicon essential.  Moreover, an experimental analysis of genetic redundancy indicated that 10-15% of chromosomal genes are functionally redundant with a pSymA or pSymB encoded gene, providing an alternative method for how secondary replicons can become essential and influence the evolution of the primary chromosome.  Finally, the work presented here provides a novel framework for forward genetic analysis of N2-fixing symbiosis and the identification of the minimal N2-fixing symbiotic genome, which will help facilitate the development of synthetic symbioses.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Many bacteria that enter into symbiotic or pathogenic relationships with plants, animals, and humans contain a genome that is divided into multiple chromosome-like molecules.  One example is the N2-fixing legume symbiont Sinorhizobium meliloti, whose genome contains three chromosome-sized molecules.  Here, the functions associated with each molecule in the S. meliloti genome were examined through a combination of experimental genetic analyses and computer based simulations.  Results from these approaches suggested that adaptation to unique environments selected for the evolution of secondary chromosome-like molecules, with each predominately contributing to growth in a specific environment, including environments associated with an eukaryotic host.  The genes on these replicons are therefore prime targets for manipulation of bacterium-host interactions, and represent reservoirs of valuable genes for use in synthetic biology applications.
Additionally, the genome reduction approach employed in this study laid out a ground work for identification of the minimal N2-fixing symbiotic genome.  This represents a crucial step towards successfully engineering improved nitrogen fixation, and the engineering of synthetic N2-fixing symbioses involving non-legumes and/or non-rhizobia.


title: Superbubble Feedback in Galaxy Evolution

contributor:
Wadsley, James
Physics and Astronomy

subject:
physics
astrophysics
interstellar medium
numerical simulation
astronomy
hydrodynamics
supernovae
galaxy formation
cosmology

abstract:
Galaxy formation is a complex, nonlinear process that occurs over scales that span orders of magnitude in space and time.  Of the many phenomena taking place within a galaxy, supernovae (SN) are among the most important.  SN heat, stir, and eject gas from the galaxy.  This has profound impact on the galaxy's evolution over cosmic time.
Numerical simulations of galaxies must often include models for feedback from SN.  We present a new model for SN feedback that captures the effects of previously ignored physics: thermal conduction.  Massive stars form in clusters, allowing their SN ejecta to merge into a superbubble, which can vent from the disc to drive a high-entropy galactic outflow.  Thermal conduction determines how much mass is mixed into this superbubble.

We use this to study SN feedback in galaxy evolution, and come to four major conclusions.  First, superbubbles drive stronger galactic outflows in compared to past models of SN feedback.  Second, these outflows are key to both preventing the overproduction of stars and the formation of too-massive central bulges.  High redshift outflows eject starforming gas, and preferentially remove bulge forming gas.  Third, we show that SN cannot prevent runaway star formation in galaxies more massive than our own $(M_{halo}>10^{12}\;\rm{M_\odot})$.  In these galaxies, SN are unable to prevent transport of gas towards the centre of the galaxy.  These results suggest a transition between regulation from stars to regulation from supermassive black holes occurs at roughly this
mass.  Finally, we use our simulated galaxies to show recent observations of the Radial Acceleration Relation (RAR) are consistent with $\Lambda$CDM cosmology.  The RAR ties galaxy kinematics to baryonic mass, in a tight, universal scaling relation. While this has been claimed as potential evidence of exotic new physics, we show this same tight relation occurs for galaxies formed in $\Lambda$CDM.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


contributor:
Qiao, Sanzheng
Computing and Software

abstract: Title: Mass-Spring Networks for Sound Synthesis, Author: Don Morgan, Location: Thode

abstract:
Physical sound synthesis produces sound by modelling the physics of musical instruments.
One way to do this is to model the musical instrument as a network of masses,
springs and dampers. This is known as a mass-spring system.

The goal of this thesis is to determine the stability and accuracy of the numerical
methods commonly used to implement mass-spring systems for sound synthesis and
determine if there are alternate methods that might provide superior results.

We show that the standard method used in mass-spring systems, when used on undamped
systems, has no numerical damping, but does have frequency warping and is
unstable at frequencies above 1/π times the sampling rate. As well, we find that for
lightly damped systems the damping is accurate, but large damping can cause instability
even at low frequencies. We present an algorithm to implement mass-spring systems
using implicit numerical methods and show how a mass-spring system can be implemented
using a wave digital filter. We compare the standard method implementing
mass-spring systems with two higher order numerical methods: the fourth order Runge-Kutta,
and the VEFRL algorithm, a fourth order symplectic algorithm. We find that
the VEFRL algorithm is much more accurate than the standard method, but that this
increase in accuracy does not noticeably affect the quality of the sound produced by the
mass-spring system when used to simulate a vibrating string. The increased accuracy
of the VEFRL method may, however, be useful for mass-spring spring systems used in
physics or engineering requiring high accuracy.

abstract: Thesis

abstract: Master of Computer Science (MCS)


contributor:
Pelinovsky, Dmitry
Mathematics

abstract: Title: Well-Posedness of a Nonlinear Wave Equations in Characteristic Coordinates, Author: Anton Sakovich, Location: Thode

abstract:
We prove global well-posedness of the short-pulse equation with small initial
data in Sobolev space H^2. Our analysis relies on local well-posedness results
of Schafer and Wayne, the correspondence of the short-pulse equation to the
sine-Gordon equation in characteristic coordinates, and conserved quantities
of the short-pulse equation. We perform numerical computations to illustrate
this result. We also prove local and global well-posedness of the sine-Gordon
equation in an appropriate vector space.

abstract: Thesis

abstract: Master of Science (MS)


title: Object-Oriented Literate Programming

contributor:
Sekerinski, Emil
Computing and Software

abstract: Title: Object-Oriented Literate Programming, Author: Ming Y. Zhao, Location: Thode

abstract:
During the past decades, programming methodology has seen an improvement by
structured programming and object-oriented programming (OOP), leading to software
that is more reliable and easier to develop. However, software engineers are still
dealing with problems in processing associated documentation. Literate programming
was introduced by Donald Knuth in the early 80's as an approach to produce programs
together with their documentation in a way that is aimed at consumption by
humans rather than by compilers. However, dated and complex features, dependence
on formatting and programming language, and a lack of methodology prevented the
method from gaining in popularity.

In this thesis, we propose an approach to "integrate" OOP with literate programming
in order to present and document the whole design in a consistent and
maintainable way. In our approach, both program code and corresponding documentation
are generated from the same source. The resulting documentation consists
of code chunks with detailed explanations, as well as automatically generated class
diagrams with varying levels of detail. A tool, Spark, has been developed and applied
to the design of a Transit Information System from requirement analysis to testing.
Spark was also used in its own development.

abstract: Thesis

abstract: Master of Science (MS)


title: Testing Grammars for Top-Down Parsers

contributor:
Franek, Frantisek
Computing and Software

abstract: Title: Testing Grammars for Top-Down Parsers, Author: Asma M. Paracha, Location: Thode

abstract:
During the past decades, the complexity of compilers has grown much and so
has the importance of testing them. Compiler is essentially a software tool, and
hence its testing should fulfill all the software testing criteria. Testing is the
process of finding errors in an application by executing it. It is one of the essential
and most time consuming phases of software development. Hence a lot of effort
is directed to fully automate this process, making it more reliable, repeatable,
less time consuming, less boring, and less expensive. Test cases for compiler
should be generated so that they cover all possible valid and invalid input
conditions. One of the major problems in generating test cases is the
completeness of coverage, and the potentially unfeasible size of the generated
test data. The test data for compilers should ideally cover all the syntax and
semantic rules of the language in all possible combinations and in all possible
contexts. When generating test cases for a compiler, the grammar act as the
foundation as it defines the language for which the compiler is being built. In this
research we addressed the issue of automatic generation of test data for parsers
by implementing Purdom's algorithm in Java and C++ and generating test data
for MAGS compiler.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: PRECARIOUS MOBILITIES: MAPPING SPACE, RACE, AND CLASS IN CONTEMPORARY BRITISH LITERATURE AND FILM

contributor:
Attewell, Nadine
English and Cultural Studies

subject:
Social Mobility
Race
Class
British Literature

abstract:
This dissertation brings together an archive of texts that both reflect and challenge the construction of a contemporary crisis of social mobility and working-class decline as a racial problem. British news media, political rhetoric, and creative work such as literature and film have increasingly represented the expansion of multicultural Britain, particularly after postwar decolonization, as responsible for the loss of the good life for the white working classes. In response to this causatively intertwined narrative of migrant mobilities and class stagnation, this doctoral project has developed an alternate dialogue between the present day and the postwar by examining social mobility as an affective genre in representations of race and class.
By exploring literary and cinematic representations of urban mobilities, the home, and the school, my thesis demonstrates the ways in which social mobility materializes as an affective structure that shapes the connections between white working-class and migrant communities in more nuanced ways than has been portrayed by British media and politicians. My analysis of literature and film reveals that the affective genre of social mobility since the postwar era has tended to shore up the continuation and preservation of white nationalism through the marginalization and continued exploitation of racialized subjects. And yet, although the contemporary rhetorical construct of social mobility and its apparently racially-caused endangerment utilizes the white working class as its litmus test and ultimate victim, what the narrative of the good (white) life obfuscates is its inaccessibility for not just the racialized other, but for the white working classes as well. Thus, while my project teases out the colonial structuring of relationships between white working class and migrant and minority ethnic subjects within narratives of class desire, it also ultimately understands classed and racialized communities as jointly — if unevenly — impacted by capitalism.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This project critically examines the common portrayal of the decline of white working-class social mobility as caused by immigration and multiculturalism in British media, politics, and culture. In particular, this narrative of racially-caused social “immobility” cultivates a comparison between the postwar era, which was supposedly a time of working-class affluence, and the twenty-first century present, which is characterized through economic austerity and lack of opportunity for lower income communities. My dissertation counters this popular and politically motivated narrative by bringing together an archive of cultural material — literature, film, political speeches, and news media coverage — that provides a more nuanced description of interactions between the white working class and migrant communities in Britain from the postwar and contemporary eras. This thesis ultimately examines social mobility as a desire that mediates relationships between classed and racialized people under capitalism, rather than a pre-existing economic and social privilege that has been “taken away” by immigrants and the expansion of multiculturalism in Britain.


title: ON ASSEMBLE-TO-ORDER  SYSTEMS WITH STOCHASTIC  LEAD TIMES

contributor:
Deza, Antoine
Huang, Kai
Computing and Software

subject:
Literature Review
Stochastic Lead Times
Assemble-to-Order
ATO

abstract:
We present and study the current research trends and advances for optimizing assemble-to-order systems with stochastic lead times. Assemble-to-order systems are widely used in several industries, where end products consist of multiple components and are customizable. Manufacturers can offer greater flexibility to their customers by delaying the assembly of the components until after the order is placed. This means they do not keep an inventory of end-products. Only components can be kept in the inventory and assembled upon demand. We
compare and contrast different formulations and the features of assemble-to-order systems studied in the literature including system configuration, replenishment policy, lead time type, and demand distribution. Single-period systems, periodic-review systems, and continuous-review systems are considered. Current assumptions, formulations, solutions, and challenges are discussed.

abstract: Thesis

abstract: Master of Science (MSc)


contributor:
Smith, Spencer
Computing and Software

abstract: Title: A Document Driven Methodology for Improving the Quality of a Parallel Mesh Generation Toolbox, Author: Wen Yu, Location: Thode

abstract:
Scientific computing software has had considerable success in producing efficient
and correct numerical results. However other software qualities, such
as usability, maintainability, testability, flexibility, and reusability, are often
neglected. Presented in this work is our proposed solution to improve the
quality of scientific computing software by using a document driven software
engineering methodology. A parallel mesh generation toolbox (PMGT) is developed
to illustrate our approach.

This thesis proposes to improve quality via a methodology that consists
of a sequence of design steps and documents, including the following: a
Software Requirements Specification (SRS), a Module Guide (MG), a Module
Interface Specification (MIS), and a Summary of Validation Testing Report
(SVTR). Where applicable, mathematical notation is used in these documents
to make them as formal as possible. This formality improves the documents
by making them less ambiguous and more validatable; therefore, the correctness
and testability of the software are improved. The proposed methodology
also requires that the traceability between the documents listed above, and the
traceability between these documents and code be explicitly specified. This allows
for verification of completeness and consistency and facilitates systematic
change management.

Quality is also promoted during the implementation stage. For instance,
a new modification is proposed to Rivara's longest side bisection algorithm.
The modified algorithm improves the quality of usability, without
sacrificing reliability. A new coarsening algorithm inspired by Oliver-Gooch is
also proposed. Instead of decimating vertices by collapsing the edges, the new
algorithm uses edge collapse to decimate the cells.

The proposed methodology promotes testing as an important way to
improve software quality. However, due to the lack of an expected answer,
testing the correctness of PMGT is difficult. To overcome this challenge, the
method promoted in our work is automated testing to verify the known properties
of a correct solution, such as checking for conformality and for boundary
closure.

abstract: Thesis

abstract: Master of Science (MS)


title: Injectable Interpenetrating Network Hydrogels for Biomedical Applications

contributor:
Hoare, Todd
Chemical Engineering

subject:
Hydrogel
Interpenetrating network
PolyNIPAM
PVP
Injectable
Biomaterials

abstract:
Interpenetrating polymer networks (IPN’s) consist of two overlapping cross-linked networks that are not bonded to each other. Hydrogel IPN’s are of application interest due to properties such as mechanical reinforcement, modulated drug release and biodegradation kinetics, dual polymer activities in vivo, and novel nanostructured morphologies. Prior IPN hydrogels reported in the literature either required surgical implantation (disadvantageous for several reasons) or were polymerized in situ (limited to a small subset of biologically safe chemistries). Alternatively, we formed IPN’s using a mixing injector to deliver orthogonally reactive functionalized prepolymer solutions that gel upon contact. Specifically, we use hydrazone chemistry to gel a thermosensitive poly(N-isopropylacrylamide) (PNIPAM) network and kinetically orthogonal thiosuccinimide or disulfide chemistry to cross-link a second network of hydrophilic poly(vinylpyrrolidone) (PVP).
The resulting IPN’s preserve the thermoresponsive properties of the PNIPAM constituent but exhibit slower, smaller, and more reversible transitions due to entanglement with the highly hydrophilic PVP network (potentially useful to reduce the problem of burst release in thermoresponsive drug delivery systems).  Mechanical reinforcement was evidenced by the increased shear storage modulus of IPN composites relative to the sum of the individual component moduli, particularly so in IPN’s employing the thiosuccinimide-cross-linked PVP.
The nanostructure of the IPN hydrogels was further studied using small angle neutron scattering with contrast matching, and was found to combine features characteristic to each single network component (PNIPAM-rich static domains embedded in PVP-rich fractal clusters). However, our results suggest some slight changes to their scattering profiles, indicative of partial mixing or influence of each network structure upon the other. Corroborating investigations with single-molecule super-resolution fluorescence microscopy, operating at a slightly larger length scale, show the formation of separate populations of mixed and individual domains or clusters of each polymer type.
These properties suggest such injectable IPN’s for further investigation as prospective biomaterials.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This thesis describes the development of overlapping but unconnected polymer networks formed by mixing of completely injectable polymer precursors. The interlocking pair of networks is based on one component that shrinks upon heating and the other component that offers the potential for biological adhesion. Entanglement between the two components renders them mutually reinforcing and changes the shrinking and reswelling behaviour of the temperature-responsive component. The structure of the composite network is also distinctive from either individual component, forming alternating, unevenly mixed regions richer in one or the other component. The composite’s properties are attractive for a potential bioadhesive drug delivery carrier and, in the future, a possible wound closure biomaterial.


title: A CFD Study on the Extraction of Geothermal Energy from Abandoned Oil and Gas Wells

contributor:
Lightstone, Marilyn
Mechanical Engineering

subject:
Computational Fluid Dynamics
Oil & Gas
Geothermal
Heat Transfer
Sustainable Energy

abstract: This thesis investigates the feasibility of converting spent oil and gas wells for use in geothermal power generation. A novel approach to heat exchange with the ground was proposed whereby two directionally drilled (L-shaped) wells are connected to create a continuous loop. A Computational Fluid Dynamics (CFD) model was developed that simulates flow through the connected wells and the associated heat exchange with the ground. The model consisted of a coupled fluid-solid domain; 1D fluid flow was explicitly coupled to the 2D cylindrical solid domain using a convection boundary condition. Temperatures in the solid domain were resolved using an Alternating Direction Implicit (ADI) solver, which suited the largely unidirectional nature of the heat transfer problem. Fluid temperatures were solved for using a Tri-Diagonal Matrix Algorithm (TDMA). The results from a series of simulations demonstrated that geothermal power generation from abandoned wells is feasible under certain conditions. The findings of this research show that the correct selection of a well, considering geothermal gradient, well diameter, and ambient temperatures (impacting the inlet temperature), will significantly influence the level of power production. Further, the simulations show that it is necessary to optimize the flow rate for the given well conditions. The research indicates that the addition of insulation to a portion of the system can lead to modest improvements in power when the system is operated continuously. In contrast, it was found that insulation was necessary for the viability of intermittent use, which would allow the system to meet the demand for peak power generation. The simulations demonstrated that the proposed system could produce approximately 200 kW to 300 kW of electricity.

abstract: Thesis

abstract: Master of Applied Science (MASc)


contributor: Veall Kanagaretnam Statistics

abstract: Title: Does Good Corporate Governance Improve Earnings Quality?, Author: Dan He, Location: Thode

abstract:
In this paper, we examine the relationship between corporate governance and earnings
quality. For earnings quality, we use two measures which are based on the
modified Jones model (1995) and the Dechow-Dichev model (2002), respectively.
Then we extract three factors from seven corporate governance variables by using
principal components analysis. Using ordinary least squares (OLS) regressions and
sensitivity tests, we find that firms with more independent boards and more efficient
board structures have higher earnings quality. The results also indicate that larger
firms and firms with higher return on assets have better earnings quality.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Berlinsky, A.J.
Kallin, C.
Physics

abstract: Title: Relaxation of a Two-Level System Coupled to a Fullerene Molecule, Author: Kiri Nichol, Location: Thode

abstract:
Insight into many-body problems in quantum mechanics may be developed
by solving simple models exactly using computational methods. The small
size of endohedral-doped fullerene molecules allows the electronic states to be
evaluated numerically using a spin model such as the Heisenberg Hamiltonian.
The Lanczos algorithm is deployed to compute a few low-energy states of
fullerene systems.

Since the spin of the dopant electrons can be manipulated using external
magnetic fields, the system can be used as a qubit. For sufficiently large couplings
between the dopant and the fullerene, the qubit may relax by releasing
energy into the carbon cage. The resulting oscillations of the qubit are found
to include a high frequency component introduced when the spin accesses multiple
states with different energies. The frequency and the amplitude of the
qubit's oscillations also depend on the magnitude of external fields and the
size of the coupling between the dopant and the fullerene.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Kallin, C.
Berlinsky, A.J.
Science

abstract: Title: Disorder Effects on AC Fluctuation Conductivity in High-Tc Superconductors, Author: Bo Zhou, Location: Thode

abstract:
For High-Tc superconductors the fluctuation regime is much wider than conventional
superconductors due to the short coherence length and high transition temperature.
AC measurements can probe the conductivity at a wide range of frequencies,
and therefore provide a test of the scaling properties predicted from theory. The
measured critical exponents and width of the fluctuation peak are sample dependent,
which suggests that the sample inhomogeneities may play an important role in the
critical region.

In this thesis we study the effects of disorder on the fluctuation conductivity in the
critical regime of zero-field normal-superconducting transition by the time-dependent
Ginzburg-Landau theory. We set up a discretized model of the superconductor and
calculate the two-dimensional and three-dimensional scaling function without disorder
above Tc. The result of the discretized model deviates slightly from previous
theoretical studies of the continuous model, which can be explained by a finite short wavelength
cutoff in Ginzburg-Landau theory. Our results agree well with other
theoretical investigations on cutoff effects from an analytical approach.

Disorder in a superconductor is modeled by a distribution of Tc's at the lattice
sites. We add random disorder to a two-dimensional lattice and calculate the scaling
functions averaged over 1000 disorder configurations. When disorder is weak, the
scaling functions are increased when T is close Tc . At strong disorder anomalous
behavior may occur at the region close to Tc.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Canty, Angelo J.
Mathematics and Statistics

abstract: Title: Empirical Bayes Analysis for Detecting Differential Expression in Microarrays, Author: Ying Wang, Location: Thode

abstract:
The purpose of gene expression microarray studies is to identify differentially expressed
genes. Due to the very large number of genes compared to the very small
sample size, and the possibility of high level of non-normal random noise, traditional
hypotheses tests cannot be used directly. In this thesis, we applied parametric and
nonparametric empirical Bayes methodologies to test the hypotheses of differential
expression in a real microarray data set from a study of Type 1 Diabetes and some
other simulated data sets. In our real data, we saw some problems of applying parametric
empirical Bayes (in terms of R software called EBarrays; nonparametric
empirical Bayes method implemented in the R packaged Siggenes also has problems
in detecting differential expression in real data when some extreme patterns show up
in the permutation matrix. We implemented a new function called EBayes based on
Efron's idea of nonparametric empirical Bayes method. EBayes performs much better
than other empirical Bayes methodologies in dealing with real data. Furthermore,
the results of simulated data show that the new function EBayes are comparable to
Siggenes EBAM function.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Sorensen, Erik S.
Physics

abstract: Title: Impurity Quantum Monte Carlo Calculations of Persistent Currents, Author: Peter Hitchcock, Location: Thode

abstract:
Recent interest in the fundamental physics of the Kondo effect has been driven
by the observation of Kondo physics in mesoscopic systems such as quantum
dots [1, 2] and carbon nanotubes [3], which can act analogously to magnetic
impurities in a bulk metal. Highly tunable mesoscopic systems such as these
present the possibility of observing the controversial Kondo length scale εK
associated with the cloud of conduction electrons that screen the spin of the
impurity [4]. This plays a similar role in scaling theories as the Kondo temperature
Tk.

One proposal [5] for detecting this length scale is to measure the finite-size
dependence of persistent currents in an isolated conducting ring coupled to a
quantum dot. The screening cloud should be 'trapped' in the closed system,
and will not form if the size of the ring L is much smaller than εK. In particular,
the current in the Kondo regime should be a universal scaling function
j = L^-1 f(Φ, L/εK, T/Tk) (here Φ is the applied flux) [6, 7]. Considerable disagreement
has arisen in the theoretical estimates of these persistent currents
as different analytical treatments yield contradictory predictions [6, 8, 9, 10].

This thesis presents a new Quantum Monte Carlo (QMC) technique for
measuring persistent currents in such systems, based on the Hirsch-Fye Impurity
QMC algorithm [11] which is ideally suited to treating systems with a
single impurity such as the quantum dot. The algorithm provides exact numerical
results at finite temperatures. The complexity of the algorithm does
not scale directly with the size of the system, making it particularly attractive
for investigating a wide range of system sizes.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Waddington, J.C.
Physics

abstract: Title: In-Beam Test of the TIGRESS Prototype Detector, Author: Lesley M .Watters, Location: Thode

abstract:
This thesis describes the preparations for the first in-beam test of a new type of
gamma-ray detector, which will be part of the TIGRESS array of segmented high-purity
Germanium clover detectors.

Gamma rays emitted from a moving nucleus are Doppler-shifted leading to a
broadening of the measured photo-peak. Through a determination of the interaction
position in the crystal, it is anticipated that most of the resolution may be recovered with
these detectors. In order to test this prediction, the detector has been tested in an
experiment. Prior to this test, a "pre-test" was done with a conventional detector. The
reasons for the choice of the reaction for the pre-test, the description of the experiment
and its results and the lessons learned will be presented.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Huang, Kai
Computational Engineering and Science

subject:
Vehicle Routing
Interdiction
Split Delivery
Mixed Integer Programming

abstract: In this thesis, we study the role of interdiction in the Vehicle Routing Problem (VRP), which naturally arises in humanitarian logistics and military applications. We assume that in a general network, each arc has a chance to be interdicted. When interdiction happens, the vehicle traveling on this arc is lost or blocked and thus unable to continue the trip. We model the occurrence of interdiction as a given probability and consider the multi-period expected delivery. Our objective is to minimize the total travel cost or to maximize the demand fulfillment, depending on the supply quantity. This problem is called the Vehicle Routing Problem with Interdiction (VRPI). We first prove that the proposed VRPI problems are NP-hard. Then we show some key analytical properties pertaining to the optimal solutions of these problems. Most importantly, we examine Dror and Trudeau's property applied to our problem setting. Finally, we present efficient heuristic algorithms to solve these problems and show the effectiveness through numerical studies.

abstract: Thesis

abstract: Master of Science (MSc)


title: Personalizing Brain Pathology Analysis Using Temporal Resting State fMRI Signal Complexity Analysis.

contributor:
Noseworthy, Michael D.
Biomedical Engineering

subject: Fractal Analysis, rs-BOLD, ASD, mTBI, CFS, Chemo-Fog, Chemo-Brain.

abstract:
Assessment of diffuse brain disorders, where the brain may appear normal, has proven difficult to translate into personalized treatments.  Previous methods based on brain magnetic resonance imaging (MRI) resting state blood oxygen level dependent (rs-BOLD) signal routinely rely on group analysis where large data sets are assessed using region-of interest (ROI) or probabilistic independent component analysis (PICA) to identify temporal synchrony or desynchrony among regions of the brain.

Brain connectivity occurs in a complex, multilevel and multi-temporal manner, driving the fluctuations observed in local oxygen demand. These fluctuations have previously been characterized as fractal, as they auto-correlate at different time scales. In this study we propose a model-free complexity analysis based on the fractal dimension of the rs-BOLD signal, acquired with MRI. The fractal dimension can be interpreted as a measure of signal complexity and connectivity. Previous studies have suggested that reduction in signal complexity can be associated with disease. Therefore, we hypothesized that a detectable differences in rs-BOLD signal complexity could be observed between patients with diffuse or heterogeneous brain disorders and healthy controls.

In this study, we obtained anatomical and functional data from patients with brain disorders where traditional methods have been insufficient to fully assess the condition. More specifically, we tested our method on mild traumatic brain injury, autism spectrum disorder, chemotherapy-induced cognitive impairment and chronic fatigue syndrome patients.
Three major databases from the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) project were used to acquire large numbers of age matched healthy controls.  Healthy control data was downloaded from the the Autism Brain Imaging Data Exchange (ABIDE), the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Human Connectome Project specifically matching our experimental design.

In all of our studies, the voxel-wise rs-BOLD signal fractal dimension was calculated following a procedure described by Eke and Herman et al. 2000. This method was previously used to assess brain rs-BOLD signal in small mammals and humans.  The method consists of estimating the Hurst exponent in the frequency domain using a power spectral density approach and refining the estimation in the time domain with de-trended fluctuation analysis and signal summation conversion methods. Voxel-wise fractal dimension (FD) was then calculated for every subject in the control and patient groups to create ROI-based Z-scores for each individual patient. Voxel-wise validation of FD normality across controls was studied and non-Gaussian voxels, determined using kurtosis and skewness calculations, were eliminated from subsequent analysis. To maintain a 95 % confidence level, only regions where Z-score values were at least 2 standard deviations away from the mean were included in the analysis.  In the case of chronic fatigue patients and chemotherapy induced cognitive impairment, DTI analysis was added to also determine whether white matter abnormalities were also relevent.  Similar Z-score analysis on DTI metrics was also performed.

Brain microscopic networks, modeled as complex systems, become affected in diffuse brain disorders.  Z-scoring of the fractal rs-BOLD frequency domain delineated patient-specific regional brain anomalies which correlated with patient-specific symptoms.  This technique can be used alone, or in combination with DTI Z-scoring, to characterize a single patient without any need for group analysis, making it ideal for personalized diagnostics.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


contributor:
Walter, Stephen
Statistics

abstract: Title: Longitudinal and Cross-sectional Reference Curves of Gross Motor Function in Children, Author: Weiling Wang, Location: Thode

abstract:
Reference curves are the most popular tool to monitor the time-related growth in children.
Both cross-sectional and longitudinal studies are widely used to collect the reference
samples. The methods used for constructing the reference curves and the interpretation of
the curves for longitudinal studies should be different from those for the cross-sectional
studies. However misunderstanding in constructing and interpreting the reference curves
for the cross-sectional and longitudinal studies is common, especially the concerning of
the effect of regression to the mean in the longitudinal studies. The LMS models of Cole
and Green[1,2] using penalized likelihood are considered to be the most powerful methods
to construct the reference curves for both cross-sectional and longitudinal studies. This
thesis focuses on the comparison of the conditional LMS regression approach for drawing
the median conditional centiles for longitudinal data to the conventional LMS model for
constructing the distance centiles for cross-sectional data. It describes the different
interpretations of the two approaches. The application of the two methods to a study of
Gross Motor Function is investigated in detail to illustrate the difference between them.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Berlinsky, A.J.
Kallin, C.
Science

abstract: Title: Spin Wave Analysis of Quasi Two-Dimensional Quantum Magnet Cs2CuCl4, Author: Junhua Zhang, Location: Thode

abstract:
The inelastic neutron scattering measurements by Coldea and co-workers on Cs2CuCl4
have attracted intense attention due to the anomalous spin correlation properties
revealed. The debate on the low-temperature magnetic phase, spiral ordered phase
or spin liquid phase, of this material has triggered mainly two theoretical scenarios,
a spin wave scenario and a spinon scenario, for the origin of the unusual scattering
continua and large quantum effects. Since there is evidence of low-energy spin wave
modes in the experimental data, a study of the spiral ordered phase using perturbation
theory, taking into account spin wave interactions, becomes important to determine
the nature of the magnetic excitations in this spin system.

Motivated by this situation, we have carried out a perturbation calculation within
the nonlinear spin wave theory framework by means of the 1/S expansion scheme.
In this work, we first develop the general formalism for a class of spiral ordered spin
systems. Then we explain how to make contact between our theoretical calculation
and experiment. After establishing the necessary formulae, we perform numerical
evaluations for Cs2CuC14 to compare with experimental data. We find that a nonlinear
spin wave analysis of this material results in significant continua in the scattering
spectra as well as large quantum renormalization of the excitation energy. However,
our results are quantitatively different from the experimental data. Further numerical
work needs to be done to better understand the remaining discrepancies between
theory and experiment.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Venus, D.
Science

abstract: Title: Structural and Magnetic Properties of a Chemically Ordered Manganese Alloy Film, Author: Zhouwei Zhou, Location: Thode

abstract:
FeMn has often been successfully used as a pinning layer in exchange bias systems.
Ultrathin FeMn films have been studied little, even though the importance of the
volume of a data storage system has been increasingly stressed recently. A 4ML
Ni/W(110) substrate is used to establish a (slightly strained) (111) f.c.c. template
upon which 3ML Fe is deposited and annealed to 580K. LEED, Auger electron spectroscopy
(AES) and crystallographic channeling of Auger electrons (Directional AES)
confirm that the resulting substrate has very good short and long range f.c.c. (111) order,
and is Fe rich at the surface. Mn is grown sequentially to 1.6ML through multiple
depositions, with annealing at 580K for 20 seconds between consecutive depositions
to maintain the epitaxial structure. LEED and AES reveal that the annealing caused
the Fe and Mn to form a chemically ordered FeMn alloy, while Ni is relatively inert
to this thermal effect. The magnetism of each alloy film is studied in situ by the
Kerr effect. The alloy films formed from 0.3 or 0.5ML of Mn have magnetic properties
similar to the FeNi substrate. Alloy films formed from 0.8 to 1.6ML of Mn
show a marked increase in the width of the susceptibility peak, and develop a slanted
hysteresis loop with a reduced coercive field that is consistent with a Mn gradient
within the film creating a wide distribution in Tc. This suggests a paramagnetic or
antiferromagnetic Mn alloy formation.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Thabane, Lehana
Statistics

abstract: Title: The Measurement of Integrated Human Service Network (The Children's Treatment Network of Simcoe York), Author: Chenglin Ye, Location: Thode

abstract:
Community-based human services have traditionally been provided by autonomous
service agencies. They have their own funding source and independent process.
Integration has been advocated as a key strategy to integrate different agencies together
to provide multiple services for a targeted community. The Children's Treatment Network
(CTN) of Simcoe York is a network of agencies and organizations providing services to
children with multiple needs and their families in Simcoe County and York Region. This
study was designed to evaluate the different levels of integrated service approaches for
children on outcomes. The study consisted of two parts: phase I and phase II
measurement. Our project covered phase I measurement with the following objectives. Clinically,
we aimed to evaluate agencies' integration in the network, promote discussion, and
determine any interrelationship between a network's integration and its functioning. The
statistical objectives were to quantify the network integration for agency, to represent the
overall integration, to quantify the association between network's integration and
functioning and to assess the sensitivity of results. We measured agencies' integration through measuring its agreement in
collaboration with other agencies in the network. The higher agreement in collaboration
indicates a better services integration. We defined four different agreement measures
from different perspectives. The agreement based on group's perception was defined to
be the primary measure. We used mean difference, percentage and the Kappa statistic
to measure the agreement for each agency. Correlation and regression analyses were
applied in investigating the association between network's integration and its functioning. The sensitivity of the results was analyzed by examining the re-sampling bias of
bootstrapping regression models. Agreement measures were consistent for each agency. In Simcoe, agencies had
an average agreement 0.874 (S.D. 0.213) in mean difference, 46.63 (S.D. 12.91) in
percentage and 0.258 (S.D. 0.143) in Kappa. Agencies of York had average agreements
of 0.662 (S.D. 0.204), 49.36 (S.D. 13.06) and 0.282 (S.D. 0.121), respectively. Agency
10 and 33 in Simcoe and Agency 14 in York were found to have the highest agreement.
Agency 3 and 21 in Simcoe and Agency 8 and 9 in York, on the other hand, were found
to have the lowest agreement. Different graphical displays illustrated that the overall
agreement in collaboration was low and the agencies in York generally had a higher
agreement. Correlation analysis showed that synergy and agencies' perception of pros
and cons were significantly correlated with the primary percentage agreement. In
regression analysis, we did not find any significant functioning component. However,
synergy was found to be much more associated with agreement than the other
components. The estimates were 11.48% (-1.03%, 24.00%) and 11.21% (-2.48%,
24.90%) in un-weighted and weighted models respectively. Bootstrapping regression
analysis showed that the results were robust to a change of sample. We concluded that the level of integration of CTN was low because the agencies
generally had poor agreement in collaboration. Synergy was the most important
component associated with the network's integration. Other functioning components
detected were also associated with the integrating process but were less clinically
important. We discussed the statistical approaches used in other contexts and some of
their strength and weaknesses. We also considered some key limitations of the study.
This study was a baseline measurement of CTN of Simcoe York for further analysis. The
results provided a basis for future enhancement of integration of the network. Our
experiences also provided ideas for improving design and analysis in integrated network
measurement.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Gaulin, B.D.
Physics

abstract: Title: Neutron Scattering Studies of Spin Glass Behaviour in LiNiO2, Author: James P. I. Clancy, Location: Thode

abstract:
We have performed time-of-flight neutron scattering measurements on two
polycrystalline samples of LiNiO2 using the Disk Chopper Spectrometer at the NIST
Center for Neutron Research. These measurements reveal an absence of magnetic
Bragg peaks, indicating a lack of magnetic order down to 1.7K. In addition, we observe
a significant narrowing in the width of the inelastic scattering at Tg ~ 9K, which
is accompanied by a simultaneous increase in the intensity of the elastic magnetic scattering.
This provides direct evidence of a spin glass transition at Tg, implying that
the low temperature magnetic state of LiNiO2 is composed of frozen, disordered moments.
Similar time-of-flight studies performed on NaNiO2 , the isostructural sister
compound of LiNiO2, have shown the existence of a simple magnetic structure below
TN ~ 23K, consisting of ferromagnetic sheets of spin 1/2 moments stacked in an
antiferromagnetic fashion [1]. From the distinct similarities observed between the
inelastic magnetic scattering in LiNiO2 and paramagnetic NaNiO2, it is implied that
the low |Q| spin response in LiNiO2 may originate from the collapse of short-lived
spin wave modes below the (0,0,1/2) position, the lowest wave vector of antiferromagnetic
ordering. It is suggested that inherent chemical disorder in LiNiO2, caused
by the substitution of Ni3+ and Li+ ions within the crystal structure, results in the
frustration of inter-layer magnetic interactions, thereby preventing the development
of a magnetically long range ordered state.

abstract: Thesis

abstract: Master of Science (MS)


title: Resilient Romans: Cross-Sectional Evidence for Long-Term Functional Consequences of Extremity Trauma

title: Long-Term Consequences of Roman Extremity Fractures

contributor:
Brickley, Megan
Prowse, Tracy
Anthropology

subject:
Palaeopathology
Biomechanics
Trauma Analyses
Extremity Fractures
Impairment
Roman Period
Post-Traumatic Dysfunction

abstract:
Long-term repercussions of extremity trauma can include fracture mal- and non-union, osteoarthritis, pain, and impairment of physical movement, which can result in disuse of the limb and eventual bone loss. Although trauma is commonly investigated in palaeopathology, the functional repercussions of injuries are not typically considered. By integrating palaeopathological fracture analyses and biomechanical investigations of cross-sectional properties, this thesis explores individual and group experiences of extremity fracture risks, responses, and consequences at two Roman sites.

Adults from 1st-4th century AD Roman cemeteries at Ancaster, UK (n=181), and Vagnari, Italy (n=66), were examined for limb fractures. Data on fracture type, location, malunion, and associated infection and osteoarthritis were collected. Bone areas and asymmetries were calculated using biplanar radiographs for individuals without fractures, and compared to those of individuals with fractures. Patterns in bone amounts and asymmetries associated with fracture attributes were identified.

Extremity fractures were observed in 39 individuals from Ancaster and 12 individuals from Vagnari, but the prevalence rates did not differ between the sites. Cross-sectional properties suggested that compared to Ancaster, individuals living at Vagnari experienced greater mechanical loading (i.e., larger bone areas). Disuse of a fractured limb was only identified in two old adult individuals from Ancaster; no Vagnari individuals had evidence for post-traumatic dysfunction. Functional consequences of injuries were not associated with observable fracture attributes (e.g., fracture type, malunion), meaning that physical impairment cannot be recognized based only on an injury’s appearance.

By incorporating biomechanical methods in palaeopathological analyses of trauma, this thesis reveals the physical experiences of injury acquisition and recovery among residents of Ancaster and Vagnari over the life course. The relative absence of post-traumatic disuse speaks to the resilience of Romans at these sites, and contributes to the growing literature on the human experience of trauma and impairment in the past.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Immobility and disuse of a fractured arm or leg can result in bone loss. Using radiographs, this research evaluated physical activity and long-term fracture complications in adult skeletons from ancient Roman communities at Ancaster, UK and Vagnari, Italy (1st-4th century AD). Compared to Ancaster, Vagnari individuals had thicker bones that indicated they were more physically active. Evidence for physical consequences were not associated with the type or location of a fracture; only two individuals from Ancaster (and none from Vagnari) had evidence of disuse.

This study of fracture consequences contributes to our understanding of injury risk and recovery in the past. Although fractures can cause lasting physical consequences, these results show that fractures that appeared ‘severe’ did not necessarily result in long-term impairment. Most residents at Ancaster and Vagnari were physically active and recovered from their injuries, a finding that emphasizes the importance of continued physical activity after injury.


title: The harvest of secession

title: A study of the dynamics of ethnic boundaries between Southern and Northern Sudanese Canadians

contributor:
Satzewich, Victor
Sociology

subject:
ethnic boundary
identity
ethnicity
nationalism
transnationalism

abstract:
This thesis examines how ethnic boundaries are constructed among, and understood by, different groups of first generation Sudanese-Canadians in Kitchener, Ontario. In particular, it seeks to examine how historical factors related to Sudanese history, contemporary events in Sudan and South Sudan, and conditions of exit from Sudan shaped boundary processes within the Sudanese diaspora in Kitchener. In this connection, this thesis examines the effect of secession/independence of South Sudan on the dynamics of this boundary and relationship between Southern and Northern Sudanese Canadians. Thus, the thesis aims to fill a gap in the literature. It also hopes to inspire further studies on Sudanese Canadians, who tend to be understudied in Canada. The research builds on the growing research tradition and theories of ethnic boundaries, identity, nationalism, and transnationalism. Qualitative approaches were used for collecting and analyzing data. Participant observation at community events, and thirty-seven semi-structured interviews were conducted with key informants in Kitchener, Ontario. The thesis emphasizes that ethnic boundaries, identities, and relations between Southern and Northern Sudanese Canadians are dynamic and ever changing, in the sense that they are sometimes undermined and broken down, and yet other times they are enforced and reinforced quite strictly.
It also finds that the concept of ‘Northern’ is no longer geographic, as my respondents have limited its meaning to the riverine/Arab people. This concept contrasts with the concept of  ‘black’ which includes many Northern Sudanese sub-national groups, in the geographic sense, along with Southern Sudanese. This indicates that the boundaries among the Southerners and riverine people have become stronger than between these Southerners and other Northerner groups.
The thesis also shows that the relationships between Southern and Northern Sudanese Canadians’ have been significantly affected by the referendum and independence/secession of  South Sudan insofar as the social gap between them has by and large become wider. Joint activities organized in collaboration between both groups before secession have since ceased. Also, the degree of general interaction between them has significantly decreased. They now tend to treat each other as strangers and avoid interaction. Even simple greetings are lacking and when interactions do happen, they are characterized by harshness, and the exchange of accusations. Moreover, instances of mutual support have also diminished. Invitations to, and attendance at private, and public events has noticeably decreased. Despite this increase in social distance at a community level some close friendships remain intact, especially among those who came to Canada from Egypt. Interestingly, Southern and Northern Sudanese continue to come together for attending death ceremonies and soccer games, and seating orders continue to be mixed at soccer games.
The dynamics of intergroup relations in Canada have mainly followed their relations in Sudan. This means that transnational ties in this case tend to be unidirectional. This implies that living in the Canadian context has had a minor and indirect effect on these groups’ relations.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Capacity Analysis of Finite State Channels

contributor:
Chen, Jun
Electrical and Computer Engineering

subject:
channel capacity
channel state

abstract:
Channels with state model communication settings where the channel statistics are not fully known or vary over transmissions. It is important for a communication system to obtain the channel state information in terms of increasing channel capacity. This thesis addresses the effect of the quality of state information on channel capacity. Extreme scenarios are studied to reveal the limit in increasing channel capacity with the knowledge of state information.

We consider the channel with the perfect state information at the decoder, while the encoder is only available to a noisy state observation. The effect of the noisy state at the encoder to the channel capacity is studied. We show that for any binary-input channel if the mutual information between the noisy state observation at the encoder
and the true channel state is below a positive threshold determined solely by the state distribution, then the capacity is the same as that with no encoder side information. A complementary phenomenon is also revealed for the generalized probing capacity. Extensions beyond binary-input channels are developed.

We further investigate the channel capacity, when the causal channel state information (available at the encoder or the decoder or both) makes it deterministic. Every such a capacity is called an intrinsic capacity of the channel. Among them, the smallest and the largest called the lower and the upper intrinsic capacities, are particularly studied. Their exact values are determined in most cases when the input or the output is binary. General lower and upper bounds are also provided for the lower and the upper intrinsic capacities with causal state information available at both sides. Byproducts of this work are a generalization of the Birkhoff-von Neumann theorem and a result on the uselessness of causal state information at the encoder.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
It is well known that with the knowledge of channel state, it is possible to increase the channel capacity. In this sense, knowing channel state never hurts. However, whether it is always bene cial to actively acquire channel state is another story. If we take into account the cost of measuring the channel state against the potential gain on the capacity, sometimes it may not appear very economic to do so. This thesis
studies the effect of the quality of observed channel states on the channel capacity. It has been found out in some circumstances the channel capacity is very sensitive to the noise on the state information. On the other hand, it appears that the maximum capacity can be achieved with the knowledge of a small portion of the total channel
state information under a slightly different setting. This thesis proves the generality of such phenomena in binary-input channels and provides the necessary and sufficient conditions for the occurrence of such phenomena for an arbitrary channel. This paper also introduces the idea of intrinsic capacity which can be used to measure the ultimate capacity potential of a channel by exploring the channel state. By viewing an arbitrary channel as a deterministic channel with state, the greatest possible and smallest possible capacities have been either derived or bounded in the thesis.


title: Development and Testing of a Chronic Pain Integration Questionnaire

contributor:
Akhtar-Danesh, Noori
Nursing

subject:
chronic pain
adjustment
integration

abstract:
Background.  Understanding how people adjust to living with chronic pain is paramount
because of the negative impact of chronic pain on quality of life.  Chronic pain integration
has been proposed as a new construct that may enhance understanding of chronic pain
adjustment.  Integration, as defined by people living with chronic pain, is an ongoing
process in which the person with chronic pain evolves becoming a mentally and
physically stronger individual; creating a sense of harmony and control in one’s life.
These positive outcomes of integration necessitate its continued investigation in chronic
pain, especially if it may positively affect life quality.
Objective.  There were two overarching purposes of this study: (a) to further refine and
test the psychometric properties of the Chronic Pain Integration Questionnaire (CPIQ);
and (b) to examine four research hypotheses based on the proposed relationships between
several constructs.
Method and Results.  Utilizing a quantitative, non-experimental design, the CPIQ
demonstrated internal consistency reliability, test-retest reliability, and evidence of
validity when tested in a sample of 201 adults living with chronic non-cancer pain.  All
four of the research hypotheses were confirmed and three domains of the CPIQ were
identified through exploratory factor analysis: self-management, self-awareness, and
intrinsic adjustment.  The favourable psychometric results of the CPIQ provide support
for its continued use to understand adjustment in chronic pain.  Ultimately, the goal of
future research with the CPIQ is to identify effective interventions that promote chronic
pain integration; leading to improved life quality for the person with chronic pain.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
A questionnaire titled the Chronic Pain Integration Questionnaire (CPIQ) was developed
and then given to 201 adults living with chronic pain in order to gain a better
understanding of how these adults have adjusted to living with chronic pain.  The
responses that these adults gave on the CPIQ were then compared to responses they gave
on additional questionnaires related to their physical and mental health, acceptance, and
social support.  These comparisons allowed for the detailed examination of people’s
adjustment to living with chronic pain.  It is hoped that the CPIQ, which has now been
developed and tested, will continue to allow health care professionals to gather more
information about the life of someone living with chronic pain.  It is also hoped that the
CPIQ could be used in future research to identify effective strategies that improve the
overall quality of life of the person suffering with chronic pain.


title: DEVELOPMENT OF A THICK GAS ELECTRON MULTIPLIER-BASED MULTI-ELEMENT MICRODOSIMETRIC DETECTOR

contributor:
Byun, Soo-Hyun
Medical Physics

abstract:
Tissue Equivalent Proportional Counters (TEPCs) are considered the standard instrument
for microdosimetry, aiming at measuring the distribution of the energy deposited
by ionizing radiation in a micrometric target, and have been employed for a number
of radiation physics, radiation protection and radiation biology applications.
This study describes development procedure and performance of a novel multi-element
TEPC. Following an extensive Geant4 simulation study, an advanced prototype
multi-element gaseous microdosimetric detector was developed using the Thick Gas
Electron Multiplier (THGEM) technique. The multi-element design was employed
to increase the neutron detection efficiency. The prototype THGEM multi-element
detector consists of three alternating layers of tissue equivalent plastic hexagons and
each layer houses a hexagonal array of seven cylindrical gas cavity elements with equal
heights and diameters of 17 mm. The final detector structure incorporates 21 gaseous
volumes. Owing to the absence of wire electrodes, the THGEM multi-element detector
offers flexible and convenient fabrication in contrast to the traditional wire-based
methods. The detector responses to neutron and gamma-ray were investigated using
the McMaster Tandetron 7Li(p,n) neutron source. The dosimetric performance of the
detector is presented in contrast to the response of a commercial tissue equivalent
proportional counter. The collected spectra exhibit the expected features of the lineal
energy distributions for given proton beam energies. Compared to the 2 inch TEPC
response, the detector gave a consistent microdosimetric response with a maximum
discrepancy of 15% in measured neutron absorbed dose. An improvement of a factor
of 3.0 in neutron detection efficiency has been accomplished. The prototype detector
offers a simple fabrication process and provides the fundamental basis for development
of a high efficiency TEPC dedicated for monitoring weak neutron radiation fields.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Universal Aqueous-Based Antifouling Coatings for Multi-Material Devices

contributor:
Fang, Qiyin
Brash, John
Biomedical Engineering

subject:
Antifouling
Polyethylene Glycol
Bovine Serum Albumin
Polydopamine
Perfluorophenyl Azide

abstract:
Biofouling is an ongoing problem in the development and usage of biomaterials for biomedical implants, microfluidic devices, and water-based sensors. Antifouling coatings involving surface modification of biomaterials is widely utilized to reduce unwanted protein adsorption and cell adhesion. Surface modification strategies, however, are reliant on the working material’s chemical properties. Thus, published procedures are often not applicable to a wide range of material classes. This constitutes a serious limitation in using surface modification on assembled multi-material devices, i.e on whole device modification. The objective of this research is to develop an antifouling coating with non-aggressive reaction conditions that can universally modify polymers and other material classes. Two strategies using polydopamine (PDA) as an anchor for polyethylene glycol (PEG) surface attachment were investigated:  (1) PDA-PEG backfilled with bovine serum albumin (BSA), and (2) PDA-PEG with light activated perfluorophenyl azide (PFPA) conjugated to the PEG. Three materials varying in surface wettability were studied to evaluate the coatings for multi-material applications: porous polycarbonate membrane (PC), polydimethyl siloxane (PDMS), and soda lime glass cover slips.
Atomic force microscopy (AFM) and ellipsometry studies revealed substantial structural differences of PDA. Differences in PDA surface roughness affected PEG grafting in solution (the first method), with higher PEG coverage achieved on PC with intermediate surface roughness to PDMS and glass. Radiolabeled Fg adsorption and E. coli adhesion experiments showed reduced fouling on all PDA-PEG modified materials when backfilled with BSA. The ability for BSA to penetrate the PEG layer indicated that low PEG grafting densities were achieved using this grafting-to approach. The use of a photoactive labeling agent, PFPA, to tether PEG was proposed to improve PEG grafting on PDA. The PFPA-PEG modification protocol was optimized by quantifying Fg adsorption. Two treatments of PFPA-PEG were required to fully block PDA active sites. Fg adsorption was not significantly improved on PFPA-PEG modified PC and glass when backfilled with BSA, indicating sufficient PEG coverage of PDA. High Fg adsorption on PFPA-PEG surfaces indicate that high density PEG brushes were still not achieved with this method. PDMS surfaces were damaged with this procedure due to increased surface handling in the protocol. This is the first, to our knowledge, successful demonstration of PFPA modification on PDA surfaces. Photopatterning of polymer-based materials can be achieved, providing opportunities for utilising new materials in cell patterned platforms. Due to low PEG coverage on PDA surfaces from solution and using PFPA, ultra-low protein adsorption cannot be achieved using these aqueous-based methods. Antifouling modifications using PDA and PEG should be applied for short-term cell studies.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Development of a multifocal confocal fluorescence lifetime imaging microscope for high-content screening applications

contributor:
Fang, Qiyin
Engineering Physics

subject:
multifocal
confocal
fluorescence
lifetime
FLIM
microscopy
high-content screening
streak camera
photonics
optics
beam scanning
SPAD
TCSPC

abstract:
Fluorescence lifetime imaging microscopy (FLIM) is an imaging modality that is able to provide key insights into subcellular processes. When used to measure Förster resonance energy transfer (FRET), for instance, it can discern protein-protein interactions and conformational changes. This kind of information is highly useful in the drug screening process in order to determine the effectiveness of drug leads and their mechanisms of action. FLIM has yet to be successfully translated to high-content screening (HCS) platforms due to the high throughput and fine temporal and spatial resolution requirements of HCS.
Our prototype HCS FLIM system uses a time-resolving instrument called a streak camera to multiplex the FLIM scanning process, allowing for 100 confocal spots to be simultaneously scanned across a sample. There have been a few major advancements to the prototype. First the fiber array used to connect the fluorescence channels to the streak camera was characterized. Its alternating fiber delay scheme was successful in greatly reducing optical crosstalk between adjacent channels. Next, an optical beam scanner for parallel excitation beams was designed and implemented, greatly improving the possible scan speeds of the system. The streak camera was upgraded to a higher repetition rate sweep, and modifications to system components and reconstruction procedures were made to accommodate the new sweep unit. A single-photon avalanche diode array was also tested as a possible replacement for the streak camera, and was found to offer photon detection efficiency advantages. Finally, improvements were made to the excitation power and optical throughput of the system in order to reduce the required exposure time.
These advances to the prototype system bring it closer to realizing the requirements of HCS FLIM, and provide a clear picture for future improvements and research directions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Fluorescent proteins are commonly used to tag subcellular targets so that they can easily be distinguished with a fluorescence microscope. While this can help visualize where different organelles and proteins are located in the cell, a great deal more information can be gained by measuring the fluorescence lifetime at each point in the sample, which is highly sensitive to the microenvironment. Fluorescence lifetime imaging microscopy (FLIM) has the potential to be a powerful technique for testing drug leads in the drug discovery process, although current FLIM systems are not able to provide the high throughput speeds and high temporal resolution required for drug screening. This thesis project has succeeded in improving a highly parallel FLIM microscope by reducing inter-channel crosstalk, implementing an optical scanner, improving power and optical throughput, and investigating future time-resolving instruments. This progress has brought the prototype setup closer to being used in a drug screening environment.


title: MAGNETICALLY ACTUATED PHYSICAL IMPINGEMENT FOR ELUTION OF ARTIFICIAL MUCOUS FROM A SWAB

contributor:
Selvaganapathy, Ponnambalam Ravi
Mechanical Engineering

subject:
Elution
Swab
Magnetic field
Recovery efficiency
Impingement
Polystyrene

abstract:
Swabs are used as a collecting device for many biological samples and its complete elution is a desired step for clinical and forensic diagnostics. Swabs are made of cotton, rayon, polyurethane, foam or polyester and come in a spun or flocked-tipped format. They are used to extract biological samples from a patient, which includes saliva, mucous, blood, semen or other body fluids. These body fluids then undergo the process of elution where the collected samples are extracted from the swabs into an elution fluid. Apart from biological samples, the importance of swabbing and elution also becomes more evident in forensics, where the concentration of available cells is very low. One such example is rape kit analysis. Another field of application is the capture and release of bacterial spores from environmental contact surfaces and food surfaces, which also indicate the use of swabs in non-biological areas.
The recovery of the biological material from the fibre matrix of the swab has a significant influence on diagnostic sensitivity of any assay. The recovery of micro-organisms from a matrix of swab fibres depends on the nature of the body fluid, the type of the swab fibres and the process of elution. Various methods are used to elute samples from swab, including the use of chemicals to digest the cotton fibres to remove intact cells (~20% recovery), centrifugation (~58% recovery), piezoelectric vibration or pressurized fluid-flow (~60% recovery). These methods are either passive (chemical elution) or provides a gentle tangential shear force through associated flow (centrifugation, piezoelectric and pressurized flow), resulting in a low recovery. The success of all the downstream processes of elution, like lysis, DNA amplification and detection, depends on the number of cells eluted from the swab fibre matrix. Hence, the recovery efficiency is an important parameter for determining the performance of elution, and higher value of the same is desired for most diagnostic assays.
This thesis reports a magnetically-actuated physical impingement method for elution and recovery of artificial sputum samples from cotton fibres. A device has been fabricated to induce a rotating magnetic field on smaller magnetic particles in a vial for striking the swab within a confined gap. Elution of samples from the swab using this device was demonstrated using artificial sputum prepared by mixing 2% methyl cellulose in deionised water, loaded with fluorescent-tagged polystyrene beads and Escherichia coli bacteria at various concentrations. The recovery efficiency was found to increase with both rotational speed and elution time, but plateaus after 400 RPM and 120s respectively. At higher concentration of polystyrene beads, a maximum recovery of ~85% was achieved at 5x108 particles/ml sample. With lower concentration (106 particles/ml), the maximum efficiency (~93%) was found to be almost twice of the static condition (46.7%), while using only 620µL of elution volume. Similar trends were found in experiments with artificial sputum loaded with E. coli cells, and the maximum recovery was found to be ~90% at 105 CFU/ml concentration.
The robust design and smaller size allows the device to be used in different clinical, forensic and laboratory settings. Also, due to cheaper means of manufacturing and assembly, the vials and smaller magnets can be discarded after every experiment, thereby preventing contamination. The device is most suitable for recovering cells from different body fluids like saliva, mucous, semen or blood, absorbed by the swab fibres. Apart from body fluids samples, swabs holding biological agents from environmental surfaces can also be eluted. A higher recovery at lower concentration facilitates the use of this device where the available analyte concentration is low.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: MUSLIMS OF INTEREST: PRACTICES OF RACIALIZATION IN THE CONTEXT OF THE WAR ON TERROR

contributor:
Beier, J. Marshall
Political Science

subject:
Popular Culture and World Politics
International Relations
Performativity
Critical Race Theory
"War on Terror"

abstract:
This dissertation explores the stereotypes of representations of Muslims in American popular culture, and specifically in television dramas and comedies. These tropes include: 1) the Muslim terrorist/villain; 2) the patriotic “Good” Muslim; 3) the Muslim “friendly cultural stereotype”; and 4) the Muslim victim (both of Western discrimination and of patriarchal “Muslim culture”). This research is also interested in portrayals of Muslims that resist these stereotypes.
Taking a performativity approach based on Critical Race Theory and intersectionality, this research is interested in the intersections of race, gender, class, and sexual orientation. Following the aesthetic turn of International Relations theory and falling within the subfield of Popular Culture and World Politics, this research takes popular culture seriously as a site of politics because representational practices are important in informing politics and societal relations at local, national, and global levels. This dissertation conducts a discursive content analysis of every American television program from 2001 to 2015 that features Muslims as main and/or recurring characters, including Homeland, 24, Sleeper Cell, and The Grid.
This project is timely and important because constructions of identities, including through performative reifications of stereotypes in popular culture, both influence and are influenced by foreign policy. Narratives about Muslim-ness are important in justifying Western intervention in the Middle East as part of the US-led “War on Terror”. Most recently, Donald Trump’s presidential campaign and early presidency illustrate in a visceral way the currency of negative and reductionist perceptions of Muslims, as illustrated in his proposed policies and widely spread societal and political support for a “Muslim ban”. Thus, it is important to think critically about the relationship between popular culture and world politics.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
This dissertation explores stereotypes of Muslims in American popular culture, and specifically in television dramas and comedies. These include: 1) the Muslim terrorist/villain; 2) the patriotic “Good” Muslim; 3) the Muslim “friendly cultural stereotype”; and 4) the Muslim victim (both of Western discrimination and of patriarchal “Muslim culture”). This research is also interested in portrayals of Muslims that resist these stereotypes.
This project is timely and important because stereotypes about Muslims are important in justifying Western intervention in the Middle East as part of the US-led “War on Terror”. Most recently, Donald Trump’s presidential campaign and early presidency illustrate the power of negative perceptions of Muslims, as illustrated by his proposed policies and widely spread societal and political support for a “Muslim ban”. Thus, it is important to think critically about the relationship between popular culture and world politics.