title: Electric Propulsion System for Exceptionally Short Takeoff and Landing Electric Air Vehicles

contributor:
Emadi, Ali
Mechanical Engineering

subject: Electric Propulsion System, ESTOL, Electric motors, Electrified air vehicle, Electric Airplane

abstract: Over the past few years, electric propulsion systems have been widely used in automotive applications. The next decade is likely to see the electrification of aerial vehicles. In the past 20 years, the passengers demand in the aviation industry has increased by roughly 5% annually. Drastic increment in the passengers demand leads to many problems such as emission, noise pollution, airports capacity shortage, and high fuel consumption. An electric airplane that can take off and land in an extremely short runway can solve all the mentioned problems. Also, an airplane that is smaller and lighter with the ability to take off and land from an extremely short runway can be used as a new transportation system in congested cities and solve the urban road traffic and compensate for people’s time wasted in traffic. With this in mind, in this thesis, the feasibility of converting a conventional fixed-wing direct-drive propeller airplane to an electric extremely short takeoff and landing airplane has been examined. An overview of the history of electric aerial vehicles and flying cars is conducted where some of these vehicles are still under development phase. The main aim of this thesis is to address the effect of takeoff and landing runway length on the electric motor main specifications, including power, torque, and speed. Also, the effect of cruising speed on the motor specifications are investigated, and it is observed that there is a considerable difference between the amount of required power for the cruising mode and takeoff mode. In the end, the impact of the braking system and airplane weight on the landing distance are examined, and It is found that for an airplane with a cruise-efficient propeller, usage of thrust reverser is not practical and hence it is not recommended. Although if the propeller is designed to have high efficiency at takeoff and landing, the thrust reverser can be a good solution to make the landing runway shorter.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: DEVELOPMENT OF A COMPUTATIONAL MODEL TO INVESTIGATE THE THERMO-MECHANICAL BEHAVIOUR OF CUTTING TOOLS

contributor:
Veldhuis, Stephen C.
Mechanical Engineering

subject: Finite Element Analysis, ALE (Arbitrary Eulerian-Lagrangian), Tool wear, Cutting Edge Geometry

abstract: During machining, the cutting tool wears out and affects the machined surface quality and overall production cost. The prediction of tool wear and analysis of cutting mechanics has significant importance for process optimization and cutting-edge design. In this present study, an efficient FE simulation approach (Arbitrary Eulerian-Lagrangian) on the Abaqus/Explicit platform has been developed to improve the predictability of flank wear and to select the appropriate tool edge geometry in the orthogonal turning operation. The FE model was calibrated by comparing the simulation and experimental force values. A new approach was applied to capture the worn tool geometry based on the frictional stress value acting on the cutting tool. The effect of wear geometry on the cutting zone was investigated with respect to temperature, normal stress, sliding velocity, and plastic deformation. The experimental tool wear pattern and characteristics for the differently prepared edges were studied and compared to the thermo-mechanical value retrieved from the FE model.  Tool wear for differently prepared edges was calculated using Usui’s wear rate equation, which was calibrated using a hybrid calibration method. The efficiency of the calibration method was investigated at different cutting speeds and feed rates. The performance of pre-coating edge preparation was evaluated in both experimental and numerical studies.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Professorial Workloads and Emotional Labour

contributor:
Lewchuk, Wayne
Work and Society

subject:
Precarity
Emotional Labour

abstract: The neoliberal university has transformed professors into front-line workers and their students into consumers of higher learning.  Research has shown there is a positive correlation between a student’s perception of supportive faculty and the completion of a degree.  Professors are expected to support their students and to engage in emotional labour, labour that tends to be invisible and, thus, often unrewarded for faculty members.  An online survey of professors - contract, tenure-track and tenure at three southwestern Ontario universities - indicates that many professors perform affective work as they mediate increasing institutional and student demands on their time and emotions.  Data, from the survey and semi-structured interviews, highlights how emotional labour is not just about meeting student expectations, but also about dealing with job insecurity and institutional pressure to provide an educational product where the emphasis is on student satisfaction.   The result is that many professors experience high levels of stress and burnout.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: This study examines the workloads of professors at three Ontario universities.  Through the use of an online survey and in-depth interviews, the working conditions of professors are revealed as well as the emotional labour professors perform in order to cope with the intensity of both institutional and student demands.  It is hoped that these findings would be useful to faculty associations to better working conditions through contract negotiations and to increase public awareness of the changing and challenging environment of academia.


title: NUMERICAL STUDY OF MECHANICAL BEHAVIOUR OF TUBULAR STRUCTURES UNDER STATIC AND DYNAMIC COMPRESSION

contributor:
Wu, Peidong
Mechanical Engineering

abstract:
Finite element analysis (FEA) is a tool used to predict responses, reproduce experiments, and improve the performance of devices. Modern production techniques, such as 3D printing, enable researchers to investigate structures with complicated shapes and made of mixed materials, thereby increasing the application of simulation and FEA. In this thesis, finite element package ABAQUS is used to numerically investigate the behavior of components subjected to axial static and dynamic loadings.
The effect of cladding a ductile material during ring compression test and energy absorption (EA) of circular tubes is evaluated. The addition of layers of a ductile material to the cross section of a ring increases its compressibility. The EA of circular tubes is improved when the layers of a soft material are located in the model.
Rings with various geometric ratios and shape factors are subjected to axial static loading. The calibration curves for different friction coefficients are plotted. The behavior of the rings and their calibration curves are predictable when the geometric ratio and shape factor of the models are the same. For the rings with the same shape factor but different geometric ratios, the calibration curves can be located lower or higher in the diagram regardless of their size.
The application of hydrostatic pressure to the inner and outer walls of a ring increases its compressibility by changing the tangential and radial stress distributions. Cladding the outer wall of a ring with a soft material changes the stress distribution and increases
iii
compressibility. The state of radial stress is easier to change from tensile to compressive in comparison with tangential stress.
The force–displacement diagrams of corrugated tubes with different number of grooves and groove sizes are divided into three parts. The optimum model that shows the best performance has the same area under the curve of each part. The grooves as triggers can control the location and value of the peak force in the diagram. The size and shape of these triggers should be optimized. The model with regular fluctuations and without any peak force can be considered the optimum model.
The addition of layers of a ductile material to the base model improves the crashworthiness of structures. The volume fraction of clad material and its location should be optimized. For the circular tubes as energy absorbers, the addition of some layers at a 45° angle increases EA and crush force efficiency.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Cortical Effects of Object Affordances on Motor Action Priming Used in Rapid Balance Recovery Actions

contributor:
Lyons, Jim
Kinesiology

subject: Reaching, Balance, Action Priming, Premotor, Perturbation, Sensorimotor, Affordances, Physical Property Affordances, fNIRS, Functional near-infrared spectroscopy, Hand orientation

abstract: There is considerable evidence to suggest that object affordances (see Gibson, 1966) can serve to moderate volitional responses by “priming” the visuomotor system toward certain actions (e.g., Tucker & Ellis, 1998). Typically, these studies assume that shorter voluntary reaction time latencies reflect more efficient movement planning. Questions remain however, as to whether object affordances offer the same motor priming benefits in situations where the temporal window to initiate motor action precludes volitional movements (e.g., during an unexpected balance perturbation). The efficiency of balance reactions to a perturbation is dependent upon the ability for the motor system to generate short latency actions at the onset of instability. Due to the rapid nature of these actions, they are suggested to be regulated by information received prior to the perturbation. In this study, participants sat in a custom-built chair that delivered posterior perturbations and, on each trial, were presented with two of three types of stimuli within their reach (two graspable poles that varied in orientation and a flat non-graspable control). They were instructed to reach and grasp one of the poles at the moment of perturbation so as to mitigate the tilt. To assess cortical activity that may be indicative of motor planning in response to the perception of object affordances, changes in oxyhemoglobin (oxy-Hb) in the right and left premotor cortices were measured using a continuous wave fNIRS system. Results revealed a significant increase (F= 4.62, p= .043) in oxy-Hb in the right and left hemisphere (M = .023 µM) in response to objects that afford an optimal form of grasping action (mitigating excessive supination or pronation of the hand), compared to when no grasping opportunity was present (M = -.051 µM). These results suggest that affordances may be used to prime the system in the event of a balance threat.

abstract: Thesis

abstract: Master of Science (MSc)


title: Housing Rights are Human Rights: Assessing the Potential for Progressive Policy Shifts in Canada’s Housing System through the Right to Housing and the National Housing Strategy

contributor:
Baker Collins, Stephanie
Social Work

subject:
Housing
Right to Housing
Canadian Housing Policy
National Housing Strategy

abstract: Utilizing critical and welfare state theory, this thesis is primarily centred on policy analysis regarding the design and implementation of the legislated right to housing in Canada alongside the National Housing Strategy. In examining Canada’s National Housing Strategy, right to housing legislation, and analysis and commentary around the 2019 Canadian federal budget, the thesis explores the potential for the right to housing to contribute to progressive policy shifts in Canada’s housing system at a time where the impacts of commodification and financialization continue to be prevalent. Additional literature related to Canada’s housing system and social welfare responses, and commentary on the right to housing in domestic and international contexts contributes to an assessment of the social and economic conditions that have led to the emergence of alternative housing policy, as well as the underlying principles and ideologies which guide and influence state intervention. Through this assessment, it is evident that while the legal space in which to claim the right to housing may be an important foundation to further highlight and challenge inequities in Canada’s housing system, the extent to which this results in tangible systemic change remains in question. Further topics are explored in the conclusion around the potential next steps and necessary considerations for implementation in the Canadian context. The research, analysis, and discussion present in this thesis is meant to contribute to a relevant and timely critical examination of the right to housing in Canada, centred within social work values, in order to better understand how to conceptualize and challenge inequities in Canada’s housing system.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: Evaluating the effects of amplitude envelope manipulation on reducing auditory alarm annoyance

contributor:
Schutz, Michael
Psychology

subject:
auditory alarms
amplitude envelope
applied music cognition

abstract: Auditory alarm annoyance plagues clinicians, which results in alarms desensitization and ultimately affects patient care. Contributing to this problem are the International Electrotechnical Commission (IEC) 60601-1-8 alarms, a standardized set of melodic alarms used to convey information to clinicians in intensive care units. By design, IEC alarms employ flat amplitude (i.e., amplitude invariant) envelopes and are not reflective of naturally occurring sounds with percussive amplitude (i.e., decaying) envelopes. We present a series of three experiments evaluating the effect of amplitude envelope manipulation (i.e., incorporating percussive envelope) on memory and annoyance in IEC alarms synthesized using pure tones (experiment 1), complex tones (experiment 2) and assessing annoyance pre and post memory assessment (experiment 3). For the memory assessment, participants were assigned to learn either the flat alarms or percussive alarms. During the memory assessment, participants were informed of the alarm–referent pairings (study phase), practised identifying alarms (training phase), had a short break, and tested on their ability to identify alarms (evaluation phase). The annoyance assessment was a two alternative forced choice task where participants identified which alarm they perceived to be more annoying from a pair of alarms differing in either envelope-type or alarm-type. Across all experiments there was no difference in alarm learnability between those learning either flat or percussive alarms during the memory assessment. Annoyance assessments revealed that all participants chose the flat alarms to be more annoying than the percussive alarms, independent of the memory assessment condition. These results showcase the potential of using percussive alarms to reduce alarm annoyance without harming learnability, a cost-efficient manipulation.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Alarms in intensive care units are perceived as annoying, ultimately negatively affecting both clinicians and patients. These alarms are mandated by the International Electrotechnical Commission to have sustained or flat amplitude envelopes (i.e., referring to the change in loudness over time), which does not reflect naturally occurring stimuli that typically have decaying or percussive amplitude envelopes. The current experiments assessed the effect of percussive envelopes on alarm learnability and annoyance. We showed in a series of experiments that there is no difference in learning alarms with flat or percussive envelopes. However, we showed that alarms with percussive envelopes are perceived to be less annoying than alarms with flat envelopes. These results offer one potential solution to reduce alarm annoyance in intensive care units without harming the learnability of these alarms.


title: “I must love her more”: Black South African male partners’ perceptions of breast cancer and their role in their partner’s access to health care in Diepsloot, Johannesburg

contributor:
Eyles, John
Mcbride, Ruari-Santiago
Global Health

subject:
breast cancer
gender relations
South Africa
health care access
hegemonic masculinity
case study
Johannesburg
Diepsloot
gender norms
gender roles
cancer

abstract:
Background: In South Africa (SA), women with breast cancer (BC) present to the health care system at advanced stages of the disease, resulting in poor prognosis. Limited awareness of the disease, large distances to health care centers, and lack of affordable transportation have all been implicated as factors delaying presentation. In addition, women in SA have limited social and financial independence, which may make it difficult for them to resolve their own health care needs. Despite this, little is known about what South African male partners know about breast cancer and what role they play in their partner’s access to health care.
Methods: This interpretive qualitative case study, guided by the theoretical framework of hegemonic masculinity(ies), used semi-structured interviews to investigate perceptions and knowledge of BC and gender norms in regards to health care access in a group of black South African males (n=20) in long-term heterosexual relationships living in a resource-poor setting. Interview data was analyzed using thematic analysis and compared to observational data collected through opportunities with local BC organizations.
Results: Participants demonstrated very little knowledge of breast cancer and cancer in general. Some specific misconceptions about cancer are reported, including confusion between cancer and HIV. Participants were positive about receiving health care for cancer but are burdened by barriers to reaching care and a lack of access to information about the disease. The men describe themselves as playing an active, mostly positive role in their partner’s access to health care. They demonstrate perspectives about gender relations that defy hegemonic forms of masculinity.
Conclusions: Major public health efforts are required to increase awareness of BC in order to encourage earlier presentation to the healthcare system. These efforts should recognize the importance of the male partner in women’s health issues.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: In South Africa, women with breast cancer often do not reach the conventional healthcare system until the disease has progressed significantly and chances of survival are poor. This occurs because of a lack of knowledge about the disease and large distances to health care centers. Furthermore, in the male-dominated society of South Africa, women have limited independence. Therefore, this study sought to determine what men in South African know about breast cancer and how they are involved in their partner’s access to health care. Interviews were conducted with 20 men living in a resource-poor setting. The men portrayed little knowledge and specific misconceptions about breast cancer and cancer in general. They appear to be playing an active and mostly positive role in their partner’s access to health care. Public health efforts should increase awareness of the disease and recognize the significant role of the male partner in women’s health issues.


title: SUPPORTING THE USE OF RESEARCH EVIDENCE TO INFORM DECISION-MAKING IN CRISIS ZONES

title: EVIDENCE-INFORMED DECISION-MAKING IN CRISIS ZONES

contributor:
Lavis, John
Health Policy

subject:
Health systems research
decision-making
research evidence
crisis zones
CIS
Case study
User testing
LMICs
knowledge translation
evidence aid
Syrian refugee crisis
health policy
Lebanon
Ontario
evidence websites
evidence-informed decision making
critical interpretive synthesis

abstract:
Many strategies can be used to support the use of research evidence in decision-making. However, such strategies have been understudied in crisis zones, where decision-making may be particularly complex, many factors may influence decision-makers’ use of research evidence, and professional judgements may be particularly relied upon. Using synthesis and qualitative research methods, this dissertation examines the role of research evidence in crisis zones and strategies to support its use in decision-making.
First, chapter 2 describes a critical interpretive synthesis, which drew upon a broad body of literature around evidence use in crisis zones to develop a new conceptual framework that outlines strategies that leverage the facilitators and address the barriers to evidence use in crisis zones in four systems, namely the political, health, international humanitarian aid, and health research systems. Second, in chapter 3, the focus narrows, and an embedded qualitative case study design was used to gain a deeper understanding into one of the four identified systems, the political system, and specifically the factors that influenced the use of research evidence in the governmental health policy-development processes for Syrian refugees in Lebanon and Ontario. Finally, in chapter 4, a user testing study design was used to zero-in on decision-makers’ experiences with a particular strategy within the health research system, namely an evidence website focused specifically on topics relevant in crisis zones.
This dissertation provides a rich understanding of research evidence use by examining knowledge translation strategies in a setting that has been largely unexplored in the broader KT map: crisis zones. The findings from this thesis point to the need for comprehensive strategies to support evidence use in decision-making that draw upon the existing literature and are adapted for crisis zones, which can occur sequentially or simultaneously within or across the four identified systems.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: In humanitarian aid, and specifically in crisis zones, there are many different types of information decision-makers can draw from when making decisions.  One specific type of information is research evidence; however, the use of research evidence, and the ways it can inform decision-making in crisis zones, has been understudied. This dissertation addresses this key gap in understanding by: 1) developing a new tool that can help decisions-makers use research evidence to inform their decisions in crisis zones within the political, health, humanitarian aid and health research systems; 2) examining the factors that influence the use of research evidence in the governmental health policy-development processes for Syrian refugees in Lebanon and Ontario; and 3) examining the perspectives of decisions-makers around using one way of supporting the use of research evidence — an evidence website — to support evidence-informed decision-making in crisis zones.


title: A new approach to modelling flooding impacts on emergency service accessibility: A case study of Calgary, Alberta

contributor:
Scott, Darren
Geography

subject:
Geographic Information Systems
Geography
Flooding
Road Network
Flood Mapping
Flood Modelling
Accessibility
Emergency Response
Service Areas
Alberta

abstract: Floods are becoming more frequent and the magnitude of direct consequences, relating to destruction of critical infrastructure and loss of life, has highlighted the importance of flood management. This thesis proposes a new methodology to quantify the impact of predicted and historic flooding events on emergency services. The approach moves beyond simple flood inundation mapping by accounting for the relationship between flood depth and vehicular speed. A case study was presented for Calgary Alberta, where the depths of a predicted 100-year flood and an historic 2013 flood event were modelled. The methodology applied geographic information systems (GIS) to flood depth mapping, utilizing digital elevation models (DEMs), flood extents, and hydrological data. Flood depths were then assigned to links comprising the road network, where the maximum vehicle speed was calculated as a function of the standing depth of water on a link. The flooded network was used to derive service areas for several types of emergency services (emergency medical services (EMS), fire, and police), following targeted response times. The results quantified and located the residential and work populations that no longer meet the targeted response times. During both flood scenarios, EMS were found to have the greatest reduction in accessibility, with 23% to 47% of residents and workers, respectively, not served. Fire services were seen to be more resilient with only 3% to 9% of residents and workers, respectively, not served. The results for police services were similar to fire services. However, the former have a greater range of response times, meaning these areas represent those that are completely isolated during both flood events. Overall, the proposed methodology quantified vulnerable populations on a partially degraded network, which can be used to develop evacuation plans and emergency response strategies, minimizing disturbances in the network and the number of people affected.

abstract: Thesis

abstract: Master of Science (MSc)


title: HIGH-TEMPERATURE PHYSICO-MECHANICAL PROPERTIES OF AS-RECEIVED STRUCTURES IN DUAL-PHASE ADVANCED HIGH-STRENGTH STEELS

contributor:
Phillion, Andre
Materials Science and Engineering

subject: Dual-phase AHSS, Hot embrittlement, Thermomechanical processing, Gleeble testing

abstract:
Dual-phase (DP) advanced high-strength steels (AHSSs) are widely used in the automotive industry due to their excellent combination of strength, ductility, and work hardening properties. However, defects occurring during processing make these ferrous alloys expensive. Toward this ends, high-temperature tensile tests using a Gleeble thermomechanical simulator have been conducted to determine the stress/strain behaviour at temperatures between 1250 to 1480 C in order to quantify the tensile strength and ductility. The results of both as-cast and transfer-bar material will be presented as well as three different sample geometries in order to better understand the effects of starting microstructure, thermal gradient, and tress/strain distribution on the reproducibility of high temperature properties. Optical and scanning electron microscopy are then performed to further elucidate the structure/property
relationships. The results show that the presence of preexisted prorosities in the as-cast structure decreases the high-temperature strength of the material, while the transfer-bar samples show lower ductility at ultra-high temperatures, (T   1450 C), due to their severe susceptibility to melting. In terms of the two mentioned thermomechanical characteristics, voids nucleation, growth, and coalescence initiated with porosity clustering are the main mechanisms behind the lower strength of the as-cast samples, whilst tearing apart of the melt plays an important role to drastically drop the ductility of transfer-bars at mentioned temperature interval. Moreover, the long-gauge-length (LGL) geometry proposes better reproducibility of data compared with the other geometries. This is attributed to a suitable combination between low stress localization and high thermal gradient during the Gleeble testing that provides a condition in which the samples experience sharp localized necking right on the hot-spot zone. The obtained data can be used as part of multi-physics process and microstructure continuous casting models.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: An in vitro and ex vivo Photodynamic Therapy Study of Methylene Blue and Natural Extracts in Association with Nail Penetration Carrier Against Trichophyton rubrum Infections

contributor:
Zhu, Shiping
Xu, Jianping
Chemical Engineering

subject:
Photo dynamic therapy
Methylene Blue
Trichophyton rubrum

abstract: Human fungal superficial infections are mainly caused by dermatophytes. These infections are distributed worldwide, common for people of all ages, in both sexes. The current treatments include taking oral antifungal drugs and topical therapy. However, treatments of superficial infections can be challenging in children and elderly mainly due to compliance issues and associated potential health risks and side-effects. Photo dynamic therapy (PDT) is a novel approach to treat fungal superficial infections. In this approach, light is used to excite a photosensitizer to turn readily available oxygen into reactive oxygen species (ROS) to kill the pathogen. In this research, we have used the pathogenic dermatophyte Trichophyton rubrum as a model to screen for photosensitizers and identify the best combinations of photosensitizer X carrier X light exposure time against T. rubrum. I obtained the In vitro photosensitizers’ Minimum Inhibitory Concentration (MIC), Minimum Fungicidal Concentration (MFC), carrier inhibitory and fungicidal combinations experimental results. In addition, ex vivo experimental results for photosensitizer and carrier systematic treatments are presented with both nail pieces and nail well apparatus. The in vitro results confirm the fungicidal ability of photosensitizer Methylene Blue and natural extracts Inula, Propolis and St. John’s Wort to T. rubrum. For ex vivo experiments, among the three natural extracts, only Inula showed promising fungicidal effect on nail pieces. Methylene Blue and carrier, Methylene Blue plus Inula and carrier combinations at certain concentrations all showed strong nail penetration ability and fungicidal effect against T. rubrum infection. These results suggest promising avenues for further clinical research and application of PDT.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Evaluation of Cardiotoxicity Using Blood Biomarkers in Breast Cancer and Lymphoma Patients Undergoing Curative Treatment

contributor: Medical Sciences (Division of Physiology/Pharmacology)

subject:
cardiotoxicity
high-sensitivity troponin
breast cancer
biomarkers

abstract:
Objective:
To evaluate whether abnormal concentrations in cardiac and inflammatory biomarkers could predict reductions in left ventricular ejection fraction (LVEF) for cancer patients undergoing curative treatment.
Materials and Methods:
Longitudinal testing was performed for high-sensitivity cardiac troponin I (hs-cTnI), N-terminal pro-B-type natriuretic peptide (NT-proBNP), heart-type fatty acid binding protein (H-FABP) and C-reactive protein (CRP) in HER2+ breast cancer (BC) patients receiving adjuvant trastuzumab treatment (n=22) and in lymphoma patients treated with radiotherapy (n=4). Sex-specific and overall upper limit of normal (ULN) cutoffs were used to identify abnormal results with a reduction in LVEF (<50% and decrease of ≥10% from baseline) indicative of cardiotoxicity. A secondary analysis was performed on the BC patients with normal LVEFs (n=12 with baseline prior to chemotherapy through to 6-months on trastuzumab) with 15 blood collections spaced between 6- and 254-days post-baseline LVEF measurement.
Results:
A majority of the BC patients had evidence of myocardial injury (hs-cTnI >female ULN=90%) or myocardial dysfunction (NT-proBNP >overall ULN=91%) at any timepoint with fewer patients having abnormal CRP or H-FABP concentrations (H-FABP >ULN=14%; CRP >ULN=45%). Myocardial injury and dysfunction were most evident during the first two cycles of trastuzumab treatment, with myocardial injury also evident during this early timeframe in the female lymphoma patients (3 with hs-cTnI >ULN). In the 12 patients who completed trastuzumab with normal LVEFs (median=60% at 6-months), myocardial injury (hs-cTnI >ULN) and dysfunction (NT-proBNP >ULN) was evident in >50% of patients. Four of the 22 patients did develop cardiotoxicity, but there was no difference in biomarker concentrations between patients with or without cardiotoxicity.
Conclusion:
The use of the recommended ULN cutoffs identified myocardial injury and dysfunction in a majority of cancer patients in this setting. Biomarker assessments did not relate to cardiac functional imaging studies. Future studies are warranted to assess different cutoffs or biomarker combinations for predicting cardiotoxicity.

abstract: Thesis

abstract: Master of Science (MSc)


title: Characterisation of a Drosophila model of cardiovascular disease

contributor:
Jacobs, Roger
Biology

subject:
Drosophila melanogaster
obesity
cardiovascular disease
extracellular matrix
fibrosis
atomic force microscopy
optical coherence tomography
confocal microscopy

abstract: The heart, as a vital organ, must pump continuously to deliver oxygenated blood to the tissues of the body. The physical stress of pumping is supported by the extracellular matrix (ECM), a dynamic protein scaffold inside and around the heart. While a regulated ECM is required to maintain heart function, aberrant or excessive ECM remodelling, called fibrosis, is associated with disease states and is a hallmark of cardiovascular disease. One major trigger of cardiovascular disease is obesity, and fibrotic remodelling is known to occur in this context. In order to study the impact of increased body size on heart function and the molecular and biophysical characteristics of the ECM, a larval overgrowth model for obesity in the genetic model Drosophila melanogaster has been developed and characterised. This model produces giant larvae twice as heavy as their wildtype counterparts, and allows a unique opportunity to study changes in the cardiac ECM in a simple genetic model. Results demonstrate a remarkable ability of the ECM to accommodate this increase in size. The muscles of the heart are particularly robust, and there are no obvious observable defects to the matrix. Preliminary results suggest Collagen fibres are thicker and more disperse. When observing heart functionality, the cross-sectional area of the heart lumen is increased significantly in giant larvae, both at diastole and systole. However, giant larvae display defects in contraction of the heart tube, characterised by an inability to contract fully at systole. This results in a less than proportional increase in stroke volume, and an increase in heart rate. Heart function of giant larvae is clearly affected by the increase in body size. To quantify the impact to the biophysical structure of the ECM, an atomic force microscopy protocol is being developed.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: A known side effect of cardiovascular disease is fibrosis of the heart, a form of pathological extracellular matrix (ECM) remodelling. Fibrosis causes the stiffening of heart muscle, leading to impaired cardiac function. One of the main risk factors for the development of cardiovascular disease is obesity, and fibrosis is known to occur in this context. I have characterised changes in the morphology and physiology of the heart in a Drosophila model for obesity. The resulting cardiac hypertrophy reveals significant plasticity in the heart ECM, while heart contraction and output is compromised.


title: THE SOCIAL AND SPATIAL DIVISIONS OF PRECARIOUS LABOR

contributor:
Newbold, K Bruce
Mills, Suzanne
Geography and Earth Sciences

subject:
Space
Precarious employment
Gender
Immigration

abstract:
The dissertation is composed of four manuscripts, positioned within the field of economic geography.   Manuscript one broadly examined how precarious forms of employment (PFEs) are spatially patterned within multiple scales and across a range of geographies. The results suggested that different PFEs exhibited distinct spatial patterns across space and scale. For example,  temporary and involuntary part-time work was more prevalent in Atlantic Canada and became gradually less prevalent moving westward. In contrast, part-time employment and employment in multiple jobs were more common in western Canada than in central and Atlantic Canada. The results also confirmed that all PFEs (except for involuntary-part-time work) were more common in rural and small-town areas, and less common in large urban areas. Second, using logistic regression models, results showed that the prevalence of PFEs was reinforced by factors such as immigration status, gender, age, education, and income. These models further confirmed that spatial patterns of PFEs were robust in finer scales i.e. CMAs (census metropolitan areas) and urban/rural geographies even when controlling for socio-demographic and socio-economic effects.

Manuscripts two and three builds on the findings in manuscript one by examining how PFEs are spatially patterned across social locations of gender and immigration status, respectively. Results showed that the east-west and urban-rural patterns observed in manuscript one were partially distorted when the analyses were disaggregated by gender and immigration status. The robustness of these spatial distortions was confirmed using logistic regression models. The fourth manuscript sought to understand the spatial characteristics influencing the spatial variations of temporary employment using ordinary least squares (OLS)  regression models. Key findings revealed that CMA/CAs (census metropolitan areas/census agglomerations)  characterized by large shares of manufacturing, utility, and management occupations were significantly negatively associated with temporary employment. Conversely, CMA/CAs with high shares of sales and service occupations were positively associated with temporary employment. Generally, population characteristics (measured by metropolitan areas characterized by a high share of  Asian immigrants, low-income earners, and employment insurance beneficiaries) contributed more to explaining positive temporary employment estimates than industry characteristics.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Automated Text Mining and Ranked List Algorithms for Drug Discovery in Acute Myeloid Leukemia

contributor:
Hope, Kristin
McArthur, Andrew
Leber, Brian
Health Sciences

subject:
Acute myeloid leukemia
Drug discovery
Deep learning
Artificial intelligence
Literature review
Natural language processing
Automated data analysis
Chatbot
Convolutional neural network
Automated pipeline

abstract: Evidence-based software engineering (EBSE) solutions for drug discovery that are effective, affordable, and accessible all-in-one are lacking.  This thesis chronicles the progression and accomplishments of the AiDA (Artificially-intelligent Desktop Assistant) functional artificial intelligence (AI) project for the purposes of drug discovery in the challenging acute myeloid leukemia context (AML).  AiDA is a highly automated combined natural language processing (NLP) and spreadsheet feature extraction solution that harbours potential to disrupt the state of current research investigation methods using big data and aggregated literature.  The completed work includes a text-to-function (T2F) NLP method for automated text interpretation, a ranked-list algorithm for multi-dataset analysis, and a custom multi-purpose neural network engine presented to the user using an open-source graphics engine.  Validation of the deep learning engine using MNIST and CIFAR machine learning benchmark datasets showed performance comparable to state-of-the-art libraries using similar architectures.  An n-dimensional word embedding method for the handling of unstructured natural language data was devised to feed convolutional neural network (CNN) models that over 25 random permutations correctly predicted functional responses to up to 86.64% of over 300 validation transcripts.  The same CNN NLP infrastructure was then used to automate biomedical context recognition in >20000 literature abstracts with up to 95.7% test accuracy over several permutations.  The AiDA platform was used to compile a bidirectional ranked list of potential gene targets for pharmaceuticals by extracting features from leukemia microarray data, followed by mining of the PubMed biomedical citation database to extract recyclable pharmaceutical candidates.  Downstream analysis of the candidate therapeutic targets revealed enrichments in AML- and leukemic stem cell (LSC)-related pathways.  The applicability of the AiDA algorithms in whole and part to the larger biomedical research field is explored.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Lead generation is an integral requirement of any research organization in all fields and is typically a time-consuming and therefore expensive task.  This is due to the requirement of human intuition to be applied iteratively over a large body of evidence.  In this thesis, a new technology called the Artificially-intelligent Desktop Assistant (AiDA) is explored in order to provide a large number of leads from accumulated biomedical information.  AiDA was created using a combination of classical statistics, deep learning methods, and modern graphical interface engineering.  It aims to simplify the interface between the researcher and an assortment of bioinformatics tasks by organically interpreting written text messages and responding with the appropriate task.  AiDA was able to identify several potential targets for new pharmaceuticals in acute myeloid leukemia (AML), a cancer of the blood, by reading whole-genome data.  It then discovered appropriate therapeutics by automatically scanning through the accumulated body of biomedical research papers.  Analysis of the discovered drug targets shows that together, they are involved in key biological processes that are known by the scientific community to be involved in leukemia and other cancers.


title: Characterization of a DNAzyme for the detection of Legionella pneumophila in cooling tower water

contributor:
Li, Yingfu
Biochemistry and Biomedical Sciences

subject:
DNAzyme
Legionella pneumophila

abstract: Ineffective bacterial monitoring in water systems represents a danger to public health and can result in costly disease outbreaks. Of interest is Legionella pneumophila, a deadly water-borne bacterial pathogen that causes Legionnaires’ disease - a severe form of pneumonia. The Center for Disease Control stated that reported cases of Legionnaires’ disease have quadrupled since 2000 and ranks L. pneumophila as the number one cause of waterborne disease outbreaks in the United States. This threat is expected to increase given an aging population who are more susceptible to L. pneumophila infection and rising global temperatures that can promote L. pneumophila growth. Presently, Public Health agencies recommend bacterial culturing for the detection of L. pneumophila in environmental samples, however, this process can take up to ten days to complete. Consequently, there is a delay between sample collection and subsequent L. pneumophila detection, creating an opportunity for a Legionnaires’ disease outbreak to occur. There is a great need to develop a field-appropriate device that can provide early-stage detection of L. pneumophila in water as a means of mitigating Legionnaires’ disease outbreaks. We propose the use of DNAzymes for the development of such a device. DNAzymes are small, catalytically-active single-stranded DNA molecules that demonstrate target-specific enzymatic activity. We have successfully isolated an RNA-cleaving fluorescent DNAzyme (RFD) specific for the detection of L. pneumophila using in vitro selection. Thorough characterization of the DNAzyme has revealed key structural features influencing kinetics, specificity and sensitivity. In addition, the ability of the DNAzyme to function in cooling tower water, and conservation of the DNAzyme target across Legionella bacteria, has been investigated. In the future we plan to incorporate this RFD into a field-appropriate paper-based device which would play a key role in managing infectious diseases and preventing large-scale outbreaks.

abstract: Thesis

abstract: Master of Health Sciences (MSc)

abstract: Legionella pneumophila is a deadly water-borne bacterial pathogen that causes Legionnaires’ disease - a severe form of pneumonia. Numerous Legionnaires’ disease outbreaks have occurred, with the most common source of exposure to L. pneumophila coming from contaminated cooling towers. Presently, bacterial culturing is used to determine if a cooling tower is contaminated with L. pneumophila, however this process can take up to 10 days to complete. To address this delay, we plan to develop a rapid paper-based test for L. pneumophila detection in cooling tower water using DNAzymes. DNAzymes are small, catalytically-active single-stranded DNA molecules that demonstrate target-specific enzymatic activity. We have isolated a DNAzyme that can specifically detect L. pneumophila and characterized its properties. In the future we plan to incorporate this DNAzyme into a field-appropriate paper-based test which would play a key role in managing Legionnaires’ disease outbreaks.


title: The Renal Transplant Experience: Patients' Post-Operative Perspectives and the Social Work Role

contributor:
Sinding, Christina
Social Work

subject:
Transplant
Critical Disability Studies

abstract: This qualitative study examines the experiences of patients who have undergone renal transplant surgery. Interviews were conducted with six patient informants who received renal transplants one to six months prior to the study. Participants’ narratives offered insight into: the variability of transplant preparation, hopes, experiences, and perspectives of recovery, meanings of recovery, significance of social and economic supports in recovery, and the role of professional staff in providing support and resources during the transplant journey. Their stories are explored in relation to literature on psychosocial aspects of renal transplant and through a critical disability studies lens. The nuances of the social work role in relation to patients’ pre- and post-operative renal transplant journey was explored in depth. Based on the findings and relevant literature, recommendations and suggestions are made on how to expand the social work role in the pre- and post-transplant clinic at St. Joseph’s Healthcare Hamilton.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: The Association of Maternal Folate and Vitamin B12 Concentrations During Pregnancy with Neonate Birth Weight in South Asians and White Europeans Living in Canada: START, FAMILY and CHILD Birth Cohorts

contributor:
Anand, Sonia
Medical Sciences

subject:
Folate
Birth weight
Vitamin B12
Neonate
Pregnancy
Canada
South Asians
White Europeans

abstract:
Background: Folate and vitamin B12 have interdependent metabolic functions that are essential for neonate growth outcomes (i.e. birth weight) based on studies from India. The objective of this research was to evaluate the association of maternal folate and vitamin B12 concentrations with neonate birth weight in South Asian (SA) and white European (WE) populations.
Methods: In this cross-sectional analysis of prospective cohort studies, maternal and neonatal data were collected during the second trimester from 3758 mother-child dyads living in Canada. Maternal diet and supplement use were assessed using a validated food frequency questionnaire. Biochemical indicators were analyzed in a subset of SA mothers. Birth weight was measured within 72 hours of delivery. All regression analyses were performed unadjusted and with adjustment for identified covariates.
Results: Maternal folate and vitamin B12 (dietary, supplemental and total) were not associated with neonate birth weight in SA and WE pregnant women. Higher consumption of milk products by SA women was associated with higher birth weight (β=0.06; p=0.01), whereas higher consumption of egg by WE women was associated with lower birth weight (β=-0.19; p<0.01). Folate and vitamin B12 deficiency in the SA subgroup was 13.7% and 17.8%, respectively. Maternal serum vitamin B12 status was inversely associated with birth weight (β=-0.16; p=0.03).
Conclusions: Folate and vitamin B12 may be proxies for poor nutritional status. Therefore, folate and vitamin B12 may have an association with neonate birth weight in a less developed area (i.e. India) rather than in a highly developed area (i.e. Canada). Highly developed countries have an adequate intake of folate and vitamin B12 and thus a higher nutritional baseline status. These findings complement current research on folate and vitamin B12 concentrations with birth weight in well-nourished populations.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Infant birth weight is an indicator of health and disease risk in adult life. The mother’s vitamin intake can influence the weight of the infant. This research aimed to study whether the mother’s folate and vitamin B12 status is related to infant birth weight. Dietary and supplemental data along with blood samples from South Asian and white European pregnant women living in Canada were collected during the second trimester. The mother’s dietary, supplemental and total folate and vitamin B12 intakes were not related to infant birth weight. In South Asian mothers, higher milk intake was related to higher birth weight and in white Europeans, higher egg intake was related to lower infant birth weight. Higher vitamin B12 in the blood was related to lower infant birth weight in South Asians. More research is needed to determine the relationship between folate and vitamin B12 with infant birth weight.


title: Development of Analytical Stochastic Models for Hydrologic Design of Stormwater Control Measures

title: ANALYTICAL STOCHASTIC MODELS FOR STORMWATER MANAGEMENT

contributor:
Guo, Yiping
Civil Engineering

abstract:
Urbanization has great impacts on hydrologic processes and can result in increased flooding, water quality deterioration, and the hazards of erosion.  To deal with the challenges caused by urbanization, stormwater control measures (SCMs) have been widely advocated and utilized.  SCMs consist of conventional centralized end-of-pipe control facilities and distributed source control or low-impact development practices (LIDs).   Combined sewer overflow (CSO) tanks, detention ponds, wetlands are examples of end-of-pipe control facilities while representative LIDs include infiltration trenches, green roofs, permeable pavements, and rain gardens.
 Methods used in the design and analysis of SCMs are generally classified into three categories: single-event design storm simulation models, continuous simulation models, and probability-based analytical models.  Among them, probability-based analytical models consist of previously developed analytical probabilistic models (APMs) and recently proposed analytical stochastic models (ASMs).  Probability-based analytical models have the advantages of being in the form of closed-form analytical equations and requiring no numerical solutions.  APMs and ASMs can be used as the surrogate of continuous simulation models for design and analysis.  APMs have the shortcoming of requiring simplifying assumptions of antecedent storage or soil moisture conditions.  Single-event design storm simulation models have limitations of relying on the assumption that the frequency of occurrence of some of the runoff hydrograph characteristics is always equal to that of some of the input rainfall hyetograph characteristics.  Continuous simulation models are time-consuming to run and require large amounts of input.  ASMs can overcome many of the drawbacks of other three types of models.
ASMs for stormwater management purposes treat rainfall inputs at a location of interest as a marked Poisson process and describe the temporal evolution of the probability distribution of the relative water level or the degree of soil saturation of a SCM by the Chapman-Kolmogorov equation.  Both rainfall event depth and inter-arrival time are assumed to be exponentially distributed in ASMs.  The concept of effective storage capacity was proposed to properly consider the effects of the instantaneous rainfall pulses represented by the Poisson process.  The steady-state probability distributions of the water content or the degree of soil saturation were analytically derived and form the basis of ASMs.  Relevant SCM performance statistics of interest were derived based on these probability distributions.
This thesis aims to develop a suite of ASMs for the design and analysis of SCMs which can significantly reduce the impact of some of the simplifying assumptions required in previously developed APMs and ASMs, while the newly developed ASMs are still in analytically tractable forms which simplify the calculation tasks required in engineering design.  In Chapter 2, an ASM is developed for evaluating the performance of CSO tanks.   In Chapter 3, instead of using constant outflow functions as in previous ASM studies, more realistic orifice outflow functions are considered in the development of ASMs for stormwater detention ponds.  In Chapter 4, considering different possible operating conditions rather than simply assuming a constant bottom infiltration rate, different ASMs are proposed for different types of infiltration facilities.   In Chapter 5, as an example application of the ASMs, the developed ASMs are applied for the sizing of infiltration trenches following local design standards and procedures.
Throughout the thesis, the developed ASMs were verified by comparing their analytical results with results obtained from continuous simulations considering various factors of climate conditions, land use conditions, soil conditions, and facility dimensions.  The usefulness of ASMs were demonstrated through cases studies at different test locations.  The developed ASMs are recommended as an efficient alternative of, or used together with, continuous simulation models in the planning, design, and analysis of SCMs.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Exploring the Perceptions, Practices and Constructs surrounding the Measurement of Dexterity in the Rehabilitation of Persons with Hand and Wrist Injuries

title: Exploring the Measurement of Dexterity in Rehabilitation

contributor:
Macdermid, Joy
Rehabilitation Science

subject:
dexterity
hand function
motor control
hand
wrist
measurement
outcome measure
qualitative
Interpretive Description
Occupational Therapy
Hand Therapy
Validity

abstract:
Introduction: Dexterity impairments are common and disabling. Measuring the extent of these impairments is important for care and service provision. Despite this, dexterity is poorly operationalized in the management of persons with hand and wrist conditions (HWC).
Thesis purpose: To understand: 1) how dexterity is defined in the management of persons with HWC and 2) how therapists working with persons with HWC perceive/understand the concept and measurement of dexterity and use of performance-based outcome measures of dexterity (PBOMD).
Methods: In study one, Interpretive Description was used to understand the perceptions and measurement practices of occupational therapists working with persons with HWC in Singapore. Study two involved a content analysis of the literature outlining the constructs measured by PBOMD that were validated for use in persons with HWC.
Results: Both studies highlighted the lack of conceptual clarity around ‘dexterity’ that is reflected in therapists’ and tool developers’ discourse. Many of the therapists we interviewed, perceive PBOMD to lack clinical value. Studies from this thesis suggest that identified PBOMD do not adequately cover dexterity.
Conclusion: Findings highlight the challenges surrounding the construct of dexterity and provide clinical practice recommendations.

abstract: Thesis

abstract: Master of Science Rehabilitation Science (MSc)

abstract: Dexterity is the ability to do tasks, successfully, quickly and accurately. Loss of dexterity is common and affects our ability to do our tasks of daily life and work. Unfortunately, there is a lack of agreement on the best way to measure dexterity. Our study aims to explore what dexterity means to health professionals. We focused on occupational therapists seeing persons with hand and arm injuries. In the first study, we interviewed therapists to understand how they measured dexterity. In the second study, we searched for dexterity tests used with persons with hand injuries. Then, we compared the tests we found to dexterity theories. We found that dexterity is measured in different ways. Therapists faced many barriers to using dexterity tests. Current dexterity tests are an incomplete reflection of a person’s dexterity. The information gained from these studies could be used to inform future research on the measurement of dexterity.


title: Multi-Site Structural Magnetic Resonance Imaging of Myelin

contributor:
Bock, Nicholas
Psychology

subject:
Magnetic Resonance Imaging
Myelin
White Matter
R1
T1
FreeSurfer
Human Connectome Project
Volume
Age Trajectory
Structural MRI
T1 weighted
Intracortical  Myelin
Surface Space

abstract: Multi-site MRI studies collect large amounts of data in a short time frame. Large sample sizes are desirable to address power and replicability issues that have been problematic for scientists in the past. Although multi-site MRI solves the sample size problem, it brings with it a new set of challenges. Scanning the same person at different sites might result in differences in MRI derived measurements. In this thesis we compared three approaches to facilitate the analysis of multi-site MRI data: quantitative R1 mapping, adding site as a covariate in a linear model, and using the ComBat method. We also investigated the relationship between two common MRI measurements: signal and volume. We collected data from 64 healthy participants across 3 GE scanners and 1 Siemens scanner at 3T. We found that signal intensity was different between vendors whereas volume was not. Our R1 method resulted in values that were different across vendor and significantly lower than those reported in the literature. B1+ maps used to calculate R1 were different across sites. Using a scale factor, we were able to compensate for mistakes in R1 mapping. We also found that adding site as a covariate corrected mean differences in signal intensity across sites, but not differences in variance. The ComBat method gave best similarity between sites. However, since different people were scanned at each site, we couldn’t evaluate the effectiveness of each method as variation in the data could have been due to site effects or heterogeneity in participants. White matter volume and signal intensity in the white matter were correlated in males but not in females. We found that this low correlation was caused by outliers in our female sample. The correlation between white matter volume and signal in males suggests that both metrics are measuring myelin and can be used as converging evidence to detect changes in brain myelination.

abstract: Thesis

abstract: Master of Science (MSc)


title: Functional and Structural Neuroplasticity in Depression

title: Functional and Structural Neuroplasticity in Major Depressive Disorder

contributor:
Minuzzi, Luciano
Hall, Geoffrey B. C.
Neuroscience

subject:
Major Depressive Disorder
functional magnetic resonance imaging
acute tryptophan depletion
neuroplasticity

abstract: The brain has the capacity to modify itself structurally and functionally, to adapt to novel circumstances. Adaptive changes in neural circuitry that become intransigent, such as continued hypervigilance after resolution of a threat situation, become maladaptive and may facilitate development of psychiatric disorders such as Major Depressive Disorder (MDD). Although MDD pathogenesis is unclear, hypothalamic-pituitary-adrenal axis dysregulation may facilitate the neuroplastic changes observed in MDD. Whether these neuroplastic changes facilitate the development of MDD or develop due to MDD remains unclear. The characterization of neuroplastic changes in MDD has resulted in sometimes contradictory findings. There are gaps in understanding the timing of neuroplastic changes in MDD, and how and when they are affected by antidepressant treatment. Characterization of neuroplasticity in MDD may uncover different phenotypes and aid in the discovery of a predictive biomarker of antidepressant treatment response. This dissertation presents the results of a series of neuroimaging studies. Chapter 1 provides an introduction to neuroplasticity and MDD. In Chapter 2 results of a study examining hippocampal memory function in treatment naïve patients with MDD are presented. Chapter 3 exhibits findings from a study examining effects of an acute tryptophan depletion paradigm in midlife women receiving estrogen-based treatment on an emotional conflict task. Chapter 4 discusses results from an examination of unmedicated patients with MDD and healthy control participants on an emotional conflict task. Chapter 5 presents longitudinal data of the sample from Chapter 4, and the effect of 8 weeks of treatment with antidepressant escitalopram on performance on an emotional conflict task. In Chapter 6 a case study is presented of a patient with long-standing overt ventriculomegaly, whose chief complaint was of mood and cognitive impairments. Chapter 7 summarizes the findings and contributions of this body of research and discusses clinical implications and future directions.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: The characterization of brain changes in Major Depressive Disorder (MDD) has resulted in contradictory findings, and gaps in understanding how the brain changes in response to antidepressant treatment. This dissertation aims to characterize brain changes in MDD through a series of neuroimaging studies. Chapter 1 provides an introduction to MDD and brain changes in MDD. Chapter 2 presents an examination of memory in treatment naïve patients with MDD. Chapter 3 presents a study of acute tryptophan depletion in midlife women receiving estrogen-based treatment on an emotional conflict task. Chapter 4 examines unmedicated patients with MDD and healthy control participants on an emotional conflict task. Chapter 5 examines the effects of antidepressant treatment on performance on an emotional conflict task. Chapter 6 presents a case study of a patient with ventriculomegaly with mood and cognitive impairments. Chapter 7 summarizes the contributions of this research and discusses implications and future directions.


title: MESH-CTEM – Development and Testing of an Integrated Biogeochemical and Watershed Hydrological Modelling System

contributor:
Arain, Arain
Earth and Environmental Sciences

subject: Carbon Watershed Hydrology Ecology CLASS CTEM MESH Modelling Streamflow Productivity

abstract: This study developed an integrated biogeochemical and hydrological modelling system by incorporating the latest versions of the nitrogen coupled Canadian Land Surface Scheme-Canadian Terrestrial Ecosystem Model (CLASS-CTEM) into the Modelisation Environmentale Communautaire (MEC) Surface and Hydrology system (MESH), hereafter referred to as MESH-CTEM. The newly developed MESH-CTEM modelling system allows simulations of energy, water, carbon and nitrogen fluxes and their feedbacks on vegetation growth and exploration of impacts of future climatic changes on catchment-scale processes. Performance of the MESH-CTEM system was tested at the Big Creek watershed within Norfolk county, Ontario, Canada, which is a 573 km2 crop-dominated catchment with areas of broadleaf and needleleaf forests, using observed eddy covariance flux, meteorological and hydrological datasets from October 2004 to December 2017 at a grid resolution of 0.02o latitude × 0.02o longitude. MESH-CTEM showed a significant increase in the simulated streamflow as compared to MESH running with only CLASS, excluding dynamic vegetation growth and carbon fluxes, resulting in an overall increase in the accuracy of streamflow with Nash-Sutcliffe Efficiency (NSE) indices of 0.38 and 0.12 respectively. Significant improvements were also seen for each Plant Functional Type (PFT) within the catchment with respect to energy fluxes, evaporation and soil water regimes. Many of these improvements in simulated fluxes were due in part by changes in the canopy conductance formulation, more realistic soil heat and water processes due to the introduction of fine soil layers, inter-grid transfers of water and other spatial components and vegetation cover feedbacks on energy, water and carbon exchanges by using dynamic vegetation growth processes. Simulated averaged gross ecosystem productivity, ecosystem respiration, latent heat flux and sensible heat flux for the entire catchment were respectively 660 g C m−2 yr−1, 640 g C m−2 yr−1, 32.5 W m-2 and 27.1 W m-2. Application and use of MESH-CTEM will help to study the impact of climate change and extreme events on energy, water and carbon fluxes and associated feedbacks at the catchment scale. Additionally, this will help bridge a major gap in hydrologic modelling studies through integration of biogeochemical processes.

abstract: Thesis

abstract: Master of Science (MSc)


title: Memory effects from cognitive control: A stage-specific account of desirable difficulty

contributor:
Scott, Watter
Psychology

subject:
desirable difficulty
cognition
cognitive control
psychology
priming
memory

abstract: This thesis investigates predictions from prominent conflict theories of cognitive control that information experienced under high conflict conditions should be better encoded. More specifically, recent research suggests that selectively attending to relevant stimuli while ignoring conflicting stimuli can lead to better memory. These ideas have been broadly discussed in the desirable difficulty literature – described by instances where increasing difficulty during initial task performance leads to better later memory. As a growing number of studies have attempted to produce these effects with mixed success, calls for more focused investigations into the underlying mechanisms have been made. This encoding benefit for high-control-demand or high-difficulty situations has been broadly conceptualized as a task-general property, where all activated representations should be better encoded. The goal of this thesis was to investigate whether memory-enhancing effects of difficulty manipulations depend on inducing additional cognitive control at particular information processing stages. This thesis documents some of the first work showing that the within-task locus of conflict and attentional control is critical to whether later memory benefits are seen – conflict/control focused on semantic item representation produces better memory, but conflict/control focused away from item representations at response selection gives no memory benefit. These findings and theory are then extended to physiological measures of pupil dilation and sequential (Grattron-like) conflict/control situations. This thesis proposes a stage-specific conflict-encoding model which complements and extends current leading theories of conflict-driven cognitive control.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: There is an intuitive notion that making a learning experience hard will hinder memory of that information later on. Contrary to this belief, in certain circumstances, making learning difficult can actually enhance the memory of that information – this has been termed desirable difficulty. The issue with these desirable difficulties is that they are only sometimes effective. Originally it was proposed that general task-wide difficulty would lead to an enhancement in memory. This thesis, however, provides evidence suggesting that task difficulty is stage-specific in nature, meaning that for the difficulty to enhance memory, the difficulty needs to be at a specific stage of cognitive processing. For difficulty to have a beneficial effect on memory, the particular difficulty needs to focus an individual’s attention on the core meaning of what they are trying to remember, or else the difficulty will direct attention away from this important information causing a possible decrease in memory. These findings provide a framework for how and when to use difficulty as a means to enhance learning.


title: Protection of the Dharma in Daoxuan’s Continued Biographies of Eminent Monks

contributor:
Benn, James A.
Religious Studies

abstract:
This study examines the section of hufa 護法 (Protection/Defence of the Dharma) in the Xu gaoseng zhuan 續高僧傳 (Continued Biographies of Eminent Monks, XGSZ for short), compiled by Daoxuan 道宣 (596–667 CE).
This study sheds light on both religious persecution and Buddhist biographical writings. While hufa could refer to a large range of activities against both external and internal challenges to the Buddhist communities, Daoxuan focuses on Daoism and anti-Buddhist imperial policies as the major threats to Chinese Buddhism. In the thesis, I annotate and summarize all the biographies in the hufa section to discuss the patterns of narrative through those biographies. I provide an annotated translation of Daoxuan’s lun 論 (evaluation) on hufa, which reflects Daoxuan’s notion of hufa as a Buddhist tradition through Buddhist history.
The study also looks into examples of hufa from other sections of XGSZ to further explore the meaning of protecting the Dharma to Daoxuan and his contemporaries.

abstract: Thesis

abstract: Master of Arts (MA)


title: Performance Evaluation of CBN Tools in High-Speed Dry Turning of AISI 1018 Low Carbon Steel

contributor: Mechanical and Manufacturing Engineering

subject:
HSDM
Low carbon steel
CBN
Dry machining
High speed machining
AISI 1018
TiAlN
Al2O3
TiCN
TiN
Coating
Binder

abstract:
Increasing productivity is a constant demand for the manufacturing industry. Low-carbon-steel is one of the most commonly used ferrous materials in the part manufacturing market. Improving productivity as well as making the process eco-friendly by implementing a dry machining condition is the essential goal of this study.
Built-up-edge (BUE) is often formed in the low-carbon-steel machining process, which, results in poor surface finish and short tool life. The high-speed-machining technique can be used to reduce the BUE formation and realize an increase in productivity. Cubic boron nitride (CBN) tools are most commonly used in hard turning and cast-iron machining at high cutting speeds. There are a limited number of studies regarding low-carbon-steel machining with CBN under a high-speed and with a dry machining condition. In this study, the investigation shows the preferable type of CBN tool and the wear mechanisms involved during finish turning operations of AISI 1018 under high speed and dry machining conditions.
Test results show that a low CBN content with a TiCN binder and smaller grain size offers the best tool life and surface integrity of the final part. Currently manufacturers use coated carbide tools with a recommended cutting speed of 200-300m/min with coolant to complete the finishing process for turning low carbon steel parts. In this study, by implementing CBN tools under the dry condition at 500 m/min cutting speed (speed was selected from the preliminary test performed using the uncoated CBN from 500 to 1200 m/min), the buildup edge formation has been reduced, tool life was measured to increase by 307% compared to the benchmark tool (Coated Carbide), and surface finish was measured in the  range of 0.8-1.6μm Ra.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Identifying the frequency and phenotype of IL-8+ T cells in cat allergic and non-cat allergic subjects

contributor:
Larché, Mark
Tonti, Elena
Medical Sciences

abstract: Advances in immunotherapy have led to the development of peptide immunotherapy (PIT) which has shown clinical efficacy in a reducing allergic symptoms and providing long-lasting benefits. In mechanistic studies, we identified that PIT reduced the transcription of IL-8 in allergen-specific T cells coinciding with no increase in blood neutrophil counts after a nasal allergen challenge. IL-8 is a chemoattractant that elicits the migration and activation of neutrophils and basophils, causing the release of histamines and leukotrienes which are effector molecules implicated in allergic diseases. We hypothesized that in allergic individuals, a novel T cell subset, ‘Th8’, may exist and are primed to produce and release IL-8 upon allergen exposure. In this study, we determined the frequency and phenotype of allergen-specific IL-8+ T cells through flow cytometry and ELISpot assays in a clinical study with 12 cat allergic and 13 non-cat allergic subjects. In cat allergics, the frequency of IL-8+CD4+ T cells was 2.14±1.02% while non-cat allergics had a frequency of 1.99±0.97% at baseline. Stimulation with cat allergens resulted in a small increase in the frequency of IL-8+ T cells in both groups. In the population of IL-8+ T cells, only a minor subpopulation were allergen-specific as <2% expressed CD154. Allergen-specificity of these cells were also assessed through MHC Class II tetramer staining, which yielded a similar result as 99.7±153.8 TET+IL-8+ T cells/million CD4 were detected in cat allergics compared to 50.9±43.5/million CD4 in non-cat allergics. Phenotyping of IL-8+ T cells suggests that these cells may have similar homing characteristics as Th2 cells due to the expression of CCR4. The presence of IL-8+ T cells detected in the study suggests that there may be a small population of allergen-specific T cells that produce IL-8 upon allergen exposure that contributes to the chemotaxis/activation of neutrophils and basophils, leading to allergic symptoms.

abstract: Thesis

abstract: Master of Science (MSc)


title: HIGH CONTENT ANALYSIS TO IDENTIFY MODULATORS OF HUNTINGTIN N17 PHOSPHORYLATION

title: HIGH CONTENT ANALYSIS OF HUNTINGTIN PHOSPHO-N17

contributor:
Truant, Ray
Biochemistry

abstract: The N17 domain in the huntingtin protein is an important modulator of mutant huntingtin toxicity in Huntington’s Disease (HD). Notably, this domain is hypophosphorylated in HD, and promoting its phosphorylation is protective in HD models. I conducted high content analysis of a library of 1163 compounds to identify modulators of phospho-N17 in order to gain mechanistic insight into the pathways which affect N17 phosphorylation. I found that the pharmaceutical compound Pranlukast promoted N17 phosphorylation by inhibiting the NFκB signaling pathway, which was also shown to modulate N17 phosphorylation in our lab’s previous work. Throughout the course of this project, I developed a novel method for screening moderately sized compound libraries that is inexpensive, unbiased, sensitive, and accurate. This new high content analysis procedure, known as the “Gladiator” screening method, can be used as a framework to screen compounds in small laboratory.

abstract: Thesis

abstract: Master of Science (MSc)


title: Nipi Mamoweenene: Indigenous Water Governance to Protect the Heart of Ohke (Mother Earth) the Great Lakes, Nayanno-Nibiimaang Gichigamiin, Kanyatare'Kó:Wa

contributor:
Garrick, Dustin
Political Science

subject: Indigenous Water Governance

abstract: The rivers and tributaries of our planet carry water through Mother Earth, like veins carry blood, and for many Indigenous Peoples, the Great Lakes are the heart of Mother Earth sustaining her life blood - water. However, centuries of water colonialism have led to the disenfranchisement of Indigenous Peoples’ water citizenship, which is connected to the evolution of Indigenous water governance in the Great Lakes. Indigenous water governance includes the intergenerational and adaptive institutions and processes by which Indigenous Peoples and Nations protect the water through decision-making, treaty relations, and resurgent kinship. Indigenous water governance is grounded in the principle of Indigenous survivence – the capacity of an Indigenous Nation or community to survive stressors to water governance through resilience building that allows for sustainability and protection of water for future generations. Understanding the roles of Indigenous Nations as rightsholders in a given social-ecological-system is necessary for understanding the institutions, policies, and processes shaping collaborative water governance in transboundary basins. The failures in equity of participation, decision-making authority, and government-to-government consultation for Indigenous Nations in the shared protection of the Great Lakes St. Lawrence River Basin (GLSLRB) represent governance crises for water security. Adaptive water governance is grounded in Indigenous inclusion as rightsholders and knowledge co-production for shared agenda setting and equitable decision-making in the face of uncertainty. This dissertation empirically investigates the norms, dynamics and mechanisms that underlie the management structure, composition, and politics of Indigenous water governance in the Great Lakes. Chapter 1 introduces the literature and background necessary for positioning the four studies of the dissertation presented in Chapters 2, 3, 4, and 5. Chapter 2 presents the history of water colonialism in the region and the transferability of Indigenous water institutions to manage the complex multilevel governance waterscape of the Great Lakes. Chapter 3 examines Indigenous attitudes towards Great Lakes protection in public opinion polls and the cross-national differences among Indigenous and non-Indigenous residents of the Great Lakes basin. Chapter 4 contains a case study of the Great Lakes Water Quality Agreement Areas of Concern, their impacts on Indigenous Nations, and the water injustices that result when Indigenous worldviews are not valued. Chapter 5 explores the reawakening of sleepy water knowledges through the Water Walks and presents the path forward set by the water walkers for rebuilding water diplomacy through Indigenous water citizenship for Great Lakes governance. Taken together, these studies help us to conceptualize Indigenous water governance within the Great Lakes and provide best practices for Indigenous leaders globally working to protect the water and enacting Indigenous water governance.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: The rivers and tributaries of our planet carry water through Mother Earth like veins carry blood, and for many Indigenous Peoples, the Great Lakes are the heart of Mother Earth sustaining her life blood - water. However, centuries of water colonialism have led to the disenfranchisement of Indigenous Peoples’ water citizenship, which is connected to the evolution of Indigenous water governance in the Great Lakes. This doctoral dissertation investigates the history of water colonialism in the region and the transferability of Indigenous water institutions to manage the complex multilevel governance waterscape; Indigenous Peoples perceptions of Great Lakes well-being; water injustices that result when Indigenous worldviews are not valued; and the path forward for rebuilding water diplomacy through Indigenous water citizenship for Great Lakes governance. Great Lakes Indigenous Nations’ reawakening of sleepy water knowledges are lessons for Indigenous Nations around the world fighting to protect the water on how to reclaim their water sovereignty for Indigenous water governance.


title: The Unity and Equality of the Divine Relations in Gregory of Nazianzus' Trinitarian Theology

contributor:
Widdicombe, Peter
Kroeker, Travis
Religion

subject:
Trinity
Theology
Patristics
Gregory of Nazianzus

abstract: In this thesis, the author examines how Gregory of Nazianzus distinguishes between the Father, Son, and Holy Spirit, while maintaining their equality and unity. In the first chapter, he examines the way theological discourse shapes Gregory's understanding of how words are predicated of God. In chapter 2, the author explores Gregory's understanding of the divine persons whom he distinguishes only on account of their subsistent relations of origin. In the final chapter, the author indicates problems with the modern scholarly interpretation of Gregory that  identifies the unity and equality of the divine persons exclusively with the person of the Father. It is concluded that Gregory relied upon the notion of the homoousios in order to establish and guarantee the divine equality and unity among the persons.

abstract: Thesis

abstract: Master of Arts (MA)


title: Social Exclusion and The Sense of Agency

contributor:
Obhi, Sukhvinder
Psychology

subject:
sense of agency
intentional binding
social exclusion
eating disorders

abstract: This thesis explored the effects of social exclusion on the sense of control. We indexed the sense of control using the sense of agency. The sense of agency refers to the feeling of control over our actions and the outcomes of those actions. We experience the sense of agency at an implicit, pre-reflective level. In other words, we routinely make movements that impact some sort of change in the environment, and simply just know that our actions cause an effect. Experimentally, we can measure the sense of agency using the intentional binding effect. Intentional binding is a temporal illusion in which we perceive the time between our voluntary action and the outcome of that action to be shorted compared to when the same effect is caused by an involuntary action. We conducted three experiments. In experiment one, we used an episodic memory recall task to prime participants to feel socially excluded or socially included. In experiment two, we used a different manipulation of social exclusion and social inclusion called Cyberball. We found that in both experiments, intentional binding was significantly reduced following social exclusion compared to social inclusion and baseline. In experiment three, we investigated the pre-reflective sense of agency in eating disorders. Eating disorders are highly associated with chronic social exclusion experiences and an altered sense of control in life. We found that individuals with higher eating disorder symptomatology experience a lower sense of agency, compared to healthy individuals. Overall, this thesis is the first to demonstrate that social exclusion has observable effects on the sense of agency. We were able to triangulate these findings using another social exclusion manipulation as well, strengthening our original findings. Lastly, we showed that a disorder characterized, in part, by social exclusion, reduces the sense of agency

abstract: Thesis

abstract: Master of Science (MSc)


title: PREDICTORS OF ORAL ANTICOAGULANT-ASSOCIATED ADVERSE EVENTS IN SENIORS TRANSITIONING FROM HOSPITAL TO HOME: A RETROSPECTIVE COHORT STUDY

contributor:
Holbrook, Anne
Health Research Methodology

subject:
Oral anticoagulants
Continuity of care
Transitions in care
Prediction models
Split-sample validation

abstract:
Background
Our objective was to identify and validate clinical and continuity of care variables associated with Oral anticoagulant (OAC)-related adverse events within 30 days of hospital discharge amongst seniors.

Methods and Analysis
This was a population-based retrospective cohort study of all adults aged 66 years or older who were discharged from hospital on an OAC from September 2010 to March 2015 in Ontario, Canada. The primary outcome was a composite of the time to first hospitalization or Emergency Department visit for a hemorrhage or thromboembolic event or mortality within 30 days of hospital discharge. A Cox proportional hazards model was used to determine the association between the composite outcome and a set of prespecified covariates. A split sample method was applied to validate the final model.

Results
We included 120 721 Ontario seniors of which 5423 suffered one of the primary adverse events. Patients discharged on a direct-acting oral anticoagulant (DOAC); dispensed the same OAC in the past 12 months; who had a history of a thromboembolic event; had a recent joint replacement or major surgery; had a cardiologist, hematologist or orthopedic surgeon as compared to a family medicine physician as the physician prescribing the OAC at discharge had a lower risk for the composite outcome. Though continuity of care was a variable in the final multivariate Cox model, it was not significant. The Cox model was stable with acceptable discrimination but poor goodness-of-fit.

Conclusion
In this study, we found that continuity of care as measured by outpatient follow-up in the 7 days post-discharge was not significantly associated with the composite outcome. Further exploration to improve the current model’s calibration and interpretation are required.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Background
Oral anticoagulants (OACs) are associated with serious adverse events, with high rates immediately post-hospitalization. We aimed to identify and validate clinical and continuity of care variables in seniors discharged from hospital on an OAC, which are associated with OAC-related harm in the short-term high-risk period following hospitalization.

Methods
Data from administrative health databases in Ontario were used to identify and validate risk factors associated with time to first OAC-related serious events including hospitalization or emergency department visit for a bleeding or thromboembolic event, and mortality. Cox proportional hazards model and split-sample methods were utilized.

Results
We included 120,721 seniors of which 5423 suffered one of the primary events. Patient-, physician- and index hospitalization-characteristics were all associated with time to the composite outcome. Though continuity of care risk factor was part of the final model, it was not a significant predictor for the outcome.

Conclusion
Exploration of this model through sensitivity analysis is required.


title: CYB5D2 PRODUCES TUMOR SUPPRESSING EFFECTS IN BREAST CANCER

title: CYB5D2 ATTENUATES BREAST CANCER AND CELL SURVIVAL

contributor:
Tang, Damu
Medical Sciences

subject: CYB5D2

subject: Breast cancer

abstract: Breast Cancer (BC) is the leading cause of cancer related deaths among women worldwide. Its etiology includes inactivation of tumor suppressors. In line with this notion, our laboratory has recently reported that CYB5D2 possesses tumor suppressing activities in cervical cancer; evidence also suggests CYB5D2 as a novel tumor suppressor of BC. I thus hypothesize that CYB5D2 mitigates cell propagation in vitro. To examine this possibility, I transiently expressed CYB5D2 in two typical BC subtype cell lines, HCC 1954 (HER2+) and MCF7 (Luminal A). Remarkably, cell population was diminished over a period of at least five days post-transfection when compared to empty vector (EV). To characterize CYB5D2-derived inhibition of BC cell proliferation, I generated a Tet-On inducible system in both cell lines in which CYB5D2 expression is induced upon addition of doxycycline. As expected, induction of CYB5D2 led to a decline of cell propagation and colony formation based on cell proliferation and colony formation assays respectively. Moreover, knockdown of CYB5D2 via lentivirus-based shCYB5D2 transfection in HCC 1954 and MCF7 cells resulted in an incline of cell propagation and colony formation when compared to the shCTRL (control) line. To examine possible apoptotic mechanism of tumor suppressor, we performed TUNEL assay analysis in cell lines expressing CYB5D2. Both HCC 1954 and MCF7 obtained similar results exhibiting evidence of apoptotic cells when compared to their respective controls. Interestingly, upon CYB5D2 expression HCC 1954 also displayed evidence of halting G1 phase progression when performing cell cycle analysis, suggesting a promising alternate tumor suppressing mechanism. Lastly, to corroborate with previous observations of an existing molecular interaction between CYB5D2 and tumor suppressor Phosphatase and tensin homolog (PTEN) we performed a Co-Immunoprecipitation (Co-Ip) assay. As expected, endogenous CYB5D2 and PTEN lysate from HCC 1954 and MCF7 were demonstrated to interact on a molecular level. These observations support the notion that CYB5D2 elicits tumor-suppressing activities in both Her2+ and Luminal A breast cancer cell lines. It is important to note that we detected a greater tumor suppressing impact of CYB5D2 in HCC 1954 when compared to MCF7 suggesting a potential mechanism to favour HER2+ status. Additional research in determining potential tumor-suppressing pathway of CYB5D2 in BC is encouraged as we established promising insight of novel tumor suppressor.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: Mediators of Decision Making in Action Planning: Assessing the Functional Costs of Alternative Movement Strategies

contributor:
Lyons, James L.
Kinesiology

subject: Decision making, biomechanics, motor behaviour, motor control, reaching, walking, action planning

abstract:
The human motor system is constantly faced with decisions about how to choose a path when navigating our environment. These types of decisions occur rapidly and constantly, from initial movement planning, through movement execution, to completion. With infinite ways to complete any given task, the central nervous system generally, and motor control systems specifically, must somehow “decide” the best way to do this while taking into account physiological and environmental constraints. In addition, these movement choices must consider the feasibility and efficiency of all movement alternatives. For example, when deciding between paths that vary in reach distance and walking distance, the path with the shorter reach distance is more likely to be chosen, as reaching is deemed to be ~10x more costly than walking a given distance (Rosenbaum et al., 2011; Rosenbaum, 2012). It is not clear, however, how much more costly the non-chosen path is, compared to the chosen path, and what factors are mediating these decisions. Thus, the purpose of this thesis was to investigate potential underlying non-cognitive mediators of behavioural decisions involved with posture selection during tasks that occur within a constrained task environment, by quantifying the biomechanical mechanisms that may be driving these decisions. Chapter 2 replicated and extended upon the work of Rosenbaum et al. (2011) by recording whole-body motion capture during a bucket transfer task. This study was the first to look at the loading of the shoulder joint and trunk during the reaching and walking decision paradigm, comparing joint loading in the chosen versus unchosen paths.
In Chapter 3, participants made decisions between movements with seemingly similar functional distances, in a four-choice reaching and walking paradigm. Behavioural outcomes suggest that the decision-making process reflects spatial coding of the movement goal that is backwards planned from the task sub-goal. Chapter 4 explored how perceived costs of multiple task variables are prioritized and integrated into action planning. Here, participants prioritized decreased reach distance over bearing an increased load. Collectively, this thesis provides evidence that bottom-up processes, namely the biomechanics of the shoulder and trunk, exert influence on cognitive decision-making and action planning, as reflected in decreased joint loading in chosen versus unchosen paths.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: The Mechanisms Governing Self-Renewal and Differentiation in Pluripotency

contributor:
Draper, Jonathan
Biochemistry and Biomedical Sciences

subject:
Biochemistry
Stem Cell Biology
Molecular Biology
Genomics

abstract:
Chapter 1: The pluripotent state is maintained by a network of “core” transcription factors (TF). REX1 (Reduced Expression-1) is a pluripotency related TF derived from retrotransposon-mediated duplication of the zinc finger TF Yin Yang 1 (YY1). Furthermore, expression of REX1 and YY1 induces changes in genes regulated by endogenous retroviral elements (ERV), suggesting an evolutionary origin of REX1 for ERV regulation. Studies suggest that murine REX1 may act in epigenetic regulation of gene expression and ERVs, but the precise mechanism remains unelucidated, so we generated FLAG-tagged REX1 pluripotent stem cell (PSC) lines, as well as a series of truncation mutants to explore the REX1 function. Our studies indicate the presence of previously undescribed isoforms of the full-length REX1 protein, suggesting that regulation by REX1 may be more complex than initially appreciated. We hypothesize that REX1 regulates the expression of a sub-set of ERVs and REX1 isoforms regulate REX1 target genes in pluripotent stem cells. Previously, we performed REX1 ChIP-seq and found enrichment for REX1 binding at specific ERVs. Here, we show that differential expression of REX1 isoforms do not change the expression of ERVs. Furthermore, our REX1 KO lines show changes in expression of ERV family members and together with the ChIP data, suggest that REX1 may act as a negative regulator of some retroviral elements. However, further experiments reveal a potential compensation of REX1 KO, possibly by the homologous factors YY1 and YY2. Due to the limited nature and time constrain of our study, we did not find conclusive evidence to further elucidate the potential compensation mechanism and the characteristics of the REX1 isoforms. Our work provided a new avenue for exploring the functional importance of REX1 isoforms and the potential, YY1 and YY2 independent, regulatory role REX1.

Chapter 2: Mitotic bookmarking describes a potential mechanism involved in the stable propagation of cellular identity through the cell cycles. Candidate based studies have identified mitotic bookmarking factors (MBFs) that are retained on the mitotic chromatin and preserve the transcriptional memory of the cell. Nevertheless, there is a poor understanding of which proteins can serve as MBFs, as well as the chromatin dynamics of bookmarked sites during mitosis and the start of G1 phase. Previously, we designed a chromatin immunoprecipitation followed by mass spectrometry (ChIP-MS) assay to develop a global unbiased approach for identifying and characterizing novel MBFs. Using ChIP-MS, we identifed putative MBFs associated with the mitotic chromatin in pluripotent stem cells (PSCs) and used ATAC-seq to identify subsets of pluripotency-associated accessible gene regions that appear to be bookmarked by a variety of transcription factors, including PARP1, PSIP1, and HDGF. Here, we characterize the interaction of a putative MBF, not found in our ChIP-MS screen, NFYa, with PARP1 and, inconclusively, another putative MBF, DNMT1. Furthermore, we found that PWWP containing putative MBF, HDGF, has a potential role in pluripotency maintenance but it is not mitosis-specific. Due to the limited nature and time constrain of our study, we did not find conclusive evidence to establish the role of PSIP1 in PSC mitotic bookmarking. Our work provided a new avenue for exploring the functional importance of mitotic bookmarks in pluripotent maintenance.

abstract: Thesis

abstract: Master of Science (MSc)


title: Adjoint-Based Optimization of Switched Reluctance Motors

contributor:
Bakr, Mohamed
Emadi, Ali
Electrical and Computer Engineering

subject:
Adjoint variable method
Geometry optimization
Sensitivity analysis
Switched reluctance motors
Topology optimization

abstract:
High-accuracy electromagnetic design and analysis of electric machines is enhanced by the use of various numerical methods. These methods solve Maxwell’s equations to determine the distribution of the electric and magnetic fields throughout the considered machine structure. Due to the complicated architectures of the machines and the nonlinearity of the utilized magnetic materials, it is a very challenging task to obtain an analytical solution and, in most cases, only a numerical solution is possible.
The finite element method (FEM) is one of the standard numerical methods for electromagnetic field analysis. The considered machine domain is divided into finite elements to which the field equations are applied. FEM solvers are utilized to develop optimization procedures to assist in achieving a design that meets the required specifications without violating the design constraints. The design process of electric machines involves adjusting the machine parameters. This is usually done through experience, intuition, and heuristic approaches using FEM software which gives results for various parameter changes.  There is no guarantee that the achieved design is the optimal one.
An alternative approach to the design of electric machines exploits robust gradient-based optimization algorithms that are guaranteed to converge to a locally-optimal model.
The gradient-based approaches utilize the sensitivities of the performance characteristics with respect to the design parameters. These sensitivities are classically calculated using finite difference approximations which require repeated simulations with perturbed parameter values. The cost of evaluating these sensitivities can be significant for a slow finite element simulation or when the number of parameters is large. The adjoint variable method (AVM) offers an alternative approach for efficiently estimating response sensitivities. Using at most one extra not-iterative simulation, the sensitivities of the response to all parameters are estimated.
Here, a MATLAB tool has been developed to automate the design process of switched reluctance motors (SRMs). The tool extracts the mesh data of an initial motor model from a commercial FEM software, JMAG. It then solves for magnetic vector potential throughout the considered SRM domain using FEM taking into consideration the nonlinearity of the magnetic material and the motor dynamic performance. The tool calculates various electromagnetic quantities such as electromagnetic torque, torque ripple, phase flux linkage, x and y components of flux density, air-region stored magnetic energy, phase voltage, and phase dynamic currents.
The tool uses a structural mapping technique to parametrize various design parameters of SRMs. These parameters are back iron thickness, teeth height, pole arc angle, and pole taper angle of both stator and rotor. Moreover, it calculates the sensitivities of various electromagnetic quantities with respect to all these geometric design parameters in addition to the number of turn per phase using the AVM method.
The tool applies interior point optimization algorithm to simultaneously optimize the motor geometry, number of turns per phase, and the drive-circuit control parameters (reference current, and turn-on and turn-off angles) to increase the motor average dynamic torque. It also applies the ON/OFF topology optimization algorithm to optimize the geometries of the stator teeth for proper distribution of the magnetic material to reduce the RMS torque ripple.
A 6/14 SRM has been automatically designed using the developed MATLAB tool to achieve the same performance specifications as 6110E Evergreen surface-mounted PM brushless DC motor which is commercially available for an HVAC system.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)