title: Domestic Violence and the Newsprint Media: A Critical Discourse Analysis of Three Canadian Newspapers in a Covid-19 Context

contributor:
Greene, Saara
Social Work

subject:
Domestic Violence
Power
Feminist Theory
Newsprint Media

abstract: This paper seeks to explore the way the print news media reported on issues related to domestic violence (DV) in the Greater Toronto/Hamilton Ontario area in the context of Covid-19 from March 2020 to March 2021. Specifically, I drew on three newspapers to include the Hamilton Spectator, the Toronto Star, and the Globe and Mail. This research is primarily concerned with the discourses that emerged about gender-based violence in the newsprint media during a time when people were required to stay in their homes and when access to community-based services that support women experiencing DV became increasing challenging. Using a Critical Discourse Analysis (CDA) that was grounded in a feminist theoretical framework, three themes emerged as particularly dominant. These included: a) the media’s use of “victim” and “survivor” discourses, b) women’s experiences of DV and access to resources, and c) public health discourses that centered on responses to DV in light of Covid-19. This paper concluded that reinforcement of dominant narratives about the socio political and gendered landscape in which DV is reported on via newsprint media sources, depict DV as an individual rather than structural issue that shifts the blame away from historical and current day social, economic, and political forces that create the conditions in which DV occurs. Importantly, the newsprint media promote a homogenous definition of ‘woman’ thus elevating dominant DV discourses that tend to centre the experiences of white, heterosexual women and that result in silencing the voices of gender diverse and racialized women. Consequently, my research suggests that there is an ongoing need to build on existing feminist literature to critically examine DV as a systemic issue that requires a response that is inclusive of the diversity of women who experience DV, the needs for services to support a diversity of women, and to do so in ways that move away from individual solutions toward shifts in practice and policy.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: Seniors Experiencing Homelessness and Their Understanding of the Meaning of Home: Using Collage to Envision Home

contributor:
Baker Collins, Stephanie
Social Work

subject:
homelessness
seniors
aging in place

abstract: This study explores the meanings and understandings of home of seniors experiencing homelessness and the supports and services these individuals need in their homes as they age. Guided by interpretive social sciences and critical gerontology this study engaged with 7 homeless seniors living in a seniors’ shelter in the City of Toronto. Using arts-based research methodology, this study had 7 seniors make collages to represent their vision and understandings of ‘home’. In addition, participants were asked what specific support and services they would need in their homes in order to support their overall health and wellbeing. Based on individual art session recordings and collages, thematic analysis was used to identify key themes in order to understand what home means, and what supports and services are required for homeless seniors. For these participants home is a unique physical space with nuanced meanings and provides unique elements that a shelter cannot. In addition, these participants identified specific in-home and community supports they would require in their homes.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: Mapping Mark: Quantitative Study of the Clause of Thematization as a Means of Illumination the Gospel Genre

contributor:
Porter, Stanley
Westfall, Cynthia

subject: Gospel, Thematization, Jewish writings, Mark, referential narrative

abstract: This project exhaustively examines the first element (theme) of each clause in Mark and in samples from other roughly contemporaneous Jewish writings. The comparative documents are divided into two categories, referential and non-referential narratives. Then statistical analyses (χ2 and t-test) are used to determine with which category of comparative documents Mark more closely aligns. The raw results of these hypothesis tests were equivocal, but their corresponding effect sizes (Cramer’s V and Cohen’s d, respectively) clearly demonstrate that Mark more closely resembles referential narrative, although the difference is small.

abstract: Thesis

abstract: Candidate in Philosophy


title: Salvation - Deliverance from the Supernatural Powers: A Register Analysis of Ephesians 1-3 and 4

contributor:
Porter, Stanley
Westfall, Cynthia
Christian Theology

subject: Ephesians, Salvation, Gentiles, Colossians, Authorship, Paul

abstract:
The study of Ephesians has been approached in multiple ways by scholars. The dominant scholarly debates on Ephesians center on the issues of authorship, to whom the letter was addressed, its comparison with Colossians, and the Jew-Gentile conflict. Scholars have discussed the theme of salvation in their textual and theological analysis and commentary. Most of these discussions do not adequately explain the meaning of salvation at the discourse level. Scholars have suggested a wide range of meanings of salvation in Ephesians: forgiveness of sins (1:7), deliverance from the grip of the evil supernatural powers that controlled them before their conversion (2:2; 6:11, 12), reconciliation between Jews and Gentiles (2:16), and reception of spiritual gifts to the service of the Church (4:7). Salvation in Ephesians is also explained as a rescue from death, sin, and disobedience; from this present world-age; from bondage to the ruler and principalities of the air; and from God’s wrath. It is being freed from the ways of the world and the ruler of the air (2:2-4); being seated with Christ in heavenly realms (2:6); being the workmanship of God; being made alive in Christ (2:5); being created in Christ Jesus (2:10). There is no consensus among scholars regarding the temporal meaning of salvation. The meaning of salvation in Ephesians must be studied in the context of the letter. There is no major study that has applied Systemic Functional Linguistic tools to the study of Ephesians.
Halliday’s model of register analysis provides tools to analyze the context of situation of Ephesians, the study of field, tenor, and mode of Ephesians. These three components of register analysis, show that the linguistic choices made by Paul describe the context of situation in which the meaning of salvation is communicated. This study shows that Paul’s idea of salvation in Ephesians is one of his prominent topics. It explains that salvation is a divinely planned entity. God executes and achieves it through Jesus Christ. Salvation is the gracious gift of God. The mystery of God’s eternal plan of salvation in Jesus Christ reveals that God has incorporated the Gentiles in his plans through adoption in Jesus Christ. It emphasizes the meaning of salvation in terms of Gentiles’ deliverance from their former spiritual bondages. Paul’s Gentile readers’ former spiritual condition corresponds to the contemporary Hindu spiritual condition. They are under spiritual bondage through their magical practices and worshiping of idols. Thus a cross-cultural application to evaluate the meaning of salvation in a Hindu context is warranted.

abstract: Thesis

abstract: Candidate in Philosophy


title: The Viability and Character of Popular Medicine in Seventeenth-century England

contributor:
Alsop, J. D.
History

subject: Popular medicine, seventeenth-century England, Stuart medicine, popular practitioners, lay medicine, female lay medical practitioners, seventeenth-century health care

abstract: This study will demonstrate that the lay or "popular" medical practitioner played a major role in the provision of health care in seventeenth-century England. The medical "professionals" have generally been accepted as providing the most expert and "scientific" medical care (within the limits of contemporary knowledge), and, as such, have been the focus of attention for the majority of studies by medical historians. This study challenges traditional studies on the basis of geography, economic factors, religious influences and contemporary medical practices. The amorphous nature of seventeenth-century medical knowledge will be demonstrated to show the similarity between lay and professional medical treatment. To this end, female lay medical practitioners have been presented as a case study to illustrate the widespread nature and diversity of popular medicine and to assist in defining the role of the popular practitioner, a vital element within seventeenth-century health care.

abstract: Thesis

abstract: Master of Arts (MA)


title: Myth and Language

contributor:
Aldwinckle, R.F.
Christian Theology

subject: Myth, language, logical analysis of language, contemporary theological writing, interpretations

abstract:
The word 'myth' appears frequently in contemporary
theological and exegetical writing. Unfortunately, it is
used with a variety of meanings by different authors, and
this gives rise to the layman’s general misunderstanding of
what is really a technical term. This thesis is an essay
in the clarification of the notion of myth, through the use
of the techniques of logical analysis of language.

abstract: Thesis

abstract: Bachelor of Divinity (BD)


title: Uphill Both Ways: Locating the Spiritual in Helping Professionals’ Narratives of Care with Adolescent Males with Adverse Childhood Experiences

contributor:
Mutter, Kelvin
Christian Studies

subject: Adverse Childhood Experiences, ACE, adolescent development, spiritual community, parrhesia, adolescent males, narratives of care, helping professionals

abstract: Adolescence is an uphill struggle. Research abundantly displays that Adverse Childhood Experiences (ACEs) have a distinct and detrimental effect on adolescents and their development. Recent research has explored the perspectives, thoughts, behaviours, and beliefs of helping professionals who integrate spirituality into their work with adolescents. The purpose of this qualitative study is to develop a thematic analysis of helping professionals’ narratives of care with this population. The narratives of helping professionals’ care of adolescent males with ACEs points to the desire to connect with spiritual community and to make meaning. Helping professionals’ narratives also highlight the constraints of locating spirituality. Theological reflection on parrhesia focuses on developing open, unencumbered discussion as an ethical, professional, and spiritually-sensitive form of integration.

abstract: Thesis

abstract: Master of Arts (MA)


title: Troubling Peer Support Institutionalization: A Mad Institutional Ethnography; Or, Everyday Documentation, De/Valuing, & Values Work in Institutionalized Peer Support

title: Peer Support Institutionalization: Troubling Everyday Work

contributor:
de Bie, Alise
Social Work

subject:
peer support
mental health
substance use
institutionalization
professionalization
institutional ethnography
addiction
mental illness
consumer/survivor movement
Mad studies
lived experience
experiential knowledge
healthcare
PHIPA
confidentiality
personal health information
compensation
professionalism
peer culture
peer community
peer drift
peer relationship
peer confidentiality
documentation
value
values

abstract: A short (11 page) plain language summary is available under the filename "Research Summary_Peer Support Institutionalization - Troubling Everyday Work.pdf"

abstract:
This study explores how the everyday work of peer supporters working within institutionalized settings are shaped by institutional forces (“ruling relations”), through a series of four (peer support) focus groups and interviews with five peer support workers in Ontario.
I explore peer supporters’ approaches to writing, reading, and verbally sharing information about their peers (“documentation work”), and reveal how their experiences and “felt troubles” relating to documentation are shaped by ideas of (clinical) confidentiality constructed in the Personal Health Information Protection Act (2004). I also explore how both lived experience and peer support are devalued through the ways organizations and clinicians determine and describe the value of healthcare roles (“de/valuing work”), and reveal how peer supporters’ experiences of being (de)valued are shaped by discourses of “professional/ism” which equate being a professional to having a post-secondary education and working through clinical frameworks.
I describe the work that peer supporters, clinicians, and organizations (can) engage in to ground peer support workers within peer values and approaches (“values work”) through accessing peer community and fostering environments of peer culture. I draw on these suggestions and the findings of the study to provide recommendations for peer support workers, organizations and clinical workers, the peer support sector as a whole, and research/ers.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: Flux-Based Dynamic Subspace Model Predictive Control of Dual-Three Phase Permanent Magnet Synchronous Motors

contributor:
Nahid-Mobarakeh, Babak
Electrical and Computer Engineering

subject: Motor Control, Model Predictive Control, Multiphase Motors, Dual-three phase motors

abstract:
ual-three phase permanent magnet synchronous motors (DTP-PMSM) are becom ing more popular in the automotive field. Their potential to increase the reliability
and efficiency of the vehicle makes them an attractive replacement for the three phase alternative. However, the increased number of phases makes the control of the
machine more complex. As a result, conventional controllers can see reduced perfor mance, especially at high speeds and torques. Currently, with the increased process ing power of modern micro-controllers and field-programmable gate arrays (FPGA),
many researchers are investigating whether finite-control set model predictive control
(FCS-MPC) can be a suitable alternative.
FCS-MPC is simple to implement and can achieve a better dynamic performance
when compared to other controllers. Furthermore, the algorithm can be augmented
for specific optimization goals and non-linearities to the system, which gives the
designer creativity in improving the system response. However, Model-Predictive
Control suffers from a variable switching frequency as well as reduced steady-state
performance. It generally has increased current ripple in the phase currents.
This thesis presents a method of reducing the steady-state ripples in FCS-MPC by
introducing the use of virtual-flux in the model equations, the incremental model, and
a dynamic vector search-space. All three of these applications make FCS-MPC have a
iv
significantly improved steady-state performance when compared to the conventional
algorithm, while still keeping the benefit of the improved dynamic response. The
benefits of the proposed techniques techniques are verified through simulation as well
as on an experimental setup.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Experimental and Computational Analysis of Mixed Convection Around In-Line Cylinders

contributor:
Novog, David
Engineering Physics

subject:
Mixed Convection
RANS
LES
Natural Convection
CANDU
Tube Array

abstract:
This work can be viewed in three separate sections, each of which build off of the prior. The first part of this study examined the flow in a 1/16th scale calandria test section based on a typical CANDU moderator layout. The experiments utilized forced flow supplied to the vessel and electrical heated rods to mimic the heat flow from calandria tubes.  The size of the vessel, flow rates, and power levels were used to scale the experiments such that the provided representative temperature fields.  The temperature field inside the vessel was measured and shown to compare well with CFD predictions over a wide range of inlet conditions and power levels. Additionally, this work addressed the scaling distortions in the experiment which occurred due to physical limitations when performing experiments at 1/16 scale (e.g., a smaller number of heater rods with a larger diameter were used in the experiment because at 1/16-scale direct fabrication of 390 fuel channel simulators is not feasible).  The work proposed the H factor addition to the Ar. This additional scaling criteria was shown to better maintain the flow regimes expected CANDU moderators by taking into account distortions introduced by surface heating instead of volumetric heating in addition to the reduction in total number of tubes.  While this work involved forced convective flows at the inlet of the vessel, in some regions of the calandria buoyancy induced forces were sufficiently high such that these phenomena altered the direction and magnitude of the flows as compared to purely forced convective behavior.  Hence further work, discussed below, was initiated to better understand and measure these local phenomena where buoyancy forces are of similar magnitude as those of forced convection.  Such local conditions we have terms mixed convection regime for the purposes of this thesis.

The second part of this work further examined the mixed convection between a subset of the CANDU calandria tubes, namely how does a lower tube effect the mixed convection heat transfer of the upper tube in an inline arrangement. To isolate and measure the phenomena with sufficient detail, a small number of tubes was studied and advanced diagnostics such as Particle Image Velocimetry (PIV) and Laser Induced Fluorescence (LIF) were employed.  This study combined fluid velocity, temperature and wall temperature measurements with CFD simulations to develop a mechanistic model and understanding of the effect of natural convection plumes from lower elevations on the natural circulation phenomena on an upper cylinder. Superposition of the natural convection phenomena combined with pseudo forced convection effects from the lower elevation cylinder’s plume was used to model the mixed convection phenomena. This model was shown to perform well, with nearly all data being predicted to with +-20% for experiments performed in this work, and experiments in literature.

A major finding from the preceding discussion is the importance of the lower elevation plume velocity on the local phenomena on the upper cylinder.  The third section further expanded upon the prior two by replacing the lower cylinder with a diffuser nozzle which could provide a forced convective component with accurately defined velocities. Such measurements allow for accurate definition of the local Ri number and allowed full access for instrumentation to observe the velocity fields. The major contribution of this work was a flow regime map that defined the phenomena around a heated cylinder under mixed convection conditions. Additionally, the establishment of a database of fluid temperature and velocity measurements for a wide range of Ri was also developed and used to further validate CFD predictions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Hybrid and machine learning based modeling, fault detection, and control of complex processes

title: Hybrid and machine learning based fault detection and control

contributor:
Mhaskar, Prashant
Chemical Engineering

abstract: The operation of industrial processes to achieve economic and safety objectives significantly depends on the use of advanced fault diagnosis and process control strategies. To design model-based fault diagnosis and control frameworks, developing sufficiently accurate models is an essential task. With the recent advance in computational power and data storage technologies, there have been growing interests in the use of machine learning techniques for process modeling and control. The performance of these techniques, however, depends on the use of a sufficient amount of high-quality data. The presence of uninformative and redundant data can hinder the model's ability to accurately predict dynamic behaviors. In this situation, the over-fitting also remains a challenging problem. As a result, it is necessary to use appropriate pre-processing tools, data mining techniques, and first-principles knowledge (if applicable) to achieve a reliable model. Motivated by the above considerations, this thesis focuses on the problem of hybrid and machine learning based modeling, fault detection, and control when collected data are not sufficient or there exist correlations between data samples. The first part of this thesis addresses the problem of system identification for heating, ventilation, and air conditioning (HVAC) systems when an insufficient amount of data is available. To this end, a hybrid machine learning based approach is developed where a pre-trained recurrent neural network (RNN) model (trained on a large amount of data from a representative zone) is leveraged to build a model for the zone in question. In the next phase, first-principles knowledge is integrated with data to develop a fault detection mechanism for HVAC systems using principal component analysis (PCA). The superior performance of the proposed approach, over the individual first-principles and data-driven based methods is shown. Finally, the problem of handling correlated data for the RNN-based model predictive control (MPC) implementations is addressed. To this end, PCA and autoencoder (AE)-based strategies are used to recognize the correlations that exist between data samples in both the input and output spaces. The constrained RNN-based MPC is then formulated by adding a PCA-based squared prediction error (SPE) constraint. PCA and AE-based optimization problems are also defined to calculate the achievable set-points. The efficacy of the proposed approaches over the nominal (standard) RNN-based MPC is demonstrated using different set-point tracking scenarios for a chemical reactor example.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Variable Selection for Skewed Clustering and Classification

contributor:
McNicholas, Paul
Mathematics and Statistics

abstract: As datasets from virtually all fields of endeavour continue to grow in size and complexity, the curse of dimensionality cannot be overlooked. Researchers in model-based clustering have recognized the need for effective dimension reduction techniques; as a result, many such algorithms exist to date. These algorithms, however, are often specific to Gaussian clustering problems and break down in the presence of skewness. We present a novel skewed variable selection algorithm that utilizes the Manly transformation mixture model to select variables based on their ability to separate clusters. We compare our approach with other asymmetric and normal variable selection methods using simulated and real-world datasets. We find that the proposed algorithm is suitable for dimension reduction in the presence of skewness.

abstract: Thesis

abstract: Master of Science (MSc)


title: Polyelectrolyte Complexes: The Effects of Charge Distribution and Charge Density

contributor:
Stöver, Harald D. H.
Chemistry and Chemical Biology

subject:
Polymer Chemistry
Physical Chemistry
Polyelectrolytes

abstract:
Polyelectrolytes are widely used as components in biomaterial applications. This thesis focuses on the design, synthesis, and investigation of polyelectrolyte complexes and their respective properties based on charge arrangement and charge density. The tunability of ionic interactions in polyelectrolyte complexes was then demonstrated in applications including alginate-based polyelectrolyte complexation for microcapsules and in strong polyampholyte hydrogels.
      Polyelectrolytes comprising methacrylic acid (MAA) and N-(3-aminopropyl)methacrylamide hydrochloride (APM) in different ratios were prepared and used to explore the interactions of different single- and multicomponent PECs with different charge arrangements using turbidimetric/potentiometric titration, UV-vis spectroscopy, microscopy, and isothermal titration calorimetry. The complexes were shown to have isoelectric points (pH(I)) at which macroscopic phase separation is induced that are highly dependent on the polymer composition as well polymer mixing ratio for multi-component PECs. Additionally, these complexes have sensitivity to [NaCl] shielding effects that are dependent on charge separation, improving with charge compensation and shifting from solid precipitates to liquid coacervates in strong complexes. The PECs exhibit cloud point temperatures indicative of lower critical solution temperature behaviours. These polyelectrolytes were then used to bind model ionic dyes and were crosslinked using naturally occurring genipin, indicating their potential as drug delivery materials.
      The system of MAA-APM polyelectrolytes was further explored as betaines were introduced to the individual polymers for three distinct coacervates: charge-balanced polyampholytes, pairs of complementary, nonstoichiometric polyampholytes, and pairs of pure polyanion-polycations. 2-methacryloyloxyethyl phosphorylcholine (MPC) was introduced into the different polyelectrolytes and drastically increased the responsiveness of complexes to pH, [NaCl], and temperature. MPC notably enhances complex hydration in single-component polyampholyte coacervates, while complex coacervates are less effectively destabilized with greater coacervate stability by charge separation.
      The exploration of structure-property relationships in polyelectrolytes was then extended to alginate-based complexation for applications in cell encapsulation, as compositional distribution and charge dilution influence the formation and stability of the complexed polyanion-polycation surface coatings. A semi-batch approach was employed to limit compositional variability in the copolymerization of APM and MPC. Different copolymers were then explored as potential low-fouling, cationic shell formers capable of covalent crosslinking with different reagents, including naturally occurring genipin. The crosslinked capsules show good mechanical and low protein adsorption.
      Finally, the underlying principles of charge density effects were demonstrated in strong polyampholyte hydrogels. Using a styrenic system of charged monomers, a near-alternating copolymerization was achieved and generated physical hydrogels with stimuli-responsive properties and high mechanical strength. Both the physical and mechanical properties are highly dependent on monomer loading during gel preparation. To tune the hydrogel properties, charge-neutral termonomers were incorporated to reduce charge density but show that termonomer selection has significant impacts on the responsive and mechanical properties. These polyampholyte hydrogels appear capable of stimuli-responsive self-healing.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: ETHICAL ANALYSES CONCERNING THE DEVELOPMENT AND USE OF GENE DRIVE MODIFIED MOSQUITOES FOR MALARIA ELIMINATION

title: ETHICS OF GENE DRIVE MOSQUITOES FOR MALARIA ELIMINATION

contributor:
Emerson, Claudia I.
Philosophy

subject:
Ethics
Policy
Gene Drive
Malaria
Global Health
Bioethics
Synthetic Biology
Stakeholder Engagement

abstract: This thesis is concerned with presenting analyses regarding key ethical issues regarding and arising from the development and potential use of gene drive modified mosquitoes for the purpose of malaria elimination. Each of the chapters constituting this thesis offers a rigorously researched analysis which attempts to answer questions thus far unanswered in the academic literature. Chapter one explores whether the development and use of this technology can be fairly considered unethical in principle; concluding it cannot be. Chapter two explores the appropriate relationship between this technology and the precautionary principle, a prominent regulatory and governance principle which has been invoked as ostensible support for an indefinite global moratorium on all gene drive technology. The chapter concludes that the precautionary principle, at least as articulated by UNESCO, does not provide justification for a global moratorium on gene drive technology. In fact, the precautionary principle is likely unfit as a regulatory norm for some kinds of gene drive products and purposes. Chapter three was co-authored with Delphine Thizy, Global Stakeholder Engagement Manager for Target Malaria, one of the leading consortiums working on research and development of gene drive biotechnology for malaria control. Together we articulate the ethical principles selected to guide Target Malaria’s stakeholder engagement, as well as provide the rationale for their selection and expound upon some early lessons from their implementation. Chapter four offers an analysis with the goal of locating the ethically appropriate locus of political organization from which to seek permission for a gene drive modified organism release into the shared environment. The chapter considers the appropriateness of each of the following levels of political organization: consent of individuals, local communities, nation states, and international governance institutions. The conclusion arrived at, with some caveats, is that such a decision is most appropriately issued by a nation state.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This thesis is concerned with presenting analyses regarding key ethical issues regarding and arising from the development and potential use of gene drive modified mosquitoes for the purpose of malaria elimination. Chapter one explores whether the development and use of this technology can be fairly considered unethical in principle; concluding it cannot be. Chapter two explores the appropriate relationship between this technology and the precautionary principle, a prominent regulatory and governance principle which has been invoked as ostensible support for an indefinite global moratorium on all gene drive technology. Chapter three articulates, expounds, and provides rationale for the ethical principles selected to guide stakeholder engagement by Target Malaria, one of the leading consortiums working on research and development of gene drive biotechnology for malaria control. Chapter four attempts to locate the ethically appropriate locus of political organization from which to seek permission for a gene drive modified organism release.


title: The role of environmental parameters in the interactions of aqueous electrolytes with graphene solid state devices

contributor:
Kruse, Peter
Chemistry

abstract:
Since the discovery of thermodynamically stable monolayer graphene, it has succeeded in overtaking a number of conventional materials in chemical sensing applications due to its exceptional chemical and electrical properties. In addition to being electrically conductive, graphene also has a large surface area which facilitates faster electronic interaction with analytes. In spite of graphene's inherent potential for chemical sensing, its application to aqueous electrolytes has been limited by an incomplete understanding of its interactions with the electrolytes’ environmental parameters. This thesis focuses on mechanisms through which graphene-based solid-state sensors (i.e., chemiresistors, Schottky diodes) respond to changes in aqueous electrolytes. Multiple environmental parameters, including pH, ionic strength, oxidation-reduction potential, as well as a target analyte (free chlorine), were chosen to examine their impacts on the performance of devices.
To begin, graphene's pH response was explored, showing that its pH sensitivity is strongly defect-dependent. The graphene defectivity was determined with the aid of Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). As revealed by measurements of the oxygen-to-carbon ratio (O/C) in XPS and the D-band/G-band intensity ratio (ID/IG) in Raman, graphene responds to pH in two main defectivity regions. In a low defect region, the graphene surface was shown to mainly interact with corresponding ions (i.e., H3O+ and OH−) through an electrostatic gating effect. However, in the high defect region, the response is dominated by protonation-deprotonation of oxygen-based functional groups. Therefore, the modulation of defectivity resulted in the change in pH responsivity. According to this result, we demonstrated that thermally reduced graphene oxide could be highly pH-sensitive to the pH range of 3-10 by dominating the defect induced pH response.
 Aside from pH, the impacts of changes in ionic strength, DO, and ORP of the electrolytes were investigated. We demonstrate that graphene chemiresistive devices can be used to investigate deviations in experimental screening lengths from the theoretical Debye length. We also present an overview of ion arrangements in the proximity of graphene, emphasizing the importance of DO in the Stern layer.
 Lastly, the development of an ultra-sensitive water quality sensor was shown by utilizing monolayer graphene in Schottky diodes. For the case study, free chlorine, a primary disinfectant of water, was chosen as the target analyte. Schottky diodes are demonstrated to offer sensitivity and LOD values competitive with current literature when environmental parameters are taken into account. I believe that this thesis provides a deeper understanding of graphene's applicability in aqueous media and opens new research avenues in graphene/aqueous interfacial interactions.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract: This thesis aims to investigate the interfacial interactions between graphene-based water quality devices and aqueous electrolytes to enhance the functionality of graphene derivatives in aqueous environments. The study focuses on the mechanisms through which graphene devices respond to changes in electrolyte parameters such as pH, oxidation-reduction potential (ORP), dissolved oxygen (DO) and ionic strength. In order to investigate the possible interference of these environmental parameters with the detection of analytes in water, multiple graphene devices (such as chemiresistive and Schottky diodes) were fabricated to better understand how graphene perceives aqueous electrolytes. This thesis explores four groups of interfacial interactions: electrostatic gating effect, surface charge transfer, substitutional doping, and ion trapping, and strives to manufacture sensitive water quality sensors based on graphene.


title: Biophysical Characterization and Bioprocessing of Proteins

contributor:
Ghosh, Raja
Filipe, Carlos. D. M.
Chemical Engineering

abstract:
Advances in biotechnology have opened up numerous new avenues for researchers in their study of proteins. These new technologies have not only resulted in a more robust understanding of protein characteristics which had hitherto only been achievable through the use of a handful of techniques - but they have also made this knowledge accessible to a wider audience. Although traditional approaches to studying proteins have performance limitations, they have remained the preferred options due to the absence of better alternatives that can accommodate similar scales of operation. Ideally such scenarios are commonly encountered during bioprocessing, which involves the extraction and purification of a pure protein from a host cell organism via the separation and removal of impurities. Here, the protein of interest undergoes through treatment to remove unwanted impure substances while at the same time preserving the targeted qualities.
This thesis introduces approaches to protein characterization and bioprocessing and discusses their limitations. In addition, newer alternatives are also introduced, particularly those that provide improved efficiency and quality of information compared to the traditional approaches. Specifically, this thesis highlights various aspects of bioprocessing and the biophysical characterization of proteins, with a focus on areas such as the processing of aggregates, impurity detection in protein samples, and the structural stability of proteins.
Overall, the results presented in this thesis were obtained with respect to the specific protein(s) under consideration. However, the nature of the presented processing techniques enables their use in the study of other similar proteins. As such, the results presented herein are not necessarily limited to a specific protein type rather, they can be generalized for application to a wide range of proteins, thus highlighting the true potential of these techniques. Finally, recommendations are made with regards to further exploring the wide scale application of these new approaches. In general, the new approaches presented in this thesis do not involve complex mechanisms; on the contrary, they are relatively easy to understand and perform.
This thesis covers the following points and presents preliminary data supporting the hypotheses:
(i)	The problem of protein aggregation is very common in the bioprocessing industry and solution(s) to remedy this problem typically involves tedious and energy intensive approaches. In this thesis, a simple and easier to perform thermal-cycling method capable of disaggregating protein clusters and refolding the resultant isolated protein chains into functional protein molecules is presented and explained.
(ii)	Another aspect of bioprocessing examined in this thesis is the impact of prolonged interaction time between a protein and substrate post adsorption. During the study it was observed that prolonged contact between a protein and adsorptive surface causes structural changes in proteins. This change was identified based on chromatographic peak broadening within an interval of 10-15 minutes.
(iii)	Heterogeneity in proteins is introduced during processing and storage, and this can adversely impact the quality of the target product. Using a rapid analytical membrane chromatographic technique, it was possible to identify monoclonal antibody charge variants. While the obtained resolution was comparable to that of column chromatography, membrane chromatography provided faster processing overall.
The work documented in this thesis provides a “proof-of-concept” methodology as an alternative to currently used protein analysis techniques. The new methods presented in this thesis lay out a platform for the further investigation of these ideas. There is immense scope for thorough and detailed studies to be performed to further bolster the principles discussed herein. Since the presented data is only a preliminary finding with a single test protein, more elaborate testing is required to validate the proposed hypotheses of this work.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Formalization of Biform Theories in Isabelle

contributor:
Farmer, William. M.
Computing and Software

subject: Isabelle, Formal Methods, Biform theory

abstract:
A biform theory is a combination of an axiomatic theory and an algorithmic
theory. It is used to integrate reasoning and computation in a common theory and
can include algorithms with precisely specified input-output relationships. Isabelle
is one of the leading interactive theorem provers. Isabelle includes locales, a module
system that uses theory morphisms to manage theory hierarchies, and that has a rich
and extensive library with multiple useful proof and formalization techniques. A case
study of eight biform theories of natural number arithmetic is described in the paper
“Formalizing Mathematical Knowledge as a Biform Theory Graph” by J. Carette
and W. M. Farmer. The biform theories form a graph linked by theory morphisms.
Seven of the biform theories are in first-order logic and one is in simple type theory.
The purpose of this thesis is to test how a theory graph of biform theories can be
formalized in Isabelle by attempting to formalize this case study. We work with
locales and sublocales in Isabelle to formalize the test case. The eight biform theories
are defined as regular axiomatic theories, while the algorithms are functions defined
on inductive types representing the syntax of the theories.

abstract: Thesis

abstract: Master of Science (MSc)


title: Incorporation of Lipid Nanoparticles into Pullulan Based Oral Thin Films for the Delivery of Vaccines

contributor:
Adronov, Alex
Chemistry

abstract:
Infectious diseases are most effectively controlled by vaccines that can elicit an immune response and create antibodies. As it stands, most vaccines are administered using subcutaneous or intramuscular injections. Injections via needle and syringe often invoke anxiety for individuals, which can result in low vaccination rates. The cost associated with administering vaccines is also high due to the requirement of trained health care professionals for administration. Additionally, administration via injection produces significant amounts of biohazardous waste. Administration of a vaccine by the swallowing of a pill or capsule also presents challenges. The active ingredient must be able to withstand passage through the gastrointestinal tract where enzymatic or acid related degradation is possible.
Two promising sites for vaccine delivery are the sublingual region which is located on the floor of the mouth and the underside of the tongue, and the buccal region located on the gums, cheeks, and inner lip. These regions, present in the oral cavity, allow for an active ingredient to be rapidly absorbed into the bloodstream without having to undergo first pass metabolism. One drug delivery method that has recently gained interest is the oral thin film. Upon placing an oral thin film on the buccal or sublingual region of the mouth, the film will rapidly dissolve and release the active ingredient to be absorbed into the bloodstream. Rapid Dose Therapeutics, a company in Burlington, Ontario, has developed the QuickStrip, an oral thin film that can deliver caffeine, vitamin B12, melatonin, and tetrahydrocannabinol (THC) through the buccal and sublingual route. Rapid Dose Therapeutics is interested in expanding the applications of the QuickStrip into vaccine delivery. Incorporating vaccines into oral thin films would allow for a pain-free, self-administrable inoculation process. This would result in a decrease in costs associated with vaccine distribution, making vaccines more accessible, while also eliminating associated biohazardous waste.
Vaccines are traditionally classified as live and non-live. Live vaccines contain a live, weakened strain of the pathogenic organism whereas non-live vaccines contain an inactivated whole pathogenic organism or a subunit of the pathogen. Over the course of the COVID-19 pandemic, a new vaccine type, messenger RNA (mRNA) -based vaccines, emerged. The mRNA within these vaccines encodes for the target antigen and employs the ribosomes within the host cell to transcribe the mRNA into the target antigen. The mRNA is encapsulated within lipid nanoparticles (LNP) which assist in delivering and protecting the RNA. mRNA based vaccines are beneficial over traditional vaccine types as they are safe and faster to manufacture.
This thesis was performed in conjunction with Rapid Dose Therapeutics and worked toward being able to use the QuickStrip as a vaccine delivery method.
In this work, lipid polymer hybrid nanoparticles were prepared using a probe sonication technique. The effect of sonication amplitude and temperature on particle size was studied. Next, ibuprofen loaded lipid polymer hybrid nanoparticles were synthesized using a nanoprecipitation technique. A fluorescent dye, fluorescein isothiocyanate, was then loaded into the hybrid nanoparticles. This allowed the acquisition of super resolution optical microscopy images of the particles, both prior to and after being incorporated into an oral thin film.
Commercially produced lipid nanoparticles were then acquired from Acuitas Therapeutics, the company that produces the lipid nanoparticles for the Pfizer-BioNTech vaccine. These lipid nanoparticles contain a model mRNA strand as well as the fluorescent dye 1,1’-dioctadecyl-3,3,3’,3’-tetramethylindocarbocyanine. Super resolution optical microscopy was employed to visualize the Acuitas Therapeutics lipid nanoparticles on a glass coverslip and in oral thin films. The images acquired suggested that the lipid nanoparticles were unharmed during the film casting process. The integrity of the mRNA within the lipid nanoparticles was then assessed and confirmed using gel electrophoresis. To ensure the mRNA was remaining encapsulated within the particles, the Quant-iT RiboGreen RNA assay was used. Initial studies indicated that the RNA was becoming unencapsulated from the nanoparticles once the film mixture had been cast. This resulted in several modifications to the preparation and formulation of the oral thin films. Ultimately, a film formulation containing a lipid-PEG molecule was used to stabilize the lipid nanoparticles within the oral thin film.

abstract: Thesis

abstract: Master of Science (MSc)


title: Influence of Electron-Poor Conjugated Polymers on the Selective  Dispersion of Carbon Nanotubes

abstract:
The unique thermal, electronic, and optical properties of single-walled carbon nanotubes (SWNTs) can be used in a variety of applications. However, all currently available production methods result in a heterogenous mixture of semiconducting and metallic species. SWNTs also self-aggregate, resulting in minimal solubility in solvents, preventing their immediate incorporation into many applications. These challenges have resulted in the development of various purification methods, but the use of conjugated polymers is considered to be the most scalable technique. Currently, conjugated polymers have allowed for the complete isolation of semiconducting SWNTs using electron-rich conjugated polymers such as polythiophenes, polycarbazoles, and polyfluorenes. Conversely, the isolation of pure metallic SWNTs still requires improvement. Recently, a two-polymer system was developed for the enrichment of metallic SWNTs using an electron-rich conjugated polymer to remove semiconducting SWNTs, followed by an electron-poor polymer to disperse the remaining metallic SWNTs. This technique represented a significant step forward in the enrichment of metallic SWNT samples using conjugated polymers, but refinement is still possible.
	The aim of this thesis is to improve this scalable technique for the enrichment of metallic SWNTs. Specially, two reactions on poly(fluorene-co-pyridine) were investigated in an effort to generate a more electron deficient polymer backbone. The first reaction involved the addition of a dinitrobenzene moiety by means of the Zincke reaction. It was found that the functionalization of the polymer backbone using the Zincke reaction was not feasible, likely due to steric hinderance. Research efforts were then redirected to a reaction involving the addition of a less bulky trifluoroacetyl group by reaction of the polymer with trifluoroacetic anhydride. This investigation led to the straightforward and complete functionalization of the polymer backbone producing acetylated poly(fluorene-co-pyridine). Next, the ideal dispersion conditions were tuned for the acetylated poly(fluorene-co¬-pyridine) to be incorporated into the two-polymer extraction system. This novel polymer showed higher dispersion concentration and improved selectivity toward metallic SWNTs than previously developed. Characterization of the polymer-SWNT dispersions were conducted using UV-vis-NIR spectroscopy, and conductivity techniques to evaluate their electronic purity.

abstract: Thesis

abstract: Master of Science (MSc)


title: Application of Atmospheric Pressure Chemical Ionization Gas Chromatography in Urine Organic Acid Analysis

contributor:
Potter, Murray
Medical Sciences

subject: Gas Chromatography

subject: Mass Spectroscopy

subject: Genetics

subject: Urine Organic Acid Analysis

subject: APCI

subject: GC-MS

subject: GCMS

subject: Inborn Errors of Metabolism

subject: Newborn Screening

abstract:
Inborn errors of metabolism (IEM) cause significant morbidity and mortality when left untreated. Urine organic acid (UOA) analysis is often a first-line investigation when an IEM is suspected. UOAs are usually qualitatively analyzed via the current gold standard, GC-EI-MS (Gas Chromatography-Electron Impact-Mass Spectroscopy). The Agilent 7890 GC in tandem with the Waters’ Xevo TQ-S MS contains an easily interchangeable LC-ESI (liquid chromatography-electrospray Ionization) and GC-APCI (Atmospheric Pressure Chemical Ionization) instrument set-up, while maintaining accuracy and sensitivity in both LC and GC applications. Utilizing this novel GC-APCI instrument, this project aims to develop and validate a new UOA method for clinical use. Furthermore, utilizing the machine’s MRM mode would increase sensitivities thus allowing for hopefully quantitative analysis.
Chemical standards and patient urine samples were extracted via a liquid-liquid ether extraction and derivatized with BSTFA for proper GC elution. Results were compared on the current gold standard GC-EI-MS instrument and the new GC-APCI-MS instrument. Initial instrument suitability and method setup was then optimized. Source moisture levels were modified to explore the wet proton transfer and the dry charge transfer mechanism using [M+H]+ and [M+*]+ ion peak ratios, respectively. Elution times and APCI ion mass spectra profiles of UOA metabolites of interest were identified from full scan mode in preparation for MRM mode analysis. Exploration into the wet and dry mode settings of the APCI source determined that the former induced via methanol had greater peak areas and signal-to-noise ratios. Suitable MRMs were determined for clinically relevant organic acids from which a quantitative assay was developed for methyl malonic acid and several other compounds.
The Waters’ Xevo TQ-S micro with Agilent 7890 GC demonstrated promising GC-APCI-MS detection of urine organic acids. With clear avenues for future work, the APCI technique hints at great benefits for biochemical genetic laboratories.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Inborn errors of metabolism (IEM) are a class of genetic diseases that when left untreated, cause reduced quality of life and sometimes death in newborns. Urine organic acid (UOA) analysis is used for detection using an instrument called GC-EI-MS (Gas Chromatography Electron Impact Mass Spectroscopy). This project explores how a new instrument, the Agilent 7890 GC and the Waters’ Xevo TQ-S MS, can detect these genetic diseases using a technique called APCI (Atmospheric Pressure Chemical Ionization) while still being accurate and sensitive.
UOAs are isolated from urine and run through the new machine. When compared to the currently used technique, results were promising but further optimization is needed. Using the new machine, various UOA compounds that were elevated and/or decreased in newborns with genetics diseases were identified and quantified. With clear avenues for future work, the APCI technique can greatly improve newborn diagnosis of IEMs.


title: Strategies for Expanding Lipid Coverage and Accelerating Biomarker Discovery Using Multisegment Injection-Nonaqueous Capillary Electrophoresis-Mass Spectrometry

contributor:
Britz-McKibbin, Philip
Chemistry

subject:
Lipidomics
Separation Science
Chemistry
Chemical Biology

abstract: The importance of biomarkers cannot be understated as they have played a key role in revolutionizing public health and disease prevention on a population level. While there is a need to discover more specific and clinically relevant biomarkers, many technical challenges exist especially in the context of the rapidly growing field of lipidomics. This thesis aims to develop new analytical strategies for nontargeted lipid profiling when using multisegment injection-nonaqueous capillary electrophoresis-mass spectrometry (MSI-NACE-MS). Chapter II greatly expands metabolome coverage in CE-MS when using a compatible non-aqueous electrolyte system for global analysis of ionic lipids differing widely in their polarity, such as lysophosphatidic acids, phosphatidylinositols, phosphatidylethanolamines and free fatty acids. For the first time, a multi-tiered data workflow was introduced in MSI-NACE-MS using an ultra-high resolution Orbitrap mass analyzer under negative ion mode for credentialing more than 270 lipid features from serum extracts based on their characteristic accurate mass and electrophoretic mobility. Of these, 128 anionic lipids were reliably measured (median CV ≈ 13%) in most serum extracts (> 75%) that were applied to stratify a cohort of Japanese non-alcoholic steatohepatitis patients (n = 85) based on their disease severity not feasible by conventional biomarkers of liver fibrosis. Chapter III expands the analytical performance of MSI-NACE-MS by introducing an innovative two-step chemical derivatization protocol as a charge-switching strategy to resolve zwitter-ionic phospholipids that otherwise co-migrate with the electroosmostic flow. Reaction conditions were optimized to achieve a quantitative yield for methylated phosphatidylcholines, which greatly improved resolution and detectability when using MSI-NACE-MS under positive ion mode. Overall, this approach expanded lipidome coverage, supported phospholipid structural identification based on their characteristic electrophoretic mobility while also demonstrating the potential for reliable quantitative determination in a human serum reference material (NIST SRM-1950). Importantly, this universal methylation strategy may prove useful in other lipidomic platforms (LC-MS/MS, DI-MS/MS) as it is less hazardous than diazomethane. Lastly, Chapter IV involved the application of MSI-NACE-MS technology to discover surrogate biomarkers of omega-3 index (O3I) in two independent placebo-controlled clinical trials involving the ingestion of high-dose omega-3 fatty acids, including fish oil, eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA). For the first time, we identified a panel of omega-3 containing phosphatidylcholines in serum and plasma ether extracts that exhibited treatment responses in participants that were also positively correlated with independent O3I measurements. This work revealed that specific circulating phospholipids may allow for rapid assessment of omega-3 index without the need for complicated erythrocyte membrane hydrolyzed fatty acid analysis as required for risk assessment of cardiovascular health and sudden cardiac death. Overall, this thesis introduced MSI-NACE-MS as a hitherto unrecognized analytical platform for lipidomics that is complementary to chromatographic methods with improved sample throughput and accelerated data workflows for biomarker discovery in clinical medicine.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Aging Black and Lonely: A Narrative Experience of Black Older Adults in Canada

contributor:
Kapiriri, Lydia
Health and Aging

subject:
Social and emotional Loneliness
Black older adults
Social participation
Exclusion

abstract:
Loneliness affects Black older adults (BOAs) in different and debilitating ways. BOAs aged 65 years and above make up 7.3% of the Black population and 15.9% of the total population of those aged 65 years and above in Canada. Also, the population of BOAs in Canada has doubled within the last two decades, highlighting the need to understand the unique experience of aging of this population, including their experiences of loneliness and social participation. Contrarily, there exist notable gaps within the loneliness literature on the experience of loneliness and social participation among BOAs living in Canada. This doctoral dissertation addresses these knowledge gaps by providing insight into the factors influencing social and emotional loneliness and lack of social participation among BOAs and proffers ways to address the issues, expressly informing future research, services, and programs targeting this group. This dissertation is comprised of four papers. Paper 1 is a scoping review of 27 articles that reveal the dearth of empirical evidence on the experience of loneliness or subjective social isolation and the contributing factors among BOAs in Canada. The data used for the remaining three papers were collected through 25 narrative interviewing conducted with 13 BOAs living in Hamilton and Windsor, Ontario. Findings from this paper shows that in addition to unavailability of social provisions (relational gains), loneliness among BOAs is exacerbated by socio-economic factors, health-related factors and behaviours, and technology, media device possession and usage. The results also indicate that there is need for inclusion of BOAs in loneliness research in Canada. Following Paper 1, Paper 2 investigates the unique experience of loneliness among BOAs living in Canada and the suitability of the social provision framework in identifying and understanding the experience of loneliness among this group. Findings from this paper demonstrates the significance of social connection, reliable relationships and relational gains in reducing and increasing experience of loneliness among
BOAs. Paper 3 analyzes the constellation of factors that contribute to loneliness among BOAs and how they cope with their experience of loneliness. The results from this paper highlight the complex overlapping factors that contribute to the experience of loneliness among BOAs including time, sense of place and belonging, weak socio-personal interaction, and level of exclusions. Paper 4 and final paper uncovers the micro and macro level factors that hinder BOAs from participating in social programs and services and suggests ways to improve their social participation. Specifically, findings from this paper uncovers the need for programs and services that are culturally diverse and sensitive to the unmet needs of racialized and minoritized groups. Collectively, the four papers contribute to knowledge on the experience of loneliness among BOAs and contributory factors and highlight the need for more inclusive research and practice on addressing loneliness among this group.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This research aims to understand how loneliness affects Black older adults (BOAs) living in Canada and how to reduce their loneliness. This is a group that is not usually included in the loneliness literature. The dissertation is organized into six chapters comprising of the introduction, four papers and the conclusion. Paper One analyzes 27 articles describing the factors that contribute to loneliness among Black older adults globally. The 27 papers reveal while loneliness is devastating for BOAs, studies that have examined the experience of loneliness among BOAs in Canada is very scanty. Paper Two, Three and Four all report results from narrative interviews conducted with 13 Black older adults living in Windsor and Hamilton, Ontario. Paper Two explores the unique experience of loneliness among BOAs. Paper Three analyzes the influence of time, place and interaction as factors that contribute to the experience of loneliness among Black older adults and their coping strategies. The final paper explores the significant factors that hinder BOAs from participating in social programs and services and ways to improve their participation. Generally, the results of these papers provide important insights into the ways to address loneliness and the lack of social participation among BOAs. The results show that programs and services targeting loneliness in Ontario need to be made more culturally sensitive and representational of minoritized groups. Lastly, it highlights the need for the inclusion of BOAs in loneliness research among older adults in Canada.


title: Development of Solutions for Rapid Simulation of Solute Transport in Fractured Aquifers

contributor:
Dickson-Anderson, Sarah
El-Dakhakhni, Wael
Civil Engineering

abstract: Understanding the flow and transport of contaminants in fractured rocks play a fundamental role in geo-environmental problems since subsurface contamination poses a serious threat to human health and the environment. Therefore, it is imperative to understand solute transport in these environments; models are an important tool in the advancement of our understanding. Aquifers in which the flow pattern is dominated by a network of connected fractures present challenges with respect to modeling due to the high degree of heterogeneity in fracture density and geometry. The goal of this research is to develop a suite of modeling tools that are accurate, computationally stable, and efficient enough to simulate solute transport in complex, discrete fracture networks (DFNs). Four research objectives have been designed to achieve this goal: (1) develop a computationally efficient analytical model for simulating two-dimensional spatial and temporal solute transport in discrete fracture networks (DFNs), (2) develop a closed-form solution describing the classical advection-dispersion equation for simulating reactive transport in single, parallel-plate fractures under a range of conditions, (3) develop a numerical model (based on the closed-form solution developed in Objective 2) to simulate solute transport in small-scale (~350 m × 350 m) discrete fracture networks considering mass exchange between the fracture and surrounding matrix, and (4) upscale the frameworks developed in Objectives 1 and 3 to develop an accurate and computationally efficient numerical model simulating solute transport in field-scale fracture networks . The developed analytical model (Objective 1) provides a useful reference tool for the verification of numerical dual-porosity fracture network simulations. The other developed numerical approaches (Objectives 2, 3, and 4) advance solute transport behavior predictions in fractured environments as they are both simpler and more computationally efficient than currently adopted techniques, which is particularly important for simulating fracture networks at the macroscopic scale.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Aquifer pollution by various contaminants is an issue of concern across Canada. It has been well-established that fractured aquifers can be highly susceptible to contamination. Contaminants are primarily transported through fractures over a period of decades or longer; however, storage occurs in the surrounding rock matrix. Contaminant transport models are important tools for understanding field conditions and developing aquifer management and remediation strategies. Unfortunately, currently available modeling approaches either lack accuracy or require extensive computational resources when applied to field-scale problems. The goal of this study is to develop a suite of modeling tools that are accurate and efficient enough to capture solute transport processes in fractured aquifers occurring at the field scale.


title: ResCoCo: Residual ConvLSTM Network with Contrastive Learning for 3D Joint Angle Estimation

contributor:
Zheng, Rong
Computing and Software

abstract:
3D joint angle is an important indicator in human gait analysis, and musculoskeletal disease diagnosis and treatment. To accurately estimate 3D joint angle, a Deep Learning approach, Residual ConvLSTM network with Contrastive Learning (ResCoCo), is proposed in this study. A sequence shortening layer is introduced in ResCoCo to discard part of the output sequence estimated by bi-directional LSTM layers from incomplete context, and a residual block is used for network depth increase. Contrastive learning is employed in ResCoCo to ensure robust and efficient representation extraction.
The model is validated on the WEVAL dataset for 3D knee joint angle estimation during walking. The experiment result shows that the sequence shortening layer and residual block benefit the 3D joint angle estimation accuracy, while contrastive learning increases the model resistance towards IMU-to-Segment (I2S) alignment and sensor placement variations. Furthermore, the sensor configuration for the model input is investigated. Using inertial data from two sensors as the model input is economical while effective, and leads to good model robustness towards I2S alignment and sensor placement variations, compared to using inertial data from a single sensor or six sensors as the model input. The model is also compared with a model-driven method. It is shown that ResCoCo not only provides accurate estimation accuracy along three rotation axes, but it is also free of calibration procedures, physical constraints, or predefined anatomical models, compared to model-driven approaches.

abstract: Thesis

abstract: Master of Science (MSc)


title: Characterizing age-related changes and protective features in the upper respiratory tract microbiota associated with healthy aging and chronic inflammation

contributor:
Bowdish, Dawn
Medicine

subject:
aging
older adults
microbiome
nasal
16S rRNA sequencing
local inflammation

abstract:
Background: The upper respiratory tract (URT) is composed of an array of microbes that can contribute to or protect against upper respiratory infections. Older adults (>65 years) are at greatest risk of acquiring respiratory tract infections, particularly pneumococcal infections, resulting in over 7,000 deaths per year in older Canadians. The increased risk of infection may be linked to diversity, high variability, and a decrease in commensal bacteria residing in the URT microbiota. The impact local inflammation has on microbial communities in the nasal cavity is not well defined. Previous research in our laboratory identified 5 dominant microbial profiles in the anterior nares URT microbiota of healthy adults. We also started building a strain collection of commensal bacteria isolated from the URT that may provide protection against pathogenic bacteria, such as S. pneumoniae. Our aim is to characterize microbial changes in the URT microbiota with age-associated changes such as specific health conditions and inflammation to determine which microbes are protective against respiratory infections.
Methods: To approach this, we collected nasal samples from 178 community-dwelling adults (18-102 years) throughout 2020 – 2022. Participants provided an additional nasal sample if they were symptomatic during cold/flu season. We collected 99 nasal samples, and 18 nasal fluid samples from 46 adults, over 3 visitations, diagnosed with either osteoarthritis or rheumatoid arthritis, to measure how local inflammatory markers (GM-CSF, Fractalkine, IL-6, IL-1 and TNF) change the nasal microbiota. The samples were processed with 16S rRNA gene sequencing, and bacterial load was measured using qPCR to determine the total 16S rRNA abundance. Phenotypic and liquid assays determine commensal microbes that exhibit resistance to S. pneumoniae colonization.
Results: We identified 7 dominant microbial profiles in the aging nasal cavity, which differed statistically with bacterial load and seasonality. We observed higher movement between these profiles within individuals who experienced a respiratory infection. We identified 8 profiles in an inflamed nasal cavity. The composition of these profiles was associated with changes in DMARDS treatment for adults living with rheumatoid arthritis. The difference between microbial profiles in the nasal cavity is due to higher variation and a diverse microbiota.
Conclusion: In addition to observing compositional changes with bacterial load, seasonality, and inflammation, we identified protective microbial strains residing in the nasal cavity. This allows us to begin identifying secondary metabolites with inhibitory activity against S. pneumoniae in the URT microbiota and non – harmful properties to the host, to develop novel drug therapeutics to reduce the risk of pneumococcal infections in older Canadians.

abstract: Thesis

abstract: Master of Science (MSc)


title: Design, Control, and Implementation of a High Power Density Active Neutral Point Clamped Inverter For Electric Vehicle Applications

contributor:
Emadi, Ali
Narimani, Mehdi
Electrical and Computer Engineering

subject:
Electric Vehicles
Multilevel Inverters
Power Density
Powertrain
Traction Applications

abstract:
Traction inverter, as a critical component in electrified transportation, has been the subject of many research studies in terms of topologies, modulation, and control schemes. Recently, some of the well-known electric vehicle manufacturers have utilized higher-voltage batteries to benefit from lower current, higher power density, and faster charging times. With the ongoing trend toward higher voltage DC-link in electric vehicles, some multilevel structures have been investigated as a feasible and efficient option for replacing the two-level inverters. Higher efficiency, higher power density, better waveform quality, and inherent fault-tolerance are the foremost advantages of multilevel inverters which make them an attractive solution for this application.
The first contribution of this thesis is to investigate and present a comprehensive review of the multilevel structures in traction applications. Secondly, this thesis proposes an electro-thermal model based on foster equivalent thermal networks for a designed three-level active neutral point clamped (ANPC) inverter, as well as a modified sinusoidal pulse-width modulation (SPWM) -based technique. This electro-thermal model and the modulation technique enable temperature estimation in the inverter and minimization of the hotspot temperature and hence, increase the power density. Based on the experimental results derived from the implemented setup, a 12% increase in power density is achieved with the proposed technique. The other contribution is a reduced-complexity model-predictive controller (MPC) for the three-level ANPC inverter without weighting factors in which the number of calculations has dropped from 27 to 12 in each sampling period.
The improvements to the structure and control system of the inverter are supported by theoretical analysis, simulation results, and experimental tests. A three-level inverter is implemented for 800 V, 70 kW operation and tested. 750 V Silicon Carbide (SiC) switches are utilized in the inverter structure. Finally, future trends and suggestions for the following studies are stated in this thesis.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Host Biomarkers of Respiratory Infection

title: CHARACTERIZATION OF CXCL10 AS A BIOMARKER OF RESPIRATORY TRACT INFECTIONS DETECTABLE BY OPEN-SOURCE LATERAL FLOW IMMUNOASSAY

contributor:
Hirota, Jeremy
Medical Sciences

subject: CXCL10

subject: SARS-CoV-2

subject: Biomarker

abstract:
Background: Respiratory tract infections are responsible for millions of deaths annually. Interferon-stimulated genes (ISGs) play a significant role in fighting off viral respiratory tract infections in the antiviral defence system. Measuring extracellular protein products of ISGs could be potential biomarkers of viral infection. Although, the feasibility and performance of ISGs as functional and robust clinical biomarkers from a non-invasive sample format remains unknown.

Methods: Three ISGs, CXCL10, CXCL11, and TNFSF10, were examined in in-vivo and in-vitro gene expression datasets (RNA-sequencing and microarray) infected with common respiratory tract infections (Rhinovirus, Respiratory syncytial virus, influenza A and SARS-CoV-2) samples and compared to negative controls. Using qualitative selection criteria of 1) elevated presence in at least one dataset with viral infection, 2) secreted protein product, and 3) commercially available antibodies for detection, CXCL10, CXCL11 and TNFSF10 gene expression levels were assessed. A correlation analysis was performed with SARS-CoV-2 infection severity and gene expression kinetics. CXCL10 was subsequently validated at the protein level in saliva as a prerequisite for developing a host-response LFA.

Results: CXCL10 and CXCL11 upregulation were positively correlated with RSV compared to control (p < 0.05). CXCL10/CXCL11/TNFSF10 were not different between samples collected from RV infected subjects relative to controls (p > 0.05). No significant association was found with influenza A for all three genes. CXCL10/CXCL11/TNFSF10 upregulation was positively correlated with SARS-CoV-2 infection compared to control (p < 0.001). CXCL10 expression correlated with COVID-19 viral load. CXCL10 was chosen as a lead biomarker candidate based on these analyses that included different virus infections, time-courses, and measures of severity. CXCL10 was not detected at the protein level in healthy saliva but was elevated in saliva from COVID-19 patients. A CXCL10 LFA was developed with a sensitivity of 2 ng/ml in a buffer and artificial saliva.

Conclusion: We establish and validate the potential of developing rapid test techniques to examine host immune response from a bioinformatic approach to developing a prototype rapid test with capabilities to be used in point-of-care settings.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Respiratory tract infections are a leading cause of death and one of the main reasons to seek primary care. Both historically and in the present day, respiratory tract infections remain a massive socioeconomic burden. Current diagnostics fail to quickly identify a respiratory tract infection's etiology, and prognosis, leading to suboptimal patient care and the over prescription of antibiotics. Advanced tools used in academia and research, including next-generation -omics sequencing and metagenomics, have capabilities to identify all nucleic acid material in a sample - including host RNA- which offers potential to improve the diagnosing of respiratory tract infections. However, these technologies have not been integrated into routine care due to economic, technical, and logistical barriers. We explored host RNA (transcriptomics), looking at antiviral interferon-stimulated genes for their potential as a biomarker of viral infection amenable to point-of-care testing platforms from non-invasive sample types.


title: EXPLORING WAYS TO SUPPORT PARENTS OF CHILDREN WITH DEVELOPMENTAL DISABILITIES

title: SUPPORTING PARENTS OF CHILDREN WITH DEVELOPMENTAL DISABILITIES

contributor:
Peter Rosenbaum
Rehabilitation Science

subject:
parents
childhood disability
family-centred care
family-centred service
children
developmental disability
well-being
services
pediatric rehabilitation
ENVISAGE
cross-cultural adaptation
transferability
pilot studies
feasibility studies

abstract: Family-centred service (FCS), which acknowledges the importance of family engagement in therapeutic processes and focuses on needs of all family members, is increasingly being recognized as an optimal care delivery model for families of children with developmental disabilities. However, services for families are oftentimes ‘child-centric’, wherein family members are seen as partners in therapy or care delivery only, while their own or family needs are not addressed. This arises from the lack of awareness of complex and highly individual family needs by professionals with whom they interact, but also from a significant lack of services oriented toward parent-specific needs in current delivery models. This thesis aims to address this knowledge gap and provides solutions for parental support in the context of pediatric developmental rehabilitation, which might also be applicable to other settings (e.g., community, education). The objectives of this thesis were: (a) to conduct a systematic review synthesizing randomized controlled trials aiming to address parents’ physical, psychological and socioeconomic well-being; (b) to perform cross-cultural and language adaptation and proof-of-concept pilot exploration of an innovative, strengths-based support program ‘ENabling VISions And Growing Expectation’ (ENVISAGE) for parents of children with neurodevelopmental disabilities in Croatia; (c) to refine the Croatian version of the program according to the pilot study results; (d) to run the first set of ENVISAGE workshops and evaluate their impact on Croatian parents’ perception of self, their child with a disability and their family; and (e) to learn about participants’ experience with the program. The findings show that interventions aiming to improve parents’ well-being have limited but promising effectiveness on parents’ health and well-being outcomes. ENVISAGE has proven to be a comprehensive, acceptable, usable, feasible and impactful program for parents of children with developmental disabilities in Croatia.

abstract: Dissertation

abstract: Doctor of Science  (PhD)

abstract: Parents raising children with developmental disabilities have unique challenges in their parenting role, which might impact their health and well-being. However, there has been very little focus on parental and family needs in the context of pediatric developmental rehabilitation. Parents are often expected to focus on their child’s issues when their own support needs are usually also significant. This thesis aimed to address this research and practice gap through: a) evaluating best quality evidence on how to support parental well-being; and b) piloting a novel ‘early intervention’ support program for parents of children with disabilities, ‘ENabling VISions And Growing Expectation’ (ENVISAGE), in a new culture and language setting, Croatia. These findings have implications for spreading awareness of innovative programs to improve well-being of parents of children with developmental disabilities in various sectors (e.g., healthcare, community).


title: Methodological considerations for the assessment of perioperative outcomes in patients with rare bleeding disorders

title: Perioperative outcomes in patients with rare bleeding disorders

contributor:
Iorio, Alfonso
Tarride, Jean-Eric
Mgbuagbaw, Lawrence
Matino, Davide
Health Research Methodology

subject: Rare bleeding disorders, Surgery, Perioperative outcomes, Methodology

abstract:
Rare bleeding disorders are a group of inherited conditions caused by a deficiency of blood coagulation factors. Due to the low prevalence of these conditions in the general population, there is a scarcity of data to make informed, evidence-based clinical decisions. In this population who are highly susceptible to excessive bleeding, surgeries and invasive procedures pose an additional level of risk for bleeding-related and non-bleeding-related complications, especially in the perioperative period. The data scarcity in patients with rare bleeding disorders is further compounded by an infrequent rate of invasive procedures, sometimes attributed to the hemostatic challenges faced by such interventions among other factors.

To address the problem of insufficient data for healthcare decision-making, as well as the assessment of perioperative outcomes in this population, this thesis explores the use of routinely collected data for the creation of a novel surgical database used for the assessment of perioperative hemostasis, complications, and initial surgical plan deviations in patients with rare bleeding disorders.

Across five chapters, this thesis provides the methodology for the creation of the Indiana Hemostasis and Thrombosis Center (IHTC) Surgical Database, a descriptive analysis of the population and procedures, and assessment of perioperative outcomes. Approaches to ensure the validity of study results including confounder adjustment by variable selection methods, data quality improvement, missing data description, and imputation methods, were explored. Evidence from randomized controlled was also reviewed using Cochrane methodology to summarize the efficacy of clotting factor concentrates for the prevention of bleeds and bleeding-related complications in patients with hemophilia.

Based on findings from the different approaches (observational study designs, randomized controlled trials, and systematic review methodology), recommendations were made regarding methodological and analytical considerations required to ensure valid and reliable perioperative outcome assessment in patients with rare bleeding disorders.

The following provides a brief outline of each chapter.
Chapter 1 is an introduction that outlines each of the studies in this thesis.
Chapter 2 is a descriptive overview of the design, structure, and exploratory analysis of data captured in the IHTC-Surgical Database over a 21-year period.
Chapter 3 is a retrospective cohort study that assessed the association between inhibitor status and perioperative hemostasis, complications, and initial surgical plan deviations in patients with hemophilia A and B.
Chapter 4 is a systematic review that examined the efficacy of clotting factor concentrates for the prevention of bleeds and bleeding-related complications in patients with hemophilia.
Chapter 5 outlines key findings, limitations, implications of the research in this thesis, and methodological considerations for the assessment of perioperative outcomes in patients with bleeding disorders.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Photoluminescence Imaging of Semiconductor Structures Grown Using Selective Area Epitaxy

contributor:
Kleiman, Rafael
Ryan, Lewis
Engineering Physics

abstract:
Selective Area Growth (SAG) is a technique developed for cost savings in semiconductor manufacturing, allowing for local area growth manipulation. In this work,
SAG was accomplished by using a lithographic direct-write laser system that creates
silica (SiO2) masks on the surface of a III-V semiconductor substrate. The III-V
semiconductor substrate used was a semi-insulating GaAs (SI-GaAs) wafer of (100)
orientation. A lattice-matched InGaP/GaAs/InGaP heterostructure was grown using
Molecular Beam Epitaxy (MBE). This heterostructure has a theoretical photoluminescence (PL) emission peak of approximately 875 nm and exhibited strong PL. A
micro-photoluminescence (μ-PL) apparatus was successfully built and consists of a
HeNe laser of 633 nm emission wavelength as the excitation source. The μ-PL apparatus captured the emission spectrum of the sample with a spatial resolution of
approximately 6 μm and a peak wavelength around 878 nm. The images are scans of
various area sizes, ranging from 0.0413-6.25 mm2. The images showed that the silica
structures are non-growth sites due to the absence of PL. The images also showed a
reduction in PL intensity in areas near silica structures. This is hypothesized to be
due to variations in the InGaP layers that ultimately affect growth quality and carrier confinement. No change in PL wavelength was observed in the growth regions, as
would be expected for a binary system grown by MBE. The PL imaging of selectively
grown heterostructure materials enables further process development for integration of
semiconductors with multiple bandgaps on a chip for fiber optic transmission.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: What mental health care experiences and outcomes matter for people with complex health and social needs?

contributor:
Lavis, John
Health Policy

abstract:
Individuals with complex health and social needs (ie. those experiencing physical and mental multimorbidity and social marginalization) are poorly served by health systems. “Complex care” programs have been developed to address these needs. However, scholarly debate surrounds the question of what problem complex care seeks to resolve, and how success can be measured. Within this debate, limited attention has been given to mental health.
This dissertation contributes to discussions of the objectives of complex care through three qualitative studies. First, a critical interpretive synthesis of literature is conducted to develop a novel framework for complex care policy. The framework integrates diverse academic and grey literature on complex care, while drawing on theoretical work on multi-level interventions. Second, a qualitative description study explores the perspectives of leaders (including operational and programmatic leaders, and individuals with lived experience in advisory roles) with respect to mental health outcomes that matter in complex care. Outcomes valued by participants include both individual-level objectives oriented along a dynamic continuum towards recovery, and system-level objectives. Finally, an interpretive description study unpacks the viewpoints of individuals with complex health and social needs on what constitutes a good experience in mental health care. Participants describe valuing mental health care that is founded on authentic relationships and that is tailored to the individual.
Taken together, these studies posit that complex care must be individualized, relationally- centred care, and situated within a flexible, multi-level system. This dissertation advances conversations on the aims of complex care and the conditions that might render these aims attainable.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: The phrase “complex health and social needs” is used to describe challenges that arise in providing healthcare for people who experience multiple physical and mental health concerns and social marginalization. Care for people with complex health and social needs is called “complex care.” Disagreement exists about the nature and goals of complex care; there is especially little evidence about the goals of complex care in relation to mental health. This dissertation aims to address these knowledge gaps by: 1) developing a new policy framework for complex care that is based on a clear definition of complex health and social needs as a policy problem; 2) exploring the mental health care outcomes that matter in complex care, from the perspective of leaders, including managers and clinicians as well as individuals with lived experience in advisory roles; and 3) exploring the mental health care experiences that matter to people with complex health and social needs.


title: X-Ray and Optical Techniques for Classification & Characterization of Tissue for Applications in Cancer

contributor:
Farquharson, Michael
Physics and Astronomy

abstract:
In this work, x-ray and optical techniques were utilized to analyze tissue for two main applications in cancer: intraoperative breast cancer margin assessment and contrast agent development for prostate cancer magnetic resonance imaging (MRI).
A clinically compatible combined time-resolved fluorescence and diffuse reflectance (TRF-DR) spectroscopy system was used to measure breast tissue from 80 patients with invasive ductal carcinoma (IDC). A procedure was developed to compare extracted optical parameters with histological analysis. Trends in optical parameters between breast tumor, adipose, and fibroglandular tissue were investigated. Optical parameters that showed statistically significant differences between tissue groups were used in multivariate analysis and tissue modelling. Tissue classification using the combined system resulted in tumor detection sensitivity and specificity of 83.9% and 96.2%, respectively. Further work studying more fibroglandular tissue and tissue of mixed composition would develop this system for intraoperative use for tumor margin detection.
In addition, micro-synchrotron radiation x-ray fluorescence (μ-SRXRF) was used to determine the efficacy of a novel gadolinium-based contrast agent for zinc-targeting in prostate cancer imaging. Trends in elements of interest such as Gd, Zn, Fe, Cu, and S between mice with prostate cancer, castrate-resistant prostate cancer, and normal mice were observed. Raster scans were collected of large regions of the prostate as well as within the lateral lobe specifically. Significant Zn and Gd co-localization was observed in both healthy and malignant tissues. Also, a marked decrease in Zn was found in the lateral lobe of the prostate obtained from mice with prostate cancer. The sample preparation and processing procedure outlined in this work provide a feasible and effective method of assessing the efficacy of MRI contrast agents in vivo. With the ability to use a beam as small as 5μm × 5μm, this optimized technique also lends itself to the investigation of other elements and contrast agents in biological tissue.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Assessment of the Long-Term Waste Management and Proliferation Resistance of Different Fuel Cycles for the Generation-IV Canadian Concept of Super-Critical Water Reactor

contributor: Engineering Physics and Nuclear Engineering

abstract:
The Canadian concept of Super Critical Water Reactor uses a mixture of reactor-grade plutonium and thorium (Pu/Th) as a fuel, in a once-through cycle. The implications of using Pu/Th on long-term waste management and proliferation resistance were investigated in this study. Other fuels were investigated as well. These fuels are Low-Enriched Uranium (LEU), a mixture of LEU and thorium (LEU/Th), re-enriched reprocessed uranium (RepU), and a mixture of Pu/Th and natural uranium (Pu/Th/U).
A quantitative estimation of the size of the deep geological repository (DGR) was done, and it was found that Pu/Th fuel would require three to four times larger DGR compared with uranium fuels. Criticality safety was investigated, and it was found that, even in the most reactive conditions, criticality safety is not hazardous.
Assessment of the occupational dose to the workers in DGR from handling and storage of Pu/Th fuel showed a higher dose, around 8%, compared with LEU. The peak dose rate to the public, in case of an accident after the closure of DGR, was 75% higher in the case of Pu/Th compared with uranium, but it is still less than the regulatory limit.
The attractiveness of the various fuel cycle for weapons were estimated using the Figure-of-Merit method. A numerical ranking system was proposed to facilitate the comparison between the different fuels from the proliferation point of view. It was found that RepU is the most proliferation-resistant fuel, while Pu/Th is the least one among all the studied fuels. Investigation of the reactivity coefficients of the studied fuel cycles showed that all fuels have the same sign of reactivity feedback. Regarding coolant void reactivity (CVR), the Pu/Th/U will have the most negative value which will help to bring the core to a safe state faster in case of an accident.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THE ROLE OF MYOGENIC CONSTRICTION IN HYPERTENSION AND CHRONIC KIDNEY DISEASE

title: MYOGENIC CONSTRICTION: ITS REGULATION, ROLE IN HYPERTENSIVE KIDNEY DISEASE, AND ASSOCIATION WITH URINARY UROMODULIN

contributor: Medical Sciences (Division of Physiology/Pharmacology)

subject: Chronic Kidney Disease, Hypertension, Myogenic Constriction, DSS, SHR, WKY, BN13, Old, Older, Salt Sensitivity, Uromodulin, Proteinuria, Albuminuria, , Renal Autoregulation, Preglomerular Arteries, Arcuate arteries, afferent arteriole, Prostaglandin, Thromboxane A2, Nitric Oxide, Endothelium, Nifedipine, High Salt, Uromodulin, Protein Casts

abstract: Chronic kidney disease (CKD) is defined as glomerular filtration rate (GFR) less than 60 mL/min/1.73 m2 for 3 months and is characterized by progressive loss of renal function. The second leading cause of CKD is hypertension. More than half of CKD patients also suffer from hypertension. Arteries and arterioles adjust to the fluctuations in the systematic blood pressure through a mechanism called autoregulation. In the kidneys, autoregulation protects the delicate glomeruli capillaries from high blood pressure and occurs through myogenic constriction (MC). MC refers to contraction of arterioles in response to an increase in the blood pressure. Chronically hypertensive individuals and animal models have an enhanced MC, leading to minimal renal injury despite their elevated blood pressure. Experimental and clinical evidence point to a role for the MC in the pathogenesis of the CKD, however, the mechanism through which preglomerular arterial MC contributes to CKD has not been fully elucidated. This thesis showed that augmented MC in chronically hypertensive animal models was due to increased thromboxane A2 prostaglandin that was not released from the endothelium (Chapter 2). Nevertheless, inhibiting MC while also reducing the blood pressure prevented salt-induced renal injury even though the blood pressure was still not normalized compared to the normotensive controls (Chapter 3). The resulting improvement in renal structure and function could be attributed to the reduction in the blood pressure, albumin, and uromodulin (UMOD) excretion (Chapter 3). UMOD is a kidney-specific glycoprotein that, based on a genome-wide association study have the strongest association to CKD (Chapter 3). Comparing two CKD hypertensive animal models further revealed that CKD progression was independent of the blood pressure and strongly associated with UMOD excretion levels (Chapter 4). Collectively, the data discussed in this thesis demonstrates potential therapeutic targets in CKD hypertensive animal models.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Theoretical studies of unconventional superconductivity in Sr2RuO4 and related systems

contributor:
Kallin, Catherine
Physics and Astronomy

subject:
Sr2RuO4
unconventional superconductivity
edge current
chiral superconductor
weak-coupling renormalization group
random phase approximation

abstract:
In this thesis, we study the unconventional superconductivity in Sr2RuO4 (SRO) and related systems. The superconducting state in SRO remains a puzzle after more than 28 years of study. Early experiments had pointed toward a topological non-trivial time-reversal symmetry breaking (TRSB) chiral p-wave order. This pairing candidate has attracted a large amount of attention, partly in relation to the possibility of topological quantum computation, and has stimulated studies on higher chirality superconducting systems. In the first part of this thesis, we study the spontaneous edge current in chiral d- and f-wave superconductors. We show that these currents, which vanish in the continuum limit at zero temperature, are generally non-vanishing but tiny, compared to the simplest chiral p-wave case. In the presence of strong surface roughness, the direction of the edge current in the chiral d-wave case can be reversed, compared with that of a specular ideal surface with specular scattering. However, it is shown that this current reversal is non-universal beyond the continuum limit.
The chiral p-wave scenario in SRO is overturned by recent Knight shift measurements, highlighting the importance of exploring different pairing symmetries for SRO. Recently, $d_{x^2-y^2} \pm ig_{(x^2-y^2)xy}$, $s' \pm id_{xy}$ and mixed helical p-wave pairings have been proposed as order parameter candidates. However, the stability of these states, especially of the $d_{x^2-y^2} \pm ig$ pairing, remains unclear. In the second part of the thesis, we study the leading superconducting instabilities in SRO in the presence of sizable atomic spin-orbit coupling (SOC), non-local SOC, and non-local interactions. We find that it is difficult to stabilize chiral p-wave pairing in SRO models; this is because, among the triplet p-wave states, the atomic SOC favors helical states over the chiral state. The presence of both d- and g-wave pairings, including a $d_{x^2-y^2} \pm ig$ state, is found when the second nearest neighbor (in-plane) repulsions, together with orbital-anisotropy of the non-local interactions and/or the B2g channel non-local SOC are included. We further analyze the properties, such as nodal structures, in-plane field spin-susceptibility, and spontaneous edge current, of the realized $d_{x^2-y^2} \pm ig$ pairing and find that this state is more compatible with existing experimental measurements than the $s' \pm id_{xy}$ and the mixed helical p-wave proposals.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)