Detection and Grading of Prostate Cancer in Temporal Enhanced Ultrasound using Convolutional Neural Networks

Prostate cancer is the most common non-dermatological cancer amongst men in the developed world. The current definitive diagnosis is core needle biopsy guided by transrectal ultrasound. However, this method suffers from low sensitivity and specificity in detecting cancer. Recently, a new ultrasound based tissue typing approach has been proposed, known as temporal enhanced ultrasound (TeUS). In this approach, a set of temporal ultrasound frames is collected from a stationary tissue location without any intentional mechanical excitation. The main aim of this thesis is to implement a deep learning-based solution for prostate cancer detection and grading using TeUS data. In the proposed solution, convolutional neural networks are trained to extract high-level features from time domain TeUS data in temporally and spatially adjacent frames in nine in vivo prostatectomy cases. This approach avoids information loss due to feature extraction and also improves cancer detection rate. The output likelihoods of two TeUS arrangements are then combined to form our novel decision support system. This deep learning-based approach results in the area under the receiver operating characteristic curve (AUC) of 0.80 and 0.73 for prostate cancer detection and grading, respectively, in leave-one-patient-out cross-validation. Recently, multi-parametric magnetic resonance imaging (mp-MRI) has been utilized to improve detection rate of aggressive prostate cancer. In this thesis, for the first time, we present the fusion of mp-MRI and TeUS for characterization of prostate cancer to compensates the deficiencies of each image modalities and improve cancer detection rate. The results obtained using TeUS are fused with those attained using consolidated mp-MRI maps from multiple MR modalities and cancer delineations on those by multiple clinicians. The proposed fusion approach yields the AUC of 0.86 in prostate cancer detection. The outcomes of this thesis emphasize the viable potential of TeUS as a tissue typing method. Employing this ultrasound-based intervention, which is non-invasive and inexpensive, can be a valuable and practical addition to enhance the current prostate cancer detection.

A Historical Materialist Approach to the Eurozone Crisis: Fictitious Capital, States, and Capital Accumulation

This dissertation examines the ongoing European sovereign debt crises that began with Greece in 2009, in the wake of the US subprime mortgage crisis. Through the application of a historical materialist approach, I attempt to understand the on-going crisis in the European Monetary Union (EMU) by investigating root causes of sovereign debt crises, relations of power, and main beneficiaries of the policy responses. My theoretical framework hinges on three contradictions in capitalism: the tendency towards overaccumulation, the tension between fictitious capital and the productive base, and the contradiction inherent in capitalist states between their role as a national state and as a class state. In contrast to the dominant positions that locate the cause of the crisis within either: debtor states; creditor states; or the framework at the EMU, I argue that these sovereign debt crises are actually a broader crisis of crisis of capitalism within the EMU itself. In order to do so, I trace the evolution of the political economy of the Eurozone in the post-Bretton woods era, with a particularly focus on the credit system. More specifically, I argue that these crises are the result of an interaction between three meso-level contradictions that have developed within the EMU region: 1) Germany’s postwar accumulation regime, which has produced a deep crisis of overaccumulation; 2) the contradictory processes associated with the neoliberal logic of the EMU, by which I mean the rush to lower barriers to credit and finance at the expense of all else; and 3) credit-fueled, consumption-based EMU integration in the periphery; and. These three contradictions came together in the wake of the 2007-2008 US subprime crisis to form an overall crisis of capitalism in the Eurozone, expressed, as I suggest, as a crisis of fictitious capital. This dissertation aims to contribute to the ongoing project among critical political economists to de-naturalize and re-politicize money, while challenging the hegemony of monetarism within neoliberalism. Second, there has yet to be a comprehensive study that examines the EMU, Germany, and the crises in the periphery from a holistic, historical materialist analysis.

“Come and live in my Shoes”: Food Access and social isolation for People living in poverty IN GANANOQUE, Ontario

This community-based research project, in collaboration with the Gananoque and Area Food Access Network (GAFAN), gathered data from self-reported food insecure residents of Gananoque and area to determine how to improve their access to healthy, personally acceptable food. In March 2016, I recruited 14 participants for three focus groups and one personal interview with those struggling to put food on the table for themselves and others in the household. Participants were single parents, adults over the age of 50, and adults who could benefit from improved access to healthy food but do not currently use existing services. Health issues, social isolation, scraping by, and lack of income were four themes that underscored the impact of poverty on the lives of participants. Lack of income, transportation, cost of food, lack of affordable or accessible childcare, and inadequate access to support services proved to be major barriers to food security: strongly influenced by the impact of rurality. The results of this research have the potential to help GAFAN improve food access for those living in this community. It may also have implications for enhancing food security in other rural Canadian communities.

A NOVEL MODELING AND STATE OF CHARGE ESTIMATION SCHEME FOR LITHIUM-ION BATTERIES

Lithium Ion (Li-Ion) batteries have got attention in recent decades because of their undisputable advantages over other types of batteries. They are used in so many our devices which we need in our daily life such as cell phones, lap top computers, cameras, and so many electronic devices. They also are being used in smart grids technology, stand-alone wind and solar systems, Hybrid Electric Vehicles (HEV), and Plug in Hybrid Electric Vehicles (PHEV). Despite the rapid increase in the use of Lit-ion batteries, the existence of limited battery models also inadequate and very complex models developed by chemists is the lack of useful models a significant matter. A battery management system (BMS) aims to optimize the use of the battery, making the whole system more reliable, durable and cost effective. Perhaps the most important function of the BMS is to provide an estimate of the State of Charge (SOC). SOC is the ratio of available ampere-hour (Ah) in the battery to the total Ah of a fully charged battery. The Open Circuit Voltage (OCV) of a fully relaxed battery has an approximate one-to-one relationship with the SOC. Therefore, if this voltage is known, the SOC can be found. However, the relaxed OCV can only be measured when the battery is relaxed and the internal battery chemistry has reached equilibrium. This thesis focuses on Li-ion battery cell modelling and SOC estimation. In particular, the thesis, introduces a simple but comprehensive model for the battery and a novel on-line, accurate and fast SOC estimation algorithm for the primary purpose of use in electric and hybrid-electric vehicles, and microgrid systems. The thesis aims to (i) form a baseline characterization for dynamic modeling; (ii) provide a tool for use in state-of-charge estimation. The proposed modelling and SOC estimation schemes are validated through comprehensive simulation and experimental results.

What's so funny? An evaluation of the relations among humour use, mirth, and depressive symptomatology

Humour production and showing mirth (i.e., smiling and laughing) confer prosocial advantages. However, there is a paucity of literature evaluating how humour manifests in psychopathology. Humour and mirth may be especially relevant in depression, wherein profound impairments are evident in emotional and social functioning. Chapters 2 and 3 present correlational and predictive relations of depressive, social anxiety, and social anhedonia symptoms with humour styles, and consider the role of motivational systems and expressivity of positive affect as they relate to humour. As expected, symptoms and avoidance-based motivation were positively related to maladaptive humour styles and negatively related to adaptive humour styles. Interestingly, the pattern of relations shifted when considered among individuals in a depressive episode; acutely depressed individuals generally shy away from any humour style rather than gravitating toward specific styles. In a mediation model, the inverse relation between depressive symptoms and affiliative humour was fully mediated by approach-based motivation and expressivity of positive emotions. Chapters 4 and 5 examined subjective and observed mirth responses (facial affect and laughter) demonstrated by depressed and healthy comparison groups. Relative to non-depressed individuals, depressed persons reported less enjoyment, lower ratings of funniness, and fewer instances and shorter durations of positive facial affect and laughter when viewing humourous videos. There was no significant change in retrospective ratings of enjoyment and funniness at a one-week follow-up. The pattern of responsivity by depressed persons shifted when they viewed humourous videos while hearing others laughing. Both groups demonstrated more mirth when hearing others laugh; there were no differences between groups on mirthful behaviours. The one exception was that the total duration of laugher produced by depressed individuals was shorter than that produced by individuals in the healthy comparison group. This research project demonstrates that facets of depressive symptomatology are differentially associated with humour use and depressed individuals show blunted emotional responsivity to humourous stimuli. However, the pattern of reduced affective responsivity is context specific in that it fluctuates in response to hearing others’ laughter. These findings have important implications for the conceptualization of depression and the subsequent avenues for the treatment of individuals with depression.

IMPACTS OF ENHANCED TEMPERATURE AND SNOW DEPOSITION ON SENESCENCE DATE, VEGETATION COVER, AND CO2 EXCHANGE IN A CANADIAN HIGH ARCTIC MESIC ECOSYSTEM

Arctic regions are expected to experience an increase in both temperature and precipitation over the coming decades, which is likely to impact vegetation dynamics and greenhouse gas exchange. To test this response, an experiment was installed at the Cape Bounty Arctic Watershed Observatory, on Melville Island, NU, in 2008 as part of the International Tundra Experiment (ITEX). Snow fences and open top chambers (OTCs) were used to manipulate snow depth and air temperature, respectively. Unlike most ITEX sites to date, enhanced temperature and snowfall were combined here in a factorial design with eight replicates. As an added control, four plots were established well outside the enhanced snow area. Senescence date was recorded at the end of the season, and at the peak of the growing season a vegetation survey was conducted within each plot in order to determine the total percent cover of each plot, as well as the percent cover of individual species. Carbon dioxide (CO2) exchange was also measured within each plot throughout the growing season. The date of senescence occurred significantly earlier in plots which had not been manipulated in any way, compared to all other treatments for all species. Salix arctica showed the greatest increase in cover over time at the species level. Lichen cover increased significantly in the deepened snow plots, and in general there were significant increases in percent cover in some functional groups over time. During June and into July the net CO2 flux was to the atmosphere. It was not until July 27 that these ecosystems became net carbon sinks. However, warming alone resulted in the ecosystem acting as a significant net carbon sink for the entire growing season. Plots exposed to warming alone were estimated to have removed approximately 19.94 g C m-2 from the atmosphere, whereas all other treatments were very similar to one another and estimated to have added approximately 3.12 g C m-2 to the atmosphere. Active layer depth and soil temperatures suggest that plots within the ambient snow zone may be receiving some additional snow due to their proximity to the fences. CO2 fluxes measured within the outer control plots suggest that the effect of warming alone could lead to this ecosystem being an even stronger net C sink under truly ambient snow conditions.

IMPROVED SAMPLE INTRODUCTION SYSTEMS FOR INDUCTIVELY COUPLED PLASMA OPTICAL EMISSION SPECTROMETRY AND THEIR APPLICATION TO THE ANALYSIS OF SIMPLE AND COMPLEX MATRICES

The objective of this thesis is to explore new and improved methods for greater sample introduction efficiency and enhanced analytical performance with inductively coupled plasma optical emission spectrometry (ICP-OES). Three projects are discussed in which the capabilities and applications of ICP-OES are expanded: 1. In the first project, a conventional ultrasonic nebuliser was modified to replace the heater/condenser with an infrared heated pre-evaporation tube. In continuation from previous works with pre-evaporation, the current work investigated the effects of heating with infrared block and rope heaters on two different ICP-OES instruments. Comparisons were made between several methods and setups in which temperatures were varied. By monitoring changes to sensitivity, detection limit, precision, and robustness, and analyzing two certified reference materials, a method with improved sample introduction efficiency and comparable analytical performance to a previous method was established. 2. The second project involved improvements to a previous work in which a multimode sample introduction system (MSIS) was modified by inserting a pre-evaporation tube between the MSIS and torch. The new work focused on applying an infrared heated ceramic rope for pre-evaporation. This research was conducted in all three MSIS modes (nebulisation mode, hydride generation mode, and dual mode) and on two different ICP-OES instruments, and comparisons were made between conventional setups in terms of sensitivity, detection limit, precision, and robustness. By tracking both hydride-forming and non-hydride forming elements, the effects of heating in combination with hydride generation were probed. Finally, optimal methods were validated by analysis of two certified reference materials. 3. A final project was completed in collaboration with ZincNyx Energy Solutions. This project sought to develop a method for the overall analysis of a 12 M KOH zincate fuel, which is used in green energy backup systems. By employing various techniques including flow injection analysis and standard additions, a final procedure was formulated for the verification of K concentration, as well as the measurement of additives (Al, Fe, Mg, In, Si), corrosion products (such C from CO₃²¯), and Zn particles both in and filtered from solution. Furthermore, the effects of exposing the potassium zincate electrolyte fuel to air were assessed.

Teen Girls’ Perspectives on Their Current Dietary Habits and Food Choices: A Qualitative Study in Jeddah, Saudi Arabia

Rapid socioeconomic development in Saudi Arabia, as a result of oil revenues, has had profound effects on people’s lifestyles, including the transformation of people’s dietary habits. Such dietary transformations, known as the nutrition transition, are common in countries undergoing rapid socioeconomic changes. This transition is significant in Saudi Arabia as the traditional Saudi diet is considered a healthy one. Adoption of the Western diet has had negative health effects on the Saudi population, especially adolescents. As evidenced in many studies, adolescents are the most affected population when it comes to changes in dietary habits and physical activity. Adolescence is a vulnerable stage of life when dietary habits are developed, often lasting into adulthood, and may not be easily changed. In the case of Saudi Arabia, youth or adolescents represent almost 60% of the population; therefore, the eating habits they develop now could have profound consequences for population health in the future. To develop effective health promotion strategies, it is important to understand the sociocultural factors that influence the dietary habits and food choices of Saudi teens. I conducted two semi-structured, open-ended interviews, using photo-elicitation techniques, with 12 Saudi girls, aged 15-16 years. Analysis of the data shows four factors that pulled the participants toward eating home cooked traditional food and five factors that pushed participants away from eating home cooked traditional foods. The research suggests that despite the attractiveness of modern, Western ways of eating for Saudi teen girls, parents still play a key role in encouraging and supporting them to eat healthy food.

An Islanding Detection Method based on Impedance Estimation and Grid Identification for Grid-Tie Distributed Power Generation Systems

Power system policies are broadly on track to escalate the use of renewable energy resources in electric power generation. Integration of dispersed generation to the utility network not only intensifies the benefits of renewable generation but also introduces further advantages such as power quality enhancement and freedom of power generation for the consumers. However, issues arise from the integration of distributed generators to the existing utility grid are as significant as its benefits. The issues are aggravated as the number of grid-connected distributed generators increases. Therefore, power quality demands become stricter to ensure a safe and proper advancement towards the emerging smart grid. In this regard, system protection is the area that is highly affected as the grid-connected distributed generation share in electricity generation increases. Islanding detection, amongst all protection issues, is the most important concern for a power system with high penetration of distributed sources. Islanding occurs when a portion of the distribution network which includes one or more distributed generation units and local loads is disconnected from the remaining portion of the grid. Upon formation of a power island, it remains energized due to the presence of one or more distributed sources. This thesis introduces a new islanding detection technique based on an enhanced multi-layer scheme that shows superior performance over the existing techniques. It provides improved solutions for safety and protection of power systems and distributed sources that are capable of operating in grid-connected mode. The proposed active method offers negligible non-detection zone. It is applicable to micro-grids with a number of distributed generation sources without sacrificing the dynamic response of the system. In addition, the information obtained from the proposed scheme allows for smooth transition to stand-alone operation if required. The proposed technique paves the path towards a comprehensive protection solution for future power networks. The proposed method is converter-resident and all power conversion systems that are operating based on power electronics converters can benefit from this method. The theoretical analysis is presented, and extensive simulation results confirm the validity of the analytical work.

TAKING ORGANIZATIONS SERIOUSLY: RESPONSIBLE AGENCY, ORGANIZATIONS AND THE CRIMINAL LAW

In the post-Enlightenment period, Anglo-American criminal law has been applied with increased force, and an ever expanding scope, to collective actors like corporations and other organizations. Recent scholarship has focused on developing “truly organizational” bases of liability that break with the conventional approach of imputing individual conduct to an organization and instead analyze culpable conduct and intent in a way that reflects the distinct and independent capacity of organizations to pursue their interests or goals collaboratively. In 2004, Canada enacted amendments inspired by these ideas in the hope they would lead to more effective criminal enforcement against organizations. Twelve years later, however, the promise of Bill C-45 is largely unfulfilled. In this thesis, I explore how much of this failure of law reform to deliver transformational change is attributable to an individualist bias that permeates how we think about what it means to be responsible and how this then shapes the responsibility ascription process. Using an analytical framework that combines criminal law theory with selected aspects of rational-structural theory and organization culture, I suggest that a promising way forward may lie in reframing the essential qualities required to be a subject of the criminal law in a way that captures the unique attributes that make organizations different from individuals. The resulting organizational concept of responsible agency allows for an integration of organizational reality into how we assess organizational culpability while keeping the ambit of criminal liability within the limits of what is practicable and fair. This better aligns with the spirit of Bill C-45: to impose criminal liability in a way that takes organizations – and their crimes – seriously.

TOWARD A POLITICAL CONCEPTION OF MINORITY RIGHTS: RECONCILING SOVEREIGNTY, HUMAN RIGHTS AND MINORITY CLAIMS

The question that I will explore in this research dissertation is whether one can defend the rights of homeland minorities as a progressive extension of the existing norms of human rights. This question calls for several deeper inquiries about the nature, the function and the underlying justifications for both human rights and minority rights. In particular, this research project will examine the following issues: on what normative grounds the available norms of human rights and minority rights are justified; if there is any methodic way to use the normative logic of human rights to support substantial forms of minority claims, such as the right to self-determination; whether human rights can take the form of group rights; and finally, whether there is any non-sectarian basis for justifying the minority norms, which can be acceptable from both liberal and non-liberal perspectives. This research project has some implications for both theories of minority rights and human rights. On the one hand, the research employs the topic of minority rights to shed light on deficiencies of the existing political theories of human rights. On the other hand, it uses the political theory to shed light on how existing theories of minority rights could be improved and amended. The inquiry will ultimately clarify how to judge the merit of the claim that minority rights are or should be a part of human rights norms.

The Impact of Community Social Capital on the occurrence of Injuries in adolescents and falls in older adults: Population-based Studies Conducted in Canadian samples

The objectives of this thesis were to study specific Canadian populations in order to examine; (1) relationships between the neighbourhood-level social capital and injuries in youth, as well as (2) falls in older adults, and; (3) to address methodological issues relevant to the study of such relationships. The thesis is comprised of four manuscripts. The first addresses methodological issues surrounding the validation of neighbourhood-level variables for the study of adolescent health, and demonstrates the existence of structural confounding in the study of related etiological relationships. Informed by the latter, the second manuscript examines the association between neighbourhood-level social capital and injuries in youth, and demonstrates that lower levels of social capital are protective factors for girls but not for boys. Manuscript 3 uses an international database focused on older adults, and shows that our existing measure of social capital is valid at neighbourhood levels, but also that there is a high possibility for the existence of structural confounding among Canadian older adults. The fourth manuscript then examines the association between neighbourhood-level social capital and the occurrence of falls in older adults and determines that differences between neighbourhoods are important factors in the occurrence of falls, and that higher levels of social capital are a risk factor for falls. Taken together, results from this thesis provide a better understanding of the role of neighbourhood-level social capital on the occurrence of injuries in Canadian youth and on the occurrence of falls in older adults. Our contributions were important both methodologically and etiologically.

New Rigorous Decomposition Methods for Mixed-integer Linear and Nonlinear Programming

Process systems design, operation and synthesis problems under uncertainty can readily be formulated as two-stage stochastic mixed-integer linear and nonlinear (nonconvex) programming (MILP and MINLP) problems. These problems, with a scenario based formulation, lead to large-scale MILPs/MINLPs that are well structured. The first part of the thesis proposes a new finitely convergent cross decomposition method (CD), where Benders decomposition (BD) and Dantzig-Wolfe decomposition (DWD) are combined in a unified framework to improve the solution of scenario based two-stage stochastic MILPs. This method alternates between DWD iterations and BD iterations, where DWD restricted master problems and BD primal problems yield a sequence of upper bounds, and BD relaxed master problems yield a sequence of lower bounds. A variant of CD, which includes multiple columns per iteration of DW restricted master problem and multiple cuts per iteration of BD relaxed master problem, called multicolumn-multicut CD is then developed to improve solution time. Finally, an extended cross decomposition method (ECD) for solving two-stage stochastic programs with risk constraints is proposed. In this approach, a CD approach at the first level and DWD at a second level is used to solve the original problem to optimality. ECD has a computational advantage over a bilevel decomposition strategy or solving the monolith problem using an MILP solver. The second part of the thesis develops a joint decomposition approach combining Lagrangian decomposition (LD) and generalized Benders decomposition (GBD), to efficiently solve stochastic mixed-integer nonlinear nonconvex programming problems to global optimality, without the need for explicit branch and bound search. In this approach, LD subproblems and GBD subproblems are systematically solved in a single framework. The relaxed master problem obtained from the reformulation of the original problem, is solved only when necessary. A convexification of the relaxed master problem and a domain reduction procedure are integrated into the decomposition framework to improve solution efficiency. Using case studies taken from renewable resource and fossil-fuel based application in process systems engineering, it can be seen that these novel decomposition approaches have significant benefit over classical decomposition methods and state-of-the-art MILP/MINLP global optimization solvers.

Genetic architecture and sexual conflict in the life history of Drosophila

Because males and females of a species express many homologous traits, sex-specific selection on these traits can shift the opposite sex away from its phenotypic optimum. This mode of sexually antagonistic selection, known as intralocus sexual conflict (IaSC), arises when the evolution of sexual dimorphism is constrained by the two sexes sharing a common gene pool. As IaSC has been historically overlooked, many outstanding questions remain. For example, what is its contribution in maintaining genetic variation for fitness in populations? What characters underlie this variation in fitness? How does the selection history of the population influence the standing genetic variation? I used the model organism Drosophila melanogaster to attempt to resolve some of these questions. The first part of my Master’s project involved assessing the detectability of sexually antagonistic alleles in populations at different stages of adaptation to the laboratory. For the second part of my Master’s project, I looked for evidence of conflict during the development of body size, a well-known sexually dimorphic trait. While the first part of my thesis proved inconclusive, the second part revealed a surprising source of sexual conflict in pre-adult stages of D. melanogaster.

Genetic Polymorphisms in Replication-related Genes and Risk of Breast Cancer Among European and East Asian Women

Background: The role of common, low to intermediate risk alleles in breast cancer need to be examined due to their relatively high prevalence. Among many cellular pathways, replication has a pivotal role in cell division and frequently targeted during carcinogenesis. Replication is governed by a host of genes involved in a number of different pathways. This study investigates the effects of replication-gene variants in relation to breast cancer and how this relationship is affected by ethnicity, menopausal status and breast tumour subtype. Methods: Data from a case-control study with 997 incident breast cancer cases and 1,050 age frequency matched controls in Vancouver, British Columbia and Kingston, Ontario were used. Unconditional logistic regression was used to calculate odds ratios between 45 replication gene variants and breast cancer risk, assuming an additive genetic model adjusted for age and centre, presented for Europeans and East Asians separately. Polytomous logistic regression was used to assess odds ratios between each SNP and four breast cancer subtypes defined by hormone receptor status among Europeans. All analyses were stratified by menopausal status. The Benjamini–Hochberg false discovery rate (FDR) was used to address multiple comparisons. Results: Among Europeans, the SNPs in FGFR2, TOX3 and 11q13 loci were associated with breast cancer after controlling for multiple comparisons. Test of heterogeneity showed the SNPs rs1045185, rs4973768, rs672888, rs1219648, rs2420946 among Europeans and rs889312 among East Asians conferred differential risk across the tumour subtypes. Conclusions: Specific SNPs in replication genes were associated with breast cancer, and the risk level differed by tumour subtype defined by ER/PR/Her2 status and ethnicity.