title: House Music: Anxiety, Order, Form, and the Domestic in the Works of Elizabeth Bishop, Gwendolyn Brooks, and Anne Sexton

contributor:
Donaldson, Jeffery
English and Cultural Studies

subject:
Elizabeth Bishop (1911-1979)
Anne Sexton (1928-1974)
Gwendolyn Brooks (1917-2000)
American poetry
metre
prosody
poetic form
the domestic

abstract:
This dissertation discusses the way in which mid-20th century American female poets Elizabeth Bishop, Anne Sexton, and Gwendolyn Brooks addressed anxieties around seeking, keeping, and surviving home spaces while incorporating elements of formal poetic structure (including metre, stanzaic configurations, and rhyme). Susan Fraiman, in Extreme Domesticity: A View from the Margins, suggests that domestic space and practice can become sites of improvisation, rebellion, and refuge. Building on this theory, I show how form and domestic subject matter can interact to signify active responses to trauma resulting from childhood abandonment, physical/sexual abuse, homophobia, madness, and systemic racism. I argue that poetic form at its most effective does not function as an homage to either patriarchal canonical models of restraint or craftspersonship but animates the work from the inside out and effectively creates poem-spaces that are metaphorical “homes” rather than “houses”.

My work adds to the fields of American poetry and prosodic scholarship by incorporating close reading techniques that neither follow New Criticism mandates that privilege authorial choice/structural integrity over biographical and sociopolitical resonances nor assign specific meaning to how form is used. Instead, this project encourages readers, students of poetry, and practitioners to rethink how formal structures in poetic work can emerge from and engage with the highly personal and how the implementation of formal technique can potentially offer shelter and a means of articulating trauma and resistance whilst extending into the public sphere (either thematically or through the vehicle of performance) to offer intimacy and forge community.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: The mid-20th century American female poets Elizabeth Bishop, Anne Sexton, and Gwendolyn Brooks addressed anxieties around seeking, keeping, and surviving home spaces while incorporating elements of poetic form (including metre, stanzas, and rhyme). I show how form and domestic subject matter can interact to signify active responses to trauma resulting from childhood abandonment, physical/sexual abuse, homophobia, madness, and systemic racism. I argue that form at its most effective should be neither a “container”—a “house” of words—nor a sign that the poet is conservative and/or old-fashioned. Rather, I invite my readers to consider the formal poem as a potential “home” in which the structure becomes an extension of the inner personal forces that animate it, helping it to offer shelter and a means of resistance to the writer and reader/listener, as well as forge connections in the public sphere, both thematically and in performance.


title: JOINT CHARGING, ROUTING, AND POWER ALLOCATIONS FOR RECHARGEABLE WIRELESS SENSOR NETWORKS

contributor:
Zhao, Dongmei
Electrical and Computer Engineering

subject: Rechargeable Wireless Sensor Network

abstract:
Prolonging the battery lifetime of sensors has been one of the most important issues in
wireless sensor networks (WSNs). With the development of Wireless Power Transfer
(WPT) technology, sensors can be recharged and possibly have infinite lifetime. One
common approach to achieving this is having a wireless charging vehicle (WCV) move
in the system coverage area and charge sensors nearby when it stops. The duration
that the WCV stays at each charging location, the amount of traffic that each sensor
carries, and the transmission power of individual sensors are closely related, and their
joint optimization affects not only the data transmissions in the WSN but also energy
consumption of the system. This problem is formulated as a mixed integer and nonconvex
optimization problem. Different from existing work that either solves similar
problems using genetic algorithms or considers charging sensors based on clusters,
we consider the optimum charging time for each sensor, and solve the joint
communication and charging problem optimally. Numerical results demonstrate that
our solution can significantly reduce the average power consumption of the system,
compared to the cluster-based charging solution.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract:
In a wireless sensor network (WSN), sensor nodes monitor the physical environment
and forward the collected data to a data sink for further processing. Sensors are
battery powered and, therefore, prolonging the lifetime of their batteries is critically
important. In a rechargeable WSN (RWSN), prolonging the battery lifetime of
sensors is achieved through reducing communication energy and recharging the batteries
periodically. Reducing the communication energy consumption is done through
choosing the best forwarding sensors (i.e., routing) for data collected by each sensor
and deciding the transmission power of each sensor (i.e., power allocation). Recharging
the batteries is achieved through harvesting energy from external sources. In this thesis,
we consider a RWSN that uses wireless power transfer as the energy harvesting
technology and jointly optimizes charging and communications in order to minimize
the power consumption of the RWSN.


title: Predicting Transfer Learning Performance Using Dataset Similarity for Time Series Classification of Human Activity Recognition

title: Transfer Learning Performance Using Dataset Similarity on Realtime Classification

contributor:
Doyle, Thomas
Biomedical Engineering

subject:
Deep Learning
Machine Learning
Transfer Learning
Similarity
GAN
Signal Classification

abstract:
Deep learning is increasingly becoming a viable way of classifying all types of data. Modern deep learning algorithms, such as one dimensional convolutional neural networks, have demonstrated excellent performance in classifying time series data because of the ability to identify time invariant features. A primary challenge of deep learning for time series classification is the large amount of data required for training and many application domains, such as in medicine, have challenges obtaining sufficient data.  Transfer learning is a deep learning method used to apply feature knowledge from one deep learning model to another; this is a powerful tool when both training datasets are similar and offers smaller datasets the power of more robust larger datasets. This makes it vital that the best source dataset is selected when performing transfer learning and presently there is no metric for this purpose.

In this thesis a metric of predicting the performance of transfer learning is proposed. To develop this metric this research will focus on classification and transfer learning for human-activity-recognition time series data. For general time series data, finding temporal relations between signals is computationally intensive using non-deep learning techniques.  Rather than time-series signal processing, a neural network autoencoder was used to first transform the source and target datasets into a time independent feature space. To compare and quantify the suitability of transfer learning datasets, two metrics were examined: i) average embedded signal from each dataset was used to calculate the distance between each datasets centroid, and ii) a Generative Adversarial Network (GAN) model was trained and the discriminator portion of the GAN is then used to assess the dissimilarity between source and target. This thesis measures a correlation between the distance between two dataset and their similarity, as well as the ability for a GAN to discriminate between two datasets and their similarity.  The discriminator metric, however, does suffer from an upper limit of dissimilarity. These metrics were then used to predict the success of transfer learning from one dataset to another for the purpose of general time series classification.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Over the past decade, advances in computational power and increases in data quantity have made deep learning a useful method of complex pattern recognition and classification in data. There is a growing desire to be able to use these complex algorithms on smaller quantities of data. To achieve this, a deep learning model is first trained on a larger dataset and then retrained on the smaller dataset; this is called transfer learning. For transfer learning to be effective, there needs to be a level of similarity between the two datasets so that properties from larger dataset can be learned and then refined using the smaller dataset. Therefore, it is of great interest to understand what level of similarity exists between the two datasets. The goal of this research is to provide a similarity metric between two time series classification datasets so that potential performance gains from transfer learning can be better understood. The measure of similarity between two time series datasets presents a unique challenge due to the nature of this data. To address this challenge an encoder approach was implemented to transform the time series data into a form where each signal example can be compared against one another. In this thesis, different similarity metrics were evaluated and correlated to the performance of a deep learning model allowing the prediction of how effective transfer learning may be when applied.


title: Mechanism of ADAMTS13 regulation

contributor: Medical Sciences (Blood and Cardiovascular)

subject: ADAMTS13, BioID, TTP, VWD, Von Willebrand Factor, Plasminogen

abstract:
Studies demonstrated ADAMTS13 possesses unique properties with a mystifying regulatory mechanism. ADAMTS13’s role is in its proteolytic function to its VWF. The disparity in the hemostatic balance between ADAMTS13 activity and the distribution of VWF multimers could result in the bleeding disorder Von Willebrand Disease (VWD) or the thrombotic disorder thrombotic thrombocytopenic purpura (TTP). ADAMTS13 is constitutively secreted as an active protease, yet VWF retains its capacity to recruit platelets. This ability makes ADAMTS13 an enigmatic protease with an unknown regulatory mechanism. Currently, the postulated regulatory mechanism of ADAMTS13 is in its open/closed conformation, yet ADAMTS13 activity is retained in both forms. Literature showed that few proteases are capable of degrading ADAMTS13 in-vitro. We hypothesize that the partial degradation of ADAMTS13 regulates its activity, thereby stabilizing VWF and promoting thrombosis. The goals of this project were to develop and optimize in-vitro plasma BioID to identify novel interactions to ADAMTS13, validate novel interactions, identify proteases capable of degrading ADAMTS13 and their proteolytic sites, and develop protease-resistant ADAMTS13 mutants as novel therapeutics to thrombotic disorders. We optimized the BioID technique to be used in-vitro in plasma, to study novel interactions with ADAMTS13. Our results identified novel potential interactions with vitronectin or plasminogen. Validation studies disregarded vitronectin’s interaction and confirmed plasminogen’s interaction through the CUB and Kringle domains in a lysine-dependent manner.
Further, the list of proteases capable of degrading ADAMTS13 was expanded to include FXIa and neutrophil-derived proteases including Cathepsin G, elastase, and hPR3. Activated neutrophils played a stronger role than coagulation proteases in degrading ADAMTS13 in vivo, while also demonstrating that elastase is a more potent regulator. Proteolytically degraded sites on ADAMTS13 were identified and proteolytic-resistant ADAMTS13 mutants were produced accordingly, which we aim to be utilized as a novel therapeutic to thrombotic disorders.

abstract: Thesis

abstract: Doctor of Philosophy (Medical Science)


title: Complex network theoretical approach to investigate the interdependence between factors affecting subsurface radionuclide migration

contributor:
Dickson-Anderson, Sarah
Guo, Peijun
Civil Engineering

subject:
Complex network theory
interdependent factors
centrality
sensitivity analysis
radionuclides
vadose zone

abstract: Mining of uranium ore and its extraction using the milling process generates solid and liquid waste, commonly termed uranium mine tailings. Uranium mine tailings is radioactive, as it consists of residual uranium, thorium, and radium, which amounts to 85% of the original ore’s radioactivity. Due to the extensively long half-lives of uranium (4.5x109 years), thorium (75,400 years), and radium (1,620 years) and their harmful radioactive, it is imperative to isolate uranium mine tailings from the environment for a longer period. Containment of uranium mine tailings in dam-like structures, called uranium mine tailings dam (UMTD), is the most followed disposal and storage method. Like a conventional water retention dam, UMTDs are also susceptible to failure, mainly due to adverse weather conditions. Once the UMTD fails, a fraction of the radioactive tailings infiltrates and migrate through the vadose zone contaminating the groundwater sources underlying it. Radionuclide behavior and migration in the subsurface are affected by several environmental factors. To minimize the uncertainty and improve current radionuclide fate and transport models, it is vital to study these factors and any interdependence existing between them. This study aims to understand these environmental factors by i) enlisting the factors affecting subsurface radionuclide migration through scoping review of articles and reports, and ii) analyzing the interdependence existing between the factors using the complex network theory (CNT) approach and identifying the dominant factors among them. Factors such as chemical and biological characteristics of soil stratigraphy, groundwater, and radioactive tailings plume, meteorological, and hydrogeological are found to influence radionuclide behavior and transport mechanisms in the vadose zone. CNT approach described soil microorganisms, fraction of organic carbon, infiltration rate of the soil, transmissivity, clay fraction in the soil, particulates in groundwater, and infiltrating rainwater as dominant factors in the NoF based on their centrality measures and sensitivity analysis of the network of factors (NoF). Any uncertainty associated with these factors will affect and propagate through the model. Hence, sufficient resources should be directed in the future to characterize these factors and minimize their uncertainty, which will lead to developing reliable fate and transport models for radionuclides.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Waste products from uranium mining and milling operations are called uranium mine tailings, which are radioactive. Generally, uranium mine tailings are disposed of and isolated in dam-like structures referred to as uranium mine tailings dams (UMTD). One of the most common causes of UMTD failure is extreme weather conditions. When a UMTD fails, a part of tailings, consisting of radionuclides uranium, thorium, and radium, infiltrate into the subsurface through the vadose zone. Radionuclide behavior and transport in the subsurface is influenced by several environmental factors. The objective of the present study is to understand the factors affecting radionuclide migration by i) conducting a scoping review on radionuclide migration in the subsurface to describe the factors studied in the literature, and ii) understanding and analyzing any relation among the factors and deriving the most dominant factors based on their relation. This study can be used further to develop accurate and reliable radionuclide fate and transport models with minimal uncertainty.


title: Quantum Bifurcations in Bose-Einstein condensates

contributor:
O'Dell, Duncan
Burgess, Cliff
Physics and Astronomy

abstract: We model an atomic Bose-Einstein condensate (BEC) near an instability, looking for universal features. Instabilities are often associated with bifurcations where the classical field theory provided here by the Gross-Pitaevskii equation predicts that two or more solutions appear or disappear. Simple examples of such a situation can be realized in a BEC in a double-well potential or in a BEC rotating in a ring trap. We analyze this problem using both Bogoliubov theory and exact diagonalization. The former describes elementary excitations which display complex frequencies near the bifurcation. We make connections to the description of bifurcations using catastrophe theory but modified to include field quantization.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Mission to Sanitize: Public Health, Colonial Authority, and African Agency in Western Nigeria, 1900-1945

contributor:
Ibhawoh, Bonny
History

subject:
African history
colonialism and development
social policy
environmental sanitation
public health
disease control
African sanitary inspector
Yorubaland
Nigeria
wole-wole
sanitary science and hygiene

abstract: Studies on empire have shown that colonialism generated new disease environments and complicated old disease experiences in Africa. These conditions necessitated a mission to sanitize Africans and their environment in British West Africa since the colonies had to be conducive for European colonial officials and their African labor, especially given the region’s image as the “white man’s grave.” However, colonial administrations lacked the skills, adequate personnel, and materials to transform territories like western Nigeria into desired healthy locations for European personnel or colonized Africans. In the first two decades of the twentieth century, most Africans resisted the preventive health measures introduced in Yoruba towns, including environmental sanitation projects to reduce mosquito breeding spots. This was not simply because the initiative threatened African livelihood but rather because many Africans were too poor to pay the cost of the British modernizing projects, including pipe-borne water and odor-proof latrine buckets. As most Africans resisted some of these initiatives and negotiated others to improve their health and social conditions, their politics of resistance shaped public health development in western Nigeria. This is significant to African history because it reveals how the administrative policing of environmental sanitation and health adds nuance to our understanding of empire, particularly the complex relationship between Africans of different social classes and between Africans and the colonial governments in Western Nigerian towns.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This dissertation is about the history of British preventive health in western Nigeria from the late nineteenth century to the end of the second world war. It contributes to the social history of medicine, health, and environment as it explores Africans’ experience of British imperial hygiene and public sanitation programs. Specifically, the study focuses on how public health projects such as potable water, public latrine, and waste management shaped people’s lives and how Africans shaped the health initiatives in return. The study argues that most of the preventive health programs the British colonial authorities introduced in western Nigerian towns during the period under review had a minimal impact on African health. This was because the colonial government and most Africans had opposing views on how public health initiatives should be executed in an environment of budget restraints and poverty. The study thus shows how Africans resisted some public health initiatives and negotiated others in an attempt to improve their health and social conditions. By exploring major colonial initiatives that sought to transform the Nigerian environment into a more healthy place and the people into environmentally responsible subjects, the study argues that colonized Africans were not passive onlookers during the transformation of their public health system. Rather, their politics of resistance shaped colonial health development.


title: An Adversarial Approach to Importance Weighting for Domain Adaptation

contributor:
Ashtiani, Hassan
Computing and Software

abstract:
Most supervised learning methods assume that the training and test data points are generated from the same distribution. Therefore, they face major challenges when this assumption does not hold.
Domain adaptation techniques aim to address this issue by adapting the learned models to new distributions. Covariate shift is a common assumption in domain adaptation, where the training and test distributions only differ in the marginal distributions.
A common idea to tackle covariate shift is estimating the importance weights of the training data points using unlabeled data from the source and target distributions and then training the classifier using importance-weighted risk minimization. Existing methods for estimating the importance weights are kernel-based which scale poorly with dataset size and underperform on high-dimensional data.
This work proposes a novel method for estimating the importance weights using generative adversarial networks. There are two neural networks used in this framework which we call the weighting and the discriminator networks. These networks are jointly trained using an adversarial learning scheme. We designed a benchmark for assessing classification performance under various forms of distribution shift and evaluated our method in this framework. We observe that while our method effectively estimates the importance weights, the improvements we get in the domain adaptation task depend on the discrepancy of the domains.

abstract: Thesis

abstract: Master of Science (MSc)


title: Patient Lifting Device Use by Caregivers in a Hospital Setting: A proposed research program

contributor:
Potvin, Jim R.
Lyons, Jim
Science

subject: patient lifting device use, musculoskeletal injuries, caregivers, nurses, barriers, patient lift, hospital

abstract: The literature cites several recurrent barriers that contribute to the under-utilization of patient lifting devices (PLDs) by caregivers (CGs), resulting in the profession being at high-risk for musculoskeletal injury. There is considerable evidence that training is a barrier to PLD use, due to the staff shortages and time constraints that result when CGs attend (provincially mandated) off-site hands-on practical training. Therefore, the current research program aims to contribute towards a better understanding of the barriers to the chronic concern of low PLD use by CGs, and, to evaluate an alternative approach that could be used to reduce the time CGs spend off the floor and enhance musculoskeletal health and well-being. Study 1 will conduct focus groups and administer a Theory of Planned Behaviour (TPB)-based questionnaire to better understand the barriers between (a) CGs’ knowledge (training/education) and intent to use PLDs, and (b) CGs’ intent to use PLDs and actual PLD use (i.e., behaviour). Also, patients and their family members will be interviewed to better understand the role of the patient as a potential barrier to PLD use. Study 2 will conduct focus groups with: (i) hospital staff who design, develop and deliver PLD training programs, (ii) unit managers, and (iii) new CG hires. Via questionnaire, Preceptors will evaluate the impact of the barrier subcategories identified on the perceived overall effectiveness of a PLD training program. Study 3 will explore the feasibility of implementing vicarious learning through observation (two intervention groups) as an effective alternative to off-site hands-on learning (control group) for new CG hires, with Preceptors evaluating the three groups’ effectiveness via a questionnaire. It is hypothesized that (a) training is an important barrier to the under-utilization of PLDs by CGs (Study 1), (b) there is a need for an effective alternative to off-site hands-on learning that does not remove CGs from units (Study 2), and (c) vicarious learning through observation is as effective as hands-on learning for the utilization of PLDs by new CG hires.

abstract: Thesis

abstract: Master of Science in Kinesiology


title: Paul and Sacrifice in Corinth: Rethinking Paul's Views on Gentile Cults in 1 Corinthians 8 and 10

contributor:
Thiessen, Matthew
Religious Studies

subject:
1 Corinthians 8 and 10
Animal Sacrifice
Paul within Judaism
Roman Corinth
The Corinthian Ekklēsia

abstract:
This thesis argues that (1) Paul’s instructions in 1 Corinthians 8 and 10 are coherent and consistent, and (2) that the apostle’s instructions does not express his departure from Judaism.
	For many years, scholars working on 1 Corinthians 8 and 10 have struggled to explain how these two chapters are connected and what Paul’s instructions within the two chapters are. I present a new reading of 1 Corinthians 8 and 10 where I argue that these chapters are connected in a coherent way and that Paul deals with two separate, yet connected, contexts in 1 Corinthians 8 and 10. In 1 Corinthians 8, he instructs the Corinthian Christ followers that they can take part in the dinners that often followed an animal sacrifice in antiquity, as long as it does not present an issue to another Christ followers. The key reason for this is the social capital at stake, would they not partake in these dinners. In 1 Corinthians 10, Paul tells the Christ followers that they cannot participate at the altar when animals are sacrificed. Doing so would be a violation against their exclusive relationship with the god of Israel and Jesus Christ.
	Many have read 1 Corinthians 8 and 10 as evidence for Paul’s departure from Judaism. I push back against this understanding by placing Paul’s instructions in the wider web of Jewish literature from the Second Temple period and the early rabbinic period. By comparing Paul’s instructions in 1 Corinthians 8 and 10 to texts from these time periods, it becomes clear that Paul is part of an ongoing Jewish conversation about how someone could remain faithful to the god of Israel while living in a gentile society.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: In this thesis, I examine Paul’s instructions regarding various level of engagement in gentile cults in 1 Corinthians 8 and 10. My thesis contributes to a new reading of these two chapters and I argue that 1 Corinthians 8 and 10 deal with two distinct, yet connected, issues. In the former chapter, Paul instructs Christ followers on how they should act when dining in temples dedicated to idols (something he in principle allows); in the latter, he instructs them to avoid all participation at the altar where the sacrifice takes place. By recognizing these two different contexts, Paul’s instructions in 1 Corinthians 8 and 10 become more understandable, coherent, and consistent. In addition, I argue that Paul’s instructions should be read within the wider context of Second Temple Judaism and early rabbinic Judaism, and not as evidence that Paul left Judaism.


title: DIGICOMP KIDS: CO-DESIGN AND USABILITY TESTING OF A HOSPITAL-TO-HOME INTERVENTION FOR CHILDREN WITH MEDICAL COMPLEXITY

contributor:
McGillion, Michael
Nursing

subject:
Digital health
Nursing
Children with Medical Complexity
Technology

abstract:
Background. Advances in healthcare have resulted in a growing population of Children
with Medical Complexities (CMC). Medical management of the complex needs of CMC has traditionally taken place in hospital settings, such as clinics, emergency departments, and hospital wards, by specialized teams of healthcare clinicians. While access to expert-level care is necessary, the hospital-based model of care is expensive and inconvenient and has resulted in harms such as medical errors conferred upon CMC. Models of care that allow for expert-delivered hospital-to-home care for CMC are needed. The aim of this dissertation was to investigate the needs, performance, and perceptions of CMC families and clinicians when using a hospital-to-home digital health system called DigiComp Kids.
Methods. This study was guided by A Holistic Framework to Improve the Uptake and Impact of eHealth Technologies, which attends to technological, human, and contextual variables influencing virtual care. A scoping review was conducted to provide an overview of how digital healthcare has been used with medically fragile children, before co-designing the DigiComp Kids system with CMC family members and clinicians. Usability testing of DigiComp Kids was conducted measuring user effectiveness, efficiency, satisfaction, and experiences.
Results. Across studies in this dissertation, technological, human, and contextual factors each played a role in the usability of digital health systems, including DigiComp Kids. In the scoping review, these factors influenced the acceptability, accessibility, and implementation success of digital healthcare systems for CMC. During DigiComp Kids co-design and usability testing, participants emphasized how these factors affected their willingness to engage with the system, how it fit into their lives and workflows, and where improvements could be made.
Conclusions. This study highlights the importance of engaging with end-users as well as attending to technological, human, and contextual factors when designing and testing digital health systems.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Synthesis and Antimicrobial Evaluation of Novel Sideromycins

contributor:
Magolan, Jakob
Biochemistry and Biomedical Sciences

subject:
Antibiotic
Siderophore
Sideromycin
Bacteria
Gram-negative
Antimicrobial Resistance

abstract:
This thesis consists of two chapters, each of which is a unique research project. Chapter 1 is focused on the synthesis and biological evaluation of novel sideromycin antibiotics. Sideromycins are bifunctional “Trojan Horse” molecules that have an iron chelator “siderophore” moiety covalently bound to an antibiotic. Such molecules exploit existing bacterial mechanisms for obtaining iron from their environment. Antibiotics that would typically not pass Gram-negative membranes are allowed access via siderophore transporter proteins. This project utilized a siderophore that has not previously been used in this capacity. The synthesis and biological evaluation of multiple sideromycin conjugates is reported.
Chapter 2 describes the chemical synthesis of coumarin natural products using a synthetic process recently developed in the Magolan laboratory that enables the efficient prenylation of phenols. These natural products are molecules of biological interest in various capacities but are rare and difficult to isolate from their plant sources. They have also previously been cumbersome to make via chemical synthesis. The chemistry described herein constitutes an inexpensive and efficient process to produce these compounds that is superior to previously known methods.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: This thesis is divided into two chapters. The first chapter is focused on the development of new sideromycin antibiotics. Sideromycins are “Trojan Horse”-like antibiotics that exploit the mechanisms of Gram-negative bacteria for obtaining iron, an essential nutrient, to enable antibiotic entry. This chapter details the synthesis of molecules that attach functionalities called “siderophores” to antibiotics, enabling them to be “smuggled” into Gram-negative microbes. This project uses a siderophore not previously utilized in sideromycin research. The second chapter is focused on the chemical synthesis of rare natural products that are phenols with prenyl substituents. Many such compounds are plant-derived and have potential for biomedical use. However, difficulty in isolating them makes them prohibitively expensive in the purity and quantity required for research. They are also challenging to make synthetically. This chapter details the application of a recently discovered process in the Magolan laboratory to synthesize coumarin-containing prenylated phenolic natural products.


title: Describing Unmet Healthcare Needs During the COVID-19 Pandemic: an Analysis of the Canadian Longitudinal Study on Aging (CLSA) COVID-19 Questionnaire Study

contributor:
Anderson, Laura N.
Health Research Methodology

subject:
Canadian Longitudinal Study on Aging
Unmet Healthcare Needs
COVID-19
Social Determinants of Health
Mental Health

abstract:
Background: The COVID-19 pandemic disrupted access to healthcare services in Canada, but little is known about the magnitude of unmet healthcare needs and characteristics associated with increased risk of unmet needs in the adult population.

Objectives: First, to describe unmet healthcare needs, including COVID-19 testing access, and to evaluate the association of the social determinants of health (SDOH) and chronic conditions with unmet healthcare needs. Secondly, to evaluate the association between symptoms of depression and anxiety with unmet healthcare needs, and test if the interaction was modified by sex.

Methods: The data of 23,972 adults who completed the Canadian Longitudinal Study on Aging COVID-19 Questionnaire Study exit survey (Sept.–Dec. 2020) was analyzed. Three outcomes were evaluated: 1) challenges accessing healthcare, 2) not going to a hospital or seeing a doctor when needed, 3) experiencing barriers to COVID-19 testing. For objective 1, a prospective cohort study was conducted. For objective 2, a cross-sectional study was conducted.

RESULTS: Overall, 25% of adults in Canada reported challenges accessing healthcare, 8% did not go to a hospital or see a doctor when needed, and 4% experienced barriers to COVID-19 testing. Several SDOH, including sex, immigrant status, racial background, education and income, were associated with unmet needs. The odds of reporting all three outcomes declined with age. Pre-pandemic unmet needs were strongly associated with higher odds of all three outcomes, while the presence of chronic conditions was associated with higher odds of the first two outcomes. Symptoms of depression and anxiety were strongly associated with all three outcomes. Interaction with sex was found for the first outcome, with stronger associations in females.

Conclusions: This thesis identified groups that experienced difficulties accessing healthcare services during the pandemic. Future research may assess consequences of unmet needs, evaluate mechanisms that cause unmet needs and determine ideal interventions.

abstract: Thesis

abstract: Master of Public Health (MPH)

abstract: The COVID-19 pandemic in Canada affected how individuals were able to access healthcare services. To understand which groups experienced a greater level of difficulties, we examined the experience of unmet healthcare needs during the first year of the pandemic using a sample of 23,972 adults that had completed the Canadian Longitudinal Study on Aging (CLSA) COVID-19 Questionnaire Study (Sept. – Dec. 2020). We found evidence that the experience of unmet healthcare needs varied by several sociodemographic characteristics, such as sex, immigrant status, racial background, education and income. Younger adults were more likely to report unmet needs. Individuals with chronic conditions and those had reported unmet healthcare needs prior to the pandemic were also more likely to report unmet needs during the pandemic. Individuals with symptoms of depression and anxiety were also more likely to report unmet healthcare needs. These results can be used to inform interventions that improve access to healthcare services for vulnerable groups.


title: Faster Design of Robust Binary Joint Watermarking and Scalar Quantization under Additive Gaussian Attacks

contributor:
Dumitrescu, Sorina Jr
Electrical and Computer Engineering

abstract:
This thesis investigates the problem of optimal design of binary joint watermarking and scalar quantization (JWSQ) systems that are robust under additive Gaussian attacks. A binary JWSQ system consists of two quantizers with disjoint codebooks. The joint quantization and embedding are performed by choosing the quantizer corresponding to the embedded message. The optimal JWSQ design for both fixed-rate and variable-rate cases was considered in the past, but the solution approaches exhibited high computational complexity.

	In this thesis, we propose faster binary JWSQ design algorithms for both the fixed-rate and variable-rate scenarios. We achieve the speed up by mapping the corresponding optimization problem to a minimum weight path problem in a certain weighted directed acyclic graph (with a constraint on the length of the path in the fixed-rate case). For this mapping to be possible we discretize the quantizer space and use an approximation for the probability of decoding error. The proposed solution algorithms have $O(LN^3)$ and $O(N^4)$ time complexity in the two cases respectively, where $N$ is the size of discretized source alphabet,  and in the fixed-rate scenario $L$ is the number of cells in each quantizer.

	The effectiveness of the proposed designs is assessed through extensive experiments on a Gaussian source. Our results show that our algorithms are able to achieve performance very close to the prior existing schemes, but only at a small fraction of their running time.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Investigating the Experimental and Correlational Reliability of Dual-Task Measures in the Psychological Refractory Period Paradigm

contributor:
Milliken, Bruce
Thomson, Sandra
Psychology

subject:
Psychological Refractory Period (PRP)
dual-task processing
backward compatibility effect (BCE)
experimental reliability
PRP Effect
correlational reliability
executive control
task interference

abstract: The Psychological Refractory Period (PRP) paradigm is frequently used to explore human cognition, executive control, and parallel processing in individuals. However, it is also important to explore the individual differences between people. Before this dual-task paradigm can be used to explore individual differences and be compared to different measures of executive control, it must be established that the effects produced are both experimentally and correlationally reliable, meaning they replicate both across sessions and within individuals. This experiment had 85 McMaster University students participate in a two day experiment that collected multiple measures of executive control and included three PRP dual-task sessions. Data from participants were analyzed to investigate the two effects found in this paradigm: the Backward Compatibility Effect (BCE) in Task 1 (T1) and the PRP Effect in Task 2 (T2). Both effects were found to be individually reliable both experimentally and correlationally. The two effects were then correlated to explore the relationship between them, and a significant positive correlation was discovered. Subsequent analyses separated by response compatibility revealed that incompatible response trials were driving the positive correlation between the PRP Effect and BCE, and that the BCE is related to T1 reaction time on incompatible trials only. These findings suggest the BCE in T1 is driven by response interference between the two tasks on incompatible trials, and this effect then propagates to T2 performance. The reliability of these measures has not previously been explored in this way and this thesis is the first to establish these findings. The results of this thesis support using the BCE and PRP Effect for exploring individual differences between people, as reliable measures that can be explored with other tasks of cognitive control and attention to investigate the presence of similar underlying cognitive processes.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The purpose of this thesis is to explore the experimental and correlational reliability of the Backward Compatibility Effect (BCE) and Psychological Refractory Period (PRP) Effect produced in the PRP paradigm that is used to investigate dual-task processing. Using a multi-day experimental design and three PRP dual-task sessions, both experimental and correlational reliability were established for both effects. This thesis is the first research to establish correlational reliability for the BCE and PRP Effect, which indicates that these measures are valid and reliable to compare with other measures used to assess individual differences in cognitive processing and executive control, especially in regards to measures assessing parallel processing (multitasking), task switching, and task interference.


title: What Is Happening Where? An Evaluation of Social Science Research Trends in Nunavut (2004-2019)

contributor:
Ljubicic, Gita
Geography

subject:
Inuit self-determination
trend analysis
northern studies
community engagement

abstract: Many Inuit feel they are not benefitting from research activities that come from colonial research licensing practices and laws enabling state control over research. In Nunavut, research licensing also helped to increase community engagement in research. The Nunavut Research Institute (NRI), based in Iqaluit, Nunavut manages research and issues physical/natural, health, and social science research licenses in the Territory. In partnership with the NRI, we examined social science and Inuit knowledge research licensed between 2004-2019, to understand the scope of research trends in Nunavut. Using the 568 project summaries from social science research licenses, thematic content analysis was conducted to: i) identify research topics in social science and Inuit knowledge projects; ii) determine frequency and diversity of topics according to leadership, location, and timeframe; iii) develop new metrics to improve tracking of research topics; and, iv) contribute to the development of a Nunavut research portal making NRI research applications/reports public. Through this analysis we learned that social science research in Nunavut increased over time. Research projects are predominantly led by Canadian academics, with the highest concentration of research being in Iqaluit. Social science research is mainly focused on cultural topics, conducted using interviews, and shared in peer-reviewed journal articles. Community engagement has also increased over time in Nunavut, and research intensity appears to be connected to the availability of research-related capacity and infrastructure in a community. This research is an important starting point in making research trends more accessible to Nunavummiut (people of Nunavut), and more useable by decision-makers regarding research intensity and potential fatigue in some Nunavut communities. Long term, improving tracking of metrics such as funding sources and reporting mechanisms can contribute to policy reform and to advancing the NRI licensing database. This is an initial step contributing to Nunavut-specific approaches to Inuit self-determination in research.

abstract: Thesis

abstract: Master of Arts (MA)

abstract:
Many Inuit feel they are not involved in the research process or seeing benefits from research outcomes.  For my MA research, I am working with the Nunavut Research Institute (NRI) licensing database analyzing summaries of social science research applications from 2004-2019.

The objectives are to:
1) Identify research topics addressed in social science projects;
2) Determine the variation of research topics across Nunavut over the past 16 years;
3) Develop new metrics to improve tracking of research topics;
4) Contribute to the development of a Nunavut research database making NRI research applications publicly accessible

Through this analysis we learned that social science research in Nunavut has increased over time. Research projects are mainly led by Canadian academics, focused on cultural topics, and concentrated in Iqaluit. Community engagement has also increased over time in Nunavut and appears to be linked with the availability of research-related capacity and infrastructure in a community. This research is an important starting point in making research trends more accessible to Nunavummiut (people of Nunavut). This work is also an initial step contributing to Nunavut-specific approaches to Inuit self-determination in research.


title: Conditioning New Behaviours in Salmonella Using Physical and Non-physical Landscapes

contributor:
Hynes, Alexander
Biochemistry and Biomedical Sciences

subject: Conditioning Training Salmonella Anticipation Evolution MEGA-plate

abstract:
Bacteria frequently encounter changes in their environment and must adapt accordingly. When these changes are predictable, there is evidence of anticipatory gene regulation. For example, the model enteric pathogen Salmonella has a well-defined natural history, typically only encountering iron in the lumen of the gut. However, this bacterium responds to the presence of iron not by upregulating genes needed to thrive in the lumen, but rather the iron-deplete epithelium, the subsequent environment it encounters. This may be similar to Pavlovian conditioning, a type of associative learning that involves pairing two unrelated stimuli and anticipatory behavioural changes.
Since conditioning has not been well explored in bacteria, we are investigating whether Salmonella can learn new conditioned responses by pairing two unrelated carbon sources, citrate and maltose. We leveraged a prototype of the Microbial Evolution and Growth Arena (MEGA)-plate motility assay to define a new natural history. By pairing stimuli across a physical landscape, we can select for bacteria that learn to use citrate to anticipate maltose and can quickly deplete the second carbon source. Time-series imaging of bacteria as they swim across the plate shows evidence of emerging variants capable of swimming faster through maltose and unique swimming behaviours through repeated passaging. This approach selects for the fastest swimming bacteria, not necessarily bacteria that have acquired anticipatory regulation. As such, further genetic and transcriptional analysis of the variants are necessary. Similar passaging of Salmonella in broth allowed us to compare anticipatory regulation across a physical and non-physical landscape.
Learning to anticipate environmental changes will provide a bacterium with a selective advantage, allowing it to outcompete its conspecifics which are slower to respond. From this investigation, we hope to provide insight into the learning capacity of bacteria and further understand how bacteria exploit memory to problem-solve.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Bacteria that encounter predictable changes in their environment can acquire anticipatory gene regulation. This may be similar to Pavlovian conditioning, a type of associative learning that involves pairing two unrelated stimuli and anticipatory behavioural changes. Since conditioning has not been well explored in bacteria, we investigate whether Salmonella can learn new behaviours by pairing two unrelated carbon sources, citrate and maltose. We leveraged a motility plate assay to define a new natural history. By pairing stimuli across a physical landscape, we can select for bacteria that learn to use citrate to anticipate maltose. Time-series imaging shows evidence of variants capable of swimming faster through maltose and unique swimming behaviours through repeated passaging. Similar passaging of Salmonella in broth allowed us to compare anticipatory regulation across physical and non-physical landscapes. From this investigation, we hope to further understand the learning capacity of bacteria and how bacteria exploit memory to solve problems.


title: Patient Engagement in Autism Research

title: Facilitators and Barriers Contributing to Patient Engagement in Autistic Children’s Research

contributor:
Stelios, Georgiades
Health Sciences

subject:
autism
patient engagement
children population

abstract:
Background: Marginalized population groups are more likely to be under-represented in autistic children’s research.

Rationale: Our understanding of the low levels of research engagement among autistic children from these marginalized groups is limited.

Objectives: (1) to examine some of the under-represented populations in autism children’s research; (2) to assess the facilitators and barriers contributing to patient engagement in autistic children’s research; (3) to suggest considerations for the development of a more equitable approach to autistic children’s research.

Methods: A scoping review was conducted on studies published during January 2011-December 2021 in five electronic research databases by two reviewers in duplicate. English qualitative/quantitative/mixed methods studies that engaged autistic children aged 2-18 and/or their parents as research participants or in the process of patient-oriented research were included.

Results: Some of the under-represented marginalized autistic children populations identified from the 21 included studies were: (1) those living in developing/under-developed countries, (2) those who received autism services from centres that do not collaborate with researchers, (3) families of ethnic minority in Western countries, (4) autistic children who received late diagnosis, (5) families whose first language is not English, (6) male parents of autistic children, (7) female autistic children, (8) families with low household income who are not enrolled in governmental healthcare financial support program and (9) those who lack technological literacy skills. Facilitators of patient engagement were: (1) building trust-based relationships among stakeholders, (2) engaging patients throughout research development, and (3) patient engagement in research funding processes. The barriers were: (1) allocation of research funding, (2) identity conflict, (3) applicability of research evidence, and (4) social stigmatization towards autism.

Discussion: To enhance patient engagement in autistic children’s research, policymakers, researchers and funders should prioritize participant’s needs in all stages of the research process.

Conclusion: The diverse identities autistic children carry should be better acknowledged. An equity approach to research is needed.

abstract: Thesis

abstract: Master of Public Health (MPH)

abstract:
Autistic children from certain marginalized population groups are less likely to be
engaged in research. This thesis aims to examine the facilitators and barriers contributing to
this phenomenon. As predicted, several child and family characteristics, socio-economic
factors, and contextual research structures appear to be associated with patient engagement in
autism research. Several recommendations are made for policymakers, researchers and funders
on ways to prioritize autistic populations’ needs, enhance patient engagement, and promote a
more equitable approach to autism research.


title: A Comparative Analysis of COVID-19 Physical Distancing Policies in South Africa and Uganda - January 2020-November 2021

abstract:
Background: COVID-19 responses internationally have depended on physical distancing policies to mitigate or contain the spread of the virus, given the initial absence of treatments and limitations on vaccine availability. Across Africa, countries have varied in their COVID-19 responses and resulting local epidemiology. These jurisdictions differ based on contextual factors affecting their responses such as past epidemic experience, ratings of epidemic preparedness, and income level, among others. This study aims to explore how policy responses affected the COVID-19 epidemiology in these jurisdictions.
Methods: A qualitative multiple embedded case study design was followed to examine the COVID-19 policy responses in South Africa and Uganda from January 2020 to November 2021. A documentary review was conducted using sources including government websites and reports, news articles, and peer-reviewed journal articles to obtain data on policy responses and contextual factors. Epidemiological data were collected from public sources. Key informant interviews conducted with relevant stakeholders were used to confirm findings and cover missing information. A comparative analysis was conducted to explore differences in implementation of different types of physical distancing policies and potential consequences of lifting or prolonging public health measures.
Results: South African and Ugandan policy responses included physical distancing measures such as lockdown, international travel bans, school closures, public transportation measures, and curfew, in addition to relief programs, vaccinations, and enforcement of policies. Differences between jurisdiction policy responses existed in terms of overarching policy response strategy, timing, and stringency.
Conclusions: This study focused on providing in-depth comparisons of COVID-19 policy responses and relevant contextual factors in South Africa and Uganda. The study showed how contextual factors such as population age, geographic distribution, and recent epidemic response experience can influence COVID-19 transmission and response. The study also showed differences in overall strategy, timing, and strictness of epidemic management policies in these jurisdictions. These findings suggest it may be important to have sustained, strict measures to limit the spread of COVID-19 and manage the course of a pandemic, which need to be further explored alongside other important social and economic pandemic outcomes.

abstract: Thesis

abstract: Master of Public Health (MPH)

abstract: COVID-19 responses internationally have depended on physical distancing policies to mitigate or contain the spread of the virus since the World Health Organization (WHO) declared a pandemic in March 2020. It is therefore worth exploring the impact of these physical distancing policies on COVID-19 epidemiology throughout the pandemic thus far. COVID-19 physical distancing policy responses in African countries have not been well-studied. This study aims to explore implementation of select physical distancing policies enacted in South Africa and Uganda, how the policies affected local epidemiology, how the policy responses compared across the jurisdictions, and how contextual factors may have affected COVID-19 policy development and timing. Responses in each jurisdiction were compared based on physical distancing policies including lockdown, international travel bans, school closures, public transportation measures, and curfew, in addition to relief programs, vaccinations, and enforcement of policies.


title: Boundary Versus Interior Defects for a Ginzburg-Landau Model with Tangential Anchoring Conditions

contributor:
Bronsard, Lia
Alama, Stanley
Mathematics and Statistics

subject:
Liquid crystals
Ginzburg-Landau
Nematics
Oseen-Frank
Weak Anchoring
Strong Anchoring

abstract: In this thesis, we study six Ginzburg-Landau minimization problems in the context of two-dimensional nematic liquid crystals with the intention of finding conditions for the existence of boundary vortices. The first minimization problem consists of the standard Ginzburg-Landau energy on bounded, simply connected domains Ω ⊂ R2 with boundary energy penalizing minimizers who stray from being parallel to some smooth S1-valued boundary function g of degree D ≥ 1. The second and third minimization problems consider the same Ginzburg-Landau energy but now with divergence and curl penalization in the interior and boundary function taken to be g = τ, the positively oriented unit tangent vector to the boundary. The remaining three problems involve minimizing the same energies, but now over the set for which all functions are precisely parallel to the given boundary data (up to a set for which their norms can be zero). These six problems are classified under two categories called the weak and strong orthogonal problems. In each of the six problems, we show that conditions exist for which sequences of minimizers converge to a limiting S1-valued vector field describing an equilibrium configuration for nematic material with defects. In some cases, energy estimates are obtained that show vortices belong to the boundary exclusively and the exact number of these vortices are known. A special case is also studied in the strong orthogonality setting. The analysis here suggests that geometries exist for which boundary vortices may be energetically preferable to interior vortices in the case where interior and boundary vortices have similar energy contributions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THERMOELECTRICITY AND HEAT CONDUCTION IN III-V NANOWIRES

contributor:
LaPierre, Ray Robert
Engineering Physics

subject: nanowire thermoelectric GaAs simulation

abstract:
Thermoelectric devices (TEDs) are useful in a variety of niche applications, but low efficiencies limit their broader application. Semiconductor nanowires (NWs) could be the key to efficient thermoelectrics, through the benefits of one-dimensional band structures and a greatly reduced thermal conductivity. This thesis explores the transport fundamentals, experimental characterization, and computational approaches relevant to prospective III-V NW TEDs.
Predictive electronic transport models are outlined for NWs and bulk III-Vs. These models are used to determine the optimum carrier concentration for maximizing the thermoelectric figure of merit (𝑍𝑇) in the bulk and in NWs of arbitrary size. We demonstrate the physical mechanisms underlying electronic thermoelectric improvements in NWs and confirm the superior performance of InSb and InAs, among other III-Vs.
Next, thermal conductivity reduction in structurally complex NWs is investigated as a means of improving 𝑍𝑇. We compare polytypic and twinning superlattice (TSL) GaAs NWs in measurements obtained by a novel application of the 3𝜔 method. We find thermal conductivities of 8.4 ± 1.6 W/m-K and 5.2 ± 1.0 W/m-K for the polytypic and TSL NWs, respectively, demonstrating a significant difference and an almost ten-fold reduction compared to 50 W/m-K of bulk GaAs.
We employ molecular dynamics simulations and the atomistic Green’s function method to address phonon engineering in generalized GaAs NW structures. In comparing twinning NWs, we find that a TSL period of 50 Å minimizes the lattice thermal conductivity across all the diameters considered. Our results also illustrate the importance of NW surfaces versus the internal crystal structure. Phonon coherence lengths are obtained by analyzing thermal conductivity trends in periodic and aperiodic structures. Transmission spectra are calculated to reveal the phonon frequencies targeted by structural engineering in NWs. These findings explain the range of thermal conductivities obtained for GaAs NWs with various crystal phases.
Finally, to inform future growths of TSL NWs, we study the influence of the substrate temperature and V/III flux ratio on TSL formation in Te-doped GaAs NWs. The crystal structure of several NWs is investigated using transmission electron microscopy, revealing a range of polytypic and TSL morphologies. We find that periodic TSLs form only at low V/III flux ratios of 0.5 and substrate temperatures of 492 to 537 °C. To explain these trends, we derive a phase diagram for TSL NWs based on a kinetic growth model.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
In a circuit of dissimilar conductors, temperature differences create voltage differences that can drive electrical currents. Similarly, electrical currents in such circuits inherently lead to heating and cooling. These phenomena are known as thermoelectric effects because they couple heat and charge transport (electricity) in a symmetric and reversible way. The goal of some thermoelectric devices (TEDs) is to exploit these effects to generate electrical power or to provide controlled cooling. However, greater conversion efficiencies are required to compete against other existing technologies.
With the advent of nanofabrication, semiconductor nanowires (NWs) have emerged as an attractive material system for efficient TEDs. In this thesis, we explore their thermal and electronic properties. We demonstrate a novel way to measure the NW thermal conductivity and employ computational methods to examine heat transport in NWs with various crystal structures. Finally, we examine how synthesis conditions can determine the morphology of NWs.


title: Functional Outcomes In Musculoskeletal Oncology

contributor: Clinical Health Sciences (Health Research Methodology)

subject: oncology

abstract:
In musculoskeletal oncology, limb salvage surgery is now the standard of care for most patients with bone or soft tissue tumors of the extremities. There has been an increased interest in quantifying functional outcomes following limb salvage with both physician reported and patient reported outcome tools utilized. However, due to the rarity of the disease and lack of prospective data, there remains significant gaps in the literature surrounding functional outcomes in this population. This thesis proposes minimal important difference values for commonly used functional outcome measures and created a predictive model for postoperative function for musculoskeletal oncology patients following lower extremity limb salvage and endoprosthetic reconstruction.

The data for this thesis was retrieved from the Prophylactic Antibiotic Regimens in Tumor Surgery (PARITY) trial database and included patients undergoing lower extremity surgical resection and endoprosthetic reconstruction for bone or soft tissue tumors. Utilizing this data, we provided answers to two important clinical questions 1) establishing minimal important difference (MID) values for commonly utilized functional outcome scoring systems and 2) determine patient and tumor factors predictive of postoperative function.

We developed both anchor-based and distribution-based MID values for both the Musculoskeletal Tumor Society Score and the Toronto Extremity Salvage Score, the two most utilized functional outcome tools in the field. Secondly, we characterized the longitudinal changes in function following endoprosthetic reconstruction and identified patient and tumor predictors of postoperative function. On average, patient function improved significantly from their preoperative baseline to 1-year follow-up, exceeding the predefined MID values. Older age, poor preoperative function, and endoprosthetic reconstruction for soft tissue sarcomas were associated with worse outcomes; reconstruction for giant cell tumors were associated with better post-operative function.

Overall, these two studies aim to provide a deeper and more meaningful understanding of functional status in musculoskeletal oncology patients.

abstract: Thesis

abstract: Master of Science (MSc)


title: Development of wrinkled thin film devices for stretchable electronics.

contributor:
Moran-Mirabal, Jose
Chemistry and Chemical Biology

subject:
Wrinkled thin films
Wearable electronics

abstract: Thin film heaters, corrosion-resistance electrode, thin film inductors

abstract:
Stretchable electronics are soft and light weight. Compared with conventional wafer-based electronics, which are rigid and planar, stretchable electronics can conform to curved surfaces and movable parts. The unique properties of stretchable electronics enable their integration with the human body, and open the door for ever more compelling applications, such as advanced surgical tools, wearable monitoring electronics, implantable prosthesis, and many others. However, the development of stretchable electronics is still at an early stage since their mechanical robustness and electrical performance are still far from satisfying.

In this work, I have developed a method to fabricate thin film stretchable devices by solvent-assisted transfer of wrinkled thin films from rigid polystyrene (PS) substrates to elastomeric polydimethylsiloxane (PDMS) substrates. Using this approach, structured thin films containing multiple materials and hybrid structures could be lifted off simultaneously, facilitating the fabrication of stretchable thin film devices. With this approach, I have built corrosion-resistant stretchable electrodes, stretchable thin film heaters, and stretchable thin film inductors. These applications demonstrate the simplicity and effectiveness of this stretchable electronics fabrication strategy. Finally, I made the first step towards fabricating dye-sensitized solar cells (DSSCs) with room temperature processes, including the preparation of mesoporous TiO2 layers through mechanical compression and the integration of an interdigitated electrode that was fabricated solely by bench-top patterning, alignment, and sputtering deposition. These steps lay the foundation for the future development of stretchable DSSC. I anticipate that the fabricated stretchable thin films electronic components will contribute to the advancement of wearable and implantable electronics.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Electronics that can be deformed and conform to the irregular surfaces are attractive because they can be better integrated with the human body. For example, they could improve disease diagnostics and therapeutic treatments by providing wearable continuous monitoring devices and more advanced surgical tools. In this work, I created wrinkled thin films that could be affixed onto an elastic substrate and stretched. The principle of operation of these wrinkled devices mimics the way that the wrinkled skin on our knuckles and elbows allows us to bend our fingers and elbows. This approach makes wrinkled thin films stretchable and could lead to robust electronic devices. I have showcased this approach building a corrosion-resistant stretchable electrode, thin films heaters that can closely conform to joints, and a spiral-shaped inductor that could be used to wirelessly transfer data or power wearable devices. I believe that this work will contribute to the development of electronics that can be worn or implanted in the human body.


title: Role of Serotonin-Autophagy Axis in Intestinal Inflammation

contributor:
Khan, Waliul
Medical Sciences

subject: 5-HT Autophagy Inflammation Intestine

abstract:
Autophagy, an intracellular degradation, and recycling process is essential in maintaining
cellular homeostasis. Dysregulated autophagy is linked to the pathogenesis of various
diseases, including inflammatory bowel disease (IBD) which consists of Crohn’s disease
and ulcerative colitis. In IBD, enterochromaffin cell numbers and one of its main product
serotonin (5-hydroxytryptamine; 5-HT) levels are elevated. Previously, we had shown
that tryptophan hydroxylase 1 deficient (Tph1-/-) mice, with reduced gut 5-HT had
decreased severity of colitis. Here, we showed that gut 5-HT plays a vital role in
modulating autophagy and thus regulating gut microbial composition and susceptibility to
intestinal inflammation. Tph1-/- mice, had upregulated colonic autophagy via the
mammalian target of rapamycin pathway (mTOR), and decreased colitis severity. Tph1-/-
mice after 5-HT replenishment, and serotonin reuptake transporter deficient (SERT-/-)
mice, which have increased 5-HT levels, showed converse results. Deletion of intestinal
epithelial cell-specific autophagy gene, Atg7, in Tph1-/- mice (DKO mice) abolished the
protective effect of Tph1 deficiency in colitis, decreased the production of antimicrobial
peptide, β-defensin 1 and promoted colitogenic microbiota. Furthermore, using cecal
microbial transplantation, we found that the colitic microbiota of the DKO mice
contributed to the increased severity of colitis. Supporting this pathway's translational
importance, we uncovered that 5-HT treatment of peripheral blood mononuclear cells
from both healthy volunteers and patients with Crohn’s disease inhibited autophagy via
the mTOR pathway. Our results in this thesis emphasize the role of 5-HT-autophagymicrobiota
axis in intestinal inflammation. Moreover, these findings suggest 5-HT as a novel therapeutic target in intestinal inflammatory disorders such as IBD that exhibit
dysregulated autophagy.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Approximately 0.7% of Canadians are currently affected with inflammatory bowel
disease (IBD). The gut hormone serotonin, which regulates many normal functions, is
elevated in gut inflammation. Reduced serotonin levels decrease the severity of
inflammation. IBD pathology has been linked to a unique cell self-eating process called
autophagy. Using cell lines, mice, and samples from IBD patients, we assessed the
interactions between serotonin signaling and autophagy during gut inflammation. I found
that an increase in serotonin levels enhances the severity of gut inflammation by
inhibiting autophagy. We also established the connection between serotonin and
autophagy in the intestinal epithelial cells, and how this modulates epithelial cell function.
Furthermore, we demonstrated the establishment of an altered gut microbiota upon
disruption of the serotonin-autophagy axis in the epithelial cells, which subsequently
influenced gut inflammation severity. Thus, we identified one of the key triggers related
to the pathogenesis and severity of IBD.


title: Mechanical Property Development, Selective Oxidation, and Galvanizing of Medium-Mn Third Generation Advanced High Strength Steel

contributor:
McDermid, Joseph
Materials Science and Engineering

subject:
Medium-Mn AHSS
Selective Oxidation
3G AHSS
Reactive Wetting
Mechanical Properties
Continuous Hot-Dip Galvanizing
Microstructure Evolution
Intercritical Annealing

abstract:
Medium Mn (med-Mn) third generation advanced high strength steels (3G AHSSs) are promising candidates for meeting automotive weight reduction requirements without compromising passenger safety. However, the thermal processing of these steels should be compatible with continuous galvanizing line (CGL) processing capabilities as it provides cost-effective, robust corrosion protection for autobody parts. Hence, the main objective of this Ph.D. research is to develop a CGL-compatible thermal processing route for a prototype 0.2C-6Mn-1.5Si-0.5Al-0.5Cr-xSn (wt%) (x = 0 and 0.05 wt%) med-Mn steel that will result in the 3G AHSS target mechanical properties (24,000 MPa%  UTS × TE  40,000 MPa%) and high-quality galvanized coatings via enhanced reactive wetting.
It was found that the starting microstructure, intercritical annealing (IA) time/temperature, and Sn micro-alloying had a significant effect on the retained austenite volume fraction and stability and, thereby, the mechanical properties of the prototype med-Mn steel. For the as-received cold-rolled (CR) starting microstructure, the intercritical austenite nucleated and grew on dissolving carbide particles and resulted in blocky retained austenite. However, Sn micro-alloying significantly effected the intercritical austenite chemical stability by segregating to the carbide/matrix interface and retarding C partitioning to the intercritical austenite. This resulted in lower volume fractions of low stability retained austenite which transformed to martensite (via the TRIP effect) at low strains, thereby quickly exhausting the TRIP effect and resulting in a failure to sustain high work hardening rates and delay the onset of necking. Consequently, the Sn micro-alloyed CR starting microstructure was unsuccessful in achieving 3G AHSS target mechanical properties regardless of the IA parameters employed. Contrastingly, the CR starting microstructure without Sn micro-alloying was able to meet target 3G mechanical properties via intercritical annealing at 675 °C × 60 s and 120 s, and at 690 °C × 60 s owing to sufficiently rapid carbide dissolution and C/Mn partitioning into the intercritical austenite such that it had sufficient mechanical and chemical stability to sustain a gradual deformation-induced transformation to martensite and maintain high work hardening rates.
On the other hand, the martensitic (M) starting microstructure produced higher volume fractions of chemically and mechanically stable lamellar retained austenite regardless of Sn micro-alloying. Intercritical annealing at 650 °C × 60 s and 675 °C × 60 s and 120 s produced 3G AHSS target mechanical properties. It was shown that the stable lamellar retained austenite transformed gradually during deformation. Furthermore, deformation-induced nano-twin formation in the retained austenite was observed, suggesting the TWIP effect being operational alongside the TRIP effect. As a result, a continuous supply of obstacles to dislocation motion was maintained during deformation, which aided in sustaining a high work hardening rate and resulted in a high strength/ductility balance, meeting 3G AHSS target properties. Based on these results, the martensitic starting microstructure without Sn micro-alloying and the M-675 °C × 120 s IA condition were chosen for the selective oxidation and reactive wetting studies.
The selective oxidation study determined the effect of a N2-5H2-xH2O (vol%) process atmosphere pO2 (–30, –10, and +5 °C dew point (Tdp)) on the composition, morphology, and spatial distribution of the external and internal oxides formed during the austenitizing and subsequent intercritical annealing cycles. The objective of this study was to identify the process atmosphere for the promising M-675 °C × 120 s heat treatment that would result in a pre-immersion surface that could be successfully galvanized in a conventional galvanizing (GI) bath. The austenitizing heat treatment (775 °C × 600 s) used to produce the martensitic starting microstructure resulted in thick (~ 200 nm) external oxides comprising MnO, MnAl2O4, MnSiO3/Mn2SiO4, and MnCr2O4, regardless of the process atmosphere pO2. However, intermediate flash pickling was successful in dissolving the external oxides to a thickness of approximately 30 nm along with exposing metallic Fe in areas which contained relatively thin external oxides. Furthermore, extruded Fe nodules that were trapped under the external oxides were revealed during the flash pickling process. Overall, flash pickling resulted in a surface consisting of dispersed external oxide particles with exposed metallic substrate and extruded Fe nodules. This external surface remained unchanged during IA owing to the multi-micron (~ 2–8 µm) solute-depleted layer that formed during the austenitizing heat treatment.
Subsequent galvanizing in a 0.2 wt% (dissolved) Al GI bath with an immersion time of 4 s at 460 °C was successful in achieving high-quality, adherent galvanized coatings through multiple reactive wetting mechanisms. The dispersed nodule-type external oxides along with exposed substrate and extruded Fe nodules on the pre-immersion surface facilitated direct wetting of the steel substrate and promoted the formation of a robust and continuous Fe2Al5Znx interfacial layer at the steel/coating interface. Additionally, oxide lift-off, oxide wetting, bath metal ingress, and aluminothermic reduction were operational during galvanizing. The galvanized med-Mn steels met 3G AHSS target mechanical properties. Overall, this Ph.D. research showed that it is possible to employ a CGL-compatible thermal processing route for med-Mn steels to successfully produce 3G AHSS target mechanical properties as well as robust galvanized coatings.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: One of the largest challenges associated with incorporating the next generation of advanced high strength steels into the automotive industry lies in processing these steels in existing industrial production lines. In that regard, a two-stage heat treatment with an intermediate flash pickling stage and process atmosphere compatible with existing industrial continuous galvanizing line technology was developed for a prototype medium-Mn steel. The heat-treated prototype steel met the target mechanical properties outlined for the next generation of advanced high strength steels. Furthermore, the heat treatment and process atmosphere utilised in this research produced a surface that facilitated the successful galvanizing of the prototype medium-Mn steel. This adherent and high-quality galvanized coating will provide robust corrosion protection if the candidate medium-Mn steel is used in future automotive structural applications.


title: The Association between Frailty Status, Multimorbidity, and Patient Demographics, and Changes in Primary Care Since the COVID-19 Pandemic: A Retrospective Cohort Study

title: Changes In Primary Care Of Older Adults Since COVID-19

contributor:
Howard, Michelle
Health Research Methodology

subject:
Frailty
Multimorbidity
Chronic Disease
Socioeconomic Status
Primary Care
COVID-19
Virtual Care
Telemedicine

abstract:
Purpose: With the start of the SARS-COV-2 pandemic in March 2020, Canadian primary care practices temporarily shifted from in-person to virtual care. The purpose of this thesis was to understand whether the pandemic impacted the primary care management of older adults with varying levels of frailty and multimorbidity in terms of care modality, volume of encounters, and visits for anxiety/depression. It also aimed to identify which patients comparatively experienced greater reductions in frequencies of routine preventive care and monitoring activities.
Methods: A research database from a sub-set of MUSIC family practice for patients ≥ 65 years of age (n=1813) was employed. Patient demographics, clinician-assessed frailty status, encounters, and chronic disease management information were retrieved. Changes from 14 months pre to 14 months since (peri) the pandemic were described and associations between patient characteristics and the extent of changes in outcomes from pre- to peri-pandemic were analyzed using regression models.
Results: The mean age was 74 years, with a mean of 2.5 chronic conditions (26% hypertension, 14% diabetes). 2.1% of patients experienced high frailty levels. The mean number of encounters increased peri-pandemic overall (peri: 10.4 (SD 11.1) vs. pre: 7.1 (SD 5.5)) and for anxiety/depression, with most visits becoming virtual. Increasing numbers of overall visits were significantly associated with female sex, increasing frailty level, and having 4+ conditions. While the frequency of routine preventive and monitoring activities related to chronic conditions decreased, the mean values (e.g., lab results) did not considerably change. In the adjusted models, generally older patients, with increasing levels of frailty, and numbers of conditions tended to receive more care, however most associations were not statistically significant.
Conclusion: Overall encounters and visits related to anxiety/depression increased peri-pandemic. Despite concerns about pandemic-related care disruptions, common elements of primary care among higher risk older patients were not notably impacted.

abstract: Thesis

abstract: Master of Health Sciences (MSc)

abstract: Many adults ≥65 years of age live with chronic conditions or frailty, requiring ongoing monitoring. Primary care physicians are fundamental in providing this continuous care. With the COVID-19 pandemic, healthcare access was restricted, many doctors switched to temporarily providing virtual care, and there were concerns about patients’ mental health. Questions arose regarding possible gaps in primary care and where efforts should be focused post-pandemic. The objectives of this thesis were 1) to understand how the pandemic impacted the management of this population and the changes in care patterns (modality, encounter numbers overall and for anxiety/depression, and chronic condition management); and 2) identify patient characteristics associated with changes. There was an overall virtual care driven increase in encounters peri-pandemic and for visits relating to anxiety/depression. Frequencies of chronic condition care activities dropped, however older patients and those with increasing levels of frailty and numbers of conditions tended to be better monitored.


title: A STUDY OF THE TEXTUAL HISTORY, DOCTRINAL CONTENT AND PHILOSOPHY OF TWELVER SHĪʿĪ LITURGY FROM THE  PERIOD OF THE IMĀMS TO ʿABBĀS AL-QUMMĪ (D.1359/1940)

contributor:
Liyakat Takim
Religious Studies

subject:
Islamic Studies
Religious Studies
Prayer
Dua
Shia
Islam
Shiism
History
Religion
Liturgy
Ziyarat

abstract: This doctoral thesis is on the subject of Islamic and Shia liturgy or prayer. it covers its history, philosophy and doctrinal content

abstract: This dissertation explores the historical, doctrinal, and philosophical aspects pertaining to Twelver Shīʿī liturgy. In doing so, it brings to light the broad historical contours which established its textual development and proliferation from the period of the Imāms until that of Shaykh ʿAbbās al-Qummī. This historical development entailed the production of the liturgical genre as a textual tradition that developed from the 2nd/8th century. It is believed that portions of this early textual tradition went on to form the basis of later liturgical collections such as al-Kulaynī’s Kitāb al-duʿāʾ, Ibn Qūlawayh’s Kāmil al-ziyārāt and al-Ṭūsī’s Miṣbāḥ al-mutahajjid. This is also indicative of a profound interest in liturgical material by both the scholars who compiled this material and the faithful who performed it, which is evidenced by the repeated copying and transmission of such texts in various parts of the Muslim world. These liturgical texts (duʿāʾ and ziyāra) are also replete with philosophical and theological motifs which underly their function as a means of developing Shīʿī piety and a religious identity that focuses upon complete submission to the Imāms of the People of the House (ahl al-bayt). Considering the above, the texts, when recited and enacted, may be described as a form of performative theology in the Twelver Shīʿī tradition. It is this performative theology which aided in the development and fortification of Twelver Shīʿī identity, especially in light of their minority and often beleaguered social-political position at various times in history. Through an in-depth investigation into the culture and practice of the rigorous and systematic transmission of liturgical texts, this dissertation provides, for the first time, clear evidence of a method for preserving the liturgical compositions that were attributed to the Imāms. With a selection of words and phrases drawn from these texts, a sensitive analysis is made of their theological and cosmological underpinnings. It is hoped that such an analysis will pave the way for further consideration of this, until now, somewhat neglected field of Islamic Studies.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Mixed Offspring in the Hebrew Bible and Second Temple Period

contributor:
Daniel, Machiela
Matthew, Thiessen
Eileen, Schuller
Religious Studies

subject: Mixed offspring; intermarriage; Second Temple Judaism; Identity; Hebrew Bible; Gender; Child-centered; Dead Sea Scrolls; Philo; Josephus; Jubilees; Purity; Profane; exogamy;

abstract:
My dissertation analyzes the status of mixed offspring in the Hebrew Bible and Second Temple texts to understand the diverse ways children from intermarried couples were presented in pre-Mishnaic Jewish literature. Prior to the Mishnah (m. Qidd 3:12), there is no evidence of a monolithic ruling to regulate the status of mixed progeny. My goal, therefore, is to examine the different ways mixed offspring were treated, and to better understand whether they endured any social repercussions due to their mixed lineage. In turn, I explore the diverse ways Jewish identity was constructed in antiquity, and how matters like gender, lineage, and geography were used to establish social boundaries. Within contemporary scholarship, the study of mixed progeny in antiquity has been incidental to other research topics, including the expulsion narrative in Ezra 9–10, genealogical purity, and the matrilineal principle in Judaism. To date, no comprehensive approach has been undertaken to trace the status of mixed progeny in pre-Mishnaic Jewish literature. My dissertation seeks to fill this lacuna.
	Following a brief introduction in chapter 1, my subsequent chapters are divided into four time periods: the pre-Persian period (chapter 2); the Persian period (chapter 3); the Hellenistic period (chapter 4); and the early Roman period (chapter 5). Within each chapter, I analyze texts generally dated to those eras that include some information about mixed offspring. In my concluding chapter, I reveal three main factors that impacted the status of mixed progeny in antiquity: genealogy, residential location, and piety. I also provide a heuristic framework to categorize my findings of mixed offspring. While there were two main responses towards mixed progeny in antiquity (accepted or rejected), not every case fits nicely into these two classifications. Therefore, the treatment of mixed progeny must be understood on a spectrum to better appreciate the nuance within each text.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Microbiota-derived D-lactate alters macrophage inflammation

contributor:
Schertzer, Jonathan
Biochemistry and Biomedical Sciences

abstract: Obesity-induced inflammation is a factor involved in the risk and progression of type 2 diabetes and non-alcoholic fatty liver disease. These diseases are associated with changes in gut microbiota composition and bacterial metabolites. Bacterial components with known innate immune receptors can cooperate with non-immunogenic metabolites derived from the gut microbiota to alter host immunity. Gut bacteria produce almost all D-lactate in the host, whereas L-lactate is host-derived. It is known that microbial-derived D-lactate in the portal circulation programs liver-resident macrophages to help combat bacterial infections. It was unknown how D-lactate and L-lactate alter cell-autonomous inflammation in macrophages exposed to low levels of bacterial cell wall muropeptides or lipopolysaccharide (LPS). It was also unknown if macrophage co-stimulation altered inflammation in macrophages exposed to bacterial metabolites and cell wall components. In vitro models showed that D-lactate had no effect (or a very small effect) on multiple markers of inflammation in the absence of interferon-gamma (IFN-γ) co-stimulation. Nevertheless, initial experiments on clonal macrophages discovered that equimolar and physiological levels of D-lactate increased Nos2 expression compared to L-lactate. Bone marrow-derived macrophages (BMDMs) co-stimulated with IFN-γ revealed a larger effect of D-lactate on immunity. Compared to L-lactate, D-lactate increased nitric oxide (NO) production and increased activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome in BMDMs co-stimulated with IFN-γ and exposed to LPS. Further, D-lactate prevented L-lactate-induced lowering of NO production and NLRP3 inflammasome-mediated release of IL-1β from BMDMs co-stimulated with IFN-γ and LPS. Identifying appropriate cell models and defining conditions that reveal the effect of D-lactate versus L-lactate on immune responses in isolated cells was a major contribution of this work. Future work should characterize the interaction of macrophages and hepatocytes. This research may lead to the identification of gut microbiota-based approaches to limit liver inflammation in obesity and metabolic disease.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Gut bacteria can influence both immunity and metabolism in the liver. It is not clear how bacteria in the gut communicate to the liver. Lactate is a key metabolite that can fuel liver metabolism and alter immunity. There are 2 types of lactate. L-lactate is host-derived, whereas D-lactate is mainly produced by gut bacteria. Bacterial-derived D-lactate can alter immune responses mediated by immune cells in the liver, including macrophages. Bacterial metabolites such as D-lactate and bacterial components that cause inflammation are increased in the blood during obesity. Our findings show that D-lactate can increase inflammation in macrophages when combined with bacterial components and that D-lactate
increases inflammation more than L-lactate. Understanding the role of D-lactate may help us understand how bacteria contribute to insulin resistance, higher blood glucose and the risk of type 2 diabetes and fatty liver disease.


title: 'It's just my home, you know?' Home-making and Belonging for People Labelled/with Intellectual Disability

contributor:
Wilton, Robert
Geography

subject:
intellectual disability
housing
home-making
belonging
Ontario
Canada

abstract:
This master’s thesis research focuses on the experiences of people labelled/with intellectual disability in their current homes and also what they want for their future home. Few studies in Canada have focused on specifically asking this population what their ideal home looks like and acknowledging the gap between this and what their reality is. Advocacy groups in Canada and the United Nations Convention on the Rights for Persons with Disabilities have been calling for years to better address the rights of people with disabilities and their place in the community, yet there has been little progress within Ontario towards this.
Using semi-structured interviews and an arts workshop, participants were asked to think about what their life is like now and what their aspirations are for their future. The research is based on a relational model of home as more than just a physical structure and expands the definition to include the neighbourhood, relationships, and support that participants experience, which shape their home and their feelings of belonging inside and outside of it. Findings show that, while there were opportunities for agency within their homes and relationships, there are many restrictions to attaining their ideal home, including funding constraints, long wait lists, and few choices for what type of housing they receive. The findings of this study have important implications for ideas of belonging and processes of home-making within geographic research, as well as for future policy based on housing for people labelled/with intellectual disabilities in Ontario.

abstract: Thesis

abstract: Master of Arts (MA)


title: Trauma and Care: Abandoned Memories in Egypt and Saudi Arabia

title: Lived Experiences of an Egyptian Family in the Diaspora

contributor:
Rethmann, Petra
Anthropology

subject: socio-cultural anthropology, memory, affect, identity, diaspora

abstract:
My research explores my Egyptian family’s migration from Egypt to Saudi Arabia and
Canada. It examines the role of photography to document memories of family reunions,
migration, and stories. The objective of my study is to foster dialogue and raise awareness about the lived experiences of an Egyptian family from the 1950s to contemporary times. The
methodology used in this series is open-ended interviews and textual analysis with family
members: my mother, father and maternal grandfather. My research aims to reconstruct the
historical effects of migration and the lived experience of an Egyptian family in the diaspora. It
looks into intergenerational psychological trauma, its several interfaces and role in familial
relationships, and modernity's emergence in Egypt. I aim to explore transnational identities
through storytelling and photography that capture historical and contemporary movements—the
role of these movements in producing complex versions of identities, belonging and trauma.

abstract: Thesis

abstract: Master of Arts (MA)


title: Developing a Reporting Item Checklist for Studies on the Prevalence of HIV Drug Resistance: A Mixed Methods Study

contributor:
Dr. Lawrence Mbuagbaw
Health Research Methodology

subject:
HIV
drug resistance
reporting guidelines
prevalence
surveillance
reporting checklist

abstract: Background: HIV drug resistance limits the effectiveness of antiretroviral therapy. Adequate surveillance of HIV drug resistance prevalence is challenged by heterogenous and inadequate data reporting. In this study, we sought to identify a list of reporting items for studies of HIV drug resistance prevalence and an understanding of why these items are important to report. Methods: We used a mixed-methods sequential explanatory design involving authors and users of studies of HIV drug resistance prevalence. In the quantitative phase we conducted a cross-sectional electronic survey (n=51). Survey participants rated various reporting items on whether they are essential to report, producing validity ratios which were used to produce a draft reporting item checklist. In the qualitative phase, two focus group discussions (n=9 in total) discussed this draft item checklist and which of the items should be reported and why. We also conducted a thematic analysis of the group discussions to identify emergent themes regarding items to be considered for the reporting guideline. Results: We identified 38 potential reporting items including participant characteristics, sampling methods, and resistance testing methods. The strongest themes that emerged from the discussions were agreement over the importance of reporting certain items, concerns over the availability and ethics of reporting certain participant data, the importance of interpretability and comparability, and the necessity for reporting guidelines to appreciate context-specific prevalence research. Conclusions: We have identified a list of reporting items for studies of the prevalence of HIV drug resistance along with an explanation of why researchers believe these items are important. The next steps involve further elaborating upon these findings in the reporting guidelines.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Drug resistant HIV is very challenging to treat and is an important global health problem. It is difficult to know how common HIV drug resistance is around the world because the studies on HIV drug resistance are not reported similarly. This is because there are no standard guidelines for these studies. In this study, we asked HIV drug resistance researchers to complete a survey on what they thought should be reported is studies measuring HIV drug resistance. Then, we had group conversations where we asked them to explain why they believed the items were important. We identified 38 potential reporting items, most of which would require authors of HIV drug resistance studies to clarify the settings, participants and methods used in their research. These items will make up a reporting checklist for authors of HIV drug resistance studies and make research in this area more comparable


title: Model Risk Management and Ensemble Methods in Credit Risk Modeling

contributor:
Racine, Jeffrey
Maheu, John
Han, Seungjin
Economics

subject:
Model Risk Management
Credit Risk
Expected Credit Loss
Basel
CECL
IFRS-9
Boosting
Bagging
Machine Learning
Fractional Response Models
Probability of Default
Loss Given Default

abstract: The number of statistical and mathematical credit risk models that financial institutions use and manage due to international and domestic regulatory pressures in recent years has steadily increased. This thesis examines the evolution of model risk management and provides some guidance on how to effectively build and manage different bagging and boosting machine learning techniques for estimating expected credit losses. It examines the pros and cons of these machine learning models and benchmarks them against more conventional models used in practice. It also examines methods for improving their interpretability in order to gain comfort and acceptance from auditors and regulators. To the best of this author’s knowledge, there are no academic publications which review, compare, and provide effective model risk management guidance on these machine learning techniques with the purpose of estimating expected credit losses. This thesis is intended for academics, practitioners, auditors, and regulators working in the model risk management and expected credit loss forecasting space.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: DEVELOPING SOFT HIERARCHICALLY-STRUCTURED BIOMATERIALS USING PROTEINS AND BACTERIOPHAGES

contributor:
Hosseini-Doust, Zeinab
Chemical Engineering

subject:
bacteriophage
biomaterials
microstructures
hydrogels
microgels
food safety
wrinkles
inkjet printing

abstract:
Bio-interface topography strongly affects the nature and efficiency of interactions with living cells and biological molecules, making hydrogels decorated with micro and nanostructures an attractive choice for a wide range of biomedical applications. Despite the distinct advantages of protein hydrogels, literature in the field has disproportionately focused on synthetic polymers to the point that most methods are inherently incompatible with proteins and heat-sensitive molecules.
We report the development of multiple biomolecule-friendly technologies to construct microstructured protein and bacteriophage (bacterial virus) hydrogels. Firstly, ordered and sphericity-controllable microbumps were obtained on the surface of protein hydrogels using polystyrene microporous templates. Addition of protein nanogels resulted in the hierarchical nano-on-micro morphology on the microbumps, exhibiting bacterial repellency 100 times stronger than a flat hydrogel surface. The developed microstructures are therefore especially suitable for antifouling applications.
The microstructures created on protein hydrogels paved the way for applying honeycomb template on proteinous bacterial viruses. We developed a high-throughput method to manufacture isolated, homogenous, pure and hybrid phage microgels. The crosslinked phages in each phage-exclusive microgel self-organized and exhibited a highly-aligned nanofibrous texture. Sprays of hybrid microgels loaded with potent virulent phage effectively reduced heavy loads of multidrug resistant Escherichia coli O157:H7 on food products by 6 logs.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Bacteriophages (bacterial viruses), also known as phages, are natural bacteria predators. These viruses act as direct missiles, each phage targeting limited groups of bacteria. In addition, phages are an endless resource for self-propagating nanoparticles that can be used as building blocks for new material.
I developed a platform for manufacturing a large quantity of microscale beads made of millions of phages. These micro-beads can be sprayed on fresh produce and meat to remove bacterial contamination (with the added benefit of not affecting taste or smell). I also printed phages on substrates, like an ink. The printed phage ink evolved into a patented technology for designing phage coatings on surfaces with very high surface area, like the small structures on our fingers. This phage coating was successfully used to test the existence of bacteria in liquids.