title: Priesthood, Cult, and Temple in the Aramaic Scrolls from Qumran

contributor:
Machiela, Daniel
Religion

subject:
Dead Sea Scrolls
Aramaic
Priesthood
Ancient Judaism

abstract:
My dissertation analyzes the passages related to the priesthood, cult, and temple in the Aramaic Scrolls from Qumran. The Aramaic Scrolls comprise roughly 15% of the manuscripts found in the Qumran caves, and testify to the presence of a flourishing Jewish Aramaic literary tradition dating to the early Hellenistic period (ca. late fourth to early second century BCE). Scholarship since the mid-2000s has increasingly understood these writings as a corpus of related literature on both literary and socio-historical grounds, and has emphasized their shared features, genres, and theological outlook. Roughly half of the Aramaic Scrolls display a strong interest in Israel’s priestly institutions: the priesthood, cult, and temple. That many of these compositions display such an interest has not gone unnoticed. To date, however, few scholars have analyzed the priestly passages in any given composition in light of the broader corpus, and no scholars have undertaken a comprehensive treatment of the priestly passages in the Aramaic Scrolls. My dissertation fills these lacunae.
	After a brief introduction to the dissertation in Chapter 1, Chapter 2 gives an overview and assessment of earlier treatments of the Aramaic Scrolls. Chapters 3 through 5 offer analyses of the passages related to the priesthood, cult, and temple found in fourteen of the approximately thirty Aramaic Scrolls, dealing with each composition in turn. In Chapter 6, I synthesize the material in the previous three chapters, and show that the Aramaic Scrolls reflect a remarkably consistent conception of Israel’s priestly institutions. By way of conclusion in Chapter 7, I situate the Aramaic Scrolls in the context of broader scholarly proposals concerning the history of the Second Temple Jewish priesthood, and demonstrate how this corpus can shed new light on an otherwise poorly documented period in Jewish history, namely, the pre-Hasmonean, Hellenistic period.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: My dissertation is a literary analysis of themes related to the Jewish priesthood in the Aramaic Dead Sea Scrolls. It uses the results of this literary analysis to understand better the history of the Jewish priesthood in the Second Temple period.


title: HIGH-ALTITUDE ADAPTATION AND CONTROL OF BREATHING IN DEER MICE (PEROMYSCUS MANICULATUS)

contributor:
Scott, Graham
Biology

subject:
Hypoxia
Genetic adaptation
Phenotypic plasticity
Carotid body

abstract: For animals at high altitude, low oxygen (hypoxia) is an unremitting stressor that has the potential to impair metabolism and performance. The hypoxic chemoreflex senses reductions in the partial pressure of O2 in the arterial blood and thus elicits many of the physiological responses to hypoxia, including increases in breathing and activation of the sympathetic nervous system. The hypoxic chemoreflex is vital to surviving acute exposure to severe hypoxia, but the advantage of this reflex during chronic hypoxia is less clear. The goals of my thesis were to examine how control of breathing by the hypoxic chemoreflex has evolved in high-altitude natives to maintain O2 transport in chronic hypoxia, and to elucidate the potential genetic mechanisms that were involved. This was accomplished using deer mice (Peromyscus maniculatus) native to high- and low-altitudes, in addition to a strictly low-altitude species (P. leucopus). I found that high-altitude deer mice breathe with higher total ventilation using preferentially deeper breaths, contributing to higher O2 saturation of arterial blood, but in contrast to lowland mice highlanders do not exhibit ventilatory plasticity in response to chronic hypoxia. These phenotypes appeared to be uniquely evolved in the highland population and arise during the onset of endothermy in early post-natal development. I then used second-generation inter-population hybrids to evaluate the effects of genetic variation (specifically, in the hypoxia-inducible factor 2a gene Epas1 and in haemoglobin genes) on an admixed genomic background. The high-altitude variant of α-globin could completely explain the deep breathing pattern of highland mice, whereas the high-altitude variant of Epas1 and possibly β-globin contributed to their apparent lack of ventilatory plasticity in response to chronic hypoxia. Together, the physiological changes elicited by these mutations contribute to maintaining O2 uptake and metabolism in the cold and hypoxic environment at high altitude.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: High-altitude environments are amongst the harshest on earth, with extremely low levels of oxygen, but some animals not only survive but thrive in these conditions. How these animals do so was previously not well understood. My thesis has uncovered how the evolution of respiratory physiology contributes to high-altitude adaptation in the deer mouse, the species with the broadest altitudinal distribution of any North American mammal, and has elucidated the genetic mechanisms involved. My work contributes to understanding nature’s solutions to oxygen deprivation – an all too common problem in many human and animal diseases.


title: The Nature of Law and Potential Coercion

contributor:
Waluchow, Wilfrid Joseph
Philosophy

subject:
Legal philosophy
Law
Coercion
Morality

abstract:
This thesis argues for a novel understanding of the relationship between law and coercion.
One of the relationships H.L.A. Hart sought to clarify is between law and coercion. In his work, Hart denies that coercion is a conceptually necessary feature of law – denies that the existence of law is in some sense determined by the presence of coercive mechanisms. According to Hart, coercion is naturally necessary to our legal practices. We humans need our law to be backed by coercive mechanisms so that it can do what it is supposed to: serve as an authoritative guide for behaviour.
Investigating the relationship between law and coercion not only depends on what one thinks about law, but also what one means by ‘coercion.’ I define an instance of coercion as a forced-choice. I also explain that understanding what it means to say, ‘law coerces’ is made difficult by the fact that what is coercive for one person may not be coercive for another. This subjective aspect of coercion means that more specific questions need to be asked in order to understand the relationship between law and coercion.
This thesis asks: is there a conceptual relationship between law and the law’s institutionalisation and utilisation of coercive mechanisms?
I argue that coercive mechanisms are not a conceptually necessary feature of law. I also argue that Hart’s work still leaves the relationship between law and coercion problematically undefined.
Rather, I put forward the claim that law is coercion-apt. I expand this claim by distinguishing law from other normative systems, like morality. Unlike law, morality, I argue, is not coercion-apt. Therefore, this thesis not only refines our understanding of the relationship between law and coercion, but also between law and morality – which is another relationship Hart sought to clarify in his work.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: This thesis explores the relationship between law and coercion. By ‘coercion’, I mean the way in which the law forces compliance with its prohibitions and requirements through the institutionalisation of sanctions (e.g., fines or prison sentences). A debate concerning the relationship between law and coercion has been present in jurisprudential literature for decades. Those who claim that that coercion is a conceptually necessary feature of law are essentially claiming that the existence of law is, in part, determined by the presence of coercive mechanisms. In this thesis I explain why such claims are erroneous. I then defend my own understanding of the relationship between law and coercion. I argue that it would be incorrect to call y ‘law’ if y is not coercion-apt. I explain what it means to say, ‘law is coercion-apt’ by distinguishing law from other normative systems like morality, religion, and voluntary associations and clubs.


title: CHARACTERIZATION OF A NOVEL MODEL OF GLUTEN SENSITIVITY

contributor:
Verdu, Elena
Medical Sciences

abstract: The gastrointestinal tract forms the largest mucosal interface between the host and the external environment and is therefore exposed to antigens from food and microbes as well as nutrients and environmental toxins. Gut functions necessary for the survival of the host, such as digestion and nutrient absorption, must be completed while ensuring protection from pathogenic microorganisms and potential toxins. This is achieved through highly coordinated interactions between the intestinal barrier, the gut immune system, neuromotor and endocrine systems, and the gut microbiota. An example of breakdown in this balance is celiac disease (CeD), an immune mediated enteropathy that is triggered by the ingestion of gluten proteins by individuals that carry either the HLA-DQ8 or DQ2 allele. Currently, the only treatment for CeD is a strict, lifelong gluten free diet and drug development in CeD has been delayed due to a lack of preclinical models. Further, most preclinical murine models are based on the expression of the HLA-DQ8 allele, the CeD risk allele that is carried by only 10% of patients. Therefore, the overall goal of my thesis is to characterize a model of gluten sensitivity based on the transgenic expression of the HLA-DQ2 allele. In Chapter 3 of this thesis, I characterized the physiological and immunological response to gluten using transgenic DR3-DQ2 mice. I determined that following gluten sensitization and an acute challenge, DR3-DQ2 mice developed a moderate level of enteropathy, anti-tissue transglutaminase 2 and anti-gliadin antibodies, and had increased il15 expression. In Chapter 4 of this thesis, I explored the impact of gluten sensitization and a long-term exposure to gluten using DR3-DQ2 mice. I demonstrated that without gluten sensitization, DR3-DQ2 mice spontaneously begin to develop anti-tissue transglutaminase antibodies, mild enteropathy, and increased paracellular permeability when exposed to gluten for a longer period of time. Together, the findings in both Chapter 3 and Chapter 4, show that mice transgenic for the DR3-DQ2 haplotype mimic different responses to gluten seen in CeD patients and will be a valuable tool in preclinical CeD research in the future. These findings also show the importance of utilizing a well-defined model to study the complex interactions between the host, immune system, and microbiota in the context of CeD.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: People with certain predisposing alleles, that consume gluten found in cereals like rye, wheat and barley, can develop a serious condition called celiac disease. The disease is characterized by damage to the lining of the upper gut and has many intestinal and non-intestinal symptoms such as anaemia, poor bone and dental health, depression, neurological problems, and infertility. Having the celiac predisposing alleles (called HLA-DQ8 and DQ2) is necessary, but not sufficient to develop celiac disease, and thus other factors have been proposed. Among those, microbes are suspected to trigger active disease in some patients. Animal models that reproduce some features of the celiac disease can help us understand mechanisms by which microbes increase risk. For this reason, I set out to characterize a novel mouse model that expresses the same human risk gene (DR3-DQ2) that is carried by the majority of celiac patients. I determined that these mice develop inflammation and blood positive tests after exposure to gluten, and reproduces some characteristics seen in patients with celiac disease. My research will allow others to use this model to study mechanisms that trigger celiac disease and test therapies preclinically that can be used with the gluten-free diet.


title: Imagining Social Work: Assembling Inter- and Trans-Generational Visions of a Modern Project

contributor:
Zhou, Rachel
Social Work

subject: Social change; generational standpoints; history of social work; critical social theory

abstract: This dissertation is about the changing imaginations of academic social work in an increasingly entangled world. Broadly, my subject area is the history and philosophy of social work, with an emphasis on engagements with critical social theory. More specifically, my research explores questions of discipline, generation, and critical social theory in the Anglophone Canadian context as a means to better understand how shared perceptions of the possible and the desirable are “situated knowledges” (Haraway, 1988). To do so, I trace and theorize changing perceptions through a survey of educators, and through integrative interdisciplinary and philosophical knowledge work considering various dynamics of disciplines in general and social work in particular. Evoking my own generational standpoint, I raise as a collective disciplinary problematic the canonization of second generation critical social theories, and the need to engage in the collective work of disciplinary reflexivity on, and accountability to, the ways in which the conditions of existence and possibility of critical academic social work are changing over time. Methodologically, I elaborate a reparative historical practice through a slightly different genre or style of writing. This is a feminist strategy, one roughly within the (generational) turn towards showing what one combines and assembles and learns through engaging with the world as a means to invite further speculative and imaginative work. This strategy is also a means to begin to imagine a “post-expert,” “post-good” and “post-progress” social work, not because knowledge and intention do not matter, but because these organizing referents have each achieved a level of saturation in what they can produce in the world. As such, this dissertation contributes some of the conditions of intelligibility necessary for the collective work of imagining and reimagining something akin to justice or improvement through social work after the fall of so many left and liberal progress narratives.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This research explores changing understandings of how social work in the Canadian state context imagines and intervenes in the world. My focus is on academic social work as both educator and knowledge producer, because the university is where some ideas and practices are refined and reproduced so that they can in turn be shared more broadly. Findings include the noteworthy influence of the university on the ideas and initiatives that do gain traction, as well as a generational structural to perceptions of the possible and the desirable. Overall, this research contributes a range of resources—historical, theoretical, empirical and speculative—to the collective work of imagining and reimagining social work for a changing world.


title: A Design Language for Scientific Computing Software in Drasil

title: Design Language for SCS

contributor:
Smith, Spencer
Carette, Jacques
Computing and Software

subject:
Code Generation
Scientific Computing
Software Design

abstract:
Drasil is a framework for generating high-quality documentation and code for Scientific Computing Software (SCS). Despite the tendency of SCS code to follow an Input-Calculate-Output design pattern, there are many design variabilities in SCS. Drasil should therefore allow its users to specify a design for their generated program. To this end, a language that encodes the design variabilities present in SCS was implemented in Drasil. Drasil's code generator was updated to generate code based on a user's design choices. A Generic Object-Oriented Language, GOOL, from which Python, Java, C#, or C++ code can be generated, was implemented. Drasil's code generator targets GOOL, enabling the choice of programming language to be included in the design language. Other choices included in the language are related to the modularity, the generation of record classes to bundle variables, the inlining of constants, the code types used to represent different mathematical spaces, which external library to use to solve ODEs, the behaviour when a constraint is violated, and the presence of
documentation, logging, or a controller. The design language is implemented as a record type in Haskell, and is designed to be understandable, extensible, and usable. A design specification can be easily changed, to generate a different version of the same program, which would often require time-consuming refactoring if the program was written manually. During the regular build process of Drasil, working code is generated in all four target languages for three examples of SCS, each using a different design specification.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: HEALTH ECONOMIC EVALUATION OF PROBIOTIC PROPHYLAXIS IN CRITICAL ILLNESS FOR PREVENTION OF HEALTHCARE-ASSOCIATED INFECTIONS

contributor:
Rochwerg, Bram
Xie, Feng
Cook, Deborah
Health Research Methodology

subject:
health economic evaluation
probiotics
healthcare-associated infections
ventilator-associated pneumonia
cost-effectiveness analysis
systematic review
protocol and statistical analysis plan
intensive care units
PROSPECT
critical care

abstract:
Ventilator-associated pneumonia (VAP) is the most common healthcare-associated infection in the intensive care unit, resulting in a high burden of illness, mortality and increased cost. The literature around the cost-effectiveness of probiotics in prevention of health-care associated infections has not been previously well-described, and a definitive health economic evaluation alongside a well-designed randomized control trial assessing probiotic prophylaxis has not been previously performed.

This thesis consists of 3 separate manuscripts (with 2 published in peer-reviewed journals and 1 pending). The theme of this thesis was to: (1) describe the literature about the cost-effectiveness of probiotics in hospitalized patients in preventing healthcare-associated infections; (2) design a protocol for an economic evaluation alongside a randomized control trial (RCT) examining probiotic prophylaxis of VAP; and then (3) perform and analyze the health economic evaluation presented in the protocol.

The first component of this thesis is a systematic review of probiotic prophylaxis of healthcare-associated infections in hospitalized patients. We performed an extensive search including multiple databases which found 7 studies. Probiotics demonstrated favourable cost-effectiveness in 6 of 7 (86%) economic evaluations, with 3 studies being manufacturer-supported, all suggesting cost-effectiveness. Certainty of cost-effectiveness evidence was very low due to risk of bias, imprecision and inconsistency using the GRADE approach. Hence further RCTs with economic evaluations were stated as a solution.

The second component of this thesis is a study protocol for an economic evaluation alongside the Probiotics to Prevent Severe Pneumonia and Endotracheal Colonization Trial (PROSPECT), which assessed the efficacy of probiotic prophylaxis in the prevention of healthcare-associated infections (specifically VAP).

The third component of this thesis is the cost-effectiveness analysis performed utilizing the individual patient data from PROSPECT to produce the economic evaluation (E-PROSPECT). As of the date of thesis submission, PROSPECT is still pending publication, and hence E-PROSPECT is also pending analysis and publication. However, I have prepared a draft manuscript (along with figures and tables) that will be produced at the conclusion of E-PROSPECT for thesis committee review.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: UNDERGRADUATE NURSING STUDENTS’ EXPERIENCES ENGAGING IN SERIOUS ILLNESS COMMUNICATION AND PERCEPTIONS OF SERIOUS ILLNESS CONVERSATION GUIDE TRAINING: A QUALITATIVE DESCRIPTIVE STUDY

contributor:
Strachan, Patricia
Nursing

subject:
serious illness communication
undergraduate nursing students

abstract:
Background: While serious illness communication is an important aspect of nursing care, it is
recognized as an area of practice for which nursing students are not adequately prepared.
Communication tools such as the Serious Illness Conversation Guide (SICG) may help address
these gaps in knowledge and skill.
Aim: The aim of this study is to explore undergraduate nursing students’ experiences engaging in serious illness communication and their perceptions about participation in a SICG workshop that aimed to improve such communication.
Methods: A qualitative descriptive approach was used. One-on-one, semi-structured interviews were conducted with eight undergraduate nursing students at McMaster University who had attended SICG training. Critical incident technique was used to elicit participant accounts of engaging in serious illness communication at their professional practice placements. Data were analyzed using qualitative techniques. Participants were surveyed to assess perceptions of the SICG workshop.
Findings: Three themes related to undergraduate nursing students’ experiences engaging in
serious illness communication after receiving SICG training were: a) serious illness
communication is challenging to enact, b) finding moral and ethical ground, and c) fitting into
the culture of the professional practice setting. Three themes related to nursing students’
perceptions of the SICG workshop were: a) applicability of SICG training to practice, b)
strengths of SICG training, and c) limited opportunities to develop competence.
Conclusions: Nursing students are challenged by serious illness communication in their practice. Findings support the integration of educational resources aimed to better prepare them for critical communication knowledge and skills on entry-to-practice.

abstract: Thesis

abstract: Master of Science in Nursing (MSN)


title: Reactive Polymers and Microcapsules

contributor:
Stover, Harald
Chemistry

abstract: In cell encapsulation, cells are embedded within a hydrogel matrix or liquid core capsule, which is designed to isolate donor cells from a patient’s immune system. This immunoisolation allows for long term transplant function of therapeutic secreting cells for potential treatment of many hormonal and enzyme deficiency disorders. The work in this thesis focuses on the use and study of reactive polymers for their application in cell application. Incorporation of covalent crosslinking into cell encapsulation by reactive polymers addresses issues of long-term stability seen in conventional alginate – poly(L-lysine) – alginate (APA) capsules, by introducing crosslinks with prolonged stability in vivo

abstract: Thesis

abstract: Master of Science (MSc)


title: Mechanical Properties of Plant Cell Wall Mimics Determined using Strain-Induced Buckling Methods

contributor:
Cranston, Emily
Moran-Mirabal, Jose
Chemical Engineering

subject: xyloglucan

subject: cellulose

subject: plant cell wall

subject: elastic modulus

subject: Fourier analysis

subject: strain-induced elastic buckling instability

abstract: A thesis submitted to the School of Graduate Studies in partial fulfilment of the requirements of the Master of Applied Science degree

abstract:
This thesis investigated structure-function relationships of materials designed to mimic the plant cell wall by comparing their mechanical properties measured using strain-induced buckling methods. The plant cell wall mimics are submicrometer-thick films composed of cellulose nanocrystals (CNCs) and various types of xyloglucan (XG), a common plant hemicellulose. Our goal was to establish links between film composition/architecture and elastic modulus, to better understand the interactions between plant cell wall components and their influence on mechanical properties.
Three buckling methods for measuring mechanical properties of supported films were compared. All methods involved compressing a thin film deposited onto a shape memory polymer or an elastomeric substrate, through thermal shrinking or mechanical compression, respectively. Two thermal shrinking methods (constrained in one axis or unconstrained) and one compression method (using a mechanical strain stage) were used. Based on the mismatch of mechanical properties between the film and the substrate, the rigid thin film “buckles” upon compression to dissipate strain. The resulting surface wrinkle sizes are characteristic of the mechanical properties of the thin film. A Fourier analysis algorithm with Gaussian curve fitting was optimized to extract wrinkle sizes accurately and reproducibly from microscopy images to reliably quantify the elastic moduli of thin films.
To select the most precise strain-induced buckling method, model layer-by-layer (LbL) thin films composed of CNCs and polyethylene imine were tested. All three buckling methods precisely quantified the elastic moduli of the films and helped us build connections between the mechanical properties and the film composition. Elastic moduli determined were 15-44 GPa (depending on composition) and films up to 350 nm-thick were tested. Based on sensitivity analyses, however, unconstrained thermal shrinking proved to be the most robust method for calculating the elastic modulus. We believe these buckling methods may find widespread use in the characterization and surface structuring of thin films for applications in biosensors, flexible electronics, point-of-care diagnostics, and for studying plant cell wall mimics.
Using the unconstrained thermal shrinking method, plant cell wall mimics were constructed using LbL thin film assembly with various concentrations of CNCs and XG. Three types of XG were compared: (1) unmodified XG, (2) XG with a fraction of the galactosyl residues removed (degalactosylated), and (3) a fragmented lower molecular weight XG. It was inferred that molecular weight impacts the stiffness of XG-CNC based on adsorption conformation of XG onto CNCs, where lower molecular weight XG results in a higher modulus film (27 ± 1 vs. 19 ± 2 GPa). As well, saccharide residues of XG, specifically galactosyl, impact XG’s capacity for self-association and interaction with CNCs, because saccharide residues hinder association through their glucan backbone. This is evidenced by the higher elastic moduli calculated for degalactosylated XG-CNC films (75 ± 6, GPa), compared to native XG-CNC films (19 ± 2 GPa). This work highlights the importance of material structure as it relates to overall performance and therefore function in natural systems, such as the plant cell wall. These studies contribute to a greater understanding of the mechanical properties of the plant cell wall and serve as a basis to extend bio-based and biomimetic materials to applications such as drug delivery, packaging, and coatings.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: The plant cell wall boasts impressive mechanical properties, balancing seemingly opposing properties of structural strength with flexibility. These natural materials have been a source of inspiration for new material design, but the phenomena that govern interactions between components and how their structures translate into function, have yet to be fully understood. In this work, we have constructed thin multilayered films to mimic the plant cell wall, composed of cellulose nanocrystals (rod-shaped nanoparticles derived from plant cellulose) and xyloglucan (a common hemicellulose “glue”). When the films on flexible supports are compressed, they buckle into wrinkled surface patterns that can be used to calculate their mechanical properties. This investigation compares three buckling methods and supports the notion that the mechanical performance of the plant cell wall is strongly dependent on the structure of the different components and the way they interact.


title: EVOLUTION OF THE GLYCOPEPTIDE BIOSYNTHETIC GENE CLUSTER FAMILY

contributor:
Wright, Gerard
Biochemistry and Biomedical Sciences

abstract:
The serendipitous discovery of antibiotics in the 20th century paved the way for safer, modern medical interventions. Bacteria in the phylum Actinobacteria are the most prolific producers of natural products, including antibiotics. The availability of low-cost, high-throughput generation of bacterial genome sequence data transforms natural product discovery, making it possible to judge the biosynthetic capacity of a strain based on its genome sequence.
I developed a software tool to compare biosynthetic gene clusters (BGCs) to show that streptothricin production is distributed among Streptomyces and that the capacity to produce common natural products does not predict the remaining potential of Streptomyces species. This approach provides a way to consider the rarity of particular natural products and grounded a biotechnological approach using CRISPR/Cas9 engineering to facilitates the identification of rare natural products in these strains.
Glycopeptide antibiotics (GPAs) are encoded by BGCs in several genera of Actinobacteria. Their diversity is the product of an intricate evolutionary history. We show that GPA biosynthesis and resistance maps to approximately 150-400 million years ago, from an older, pre-existing pool of components. We find that resistance appeared contemporaneously with biosynthetic genes, raising the possibility that the mechanism of action of glycopeptides was a driver of diversification in these gene clusters.
In a set of GPA BGCs, we identify several scaffolds distinct from the traditional D-Ala-D-Ala binding antibiotics. while complestatin, kistamicin, and longer peptides like enduracidin and ramoplanin are known, others are uncharacterized. Through phylogenetic analysis of these BGCs we develop a new classification scheme to organize these BGCs into four major classes. Structural predictions led us to purify complestatin and a novel compound we named corbomycin. Both possess antibacterial activity. Mutations conferring decreased susceptibility to these compounds suggest a novel mechanism of action distinct from known compounds in the GPA family.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The discovery of antibiotics is a triumph of the 20th century. Most antibiotics are derived from microorganisms – they are natural products. The biosynthetic gene clusters (BGCs) encoding their production are being revealed through an unprecedented genomic sequencing. My work considers the way BGCs are represented and ways of comparing the biosynthetic potential of different strains. Glycopeptide antibiotics (GPAs) are chemically diverse, made by several genera of Actinobacteria. Using BGCs derived from our in-house and public databases I build a natural history of these molecules, dating their emergence to 150-400 million years ago and connect it with GPA resistance. I further explore their evolution by considering the wider set of related BGCs to propose an expanded classification system that naturally points the way to the discovery of novel molecules. This culminates in discovery of corbomycin, shown to possess a new mechanism of action shared by other molecules in my classification.


title: Cognitive Dynamic System for Control and Cyber Security in Smart Grid

contributor:
Haykin, Simon
Hurd, Thomas
Computational Engineering and Science

subject:
Cognitive Dynamic System
Smart Grid
Cognitive Control
Cognitive Risk Control
Reinforcement Learning
Kalman Filter
Cyber Security
False Data Injection
Power System Security
Adaptive Control
DC State Estimation
AC State Estimation

abstract:
The smart grid is forecasted to be the future of the grid by integrating the traditional grid with information and communication technology. However, the use of this technology has not only brought its benefits but also the vulnerability to cyber-attacks. False data injection (FDI) attacks are a new category of attacks targeting the smart grid that manipulates the state estimation process to trigger a chain of incorrect control decisions leading to severe impacts.
This research proposes the use of cognitive dynamic systems (CDS) to address the cyber-security issue and improve state estimation. CDS is a powerful research tool inspired by certain features of the brain that can be used to study complex systems. As two of its special features, Cognitive Control (CC) is concerned with control in the absence of uncertainty, Cognitive Risk Control (CRC) uses the concept of predictive adaptation to bring risk under control in the presence of unexpected uncertainty.
The primary research objective of this thesis is to apply the CDS for the SG with emphasis on state estimation and cyber-security. The main objective of CC is to improve the state estimation process while CRC is concerned with mitigating cyber-attacks. Simulation results show that the proposed methods have robust performance for both state estimation and cyber-attack mitigation under various challenging scenarios.
This thesis contributes to the body of knowledge by achieving the following objectives: proposes the first theoretical work that integrates the CDS with the DC model of the SG for control and cyber-attack detection; demonstrates the first experimental work that brings a new concept of CRC for cyber-attack mitigation for the DC state estimator; introduces a new CDS architecture adapted for the AC model of the SG for state estimation and cyber-attack mitigation which builds upon all the research efforts made previously.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The smart grid is forecasted to be the future of the grid by integrating the traditional grid with information and communication technology. However, the use of this technology has not only brought its benefits but also the vulnerability to cyber-attacks. False data injection attacks is a new category of attacks targeting the smart grid that can cause serious damage by manipulating the state estimation process and starting a chain of incorrect control decisions. The cognitive dynamic system is a powerful research tool inspired by the brain that can be used to study real time cyber physical systems. The key goal of this thesis is to apply cognitive dynamic systems to the smart grid to improve the state estimation process, detect cyber-attacks and mitigate their effects. Simulation results show that the proposed methods have robust performance in both state estimation and cyber-attack mitigation under various challenging scenarios.


title: THE USE OF ARTIFICIAL INTELLIGENCE FOR THE DEVELOPMENT AND VALIDATION OF A COMPUTER-AIDED ALGORITHM FOR THE SEGMENTATION OF LYMPH NODE FEATURES FROM THORACIC IMAGING

contributor:
Hanna, Waël
Health Research Methodology

subject:
Lung Cancer
Artificial Intelligence
Mediastinal Staging
Segmentation

abstract:
Background- Mediastinal staging is the rate-limiting step prior to initiation of lung cancer treatment and is essential in identifying the most appropriate treatment for the patient. However, this process is often complex and involves multiple imaging modalities including invasive and non-invasive methods for the assessment of lymph nodes in the mediastinum which are error prone. The use of Artificial Intelligence may be able to provide more accurate and precise measurements and eliminate error associated with medical imaging.
Methods-This thesis was conducted in three parts. In Part 1, we synthesized and critically appraised the methodological quality of existing studies that use Artificial Intelligence to diagnosis and stage lung cancer from thoracic imaging based on lymph node features. In Part 2, we determined the inter-rater reliability of segmentation of the ultrasonographic lymph node features performed by an experienced endoscopist (manually) compared to NeuralSeg (automatically). In Part 3, we developed and validated a deep neural network through a clinical prediction model to determine if NeuralSeg could learn and identify ultrasonographic lymph node features from endobronchial ultrasound images in patients undergoing lung cancer staging.
Results- In Part 1, there were few studies in the Artificial Intelligence literature that provided a complete and detailed description of the design, Artificial Intelligence architecture, validation strategies and performance measures.  In Part 2, NeuralSeg and the experienced endosonographer possessed excellent inter-rater correlation (Intraclass Correlation Coefficient = 0.76, 95% CI= 0.70 – 0.80, p<0.0001). In Part 3, NeuralSeg’s algorithm had an accuracy of 73.78% (95% CI: 68.40% to 78.68%), a sensitivity of 18.37% (95% CI: 8.76% to 32.02%) and specificity of 84.34% (95% CI: 79.22% to 88.62%).
Conclusions- Analysis of staging modalities for lung cancer using Artificial Intelligence may be useful for when results are inconclusive or uninterpretable by a human reader. NeuralSeg’s high specificity may inform decision-making regarding biopsy if results are benign. Prospective external validation of algorithms and direct comparisons through cut-off thresholds are required to determine their true predictive capability. Future work with a larger dataset will be required to improve and refine the algorithm prior to trials in clinical practice.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Before deciding on treatment for patients with lung cancer, a critical step in the investigation is finding out whether the lymph nodes in the chest contain cancer cells. This is accomplished through medical imaging of the lymph nodes or taking a biopsy of the lymph node tissue using a needle attached to a scope that is entered through the airway wall. The purpose of these tests is to ensure that lung cancer patients receive the optimal treatment option. However, imaging of the lymph nodes is heavily reliant on human interpretation, which can be error prone. We aimed to critically analyze and investigate the use of Artificial Intelligence to enhance clinician performance for image interpretation. We performed a search of the medical literature for the use of Artificial Intelligence to diagnosis lung cancer from medical imaging. We also taught a computer program, known as NeuralSeg, to learn and identify cancerous lymph nodes from ultrasound imaging. This thesis provides a significant contribution to the Artificial Intelligence literature and provides recommendations for future research.


title: Three Essays on Forecasting Return Distributions with Mixture Modelling

contributor:
Maheu, John
Business

abstract:
This thesis examines three important topics in finance: co-jumps among risky assets and portfolios, proposing a new Bayesian semiparametric stochastic volatility model with Markovian mixtures, and whether better return density forecasts lead to economic gains in portfolio allocation practice.
First, jump models are useful in capturing skewed and/or leptokurtic financial returns. So far, research has focused on jumps in a single asset, including co-jumps between return and volatility. On the other hand, co-jumps among assets are also important especially in practices such as beta dynamics and portfolio allocation. I propose a parsimonious yet flexible multivariate GARCH-jump mixture model (MGARCH-jump model) with multivariate jumps that allows both jump sizes and jump arrivals to be correlated. The model identities co-jumps well and shows that both jump arrivals and jump sizes are highly correlated. The model also provides better prediction and better investment outcomes as opposed to the benchmark multivariate GARCH model with normal innovations (MGARCH-N model).
Second, I extend the Bayesian semiparametric stochastic volatility (SV-DPM) model of Jensen and Maheu (2010). Instead of using a Dirichlet process mixture (DPM) to capture return innovations, we use an infinite hidden Markov model (IHMM). This allows for time variation in the return density beyond that attributed to latent volatility dynamics. The new model (SV-IHMM) also nests the SV-DPM as a special case and improves the density forecast from the SV model with Student-t innovations, SV-DPM and other benchmark models. Our model is applied to equity stock returns, foreign exchange rates, commodity prices and industrial growth rates. The model demonstrates robust and consistent gains in out-of-sample performance against other benchmarks. Furthermore, predictive densities from the SV-IHMM exhibit clear distributional change over time.
Third, I investigate the relationship between statistical improvements in density forecasts of returns and actual economic gains in portfolio allocation for a risk-averse investor. To aid this investigation, this chapter proposes a new multivariate Bayesian semiparametric model that has better out-of-sample density forecasts than benchmark models. Results show that this more sophisticated econometric model does provide positive economic gains whether the investor’s utility is CRRA, CARA or quadratic. The economic gain diminishes when the investor is more risk-averse because she is moving away from risky investment positions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THE IMPACT OF MATERNAL POSTPARTUM DEPRESSION AND/OR ANXIETY ON MOTHER AND INFANT PERFORMANCE ON THE FACE-TO-FACE STILL-FACE TASK

contributor:
Van Lieshout, Ryan
Global Health

subject:
Postpartum depression
Postpartum anxiety
Face-to-Face Still Face Task
Cognitive behavioural therapy
Social Interactions

abstract:
Objective 1: To examine the influence of maternal depression and/ or anxiety on infant, maternal and dyadic FFSF task performance

Objective 2: To investigate the changes in infant and maternal FFSF task performance before and after Cognitive Behavioural Therapy (CBT) treatment of maternal depression

abstract:
Background: Research suggests that postpartum depression (PPD) and postpartum anxiety (PPA) impact both mothers and their infants, leading to adverse behavioural outcomes across the lifespan. The face-to-face still-face (FFSF) task is a validated observational tool used to measure the quality of mother-infant interactions. This thesis aimed to investigate the differences in responses to the FFSF task between dyads consisting of mothers with PPD and/or PPA and healthy dyads. Another goal was to examine whether PPD treatment could improve mother and infant FFSF outcomes.
Methods: A systematic search was performed in PubMed/MEDLINE, EMBASE, CINAHL, PsycINFO and Web of Science. Meta-analyses were conducted to examine the differences in infant, maternal and dyadic FFSF outcomes in mothers with PPD, PPA or comorbid PPD and PPA in comparison to healthy control dyads. Second, we examined whether group cognitive behavioural therapy (CBT) for PPD could help improve infant and maternal FFSF outcomes. A case-control design study was conducted with three different assessment points (i.e., pre-CBT treatment, immediately after CBT and three months post-CBT).
Results: Meta-analyses suggested that the infants of mothers with PPD display lower levels of positive affect during the play and reunion phases compared to the infants of healthy non-depressed mothers. Also, mothers with PPD may engage less positively with their infants at the reunion phase, and mother-infant dyads affected by PPD show less positive interactive matching during the play phase compared to healthy control dyads. Finally, object/environment engagement was higher in infants of PPA mothers compared to healthy controls at still-face.
Conclusion: The results suggest that mothers with PPD and/or PPD (and their infants) may exhibit different interaction patterns compared to healthy dyads. Also, it appears that the benefits of CBT for maternal PPD may extend to their infants through reductions in maladaptive infant withdrawn behaviours to normal, healthy levels.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Maternal postpartum depression (PPD) and postpartum anxiety (PPA) are the most common mental health complications of birth. Apart from unfavourable effects PPD and PPA have on mothers, it may also impact the mother-infant relationship, leading to adverse infant outcomes. Given the relatively high prevalence of maternal PPD, PPA, and comorbid PPD and PPA, this thesis aimed to examine the differences in how mothers suffering from PPD and/or PPA and their infants coordinate their behaviour, in comparison to healthy mothers and their infants using a validated observational task (face-to-face still-face [FFSF] task). Another goal of this thesis was to investigate whether the benefits of maternal treatment for PPD with cognitive behavioural therapy may extend to infants and improve mother, as well as infant behaviour. These investigations may provide new insights on how maternal PPD and/or PPA affects mother-infant interactions, and consequently, infant socio-emotional development.


title: OVERCOMING INTRINSIC AND ACQUIRED ANTIBIOTIC RESISTANCE WITH OUTER MEMBRANE PERTURBATION

title: OUTER MEMBRANE PERTURBATION AS AN ANTIBIOTIC APPROACH

contributor:
Brown, Eric David
Biochemistry and Biomedical Sciences

subject:
outer membrane
antibiotic discovery

abstract: There is an urgent need to identify novel antibiotics for multidrug-resistant Gram-negative pathogens. These bacteria are intrinsically resistant to many antimicrobials due to a formidable outer membrane barrier. Herein we investigate the potential of perturbing the outer membrane to sensitize Gram-negative bacteria to otherwise inactive antibiotics. In chapter 2, we identify the ability of mcr-1 mediated resistance to confer protection from the lytic but not outer membrane-perturbing activity of colistin. Exploiting this sensitivity, we show that colistin and clarithromycin in combination are efficacious against mcr-1-expressing Klebsiella pneumoniae in murine infection models. This demonstrates the viability of colistin combination therapies against Gram-negative pathogens harbouring mcr-1, and points to a mechanism of mcr-1-mediated resistance extending beyond the predicted reduction in binding affinity of polymyxins to the outer membrane. We continue to investigate the potential of using outer membrane perturbants with otherwise inactive antimicrobials in chapter 3. In this work, we identify the ability of OM disruption to change the rules of Gram-negative entry, render pre-existing resistance ineffective, reduce the development of spontaneous resistance and attenuate biofilm formation. Together, these data suggest that OM disruption overcomes many traditional hurdles encountered during antibiotic treatment and is a high priority approach for further development.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Cannabis use and cardiometabolic risk in patients with psychiatric conditions

contributor:
Samaan, M. Constantine
Medical Sciences

subject:
cannabis use
psychiatric conditions
cardiometabolic risk
glycemia
blood pressure
lipids
body mass index
BMI

abstract:
Introduction: The homeostatic role of the endocannabinoid system (ECS) is mediated through the actions of endocannabinoids. Intake of exogenous cannabinoids found in Cannabis sativa alter the function of the ECS which may then impact other organ systems. Use of cannabis has been inconsistently linked to adverse cardiometabolic outcomes. Rates of cannabis use are high among patients with psychiatric conditions who are already at higher risk of cardiometabolic diseases when compared to the general population. Cannabis use patterns and cardiometabolic risk variables in this population need further study to clarify the links between use and outcomes.
Methods: Patients with psychiatric conditions from the St. Joseph’s Healthcare Hamilton Hospital were enrolled into the Cannabis and Physical Health study. Sociodemographic data, medical history, cigarette use, and cannabis use patterns were collected. In addition, cardiometabolic profile data were collected including body mass index, blood pressure, lipids, and HbA1c. Multivariable regression analyses were conducted, and a Bonferroni correction applied.
Results: This cross-sectional study enrolled 200 patients (female: n=86, 43.0%), 18 years of age and older. Among 79 cannabis users (female: n=34, 43.0%), the majority (n=53, 67.1%) consumed cannabis daily and had a diagnosis of a moderate cannabis use disorder (CUD; n=57, 72.2%, CUD score = 4.3 ± 3.4). Use of cannabis was initiated on average at 15.2 ± 3.5 years of age and used for an average of 13.5 ± 11.0 years.  There was no association between cannabis use and cardiometabolic risk factors when adjusted for age, sex, psychiatric diagnosis, antipsychotic medication use, and cigarette smoking (P>0.006 for all outcomes).
Conclusions: Our findings indicate that in this sample of patients with psychiatric diagnoses, patients who use cannabis had a similar cardiometabolic profile to non-users. Patterns of cannabis use highlight the importance of reducing cannabis consumption and preventing or slowing the progression of CUD in this population, as well as limiting adolescent exposure to cannabis.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
The endocannabinoid system regulates several processes in the body via endocannabinoid signaling, and cannabinoids found in cannabis can change endocannabinoid system function. Cardiovascular events and changes in appetite have been noted with cannabis use, and this is especially important in some vulnerable populations at risk of increased cannabis use; one of these groups include patients with psychiatric conditions who tend to use cannabis but also already have an increased cardiometabolic risk. In this thesis, the relationship between cannabis use and cardiometabolic risk was examined in 200 patients, and patterns and determinants of cannabis use explored.
Our results demonstrated that of the 79 cannabis users, most consumed cannabis daily, and had a moderate cannabis use disorder. On average, users began cannabis consumption at 15 years of age and for an average duration of 14 years. Moderate cannabis use was not related to cardiometabolic risk in these patients.
Our data demonstrate the need to prevent or slow the progression of cannabis use disorder in these patients and the importance of reducing early exposure of adolescents to cannabis.


title: Deep Learning on the Edge: Model Partitioning, Caching, and Compression

contributor:
Zheng, Rong
Computing and Software

subject:
Deep Learning
Edge Artificial Intelligence

abstract:
With the recent advancement in deep learning, there has been increasing interest to apply deep learning algorithms to mobile edge devices (e.g. wireless access points, mobile phones, and self-driving vehicles). Such devices are closer to end-users and data sources compared to cloud data centers, therefore deep learning on the edge leads to several merits: 1) reduce communication overhead (e.g. latency), 2) preserve data privacy (e.g. not leaking sensitive information to cloud service providers), and 3) promote autonomy without the need of continuous network connectivity. However, it also comes with a trade-off that deep learning on the edge often results in less prediction accuracy or longer inference time. How to optimize such a trade-off has drawn a lot of attention among the machine learning and systems research communities. Those communities have explored three main directions: partitioning, caching, and compression to solve the problem.

Deep learning model partitioning works in distributed and parallel computing by leveraging computation units (e.g. edge nodes and end devices) of different capabilities to achieve the best of both worlds (accuracy and latency), but the inference time of partitioning is nevertheless lower bounded by the smallest of inference times on edge nodes (or end devices).

In contrast, model caching is not limited by such a lower bound. There are two trends of studies in caching, 1) caching the prediction results on the edge node or end device, and 2) caching a partition or less complex model on the edge node or end device. Caching the prediction results usually compromises accuracy, since a mapping function (e.g. a hash function) from the inputs to the cached results often cannot match a complex function given by a full-size neural network. On the other hand, caching a model's partition does not sacrifice accuracy, if we employ a proper partition selection policy.

Model compression reduces deep learning model size by e.g. pruning neural network edges or quantizing network parameters. A reduced model has a smaller size and fewer operations to compute on the edge nodes or end device. However, compression usually sacrifices prediction accuracy in exchange for shorter inference time.

In this thesis, our contributions to partitioning, caching, and compression are covered with experiments on state-of-the-art deep learning models. In partitioning, we propose TeamNet based on competitive and selective learning schemes. Experiments using MNIST and CIFAR-10 datasets show that on Raspberry Pi and Jetson TX2 (with TensorFlow), TeamNet shortens neural network inference as much as 53% without compromising predictive accuracy.

In caching, we propose CacheNet, which caches low-complexity models on end devices and high-complexity (or full) models on edge or cloud servers. Experiments using CIFAR-10 and FVG have shown on Raspberry Pi, Jetson Nano, and Jetson TX2 (with TensorFlow Lite and NCNN), CacheNet is 58-217% faster than baseline approaches that run inference tasks on end devices or edge servers alone.

In compression, we propose the logographic subword model for compression in machine translation. Experiments demonstrate that in the tasks of English-Chinese/Chinese-English translation, logographic subword model reduces training and inference time by 11-77% with Theano and Torch. We demonstrate our approaches are promising for applying deep learning models on the mobile edge.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Edge artificial intelligence (EI) has attracted much attention in recent years. EI is a new computing paradigm where artificial intelligence (e.g. deep learning) algorithms are distributed among edge nodes and end devices of computer networks. There are many merits in EI such as shorter latency, better privacy, and autonomy. These advantages motivate us to contribute to EI by developing intelligent solutions including partitioning, caching, and compression.


title: The Association Between Mobile Dating Apps Use, Sexually Transmitted Infections and Risky Sexual Behaviour in Ontario University Students

title: Dating Apps, Sexually Transmitted Infections and Risky Sexual Behaviour

contributor:
Marshall, Tara
Health Research Methodology

subject:
sexual health
public health
sexually transmitted infection
sexual behaviour

abstract: Over the last decade, the incidence rates of many sexually transmitted infections (STI) have been on the rise, especially amongst young adults. Popular Canadian media outlets have speculated that the reason behind these increases is the use of mobile dating applications which foster romantic and sexual connections. This cross-sectional study assesses whether students who use mobile dating apps are more or less likely to have been diagnosed with an STI in the previous 12 months and engage in risky sexual behaviour, compared to students who did not use mobile dating apps in the previous 12 months. An anonymous online questionnaire was used to collect data from 965 study participants currently enrolled at an Ontario university. The survey required participants to self-report STI testing behaviour and diagnoses, as well as sexual behaviours, including number of sexual partners, relationship type, condom use, substance use and sex work. I found that Ontario university students who used dating apps in the previous 12 months were more likely to have a greater number of sexual partners in the previous year (p<0.05), have multiple concurrent sexual partners (OR=10.72, 95% CI: 6.10-18.84),  frequently use alcohol (OR=3.94, 95% CI:2.17-7.14) and cannabis (OR=3.36, 95% CI:1.45-7.78) in combination with sexual activity, and were more likely to have been tested for STIs in the previous 12 months (OR=2.25, 95% CI: 1.73-2.94) compared to non-dating app users. However, mobile dating app users were not more likely to have been diagnosed with an STI in the previous 12 months compared to non-dating app users.

abstract: Thesis

abstract: Master of Public Health (MPH)

abstract: This study investigated whether students who use mobile dating apps are more or less likely to engage in risky sexual behavior, and to have been tested for and diagnosed with a sexually transmitted infection (STI) in the previous 12 months, compared to students who do not use mobile dating apps. An anonymous online survey was used to collect data on sexual behaviour and STI history from Ontario university students. I found that Ontario university students who used dating apps in the previous 12 months were more likely to have a greater number of sexual partners in the previous year, have multiple concurrent sexual partners, use alcohol and cannabis in combination with sexual activity, and get tested for STIs more frequently than non-dating app users. However, mobile dating app users were not more likely to have been diagnosed with an STI in the previous 12 months compared to non-dating app users.


title: Improvement of a detection system for in-vivo Al measurements, and in-vivo Al measurements of a population of miners.

contributor: Radiation Sciences (Medical Physics/Radiation Biology)

abstract:
The following thesis seeks to investigate potential alternatives to the 4π system employed by the Tandem Accelerator Laboratory (TAL) at McMaster University for use in the investigation of in-vivo aluminum levels using in-vivo neutron activation analysis. It also aims to measure the levels of aluminum in miners who were exposed to it via inhalation of the Aluminum containing McIntyre powder from ~ 1944-1979.
The same protocol for creation and irradiation of phantoms was followed as in [1], namely tissue equivalent phantoms were created and irradiated under a proton current of 400 μA, with a proton energy of 2.3 MeV which led to neutron energies of 0.55 MeV. These phantoms were then counted using three different detectors. These detectors consisted of two scintillators (the currently used 4π NaI(Tl) system, and a single LaBr3(Ce)) and a semi-conductor, a single closed-end coaxial HPGe. MDLs for these detectors were found to be 15.85   μgAl/gCa (236.17 μgAl) for the 4π NaI(Tl) system, 56.51 μgAl/gCa (842.0 ugAl) for the HPGe and 98.67 μgAl/gCa (1470.20 μgAl) for the LaBr3(Ce).
The next part of the thesis involved in-vivo measurements on a group of 15 miners from Northern Ontario who had been exposed to McIntyre powder previously throughout their careers in the mines. Each patient was irradiated under the same proton current and energy as above, and was transferred to the 4π system for counting for 10 1 minute cycles. The MDL for these in-vivo measurements was found to be 22.57  μgAl/gCa. The highest value was 206.36±14.76 μgAl/gCa and the lowest value was 18.55±3.95 μgAl/gCa, with a median value of 18.56±11.28 μgAl/gCa and average value of 21.78±2.27 μgAl/gCa for IVWM, and 17.43±13.78 μgAl/gCa for regular mean . Of the miners, 7 had negative concentrations, indicating that the concentrations were below the detection limit of the system.
Data analysis for all experiments was performed the same way. The Al/Cl peak for the NaI was fit using a FORTRAN algorithm, as well as the Ca peak. The areas for these peaks were then calculated, then the MDL was calculated by taking the average of the low concentration phantoms, and the error was multiplied by 2, then was divided by the calibration slope for the first three time cycles. These values were then added via the inverse variance weighted mean (IVWM) method, and the final concentration of μgAl/gCa was calculated .
Given that the HPGe had a significantly better MDL than the LaBr3(Ce) (56.51 vs 98.67 μgAl/gCa), that the HPGe may be a good candidate to improve the current 4π in-vivo system. Also given the high amount of Al found in the bones of the miners, this indicates that it can be a good indicator of how much Al each miner was exposed to and may help with assessing the health effects of McIntyre powder.

abstract: Thesis

abstract: Master of Science (MSc)


title: An Efficient Implementation of Guard-Based Synchronization for an Object-Oriented Programming Language

contributor:
Sekerinski, Emil
Farmer, William M.
Computer Science

subject: Synchronization, Guard-based, OOP, Stack Mechanism

abstract:
Object-oriented programming has had a significant impact on software development because it provides programmers with a clear structure of a large system. It encapsulates data and operations into objects, groups objects into classes and dynamically binds operations to program code. With the emergence of multi-core processors, application developers have to explore concurrent programming to take full advantage of multi-core technology. However, when it comes to concurrent programming, object-oriented programming remains elusive as a useful programming tool.

Most object-oriented programming languages do have some extensions for concurrency, but concurrency is implemented independently of objects: for example, concurrency in Java is managed separately with the Thread object. We employ a programming model called Lime that combines action systems tightly with object-oriented programming and implements concurrency by extending classes with actions and guarded methods. This provides programmers with a unified and straightforward design view for a concurrent object-oriented program.

In this work, using coroutines with guarded methods and actions is proposed as a means of implementing the concurrency extension for objects.  Mapping objects to coroutines can result in stack overflow as the number of objects increases. A dynamically segmented stack mechanism, which does not introduce runtime overhead, is implemented to support large-scale concurrency. Since Lime allows guarded methods and actions to "get stuck," a new user-level cooperative scheduler, and a fast coroutine context switch mechanism are implemented to improve the performance.

Compared with the traditional segmented stack mechanisms, the new dynamically segmented stack mechanism gets equal performance for more common scenarios. Besides, it outperforms the contemporary stack mechanisms for deep recursion scenarios. Above all, Lime does not only provide the programmers with a unified and straightforward object-oriented programming model for concurrency, but also accomplishes a better performance than concurrent programming languages such as Erlang and Go, in fine-grained, highly concurrent benchmarks.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Chemistry of Lycopodine

contributor:
MacLean, D.B.
Chemistry

subject: chemistry lycopodine

abstract:
Hydride reductions of a-cyanobromolycopodine and simple derivatives provided a number of derivatives of these compounds useful for oxidation and dehydrogenation studies. Dehydrogenation of a-des-tetrahydrolycrodine yielded a
quinoline derivative. This result together with other evidence indicated that three of the four rings of lycopodine are six-membered. Two conjugated enols were isolated from oxidation experiments on a -cyanlyopodine. This indicated the presence of an active methylene group and from examination of these enols it appears unlikely that the carbonyl and nitrogen can be in the same ring. A benzal derivative was prepared from a-cyanolycopodine. This derivative was converted into a tertiary base which under-went a bond scission reaction with methyl sulfate. A selenium dioxide oxidation product of benzal-a -cyanolyco-podine gave some indication of the relationship of the carbonyl to the nitrogen in lycopodlne.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Some Effects of Prior Experience with Electric Shock on the Acquisition of a Conditioned Emotional Response

contributor:
Kamin, L. J.
Psychology

subject:
electric shock
conditioned emotional response

abstract: This thesis is concerned with the effects of previous experience with electric shock on the acquisition of a conditioned emotional response (CER) to a signal preceding shock. Rats with prior shock experience were slow to acquire the normal CER, which is manifested by a decrease in the rate of food-motivated lever pressing. However, this slow acquisition did not seem to result from adaptation or habituation to shock, as had previously been proposed. Rather, prior experience with unsignalled shock tended in itself to inhibit the rate of lever pressing. When later presented with a warning signal preceding shock, rats with prior shock experience increased their rate of responding. This "dis-inhibition" persisted for several days, after which the usual decrease in rate occurred.

abstract: Thesis

abstract: Master of Arts (MA)


title: Virus Influence on Pigments in Dark-Growth Light-Grown Plants

contributor:
MacClement, D.
Biology

subject:
pigment assay
dark-green plant
light-green plant

abstract: Three issues were investigated; first, the influence of virus on pigment production in diseased plants; second, the increase of virus as indicated by a resulting change in carotene concentration; third, the function of pigments other than chlorophyll in photosynthesis in young potato leaves. Results on the first issue demonstrated an increase in carotene and xanthophyll concentration, and a decrease in chlorophyll concentration in diseased relative to normal plants. Evidence on the second issue suggested a close relationship between virus increase and carotene concentration. Data on the third issue indicated a soil and possibly significant photosynthesis due to leaf carotenoids

abstract: Thesis

abstract: Master of Science (MS)


title: On Thorium Oxinates and Their Analytical Properties

contributor:
Graham, R. P.
Chemistry

subject:
thorium
thorium oxinates
analytical properties

abstract: 2-Methyloxine is shown to be superior to oxine as a reagent for the determination of thorium. The conditions under which thorium is precipitated quantitatively and solely as 1:4 thorium 2-methyloxinate have been carefully investigated, and the results shown to lead to precise, accurate, and sensitive gravimetric, bromometric, and polaro-graphic methods for the determination of thorium. The polarography of 2-methyloxine in alkaline solution has been studied, and an attempt to elucidate the reduction process has been made. In contrast to 2-methyloxine, and in contrast to what has been believed, oxine precipitates thorium only as a compound of 1:5 stoichiometry. An accounting for this difference is made in terms of steric considerations. The structural nature of 1:5 thorium oxinate is considered, this being based on studies involving radioactive oxine and the stoichiometry of the heretofore unprepared thorium 5- and 4-methyl-oxinates.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A Mesozoic Fossil Flora from Arctic Ellesmere Island

subject:
mesozoic fossil
fossil flora
ellesmere island

abstract:
Macrofossils from a Mesozoic fossil flora from Ellesmere Island, North West Territories are described and their affinities discussed, Several rarely occurring genera and species ore discussed in detail. The deposit in which they occur is dated using the known ranges of identified macro fossils and miospores, rand the results compared with those of other workers. The described flora is compared with floras of similar age in other parts
of the world.

abstract: Thesis

abstract: Master of Science (MS)


title: Study of Distribution of Digestive Enzymes in the Ammocoete and Adult of Petromyzon Marinus

contributor:
Kleerekoper, H.
Biology

subject:
distribution
digestive enzymes
ammoete
Petromyzon marinus

abstract: This dissertation deals with a study of certain aspects of the physiology of digestion of Petromyzon marinus with emphasis on the localization of certain enzymes. It was found that the physiology of digestion adjusted to the drastic change in feeding habits at metamorphosis.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: (n, n', y) Reactions with Stable Light Nuclei in the Region Z-13 to 17

contributor:
Keech, G. L.
Physics

subject:
n n' y reactions
Z = 13 to 17
stable light nuclei

abstract:
This thesis describes the investigation of the Y-rays arising from the inelastic scattering of a fission produced neutron spectrum by stable light nuclei in the region 2 > 15 to 17. The high resolution of a Ge(Li) detector was employed to indicate some discrepancies with previously reported data for the decay schemes of the above mentioned nuclei. The correlation between the primary population values of the levels and their spin and parity assignments
was also considered.

abstract: Thesis

abstract: Master of Science (MSc)


title: Cumulative Yields of the Heavy Fragments in U235 Thermal Neutron Fission

contributor:
Tomlinson, R. H.
Physics

subject:
cmulative yields
heavy fragments
thermal neutron fission

abstract: Isotopic abundances of the elements barium, cerium, neodymium, samarium and europium formed in the thermal neutron fission of have been studied with a mass spectrometer. Suitable analyses of very young and old fission products have made possible the normalization of the isotopic abundances of each of these elements through isobaric nuclides. In this manner the relative cumulative fission yield of every fission chain from mass 137 to 154 has been obtained. These yields, together with previously reported relative yields of masses 131 to 137 when normalized to total 100%, give the absolute cumulative yield of all the significant heavy fragment chains. The origin of the fine structure found in this mass yield distribution is discussed. It has been found that all fine structure can be explained in terms of a smooth primary mass-yield curve and a simple neutron distribution both of which are compared with experimental data from other laboratories.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Framework for a Virtual Material Testing Laboratory

contributor:
Smith, Spencer
Software Engineering

subject:
virtual material testing laboratory
material testing laboratory

abstract:
This thesis presents a framework for a virtual laboratory for material testing, called Virlab. A virtual laboratory is an open and flexible environment that is used to simulate a set of experiments using a computer. It is beneficial and valuable for researcher and educators to simulate real problems and to conquer some challenges such as a weightless body. The virtual laboratory for material testing contributes both to the field of mechanics of materials and the field of software engineering.
In the field of material mechanics Virlab can be used for material testing education and research. Students can rapidly investigate many experiments for materials and the difference between kinematics quantities and stress measures. Virlab also offers a convenient platform for researchers to investigate and test new constitutive equation and implement their new algorithms. Virlab also encourages unambiguous definitions of mechanics terms and principles. In the field of software engineering the contribution is to provide an example of the application of software engineering approaches to an important scientific computing problem. By showing the successful application of software engineering methodologies for a virtual laboratory, it is hoped that software engineering ideas will spread to other scientific applications. In terms of software engineering methodologies, this thesis presents a component-based design for the virtual laboratory for material testing. In this thesis we conduct a commonality analysis for material testing, decompose the system into modules with the information hiding principle, provide an easy way to identify components from the module decomposition, and build the component-based system architecture. In this procedure we apply the concept of design through documentation at each stage.

abstract: Thesis

abstract: Master of Applied Science (MASc)


contributor:
Nicholson, P.S.
Materials Science and Engineering

subject: Flaw Tolerant Alumina/Zirconia Multilayered Composites for High Temperature Applications

abstract:
Ceramic composites for high temperature applications must be designed with crack arrest capability to improve the resistance to flaws produced in service, such as by thermal shock.
Laminated composites containing Al2O3 layers in 3mol%Y2O3-ZrO2 (TZ3Y) were fabricated by electrophoretic deposition (EPD) and pressureless sintering. The layering design (Al2O3 layer thickness and volume fraction) was varied to determine the influence on fracture behaviour. The residual stress in Al2O3 layers was measured using a fluorescence spectroscopy technique.
The fracture strength of 15 different laminates, and monolithic Al2O3 and TZ3Y, was tested in 4-point bending at room temperature. Vickers indentation (10 kg load) was used to simulate natural flaws at the sample surface before testing as a measure of flaw tolerance. Fracture ranged from catastrophic failure, to multi-stage failure and complete delamination (in processing). Transitions in behaviour were found related to a geometrical parameter derived from the strain energy release rate for edge cracks. The strength of three Al2O/TZ3Y composites was compared with monolithic Al2O3 and TZ3Y for a range of indentation loads (up to 20 kg). The strength of the composites was similar to monolithic TZ3Y but the flaw tolerance was improved due to multi-stage fracture. The strength and flaw tolerance (using 10 kg indentation) of two Al2O3/TZ3Y composites and monolithic TZ3Y was measured < 1300°C. The multi-stage fracture behaviour disappeared > 25 °C, and there was no beneficial effect of the Al2O3 layers on the strength. Superplastic deformation of the TZ3Y layers at 1300°C was prevented by the constraint of the Al2O3 layers. Recommendations are made about the design of flaw tolerant ceramic laminates for high temperature use.

abstract: Thesis

abstract: Master of Engineering (ME)


title: An Experimental and Numerical Study of the Effects of Surrounding Disturbances on Vortex Rings

contributor:
Latto, Brian
Mechanical Engineering

subject:
experimental study
numerical study
surrounding disturbances
vortex rings

abstract: In this thesis, the effect of the following three aspects related to the generation and efficient transport of vortex rings were studied. They included: 1) the initial boundary condition where the vortex ring is generated. A comparison between previous results and the data obtained in this study showed that vortex rings generated at a tube orifice were both slower in velocity and larger in size than vortex rings generated at a plate orifice under similar conditions. 2) the presence of a stratified layer of fluid in a vessel. Flow visualization experiments showed that after a vortex ring penetrated through the interface of the stratified layer, it was able to mix the fluid inside the ring with the surrounding fluid. The amount of mixing depended on the depth of penetration of the ring into the stratified layer. An empirical relationship was obtained to predict the maximum penetration depth of a vortex ring into a stratified layer. It is: Xp/Rm - -29.7 log10Ri - 22.7 3) the proximity of a wall or another vortex ring to the path of the primary ring. Through numerical simulation, it was shown that the primary ring would slow down and turn away from its original path. Eventually, this ring would either crash into the wall or collide with another ring. In order to prevent this turning of a vortex ring from happening, the centre of the generation orifice should be 7.5 times the radius of the injection orifice (Rm) from the wall or (Rm) between two generation orifices. These results can be used to optimize the design and positioning of vortex ring mixers for various mixing vessel geometries and mixing processes.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Processing and Characterization of Interpenetrating Ni-ZrO2 Composites

subject: interpenetrating Ni-ZrO2 composites

abstract: This thesis describes the processing and characterization of uniform, interpenetrating, nickel-cubic stabilized zirconia composites. This work was performed in support of future development in the study and modelling of Metal-Ceramic (M/C) Functionally Graded Materials. Since it is of fundamental interest to understand the relationship between microstructure and behaviour in these materials, the characterization has focused on uniform composites. To minimize experimentation while maximizing productivity, the material grades selected for this study include M:C ratios by volume of 25:75, 50:50, and 75:25, along with the elemental materials (i.e. 100% nickel and 100% cubic zirconia). Solid state powder processing was developed including the steps: colloidal processing (by tape casting), lamination, organic burnout, hydrogen reduction of metal oxides, and hot press consolidation. These techniques support the even distribution of phases and yield high density composites (>98% of theoretical). Unfortunately the nickel powder used in this study produced atypical properties which complicated the analysis of mechanical behaviour. Composite thermal dilation, elastic, and mechanical properties were determined. Through analysis of residual stresses and fracture behaviour ideas regarding the modelling of M/C composites and FGMs are addressed. Continuum modelling approaches seem appropriate.

abstract: Thesis

abstract: Master of Engineering (ME)


title: An Experimental Study on the Local Void Fraction Measurements in Large-Diameter Vertical Pipes using Optical Fiber Probes

contributor:
Shoukri, M.
Mechanical Engineering

subject:
experimental study
local void fraction
large-diameter vertical pipe
optical fiber probe

abstract: This thesis contains the details of an experimental study on the local void fraction measurements in large-diameter vertical pipes using optical fiber probes. The experiments were conducted in vertical transparent acrylic pipe of a 20-cm diameter. An experimental test facility used for performing of experiments, was designed as a low-pressure air-water loop, which can operate in either a natural circulation mode or a forced circulation mode. Radial void fraction profiles were measured using an optical fiber probe. An average cross-sectional void fraction was calculated by integration of the data obtained by the optical fiber probe. The average void fraction was also calculated using two-phase pressure-drop measurements . The results were compared and the resulting good accuracy of the optical fiber probe was determined. The flow regime results were plotted in terms of superficial gas and liquid velocities using flow regime maps of several researchers. Absence of the slug flow regime in large-diameter pipes was observed during the experiments. The data were correlated using the drift-flux model. A near unity distribution parameter showed that nearly uniform radial distribution of the void fraction dominates in two-phase flow through large-diameter vertical pipes.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Palaeobotanical Analysis of Certain Upper Ordovician Sedimentary Rocks Emphasizing Microfossil Fragments

contributor:
Radforth, N.W.
Biology

subject:
palaeobotanical analysis
upper ordovician
sedimentary rocks
microfossil fragments

abstract: Several methods for the palaeobotanical analysis of inorganic rocks are developed and through the employment of these methods both microfossils and macrofossils have been recovered from certain Upper Ordovician Strata. These fragments are assigned to series, basing such designation upon their sources and individual morphological characteristics. The problematical identity and biological importance of these fragments is discussed, and their practical usage in problems of correlation is considered.

abstract: Thesis

abstract: Master of Science (MSc)


title: Cost-Utility Analysis of Using Polygenic Risk Scores to Guide Statin Therapy for Cardiovascular Disease

contributor:
Paré, Guillaume
Health Research Methodology

subject:
health economics
health research methodology
health technology assessment
genetic epidemiology
polygenic risk score
cardiovascular disease
statins
cost-effectiveness
cost-utility analysis

abstract:
Introduction: There are no economic evaluations to determine the value of PRSs. The objective of this study was to determine if the addition of a PRS to traditional risk factors to guide statin therapy is a cost-effective intervention for the prevention of primary MI cases in the Ontario healthcare payer perspective.

Methods: A PRS cost-effectiveness model was constructed to produce various statin prescription strategies in conjunction with the FRS. Upper PRS thresholds (between 25% to 70%) were set such that individuals falling into them would be eligible for statins while those in lower PRS thresholds (between 1% to 25%) were deemed protected and removed from consideration. The model determined number of incident MIs saved or not saved by statins, costs, quality of life, and the effect of statins on preventing MIs over a 10-year time horizon, discounted at 1.5% annually. One-way sensitivity analysis and a PSA were performed by varying all model parameters. Non-related participants of white British descent from 96,736 participants in the UK Biobank at intermediate risk for cardiovascular disease, determined using the Canadian Cardiovascular Society dyslipidemia guidelines of 2016, were used for the study.

Results: The optimal clinical and economic strategy was one whereby the top 70% PRS individuals are eligible for statins, with the lower 5% PRS excluded. A base-case analysis at a PRS cost of $70 produced an ICER of $747,184.10/QALY, ranging from $525,678.90/QALY to $930,144.40/QALY in a one-way sensitivity analysis. In the PSA, the intervention has approximately a 50% probability of being cost-effective at $750,000/QALY. At a genotyping cost of $0, statin strategies guided by PRS dominated standard care when at least 12% of the lower PRS individuals were withheld from statins. When the predictive performance of the PRS is increased, the ICER drops drastically depending on the cost of genotyping and statin strategy.

Conclusion: The cost-effectiveness model considers MI cases exclusively and a short, 10-year time horizon which likely overestimate the ICER. However, this study elucidates that the PRS has the potential to be extremely cost-effective in the future.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Approximately 1 in 3 Canadians live with at least one genetically linked chronic disease. Together, these diseases constitute a large economic burden on the healthcare system and well-being of individuals. Recent advancements in genetics allow risk prediction of developing complex, but common chronic diseases such as cardiovascular disease. Termed as polygenic risk scores, they have the potential to carry beneficial clinical outcomes such as an improved quality of life. However, the economics is not yet understood. This study determined that when targeting heart attacks, approximately $750,000 is required to gain an additional life-year for an adult. Although this may seem high, the result is closer to an upper-limit estimate than the true cost since polygenic risk scores have more benefits than solely for heart attacks. In the future, when accounting for their entire potential, the cost per life-year is likely to be lower, and perhaps even a money-returning investment.


title: THE ROLE OF REFLECTION IN LEARNING THROUGH EXPERIENCE:  A FRAMEWORK AND GUIDE FOR STUDENTS AND EDUCATORS

contributor:
Paez, Antonio
Geography

subject:
Bloom’s Taxonomy
comparison of means
interrater reliability
metacognition
grounded theory
sustainability education
experiential learning
reflection
cognition

abstract:
The research reported here covers the following items:
1. The development of the Reflective Learning Framework (RLF). This framework was developed based on a grounded theoretical approach combined with an exploration of existing student reflections; then-current literature; and years of multiple iterations through real-world trials. This framework has now successfully been used by many educators in courses at McMaster and other institutions of higher education.
2. An investigation of students’ responses to the RLF. Following the development of the RLF, third-year students who had used the RLF to guide, assess, and evaluate their course reflections were surveyed and interviewed about their perceptions of using the RLF. Results of this study demonstrate that students see reflection as a tool to develop and use cognitive and metacognitive skills, and also as a tool to support knowledge retention and transfer. Furthermore, findings suggest how reflection, as studied, contributes to the acquisition of higher-order thinking skills required to address the complex challenges of improving sustainability.
3. Determining the effectiveness of the RLF. Finally, to determine the effectiveness of the RLF to support students in applying and demonstrating their higher-order thinking skills, a comparison of two sets of reflections was performed – one that used the RLF and one that did not. The comparison was based on tests of interrater reliability and a comparison of means was conducted. The results of this study demonstrate the reliability of the Framework to be used by multiple raters and that significantly different reflection outputs were obtained from students who used the RLF compared to those who did not.
	The results of these studies demonstrate the overall effectiveness of the RLF as a tool to guide, assess, and evaluate reflection through experiential education in university courses.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The research reported here covers the following items: (1) the development of the Reflective Learning Framework (RLF), which was accomplished through a bottom-up approach, and which began with reading and re-reading over 100 student reflections and then reviewing the wealth of literature on the topics of reflection and experiential learning; (2) an investigation of students’ responses to the RLF, which was accomplished through an online survey and in-person interviews; and (3) determining the effectiveness of the RLF by comparing the grades of students who used the RLF to those who did not. The results of these studies demonstrate the overall effectiveness of the RLF as a tool to guide, assess, and evaluate reflection through experiential education in university courses.


title: The Microwave Measurement of the Conductivity of a Semiconducting Film

contributor:
Gunn, M.W.
Electrical Engineering

subject:
microwave measurement
conductivity
semiconducting film

abstract:
Indium-antimonide films have been prepared for experiments involving the application of high electric fields to this semiconducting material. The films have been deposited onto a mica substrate. To obtain high mobilities, a multilayer construction with subsequent annealing was used.
Measurements of the complex propagation coefficient of a section of waveguide containing the film have been made and the results agree closely with a numerical solution of a theoretical model proposed for the structure.
The design of a new type of a pulse generator for these high electric field experiments is described.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Predictors of Weight Change in First-Year Undergraduate Students

contributor:
Meyre, David
Health Research Methodology

abstract: Obesity is a multifactorial and largely preventable condition resulting from complex interactions between different biological and environmental factors. In recent decades, the disease has reached epidemic proportions as over one-third of the global population today is either overweight or obese. Adolescence and young adulthood may be critical periods for obesity development as elevated BMI during these periods have been associated with chronic obesity later in life. As such, young adulthood may be considered a favorable period for effective obesity prevention. Interestingly, while education status is negatively correlated with BMI in the general population from high-income countries, young adults with higher education have been shown to be at greater risk for weight gain than those without a post-secondary education. The “Freshman 15” is a popular theory that suggests that undergraduate students gain 15 pounds during their first year in university. While previous studies have found this to be an exaggerated estimate, they have indicated that, on average, students still tend to gain around 3-5 pounds during this period. Given that young adults pursuing undergraduate studies represent an at-risk group for increased BMI and the development of obesity later in adulthood, the predictors of weight gain in this population must be explored for the development of effective prediction and prevention strategies. This thesis compiles a series of investigations focused on identifying the effect of certain demographic and environmental factors on change in obesity traits among first-year university students from Ontario, Canada. Our investigations confirm the trend of weight gain among students during the first year of university, and implicate ethnicity and type of living arrangement, but not sex, as potential predictors within this context. These results may help promote further research in this area, and ultimately help us have a better understanding of the risk factors that make students susceptible to weight gain during first of university.

abstract: Thesis

abstract: Master of Science (MSc)


title: DEVELOPMENT OF AN ULTRA-WIDEBAND (UWB) PULSE GENERATOR AND PRINTED ANTENNA FOR CONCEALED WEAPONS DETECTION RADAR

title: DESIGNING A UWB GENERATOR AND ANTENNA FOR CWD RADAR

contributor:
Nikolova, Natalia Koleva
Electrical and Computer Engineering

subject:
Electromagnetics
Antennas
Ultra-wideband (UWB) Technology
Radar
Microwaves
Concealed Weapons Detection (CWD)
Simulation
Fabrication
Engineering
Public Safety

abstract:
This thesis demonstrates the further development of an ultra-wideband (UWB)
pulse generator and of an UWB antenna. Custom prototypes of these devices were
initially developed for an ongoing research project. The project topic is a compact and
portable concealed weapons detection (CWD) radar system to find objects such as
firearms, knives, and grenades hidden on persons as they pass by. The system uses the
UWB pulse generator as a transmitter, while the UWB antenna radiates the pulse and
receives the corresponding backscatter from targets and other objects. Initial device
prototypes do not perform adequately according to project specifications. A key
specification is of adequate operation over the entire 0.5 GHz to 5 GHz frequency band,
where adequate operation is defined distinctly for the antenna and pulse generator.
In this work, empirical investigations of both devices are performed using techniques
such as simulation, fabrication, and measurement. Through these investigations, the
designs of the devices have been incrementally modified. Measured performance data
suggest that the research has yielded designs with substantially improved bandwidth
as a result. Bandwidth increases from 3.31 GHz to 4.36 GHz (31.7%) for the pulse
generator and from 0.46 GHz to 4.98 GHz (983%) for the antenna are demonstrated.
Future work is needed to establish the effects of fabrication tolerance, component
tolerance, and human error on the variation of the observed device performance.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract:
This thesis is about the improvement of a radio antenna and a transmitter. These
are ultimately intended as components in a system for detecting weapons (such as
firearms, knives, etc.) concealed within the clothing or bags of nearby persons. The
detection happens by transmitting specific radio signals which interact harmlessly
with a person being scanned, and then are received back by the system. This is a
form of radio detection and ranging (RADAR). The research on these devices has
consisted of computer simulations and real-life measurements. As a result, it appears
that the transmitter and radio antenna have been improved to be more suitable for
the desired application than they were originally.


title: Fractal-based magnetic resonance imaging coils for 3T Xenon imaging

contributor:
Noseworthy, Michael, D.
Electrical and Computer Engineering

subject: xenon imaging magnetic resonance fractal mri coil rf radiofrequency design simulation verification

abstract:
Traditional 1H lung imaging using MRI faces numerous challenges and difficulties due
to low proton density and air-tissue susceptibility artifacts. New imaging techniques
using inhaled xenon gas can overcome these challenges at the cost of lower signal to
noise ratio. The signal to noise ratio determines reconstructed image quality and is
an essential parameter in ensuring reliable results in MR imaging. The traditional RF
surface coils used in MR imaging exhibit an inhomogeneous field, leading to reduced
image quality. For the last few decades, fractal-shaped antennas have been used to
optimize the performance of antennas for radiofrequency systems. Although widely
used in radiofrequency identification systems, mobile phones, and other applications,
fractal designs have yet to be fully researched in the MRI application space. The use of
fractal geometries for RF coils may prove to be fruitful and thus prompts an investiga-
tion as the main goal of this thesis. Preliminary simulation results and experimental
validation results show that RF coils created using the Gosper and pentaflake offer
improved signal to noise ratio and exhibit a more homogeneous field than that of a
traditional circular surface coil.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Advanced Flux-Weakening Control Methods for Interior Permanent Magnet Synchronous Motors with Torque Performance Improvement

contributor:
Emadi, Ali
Electrical and Computer Engineering

subject:
Flux-weakening control
IPMSMs

abstract:
The flux-weakening control (FWC) methods for interior permanent magnet synchronous motors (IPMSMs) with torque performance improvement are studied in this thesis.
A FWC strategy with constant parameters is proposed, which achieves the extended dc-link voltage utilization and improves the tracking performance. The voltage trajectory is extended to the overmodulation region to increase the dc-link voltage utilization rate and torque. Moreover, a current predictive controller is implemented to improve tracking performance.
A FWC method considering the resistive voltage drop and magnetic saturation is proposed. The proposed method achieves the voltage extension, torque improvement, and improved dynamic performance by establishing a new stator flux linkage adjustment method. The stator flux linkage reference is adjusted based on the torque reference, operating speed, and modulation index. Two voltage feedback paths are established and chosen based on the torque reference and operating speed. The stator resistance and nonlinear inductance characteristics are constructed based on the experimental test. Thus, accurate current control is achieved. Compared to feedforward-based FWC methods, the proposed method improves the output torque and power. Compared to feedback-based FWC methods, the proposed method improves the dynamic performance and avoids the voltage saturation and windup problem. Compared to the mixed FWC methods, which only have one feedback path, the proposed method improves the dynamic performance.
The influence of extended dc-link voltage utilization is analyzed. The nonlinear relationship between voltage and torque is solved mathematically. The torque, torque ripple, and current ripple trends with modulation index in voltage extension region are analyzed, and the harmonic spectra of voltage, current, and torque with or without voltage extension are compared, which provide the guidance to make the tradeoff between maximizing the torque and torque ripple alleviation.

abstract: Thesis

abstract: Master of Applied Science (MASc)