title: Regioselective and Stereospecific Rhodium-Catalyzed Allylic Substitution Reactions With Nitrile-Stabilized Anions: Construction Of Acyclic Remote Stereocenters and Chemoselective Hydrogenation of Nitroarenes to Anilines using Heterogeneous Nickel Foams

contributor:
Evans, P. Andrew
Chemistry

subject:
rhodium catalysis
nitrile anions
hydrogenation
allylic alkylation
asymmetric catalysis

abstract:
The thesis is divided into three chapters, featuring a comprehensive literature review, followed by two research chapters that are split into two different areas of research in homogeneous rhodium and heterogeneous nickel catalysis.

Chapter 1 commences with a brief introduction on nitrile-stabilized anions and historical developments on the transition metal-catalyzed allylic alkylation reaction, which is followed by a detailed account on nitrile-stabilized anions in asymmetric transition metal-catalyzed allylic alkylation reactions.  The review is divided into three major subsections focused on the type of selectivity, namely, diastereoselective, enantiospecific and enantioselective transformations featuring nitrile-stabilized anions and delineates the achievements in each area.

Chapter 2 features the development of silyl-stabilized nitrile anions in the regioselective and stereospecific rhodium-catalyzed allylic alkylation reaction for the construction of remote stereocenters.  The chapter opens with the discovery and development of the rhodium-catalyzed allylic substitution reaction and follows by highlighting the utility of organosilicon compounds with particular focus on their utility as nucleophiles in transition metal-catalyzed allylic substiution reactions. The following two sections will discuss our work on the regioselective and stereospecific rhodium catalyzed allylic cyanomethylation using a silyl-stabilized acetonitrile equivalent for the construction of acyclic β-quaternary and ternary stereogenic nitriles.  Finally, our initial progress towards the development of a regioselective and stereospecific rhodium-catalyzed allylic substitution reaction with γ-silyl allylic α-amino nitrile as homoenolate equivalents for the construction of acyclic γ-functionalized carboxylic acids shall be discussed.

Chapter 3 highlights our efforts towards the chemoselective hydrogenation of substituted nitroarenes to anilines using heterogeneous open-pore nickel foams.  After a brief introduction on the hydrogenation of nitroarenes to anilines using heterogeneous catalysis, our development of a highly chemoselective nickel foam variant of this process is discussed.  We showcase the utility of the transformation for the synthesis of highly substituted anilines using mild conditions.  Additionally, the structural integrity and morphology of the nickel foams are analyzed using scanning electron microscopy (SEM), which give insight into the unique etching pattern of the heterogeneous nickel catalyst.

abstract: PhD


title: Primary Fixation and Anchorage of Dental Implants in Bone Surrogate

contributor:
Ploeg, Heidi-Lynn
Mechanical and Materials Engineering

rights: Queen's University's Thesis/Dissertation Non-Exclusive License for Deposit to QSpace and Library and Archives Canada

rights: ProQuest PhD and Master's Theses International Dissemination Agreement

rights: Intellectual Property Guidelines at Queen's University

rights: This publication is made available by the authority of the copyright owner solely for the purpose of private study and research and may not be copied or reproduced except as permitted by the copyright laws without written authority from the copyright owner.

subject:
FEA
Analytical Model
Dental Implant
Primary Fixation
Anchorage

abstract: Edentulism (toothlessness) changes dietary habits resulting in obesity, diabetes, and coronary artery disease; and, thirty percent of people aged 65-74 years suffer from edentulism, globally. Dental implants, as anchors to replace the natural root of the tooth and support dental prostheses, have become a standard treatment for edentulous patients. Sufficient anchorage (mechanical engagement between bone and implant during insertion) and primary fixation (mechanical engagement under loading) of dental implants have been recommended for positive clinical outcomes. Rigid polyurethane (PU) foam as standard bone surrogate material has been widely used in preclinical studies and dental implant designs. However, the mechanics of anchorage and primary fixation and their relationship for bone surrogate-implant system is not well understood. Two main mechanics dominate anchorage and primary fixation of dental implants: thread mechanics and press-fit established by tapered body. Therefore, the objective of this research was to comprehensively investigate effects of implant design such as tapered body on anchorage and primary fixation of dental implants in PU foam combining mechanical experiments, analytical models, and finite element analyses (FEAs). A new analytical model for the insertion torque (IT) was proposed to differentiate contributions of the thread and press-fit mechanics on IT with two parameters: effective force, F^', and effective pressure, p^'. Including the PU foam damage during insertion and under loadings, FEA models for both insertion and primary fixation presented in this study were validated against experimental results. By combining the mechanical testing, analytical modelling and numerical modelling, this research found: the dental implant insertion process played a crucial role in primary fixation; tapered implants with high insertion press-fit and non-zero p^' promoted anchorage with high IT, and primary fixation with lower implant motion and higher bone surrogate-implant stiffness under an axial loading compared to parallel-walled implants. These major findings not only contribute a unique dataset to current dental biomechanical field but also provide new findings and assessment methods for anchorage and primary fixation of dental implants. This research work presents new understanding of the mechanics of dental implant anchorage and primary fixation and new methods in support of dental implant design and their preclinical assessment.

abstract: PhD


title: (Re)Defining Nonsense Literature as an Intermedial Genre

contributor:
Willmott, Glenn
English Language and Literature

subject:
Intermediality
Nonsense Literature
Literary Nonsense
Comics Studies
Image and Word
Lewis Carroll
Edward Lear
Nonsense Verse
Nonsense Prose
Contemporary Literature
Canadian Literature
Edward Gorey
Dr. Seuss
Shel Silverstein

abstract: This dissertation argues that literary nonsense is an inherently intermedial genre and offers a new definition of the genre based on this understanding. Focusing on media that combine image and word – including picture books, illustrated verse, graphic novels, comic books, comic strips, magazines, zines, and more – this dissertation explores how nonsense is generated between the verbal and visual components of the text, offering four new categories of visual/verbal nonsense combinations. From this new perspective, the study then explores how nonsense storyworlds and world building are generated across media before offering a new taxonomy and discussion of nonsense characters. In both these sections, the focus is on building a set of criteria to differentiate between nonsense settings/characters and other, similar genres (such as fantasy or science fiction). The next section looks at format, exploring how changes in the genre often come from innovation in format and offers a loose overview of the genre since the Victorian period to more contemporary additions, expanding the canon to include various forms of comics and independent/self-published texts. The next section also focuses more on contemporary texts and expands the canon by looking at contemporary nonsense content, with a specific focus on women’s, racialized, and queer nonsense, arguing that each of these categories represent a distinct subgenre. In the conclusion of the project, the focus shifts to potential futures for literary nonsense by looking at Canadian contributions to nonsense, with an additional analysis of the works of Marc Bell.

abstract: PhD


title: Investigating the Intensity-Dependent Molecular Signalling Response to Acute Maximal and Supramaximal Intensity Exercise in Recreationally-Active Men and Women

contributor:
Gurd, Brendon
Kinesiology and Health Studies

subject:
Exercise
Intensity
PGC-1a
AMPK
Mitochondria
Mitochondria biogenesis
High intensity interval exercise
Skeletal muscle
Molecular signaling

abstract:
Mitochondria are responsible for producing energy for our bodies - their dysfunction has been linked to numerous diseases. One of the many benefits of high-intensity interval exercise (HIIE) is that it creates more mitochondria in our skeletal muscle - a process known as mitochondrial biogenesis. HIIE induces mitochondrial biogenesis by regulating numerous signaling proteins (proteins that activate other proteins) and transcription factors (proteins that activate genes). An important transcription factor – recognized as the “master regulator” of exercise-induced mitochondrial biogenesis – is peroxisome proliferator-activated gamma coactivator 1-alpha (PGC-1α). Due to its profound role in coordinating other mitochondrial genes and transcription factors, understanding the mechanisms that underlie PGC-1α’s expression and regulation represents an important area for research

As exercise gets harder (i.e. higher intensities), PGC-1α and the proteins that 'turn on'  PGC-1α are activated in an “intensity-dependent” manner. This observation is consistent as long as exercise bouts occur below the power output associated with maximal aerobic capacity (aka submaximal intensities). However, there is a knowledge gap within this intensity-dependent relationship at exercise intensities past maximal to supramaximal efforts. Thus, our main question was “is there a threshold of intensity where more effort becomes less beneficial?”

Our results indicated that between work-matched maximal (max) and supramaximal (supra) HIIE, though exercise at supra intensities was significantly harder (RPE: p < 0.05) and physiological stress was significantly higher (Blood lactate: p < 0.05), post-exercise increase in PGC-1𝛼 expression (p<0.001) and proteins that turn on PGC-1𝛼 (p<0.05) did not differ between intensities (p = 0.71; p = 0.08 ). Therefore, our findings demonstrate that supramaximal intensities of exercise do not elicit greater molecular adaptations (Upstream PGC-1𝛼 signaling and gene expression) in skeletal muscle.

abstract: M.Sc.


title: Kinesthetic Haptic Actuators: A Comparative Study of Motor Technology

contributor:
Hashtrudi-Zaad, Keyvan
Pahlevani, Majid
Electrical and Computer Engineering

subject:
Haptics
Haptic Actuators
BLDC Motors

abstract: This thesis evaluates a BLDC motor for use as a direct drive haptic actuator. This is done by a comparison of the performance and specifications of a direct drive BLDC motor with those a of the actuator used in a common haptic device, comprised of a DC motor and capstan mechanism. To facilitate this comparison, an experimental platform, consisting of the two actuators and all associated mechanical and electrical systems, was constructed. The actuators are compared using a variety of metrics, which were first calculated using time-domain, Laplace-domain, and discrete time models, as well as PSIM simulation. The comparison metrics were then determined experimentally and compared. These metrics include datasheet parameters, peak torque determined using a thermal simulation, current and position step responses, uncoupled stability regions, and rendering areas. Based on this comparison, it can be concluded that a direct drive BLDC motor offers both a higher peak and continuous torque, while having lower inertia and therefore higher acceleration than the DC motor and capstan. The DC motor and capstan is lighter than the BLDC motor, but has significantly more friction. Because on these differences, the BLDC motor has a larger rendering area than the DC motor and capstan, as well as a larger uncoupled stability region. These results indicate that BLDC motors are a promising technology for effective direct drive haptic actuation.

abstract: M.A.Sc.


title: Understanding Strategy Monitoring and Real-World Transfer in Cognitive Remediation Within the Context of Mood and Psychotic Disorders

contributor:
Bowie, Christopher
Psychology

subject:
Cognitive Remediation
Cognition
Functioning
Outcomes

abstract: Cognitive Remediation (CR) is a behavioural intervention designed to enhance cognitive abilities and improve functioning in several psychiatric disorders. CR programs involve cognitive training as well as therapist-facilitated procedures for strategy monitoring and the transfer of cognitive skills and strategies to real-world activities. Research focusing on strategy monitoring and real-world transfer treatment processes has been limited to date. Chapter 2 of this dissertation examined correlates of strategy monitoring and transfer skills development, and the relationships of these skills with treatment outcomes. Results showed that participants with less impaired baseline neurocognition produced higher quality strategies at session one. Over treatment, there was a significant improvement in strategy quality among more neurocognitively impaired individuals, but not among less neurocognitively impaired individuals. By the final session, participants with different levels of baseline neurocognitive impairment generated strategies of comparable quality. Additionally, participants at all levels of baseline real-world functioning showed improvements in transfer skills, however, individuals with higher baseline real-world functioning consistently produced higher quality transfer ideas from the beginning through the end of treatment. In terms of treatment outcomes, the development of strategy monitoring skills was associated with improvements in neurocognition, whereas the development of transfer skills was associated with improvements in real-world functioning. Chapter 3 examined the reliability and validity of a novel clinician-rated measure of strategy monitoring and real-world transfer skills. The strategy monitoring and transfer subscales showed evidence of good and moderate inter-rater reliability, respectively. Regarding validity, the strategy monitoring subscale showed evidence of convergent and discriminant validity, while the transfer subscale showed evidence of discriminant validity. Together, these studies support the notion that strategy monitoring and real-world transfer are active ingredients of CR, and build on existing research by developing a novel clinician-rated measure of these skills. Our studies represent a promising step toward developing a measure for use in empirical research and clinical settings implementing CR, however, further revision is needed.

abstract: PhD


title: Petroleum Activities in Disputed Maritime Areas: Guyana, a New Petroleum Frontier

contributor:
Pardy, Bruce
Law

subject:
international law
maritime law
treaties
joint development agreement
unitization agreement
rule of capture
law of the sea
petroleum
oil and gas law
environmental law

abstract:
New emerging oil and gas exploration and production frontiers like Guyana need clarity on the legal framework governing oil and gas law exploration and production in disputed maritime territories. The existing literature in this area fails to provide a comprehensive analysis of the possible solutions to resolving such disputes from a positivist international law perspective. This work attempts to fill that gap and provide an outline of the legal obligations and restrictions concerning oil and gas development and exploration which can be undertaken in a unilateral manner. This is an area of law which can have huge economic implications for the states concerned and it is therefore very important to promote certainty to the extent possible, about the legal framework in this area. This thesis will clarify the law in this area for states like Guyana, investors, international oil companies, and other relevant stakeholders. It attempts to clarify the legal rights and obligations to conduct unilateral petroleum activities in disputed maritime zones and the legal status of absolute and permanent sovereignty over petroleum resources in the maritime zones.
My dissertation advances a limited argument about the positivist international law approach and its application to the area of maritime law under review. It examines several relevant sources of international law in this area. It argues that the positivist international law approach helps to promote certainty to a certain extent, and the peaceful settlement of disputes. Apart from the positivist approach to international law in the area under review, another point which is examined in this dissertation is the modern conception of state sovereignty. It demonstrates how state sovereignty is impacted by the development of maritime law and the control of resources in offshore areas. It also demonstrates that the current state of the law is certain only to the extent that absolute sovereignty doesn’t exist.
Some of the principal conclusions of this research include that the requirements for the formation of customary international law from a positive international law perspective promotes certainty in the law. This research also concludes that treaties such as joint development zone agreements and unitisation agreements are good examples of positive sources of international law which help to provide solutions for maritime boundary disputes. However, these agreements do not represent customary international law. It argues that there is a customary international law requiring states to cooperate but there is no customary international law requiring states to enter into joint development zone agreements and unitisation agreements. It also concludes that there is no customary international law creating a rule of capture in international law. Importantly, it also discusses the varying degrees of limitations on state sovereignty in the various maritime zones, such as in the exclusive economic zone and the continental shelf. Another conclusion is that Articles 74(3) and 83(3) of United Nations Convention on the Law of the Sea (UNCLOS)  are useful to help resolve maritime boundary disputes, but these treaty provisions do not reflect customary international law obligations. The point here is that there is often a leap from treaty law to customary international law and I will closely examine the relationship between the two to demonstrate that the criteria for the establishment of customary international law are not satisfied in this instance.

abstract: PhD


title: Defining the Neurochemical Phenotype of Myenteric Neurons that Display Nerve Growth Factor Promotor Activity in Adult Transgenic Mice - Implications for Colonic Inflammation

contributor:
Kawaja, Michael
Neuroscience Studies

subject:
Myenteric
NGF
Nerve growth factor
Colon
Inflammation
Pain

abstract: Nerve growth factor (NGF) has demonstrated a wealth of functions in the body in addition to the neurotrophin’s main growth effects on sensory and sympathetic axons. Although this neurotrophin is well-studied, the specific function of NGF-producing neurons of the myenteric plexus has yet to be characterized. Using transgenic mice that express enhanced green fluorescence protein (EGFP) under the control of the NGF promotor, we provide evidence for a role in nociceptive signalling by NGF in the inflamed colon. Gut inflammation induces the increased production and release of NGF from specific myenteric neurons. These NGF-producing neurons express and upregulate the pain-signaling peptide, calcitonin gene-related peptide (CGRP) in surrounding clusters of neurons. This study demonstrates high colocalization of CGRP and the nociceptive signalling, ATP-gated ion channel, P2X purinoceptor 3 (P2X3) in myenteric NGF-producing neurons and surrounding neuronal clusters. The induction of sensory axonal growth around these clusters by NGF, functionally increases the gut’s ability to perceive and respond to painful stimuli. These results suggest that NGF-regulated neuron clusters transmit chemical signals concerning gut condition to sensory axons of the DRG in the mouse myenteric plexus, following the inflammation-mediated release of CGRP and ATP. This alludes to the function of NGF as a pain sensitizing factor of the descending colon in response to inflammation.

abstract: M.Sc.


title: Large-eddy Simulations of the Flow over Airfoils with Leading-Edge Roughness

contributor:
Piomelli, Ugo
Mechanical and Materials Engineering

subject:
Large eddy simulation
Surface roughness
Aircraft icing
boundary-layer flow
flow separation

abstract:
We performed large-eddy simulations of the flow over a NACA4412 airfoil to understand the effects of leading-edge roughness designed to mimic ice accretion. The roughness elements protrude outside the boundary layer, which, near the leading edge, is very thin; thus, the configuration does not represent a classical rough-wall boundary layer, but rather the flow over macroscopic obstacles. A grid convergence study is conducted and results are validated by comparison to numerical and experimental studies in the literature. The main effect of the obstacles is to accelerate transition to turbulence. Significant variations in structure generation are observed for different roughness shapes. The three-dimensionality of the irregularities has a strong impact on the flow: it creates alternating regions of high-speed (“peaks”) and low-speed (“valleys”) regions, a phenomenon termed “channelling”. The valley regions resemble a decelerating boundary layer: they exhibit considerable wake and higher levels of Reynolds stresses. The peak regions, on the other hand, are more similar to an accelerating one. Implications of the channelling phenomenon on turbulence modelling are discussed.
In the second part of the thesis, we investigate further the channelling phenomenon by performing simulations at three angles of attack. Downstream of the roughness zone, the fast regions slow down under the action of hairpin vortices generated by the roughness elements, and merge with neighbouring slow regions. The flow channels remain coherent over the boundary layer developing on the suction side of the airfoil and affect the trailing-edge separation. With increasing angle of attack in the linear- lift regime the intensity of flow-channelling can increase or decrease depending on the topology of the leading-edge roughness. Its effect on the trailing-edge separation remains, however, significant. The mean-separation line is highly distorted, and the separation length can vary by up to 30% of the chord length along the span.

abstract: PhD


title: Inhibitory Control Changes in Healthy Aging, Alzheimer’s Disease and Amnestic Mild Cognitive Impairment: An FMRI Study of the Stroop Task

contributor:
Munoz, Douglas
Neuroscience Studies

subject:
Alzheimer's Disease
Amnestic Mild Cognitive Impairment
Healthy Aging
Stroop Task
Inhibitory Control

abstract: Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by impairments in cognition coupled with a predictive pattern of neural atrophy beyond changes associated with healthy aging. Divergence from normative aging occurs years before clinical diagnosis of AD, a prodromal period classified as amnestic mild cognitive impairment (aMCI). Inhibitory control has been investigated across healthy aging, AD and aMCI through utilization of the Stroop task. Inhibition is required to suppress the automatic reading response in order to identify the ink color of word stimuli with matching (congruent) or non-matching (incongruent) ink color. Whether differences exist behaviorally, or if compensatory brain mechanisms to maintain task performance occur across these groups remains unclear. To address this knowledge gap, we utilized functional magnetic resonance imaging (fMRI) to evaluate the relationship between behavioral measures, neural correlates, and functional connectivity during performance of the Stroop task in young, middle-aged, and older adults, as well as patients with AD and aMCI. We found evidence of over-recruitment in middle-aged adults, which became more discernable after age 65 with both over-recruitment and loss of specificity to stimuli. Despite changes detected using fMRI, behavioral performance was similar across groups, with generalized slowing in older adults. Patients with aMCI performed similarly to controls, however showed reduced BOLD response within the parietal ROIs and over-recruitment of frontal ROIs when faced with incongruent trials. Patients with AD did not elicit different activity from controls in any ROI but did produce significantly more incongruent errors. Patients with AD had reduced functional connectivity in frontal brain areas, which correlated with default mode network (DMN) seeds. Functional connectivity was similar between aMCI and controls, suggesting that functional connectivity of Stroop and DMN ROIs remain spared early in the disease. Our results suggest that reaction times alone may not be sensitive enough to show changes in aging or aMCI, but incongruent errors may be particularly useful at discriminating AD. Our studies support the literature indicating compensation, as we found evidence of neural plasticity in both healthy and pathological aging. Methodological factors including Stroop design, fMRI analysis, and participant variability may contribute to inconsistencies within the literature.

abstract: PhD


title: The Matter of Britain:  How the Tudors Adapted British Historic Tradition to Legitimise their Dynasty

contributor:
Woolf, Daniel
History

rights: Attribution-NonCommercial-NoDerivs 3.0 United States

subject:
British History
Welsh History
English History
British Isles
Arthurian
Galfridian
History of Memory
Historry of Ideas
Political History
Mythology
Nation
Nationalism
Britain
England
Wales
Shakespeare
Henrician
Elizabethan
Tudor
Early Modern
Medieval
Imperialism
Cartography
Chronicles

abstract: The subject of this paper is the relationship between the Tudors who ruled England 1485-1603 and their Welsh ancestry. The Welsh of the sixteenth century viewed themselves as Britons with a tradition dating back before Roman Britain. Recent scholarship has highlighted the ongoing importance of Welsh and British narratives in Tudor England. This thesis shows that the importance of the British past to the Tudors is not a series of isolated instances but clearly related parts of an ongoing discourse by them to legitimise their claims to authority. Whether initially with the weak genealogical claims to the throne with Henry VII, or the supremacy over the Church in England during the Reformation, or even at the end of the sixteenth century when Elizabeth I began to sponsor what would become the British Empire. The Tudors successfully applied their British pedigree to the crises of legitimacy throughout the sixteenth century and created a new concept of Britain, a Tudor Britain.

abstract: PhD


title: Geomechanics of hydrothermal veins: Insights from laboratory direct shear and numerical triaxial experiments

contributor: Geological Sciences and Geological Engineering

subject:
Geomechanics
Rock mechanics
Triaxial Compressive Strength
TCS
UCS
Uniaxial compressive strength
DS
Direct Shear Strength
RS2
Numerical modelling
Numerical calibration

abstract:
Geotechnical rockmass strength characterization is a task regularly undertaken by rock engineering practitioners for underground and open pit excavations. As the demand for mineral resources drives extraction into deeper, more challenging and complex geological environments, the effect of intrablock structure is commonly overlooked in conventional field and laboratory characterization practice though it may be particularly important to rockmass behaviour in high stress environments. This research focuses on the characterization of the shear strength of intact hydrothermal veins through laboratory direct shear and triaxial numerical experiments. Direct shear testing of basaltic and dacitic rocks with calcite veins produced recommendations for direct shear sample selection and preparation, and a greater understanding of the challenges with testing intact specimens in direct shear was gained. Laboratory uniaxial compressive strength and triaxial compressive strength results of mafic rocks with and without sulfide veins from the El Teniente mine were used to calibrate numerical input parameters for triaxial simulations of veined core specimens. This investigation, whereby the vein orientation and vein thickness of veined specimens was systematically varied, was used to evaluate the effect of sample geometry on strength and elastic model output properties, with the ultimate purpose of being used to represent intact joints in excavation scale models.
Vein orientation played the most significant role on peak strength with the highest reduction in strength, compared to the homogeneous wallrock, occurring in samples with veins oriented at 20° < α < 35°. To incorporate the results of the laboratory scale tests of intact veins into excavation scale numerical models, the practitioner must decide which method will be utilized for the excavation scale model. To include veins as discrete structures in the excavation scale model, the shear strength of the fractured vein in the laboratory scale model should be calculated. For this method, a range of vein orientations must be tested at a variety of confining pressures. Alternatively, the intact rock strength can be modified to account for the presence of the veins and in this case, the strength of the laboratory scale specimens as a whole should be utilized.

abstract: M.A.Sc.


title: A Tensor Decomposition Method for Calculating Vibrational Energy Levels of Molecules

contributor:
Carrington, Tucker
Chemistry

subject:
vibrational energy calculation
tensor decomposition format
CP format
MSBII
inverse iteration

abstract:
Computation of vibrational energy levels of molecules is useful for predicting and interpreting experimentally observed spectra. It is also used to analyse and generate potential energy surfaces. Standard techniques for calculating vibrational energy levels of polyatomic molecules by solving time independent vibrational Schrödinger equation, suffer from the so-called curse of dimensionality: the exponential increase of the cost of the calculation with the size of the molecule.
We developed a method that avoids storing large vectors and matrices. We use a tensor format called Canonical Polyadic (CP) format to represent vectors. As a result,  the memory cost scales linearly with the dimensionality of the molecule. Our method of solving the Schrödinger equation is called the Multiple Shift Block Inverse Iteration(MSBII) eigensolver. In CP format a vector is represented as a sum of terms. An Alternating Least Squares (ALS) approach is used so that the number of terms in the CP vectors is constant. We improved the MSBII method by using a tree-like structure, thereby solving Schrödinger equation sequentially in reduced dimensions. This improvement results in a significant reduction in the CPU time of the calculation. These ideas are tested by computing vibrational energy levels of a 64-D bilinearly coupled model Hamiltonian and acetonitrile (12-D) molecule.

abstract: PhD


title: Have lakes within the Rideau Canal system responded to impacts of recent anthropogenic stressors over the past ~25 years: A diatom-based paleolimnological re-assessment

contributor:
Smol, John
Paterson, Andrew
Biology

subject:
Diatoms
Paleolimnology
Rideau Lakes
Climate Warming

abstract: Earlier paleolimnological studies examined diatom compositional changes in dated sediment cores retrieved ~25-30 years ago to track long-term environmental impacts following the construction of the Rideau Canal (ca. 1828). My thesis examines sedimentary diatom records collected in 2019-2020 from these same study lakes [(i.e., Big Rideau L., Indian L., Upper Rideau L., Lower Rideau L., L. Opinicon, Otter L. (canal reference)], focusing on the most recent lake responses (post-1990) to multiple environmental stressors (i.e., climate warming, shoreline development, zebra mussels) by examining changes in diatom composition, spectrally inferred chlorophyll-a, and water quality monitoring data (TP and Secchi disk depth). The most notable diatom compositional changes in the ~150-year sediment records occurred in the past ~25-30 years across all of the study lakes despite intense, early 19th-20th century cultural disturbances within the Rideau Canal system (e.g., deforestation, flooding). This response to recent environmental stressors was registered as increases in planktonic diatom taxa with concurrent declines in Aulacoseira taxa in the majority of our study lakes (excluding Upper Rideau L.). However, in Big Rideau L., this recent response also included a shift among planktonic taxa, as well as a clear increase in epiphytic diatoms. These recent shifts in diatom assemblage composition could not be explained by nutrient enrichment, as measured TP concentrations have declined significantly in all lakes since the 1970s. The recent diatom compositional shifts also pre-date the documented arrival of zebra mussels within the Rideau Canal system (ca. 1990). Instead, these recent changes could be best explained by accelerated regional climate warming, particularly significant increases in air temperatures and declines in wind speed, affecting the physical and thermal regimes of these lakes. These conditions allowed for the proliferation of small cyclotelloid and elongate planktonic taxa, while heavier Aulacoseira taxa were less competitive, as well as the recent emergence of cyanobacterial algal blooms despite the lack of nutrient increases. The nature and magnitude of diatom compositional change over the past ~ 25-30 years appears to track a response to limnological changes linked to warming, which are a continuation of diatom assemblage trends initially observed in the earlier paleolimnological studies.

abstract: M.Sc.


title: Nonlinear Optical Generation of Multimode Entangled Squeezed Thermal States

contributor: Physics, Engineering Physics and Astronomy

subject:
Squeezed light
Entanglement
Nonlinear quantum optics

abstract: Squeezed states of light exhibit a reduction of quantum noise in one of their phase-space quadratures. They can be generated via a nonlinear interaction  between a laser and  a nonlinear dielectric material. Multimode squeezed states of light contain entanglement in the form of correlations between the quadratures of the modes in the state. Scattering loss in the dielectric material used to generate the squeezed state reduces the amount of squeezing and the strength of the correlations between the modes in the state. In this thesis, I consider the nonlinear generation of multimode squeezed states in resonant structures. The modes of these structures are inherently lossy due to scattering and coupling loss and also form a nonorthogonal basis in general. The central result of this thesis is that I show the analytic solution of the Lindblad master equation for the density operator of the generated light in the multiple lossy nonorthogonal modes of a structure has the form of a \textit{multimode squeezed thermal state}. I show that  using the analytic solution makes it fast to calculate the amount of quadrature squeezing and the strength of  the correlations between modes in the state as a function of time. I apply this theory to the nonlinear generation of a single-mode and two-mode squeezed thermal state in a microring resonator, and I optimize the coupling parameters of the ring to maximize the squeezing in the presence of loss or to obtain a two-mode squeezed thermal state in which the two modes are highly-correlated despite the loss. In addition, I derive a squeezing criterion that if the multimode squeezed thermal state obeys it can be considered as a  cluster state and be used for continuous-variable quantum computing. Therefore, the multimode squeezed thermal state is the natural state to describe the nonlinearly generated light in systems of coupled-cavities and it provides a simply way to incorporate loss into a practical theory of entangled squeezed light generation, which opens a path to optimize this light for applications in quantum technologies.

abstract: PhD


title: Cosmopolitan Guilt: Reading African Narratives of Children in Crisis

contributor:
Bongie, Chris
English Language and Literature

subject:
Cosmopolitanism
African crisis literature
Mariatu Kamara
Ishmael Beah
Bite of the Mango
A Long Way Gone
Cosmopolitan guilt
Affect
Empathetic reading

abstract: This dissertation investigates how literature that depicts turbulent events taking place in foreign locations demands to be read through a cosmopolitan lens. This becomes particularly relevant for Western readers such as myself when they encounter real-life stories about children in crisis and are forced to navigate their emotional reactions to learning about this suffering. At its core, cosmopolitanism is an outlook that captures the feeling of being a citizen of the world. This belief encompasses an array of ethical responsibilities. Crisis narratives (such as memoirs about African children in crisis) challenge cosmopolitan believers’ worldviews by testing their local and global solidarities to close and distant neighbors. To unpack how cosmopolitanism functions as a “natural” method for people to relate to and understand each other across geographical and cultural divides, it is important to look at how it has been conceptualized by philosophers in the past and in our own globalized present, a theoretical overview that I undertake in the opening two chapters of this dissertation. I conceptualize cosmopolitanism as an approach that allows readers to use their imagination (i.e. their ability to create meaning using their awareness of the world) to understand and identify with the conditions of the characters in the text as fellow global citizens. In the remaining chapters, I engage in a close analysis of two primary texts, the memoirs Bite of the Mango by Mariatu Kamara and A Long Way Gone by Ishmael Beah, in order to flesh out the process through which Western readers such as myself and African storytellers such as Kamara and Beah do, and do not, interact as cosmopolitan agents and to explore how reading as a cosmopolitan act reveals both the reader’s and the storyteller’s views on local and global issues.

abstract: PhD


title: Immanent Criticism as Method in Social Philosophy: Avoiding the Risks of Arbitrariness and Authoritarianism

contributor:
Sypnowich, Christine
Philosophy

subject:
critical theory
social philosophy
immanent critique
left-Hegelianism
social pathology

abstract: The subject of this dissertation is immanent critique as a critical methodology in social philosophy: what its core features are, what kind of claim to rational validity it can make, and how we should understand the processes of social change to which it aims to contribute. Drawing on the recent work of Axel Honneth and Rahel Jaeggi, I show how a wholly immanent approach to social criticism allows us to criticize society on explicitly ethical grounds, in terms of whether our social relations enable or obstruct the flourishing of participants. I argue this is possible because the norms against which we can measure social formations are said to be produced as an immanent part of their historical development and ongoing reproduction. This involves giving a social ontological account of what I call ethical norms: norms embedded in social practices that confer normative obligations on to participants in terms of their occupying specific social roles. Once we have an account of what a social formation is, we can evaluate whether a given institution or social formation is behaving as the kind of thing that it is, by asking whether it is successful in solving the problems it posits as worth solving, or whether it regularly comes into contradiction with and violates the normative expectations that participants have for it. Consequently, the immanent social critic can justify the judgment that their form of life is unhealthy by (i) reconstructing the norms which are already effective in establishing and regulating ethically significant social practices, (ii) explaining their (defeasible) authority in relation to the members of a particular ethical community, and (iii) explaining how or why they are inadequately realized. Ultimately, I argue that the principle of immanence not only best explains how social critics can acquire authority in addressing a particular audience without becoming dogmatic or authoritarian in their prescriptions but enables a wider account of the immanent normativity of social life than do modern neo-Kantian approaches to normative theory.

abstract: PhD


title: Schizoanalytic Floorplanning and Curatorial Refrains

contributor:
Lord, Susan
Cultural Studies

subject:
curatorial
curation
curatorial research
cultural studies
curating

abstract: While art institutions are beginning to decolonise, curating is integrating uneasily with likewise decolonising university pedagogical structures and discourses. Simultaneously, the professional is surrounded by new amateur and consumerist “curation” and “curatorial subjectivities” emerging in neoliberal society. This project seeks to contribute critically to curatorial practice and studies by considering pathways made possible by the conjunction of different models of the curatorial. It rereads a portfolio of five of my texts published over the last ten years; speaking as a practitioner, the project applies a curatorial research method to reorganise and reread the portfolio of my own writing for gallery publications on artistic projects by Ciara Phillips, Les Levine, Yam Lau, Chris Kline, Ibghy and Lemmens, Nadia Lichtig, Josèfa Ntjam, Anne Riley and Jol Thoms. A critical and speculative framing text borrows theoretical tools from Félix Guattari’s militant “meta-modeling” to forage for components of mental and social ecologies of the curatorial and explore the potential of curating and thinking with the notion of the refrain. This new curatorial essay folds the portfolio across an interpretation of schizoanalytic cartography. Attending to broader ecologies that condition the breaks and sutures of curating, the curatorial and curation, the project speculates on a direction of curatorial practice-studies; so that it might venture off its foundations and develop a processual, listening, and trans-disciplinary ethos, I chart movements through a mental ecology toward a yet-speculative intervention in the social ecology of the curatorial.

abstract: PhD


title: Examining the structure and role of the C-terminal tail domain of a motile microtubule-depolymerizing kinesin

contributor:
Allingham, John
Biochemistry

subject: Biochemistry Protein Kinesin Microtubule

abstract: Kinesins are a family of force-generating enzymes that transport cellular cargos along microtubule trackways and restructure the mitotic spindle to segregate chromosomes. Members of the kinesin-8 family possess the dual ability to move along microtubules and change microtubule structure by actively removing αβ-tubulin subunits from microtubule ends. Some kinesin-8s combine these two activities to regulate the length and position of the mitotic spindle to ensure that divided nuclei reach the center of daughter cells at the end of mitosis. These activities are mainly powered by their highly conserved motor domain, but where and when they act is tightly regulated by their unique C-terminal tail domain. This thesis examined the structure and function of two distinct regions of the tail domain of kinesin-8 in the opportunistic human fungal pathogen Candida albicans (Ca). The region closest to the C-terminus, dubbed the distal tail, was found to harbour an additional microtubule binding interface that is also capable of binding curved tubulin rings and tubulin dimers using electrostatic interactions. Evidence is provided that the microtubule binding site of the distal tail overlaps, at least in part, with the motor domain. The other region of the C. albicans kinesin-8 tail, named the proximal tail, does not overtly associate with microtubules. Instead, this part of the kinesin seems to form a structure that tethers two kinesin-8 proteins together as a homodimer.  The protein structure model prediction platforms, AlphaFold and AlphaFold Multimer, predict that the proximal tail folds as a nine-helix bundle that dimerizes with the help of a predicted coiled-coil forming helix that is immediately N-terminal to the proximal tail. Sedimentation velocity analysis of a purified proximal tail construct supports dimer formation in solution. Together, these findings expand our knowledge of the structural configuration of kinesin-8s and reveal more about how the unique C-terminal tail domain of kinesin-8s regulates the motile and microtubule remodelling activities of the motor domain.

abstract: M.Sc.


title: What About Women coaches? An Examination of Barriers and Facilitators that Affect Progression in Leadership Roles

contributor:
Côté, Jean
Kinesiology and Health Studies

subject:
women coaches
leadership
personal assets framework
timeline interview

abstract:
Although we are aware of the underrepresentation of women coaches, the problem persists in both the literature and within the field (Norman et al., 2018). The underrepresentation of women coaches across sport suggests that sport structures and organizations privilege men and perpetuates a highly gendered system (Reade et al., 2009). Underrepresentation of women in coaching can often be attributed to external, social, and structural barriers, such as unequal assumptions of competence, hiring from principle similarity, homophobia, microaggressions, and a lack of role models (LaVoi et al., 2019; Norman & Simpson, 2022). With this in mind, the purpose of the present study was to highlight the experiences of women coaches who have sustained a career in coaching by exploring the facilitators and barriers that affected their progression toward important leadership roles within the sport system.
Participants consisted of 13 engaged, four partially engaged, and three disengaged model women coaches who were asked to reflect upon their unique leadership journeys. The participants were recognized by sport governing bodies as “model” because of the positive impact they had on their athletes for a sustained period. Data was collected following a two-phased interview approach. In phase one, the coaches were asked to create a career timeline by reflecting on their coaching roles and positions that were then separated into early and late stages. In phase two, open-ended questions focused on coaches’ career facilitators and barriers in the coaches’ early and late stages. Interview transcripts were analyzed using a thematic analysis. The results indicate that career progressions were facilitated by intrinsic motivations of growth, supportive mentors, and a passion for sport. The coaches also discussed many barriers including having to ask for respect, unrealistic expectations, and balancing work and life.
Herein, we summarize the relevant literature about women coaches, describe the methodological processes adopted for this study, present the results, discuss the theoretical and practical implications of the findings, and conclude by highlighting the study's strengths, limitations, and possible future directions.

abstract: M.Sc.


title: Development of a Quantitative Microbial Risk Assessment for Private Drinking Water Wells in Rural and Remote Ontario

contributor:
Majury, Anna
Hynds, Paul
Brown, Stephen
Environmental Studies

subject:
private water wells
quantitative microbial risk assessment
waterborne illness
groundwater

abstract: The province of Ontario comprises the largest groundwater reliant population in Canada serving approximately 1.6 million individuals. Private well users are responsible for ensuring the potability of their own private drinking water source through protective actions (i.e., water treatment, well maintenance, and regular water quality testing).  Infections associated with private drinking water wells are rarely documented given their sporadic nature, thus the human health effects remain relatively unknown, representing a significant gap in water safety management and public health action.  In the absence of regulation and limited surveillance, quantitative microbial risk assessment (QMRA) represents the most feasible and robust approach to estimating the human health burden attributable to private wells. The current thesis sought to quantify the risk of waterborne acute gastrointestinal illness (AGI) attributed to Giardia, shiga-toxin producing E. coli and norovirus from private drinking water wells in Ontario using simulation-based hydrogeologically- and socio-cognitively- (i.e., Clusters) delineated QMRA. The effects of various geographical and societal factors on E. coli detection rates informed delineation of QMRA models. The current study employed a large groundwater quality dataset (>700,000 samples), permitting spatio-temporally-specific exposure distributions for model inputs, including private well water consumption and annual contamination duration. Developed models were used to explore the effect of varying socio-cognitive scenarios on baseline simulations. Consumption of contaminated private well water in Ontario is estimated to cause 4,648 AGI cases annually, with 3,420 and 1,228 AGI cases predicted to occur among well users located in consolidated and unconsolidated aquifers, respectively. These estimates would increase by 1,596 cases per year in the (unlikely) event of total treatment failure. Further, socio-cognitive-specific QMRA findings suggest significant differences in the level of exposure among Cluster sub-groups of private well users. Private well users within Cluster 3 are characterised by higher levels of exposure and annual illness than Clusters 1 and 2. An efficacious public health intervention would be predicted to decrease AGI cases among well users within Cluster 3 by approximately 91% (5,345 to 536 cases). Developed models provide a transferable tool for public health authorities and governments globally to preserve and protect private well water for current and future well users.

abstract: PhD


title: Characterization of Natural Anti-FVIII Antibodies and the Regulatory Role of the Gut Microbiota in FVIII Immunogenicity

contributor:
Lillicrap, David
Pathology and Molecular Medicine

subject:
hemophilia A
factor VIII
inhibitors
antibodies
gut microbiota

abstract:
Patients with hemophilia A bleed spontaneously into the soft tissues and joints due to deficiencies in the coagulation protein Factor VIII (FVIII). One-third of patients develop neutralizing antibodies to standard intravenous replacement therapy, rendering it ineffective. A significant area of research focuses on identifying risk factors associated with the development of FVIII inhibitors and investigating mechanisms of inhibitor pathogenesis. Translating this knowledge into effective strategies or therapeutics to prevent FVIII inhibitor development is highly desired. Here, we have investigated the role of the gut microbiota and natural anti-FVIII antibodies in modulating one’s risk of developing FVIII inhibitors.
	The gut microbiota is an expansive network of microorganisms that line the gastrointestinal tract and has been shown to modulate the immune system in mice and humans. We first sought to determine if the gut microbiota plays a role in regulating FVIII inhibitor development by developing a hemophilia A mouse model of antibiotic-induced gut perturbation. Gut perturbation was associated with an enhanced FVIII immune response, decreased short-chain fatty acid (SCFA) production, and an altered transcriptomic environment in the spleen and draining mesenteric lymph nodes.
	We further characterized the effects of SCFAs on immune cells and found that only butyrate was able to potently inhibit B cell function ex vivo. Attempts to endogenously increase SCFA production and inhibit FVIII inhibitor formation through a high-fiber diet yielded subtle yet significant changes in the immune response and blood metabolome, revealing complex relationships between gut bacteria and host.
	Lastly, natural anti-FVIII antibodies are found in healthy human donors but appear to enhance immunogenicity to the FVIII protein in patients with hemophilia A. We characterized this natural antibody repertoire and found striking differences in the peripheral blood between mice and humans. We discuss how these findings fit into our current understanding of FVIII inhibitor development and shed light on how natural antibodies may modulate peripheral tolerance to the FVIII protein.
	Ultimately, this work explores two unknown factors related to the FVIII immune response and highlights the diversity of influences contributing to one’s FVIII inhibitor risk profile.

abstract: PhD


title: “Any Technology Creates its Own Environment”: Progressive Education in Marshall McLuhan’s Electronic Age

contributor:
Christou, Theodore
Education

subject:
Marshall McLuhan
The Living and Learning Report (1968)
Mosaic
Progressive Education
Tools of Perception
Media
Technology
Pedagogy
The Electronic Age
1960's Ontario Education
The Medium is the Message
Communications

abstract: Published with much fun-fare, The Living and Learning Report (1968) arrived as an educational panacea for progressive, radical, technologically-savvy pedagogical approaches that would revolutionize and improve the student-focused experience. Besides much enthusiasm, the Report attracted somber criticism, especially for the absence of concrete curriculum directions. Marshall McLuhan made a presentation in support of one of the committee’s major goals: the advancing and expansion of technology within the classroom. In “Education in the Electronic Age” (1967), McLuhan proposed experimental, experiential, collaborative, student-centered, project-based, integrated learning to be achieved through “the training of [students’] perception.” The few references to McLuhan in the Report skim over his pedagogical vision, especially his notions of the “mosaic,” his media ecology and pedagogy, an “educational task,” which could “provide [the] basic tools of perception, but also . . . develop judgment and discrimination with ordinary social experience.” Largely ignored in the Report and by progressive reformers alike, McLuhan’s “mosaic,” his “kit of tools for analysis and perception,” turned out to be a missed opportunity. Rooted in his modernist training at Cambridge (1936-1942), it aims to shift attention from learning and communication approaches grounded in conventional, visually-focused, connected, continuous, static technologies--including those of the linear, alphabetic practice of print--to a genuine transformation of perception grounded in a post-visual, physical, multi-sensory, dynamic, discontinuous experience. A heuristic probe that focuses on textual and perceptual gaps or intervals (“the interval is where the action is”), McLuhan’s mosaic approaches media as sites of the transference of maximal energy across visual and acoustic fissures. Touted as a technophile who prophesized the death of the book, McLuhan’s work constitutes a critique of both technology and curricula, promoting a pedagogy of “exploration,” of experimental learning that blasts the sequential, linear, prescriptive approaches of traditional humanist learning without, nonetheless, rejecting its continued relevance. It turns out that progressive educators and reformers over the past several decades have proposed the kinds of radical changes (from open classrooms and collaborative learning to critical pedagogy and the rejection of conventional canons) contemplated by McLuhan, almost always without being conscious of the impact of his media theory and pedagogy.

abstract: PhD


title: Selection and genetic constraints on clonal investment in a perennial plant

contributor:
Friedman, Jannice
Biology

subject:
Clonality
Life history
Artificial selection
Quantitative genetics
Evolution
Mimulus guttatus

abstract: Many plant species can reproduce both clonally and sexually. Why, then do some plants invest resources into both?  The relative importance of the two modes of reproduction likely varies in different ecological conditions. The ability for selection to drive different investment strategies will depend on phenotypic variation and genetic constraints between the two modes of reproduction. Genetic correlations between traits can either facilitate or constrain evolutionary responses depending on the direction and strength of selection. Here, I use an artificial selection experiment to investigate the capacity for clonal investment to respond to high or low truncation selection in perennial Mimulus guttatus. The aims of my research are to quantify the standing variation and heritability of clonal reproduction, and then to estimate the magnitude of phenotypic responses to artificial selection on clonal growth and identify genetically correlated traits. To address these aims, I established an outbred population from field collected seed in a greenhouse, then imposed four generations of divergent, truncation selection on clonal growth for two replicate high lines, two low lines, and a control line. I used quantitative genetics to investigate additive genetic variance, heritability, and the response of clonal growth through time. I investigated how genetic correlations in life history traits measured throughout the lifecycle might constrain evolutionary trajectories. My results showed that selection elicited the predicted divergent response in clonal growth; however, high clonal lines respond more strongly to selection compared to low clonal lines. I found that selection did not drastically change investment strategies but did affect trait means among selection lines. These findings suggest that populations have greater capacity to increase clonality in the face of selection, and that selection on an increase in clonal investment might be more straightforward. This study tests a classic, yet unresolved, evolutionary question and suggests populations harbour sufficient standing genetic variation to respond rapidly to selection and that the underlying genetic architecture and trait covariation could constrain evolutionary trajectories and adaptive divergence.

abstract: M.Sc.


title: The Role of Daily Interpersonal Difficulties in the Relationship between Perfectionistic Concerns and Change in Anhedonic Depressivity

contributor:
Flores, Luis E.
Psychology

subject:
Perfectionism
Social Difficulties
Depressive Symptoms
Emerging Adulthood

abstract: Perfectionistic concerns are an individual difference factor that play an important role in predicting depressive symptoms among emerging adults. However, comparatively less is known about how and why perfectionistic concerns engender depressive symptoms among emerging adult populations. The Perfectionism Social Disconnection Model (PSDM) posits that high levels of perfectionistic concerns lead to social difficulties that consequently give rise to depressive symptoms (Sherry et al., 2016). Thus, the aim of the current study is to empirically test the PSDM and investigate daily interpersonal experiences that explain the relationship between perfectionistic concerns and change in depressive symptoms. Indicators of daily social disconnection (including daily loneliness) and daily social connection (including daily social positivity and closeness and daily emotional closeness behaviours) that may uniquely mediate the relationship between perfectionistic concerns and change in one-month anhedonic depressivity were tested. The role of trait worry in my hypothesized model was also tested. Lastly, the role of instability of interpersonal experiences in the PSDM was investigated. The current study included 133 first-year post-secondary students who completed a one-month mixed longitudinal and daily-diary study protocol. Results found that daily loneliness and daily social positivity and closeness uniquely mediated the relationship between perfectionistic concerns and change in one-month anhedonic depressivity, above and beyond other daily interpersonal difficulties and trait worry. Contrary to hypotheses, perfectionistic concerns did not predict greater instability in interpersonal experiences, and instability in interpersonal experiences did not predict change in one-month anhedonic depressivity. Overall, results underscore the critical need for future work to investigate prevention and intervention strategies that may help increase feelings of social connection and decrease feelings of social disconnection among emerging adults with high levels of perfectionistic concerns.

abstract: M.Sc.


title: Deliberating in an Emergency: Participant Experiences and Public Perceptions of Deliberative Mini-Publics on Climate Change in Canada and the United Kingdom

contributor:
Rose, Jonathan
Political Studies

subject:
political participation
deliberative democracy
climate change

abstract:
This article-based dissertation project includes three distinct empirical studies which consider different aspects of deliberative mini-publics (DMPs). A deliberative mini-public is a process in which randomly-selected citizens are gathered to learn about, deliberate on and provide recommendations dealing with a specific policy issue. These processes have become increasingly popular as a tool for policy-makers who are facing complex or controversial policy decisions, and many recent cases have considered the issue of climate change.

The introductory paper of this dissertation provides a brief history of the use of DMPs and introduces current debates in the study of DMPs, particularly in terms of their implications for political behaviour and public opinion. The first study compares the political efficacy and behaviour of DMP members before and one year after participating in a DMP (Climate Assembly UK). This study shows that members reported higher internal political efficacy, higher political capacity scores, and increases in the rates of their political participation after Climate Assembly UK. The second study asks why members chose to participate in a DMP. Drawing on interview data with participants, I find that both interest in the topic of deliberation and the design of the deliberative experience is crucial to a member’s decision to participate in a DMP. The third study outlines how DMPs have been used differently in the Canada and UK context and examines how the public perceives DMPs in these two country countries. I find no differences in public perceptions attributable to country context and a strong preference for more traditional methods of citizen engagement over the DMP model.

This project provides insights into the broader political implications of this relatively novel method of citizen participation. I contribute to debates about the capacity of citizen engagement to address the issues of democratic malaise and disengagement from traditional avenues of citizen participation.

abstract: PhD


title: Electro-optical Spiking Neurons in Silicon Photonics

subject:
Spiking Neurons
Silicon Photonics
Graphene
Nonlinear Dynamics
Neuromorphics

abstract: Artificial intelligence (AI) has shown it is capable of completing a large variety of tasks, such as prediction, control, classification, simplification, memory, and generation. These tasks are diverse and have applications in self-driving cars, medical diagnosis, physical system simplification, language tasks, and art creation. The versatility of AI is one of its greatest strengths. Currently, most machine learning tasks are performed using digital computers with graphic processing units (GPUs). These devices can perform these tasks, but their energy usage is atrocious, since these devices were not originally designed to perform AI computations. A neuromorphic system is hardware designed specifically to run AI tasks. In particular, spiking neuromorphic systems have great promise for incredible energy efficiency. Artificial spiking neurons more closely emulate the neurons in the human brain and primarily consume power when they fire a spike and are in use. The construction of spiking neurons is non-trivial due to the inherently non-linear nature of their time dynamics. There are different types of spiking neurons and their dynamical behavior involve sudden shifts (known as bifurcations) from steady state to oscillatory behavior. Simulations of these devices can be difficult due to convergence issues of studying a system that intentionally switches from stable to unstable behavior. This thesis focuses on how to create and simulate spiking systems using physics present in silicon photonic platforms. Silicon photonics is known for its scalable, high bandwidth, low-loss interconnects. Since computations in neural networks are distributed over a large number of interconnected neurons in large networks, silicon photonics is well-suited for neuromorphic devices. This thesis discusses the various types of bifurcations required for different classes of spiking neurons and gives an in depth look at simulations of three different silicon photonic devices capable of spiking. The devices are electrooptical and exhibit nonlinear optical and electrical physics. In particular, there are plenty of applications at cryogenic temperatures for spiking neural networks, so the cryo-compatibility of these effects are discussed.

abstract: M.A.Sc.


title: Predicting Atmospheric CO2 Sequestration in Ultramafic Mine Tailings using an Empirically-Derived Model

contributor:
Ghahreman, Ahmad
Davis, Boyd
Mining Engineering

subject:
Sustainability
Mining
Carbon Capture and Storage
Ultramafic
Tailings Storage Facility

abstract:
Mineral carbonation is a spontaneous reaction which sequesters carbon dioxide in mineral form. Mining companies are interested in mineral carbonation because ultramafic mine tailings can undergo this reaction and sequester CO2. In partnership with Canada Nickel Company (CNC), a junior mining company located in Timmins, ON, this project set out to quantify CO2 sequestration in CNC’s mine tailings and model CO2 sequestration in their prospective tailings storage facility (TSF).
A column experiment with 10 cm deep of CNC’s tailings determined the maximum 19 kg CO2 / t tailings sequestration capacity, reached between 56-112 days of reaction in the surface 0-1 cm layer. Reaction stopped both at the surface where the maximum conversion was reached and below the surface where reaction extent was significantly lower. Passivation of reaction throughout the column was attributed to cementation of the tailings surface from the mineral carbonation reaction, inhibiting CO2 ingress below the surface. Empirical relationships were developed for reaction passivation and depth in the column experiment. A second experiment developed empirical relationships for the effect of temperature and water saturation by estimating CO2 flux into the tailings. An empirical rate expression was proposed and used to model the rate of reaction as a function of these reaction parameters.
CO2 sequestration was modelled for three scenarios: the column experiment for tuning the model, a static TSF with a singular deposition event, and a dynamic TSF with regular deposition. The column experiment results were reproduced by tuning the model to a baseline reaction rate of 0.7 kg CO2/t tailings/day at 30% water saturation in the 0-1 cm reaction layer. The static TSF scenario estimated a net 4 kg CO2 sequestered/t tailings between 0-10 cm deep from May to October. The dynamic tailings storage facility model predicted CO2 sequestration between May and October with varying deposition cycle rates. The dynamic TSF had an optimal deposition cycle rate of 14-16 days with a net 14 kg CO2 sequestered /t tailings between 0-10 cm deep.

abstract: M.A.Sc.


title: Sensor Characterization and Fiducial Volume Studies for the NEWS-G Dark Matter Experiment

subject:
Dark Matter
NEWS-G
Spherical Proportional Counter
SPC
WIMPs
Direct Detection
Achinos
Linearity
LSM
pure methane
fiducial volume
sensor
SNOLAB
Stability
Gain
neon
argon

abstract: The evidence of dark matter from astrophysical and cosmological observations has led to the development of various detectors searching for the elusive matter. The NEWS-G detector, exploiting its low-energy threshold, has been implemented in the search for low-mass dark matter at sub-GeV masses. The development of the multi-anode \emph{achinos} sensor has enabled the detector for the low threshold in large volume SPCs thanks to the high electric field providing efficient charge collection at large distances from the center and high avalanche amplification. Two different achinos models were characterized and compared, selecting the one best suiting the experiment for dark matter search at SNOLAB. Before the SNOLAB installation, the detector was installed at LSM (Laboratoire Souterrain de Modane) where physics data were obtained in 135 mbar pure methane, thus taking advantage of the nuclear recoils on protons. Estimation of the fiducial volume was required to determine the final target mass of the detector and was achieved from \ce{^{37}Ar} calibrations. Currently, the NEWS-G detector is installed and operating at SNOLAB, undergoing background calibrations and noise reduction, and will soon begin its physics runs using neon-methane mixtures.

abstract: PhD


title: Investigating the Effects of In Utero Benzene Exposure on Murine Fetal Placenta DNA Repair Gene Expression

contributor:
Winn, Louise
Biomedical and Molecular Sciences

subject:
Benzene
In utero
Gene expression
Placenta
Non-homologous end joining
Homologous recombination
Environmental pollutant
Leukemia
Hematapoiesis
Reactive oxygen species

abstract: Benzene is a ubiquitous pollutant found in the environment, in car emissions, cigarette smoke, and at elevated levels in the industrial manufacturing of plastics, resins and dyes. Exposure to benzene results in carcinogenic and hematotoxic effects. In humans, adult exposure to the environmental pollutant is positively correlated with the development of leukemia and benzene may be associated with childhood leukemia following in utero exposure. The evidnce suggests that benzene and its metabolites are more toxic to the developing fetus, since the fetus has decreased detoxification and DNA repair abilities. While numerous studies implicate benzene crossing the placenta, being metabolized and causing oxidative stress and DNA damage ultimately leading to childhood leukemia, the mechanism by which it does this is unclear. It is possible that fetal exposure to benzene results in increased DNA damage that may be left mis repaired or unrepaired, leading to genotoxicity. By using a molecular toxicological approach, employing a CD-1 mouse in utero model, we tested whether in utero benzene exposure alters gene expression of critical DNA repair genes in fetal placentas. By conducting qRT-PCR tests for mRNA expression of critical NHEJ (non-homologous end joining) and HR (homologous recombination) genes, we showed that in utero benzene affects the regulation of 5 DNA repair genes following in utero exposure using two-way ANOVA. Xrcc4 showed significant increased gene expression at 24h, Xrcc5 showed significant increased expression at 6h, Xrcc6 showed no changes at any time point, Rad51 showed significant increased expression at 24h and Brca2 showed significant decreased expression at 2h and 6h. Results summarized in this thesis add to the growing evidence of the effects of in utero benzene exposure on fetal and placental DNA repair genes.

abstract: M.Sc.


title: A Curriculum History of Postgraduate Medical Education in Canada, 1990-2020

contributor:
Chahine, Saad
Education

rights: Attribution-NonCommercial-ShareAlike 3.0 United States

subject: Change Leadership

subject: Glocalization

subject: Competency-Based Medical Education

subject: CanMEDS Roles Framework

subject: Modified CanMEDS

subject: CanMEDS-2025

subject: GLOCALS

subject: Leadership

subject: Leadership in Medical Education

subject: Postgraduate Medical Education

subject: Leadership in Postgraduate Medical Education

subject: PGME

subject: CBME

subject: CBD

subject: Longue Durée framework

subject: Braudel’s Longue Durée

subject: exploratory sequential multi-manuscript mixed methods

subject: Multi-Manuscript

subject: Configurations

subject: Ideological factors

subject: Skinner

subject: hermeneutic approach

subject: theory of intentionality

subject: Curriculum History

subject: Historical research

subject: Archives

subject: Arksey and O’Malley Scoping Review

subject: Modified Delphi Study

subject: Pan-Canadian

subject: Consensus

subject: Curriculum Change

subject: Inclusive Governance

subject: EDII

subject: Indigenization - Equity, Diversity, Inclusion, Anti-Racism, and Accessibility (I-EDIAA)

subject: Digital Health Literacy

subject: Expert Panel

subject: think globally

abstract:
Curricular reforms and change initiatives in PGME are often reactive responses to global or local crises, risks, and opportunities. This reality renders our understanding of PGME curriculum incomplete. To better design and understand curricular change in a complex adaptive human system such as PGME, it is necessary to “think globally, act locally,” concomitantly looking back while thinking forward. Since 1990, PGME curricula in Canada has undergone many reform iterations including the EFPO project, the CanMEDS Roles framework, the CBME/CBD initiative, and the recent emergency response to the ongoing COVID-19 pandemic. To unpack these curricular transformations, contextualize drivers behind change, and examine change leadership, this multi-manuscript dissertation employed a curriculum-history approach using Braudel’s (1960) interdisciplinary Longue Durée framework in an exploratory sequential mixed methods design. This dissertation contributes to the body of knowledge in PGME by documenting national and international social, cultural, political, and ideological configurations and lived experiences that shaped PGME curricula between 1990 and 2020, providing an understanding of how the current system of training residents has evolved in Canada, and why PGME curricula is the way it is today.
In Study 1, Skinner's (2002) hermeneutic approach and theory of intentionality were utilized to thematically analyze archival collections going back to 1970. In Study 2, Arksey’s and O’Malley’s (2005) framework for scoping reviews was employed to map the literature relevant to the CBME paradigmatic shift in Canada since 1990. In Study 3, a modified Delphi study of three rounds was conducted to gain consensus from 30 pan-Canadian CBME experts about the role of change leadership and driving forces behind curricular changes in PGME over the last 30 years. The findings of the three studies suggest that change in PGME is a learning process involving stakeholders’ co-creation, contextualization, and actualization of curricular change to meet the needs of local population served. The resultant GLOCALS model calls for a distributed and participatory change leadership approach, as well as an inclusive and engaging PGME governance at the global and local levels to guide successful curricular reforms. The results further recommend the addition of digital health literacy and equity, diversity, inclusion, and indigeneity (EDII) to the CanMEDS-2025 version.

abstract: PhD


title: Gregory Palamas and Demetrios Kydones on God, Knowledge, and Humanity  at the End of Byzantium

contributor:
Greenfield, Richard
History

subject:
Byzantium
Byzantine history
Hesychasm
Gregory Palamas
Demetrios Kydones
Orthodoxy
Existential Threat
Epistemology

abstract: Palaiologan Byzantium is conspicuous not only for the gradual erosion of its autonomy and any pretence to empire, but also for the severity of its religious controversies. Among these, the so-called "Hesychast Controversy" of the fourteenth century has proven to be as difficult now to characterize as it was impossible then to ignore. Modern scholarship has described it variously as a conflict between the monastery and the secular church, between traditionalists and innovators, and between the advocates of a mystical theology and those who favoured a dogmatic or philosophical alternative. While there is truth to each of these descriptions, they are also misleading insofar as each is incomplete. The present dissertation proposes a way of integrating and expanding some of these characterizations. In particular, it attempts to consider what the debates of the early and late controversy reveal of pre-existing and newly crystalizing beliefs about intellection, the human person, and the relationship between humanity and the divine, as well as how a climate of existential threat enabled or modulated expression of these beliefs. Gregory Palamas’ hesychast doctrine not only grounds apodictic cataphatic theology in hesychia, it indicates that the fullness of the human person is only realized in the divinization of that holy silence. That divinization requires the intellect be made completely silent. Contrastingly, Demetrios Kydones presents a vision of the human person as most fully realized while deliberately engaging the intellect. For Demetrios, intellection is nothing less than the act which distinguishes humanity from animal creation. It follows that knowledge of God can also be achieved through intellection. These are the more fundamental and opposed visions of humanity which are revealed in the major texts of that controversy, and whose expression was catalyzed by that climate of chronic existential threat.

abstract: PhD


title: An Exploration of Heuristics Applied to Genetic Algorithms on the Capacitated Pickup and Delivery Problem with Time Windows

contributor:
Choudhury, Salimur
Salomaa, Kai
Computing

subject:
Vehicle Routing
Combinatorial Optimization
Operations Research
Pickup and Delivery
Genetic Algorithm
Heuristics

abstract:
Pickup and delivery is a ubiquitous part of everyday life. Being able to move goods and people between locations in the shortest amount of time and with the fewest vehicles allows packages to arrive on time, allows the just-in-time delivery paradigm that much of our industries rely on, and much more. Solving this problem is a complex task that interests both academia and industry.

As time goes on the size and complexity of the problems we wish to solve also increase. Additionally, time is often a critical parameter that cannot be changed. This in turn leads to a need for better and more efficient algorithms. Due to the scale of the problems, exact solutions are often eschewed in exchange for satisfactory solutions. Many heuristics and algorithms have been designed to try and improve the solutions while not increasing the time to completion. These algorithms use local search operations to iteratively improve solutions in hopes they become better over time.

This thesis aims to address the need for better algorithms. The first problem that we approach is an exploration of how different local search operations compare against each other. By identifying the operators that most improve the final solution, more intelligent algorithms can be constructed. Using genetic algorithms as the base, typical genetic algorithm operators are compared against vehicle routing operators to determine which most improves the solution.

The second problem introduces a new heuristic that uses historical information to improve solutions. Previous solutions can be deconstructed into subroutes, with the most frequently occurring being extracted. Using these previously found subroutes, the new heuristic attempts to insert them into newly created solutions. This is done by removing each part of the pattern from the solution, creating route fragments. These fragments can then be recombined to create a new solution. The two principal ideas are that common routes will tend to be good routes and this process allows higher-order operations to be performed.

abstract: M.Sc.


title: Feral Familiars and Cat Tales: Deconstructing Domesticity in Wilkie Collins' Heart and Science

contributor:
Cameron, Sally Brooke
English Language and Literature

subject:
Ferality
Domestication
Jacques Derrida
Eve Sedgwick
Wilkie Collins
Nineteenth-Century Studies
Literature
The Sensation Novel

abstract: Through an examination of Victorian artifacts, including contemporary paintings and literature, this thesis explores the ways in which the concept of the feral cat challenges the image of not only the Victorian family and its domestic sphere, but how the animal functioned within this space. In a period so forcefully defined by domestication and the taming of the beast, cats during the Victorian era walked against the path of human domination marking a defiant power. I look to the theoretical work of Jacques Derrida, Eve Sedgwick (and her term “feline pedagogue”) and Teresa Magnum to illustrate how the cat’s challenge to humanistic ideology opens up a feral pedagogue. Feral Pedagogy requires that the critic risks rhetorical, ideological and narratological certainty in the name of evoking fear, shame and uncertainty. It requires a reorientation of space as no longer ordered by the lines of domestic/wild boundaries in and beyond Victorian literary fields. I extend this methodology to the works of Wilkie Collins, in particular, his use of the sensation novel in Heart and Science. Through the animal’s escape beyond domestic structures, Collins’ work presents a feral reading of the Victorian family. By reading representations of ferality, as inspired by the cat’s power, I hope to reimagine the bounds of Victorian animal studies. As a field of study which is so heavily inspired by the Victorian ideas surrounding the animal, the prospect of recognizing feral familiars in Victorian cat tales opens up a new analytical field: cat studies. I hope to incite further revisits to and reexaminations of the way feline potential rewrites the discourse on animals, especially discourses rooted in the Victorian conceptions of human domination. Reading “ferally” requires an opening of space, taken up by many kinds of relationships that are no longer ordered by human domination and nonhuman subjugation.

abstract: M.A.


title: Privacy Preservation and Verifiability for Federated Learning

contributor:
Ni, Jianbing
Electrical and Computer Engineering

rights: Attribution-NonCommercial 3.0 United States

subject:
Federated Learning
Secure Machine Learning

abstract:
Federated learning is a distributed machine learning framework to address the bottleneck of traditional machine learning on data collection and privacy leakage, which allows training a learning model using distributedly stored data without exposing them. In federated learning, multiple clients collaboratively train a single global model that is improved iteratively through clients' local data. Each client receives the global model from an aggregation server. Then, they train it on their private data, and send locally trained models back to the server, which are later integrated into the global model. Iteration after iteration, the federated training continues until the global model is considered well-trained.

Federated learning provides basic privacy protection against outsider attackers, but it does not mean user privacy would not be leaked. It has been proved that the local models shared with the server are vulnerable to leaking the raw data maintained by users. To preserve the privacy of users, shared models shall not be in the form of plaintext. However, the encryption of the local models in sharing brings the challenge of model aggregation for the server, which is important to ensure fast convergence of the global model. In addition, it is hard to ensure that the server could honestly aggregate the local models, especially in cross-silo federated learning. If the server does not have enough motivation to coordinate the training, the performance of federated learning cannot be guaranteed.

In this thesis, we aim to prevent user privacy leakage from the shared local models, and guarantee the correctness of the global models output by the server. Specifically, we first propose PPA-AFL, a fully asynchronous secure federated learning protocol, which addresses the privacy issue in the asynchronous federated aggregation. The disadvantage of PPA-AFL is that it requires two non-colluding servers and cannot provide a correctness guarantee for the global model. Then, we design PPVA-AFL, a secure and verifiable aggregation protocol for asynchronous federated learning, which simultaneously guarantees the privacy of the local model and the correctness of the global model. In short, we have investigated security issues in federated learning and developed two novel schemes that enhance privacy preservation and introduce verifiability for federated learning.

abstract: M.A.Sc.


title: Pedestrian Data Generation Through Simulation, Diffusion, and Conditional Image Synthesis

contributor:
Greenspan, Michael
Electrical and Computer Engineering

subject:
Supervised Learning
Simulation
Pedestrian Detection
Sim2Real Transfer
Conditional Image Synthesis
Diffusion
Conditional Diffusion
Dataset Generation
CARLA
Cross-Dataset Evaluation

abstract: Simulated data has been proposed as a solution to the costly process of creating large datasets that deep learning models require through simulation platforms such as CARLA. However, creating a dataset synthetically introduces the sim2real gap where models trained on this data do not perform well when transferred to the real world. To fix this, sim2real transfer has been proposed in many works which transforms the simulated data to match its real-world counterparts. As such, we explore the use of simulation and sim2real transfer using the task of pedestrian detection as a reference frame evaluated using the M R−2 score. After implementing and iterating upon simulated datasets with sim2real transfer, we found this data lacking in terms of cross-dataset evaluation capability when tested against our real-world benchmark. To improve this result, we look to other methods of synthetic data creation. Specifically, diffusion models and pretrained pedestrian detection models are used to generate additional data which then augments the simulated dataset. Diffusion has the advantage of creating arbitrarily large datasets more quickly than simulation and represents the real-world target dataset more effectively. This thesis presents a pipeline for generating pedestrian detection data using a simulation platform, our sim2real transfer method, and our method of generated data through diffusion. We show that using these methods together results in the closest cross-dataset evaluation to the real-world benchmark. The best CARLA trained pedestrian detection model was able to achieve a 59.08% reasonable M R−2 score. When combined with diffusion generated data, the model was able to achieve 42.97% reasonable M R−2 score which is a 16.11% improvement over CARLA’s performance.

abstract: M.A.Sc.


title: Modulation of Electrical Transmission in Aplysia Bag Cell Neurons by cAMP Through a Postsynaptic Mechanism

contributor:
Magoski, Neil
Biomedical and Molecular Sciences

subject:
neuroscience
PKA
aplysia
bag cell neuron
gap junction
postsynaptic
cAMP
neurophysiology
electrical coupling
neuroendocrine
electrophysiology

abstract: Direct electrical communication between neurons occurs via electrical coupling, which is achieved through paired hemi-channels known as gap junctions. These inter-cellular channels promote synchronized, rapid, and reliable information transfer, thereby affecting the frequency, coordination, and pattern of firing. The present study concerns the electrically coupled bag cell neurons from the sea snail, Aplysia californica. These neuroendocrine cells undergo an ~30-min afterdischarge of continuous firing, culminating with the secretion of egg-laying hormone into the bloodstream. During the afterdischarge, cyclic adenosine monophosphate (cAMP) is quickly increased, and its effector, protein kinase A (PKA), is subsequently upregulated. Yet, it is unknown if cAMP/PKA impact bag cell neurons gap junctions. In culture, paired electrically coupled bag cell neurons present a non-rectifying and voltage-independent junctional conductance. Compared to control, PKA activation with IBMX, a membrane-permeable phosphodiesterase inhibitor, or 8-CPT-cAMP, a cAMP analogue, significantly augmented (~40%) coupling coefficient, a gauge of how well the inter-cellular signal spreads. The height of the electrotonic potential (ETP) evoked by a presynaptic action potential-like waveform was also significantly increased (~30 and ~40%, respectively) by these two reagents, indicative of enhanced electrotonic transmission. However, neither compound altered junctional conductance, suggesting a postsynaptic mechanism. When a junctional-like current was applied to single cells, the resulting ETP-like response was significantly elevated (20-40%) by cAMP, and this was prevented by pretreatment with the PKA inhibitor, KT5720. Next, recordings of either delayed rectifier K+ current, evoked by voltage steps, or more modest K+ current, evoked by an ETP-like voltage change, showed a significant reduction (~25%) after cAMP. Again, these outcomes were eliminated by KT5720, confirming that the effect was PKA-dependent. Moreover, cAMP significantly boosted synchrony and feed-forward excitation, ie, the ability of the presynaptic neuron to evoke postsynaptic action potentials. Overall, these results suggest that PKA enhances electrical transmission by reducing postsynaptic K+ current, making bag cell neurons more responsive to junctional current. Given the critical physiological role of electrically coupled neuroendocrine cells, including those in the vertebrate hypothalamus or adrenal medulla, the insect corpus cardiacum, and the crustacean X-organ, this has implications for the hormonal control of fundamental behaviour.

abstract: M.Sc.


title: Heterologous expression strategies to elicit the production of novel lanthipeptides, flavipuricin I and flavipuricin II, identified from a gram-negative proteobacterium, Pseudoalteromonas flavipulchra 2ta6 in the host, Escherichia coli

contributor:
Ross, Avena
Chemistry

subject:
Natural Products
Lanthipeptides
RiPPs
Heterologous expression
post-translational modifications
biosynthesis
marine proteobacteria
Pseudoalteromonas

abstract:
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs). The diverse group of polycyclic lanthipeptides is structurally identified by non-proteinogenic amino acids, lanthionine, and methyllanthionine, and their rich bioactivities make them desirable candidates for natural product (NP)-based drug discovery applications. Most lanthipeptides characterized so far have been from gram-positive bacteria, with an abundance of their biosynthetic gene clusters (BGCs) reported in gram-negative bacteria as well. However, to date, there is only one example of lanthipeptides characterized from a gram-negative marine proteobacterium, Thalassomonas actiniarum.
Genomic analysis of gram-negative proteobacterium, Pseudoalteromonas flavipulchra 2ta6, identified a putative class I lanthipeptide BGC. Previous investigations identified flavipuricin I and flavipuricin II as potential products of the BGC. Isolation attempts from the native organism along with heterologous expression of the BGC in Escherichia coli BL21(DE3) resulted in low yields hindering complete structural characterization of the flavipuricins.
The aim of this research is to boost the heterologous production of the flavipuricins to get enough material for complete structural characterization by nuclear magnetic resonance (NMR) spectroscopy. Previous studies suggested using codon-optimized precursor peptide encoding gene, flnA(c.o.) during heterologous expression experiments might overcome the low availability of starting material for the biosynthetic enzymes and enhance flavipuricin production. Multiple attempts were made to heterologously express the putative flavipuricin BGC with the codon-optimized gene, modification of various conditions like IPTG concentration, time, temperature, and ZnCl2 concentration were investigated but the flavipuricin peptides were not detected. Hence, an alternate strategy was then followed in which mutated versions of flnA with artificial protease cleavage sites incorporated strategically into its sequence, were heterologously expressed alongside the dehydratase (flnB) and the cyclase (flnC) encoding genes in E. coli to yield putative modified flavipuricins. Finally, attempts were made to cleave the modified peptides with an external protease, endoproteinase LysC to yield mature flavipuricins in vitro. A successful overexpression of the potentially modified flavipuricins was observed however the experimental masses of the peptides were found to be higher than the calculated masses. In vitro endoproteinase LysC proteolysis assays did not result in the detection of mature flavipuricins.
Future investigations to determine the extent of post-translational modifications and analysis using tandem mass spectrometry would help unravel the identities of the putative modified peptides and shed light on the mass difference observed. Additionally, employing a modified purification protocol with high concentration organic solvents following proteolysis could lead to the detection of mature flavipuricins. Acquiring purified flavipuricins in significantly higher yields for future NMR experiments will help determine the macrocyclization pattern within their structures.

abstract: M.Sc.


title: The Use of Surface Energy Traps as a Platform for Particle Separation and Sample Deposition

contributor:
Oleschuk, Richard
Chemistry

subject: microfluidic

subject: liquid micro junction surface sampling probe

subject: mass spectrometry

subject: particle separation

subject: sample deposition

subject: wettability-patterned microchip

subject: microarray

subject: analyte detection

abstract:
Microfluidics is the science investigating the behaviour of fluids that are transferred and manipulated through microfluidic channels. It has become a distinct and major technological field that allows for miniaturization of complex systems built into a chip. Digital microfluidics (DMFs), on the other hand, is an alternative approach to channel-based microfluidic systems. Droplets in this case containing reagents or analyte samples are manipulated on two-dimensional planar chips, contrary to microfluidic channels. No or negligible cross-mixing and excellent reagent economy of such systems make them unparalleled. Apart from microfluidics, mass spectrometry (MS) is an important tool in analytical chemistry. Mass spectrometry not only is able to provide compositional information for a sample but has the potential to carry out external calibration by relating the peak area with known concentrations to analyze a sample with unknown concentration. This thesis seeks to use a liquid micro-junction surface sampling probe (LMJ-SSP) as a bridge to connect microfluidics and mass spectrometry together to investigate particle trapping and sample analysis in a more analyte and time efficient way.
          A discontinuous de-wetting process is applied on an array of surface energy traps (SETs) which are hydrophilic ablated surfaces along with milled broadening zones (MBZs) formed from the laser ablation of a glass chip coated with hydrophobic coating. By sliding a large droplet on the chip surface, much smaller individual droplets are formed (nanolitre to femtolitre range). The size and shape of the SETs can be simply manipulated by varying the laser micromachining conditions. Ultra-high density is achieved using surface treatments to remove the MBZs such that roughly 5,000 to 45,000 of SETs can be packed on a 25 mm by 75 mm standard microchip glass slide to trap and separate microparticles. To limit sample preparation time and better improve detection efficiency, a microfluidic approach is used with Electrospray Ionization Mass Spectrometry (ESI-MS) coupled with LMJ-SSP for rapid organic/biological sample analysis. The correlation between cell concentration and peak area can be used as a rapid real-time sample detection technique for laboratory purposes.

abstract: M.Sc.


title: A Simple Approach to Modify Cellulose Nanocrystals: The Adsorption of Statistical Copolymers

contributor:
Champagne, Pascale
Cunningham, Michael
Chemical Engineering

subject:
Cellulose Nanocrystals
Polymer Modification

abstract: Cellulose nanocrystals (CNCs) are biologically sourced nanoparticles with vast potential in the design of sustainable, composite materials. Due to their exceptional mechanical properties, CNCs have been investigated as reinforcing agents in polymer nanocomposites, including foams, paints, coatings, and adhesives. Unfortunately, the hydrophilic surface is not conducive to a variety of applications, namely the formation of nanocomposites based on hydrophobic polymers. Various modification routes have been developed to introduce hydrophobic character and expand the application range of CNCs. Modifications typically suffer from complexity and cost, which jeopardize the commercialization and environmental sustainability of CNC-based technologies. In this work, cationic poly(2-(dimethylamino)ethyl methacrylate-co-butyl acrylate) (Q-P(DMAEMA-co-BA)) statistical (random) copolymer dispersants were adsorbed to anionic CNCs in a single step. Solid-state NMR, FTIR, and TGA were used to characterize Q-P(DMAEMA-co-BA) at the CNC interface. The loading, molecular weight, and cationic character (e.g., degree of quaternization) of Q-P(DMAEMA-co-BA) were tuned to improve the dispersion of polymer-modified CNCs in organic solvents. Well-dispersed CNCs are identified as promising reinforcing agents in analogous polymer systems. This simple modification strategy is attractive on an industrial scale and offers several environmental advantages versus conventional techniques. Preliminary studies using copolymer dispersants of butyl vinyl imidazolium bromide and either styrene (P(BuVIm-co-Sty)) or BA (P(BuVIm-co-BA)) demonstrate the versatility of this modification route. Further adaptation may simplify the design of stimuli-responsive CNCs, along with CNC-based Pickering emulsifiers, adsorbents, and flocculants.

abstract: M.A.Sc.