title: Stellar Feedback in a Vertically-Stratified ISM

contributor:
Wadsley, James
Couchman, Hugh
Wilson, Christine
Physics and Astronomy

subject: stellar feedback

subject: interstellar medium

subject: star formation rate

subject: supernova

subject: photoionization

subject: numerical

subject: Stars, Interstellar Medium and the Galaxy

abstract: The effect of stellar feedback on the interstellar medium is investigated using numerical simulation. In particular, the roles of supernova feedback and ionization feedback on the star formation rate and structure of the interstellar medium are compared. We use Enzo, an adaptive mesh code, and employ the MUSCL-Hancock hydrodynamics scheme to run simulations of a section of a stratified galactic disk. A turbulent velocity field is imposed in the central region of the disk and self-gravity is applied. Star clusters are formed when density and temperature conditions are met, which, in turn, provide ionization and supernova feedback into the interstellar medium. Simulations were run with and without supernova and ionization feedback and the runs are compared. Ionization feedback is found to dominate over supernova feedback in regulating star formation rates. With no feedback, all the gas is converted to stars by 200 Myr. When supernova feedback is added, 98% of the gas is used to create stars by 300 Myr. With ionization feedback instead, at 1 Gyr into the run, only 30% of the gas is in stars. Even with supernova feedback added to ionization feedback, the gas converted to stars is just 29% at 1 Gyr. Very strong supernovae take this fraction down to 25%. The star formation rates in the runs with supernova feedback are consistent with the low end of the Kennicutt-Schmidt relation, while the runs without ionization feedback have star formation rates that are an order of magnitude larger. Gas phase masses and volumes produced in the ionization runs are broadly consistent with observations.

abstract: Master of Science (MSc)


title: A Study of IMRT Pre-Treatment Dose Verification Using a-Si Electronic Portal Imaging Devices

contributor:
Ostapiak, Orest
Medical Physics

subject:
IMRT dose verification
portal dosimetry
EPID dosimetry
amorphous silicon
Other Physics
Other Physics

abstract: Intensity-Modulated Radiation Treatment (IMRT) requires patient-specific quality assurance measurements, which can benefit from the convenience of using an Electronic Portal Imaging Device (EPID) for dose verification. However, EPIDs have limitations stemming from the non-uniform backscatter due to the support-arm as well as from scatter, glare, and an increased sensitivity to low-energy photons. None of these effects is typically accounted for in a treatment planning system (TPS) model, resulting in errors in calculated EPID response of up to 6%. This work addresses the non-uniform backscatter by directly incorporating a support-arm backscatter region into the TPS geometry. The shape of the backscatter region is adjusted iteratively until the TPS-calculated flood-field planar dose matches the flood-field EPID image The scatter, glare and increased low-energy response are addressed by using a radially-dependent Point-Spread Function (Kernel). The kernel is fitted using a least-squares method so that it best reproduces the EPID-acquired image for a checkerboard field. The backscatter-correction method is implemented for a Varian Clinac equipped with a 40 cm x 30 cm (512 x 384 pixel) EPID and a Pinnacle3 TPS and tested for several rectangular and IMRT fields. The scatter, glare and energy-response correction kernel is implemented and tested for a simulated checkerboard field and a simulated IMRT field. Agreement between the EPID-measured image and TPS-calculated planar dose map is seen to improve from 6% to 2% when the backscatter region is added to the Pinnacle3 model. Agreement between the simulated EPID images and simulated TPS images is improved from 14% to approx. 1% when the radially-dependent kernel is used. Simultaneous application of both the backscatter region and Point-Spread Function is a promising direction for future investigations.

abstract: Master of Science (MSc)


title: Alexander Pope's Pastorals: a Study of Their Genesis and Evolution

contributor:
King, James
English

subject:
English Language and Literature
English Language and Literature

abstract:
The following study describes the evolution of Alexander Pope's Pastorals from their embryonic state in the earliest extant manuscript of them, the Houghton holograph, to their final resting place in the last authorized version of them, the posthumous 1751 edition of the poet's Works edited by his friend and literary executor, Rev. William Warburton. During this period the four poems -- "Spring", "Summer", "Autumn" and "Winter" -- and the brief critical treatise that accompanied them underwent hundreds of alterations, from single words to entire stanzas. A careful examination of the earliest extant version, in conjunction with a close study of the many changes and additions Pope made during his lifetime, provides a considerable amount of information concerning precisely what Pope endeavours to accomplish in creating this cycle of poems. A xerox copy of the Houghton holograph, together with a diplomatic transcript of it and a list of all subsequent authorized alterations to the text has been included to facilitate the study. Though some of the variants of this holograph have been cited (with varying degrees of accuracy) in previous editions of Pope's poetry, the manuscript itself has never before been reproduced in its entirety.

This study concentrates particularly upon the evolution of the Pastorals primarily because a comparison of the final version of any given passage with earlier versions often makes the poet's intentions clearer. Pope himself would seem to have been aware of this fact since he includes a number of variant readings from manuscripts and earlier printed texts in the notes he appends to these poems in the 1736 edition of his Works. Likewise, an examination of the sources of Pope's allusions to other poems in the pastoral tradition -- some though by no means all of which he also records in his 1736 notes -- sheds additional light on the poet's meaning. Though the vast majority of these allusions have been identified by previous scholars, their function in the poems themselves has to date been for the most part, ignored. Yet, as this study demonstrates, these allusions and their contexts form an integral part of the poet's design, frequently providing an oblique, but highly pertinent comment upon what is actually taking place.

This study leads ultimately to a new reading of the Pastorals, one that focuses upon the numerous alterations and additions to them between 1704 -- the supposed date of the Houghton holograph which may be regarded as their first limited "edition" -- and 1751. Particular emphasis is placed on the major additions -- the dedicatory stanzas inserted into the first three poems in 1709, the revised version of the prose treatise added in 1717 and the apparatus of notes appended in 1736. For, in each of these Pope would appear to be providing his readers with the necessary direction to comprehend precisely what he is endeavouring to accomplish. To study Pope's creation without reference to these and the other factors previously mentioned is to miss much that is of the utmost importance in them. Only through a reconstruction of their evolution can the Pastorals be fully understood and appreciated.

abstract: Doctor of Philosophy (PhD)


title: PROCESSING OF FACIAL EXPRESSIONS BY OLDER AND YOUNGER ADULTS

contributor:
Bennett, Patrick J.
Sekuler, Allison B.
Rutherford, Mel D.
Psychology

subject:
aging
facial expression
face perception
vision science
face inversion
Cognition and Perception
Cognition and Perception

abstract: Older adults tend to show overall recognition deficits and qualitatively different patterns in the particular expressions that are most difficult to identify (Ruffman et al., 2008). In the current study, 23 younger (18-33 years old) and 23 older (60-80 years old) adults performed a 4AFC (angry, fearful, happy, sad) facial expression categorization task varying orientation (upright/inverted) and stimulus duration (100, 500, 1000 ms). For both groups, happiness was the easiest expression to identify and fear and sadness were the most difficult. Compared to younger adults, older adults were more affected by stimulus orientation, and generally benefit less from increased stimulus duration. For upright faces, there was no age difference in response accuracy but response latency was longer in older subjects. For inverted faces, older adults showed lower accuracy and longer latencies for expressions of anger, fear, and sadness. Recognition of inverted happy faces was spared in older adults for accuracy, but not response latency. These findings could not be explained by impaired detection sensitivity, as no systematic age differences were found for perceived intensity ratings. Finally, the expressions that were most to least difficult to identify was the same in each age group at both orientations. Overall, these results suggest that older individuals process expressive faces in a qualitatively similar way to their younger counterparts, but are less efficient at extracting the diagnostic information.

abstract: Master of Science (MSc)


title: "The Streets Belong to the People": Expressway Disputes in Canada, c. 1960-75

contributor:
Weaver, John
History

subject: Canadian urban history; development controversies; urban governance; citizen activism

subject: Cultural History

subject: History

subject: Political History

subject: Cultural History

abstract:
In Canada, as in the United States, cities seemed to many to be in complete disarray in the 1960s. Growing populations and the resultant increased demands for housing fed rapid suburban sprawl, creating a postwar burst of urban and suburban planning as consultants were hired in city after city to address the challenges of the postwar era. During this period expressway proposals sparked controversy in urban centres across the developed world, including every major city in Canada, namely Vancouver, Edmonton, Winnipeg, Toronto, Montréal and Halifax. Residents objected to postwar autocentric planning designed to encourage and promote the continued growth of city centres. Frustrated by unresponsive politicians and civic officials, citizen activists challenged authorities with an alternate vision for cities that prioritized the safeguarding of the urban environment through the preservation of communities, the prevention of environmental degradation, and the promotion of public transit. As opponents recognized the necessity of moving beyond grassroots activism to established legal and government channels to fight expressways, their protests were buoyed by the rapidly rising costs that plagued the schemes. By the latter half of the 1960s, many politicians and civil servants had joined the objectors. Growing concerns over the many costs of expressways -- financial, social, environmental, and eventually, political -- resulted in the defeat of numerous expressway networks, but most were qualified victories with mixed legacies.

Expressway disputes were an instrumental part of a wider struggle to define urban modernity, a struggle that challenged the basis of politicians and civil servants power by questioning their legitimacy as elected leaders and uniquely qualified experts, respectively. The subsequent emergence of urban reform groups that sought to change the direction of city development by challenging the autocratic municipal bureaucracies was the direct legacy of expressway and other development battles. Despite this, autocentric planning continued and demands for greater citizen participation did not result in significant changes to the form and function of municipal governments.

abstract: Doctor of Philosophy (PhD)


title: THE EFFECT OF PHYSICAL ACTIVITY ON MEDIAL TIBIAL CARTILAGE HEALTH IN CLINICAL KNEE OSTEOARTHRITIS

contributor:
Maly, Monica
Beattie, Karen A.
Stratford, Paul
Rehabilitation Science

subject:
Osteoarthritis
Physical Activity
Cartilage Volume
Cartilage Thickness
Biomechanics
Exercise Science
Rheumatology
Biomechanics

abstract:
Knee osteoarthritis (OA) is a common chronic disease that often occurs in older adults, affecting their quality of life. The purposes of this study were to examine 1) the relationship between physical activity and medial tibial cartilage volume and thickness in participants with clinical knee OA; and 2) the test-retest reliability of daily step counts produced by participants with knee OA.

The study included 34 participants (age 60.6 ± 6.5 years; body mass index 28.5 ± 5.4 kg/m2). Dependent variables were medial tibial cartilage volume and thickness, measured from magnetic resonance images. Independent variables were average step counts and average time spent in light intensity activity, measured with an accelerometer. These data were then was analyzed using linear and second degree polynomial regression analyses to determine the relationship between dependent and independent variables along with age, sex and BMI as covariates. The test-retest reliability of step counts collected over 5 days was evaluated with an intraclass correlation coefficient (ICC).

Average time engaged in light intensity activity, average daily step counts, sex and age accounted for 56.3% of the variance in medial tibial cartilage volume. Age and average time in light intensity activity explained 33.2% of the variance in medial tibial cartilage thickness. Results from the second degree polynomial analyses were not significant. The ICC for the daily step counts over first 5 days of 10 hours wear time was 0.929 (95% [CI] =0.883, 0.961).

A weak linear relationship existed between physical activity and cartilage volume and thickness within the knee joint. The greatest medial tibial cartilage volume was found in men who were engaged in longer durations of low intensity physical activity. The test-retest of step counts data by participants with knee OA was very reliable over the 5 days. Findings from this study augment current knowledge of knee OA.

abstract: Master of Science (MSc)


title: Epistemic Contextualism and Its Problems: A Philosophical Critique

contributor:
Griffin, Nicholas
W., Richard T.
Vorobej, Mark
Philosophy

subject:
Epistemology
Epistemic Contextualism
Contrastivism
Skepticism
Fallibilism
Epistemology
Epistemology

abstract: The purpose of this dissertation is to argue that epistemic contextualism, which proposes that the word ‘know’ is a context-sensitive term, is seriously deficient and therefore indefensible. Since epistemic contextualists claim that their semantic theory of ‘know’ contributes not only to a linguistic model of knowledge ascription but also to a unified solution to some important puzzles in epistemology, I divide my thesis into two basic parts. In the first part (i.e., Chapters 2 and 3), I argue that the proponents of both binary and ternary accounts of the supposed context-sensitivity of ‘know’ fail to provide a reasonable linguistic model of knowledge ascription. My argument in Chapter 1 indicates that ‘know’ cannot be treated as a binary context-sensitive term that is similar to paradigmatic indexical terms or gradable adjectives. Chapter 2 takes contrastivism as a representation of the ternary account of the supposed context-sensitivity of ‘know’ and argues that this theory is in an even worse position because it even fails to capture the supposed phenomena of the context-sensitivity of knowledge ascription. The second part (i.e., Chapters 4, 5, and 6) argues that epistemic contextualism does not provide us with a really satisfactory solution to the puzzles of skepticism, the epistemic closure principle and fallibilism. On the contrary, its rival, invariantism, with some support from pragmatics, psychology of belief and experimental philosophy, is able to solve the above puzzles in a quite nice way. At the end of my thesis (i.e., Chapter 7), I systematize the observations, the evaluations and the critiques of epistemic contextualism from the previous chapters and indicate that epistemic contextualists even fail to establish their supposed phenomena of the context-sensitivity of ‘know.’

abstract: Doctor of Philosophy (PhD)


title: CALCULATING THE GROUNDWATER CONTRIBUTION OF PHOSPHORUS AND NITROGREN TO A SMALL URBAN STREAM, BARRIE, ONTARIO

contributor:
Smith, James
Roy, James
Geography and Earth Sciences

subject:
Groundwater
Hydrology
Hydrogeology
Streams
Contaminant Hydrogeology
Hydrology
Water Resource Management
Hydrology

abstract: Excess nutrients are currently impacting the ecosystem, fisheries, and recreational use of Lake Simcoe. The objective of this study was to determine the importance of groundwater as a pathway for nutrient input during base flow periods to a landfill impacted urban stream in Barrie, Ontario, which flows directly into the lake. A characterization of a 28 m reach was created using sediment and water level data, and a groundwater flux map of the stream was creating using heat tracer methods. This data was combined with the shallow groundwater nutrient concentration distribution measured with multi-level piezometers and diffusion samplers to calculate nutrient discharge. Such fine-scale measurements of nutrient discharge using groundwater-based data like these have not previously been reported. The water flux results were then extrapolated to a larger 460 reach (Site B) of Dyment’s Creek, and combined with groundwater contaminant data from that reach to derive a crude estimate of nutrient discharge at a larger scale. Groundwater soluble reactive phosphorus (SRP) and ammonium concentrations were much higher than stream concentrations. Estimates of total SRP discharge ranged from 3.6 to 8.1 g/d at Site A and 38 to 108 g/d at Site B, and ammonium discharge ranged from 66 to 218 g/d at Site A and 757 to 2043 g/d at Site B. This study showed that groundwater is an important pathway for nutrients to enter Dyment’s Creek, and this pathway that must be considered when addressing nutrient input to Lake Simcoe.

abstract: Master of Science (MSc)


title: Experimental Study of DKPP-βT Polymeric Thin Film Transistor

contributor: P. Ravi Selvaganapathy, Yaser M. Haddara

subject: polymeric thin film transistors (PTFTs)

subject: microfluidic PTFTs

subject: stability

subject: sensor

subject: characterization techniques

subject: Electronic Devices and Semiconductor Manufacturing

abstract:
In the last 30 years, the possibility of using polymeric thin film transistors (PTFTs) in flexible display, sensors, radio-frequency identification tag and the potential of using printing or low-cost reel-to-reel fabrication techniques has stimulated much research and technology development in these devices. However, the utilization of PTFTs needs better understanding of the organic semiconductor material’s properties and their physical and chemical mechanisms. In addition, the PTFTs show poor stability compared to the crystalline transistors. The PTFTs can have significant variations of threshold voltage, mobility, on/off ratio even when deposited using the same conditions on the same substrate. Therefore, better understanding of the PTFTs’ physical and chemical properties and the improvement of the characterization techniques are needed.

The design and fabrication of the novel polymeric semiconductor, diketopyrrolopyrrole β-unsubstituted quaterthiophene (DKPP-βT) based bottom-gated top-contact PTFT and microfluidics PTFT are introduced in this thesis. The microfluidic PTFT consists of polydimethylsiloxane (PDMS) microchannel which guides liquids flowing over the top of the semiconductor channel.

From consecutive electrical measurements, it was found that the threshold voltage (VT) follows a logarithmic law function of the time. Illuminating the PTFTs results in shifts of the initial value of the threshold voltage linearly towards more positive value. The mobility is unaffected by time or by illumination. However, the off current increased proportionally with light. Also, the contact resistance extracted by the parameter compensated transmission line model (TLM) method is ohmic and gate bias independent for high gate biases.

The novel microfluidic PTFT enables the study of the sensing property of the DKPP-βT PTFT of liquid analytes. The threshold voltage evolution in the deionized (DI) water measurements also follows logarithmic function of the time with a slightly steeper slope than in air. The mobility only slightly decreases initially on exposure to DI water. The off current in DI water measurements decrease compared with air measurements. In acid solution measurements, the threshold voltage remains stable and the mobility slightly increased, compared with measurements in water. Additionally, the subthreshold slope and off current in both acid solution and salt water measurements show similar results to the DI water measurements. While the base solution damages the device immediately. The stable performance of DKPP-βT PTFTs with DI water and low-concentration salt water in the microchannel makes it a promising biosensor.

abstract: Master of Applied Science (MASc)


title: Extended Ocular Drug Delivery using Hyaluronic Acid-Containing Model Silicone Hydrogel Materials

contributor:
Sheardown, Heather
Jones, Lyndon
Chemical Engineering

subject: ocular drug delivery

subject: silicone hydrogels

subject: contact lenses

subject: extended release

subject: hyaluronic acid

subject: glaucoma

subject: Biochemical and Biomolecular Engineering

subject: Biomaterials

subject: Polymer Science

abstract:
While eye drops are a well-accepted and convenient method for ocular drug delivery, they exhibit significant limitations such as poor drug bioavailability, low ocular residence time, pulsatile delivery profiles in the tear fluid as well as the need for patient compliance. Silicone hydrogel (SH) contact lenses have been proposed as alternative ocular drug delivery systems due to their potential for targeted delivery to the corneal surface and high oxygen permeability. The ability of novel hyaluronic acid (HA)-containing silicone hydrogel materials to release timolol maleate (TM), an antiglaucoma drug, or ketotifen fumarate (KF), an anti-histamine administered for ocular allergies, was examined.

The releasable wetting and the therapeutic agent were added to the pre-polymer mixture of the SH during synthesis through direct entrapment, while the reaction was performed by UV induced free-radical. The impact of the wetting agent on the swellability, surface wettability, optical transparency and in vitro drug release was studied.

Simultaneous drug and wetting agent incorporation resulted in modified SH materials with slightly increased water content and significantly improved surface wettability. In addition, the optical transparency of these materials was not affected by drug loading. However, direct entrapment of HA decreased their optical clarity. In vitro release showed that TM was released over a 14 day period, whereas KF release lasted up to 36 days. For both therapeutic agents used in the current research, non-covalent entrapment of wetting agent and its MW did not significantly change the release kinetics, however the release rate of TM was slowed and controlled by the release of the HA, due to electrostatic interactions between the protonated TM and the anionic HA.

The development of SH materials capable of simultaneously releasing a therapeutic and a wetting agent for an extended period of time and in a sustained manner can have a significant potential as extended drug delivery systems for the treatment of front of the eye diseases while also possibly providing comfort during wear.

abstract: Master of Applied Science (MASc)


contributor:
Habibi, S. R.
Mechanical Engineering

subject:
Electro-Hydrostatic Actuator
Fault Detection and Diagnosis
Extended Kalman Filter
Smooth Variable Structure Filter
Interacting Multiple Model
Electro-Mechanical Systems
Electro-Mechanical Systems

abstract:
Abstract

As a compact, robust, and reliable power distribution method, hydraulic systems have been used for flight surface control for decades. Electro-hydrostatic Actuator (EHA) is increasingly replacing the conventional valve-controlled system for better performance, lighter weight and higher energy efficiency. The EHA is increasingly being used for flight control. As such its reliability is thereby critical important for flight safety. This research focuses on fault detection and diagnosis (FDD) for the EHA to enable predictive unscheduled maintenance when fault detected at its inception.

An EHA prototype previously built at McMaster University is studied in this research and modified to physically simulate two faults conditions pertaining to leakage and friction. Nine different working conditions including normal running and eight fault conditions are simulated. Physical model has been derived mathematically capable of numerically simulating the fault conditions. Furthermore, for comparison, parametric model was obtained through system identification for each fault condition. This comparison revealed that parametric models are not suitable for fault detection and diagnosis due to the computation complexity.

The FDD approach in this research uses model-based state estimation using filters. The filter based combined with the Interacting Multiple Model fault detection and diagnosis algorithm is introduced. Based on this algorithm, three FDD strategies are developed using a combination of the Extended Kalman Filter and IMM (IMM-EKF), the Smooth Variable Structure Filter with Varying Boundary and IMM (IMM-SVSF (VBL)), and the Smooth Variable Structure Filter with Fixed Boundary and IMM (IMM-SVSF (FBL)). All the three FDD strategies were implemented on the EHA prototype. Based on the results, the IMM-SVSF (VBL) provided the best performance. It detected and diagnosed faults correctly at high mode probabilities with excellent robustness to modeling uncertainties. It also was able to detect slow growing leakage fault, and predicted the changing trend of fault conditions.

abstract: Master of Applied Science (MASc)


title: MECHANISMS OF TGFβ ACTIVATION IN LUNG FIBROSIS

contributor:
Kolb, Martin
Gauldie, Jack
Margetts, Peter
Medical Sciences

subject:
TGFbeta
Mechanical Activation
Lung Fibrosis
Pathogenesis
Animal Models
Medicine and Health Sciences
Medicine and Health Sciences

abstract: This PhD thesis focuses on the mechanical activation of TGFβ in the context of pulmonary fibrosis. Mechanical TGFβ activation occurs by physical force of breathing and signals to the nucleus via phospho‐Smad2. This activation occurs in presence of strong pan‐serine protease and matrix metalloproteinase inhibition. The augmented expression of latent TGFβ in lung tissue also lead to TGFβ activity following tissue stretch. Tissue biopsies from pulmonary fibrosis patients exhibited the same mechanical TGFβ activation and subsequent accumulation of phospho‐Smad2 as was seen in animal models. In rodent models and human control tissue, TGFβ was not released in detectable quantities, nor was there any significant upregulation of phospho‐Smad2. These data show that mechanical TGFβ activation is a relevant and limited to the context of a fibrotic disease process. Non‐invasive investigation of lung fibrosis was evaluated for correlation to classical assessments. We found that non‐invasive lung function parameters measured by a rodent ventilator, and small animal CT imaging correlated significantly with histomorphometic Ashcroft scoring. Exercise testing and quantification of the maximal oxygen consumption rate was a valuable indicator of overall rodent lung health but did not correlated significantly with Ashcroft scoring. Non‐invasive investigation tools evaluated here represent important advances in the quality of interpretation of preclinical lung fibrosis trials. Finally, collagen turnover was investigated by measurement of pyridinolines and serum collagen metabolic peptides. A novel method was developed and tested to detect pyridinolines in facile procedure. We found that deoxypyridinolines, but not pyridinolines, were significantly increased in the serum of lung fibrosis patients with respect to healthy controls. Furthermore, collagen type 1 telopeptide, a collagen breakdown product, was significantly increased in lung fibrosis patient serum. These data intriguingly indicate that under stable lung fibrosis conditions, more collagen appears to be breaking down into the serum then is synthesized.

abstract: Doctor of Philosophy (PhD)


title: TRADE IN FEELINGS: SHAME IN EIGHTEENTH-CENTURY BRITAIN

contributor:
Walmsley, Peter
Zuroski-Jenkins, Eugenia
Brophy, Sarah
English

subject:
history of the novel
affect theory
Literature in English, British Isles
Literature in English, British Isles

abstract: “Trade in Feelings: Shame in Eighteenth-Century Britain,” traces a genealogy of shame, a difficult feeling which is transformed and reworked in eighteenth-century narratives and which provides a ground for the self-reflective interiority required of commercial subjects. The stakes of this project are twofold. First, while cultural critics (e.g., Ahmed, Probyn, and Sedgwick) have recently theorized shame and suggested its potential for political activism, histories of this feeling have yet to be written. Reading narratives of shame in George Lillo’s London Merchant ( 1731) , Eliza Haywood’s The British Recluse (1722), multiple editions of Defoe’s Roxana (1724, 1730, 1745[49]), Samuel Richardson’s Clarissa (1747-48), and Frances Burney’s Evelina (1778), this chronologically organized study supplies one part of such a history. As such, the analysis builds on and reframes Foucault’s historical narrative of the emergence of the modern disciplined and divided self-consciousness by focusing on the affects that produce and re-produce it, particularly the affect of shame. Second, while Michael McKeon has identified the formative force of questions of virtue and truth on the novel, this thesis suggests that these questions are critically condensed in narratives of shame. The dissertation argues that private shame and the psychological interiority of the eighteenth-century novel are mutually productive. Once a passion which could lead to vice and even murder, by the late eighteenth century shame becomes a feeling which is internalized, and which divides the self. Connected both to the question of truth and the question of virtue, as well as to the status of passion itself, shame informs our sense of emotions as interior, yet remains inextricable from questions of reputation, credit, and civility.

abstract: Doctor of Philosophy (PhD)


title: Growth of InAs/InP Nanowires by Molecular Beam Epitaxy

contributor:
LaPierre, R. R.
Engineering Physics

subject:
Nanowire Heterostructures
Molecular Beam Epitaxy
Semiconducting III-V Materials
Transmission Electron Microscopy
Nanoscience and Nanotechnology
Nanoscience and Nanotechnology

abstract: InP nanowires with short InAs segments were grown on InP (111)B substrates by Au assisted vapour-liquid-solid growth in a gas source molecular beam epitaxy system. Nanowire crystal structure and morphology were investigated by transmission electron microscopy as a function of temperature, growth rate, and V/III flux ratio. At 370C predominantly kinked nanowires with random morphology and low areal density were observed with a rough parasitic 2D film. At 440C, nanowire density was also reduced but the 2D film growth was smoother and nanowires grew straight without kinking. An optimum temperature of 400C maximized areal density with uniform nanowire morphology. At the optimum temperature of 400C, an increase in V/III flux ratio changed the nanowire morphology from rod-shaped to pencil like indicating increased radial growth. Growth rate did not affect the crystal structure of InP nanowires. For InAs nanowires, changing the growth rate from 1 to 0.5 μm/hr reduced the presence of stacking faults to as low as one per nanowire. Short InAs segments in InP nanowires were found to grow through two mechanisms for nanowires of length L and diameter D. The first mechanism described the supply of In to the growth front via purging of In from the Au droplet where L was proportional to D. The second mechanism involved direct deposition of adatoms on the nanowire sidewall and subsequent diffusion to the growth front where L was proportional to 1/D. For intermediate growth durations, a transition between these two mechanisms was observed. For InP and InAs nanowires, the growth mode was varied from axial to radial through the inclusion of Al to form a core shell structure. AlxIn1-xAs(P) shells were grown on InAs cores with Al alloy fractions between 0.53 and 0.2. These nanowires were examined by transmission electron microscopy and it was found, for all values of x in InAs-AlxIn1-xP structures, that relaxation had occurred through the introduction of dislocations. For InAs-AlxIn1-xAs structures, all values except x=0.2 had relaxed through dislocation formation. A critical thickness model was developed to determine the core-shell coherency limits which confirmed the experimental observation of strain relaxation. The effects of passivation on the electronic transport and the optical properties were examined as a function of structural core-shell passivation and chemical passivation. The mechanisms for the observed improvement in mobility for core-shell versus bare InAs nanowires was due to the reduction in ionized impurity scattering from surface states. Similarly an increase in photoluminescence intensity after ammonium sulfide passivation was explained by the reduction of donor type surface states.

abstract: Doctor of Philosophy (PhD)


title: WAX-BASED EMULSIFIERS FOR WAX EMULSIONS FOR USE IN ENGINEERED WOOD PRODUCTS

contributor:
Zhu, Shiping
Chemical Engineering

subject:
Wax
Maleation
Engineered Wood Product
Emulsion
Grafting
Polymer Science
Polymer Science

abstract: In this study new value-added products were developed from four commercially available refined waxes for use as commercial emulsifiers via the technique of maleation. This research was performed in collaboration with an industrial partner with the hope of developing a wax emulsifier product that could replace commercially used wax emulsifiers in engineered wood product emulsions at a cost reduction by beginning with the design of a cost effective process that could be incorporated into an existing factory production line. Through the investigation and subsequent optimization of this process, a highly maleated product was achieved using 6 different quick and simple approaches. A standardized experimental design was applied to the parameters of the experiment: reaction time, peroxide, starting wax, maleic anhydride concentration, and temperature to observe and understand the individual effects of each on the resultant final product. Three organic peroxide initiators were evaluated; di-tert-butyl peroxide, di-tert-butyl peroxybenzoate and benzoyl peroxide, as well as a thermally initiated approach. The resultant waxes were then identified by their acid number and drop melt point; and from this, the overall efficiency of the combined parameter levels was calculated as a function the initial maleic anhydride amount versus that of the final. The maleated wax emulsifiers were incorporated into emulsions and applied to engineered wood products. Emulsifiers made via the thermally initiated approach showed statistically significant improvements in the desired properties, water absorbance and thickness swell, of the engineered wood products as compared to a commercial control formulation.

abstract: Master of Science (MSc)


title: Computational Investigation of Steady Navier-Stokes Flows Past a Circular Obstacle in Two--Dimensional Unbounded Domain

contributor:
Protas, Bartosz
Computational Engineering and Science

subject:
Fluid Mechanics
steady Navier-Stokes Equation
Oseen Equation
Spectral Methods
Fluid Dynamics
Numerical Analysis and Computation
Partial Differential Equations
Fluid Dynamics

abstract: This thesis is a numerical investigation of two-dimensional steady flows past a circular obstacle. In the fluid dynamics research there are few computational results concerning the structure of the steady wake flows at Reynolds numbers larger than 100, and the state-of-the-art results go back to the work of Fornberg (1980) Fornberg (1985). The radial velocity component approaches its asymptotic value relatively slowly if the solution is ``physically reasonable''. This presents a difficulty when using the standard approach such as domain truncation. To get around this problem, in the present research we will develop a spectral technique for the solution of the steady Navier-Stokes system. We introduce the ``bootstrap" method which is motivated by the mathematical fact that solutions of the Oseen system have the same asymptotic structure at infinity as the solutions of the steady Navier-Stokes system with the same boundary conditions. Thus, in the ``bootstrap" method, the streamfunction is calculated as a perturbation to the solution to the Oseen system. Solutions are calculated for a range of Reynolds number and we also investigate the solutions behaviour when the Reynolds number goes to infinity. The thesis compares the numerical results obtained using the proposed spectral ``bootstrap" method and a finite--difference approach for unbounded domains against previous results. For Reynolds numbers lower than 100, the wake is slender and similar to the flow hypothesized by Kirchoff (1869) and Levi-Civita (1907). For large Reynolds numbers the wake becomes wider and appears more similar to the Prandtl-Batchelor flow, see Batchelor (1956).

abstract: Doctor of Science  (PhD)


title: Leptonic Dipole Transitions: A New Signature for Physics Beyond the Standard Model

contributor:
Yavin, Itay
Burgess, Cliff
O`Dell, Duncan
Physics and Astronomy

subject: lepton flavour violation

subject: muonium oscillations

subject: Standard Model Extensions

subject: Extra Gauge Bosons

subject: Large Electron Positron Collider

subject: Tests of Symmetries

subject: Elementary Particles and Fields and String Theory

abstract: In this work, we consider the addition of a single neutral massive vector boson to the Standard Model (SM). This boson, which we refer to as N0, induces dipolar transitions between electrons and muons. We obtain bounds on the strength of its coupling and its mass: from the scattering process e+e- to mu+mu-; from its contribution to muonium-antimuonium oscillations; and from its possible contribution to the rare muon decay mu- to e+e-e-. In particular, we examine the two cases where the mediator is both heavy and light compared with the scattering energies for, and place constraints on the relevant parameters based on their contributions to the cross section and the forward-backward asymmetry. For muonium-antimuonium oscillations, we consider only the case where the mediator is heavy compared to all other scales, reducing its effect to an effective contact interaction. Finally, we consider an SU(2) invariant theory from which the N0 interaction emerges, and find that flavour diagonal interactions also emerge, giving a tree-level path for the decay mu- to e+e-e-. We find that the heavy N0 is not strongly constrained by this contribution, while the light N0 is very strongly constrained by it. Very generally, we find that the heavy N0 is much less constrained than other lepton flavour violating processes, while the constraints on the light N0 vary in strength between processes.

abstract: Master of Science (MSc)


title: Les Diplômés des Proqrammes d'immersion.

contributor:
Lepicq, Dominique
French

subject: French

subject: French and Francophone Language and Literature

abstract: Cette recherche examine l'incidence de l'arrivée des diplômés des programmes d'immersion en français sur les universités anglophones au Canada. Pour ce faire, nous décrivons les perceptions que les élèves de ces programmes peuvent avoir sur leurs compétences en français (orales, écrites, actives, réceptives), leurs attitudes envers la compétence de communication, leur motivation et leur fréquence d'utilisation du français en dehors du contexte académique et scolaire, leurs intentions de poursuivre des études post-secondaires en français et leurs besoins et désirs en matière de cours et de programme, et finalement leurs aspirations professionnelles. Nous divisons l'étude en deux parties, chacune correspondant à un groupe de sujets, soit au niveau secondaire soit au niveau universitaire. Dans la partie 1 (universitaire), nous présentons les résultats d'un questionnaire rempli par 29 étudiants inscrits à l'Université McMaster. Dans la deuxième partie, nous examinons les réponses de 43 élèves du niveau secondaire à un questionnaire en plus des résultats obtenus à un test de rendement en français. Le rapport est divisé en trois chapitres. Dans le premier, nous exposons nos objectifs d'étude. Dans le deuxième, nous faisons la description de la dėmarche méthodologique. Le troisième chapitre est consacré a la présentation, a l'analyse et a la discussion des résultats obtenus. Dans la conclusion, nous faisons des suggestions pour l'aménagement des programmes aux niveau secondaire et universitaire. Les résultats de cette recherche et d'autres montrent que les diplômés des programmes d'immersion ont des capacités réceptives en français (compréhension auditive, lecture) qui surpassent leurs capacités actives (production orale et écrite). Les résultats des diplômés d'immersion diffèrent beaucoup de ceux normalisés sur des francophones du même âge. En ce qui concerne I' Auto-évaluation faite par les sujets, ils se jugent de façon assez positive (ils sont plus positifs envers leurs capacités réceptives). Bien qu'ils manifestent un vif désir de parler le français et de s'améliorer, ils utilisent cette langue très rarement en dehors du contexte scolaire et académique. Une grande majorité des élèves du secondaire ont l'intention d'aller à l'université. Le choix d'université ne semble pas influencé par la possibilité de suivre des cours de/en français. Il est plutôt influencé par toute une variété de programmes et de cours. Les étudiants universitaires font peu de cours de/en français soit parce qu'ils ont un horaire trop charge, soit parce qu'ils sont satisfaits de leur niveau de compétence actuel ou bien parce qu'ils ont peur de faire baisser leurs notes. Dans la conclusion, nous livrons plusieurs suggestions pouvant concerner à la fois les systèmes d'éducation provinciale et les universités. De plus, nous mettons en valeur l'importance de la communication et l'échange d'idées entre enseignants, administrateurs, conseillers pédagogiques des universités et du système d'education provinciale.

abstract: Master of Arts (MA)


title: The Effect of Prenatal Stress on a Mouse Model of Allergic Airway Disease

contributor:
Forsythe, Paul
Health Sciences

subject:
Prenatal Stress
Allergic Airway Disease
Mouse Model
Immunopathology
Medical Immunology
Immunopathology

abstract: Prenatal life events have been long observed to be able to influence disease into adulthood in both epidemiological and animal studies. Prenatal stress (maternal stress during gestation) is one of such factors that has been shown to impact cognition and behaviour of the offspring. However, the effects of prenatal stress on the immune system are not understood. This study has evaluated the effects of prenatal stress on a murine model. Prenatal stress increased allergic airway inflammation in male, but not female offspring following sensitization and challenge with cockroach extract. This corresponded with stress-induced changes in the immune environment of non-sensitized animals. These changes included a decrease in regulatory T cells at baseline in males compared to non-stressed controls and increased splenic dendritic cell percentage and cytokine, particularly IFN-γ, secretion compared to prenatally stressed females. In females, prenatal stress decreased allergic inflammation, which corresponded to a decreased percentage of dendritic cells in the lung and mesenteric lymph node. Prenatal stress did not affect dendritic cell antigen presentation in ether male or female offspring. There was no evidence to suggest a prenatal stress induced change in glucocorticoid sensitivity of dendritic cells. In order to explore the possibility of prenatal stress induced decrease of parasympathetic output, a vagotomy model was used as a proof of concept in naïve animals not exposed to prenatal stress. Vagal modulation of dendritic cell phenotype and function was assessed. While there was some evidence that vagotomy may indirectly modulate dendritic cell function, its effects on the immune system were different then the changes caused by prenatal stress and thus it is a role of reduced parasympathetic output was not supported. Overall this data indicates a role of prenatal stress on the immune system with clear sex differences, but the mechanism for how this occurs is currently unknown. Further research is needed to investigate the role of TLRs and IFN-γ in this model, as well as other possible mediators of prenatal stress such as the changes to the parasympathetic nervous system that may in turn mediate alterations to the immune system. Differences in when the effects of prenatal stress are expressed during postnatal life are discussed.

abstract: Master of Science (MSc)


title: THE EFFECTS OF PPAR AGONISTS ON EOSINOPHIL FUNCTION

contributor: Medical Sciences (Division of Physiology/Pharmacology)

subject:
Migration
Differentiation
Progenitor cell
Rosiglitazone
Medical Immunology
Medical Immunology

abstract: PPAR agonists have been suggested as novel therapeutics for the treatment of inflammatory lung disease, such as allergic asthma. Treatment with PPAR agonists have been shown to inhibit peripheral eosinophilia in murine models of allergic asthma, which can occur through several mechanisms including decreased cytokine/chemoattractant (IL-5/eotaxin) release, decreased eosinophil migration and/or decreased eosinophil differentiation. This is the first study to show that PPARγ is expressed at the protein level in human airway eosinophils sampled from induced sputum, and confirms PPARγ protein expression in human peripheral blood eosinophils. We demonstrated the novel observation that peripheral blood eosinophil PPARγ protein expression, as measured by flow cytometry, is not different in eosinophils purified from asthmatic subjects compared to healthy controls and these observations suggest that the level of PPARγ expressed in human eosinophils is not related to asthmatic status. Our study also confirms, by real time PCR, the detection of mRNA for PPARγ in airway-derived leukocytes, collected from bronchial washings, increases 24hrs after whole lung allergen challenge. This increase is regulated by Symbicort® and Pulmicort® treatment in most subjects. This is the first study to show increased chemokinesis (random stimulated movement) of eosinophils in vitro at low concentrations of a PPARγ agonist. We have generated data to suggest this is through an effect on calcium signalling. We also observed that higher concentrations of PPAR agonists directly inhibit eotaxin-stimulated eosinophil directional migration. Finally, using methycellulose cultures of non-adherent mononuclear cells and CD34+ progenitor cells, we demonstrate that PPAR activation can inhibit the differentiation of eosinophils in vitro. Collectively, these data demonstrate that PPARγ is expressed consitutively on eosinophils in peripheral blood and airways, and suggest signaling through this receptor with nanomolar concentrations of agonist regulates eosinophilia through inhibition of both eosinophil migration and eosinophil differentiation.

abstract: Doctor of Philosophy (PhD)


title: Dengue and development: a critical political ecology

contributor: Corinne Schuster-Wallace, William Coleman

subject:
dengue
development
urban
political ecology
global health
putrajaya
malaysia
critical discourse analysis
systematic review
poverty
urban planning
neglected tropical diseases
Other Geography
Other Geography

abstract:
Policies for the control of dengue fever often construct the mosquito-borne virus as a disease of poverty, and call for disease control through “development” to meet the needs of poor populations and impoverished or unsanitary spaces. However, exceptions to the narrative of a rich/poor dengue divide persist in non-poor urban environments across the world. One example is Malaysia's new administrative capital city of Putrajaya – a wealthy and centrally planned new city with among the highest rates of dengue in the country.

This dissertation drew on theories of ecosocial epidemiology and urban political ecology to investigate and contextualize the geography of dengue and development in Putrajaya. Key informant interviews and critical discourse analysis found that infectious disease control fell well below other urban priorities for the city, and that globally dominant dengue control strategies targeted toward poor populations were inappropriately transferred to Putrajaya's non-poor local environment. A systematic review of the research literature found no clear evidence showing an association between dengue and conditions of poverty. These findings challenge conventional thinking by policy makers about epidemiological transition and the social determinants of health.

The dissertation addresses the dearth of research into the world's neglected tropical diseases (NTDs); in particular, gaps in our understanding of the biopolitical and socioecological contexts (sites of urban governance, sites of health policy development and implementation, and sites of academic research) in which policies for NTDs like dengue are determined, enacted and justified. The dissertation further identifies non-poor urban environments – in particular those undergoing rapid development, such as Putrajaya – as key spaces for future geographic and political ecological research related to epidemiological transition, economic development and the social and environmental determinants of health.

abstract: Doctor of Philosophy (PhD)


title: Perception and Production in Autism Spectrum Disorder

contributor:
Trainor, Laurel
Psychology

subject:
perception
production
auditory processing
Autism Spectrum Disorder
adolescents
adults
Psychology
Psychology

abstract: Many behavioural theories describe Autism Spectrum Disorder (ASD) as having roots as a social disorder. However, our research adds to previous studies showing that those with ASD with normal intelligence have perceptual problems that affect their social functioning. We report that those with ASD perform worse than controls in all of our speech tasks that measure the ability to filter speech in noise, specialization for native speech sound categories, and audio-visual integration of speech sounds. Those with ASD also performed worse on tasks measuring specialization for native musical meters, but not on tasks measuring absolute pitch or knowledge of tonal harmony. This research provides some explanation for why perceptual areas that develop early instead of late are most impaired in ASD, which can have implications for remediation. Besides perceptual problems, we found in other research that those with ASD have abnormal prosody, which varies according to language ability. We report that those with Autism Moderate Language Functioning (A-moderateL) use a restricted pitch range relative to those with Autism High Language Functioning (A-highL) and controls, whereas those with A-highL use a larger pitch range relative to those with A-moderateL and controls. We also found that A-moderateL speakers and controls, but not A-highL speakers vary acoustic features to mark words representing focus relative to topic. This research is important because identifying different ASD language subgroups might lead to more appropriate speech and language therapy.

abstract: Doctor of Philosophy (PhD)


title: Interactions of Self-Trapped Beams Generated with a Miniature Green Laser in a Photopolymerizable Medium

contributor:
Xu, Chang-qing
Saravanamuttu, Kalaichelvi
Knights, Andrew
Engineering Physics

subject:
nonlinear optics
green laser
self-trap
photopolymerization
beam interactions
filamentation rings
Other Engineering
Other Engineering

abstract: This study examined the self-trapping of light emitted by a miniature green laser in a photopolymerizable medium and the interactions between two parallel-propagating self-trapped beams. The work included the design and fabrication of an Intra-Cavity Frequency-Doubling (IC-FD) Nd: YVO4/MgO: PPLN miniature green laser with a stable and tunable output intensity. Emission from this laser enabled a systematic examination of self-trapping phenomena at incident intensities spanning 8 orders of magnitude (3.2× W·cm-2 to 6368 W·cm-2). When launched into a photopolymerizable medium, light emitted by the miniature green laser self-trapped by initiating polymerization and corresponding changes in refractive index along its propagation path. The evolution and dynamics of the self-trapped beam corresponded to the behaviour of self-trapped beams of coherent light. Interactions between a pair of parallel-propagating self-trapped beams were also characterised at a range of intensities. This study shows that the miniature green laser is an efficient, coherent source with a large range of output intensities for the excitation of self-trapped beams. This opens opportunities for its incorporation into small-scale optical systems designed to operate based on the generation and interactions of self-trapped beams.

abstract: Master of Applied Science (MASc)


title: Inhibition of the prothrombinase complex on phospholipid vesicles, activated platelets, and red blood cells by a covalently-linked antithrombin-heparin complex

contributor: Medical Sciences (Blood and Cardiovascular)

subject:
antithrombin
covalent antithrombin-heparin complex
heparin
platelets
phospholipid vesicles
prothrombinase complex
red blood cells
Medical Sciences
Medical Sciences

abstract: Prothrombinase is composed of a proteinase, factor Xa (Xa), its cofactor Va (Va), Ca2+ and a zymogen, prothrombin (II), assembled on a phospholipid surface. During coagulation, prothrombinase accelerates II to thrombin conversion; but during anticoagulation, it protects the proteinase from inhibition by antithrombin (AT) ± unfractionated heparin (UFH). Although the degree of Xa protection by prothrombinase varies according to the reports in literature, moderate to significant protective effects have been consistently reported by most investigators. To overcome the limitations of UFH, our laboratory has developed a covalent complex of AT and UFH (ATH) with superior anticoagulant responses. To further understand the mechanisms of enhanced anticoagulant activity of ATH, we proceeded to study inhibition of the prothrombinase complex on synthetic vesicles, activated platelets and red blood cells (RBCs). Using discontinuous inhibition assays, we determined the rate of inhibition of prothrombinase-complexed Xa compared to control Xa. With synthetic vesicles, Xa was protected from inhibition by AT+UFH when in prothrombinase, while only a mild protective effect was observed with ATH. Omission of various components of the prothrombinase led to a reduction in Xa protection for AT+UFH. However, an increased Xa protection against ATH was observed when II was omitted from the prothrombinase. In comparison to the synthetic vesicle system, activated platelets showed a similar trend for protection of Xa in reactions involving prothrombinase ± components, while no protection of Xa was observed for ATH reactions. Alternatively, RBCs showed differences relative to vesicles in that increased protection of Xa occurred with omission of II and Va for AT+UFH, whereas omission of Va increased protection against ATH inhibition. In addition, ATH had improved inhibition of thrombin generation, fibrin formation and plasma coagulation compared to AT+UFH. Studies of fluorescently labelled Xa and inhibitors detailed binding interactions with prothrombinase subunits. Overall, the results suggest that a covalent linkage between AT and heparin improves inactivation of prothrombinase complexed-Xa leading to down-regulation of prothrombinase function.

abstract: Doctor of Philosophy (Medical Science)


title: Detection and Localization of Power and Coherence Dynamics with EEG

contributor:
Wong, Kon Max
Jeremic, Aleksandar
Jian-Kang Zhang, Nicola Nicolici
Electrical and Computer Engineering

subject:
EEG
spatial filter
magnitude-squared coherence
imaginary component
Biomedical
Biomedical

abstract: It has been observed by researchers that periodic auditory stimuli can cause the activities in different brain areas to be periodically synchronized. Fast auditory stimuli have been shown to cause the brain sources to synchronize at the rate of stimuli. Brain sources respond to them not only by increase in local synchronization, but also in the global synchronization of cortical regions often regarded as functional connectivity. Spectral power and coherence are often used to characterize such neural synchronization. Beta band oscillations have been reported to underlie the neural mechanism during repetitive auditory stimuli. Cortical generators of these underlying beta oscillations were investigated in several studies based on MEG measurements. This research is intended to investigate (1) EEG can be used to detect and localize neural sources changing in power and coherence and (2) beta oscillations underlie such neural synchronization during fast repetitive auditory stimuli based on EEG measurements. The procedure of this study consists of several steps. First, the minimum variance (MV) scalar beamformer, an adaptive spatial filter, is used to estimate the temporal signals in the brain source space, given EEG recordings. The analysis of the estimated source temporal signals then consists of two stages firstly the power analysis and secondly the coherence analysis. The dynamics of power and coherence is investigated instantaneously over time and in the lower beta frequency band [14,20Hz]. This is done by detecting the most prominent changes in the two spectral parameters through singular value decomposition (SVD). Two coherence measures imaginary component (IC) and magnitude-squared coherence (MSC) are employed and compared in terms of their performance both mathematically and experimentally. In the simulations, we show the capability of using EEG to detect and localize power co-variations and dynamic functional connectivity in the cortical regions. We also perform the procedure on the recorded real data from subjects passively listening to rhythmic auditory stimuli. Beta oscillations are found to underlie the neural activity to percept auditory stimuli. This is shown by localization of auditory cortices and detection of power co-variation in this frequency band. We demonstrate the feasibility of using EEG to identify coupled and co-activated brain sources similar to those obtained from MEG signals in the previous studies. These include auditory and motor regions which were found to be functionally coherent and have a functional role in the auditory perception. The superiority of IC over MSC measure is proven mathematically and validated in both simulations and real data experiments.

abstract: Master of Applied Science (MASc)


title: Huntingtin Nuclear Localization: Current Insights into Mechanism and Regulation

contributor:
Truant, Ray
Biochemistry

subject:
Huntington's Disease
Nuclear Transport
Huntingtin
Cell Biology
Cell Biology

abstract: Huntington's Disease brains display a striking accumulation of huntingtin in the nucleus of striatal and cortical neurons, suggesting that nuclear functions may be key to the onset of cellular pathogenesis. Entry to the nucleus is tightly regulated by a family of import receptors called karyopherins that limit their binding to proteins bearing specific nuclear localization signals (NLS). Although huntingtin is primarily cytoplasmic in healthy neurons, it is also found in the nucleus at low levels and contains a nuclear export signal (NES), suggesting that shuttling to and from the nucleus is part of the protein's normal function. Indeed, recent publications from our lab (Atwal et al. 2007 and 2011, and Munsie et al. 2011) describe huntingtin's ability to enter the nucleus in response to cell stress, and localize to cofilin-actin rods. We have identified an active NLS near the amino terminus of huntingtin between amino acids 174-207, which is recognized by both karyopherin β2 and β1. While functional in STHdh and NIH 3T3 cells, the huntingtin NLS lacks activity in HEK 293 and MCF-7 cell lines. This surprising observation suggests that additional levels of regulation exist amongst cell types. We have isolated a shorter sequence within the NLS that localizes to membrane structures throughout the cell (such as the plasma membrane and vesicles). This thesis explores several putative secondary regulatory mechanisms, such as, nuclear export activity, transcriptional dependence, palmitoylation and acetylation. However, the most promising mechanism thus far is masking of the NLS by HAP1 and HMGB1. The functions of these proteins, in vesicular trafficking and autophagy/apoptosis, respectively, may offer further insight into huntingtin’s nuclear function. By understanding the underlying regulatory mechanisms of huntingtin nuclear import, we hope to gain further insight into why huntingtin accumulates in the nucleus of specific neurons in HD, and whether or not this mislocalization directly contributes to disease.

abstract: Doctor of Philosophy (PhD)


title: SsrB-dependent regulation during Salmonella pathogenesis

contributor:
Coombes, Brian K.
Nodwell, Justin
Schellhorn, Herb
Biochemistry

subject:
gene regulation
pathogenicity
virulence
type-3 secretion systems
bacteriophage
Biochemistry
Molecular genetics
Pathogenic Microbiology
Biochemistry

abstract: Bacteria demonstrate an extraordinary capacity to survive and adapt to changing environments. In part, this ability to adapt can be attributed to horizontal gene transfer, a phenomenon which introduces novel genetic information that can be appropriated for use in particular niches. Nowhere is this more relevant than in pathogenic bacteria, whose acquisition of virulence genes have provided an arsenal that permits them to thrive within their selected host. Regulatory evolution is necessary for timely regulation of these acquired virulence genes in the host environment. Salmonella enterica serovar Typhimurium is an intracellular pathogen which possesses numerous horizontally-acquired genomic islands encoding pathogenic determinants that facilitate its host lifestyle. One island, Salmonella Pathogenicity Island (SPI)-2, encodes a type-III secretion system (T3SS) which is regulated by the two-component regulatory system SsrA-SsrB. This system coordinates expression of the SPI-2 T3SS as well as an array of virulence effectors encoded in horizontally-acquired regions throughout the Salmonella genome. The studies presented here investigated the mechanisms in which the transcription factor SsrB functions to integrate virulence processes through regulatory adaptation. This work identified the regulatory logic controlling SsrB and defined the associated SsrB regulon. Furthermore, SsrB was found to induce a regulatory cascade responsible for the expression of bacteriophage genes encoded within SPI-12, an island that also contributes to Salmonella virulence. These findings demonstrate the important contribution of regulatory evolution in pathogen adaptation to the host, and show that horizontally-acquired genes, once integrated into appropriate regulatory networks, can contribute to pathogen fitness in specific niche environments.

abstract: Doctor of Philosophy (PhD)


title: The Human Right to Water and Water Security

contributor:
Gedge, Elisabeth
Adeel, Zafar
Igneski, Violetta
Philosophy

subject:
Human Rights
Water Security
Bottom Billion
Ethics and Political Philosophy
Ethics and Political Philosophy

abstract: In this thesis I argue that the utility of employing the human right to water within discussions of water security is intimately related to the population under consideration, such that its use can be more or less effective depending on whose water security one is considering. This is owed to the fact that employing the human right to water in discussions of water security is useful only in the case of states that are able to satisfy the conditions necessary for the successful implementation of the human right to water as a positive legal right: i) being possessed of adequate amounts of the resource in question, ii) being possessed of the political willingness to provide the resource, and iii) being possessed of the capacity, including the infrastructure, to supply the end user with the resource.

abstract: Master of Arts (MA)


title: Computational and Structural Approaches to Periodicities in Strings

contributor:
Deza, Antoine
Franek, Frantisek
Computing and Software

subject:
string
algorithm
run
word
periodicity
string algorithm
Theory and Algorithms
Theory and Algorithms

abstract: We investigate the function ρd(n) = max { r(x) | x is a (d, n)-string } where r(x) is the number of runs in the string x, and a (d, n)-string is a string with length n and exactly d distinct symbols. Our investigation is motivated by the conjecture that ρd(n) ≤ n-d. We present and discuss fundamental properties of the ρd(n) function. The values of ρd(n) are presented in the (d, n-d)-table with rows indexed by d and columns indexed by n-d which reveals the regularities of the function. We introduce the concepts of the r-cover and core vector of a string, yielding a novel computational framework for determining ρd(n) values. The computation of the previously intractable instances is achieved via first computing a lower bound, and then using the structural properties to limit our exhaustive search only to strings that can possibly exceed this number of runs. Using this approach, we extended the known maximum number of runs in binary string from 60 to 74. In doing so, we find the first examples of run-maximal strings containing four consecutive identical symbols. Our framework is also applied for an arbitrary number of distinct symbols, d. For example, we are able to determine that the maximum number of runs in a string with 23 distinct symbols and length 46 is 23. Further, we discuss the structural properties of a shortest (d, n)-string x such that r(x) > n-d, should such a string exist.

abstract: Doctor of Philosophy (PhD)


title: THE DESIGN, FABRICATION AND CHARACTERIZATION OF SILICON OXIDE NITRIDE OXIDE SEMICONDUCTOR THIN FILM GATES FOR USE IN MODELING SPIKING ANALOG NEURAL CIRCUITS

contributor:
Mascher, Peter
Bruce, Ian C.
Preston, John
Engineering Physics

subject:
Neuromorphic Engineering
SONOS
Organic Electronics
Spiking Analog Neural Circuits

abstract:
This Thesis details the design, fabrication and characterization of organic semiconductor field effect transistors with silicon oxide-nitride-oxide-semiconductor (SONOS) gates for use in spiking analog neural circuits. The results are divided into two main sections. First, the SONOS structures, parallel plate capacitors and field effect transistors, were designed, fabricated and characterized. Second, these results are used to model spiking analog neural circuits. The modeling is achieved using PSPICE based software.

The initial design work begins with an analysis of the basic SONOS structure. The existence of the ultrathin layers of the SONOS structure is confirmed with the use of Transmission Electron Microscopy (TEM) and Energy Dispersive Spectroscopy (EDS) scans of device stacks. Parallel plate capacitors were fabricated prior to complete transistors due to the significantly less processing required. The structure and behaviour of these capacitors is similar to that of the transistor gates which allows for the optimization of the structures prior to the fabrication of the transistors. These capacitors were fabricated using the semiconductor materials of; crystalline silicon, amorphous silicon, Zinc Oxide, copper phthalocyanine (CuPc) and tris 8-hydroxyquinolinato aluminium (AlQ3). These devices are then subjected to standard capacitance voltage (C-V) analysis. The results of this analysis demonstrate that the inclusion of SONOS structures in the capacitors (and transistors) result in a hysteresis which is the result of charge accumulation in the nitride layer of the SONOS structure. This effect can be utilized as an imbedded memory. Standard control devices were fabricated and analysed and no significant hysteresis effect was observed. The hysteresis effect is only observed after the SONOS devices are subject to high voltages (approximately 14 volts) which allows tunneling through a thin oxide layer into traps in the silicon nitride layer. This analysis was conducted to confirm that the SONOS structure causes the memory effect, not the existence of interface states that can be charged and discharged.

The next step was to design and fabricate amorphous semiconductor field effect transistors with and without the SONOS structure. First FETs without the SONOS gates were fabricated using amorphous semiconductor materials; Zinc Oxide, CuPc and AlQ3 and then the devices were characterized. This initial step confirmed the functionality of these basic devices and the ability to fabricate working control samples. Next, SONOS gate TFTs were fabricated using CuPc as the semiconductor material. The characterization of these devices confirmed the ability to shift the transfer characteristics of the devices through a read and write mechanism similar to that used to shift the C-V characteristics of the parallel plate capacitors. Split gate FETs were also produced to examine the feasibility of individual transistors with multiple gates.

The results of these characterizations were used to model spiking analog neural circuits. This modeling was carried out in four parts. First, representative transfer and output characteristics were used to replicate analog spiking neural circuits. This was carried out using standard PSPICE software with the modification of the discrete TFT device characteristics to represent the amorphous CuPc organic transistors. The results were found to be comparable to circuits using crystalline silicon transistors. Second, the SONOS structures were modeled closely matching the characterized results for charge and voltage shift. Third, a simple Hebbian learning circuit was designed and modeled, demonstrating the potential for imbedded memories. Lastly, split gate devices were modeled using the device characterizations.

abstract: Doctor of Philosophy (PhD)


title: Improving specimen identification: Informative DNA using a statistical Bayesian method

contributor:
Golding, G. B.
Biology

subject:
Theory of segregating sites
Bayesian theory
Species identification
Mitochondrial DNA
DNA barcoding
Treeless statistical assignment method
Computational Biology
Ecology and Evolutionary Biology
Evolution
Genetics and Genomics
Population Biology
Computational Biology

abstract: This work investigates the assignment of unknown sequences to their species of origin. In particular, I examine four questions: Is existing (GenBank) data reliable for accurate species identification? Does a segregating sites algorithm make accurate species identifications and how does it compare to another Bayesian method? Does broad sampling of reference species improve the information content of reference data? And does an extended model (of the theory of segregating sites) describe the genetic variation in a set of sequences (of a species or population) better? Though we did not find unusually similar between-species sequences in GenBank, there was evidence of unusually divergent within-species sequences, suggesting that caution and a firm understanding of GenBank species should be exercised before utilizing GenBank data. To address challenging identifications resulting from an overlap between within- and between species variation, we introduced a Bayesian treeless statistical assignment method that makes use of segregating sites. Assignments with simulated and Drosophila (fruit fly) sequences show that this method can provide fast, high probability assignments for recently diverged species. To address reference sequences with low information content, the addition of even one broadly sampled reference sequence can increase the number of correct assignments. Finally, an extended theory of segregating sites generates more realistic probability estimates of the genetic variability of a set of sequences. Species are dynamic entities and this work will highlight ideas and methods to address dynamic genetic patterns in species.

abstract: Doctor of Philosophy (PhD)


title: The Growth Curve Model for High Dimensional Data and its Application in Genomics

contributor:
Hamid, Jemila S
N. Balakrishnan, R. Viveros
Mathematics and Statistics

subject: Generalized multivariate analysis of variance

subject: growth curve model

subject: high-dimensional data

subject: Euclidean distance

subject: multivariate bias and mean square error

subject: moderated trace test

subject: Moore-Penrose generalized inverse

subject: Biostatistics

subject: Multivariate Analysis

subject: Biostatistics

abstract:
Recent advances in technology have allowed researchers to collect high-dimensional biological data simultaneously. In genomic studies, for instance, measurements from tens of thousands of genes are taken from individuals across several experimental groups. In time course microarray experiments, gene expression is measured at several time points for each individual across the whole genome resulting in massive amount of data. In such experiments, researchers are faced with two types of high-dimensionality. The first is global high-dimensionality, which is common to all genomic experiments. The global high-dimensionality arises because inference is being done on tens of thousands of genes resulting in multiplicity. This challenge is often dealt with statistical methods for multiple comparison, such as the Bonferroni correction or false discovery rate (FDR). We refer to the second type of high-dimensionality as gene specific high-dimensionality, which arises in time course microarry experiments due to the fact that, in such experiments, sample size is often smaller than the number of time points ($n

In this thesis, we use the growth curve model (GCM), which is a generalized multivariate analysis of variance (GMANOVA) model, and propose a moderated test statistic for testing a special case of the general linear hypothesis, which is specially useful for identifying genes that are expressed. We use the trace test for the GCM and modify it so that it can be used in high-dimensional situations. We consider two types of moderation: the Moore-Penrose generalized inverse and Stein's shrinkage estimator of $ S $. We performed extensive simulations to show performance of the moderated test, and compared the results with original trace test. We calculated empirical level and power of the test under many scenarios. Although the focus is on hypothesis testing, we also provided moderated maximum likelihood estimator for the parameter matrix and assessed its performance by investigating bias and mean squared error of the estimator and compared the results with those of the maximum likelihood estimators. Since the parameters are matrices, we consider distance measures in both power and level comparisons as well as when investigating bias and mean squared error. We also illustrated our approach using time course microarray data taken from a study on Lung Cancer. We were able to filter out 1053 genes as non-noise genes from a pool of 22,277 genes which is approximately 5\% of the total number of genes. This is in sync with results from most biological experiments where around 5\% genes are found to be differentially expressed.

abstract: Master of Science (MSc)


title: Developing Generally Applicable Tools to Investigate TetR Family Transcriptional Regulators

contributor:
Nodwell, Justin
Biochemistry

subject:
transcription
TetR family transcriptional regulator
target
ligand
genomics
screening
Bacteriology
Bacteriology

abstract: Bacteria adapt to changes in their environment by regulating gene transcription. TetR family transcriptional regulators (TFRs) constitute one of the largest groups of bacterial transcription factors and thus, characterization of TFRs is anticipated to be crucial for a better understanding of prokaryotic physiology. Of significant importance, the majority of TFRs are predicted to respond to small-molecule signals and an emerging paradigm suggests that identifying ligands of TFRs can provide direct insight into the biochemical functions of the genes they regulate. Regulatory target genes and small-molecule ligands are unknown for all but a few TFRs and therefore, generally applicable tools for identifying these basic elements of TFRs are highly desirable. We first investigated the use of genome context as a predictive tool for identifying regulatory targets of TFRs. We find that the majority of TFRs are divergently oriented from a neighboring gene, and those with a“200 bp rule” should allow us to predict at least one regulatory target for more than half of all TFRs in the public databases. Second, we developed a biosensor mechanism amenable to high-throughput screening for identifying ligands of TFRs of unknown function. Significantly, one of our biosensors has played an integral role in characterizing the ligands of a previously uncharacterized TFR. Thus, the combined use of the tools we have developed will provide considerable benefit in understanding bacterial small-molecules responses mediated by TFRs.

abstract: Doctor of Philosophy (PhD)


title: Neutron Scattering and Nuclear Spin Species Conversion in the Solid Methanes

contributor:
Morrison, J. A.
Chemistry

subject: Chemistry Chemistry

abstract:
An understanding of the interconversion between the nuclear spin symmetry species in the solid methanes is essential for characterising the unusual low temperature behaviour of these solids. In this thesis, the measurement of the total neutron scattering cross-sections of the methanes is used to study quantitatively the extent and kinetics of the spin conversion process.

A method of accurately measuring total cross-sections of molecular solids, at low temperatures (0.75 K

Three of the solid isotopic methanes were studied (CH₄, CH₃D and CH₂D₂). In CH₄, extensive measurements were made on solid in phase II, in which spin conversion occurs at different rates on the two different kinds of sublattice. The conversion lifetime of the molecules on the ordered sublattice sites was found to be 75 hours. On the disordered sublattices, the lifetimes were much shorter and strongly temperature dependent. The equilibrium cross-section data were used to critically test a theoretical description of solid CH₄. It was found to be satisfactory.

Spin conversion in CH₃D was studied quantitatively and found to occur primarily below T = 4 K. In contrast to CH₄, the spin conversion process in CH₃D was very fast. The cross-section data were also used to guide the analysis of some existing thermodynamic data for CH₃D, and to derive the characteristics of the low-lying tunnelling levels. Some inferences about the nature of the lowest temperature phase (phase III) are made.

Little is known about CH₂D₂, and the cross-section measurements were made to determine if spin conversion occurs, especially below T = 4 K. A change in cross-section was found in this temperature region and an argument is presented which could ascribe such a change to spin conversion.

abstract: Doctor of Philosophy (PhD)


title: Revitalizing Hamilton's Heart: Business Owners and the Prospects for King Street Downtown

contributor:
Harris, Richard
Dunn, Jim
Peace, Walter
Geography

subject: Downtown

subject: Revitalization

subject: Business Owners

subject: Commercial Gentrification

subject: Main Street

subject: Hamilton

subject: Community-based Research

subject: Community Engagement

subject: Critical and Cultural Studies

subject: Cultural Resource Management and Policy Analysis

subject: Environmental Design

subject: Growth and Development

subject: Historic Preservation and Conservation

subject: Human Geography

subject: Inequality and Stratification

subject: Infrastructure

subject: Landscape Architecture

subject: Other Geography

subject: Political Economy

subject: Public Administration

subject: Public Economics

subject: Recreation, Parks and Tourism Administration

subject: Social and Cultural Anthropology

subject: Social History

subject: Social Influence and Political Communication

subject: Social Policy

subject: Tourism

subject: United States History

subject: Urban, Community and Regional Planning

subject: Urban Studies

subject: Urban Studies and Planning

subject: Community-based Research

abstract: Since the 1960’s, post industrial downtowns across North America and Europe have suffered economic and population losses. Downtown revitalization theory is now a major subject in urban geography. Although each city is unique and requires customized revitalization techniques, certain approaches have worked better than others. Hamilton, Ontario, is a city of roughly 520,000 located just outside the Greater Toronto Area. Its downtown has struggled since the 1970’s. In the last ten years, however, certain areas of downtown have shown signs of revitalization. Conversation about this change has largely focused on attracting creative industries. King Street, Hamilton’s most downtown street, has yet to experience significant improvement, but is surrounded by changing areas and expected to follow suit. This study looks at two theories of revitalization: the Creative Capital theory, and the Main Street approach. It also discusses commercial gentrification. City officials and business owners along King Street were interviewed about what they expect for King Street downtown. Business owners, this study found, are underutilized agents of revitalization in the area. They want and expect the area to improve, but have yet to make significant changes to their own establishments. More could be done to include incumbent business owners in King Street's revitalization processes in Hamilton, and to acknowledge them as agents of change within the commercial gentrification literature.

abstract: Master of Arts (MA)


title: Analysis of Transuranic Mixed Oxide Fuel in a CANDU Nuclear Reactor

contributor: Engineering Physics and Nuclear Engineering

subject:
CANDU
Actinide Burning
Nuclear Safety Analysis
Mixed Oxide Fuel
Nuclear Engineering
Nuclear Engineering

abstract: The reprocessing of spent fuel is a key component in reducing the end waste from nuclear power plant operations and creating a sustainable closed fuel cycle. Central to this effort is the extraction and reprocessing of actinide materials to be recycled into fast or thermal reactors. Reprocessed actinides can contribute additional energy and may be partially transmuted in current thermal systems using mixed oxide fuels before being sent to fast reactors. The use of current thermal reactors as an intermediary step significantly reduces the fast reactor infrastructure needed to handle the spent fuel inventory in the long term, and also provides a source of additional energy from existing mined resources in the short term. An optimization of the fast and thermal systems in a closed fuel cycle reduces the end cycle waste to primarily fission products which have little residual value and manageable disposal and monitoring demands. The dissertation explores the design and analysis of an actinide transmutation solution utilizing a current thermal reactor design. The TRUMOX-30 CANDU-900 system defined herein uses a mixed oxide fuel containing 3.1% transuranic actinides extracted from 30 year cooled spent fuel from a prototypical Pressurized Water Reactor (PWR) and mixed with natural uranium. A significant constraint imposed on the design is that the actinide burning is to occur in an existing CANDU design without major changes or infrastructure replacement. Hence the standard CANDU design and analysis methodology was employed to produce and evaluate the system. The phased approach includes extensive neutron transport modeling of the lattice and control device super-cell configurations, which feed forward in to a detailed full core diffusion model of the TRUMOX-30 CANDU-900 design. Suitable fuel burnup and significant actinide conversion was achieved while remaining within the prescribed operational envelope of the CANDU reactor. The design was evaluated against existing operational constraints and limits, performing well and achieving the goal of actinide transmutation with no changes to the reactor design. This effort demonstrated the adaptation of a current CANDU-900 reactor as a platform for intermediary actinide transmutation which may form part of a sustainable and efficient fuel cycle.

abstract: Doctor of Philosophy (PhD)


title: Speculative Matter: Generic Affinities, Posthumanisms and Science-Fictional Imaginings

contributor:
Savage, Anne
Fast, Susan
Rethmann, Petra
English and Cultural Studies

subject:
science fiction
fantasy
posthumanism
print fiction
television
genre
Arts and Humanities
Feminist, Gender, and Sexuality Studies
Literature in English, North America
Television
Arts and Humanities

abstract: The boundaries of science fiction, as with any genre, are relational rather than fixed, and critical engagements with Western/Northern technoscientific knowledge and practice and modern human identity and being may be found not just in science fiction “proper,” or in the scholarly field of science and technology studies, but also in the related genres of fantasy and paranormal romance. This thesis offers an interdisciplinary examination – a science-fictional and posthumanist reframing – of the lines of affinity and relationality between these discursive and imaginative domains. Bringing together genre theory and critical posthumanism – itself informed by postmodern and poststructuralist feminism, postcolonialism, science and technology studies, and critical animal studies – with readings of several series in print (Christine Feehan’s Ghostwalkers, Kim Harrison’s The Hollows, and Justina Robson’s Quantum Gravity) and on television (Fringe, True Blood, and Sanctuary), I argue that such narratives’ powerful abiding interest in the domains of knowledge, experience and imagination that lie within, along and outside the margins of scientific orthodoxy, registers a broader cultural apprehension of the conditions and critical perspectives by which Western/Northern humanism, anthropocentrism, modernity, and technoscientific authority have been and can be seen to be destabilized.

abstract: Doctor of Philosophy (PhD)


title: Adults’ and Infants’ Perception of Pitch-Evoking Stimuli with No Resolvable Spectral Cues

contributor:
Trainor, Laurel J.
Psychology

subject:
Developmental Neuroscience
Developmental Psychology
Developmental Neuroscience

abstract: Pitch perception depends on two types of cues provided by acoustic stimuli: spectral cues arise from the tonotopic organization of the basilar membrane, while temporal cues are contained within the pattern of action potentials generated in auditory nerve fibers. Filtered iterated rippled noise (IRN) can be used to examine how adults and infants perceive stimuli without resolvable spectral cues. Chapter 2 uses event-related potentials (ERPs) to compare adult perception of IRN and complex harmonic stimuli. Functional imaging studies have revealed a common pitch centre along lateral Heschl’s gyrus, but lack the temporal resolution to index different stages of processing. Chapter 2 reveals differences between feature extraction-related ERP components elicited in response to different pitch-evoking stimuli. However, no differences were observed in the mismatch negativities (MMN), suggesting pitch percepts formed at this stage of processing are independent of stimulus type. Moreover, source estimates for the MMN were consistent with fMRI studies. Chapter 3 demonstrates that infants can perceive the pitch of stimuli that lack resolvable spectral cues. Eight-month-old infants discriminated between 167 Hz and 200 Hz IRN stimuli. However, performance was poor relative to when resolvable spectral cues were present, and required a period of pitch-priming (Experiment 2). Chapter 4 uses ERPs to further examine infants’ perception of IRN. Using an oddball paradigm, 4- and 8-month-old infants were shown to discriminate between 167 Hz and 200 Hz stimuli. However, successful discriminations again required pitch-priming (Experiment 2). Together, these findings suggest that infant pitch percepts are dominated by resolved spectral cues. Infants discriminate between stimuli without resolvable spectral cues, but appear to require a period of priming to do so, at least until 8 months of age. Thus, infant pitch perception may be impaired in challenging listening situations, such as extracting vocal pitch cues in the presence of background noise.

abstract: Doctor of Philosophy (PhD)


title: INVESTIGATION OF CD36 SCAVENGER TYPE B RECEPTOR EXPRESSING MACROPHAGES IN INTESTINAL INFLAMMATION

contributor:
Yang, Pingchang
Paul Forsythe, Damu Tang
Medical Sciences

subject:
Crohn's Disease
Ulcerative Colitis
LCFA
TNBS
Medical Immunology
Medical Immunology

abstract: Currently, there is no effective cure for Inflammatory Bowel Disease (IBD), medications are aimed solely at alleviating symptoms and not curative. Great scientific efforts have been aimed at elucidating the mechanisms underlying the pathogenesis of IBD. Macrophages—antigen presenting cells—play a chief role in the pathophysiology of IBD. It has been proposed that CD36 receptor present on the surface of macrophages, may play a role in the inflamed intestine. CD36-expressing macrophages have been implicated in a variety of human diseases; however the role of CD36+ macrophages in the intestine has been limited. The aim of this study was to decipher whether or not CD36+ F4/80+ macrophages are inflammatory in the colonic intestine. Our study discovered the proportion of CD36+ F4/80+ macrophages were markedly upregulated in active IBD patients and TNBS-induced colitis mice. CD36+ macrophages isolated from the LPMC of the small and large intestine of Balb/c treatment groups(a) 12TNBS, (b) MHS+12TNBS, and (c) MHS+PA mice confirmed these macrophages expressed some level of proinflammatory cytokine TNF-α. Two macrophage ligands, LCFA: Palmitic Acid and PGN, in conjunction or separately, appeared to be two culprits which induced MHS macrophages to produce TNF-α both in vitro and in vivo. It is possible these two ligands may work in concert, however the mouse model has yet to be examined. The precise role(s) of these CD36+ F4/80+ macrophages requires further scientific inquiry and elucidation in the context of intestinal inflammation. It is quite possible understanding the mechanisms and roles of these macrophages will greatly advance our knowledge in the pathophysiology of IBD and potential therapeutic treatments or targets.

abstract: Master of Science (MSc)


title: LUNG-HOMING OF ENDOTHELIAL PROGENITOR CELLS AND ANGIOGENESIS IN ASTHMA: ROLE OF EOSINOPHILS

contributor:
Sehmi, Roma
Inman, Mark
Gauvreau, Gail
Medical Sciences

subject:
asthma
angiogenesis
endothelial progenitor cell
stromal-derived factor-1α
eosinophils
house dust mite
Circulatory and Respiratory Physiology
Immune System Diseases
Medical Immunology
Respiratory System
Respiratory Tract Diseases
Circulatory and Respiratory Physiology

abstract:
Asthma involves a systemic element that includes the mobilization and lung-accumulation of bone marrow-derived endothelial progenitor cells (EPC). This traffic may be driven by the stromal cell derived factor-1α (SDF-1α)/CXCR4 axis, where SDF1-α is a potent progenitor cell chemoattractant.

Interfering with EPC lung-accumulation by administering AMD3100, a CXCR4 antagonist, was previously shown to be associated with the modulation of airway angiogenesis and airway hyperresponsiveness. However, since eosinophils express CXCR4, it is unknown whether AMD3100 acted directly on EPC or indirectly through its anti-inflammatory effects on eosinophils.

We investigated the role that eosinophilic inflammation plays in the lung-homing of EPCs and airway angiogenesis in allergic asthmatic response by utilizing eosinophil deficient (PHIL) mice.

Wild-type BALB/c (WT) and PHIL mice underwent a chronic house dust mite (HDM) exposure protocol. Treatment groups were administered AMD3100. Outcome measurements were made 24hrs post final exposure and included: flow cytometry to enumerate lung-extracted EPCs, immunostaining for von Willebrand factor to assess bronchial vascularity, bronchoalveolar lavage for airway inflammation, haematoxylin and eosin stain to enumerate eosinophils, picrosirius red stain to assess collagen deposition, and measurement of airway resistance to increasing intranasal doses of methacholine.

HDM exposed mice had a significant increase in EPC lung accumulation, bronchial vascularity, airway inflammation, collagen deposition and airway hyperresponsiveness (AHR) in both WT and PHIL groups, with some indices at lower levels in PHIL mice. Concurrent treatment with AMD3100 significantly attenuated EPC lung homing, bronchial vascularity, eosinophil numbers in lung tissue and AHR, but not collagen deposition in WT mice. AMD3100 treatment significantly attenuated all indices in PHIL mice.

The findings of this study show that, EPC-driven angiogenesis and the development of AHR in allergic airway responses are independent of eosinophils, the presence of these cells, however, may have a role in worsening of the pathology of allergic airways disease.

abstract: Master of Science (MSc)


title: Non-Equilibrium Topographies: Surface Tension Driven Flows Reveal Polymer Properties at the Nanoscale

contributor:
Dalnoki-Veress, Kari
Shi, An-Chang
Rheinstädter, Maikel
Physics and Astronomy

subject:
polymer
thin films
experimental
nanofluidics
entanglement
condensed matter
Condensed Matter Physics
Fluid Dynamics
Condensed Matter Physics

abstract: The most important results in this thesis are those concerned with the levelling of a stepped film’s height profile. Films are prepared such that their height profiles are well described by a Heaviside step function and to a good approximation, they are invariant in one dimension. The temporal dependence of the levelling gives rheological information about the molecules making up the stepped films. For the range of heights that is much larger that the typical size of molecules making up the film, we use classical hydrodynamics to model the flows in these stepped films. Having measured the temporal and geometric dependence of the energy dissipation in time, we find that the hydrodynamic models are in excellent agreement.

abstract: Doctor of Philosophy (PhD)


title: Steroid transfer between conspecifics and its potential impacts on the reproductive endocrinology of female mice

contributor:
deCatanzaro, Denys
Psychology

subject:
estradiol
progesterone
[3H]steroids
pheromones
steroid transfer
reproductive endocrinology
Endocrinology
Endocrinology

abstract: Sex steroids are critical for the post-natal development of the female reproductive system, and are involved in ovulatory cycling and pregnancy. In mice, Mus musculus, female development, cycling, and pregnancy can be affected by the urine of conspecifics, which is known to contain active steroids. Specifically, puberty can be accelerated (the Vandenbergh effect), estrous cycling can be prolonged (the Lee-Boot effect) or synchronized (the Whitten effect), and blastocyst implantation can be disrupted (the Bruce effect). Since steroids alone can affect females in ways that are indistinguishable from these social reproductive effects, I hypothesized that urinary steroids of conspecifics may be absorbed by females, arrive in the reproductive system, and thereby affect females through known mechanisms. First I showed that tritium-labelled 17β-estradiol (3H-E2) injected into males is excreted in their urine, and that application of urine from these males to the nose of an inseminated female results in detectable levels in her uterus. When I paired inseminated females with non-sire males injected with 3H-E2, radioactivity was detected in the brain and reproductive tissues of the females. This was the first demonstration of steroids from one animal directly entering the body of another. Similar results were found when I exposed juvenile females to adult males injected with 3H-E2, and when I exposed nulliparous adult females to same-strain 3H‑E2- or 3H-progesterone- (3H-P4) treated adult males or females. Taken with the existing literature, these results suggest that steroid transfer may underlie various social reproductive phenomena in mice, with potential implications for many other species.

abstract: Doctor of Philosophy (PhD)