title: Effects of Transcatheter Intervention on Hemodynamics of Coarctation of the Aorta

contributor:
Keshavarz Motamed, Zahra
Mechanical Engineering

subject: Coarctation of the Aorta, LES Model, CFD Simulation

abstract:
Coarctation of the aorta (CoA) is a congenital heart disease in which the aorta witnesses localized obstruction. CoA can be fatal if left untreated. Endovascular stenting
of CoA is an attractive treatment of choice in adolescents and adults; however, it can
be associated with problems like stent malapposition and inappropriate stent expansion. The main objective of this study is to investigate the effects of stent implantation
on the hemodynamic factors in a patient with mild coarctation.
Computational fluid dynamics was utilized to illustrate the hemodynamic factors
like velocity distribution, wall shear stress, and trans-coarctation pressure drop in
pre- and post-intervention states. These factors were used to assess the success of
stent deployment in this patient. Large Eddy Simulation (LES) model is employed in
this work to provide detailed information on hemodynamics in patient-specific preand post-intervention geometries of the aorta. The results of an in-house lumped
parameter code, in which its input parameters are obtained from patient-specific
clinical data, were applied as the boundary conditions in this study.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Predictors and Outcomes in Patients with Opioid Use Disorder

contributor:
Samaan, Zainab
Medical Sciences

subject:
opioid use disorder
medication assisted treatment
patient important outcomes
systematic review

abstract:
Background
Opioid use has become a huge public health crisis and opioids are now one of the leading causes of deaths related to drugs worldwide. Identifying differences in predictors and treatment outcomes for people with opioid use disorder (OUD) that were introduced by prescription versus other means is important. It is also vital to understand what the goals are and needs that patients want to achieve out of OUD treatment.
Methods
We used systematic review methodology to first examine any adverse outcomes that may be associated with prescribing opioids for acute low back pain. We also conducted a systematic review and meta-analysis examining what are the differences in patients with OUD that were initially introduced to opioids by prescription in comparison to those introduced by recreational means. We then conducted an observational study using data obtained from the GENetics of Opioid Addiction (GENOA) research collaborative. We examined treatment outcome differences between individuals introduced to opioids through a licit prescription and those introduced through illicit means. We conducted a mixed-methods study asking what the desired goals of patients with OUD from the Pharmacogenetics of Opioid Substitution Treatment (POST) project are. Using data from POST, we also examined the treatment outcome differences between those that were receiving methadone treatment in comparison to those that were on buprenorphine. Results
The systematic review examining adverse outcomes of prescribing opioids for acute low back pain found that prescribing opioids for ALBP was significantly associated with long-term continued opioid use (1.57, 95% CI 1.06,2.33). The second systematic review found that those who were introduced to opioids through a legitimate prescription were significantly less likely to have illicit opioid use (0.70, 95% CI 0.50, 0.99) while in treatment. Our results from GENOA also showed that those introduced to opioids by prescription were more likely to have chronic pain, an older age of onset of opioid use, less likely to have hepatitis C and use cannabis. When we asked patients what goals they desired out of treatment, we found that the most frequently reported patient important outcomes were to stop treatment (39%) and avoid all drugs (25%). When comparing OUD patients by treatment we discovered that those receiving buprenorphine were less likely to consume illicit opioids and amphetamines but more likely to have used alcohol in comparison to those on methadone.
Conclusion
With this knowledge, we can recognize unique risk factors for each patient and provide more tailored treatment that can incorporate this into clinical practice to address specific concerns in various cohorts of OUD patients. Additionally, the variation in the selection of outcomes demand the need for further research to establish a set of outcomes that considers patients’ goals and preferences for OUD treatment.

abstract: Thesis

abstract: Candidate in Philosophy


title: Developing signal enhancement strategies for photoelectrochemical nucleic acid sensing

contributor:
Soleymani, Leyla
Biomedical Engineering

subject:
Photoelectrochemistry
Electrochemistry
Biosensor
Point-of-Care
DNA detection
Differential Signal

abstract:
Recently, photoelectrochemical (PEC) signal transduction, with optical excitation and electronic readout, has been identified as a powerful transduction strategy for bioanalysis due to its high sensitivity and low limit-of-detection. Semiconductive materials have been used as the building blocks of PEC transducers, while plasmonic nanoparticles (NPs) are frequently used as signal amplifiers in these biosensors. Though these approaches have been previously used in PEC biosensing, the interaction between plasmonic and semiconductors NPs linked together through biomolecules are not currently well-understood. Herein, we developed new strategies for preparing photoelectrodes using solution-based methods to enhance the photocurrent of PEC transducers. These transducers were then used to investigate the interaction mechanisms between plasmonic NPs and the photoelectrodes with the goal of enhancing the limit-of-detection of PEC biosensors.
In order to create photoelectrodes that were fabricated using facile benchtop methods designed to enhance the photocurrent of PEC transducers, wrinkled scaffolds were used to fabricate photoelectrodes that show an order of magnitude enhancement in photocurrent compared to the planar electrodes. These electrodes were further used in label-free signal-off DNA biosensing without any amplification steps. Limit-of-detection of 200 times lower were reported using these wrinkled photoelectrodes, than planar electrodes.
Gold (Au) and TiO2¬ NPs were used as model materials to investigate the interaction between plasmonic and semiconductor NPs on a photoelectrode. The modulation of photocurrent was examined by varying the concentration of Au NPs and under different optical excitation wavelengths. UV light excitation provided larger photocurrent enhancement – at low concentration of Au NP – than visible light excitation. Furthermore, anodic photocurrent generation efficiencies by the photoelectrodes, which were prepared by using only Au NPs, were compared between interband and intraband excitation. The Au NP photoelectrodes demonstrated higher anodic photocurrent at interband excitation than intraband excitation and were further optimized by varying the size and deposition time of the Au NPs. Following this, Au NP- labeled DNA was used to study the effect of the distance between Au NPs and TiO2 NPs on the magnitude of the measured photocurrent. When Au NPs were in proximity with TiO2, they increased the generated photocurrent; however, they reduced the measured photocurrent when they were positioned further away from TiO2 NPs. Utilizing this switching behavior of PEC signals, a differential signal generation strategy was adopted to achieve a biosensor with enhanced sensitivity and signal-to-noise ratio.
Ultimately, we designed a PEC signal transduction strategy to detect nucleic acids without target labeling. In this assay, Au NP-labeled DNA was used as a signal-amplification-barcode that was introduced to the assay following target binding. This label-free PEC biosensor showed a low limit-of-detection (3 fM), broad (1 fM – 100 pM) linear range, and capability to detect single and double base-mismatched sequences of DNA. Thus, this work presents materials and signal transduction innovations that enhance the performance metrics of biosensors.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Detection and quantification of biomolecules is of utmost importance in early diagnosis, disease monitoring, prognosis, and disease management. In the past few decades, enormous efforts have been put towards utilizing photoelectrochemical (PEC) processes for biomolecular detection due to their high sensitivity. Gold nanoparticles are frequently being used to amplify the signal in the PEC bio-detection assay due to their plasmonic properties. However, the exact nature of the interaction between gold nanoparticles and the electrode material has not been determined. In this thesis, we investigated the interaction of gold nanoparticles with photoelectrode materials when they are separated by nucleic-acid sequences. Excitation energy and nucleic-acid length were varied to modulate the PEC current. The improved understanding of this interaction was further utilized to achieve a programmable response of nucleotide sensor from the photoelectrodes upon detecting the analyte of interest. We further developed different types of biosensing assay designs and examined their performance in terms of limit-of-detection, sensitivity, and specificity. Finally, we developed a new class of biosensor for detecting nucleic acids in bodily fluid and assessed the assay by using both electrochemical and PEC signal readout.


title: High Precision and Safe Hybrid Pneumatic-Electric Actuated Manipulators

contributor:
Bone, Gary M.
Mechanical Engineering

subject:
Hybrid pneumatic electric actuator
Collaborative robots
Inherent safety
Position control
Pressure control
Impact safety
Force allocation
Actuator redundancy
Manipulator control
High precision control
Friction compensator
Payload estimation

abstract:
Robot arms require actuators that are powerful, precise and safe. The safety concern is amplified when these robots work closely with people in collaborative applications. This thesis investigates the design and implementation of hybrid pneumatic-electric actuators (HPEA) for use in robot arms, particularly those intended for collaborative applications. The initial focus was on improving the control of an existing single HPEA-driven rotary joint. The torque is produced by four pneumatic cylinders connected in parallel with a small DC motor. The DC motor is directly connected to the output shaft. A cascaded control system is designed that consists of an outer position control loop and an inner pressure control loop. The pressure controller is based on a novel inverse valve model. High precision position tracking control is achieved due to the combination of the model-based pressure controller, model-based position controller, adaptive friction compensator and offline payload estimator. Experiments are performed with the actuator prototype rotating a link and payload with a rotational inertia equivalent to a linear actuator moving a 573 kg mass. Averaged over five tests, a root-mean-square error of 0.024° and a steady-state error (SSE) of 0.0045° are achieved for a fast multi-cycloidal trajectory. This SSE is almost ten times smaller than the best value reported for previous HPEAs. An offline payload estimation algorithm is used to improve the control system’s robustness. The superior safety of the HPEA is shown by modeling and simulating a constrained robot-head impact, and comparing the result with equivalent electric and pneumatic actuators. This research produced two journal papers.
Since HPEAs are redundant actuators that combine the large force, low bandwidth characteristics of pneumatic actuators with the large bandwidth, small force characteristics of electric actuators, the effect of using optimization-based input allocation for HPEAs was studied. The goal was to improve the HPEA’s performance by distributing the required input (force or torque) between the redundant actuators in accordance with each actuator’s advantages and limitations. Three novel model-predictive control (MPC) approaches are designed to solve the position tracking and input allocation problems using convex optimization. The approaches are simulated on a HPEA-driven system and compared to a conventional linear controller without active input allocation. The first MPC approach uses a model that includes the dynamics of the payload and pneumatics; and performs the motion control using a single loop. The latter methods simplify the MPC law by separating the position and pressure controllers. Although the linear controller is the most computationally efficient, it is inferior to the MPC-based controllers in position tracking and force allocation performance. The third MPC-based controller design demonstrated the best position tracking with root mean square errors of 46%, 20%, and 55% smaller than the other three approaches. It also demonstrated sufficient speed for real-time operation. This research produced one journal paper.
The research continued with the design and implementation of a two degree-of-freedom HPEA-driven arm. A HPEA-driven “elbow” joint is designed and added to the existing “shoulder” joint. The force from a single pneumatic cylinder is converted into torque using a 4-bar linkage. To eliminate backlash and keep the weight of the arm low, a 2nd smaller DC motor is directly connected to the joint. The kinematic and kinetic models of the new arm, as well as the geometry of the new elbow joint are studied. The resulting joint design is implemented, tested and controlled. This joint could achieve a SSE of 0.0045° in spite of its nonlinear joint geometry. The arm is experimentally tested for simultaneous tracking control of the two joints, and for end-effector position tracking in Cartesian space. The end-effector is able to follow a circular trajectory in pneumatic mode with position errors below 0.005 m.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Robots that work with, or near, humans require greater safety considerations than other robots. A significant concern is collisions between the robot and humans that may happen when sensors or software fails. An actuator for robots that combines the inherent safety of pneumatic actuators with the accuracy of electric actuators, termed a “hybrid pneumatic electric actuator” (HPEA), is investigated. The design, instrumentation, modelling, and control of HPEAs are studied theoretically and experimentally. The proposed actuator could achieve high position control accuracy in a variety of experiments, with steady state error of less than 0.0045 degrees. Simulated impacts with a human head also showed that a HPEA-driven robot arm can achieve a 52% lower impact force, compared to an arm driven by conventional electric actuators. The HPEA design and control experiments are performed on a single HPEA-driven joint and extended to an arm consisting of two HPEA-driven revolute joints.


title: Can We Predict the Magnitude and Direction of Epistasis from Individual Allelic Effects?

contributor:
Dworkin, Ian
Biology

subject: Epistasis

abstract: Linking allelic variants to variation for complex traits has been a major focus in modern genetics. However, the ability to assess and predict how genetic factors influence complex traits (including human disease) requires an understanding of the specific genes that influence a trait, but also a broader understanding of the genetic architecture of complex traits. Epistatic interactions are crucial when mapping genotypic to phenotypic effects, as mutations in two (or more) genes can produce a phenotype that differs substantially from the expectation of the sum of individual effects. Epistatic interactions are both common and vary considerably in magnitude. Yet little current research focuses on identifying and predicting when mutations will have epistatic interactions and the extent of such effects. I examined the extent of epistatic interactions as a function of individual allelic effects (magnitudes) and wild-type genetic background using the Drosophila melanogaster wing as a model system. The aim of this research is to demonstrate whether individual mutational effects are predictive of the magnitude and direction of epistatic interactions. My results indicate 1) relationships between the average mutant effect and the resulting epistasis and 2) the genetic background can have a strong influence on epistasis.

abstract: Thesis

abstract: Master of Science (MSc)


title: Investigating the Role of LAMP3 in HIV-1 Uptake and Transcytosis Across Vaginal Epithelial Cells

contributor:
Kaushic, Charu
Medical Sciences

subject: HIV-1

subject: Reproductive Health

abstract:
It is estimated that 38 million people currently live with HIV-1. Of the 38 million currently infected, 19.2 million women are infected compared to 17 million men, indicating a clear
disproportion. As such, understanding mechanisms that result in increased susceptibly in women is critical to develop more efficacious prevention strategies. The epithelial cells that line the lower female reproductive tract are the first line of defense against invading pathogens. The current consensus in the field is that HIV-1 can cross the mucosal epithelium in two ways: paracellular passage and transcytosis. There are several endocytic pathway associated proteins within vaginal epithelial cells that may have a role in viral transcytosis, however, little is known about their role. One of these is Lysosomal Associated Membrane Protein 3 (LAMP3), which has been shown to be upregulated following viral exposure and involved in viral trafficking. The mechanisms regarding the early events of transmission of HIV-1 across vaginal epithelial cells remains unclear and warrant further investigation. This study was designed to examine the mechanism of how HIV1 crosses vaginal epithelial cells and potential interactions of LAMP3 and HIV-1.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Role of Spatial Heterogeneity in Sexual Selection and the Evolution of Exaggerated Animal Weapons

subject:
Evolution
Sexual Selection
Animal Weaponry
Drosophila

abstract: Sexually selected male weaponry are among the most diverse and elaborate traits seen in the animal kingdom and often aid males in securing resources and mates, providing a fitness advantage to those that bear them. Yet, while intra-sexual competition between males to secure mates is common, weaponry is a rare trait that is observed in few taxa. Building upon previous theory, Emlen predicted that exaggerated animal weaponry evolves when, (i) there is intense competition between males for access to females, (ii) the biology or behaviour of a species generates high variance in male reproductive success, and (iii) competitions between males promote extreme weapon size evolution. While there are many species bearing weaponry that appear to fit these contexts, it has yet to be tested if these conditions are sufficient to initiate the evolution of exaggerated weaponry. For my research, I created three environmental treatments that emulated the three conditions proposed by Emlen. Using these treatments, I conducted experiments using Drosophila melanogaster to examine the effects of spatial structure on natural and sexual selection with a focus on the initial stages of the evolution of exaggerated trait weaponry that arise from this process. From these experiments, I found that the strength of sexual and other components of natural selection vary with environmental complexity and mutational effect. I also found that these environmental treatments generate weak differences in condition dependence and allometry of fly morphological traits that could be indicative of early weapon evolution. With these experiments, I provide the initial framework to test whether the conditions proposed by Emlen are both necessary and sufficient to lead to the initial evolution of exaggerated animal weaponry and demonstrate that these conditions may indeed create the circumstances that allows this evolution to occur.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Sexual selection drives the evolution of extreme animal weapons that are used in competition between individuals for access to mates, however while competition is common, these traits are rare. Theory predicts that animal weapons will evolve when (i) there is intense competition between males for mates, (ii) there is high variance in male reproductive success, and (iii) competitions between males mostly occur as duels. For my research, I created three environments that emulated these conditions to differing extents and used the fruitfly as a model to see how these conditions influence the initial stages of animal weapon evolution. I found that these environments are variable in their effects on sexual selection and create morphological differences that could indicate early weapon evolution. With this research, I provide the initial framework to test whether these conditions can create the circumstances for the initial evolution of exaggerated animal weaponry to occur.


title: Understanding Competence Committee Implementation and Decision-Making Practices in the Era of Competency-Based Medical Education

contributor:
Sonnadara, Ranil R.
Psychology

subject:
competence committees
clinical competency committees
competency-based medical education
health professions education
implementation
decision making
applied psychology

abstract:
Competence committees are groups of educators that monitor the progress of medical
trainees and decide when they should be promoted to the next stage of training. They
represent an important part of modern-day competency-based medical education
programs, yet relatively little is known about their implementation and decision-making
practices. This thesis seeks to fill a critical gap in the literature by generating empirical
evidence with respect to competence committee implementation and decision-making
practices across multiple programs. The first data chapter uses a multi-method approach
to examine competence committee implementation practices at a Canadian institution
over a three-year period. The second and third chapters examine how individuals and
groups make promotion decisions, respectively. These chapters also consider the role of
non-traditional data sources, such as anecdotal evidence, in competence committees’
decision-making processes. The final data chapter considers the role of social influences
and power and examines how factors such as members’ position on the committee,
gender, and race/ethnicity influence their contributions to the committee. This thesis
provides insight into some of the challenges that exist with respect to competence
committee implementation and offers potential solutions based on best practices across
multiple programs. It also highlights factors that can influence competence committee
decision making and discusses ways that their decision-making processes can be
optimized. Broader implications of this thesis, including the role of groups in solving
complex problems and the importance of diversity (both in terms of demographics and
functional specialization) in ensuring good decision-making outcomes, are also discussed.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Competence committees are groups of experienced health professionals and educators
whose job is to determine whether physician learners (i.e., residents) are ready to
progress to the next stage of training and responsibility. These committees are relatively
new, and as a result, we do not know very much about how they make decisions. Given
the importance of competence committees in ensuring that physicians are able to provide
high-quality and safe patient care, the purpose of this thesis was to examine competence
committee implementation and decision-making practices at a Canadian academic centre.
This took place in two parts. First, we studied competence committees over a three-year
period using surveys, interviews, and observations. This helped us understand some of
their benefits and challenges. Next, we conducted a series of experiments to understand
how competence committee members make decisions both individually and as part of a
group. These experiments also helped us understand how competence committees make
sense of different types of data, such as prior knowledge about a resident or their
assessors. Finally, we examined how various aspects of members’ social identities, such
as their position on the committee, their gender, and their race/ethnicity, influence their
contributions to the committee. Collectively, the findings of this thesis help to advance
the scientific literature in the areas of medical education and group decision making. They
can also be used to optimize competence committee operations, which can in turn
positively impact patients, healthcare, and society.


title: Design and Optimization of DSP Techniques for the Mitigation of Linear and Nonlinear Impairments in Fiber-Optic Communication Systems

title: DESIGN AND OPTIMIZATION OF DIGITAL SIGNAL PROCESSING TECHNIQUES FOR THE MITIGATION OF LINEAR AND NONLINEAR IMPAIRMENTS IN FIBER-OPTIC COMMUNICATION SYSTEMS

contributor:
Bakr, Mohamed H
Kumar, Shiva
Electrical and Computer Engineering

subject:
optical fiber
artificial neural network
nonlinear feed-forward equalizer
nonlinear Schrödinger equation
adjoint sensitivity analysis
adaptive digital backpropagation

abstract:
Optical fibers play a vital role in modern telecommunication systems and networks. An optical fiber link imposes some linear and nonlinear distortions on the propagating light-wave signal due to the inherent dispersive nature and nonlinear behavior of the fiber. These distortions impede the increasing demand for higher data rate transmission over longer distances. Developing efficient and computationally non-expensive digital signal processing (DSP) techniques to effectively compensate for the fiber impairments is therefore essential and of preeminent importance. This thesis proposes two DSP-based approaches for mitigating the induced distortions in short-reach and long-haul fiber-optic communication systems.

The first approach introduces a powerful digital nonlinear feed-forward equalizer (NFFE), exploiting multilayer artificial neural network (ANN). The proposed ANN-NFFE mitigates nonlinear impairments of short-haul optical fiber communication systems, arising due to the nonlinearity introduced by direct photo-detection. In a direct detection system, the detection process is nonlinear due to the fact that the photo-current is proportional to the absolute square of the electric field intensity. The proposed equalizer provides the most efficient computational cost with high equalization performance. Its performance is comparable to the benchmark compensation performance achieved by maximum-likelihood sequence estimator. The equalizer trains an ANN to act as a nonlinear filter whose impulse response removes the intersymbol interference (ISI) distortions of the optical channel. Owing to the proposed extensive training of the equalizer, it achieves the ultimate performance limit of any feed-forward equalizer. The performance and efficiency of the equalizer are investigated by applying it to various practical short-reach fiber-optic transmission system scenarios. These scenarios are extracted from practical metro/media access networks and data center applications. The obtained results show that the ANN-NFFE compensates for the received BER degradation and significantly increases the tolerance to the chromatic dispersion distortion.

The second approach is devoted for blindly combating impairments of long-haul fiber-optic systems and networks. A novel adjoint sensitivity analysis (ASA) approach for the nonlinear Schrödinger equation (NLSE) is proposed. The NLSE describes the light-wave propagation in optical fiber communication systems. The proposed ASA approach significantly accelerates the sensitivity calculations in any fiber-optic design problem. Using only one extra adjoint system simulation, all the sensitivities of a general objective function with respect to all fiber design parameters are estimated. We provide a full description of the solution to the derived adjoint problem. The accuracy and efficiency of our proposed algorithm are investigated through a comparison with the accurate but computationally expensive central finite-differences (CFD) approach. Numerical simulation results show that the proposed ASA algorithm has the same accuracy as the CFD approach but with a much lower computational cost.

Moreover, we propose an efficient, robust, and accelerated adaptive digital back propagation (A-DBP) method based on adjoint optimization technique. Provided that the total transmission distance is known, the proposed A-DBP algorithm blindly compensates for the linear and nonlinear distortions of point-to-point long-reach optical fiber transmission systems or multi-point optical fiber transmission networks, without knowing the launch power and channel parameters. The NLSE-based ASA approach is extended for the sensitivity analysis of general multi-span DBP model. A modified split-step Fourier scheme method is introduced to solve the adjoint problem, and a complete analysis of its computational complexity is studied. An adjoint-based optimization (ABO) technique is introduced to significantly accelerate the parameters extraction of the A-DBP. The ABO algorithm utilizes a sequential quadratic programming (SQP) technique coupled with the extended ASA algorithm to rapidly solve the A-DBP training problem and optimize the design parameters using minimum overhead of extra system simulations. Regardless of the number of A-DBP design parameters, the derivatives of the training objective function with respect to all parameters are estimated using only one extra adjoint system simulation per optimization iterate.  This is contrasted with the traditional finite-difference (FD)-based optimization methods whose sensitivity analysis calculations cost per iterate scales linearly with the number of parameters.

The robustness, performance, and efficiency of the proposed A-DBP algorithm are demonstrated through applying it to mitigate the distortions of a 4-span optical fiber communication system scenario. Our results show that the proposed A-DBP achieves the optimal compensation performance obtained using an ideal fine-mesh DBP scheme utilizing the correct channel parameters.  Compared to A-DBPs trained using SQP algorithms based on forward, backward, and central FD approaches, the proposed ABO algorithm trains the A-DBP with 2.02 times faster than the backward/forward FD-based optimizers, and with 3.63 times faster than the more accurate CFD-based optimizer. The achieved gain further increases as the number of design parameters increases. A coarse-mesh A-DBP with less number of spans is also adopted to significantly reduce the computational complexity, achieving compensation performance higher than that obtained using the coarse-mesh DBP with full number of spans.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This thesis proposes two powerful and computationally efficient digital signal processing (DSP)-based techniques, namely, artificial neural network nonlinear feed forward equalizer (ANN-NFFE) and adaptive digital back propagation (A-DBP) equalizer, for mitigating the induced distortions in short-reach and long-haul fiber-optic communication systems, respectively. The ANN-NFFE combats nonlinear impairments of direct-detected short-haul optical fiber communication systems, achieving compensation performance comparable to the benchmark performance obtained using maximum-likelihood sequence estimator with much lower computational cost. A novel adjoint sensitivity analysis (ASA) approach is proposed to significantly accelerate sensitivity analyses of fiber-optic design problems. The A-DBP exploits a gradient-based optimization method coupled with the ASA algorithm to blindly compensate for the distortions of coherent-detected fiber-optic communication systems and networks, utilizing the minimum possible overhead of performed system simulations. The robustness and efficiency of the proposed equalizers are demonstrated using numerical simulations of varied examples extracted from practical optical fiber communication systems scenarios.


title: Improving the Tool Performance by Using Soft Coatings During Machining of Inconel 718

contributor:
Veldhuis, Stephen. C
Mechanical Engineering

subject:
Difficult-to-cut materials
Inconel 718
Soft coating

abstract:
Increasing tool life is a significant objective in production. Achieving this objective in a machining process poses a significant challenge, especially during cutting hard-to-cut materials such as superalloys, due to the severe tool chipping/failure at the beginning of the cut. Although numerous attempts have been carried out to improve tool performance and prolong tool life during the machining of difficult-to-cut materials over the past several years, researchers have not obtained sufficient control over sudden tool failure/chipping. The focus of this study is to prolong tool life and control tool chipping by developing an ultra-soft deposited layer on the cutting tool that can protect it during the machining of difficult-to-cut materials such as Inconel 718. In the current study, an ultra-soft layer of material is deposited on the tool through two different techniques; a typical physical vapor deposition (PVD) technique and a novel developed method called “pre-machining”. In the PVD method, the soft layer is deposited under a high vacuum environment using a PVD coater. In the novel pre-machining method, the soft layer is deposited through a very short machining process involving Al-Si. It should be mentioned that soft coatings have never been used before for machining applications of difficult-to-cut materials including Inconel 718.
This study shows that in contrast to what is expected, depositing an ultra-soft layer on the cutting tool significantly improves tool performance, by reducing chipping, and improving the machined surface integrity during cutting of Inconel 718. The obtained results show up to a 500% ± 10% improvement in tool life and around a 150% ± 10% reduction in cutting forces. Significant reductions in work hardening, residual stress, and surface roughness on the machined surface were other main achievements of the current study.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Inconel 718 is considered to be a difficult-to-cut material due to its poor machinability. Significant tool failure at the early stage of cutting is the main challenge of machining this material and is the most significant contributing factor to its high manufacturing costs. Studies show that the common methods used to tackle this issue have not been completely successful. The goal of the present study is to tackle the machining challenges of Inconel 718 by developing tool coatings that meet the specific needs of the material to eliminate tool failure and thereby improve overall machining performance. For this purpose, a new tool coating material and a novel deposition technique that can be used as an alternative for commonly used coatings were developed in this study to improve the tool performance during the machining of Inconel 718. In addition, thorough studies have been carried out to gain a better understanding of the dominant wear phenomena and tool surface treatments that result in an improvement in the machinability of Inconel 718.


title: The Cult of Aphrodite Under the Ptolemies: The Consolidation and Legitimization of a Dynasty

contributor:
Corner, Sean
Classics

subject:
Aphrodite
Arsinoë
Berenice
Egypt
Hellenistic History
Isis
Ptolemy

abstract:
Aphrodite is one of the oldest deities of the Graeco-Roman pantheon, and her cult has a rich and varied history in its development throughout the Mediterranean and beyond. The goddess has been associated with numerous female deities from other cultures, including Astarte, Inanna, and Ishtar from the Near East; Hathor and Isis from Egypt; and Venus from Rome. The origins and development of the cult of Aphrodite have long been favoured topics in Classical scholarship, with notable works including Friedrich’s "The Meaning of Aphrodite" (1978) and Budin’s "The Origin of Aphrodite" (2003). The nature of syncretism between deities continues to be a popular topic of debate, and collections such as "Transformation of a Goddess: Ishtar-Astarte-Aphrodite" (2014) are produced from conferences and symposiums. Likewise, interest in the history of the Ptolemaic dynasty remains high; in particular, the field of numismatics eagerly anticipates the final release of Lorber’s "Coins of the Ptolemaic Empire" (2018 - ), which will replace the seminal work of Svoronos (1904) as the primary catalogue.
	Although it is common for works concerning the Ptolemaic dynasty to reference Aphrodite, detailed discussion of her cult often arises only in the context of Arsinoë II, with whom she was syncretized. This thesis aims to bring Aphrodite to the forefront, and produce a cohesive narrative which highlights the role of her cult in the development of the Ptolemaic dynasty. It surveys the presence of the goddess in Egypt to determine her nature and significance, before examining the manner in which her cult was manipulated to the benefit of the Ptolemaic dynasts, predominantly through syncretism to the queens Arsinoë II and Berenice II. The discussion of syncretism is extended to include Isis, whose increasing popularity is connected to the eventual decline of the cult of Aphrodite in Egypt.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: Following the death of Alexander the Great in 323 BCE, his empire was divided between his generals. Ptolemy I obtained control of Egypt, and established a dynasty that endured for over two centuries before falling to Rome. This thesis examines the foundation of the dynasty, and the manner in which Ptolemy I and his early successors secured their power. It focuses on Greek and Egyptian religion, and argues that the cult of Aphrodite was integral to the legitimization and consolidation of the dynasty. Discussion extends beyond Aphrodite to those with whom she was associated, including the Egyptian goddess Isis, and the Ptolemaic queens Arsinoë and Berenice. The aim of the thesis is to highlight the complexities of religious practice, and demonstrate the significance of Aphrodite and the sociopolitical impact of her cult in Egypt and throughout the Hellenistic world.


title: Characterizing the functional nature of nervous communication between gut and brain

contributor:
Kunze, Wolfgang
Biology

subject: vagus gut-brain

abstract: Vagal afferents in the gut are polymodal for a multitude of chemical mediators, including beneficial and noxious sensory stimuli, and therefore must encode sensory information for the brain about the luminal environment. This sensory information has profound influence on related reflex pathways, gut function, and mood and behaviour via the gut-brain axis. Using an established mesenteric nerve recording protocol, we investigated how vagal afferents from the small intestine signal and encode information about luminal stimuli and somatic age to the brain. We investigated the role of an intramural sensory synapse between intrinsic primary afferent neurons (IPANs) of the enteric nervous system (ENS) and extrinsic vagal afferents in the gut wall in the excitatory response to luminal application of the vagus-dependent selective serotonin reuptake inhibitor (SSRI) sertraline. Vagal afferent excitation by sertraline was inhibited by intramural sensory synaptic blockade, indicating a potential role of IPAN to vagal crosstalk in the vagal response to sertraline. We examined patterns of vagal afferent firing produced by stimuli with opposing effects on behaviour to determine how the vagus encodes information pertaining to antidepressant stimuli. A distinct temporal pattern code of antidepressant vagal afferent signaling was identified that was different from the pattern code produced by non- antidepressant stimuli. Lastly, we examined how vagal afferent signaling to the brain differed in aged mice and in an aged Parkinson’s disease (PD) model. There was a significant reduction in vagal afferent firing in old and PD model mice, but this reduction was partially reversed by treatment with the excitatory aminosterol squalamine. These studies demonstrate that vagal afferent firing is critical to the communication of sensory information from the gut lumen to the brain and that this information is encoded in specific patterns of firing that are influenced by the type of stimulus and the welfare of the signalling pathway.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: The vagus nerve connects the brain and gut enabling the transfer of bidirectional nervous signals, of which 80-90% transmit towards the brain. Some of these vagal signals that travel from the gut to the brain can modify behaviour or mood. We investigated a potential mechanism by which vagal afferents change firing in response to stimuli inside the gut to communicate mood-altering information to the brain and explored whether vagal signaling is vulnerable to aging. We presented evidence that the antidepressant sertraline increased vagal firing by synaptic signaling between neurons in the gut wall and vagal afferents. We demonstrated that antidepressant agents produced a specific pattern of action potential firing that might encode mood-altering information to the brain. Lastly, we found that aging and Parkinson’s disease decreased vagal afferent firing, but not insurmountably. This work identifies novel mechanisms by which intestinal vagal afferents signal the brain, which may have therapeutic applications.


title: Ancient environmental DNA as a means of understanding ecological restructuring during the Pleistocene-Holocene transition in Yukon, Canada

contributor:
Poinar, Hendrik Nicholas
Anthropology

subject:
Ancient DNA
Environmental DNA
Late Quaternary Extinctions
Pleistocene/Holocene Transition
Megafauna
Beringia
Archaeology
Palaeontology
Palaeoecology
Metagenomics
Palaeogenetics
Mitogenome
Environmental turnover
Human ecology
Anthropocene
Yukon
Woolly mammoth
Steppe bison
Yukon wild horse
Palaeoamerica
Palaeochip Arctic-1.0
Targeted capture enrichment
DNA extraction
Permafrost

abstract: Humans evolved in a world of giant creatures. Current evidence suggests that most ice age megafauna went extinct around the transition to our current Holocene epoch. The ecological reverberations associated with the loss of over 65% of Earth’s largest terrestrial animals transformed ecosystems and human lifeways forever thereafter. However, there is still substantial debate as to the cause of this mass extinction. Evidence variously supports climate change and anthropogenic factors as primary drivers in the restructuring of the terrestrial biosphere. Much of the ongoing debate is driven by the insufficient resolution accessible via macro-remains.  To help fill in the gaps in our understandings of the Pleistocene-Holocene transition, I utilized the growing power of sedimentary ancient DNA (sedaDNA) to reconstruct shifting signals of plants and animals in central Yukon. To date, sedaDNA has typically been analyzed by amplifying small, taxonomically informative regions. However, this approach is not ideally suited to the degraded characteristics of sedaDNA and ignores most of the potential data. Means of isolating sedaDNA have also suffered from the use of overly aggressive purification techniques resulting in substantial loss. To address these limitations, I first experimentally developed a novel means of releasing and isolating sedaDNA. Secondly, I developed a novel environmental bait-set designed to simultaneously capture DNA informative of macro-scale ecosystems. When combined, we identify a substantial improvement in the quantity and breadth of biomolecules recovered. These optimizations facilitated the unexpected discovery of horse and mammoth surviving thousands of years after their supposed extirpation. I followed up these results by extracting DNA from multiple permafrost cores where we confirm the late survival signal and identify a far more complex and high-resolution dataset beyond those identifiable by complementary methods. I was also able to reconstruct mitochondrial genomes from multiple megafauna simultaneously solely from sediment, demonstrating the information potential of sedaDNA.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: A new addition to the rapidly growing field of palaeogenetics is environmental DNA (eDNA) with its immense wealth of biomolecules preserved over millennia outside of biological tissues. Organisms are constantly shedding cells, and while most of this DNA is metabolized or otherwise degraded, some small fraction is preserved through sedimentary mineral-binding. I experimentally developed new ancient eDNA methods for recovery, isolation, and analysis to maximize our access to these biomolecules and demonstrate that this novel approach outperforms alternative protocols. Thereafter, I used these methods to extract DNA from ice age permafrost samples dating between 30,000–6,000 years before present. These data demonstrate the power of ancient eDNA for reconstructing ecosystem change through time, as well as identifying evidence for the Holocene survival of caballine horse and woolly mammoth in continental North America. This late persistence of Pleistocene fauna has implications for understanding the human ecological and climatological factors involved in the Late Pleistocene mass extinction event. This effort is paralleled with megafaunal mitogenomic assembly and phylogenetics solely from sediment. This thesis demonstrates that environmental DNA can significantly augment macro-scale buried records in palaeoecology.


title: Parallel Windowed Method for Scalar Multiplication in Elliptic Curve Cryptography

contributor:
Anand, Christopher
Kahl, Wolfram
Computing and Software

subject:
cryptography
parallel computing

abstract:
Commercial applications, including Blockchain, require large numbers of cryptographic
signing and verification operations, increasingly using Elliptic Curve Cryptography. This uses a
group operation (called point addition) in the set of points on an elliptic curve over a prime field. Scalar multiplication of the repeated addition of a fixed point, P , in the curve. Along with the infinity point, which serves as the identity of addition and the zero of scalar multiplication, this forms a vector space over the prime field. The scalar multiplication can be accelerated by decomposing the number of additions into nibbles or other digits, and using a pre-computed table of values P , 2P , 3P, . . . This is called a windowed method. To avoid side-channel attacks, implementations must ensure that the time and power used do not depend on the scalar. Avoiding conditional execution ensures constant-time and constant-power execution.
This thesis presents a theoretical reduction in latency for the windowed method by introducing parallelism. Using three cores can achieve an improvement of 42% in the latency versus a single-threaded computation.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Effects of Different Forest Management Practices on Mercury Contamination in Slimy Sculpin (Cottus cognatus)

contributor:
Kidd, Karen
Science

subject:
mercury
stream food web
forest management
stable isotopes
ecotoxicology

abstract: Forested catchments support an important ecological relationship between forests and streams. For example, forests filter nutrients and sediments from runoff and contribute terrestrial energy inputs (e.g. leaf litter) that support aquatic food webs. Consequently, disturbance from activities like forestry can affect the transport of matter into streams. A growing concern is the role of forestry in mobilizing mercury (Hg) from terrestrial sources into streams, which is poorly understood at catchment-sized scales. The objectives of my thesis were to evaluate the effect of forest management on spatial distributions of Hg in slimy sculpin (Cottus cognatus) within a catchment and between three catchments managed at different intensities in New Brunswick: minimally, extensively, and intensively harvested (NBR, NBE, and NBI, respectively). Alongside Hg analysis, stable isotopes of carbon, nitrogen, and hydrogen were measured to distinguish the relative contributions of terrestrial and aquatic energy to sculpin diet and trace the movement of Hg across trophic levels. During the fall of 2017, sculpin were sampled from five or six upstream to downstream reaches in each catchment. Where possible, 10 males and 10 females were selected for analyses (n = 287). Total Hg (THg) was measured in dried, homogenized whole body tissue (n = 258) using a Direct Mercury Analyzer, and δ13C, δ15N, and δ2H were measured in dried, homogenized muscle fillets (n = 245). Stable isotope ratios were used in Bayesian mixing models to predict the contribution of terrestrial and aquatic food sources to sculpin diet. Results showed that female sculpin in the minimally disturbed catchment had significantly lower THg levels compared to sculpin from NBE (p = 0.0141). The effect of stream order on THg concentration was significant in all three catchments (ANOVA, p < 0.01), but there were no clear spatial trends. Stable isotope results showed that variations in THg levels could be related to differences in diet, and results in one of the mixing models found that terrestrial inputs in the diet of sculpin in NBE and NBI decreased along the upstream-downstream gradient. Overall, results suggest that variations in THg between catchments could be due to differences in diet and this could be related to forest management. This study contributes to a better understanding of how forestry affects stream food webs and Hg contamination across catchment-sized scales.

abstract: Thesis

abstract: Bachelor of Science (BSc)


title: Cumulative Impacts of Forest Management on the Accumulation and Biomagnification of Mercury and its Relationship to Autochthony in Stream Food Webs in New Brunswick, Canada

contributor:
Kidd, Karen
Biology

subject:
Forest Management
Mercury
Biomagnification
Autochthony

abstract: Forests provide a multitude of ecological services and are one of Canada’s most important natural resources that support a profitable industry, especially in New Brunswick. The activities associated with harvesting and forest management have documented ecological impacts such as the increased mobilization of mercury from the land to adjacent streams. Methylated mercury bioaccumulates and biomagnifies (concentrates) through food webs and in headwater streams forestry has been shown to change its accumulation. However, not much is known about the spatial trends of mercury accumulation and biomagnification through stream food webs and how different forest management practices affect these trends. To delineate these patterns, food webs were sampled across a spatial gradient from three basins experiencing different levels of forest management intensity. At a basin scale, methylmercury concentrations were greatest in filtered water, food sources, and one invertebrate taxa in a harvested but less intensively managed basin, likely due to increased inorganic sediments and dissolved organic carbon also observed. Biomagnification was lower in this same basin, possibly from inefficient trophic transfer of methylmercury from food sources. Longitudinally this basin also showed differences in fine particulate organic matter (FPOM) and coarse particulate organic matter (CPOM) mercury compared to the other basins, likely due to similar spatial patterns in organic matter. In conclusion, mercury dynamics in stream food webs were impacted by forestry primarily in water and basal food sources at a basin scale, but spatial patterns were inconsistent.

abstract: Thesis

abstract: Master of Biological Science (MBioSci)

abstract: Forest harvesting is an essential and large part of Canada’s economy, and it is important to ensure that its impacts on freshwater systems are minimal. Forest management can increase the amount of the toxic metal mercury entering streams and this can have harmful effects in top predators, like fish, since mercury concentrates through food webs. The knowledge lacking is how different harvesting practices change the amount of mercury in these food webs and whether impacts increase as streams get larger. Of the three basins I studied, the one with harvesting but little assisted regeneration (moderately impacted) had the highest mercury levels in water, leaves, and algae. From upstream to downstream the leaves and biofilm from the moderately impacted basin accumulated less mercury compared to the least harvested basin. Additionally, mercury concentrated less through the food web of this basin. The changes in the moderately impacted basin may be caused by sediments and other materials that transport mercury into the stream and increase water and food levels, but this high mercury was not being transferred to the other organisms in the food web. In conclusion, forest management had some effects on mercury at the base of food webs at a large scale, but patterns through space were inconsistent.


title: Behavioural and Neuroimaging Investigation into the Experience of Moral Injury

contributor:
McKinnon, Margaret
Lanius, Ruth
Psychology

subject: moral injury;

subject: neuroimaging;

subject: shame;

subject: posttraumatic stress disorder (PTSD)

subject: viscerosensory;

subject: tonic immobility

subject: EmBODY tool

subject: Scale for Tonic Immobility Occurring Post-trauma (STOP);

subject: alexithymia

subject: bodily sensation maps;

abstract: Moral injury (MI) is associated with severe blame-related emotion and the development of psychopathology including posttraumatic stress disorder (PTSD). Little is known about how MI events are neurally processed when PTSD is comorbid, limiting the development of tailored interventions. Thus, this thesis sought to provide a novel, multi-method examination of the biological underpinnings of moral injury and relevant behavioural correlates. Study one provides the first investigation into the neural activation patterns elicited during MI event recall in military members and public safety personnel with PTSD, relative to MI-exposed civilian controls. In PTSD, emotional processing is challenged by heightened sensory information. Here, we provide evidence of heightened viscerosensory information processing (i.e. internal gnawing or gastrointestinal constriction related to blame-based emotion) during MI event recall, which appears to exert a strong influence over cortical regions facilitating moral cognitive processes including emotion regulation, autobiographical memory integration, and social cognition. Overwhelming visceral sensations can elicit defensive behaviour including tonic immobility (TI), a defensive response that facilitates viscerosensory dampening. Interestingly, more severe negative alterations in cognition and mood were associated with viscerosensory dampening in our PTSD group, pointing towards a compensatory pattern of emotional numbing. Studies two and three explore two posttraumatic symptoms consistent with emotional numbing: alexithymia and posttraumatic TI. In study two, we explore posttraumatic TI as a survival-based dissociative response and test a new measure of posttraumatic TI. In study three, we provide evidence that alexithymia is associated with an altered (muted) pattern of emotion-specific bodily sensation. This thesis provides a framework for embodied MI event processing in PTSD and highlights the importance of assessing the somatic experience of MI and screening for TI responses and emotional numbing as part of PTSD symptomatology. The evidence presented here suggests sensorimotor-based approaches and bottom-up regulatory strategies may be useful adjuncts to MI event processing.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Moral injury (MI) is a psychosocial-spiritual injury that can occur when deeply held values are violated either by oneself or a trusted other; it produces considerable pain and social alienation. MI has been linked to suicide and the development of posttraumatic stress disorder (PTSD), a mental health condition associated with distressing symptoms and reduced functioning in important areas of life, including social relationships. This thesis focuses on how MI events are processed by military members and public safety personnel, who are both at risk for MI and PTSD. We investigate how shame is experienced in the brain and body, and explore how intensified visceral sensations may become overwhelming (e.g., pit in stomach, vomiting) prompting emotional numbing or difficulties remaining embodied in the present moment (e.g., zoning out, freezing up). By understanding MI event processing when PTSD is present, we hope to gain insight into more effective treatments for these individuals.


title: Total Asymmetric Synthesis of Ring-A Derivatives of (+)-Trans-Dihydronarciclasine

contributor:
McNulty, Jim
Chemical Biology

subject: Amaryllidaceae, alkaloid, Sonogashira, organocatalytic, cycloaddition, alkyne-tag Raman imaging

abstract:
Significant attention from the medicinal and pharmaceutical communities has been pushed towards the design and development of natural products for defence against many forms of illnesses. The Amaryllidaceae plant family has shown their prevalence over time aiding towards our needs and becoming viable sources of alkaloids due to their wide variety of bioactivities presented. The low availability towards these often-complex structures with at times comprising up to six contiguous chiral centers have made practical testing scarce. More dominantly the isocarbostyrils are well recognized, being hydroxylated phenanthridones providing increased activities making them model targets to test and develop new synthetic strategies towards. These compounds represent a subset of the Amaryllidaceae alkaloids that lack a basic nitrogen center.
This thesis describes the total synthesis of four derivatives of the antiviral natural product (+)-trans-dihydronarciclasine from α-azidoacetone and m-anisaldehyde. Herein we demonstrate constructive routes towards ring-A modified, fully functionalized rings-B/C derivatives synthesized via asymmetric chemical syntheses providing further insight into SAR studies. This thesis expands on the organocatalytic [3+3]-cycloaddition sequence to produce aminocyclitol cores providing effective routes towards the development of five stereogenic centers in all targeted ring-C structures. Such studies were attributed to the enal adducts isolated from the Wittig reaction towards four natural product derivatives gaining knowledge related to the targeted molecules mode of action. One additional (+)-transdihydrolycoricidine analogue will be communicated, that enables the imaging while inside live cells with use of alkyne-tag Raman imaging.
Limitations of the alkaloids include the toxicity that accompanies these agents and the poor aqueous solubilities they provide, eliciting an increased need for new antiviral agents. The syntheses communicated provide effective routes towards unnatural alkaloids and can be pushed towards alternative chiral aminocyclitol targets for future studies. All
compounds have been sent away for screening including against coronavirus at Johns Hopkins.

abstract: Thesis

abstract: Bachelor of Science (BSc)

abstract:
This thesis is primarily driven towards the development of four antiviral lycorane structural type alkaloids, and an analogue synthesized via a copper-cocatalyzed Sonogashira reaction, utilizing a labile phenol-derived sulfonated hydroxyl group in its coupling towards an alkyne tagged structure. This method provides easy access for a variety of compounds without a fluorescent tag, taking steps forward in elucidating how the
Amaryllidaceae alkaloids are delivering their biological effects.
The densely substituted ring-C was obtained via an asymmetric organocatalytic [3+3] sequence for the assembly of the aminocyclitol core and is described. This sequence has provided effective regio, diastereo, and enantioselective access to five unnatural products. Preparation of the precursors were prepared using a Wittig methodology previous reported by the McNulty group that has been used in many syntheses for various
Amaryllidaceae alkaloids


title: Some Flexible Families of Mixture Cure Frailty Models and Associated Inference

contributor:
Balakrishnan, Narayanaswamy
Mathematics and Statistics

subject:
Survival analysis
PH
AFT
Mixture cure frailty model

abstract:
In survival analysis or time-to-event analysis, one of the primary goals of analysis is
to predict the occurrence of an event of interest for subjects within the study. Even
though survival analysis methods were originally developed and used in medical re-
search, those methods are also commonly used nowadays in other areas as well, such
as in predicting the default of a loan and in estimating of the failure of a system.
To include covariates in the analysis, the most widely used models are the propor-
tional hazard model developed by Cox (1972) and the accelerated failure time model
developed by Buckley and James (1979). The proportional hazard (PH) model as-
sumes subjects from different groups have their hazard functions proportionally, while
the accelerated failure time (AFT) model assumes the effect of covariates is to accel-
erate or decelerate the occurrence of event of interest.
In some survival analyses, not all subjects in the study will experience the event. Such
a group of individuals is referred to `cured' group. To analyze a data set with a cured
fraction, Boag (1948) and Berkson and Gage (1952) discussed a mixture cure model.
Since then, the cure model and associated inferential methods have been widely stud-
ied in the literature. It has also been recognized that subjects in the study are often
correlated within clusters or groups; for example, patients in a hospital would have
similar conditions and environment. For this reason, Vaupel et al. (1979) proposed a frailty model to model the correlation among subjects within clusters and conse-
quently the presence of heterogeneity in the data set. Hougaard (1989), McGilchrist
and Aisbett (1991), and Klein (1992) all subsequently developed parametric frailty
models. Balakrishnan and Peng (2006) proposed a Generalized Gamma frailty model,
which includes many common frailty models, and discussed model fitting and model
selection based on it.
To combine the key components and distinct features of the mixture cure model
and the frailty model, a mixture cure frailty model is discussed here for modelling
correlated survival data when not all the subjects under study would experience
the occurrence of the event of interest. Longini and Halloran (1996) and Price and
Manatunga (2001) developed several parametric survival models and employed the
Likelihood Ratio Test (LRT) to perform a model discrimination among cure, frailty
and mixture cure frailty models.
In this thesis, we first describe the components of a mixture cure frailty model, wherein
the flexibility of the frailty distributions and lifetime survival functions are discussed.
Both proportional hazard and accelerated failure time models are considered for the
distribution of lifetimes of susceptible (or non-cured) individuals. Correlated ran-
dom effect is modelled by using a Generalized Gamma frailty term, and an EM-like
algorithm is developed for the estimation of model parameters. Some Monte Carlo
simulation studies and real-life data sets are used to illustrate the models as well as
the associated inferential methods.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Antifouling Surface Modifications for Multiple Materials

contributor:
Fang, Qiyin
Biomedical Engineering

subject:
Surface Modification
Antifouling
Zwitterion
CBMA
SBMA

abstract:
Biomaterials used in biomedical implants, diagnostic devices, and in-situ sensors, all face the issue of biofouling. Surface modification of biomaterial surfaces with antifouling polymers can prevent non-specific adsorption of proteins and other bio-foulants onto these surfaces. Although there are many antifouling polymers to chose from, getting the polymers onto different materials is challenging as the surface modification process is dependent on the substrate’s surface chemistry. This limits the kinds of materials that are able to be modified, especially in devices made with several materials that must be modified as a single unit. Therefore, the goal of this research is to develop an effective antifouling surface modification that is compatible with different types and classes of biomaterials. A three-step modification approach was taken to form dense antifouling polymer brushes. The surfaces were first activated using oxygen plasma to increase the density of surface hydroxyl groups. Next, a silane coupling agent with an Atom Transfer Radical Polymerization (ATRP) initiator was attached to the activated surfaces. Finally, an antifouling zwitterionic monomer was polymerized on the surface using an aqueous controlled living radical polymerization technique, Surface Initiated - Activators Regenerated by Electron Transfer – Atom Transfer Radical Polymerization (SI-ARGET-ATRP). Two zwitterionic antifouling polymers, poly(carboxybetaine methacrylate) (pCBMA), and poly(sulfobetaine methacrylate)  (pSBMA) were investigated.
Clinically- and environmentally-relevant materials were studied and include poly(dimethylsiloxane) (PDMS), poly(ether ether ketone) (PEEK), titanium, silicon, and 3D printed stainless steel. Water contact angle (WCA) analysis showed that surfaces modified with zwitterionic polymers became more hydrophilic. WCA analysis may not be suitable for evaluating non-modified 3D printed surfaces due to their poor surface finish, and this material requires further surface topography characterization. Atomic force microscopy (AFM) and ellipsometry showed that the zwitterionic polymer layers did not necessarily have to be thick to produce their hydrophilic effect. AFM also revealed that each step of the surface modification process produced different roughness effects on all of the different surfaces. The zwitterionic layer with the smoother surface tended to better resist bovine serum albumin (BSA) adsorption. Radiolabelled BSA experiments showed reduced fouling on all 2D samples but to different degrees. The pCBMA modification was not successful in preventing BSA fouling on 3D printed 316L stainless steel. Full or partial BSA fouling may be due to the hydrolytic instability of the silane coupling agent, used to form covalent bonds between the antifouling polymers and the different surfaces, although further investigation is required to validate this hypothesis. Improving the long-term stability of silanes or research with other multi-surface compatible coupling agents that have better long-term stability in aqueous solutions should be pursued.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: New Transition State Optimization and Reaction Path Finding Algorithm with Reduced Internal Coordinates

contributor:
Ayers, Paul
Chemistry and Chemical Biology

subject:
Geometry Optimization
Reaction Modelling
Theoretical Chemistry
Reaction Path Finding

abstract:
Geometry optimization is a fundamental step in the numerical modelling of chemical reactions. Many thermodynamic and kinetic properties are closely related to the structure of the reactant, product, and the transition states connecting them. Different from the reaction and product, which are local minima on the potential energy surface, a transition state is the first-order saddle point with only one negative curvature. Over years, many methods have been devised to tackle the problem. Locating stable structures is relatively easy with a reliable algorithm and high accuracy. One can follow the gradient descent direction to pursuit the local minimum until convergence is reached. But for the transition state, the determination is more challenging as either the up-hill or down-hill direction is allowed in the process.

Motivated by the difficulty, many well-designed optimization algorithms are elaborated specifically to stress the problem. The performance of geometry optimization is affected by various aspects: the initial guess structure, the coordinate system representing the molecule, the accuracy of the initial Hessian matrix, the Hessian update schemes, and the step-size control of each iteration. In this thesis, we propose a new geometry optimization algorithm considering all the important components. More specifically, in Chapter 2, a new set of robust dihedral and redundant internal coordinates is introduced to effectively represent the molecular structures, as well as a computational efficient transformation method to generate a guess structure. In Chapter 3 and 5, a sophisticated robust algorithm is presented and tested to solve intricate transition state optimization problems. In Chapter 4, a new algorithm to exploring reaction pathways based on redundant internal coordinates is illustrated with real chemical reactions. Last but not least, in Chapter 6, a systematic test to explore the optimal methods in each procedure is presented. A well-performed combination of optimization methods is drawn for generic optimization purposes.

All the methods and algorithms introduced in this thesis is included in our forth-coming open-source Python package named GOpt. It's a general-purpose library that can work in conjunction with major quantum chemistry software including Gaussian. More features are under development and await to be released in the coming update.

abstract: Thesis

abstract: Doctor of Science  (PhD)


title: The Effects of Random and Rhythmic Lower Limb Force-Tracking on the Hemodynamic Response Function

contributor:
Nelson, Aimee J
Kinesiology

subject:
fNIRS
neuroimaging
force tracking

abstract:
Complexity-modulated tasks elicit differential hemodynamic activations in the primary
motor cortex for upper limb motor representations. However, much is yet to be learned regarding lower limb complexity modulation, as most fNIRS complexity modulation studies focus on the upper limb. It is currently unknown whether hemodynamic activations from single-joint lower limb motor tasks are detectable by fNIRS, and further, if fNIRS can detect differences between activations from simple and complex lower limb motor tasks. An fNIRS study was conducted to investigate the effects of an unpredictable, complex force-tracking task vs. a predictable, simple force-tracking task on hemodynamic activations in the TA motor representation. No significant TA motor cortex activations were found for 4/5 participants, with one participant showing a significant activation in one channel. Lack of activation in the TA motor representation was attributed to the depth of the area within the central sulcus. Significant hemodynamic activations were also found in areas assumed to overly STG/SII, and pre-SMA/SMA. These activations were attributed to sensory integration and motor learning, respectively. An fNIRS processing review was also conducted to inform processing decisions in the first experiment and to further fNIRS usage in our lab. Common techniques were identified as low-pass, band-pass, and high-pass filters, smoothing filters, wavelet filters, and the GLM. More appropriate alternative techniques were provided, including short-separation regression, pre-whitening, and spline interpolation with a Savitsky-Golay filter. Future studies may elucidate the lack of activity in the TA motor representation, and will further basic neuroscience regarding fNIRS.

abstract: Thesis

abstract: Master of Science in Kinesiology


title: Three Essays on Credit Risk Modeling

contributor:
Miu, Peter
Finance

subject: Credit Risk

abstract:
This thesis explores three important issues in credit risk modeling: the nonlinear credit risk stress testing models, the recovery term structure of point-in-time (PIT) loss given default (LGD), and the estimation of LGD by mixture beta regression model.

In the first essay of this thesis, we study the credit risk stress testing models. By incorporating the regime-switching and quantile regression techniques into credit risk stress testing models, we propose two new dynamic models that outperform the traditional linear regression model according to both the point estimate accuracy and the confidence interval breaches. This confirms the importance of nonlinear regression approaches in the estimation and the prediction of credit risk determinants. The proposed models perform especially well in capturing the extreme values on the tail of the estimated distribution of the credit risk measure. The proposed models could be used for both the International Financial Reporting Standard 9 (IFRS9) expected loss calculation and Basel’s Advanced Internal Rating-Based (AIRB) regulatory capital calculation purposes.

In the second essay, we examine and model the time-series pattern of recovery throughout the bankruptcy and workout process of a retail credit portfolio; whereas other researchers are concerned with predicting the overall recovery rates of debt instruments, we model the amounts a creditor can recover at different points in time subsequent to the default event. This is of practical interest to commercial banks in managing the risk of their default loan portfolios. Like managing performing loan portfolios, banks must assign loss provision and determine the capital requirement associated with non-performing (i.e., defaulted) loan portfolios. Given the fact that it usually takes two to three (up to five or more) years to complete the recovery process for a typical defaulted retail (corporate) loan, it is important to understand the time-varying risk characteristic of the defaulted portfolio as a function of its vintage in the recovery process. An accurate point-in-time (PIT) risk assessment enables financial institutions to manage their defaulted loan portfolios in a timely fashion.

In the third essay, we further extend our understanding of the distribution of LGD. For credit risk management purposes, the LGD of credit instruments is one of the key determinants in estimating capital requirements for financial institutions. To address the practical problems encountered in implementing LGD prediction model (e.g., in capturing the bimodal characteristic of the LGD distribution), we propose to develop a mixture beta regression LGD model. By using the maximum likelihood estimation and the method of moment approaches, the parameters of the mixture beta regression model can be estimated. Furthermore, we examine the impact of the systematic factors and model the time-series variation of the LGD distribution as a function of these systematic factors. Finally, through a number of empirical analyses, we demonstrate the superior performance of our proposed mixture beta models in comparison with the single-beta logit-linked model commonly considered in the literature.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Dynamic Probabilistic Risk Assessment of Nuclear Power Generation Stations

contributor:
El-Dakhakhni, Wael
Wiebe, Lydell
Civil Engineering

subject:
Nuclear Power Plant
Dynamic Probabilistic Risk Assessment
Text Mining
Latent Dirichlet Allocation
System dynamics
Thermal dynamic processes
Temporal Probability of Core Damage
Uncertainty Analysis
Machine learning
Artificial Neural Network

abstract: Risk assessment is essential for nuclear power plants (NPPs) due to the complex dynamic nature of such systems-of-systems, as well as the devastating impacts of nuclear accidents on the environment, public health, and economy. Lessons learned from the Fukushima nuclear accident demonstrated the importance of enhancing current risk assessment methodologies and developing efficient early warning decision support tools. Static probabilistic risk assessment (PRA) techniques (e.g., event and fault tree analysis) have been extensively adopted in nuclear applications to ensure NPPs comply with safety regulations. However, numerous studies have highlighted the limitations of static PRA methods such as the lack of considering the dynamic hardware/software/operator interactions inside the NPP and the timing/sequence of events. In response, several dynamic probabilistic risk assessment (DPRA) methodologies have been developed and continuously evolved over the past four decades to overcome the limitations of static PRA methods. DPRA presents a comprehensive approach to assess the risks associated with complex, dynamic systems. However, current DPRA approaches are faced with challenges associated with the intra/interdependence within/between different NPP complex systems and the massive amount of data that needs to be analyzed and rapidly acted upon. In response to these limitations of previous work, the main objective of this dissertation is to develop a physics-based DPRA platform and an intelligent data-driven prediction tool for NPP safety enhancement under normal and abnormal operating conditions. The results of this dissertation demonstrate that the developed DPRA platform is capable of simulating the dynamic interaction between different NPP systems and estimating the temporal probability of core damage under different transients with significant analysis advantages from both the computational time and data storage perspectives. The developed platform can also explicitly account for uncertainties associated with the NPP's physical parameters and operating conditions on the plant's response and probability of its core damage. Furthermore, an intelligent decision support tool, developed based on artificial neural networks (ANN), can significantly improve the safety of NPPs by providing the plant operators with fast and accurate predictions that are specific to such NPP. Such rapid prediction will minimize the need to resort to idealized physics-based simulators to predict the underlying complex physical interactions. Moving forward, the developed ANN model can be trained under plant operational data, plants operating experience database, and data from rare event simulations to consider for example plant ageing with time, operational transients, and rare events in predicting the plant behavior. Such intelligent tool can be key for NPP operators and managers to take rapid and reliable actions under abnormal conditions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Clinical trials for symptoms in patients receiving dialysis

contributor:
Walsh, Michael
Health Research Methodology

subject:
Symptoms
Dialysis
Run-in period
Clinical trial
Cannabinoids

abstract:
Symptoms in patients receiving dialysis are common and associated with impaired quality of life.
Symptoms are a top research priority because effective therapies are lacking and even with appropriate diagnosis and treatment, residual symptoms often persist. Clinical trials in the setting of kidney disease are challenging to conduct and as a result, nephrology lags behind other specialties regarding the degree to which clinical trials inform the care of patients with kidney disease, including those receiving dialysis. The studies in this thesis inform the design of randomized controlled trials with regards to run-in periods and the treatment of symptoms in patients with kidney disease. Chapter 2 describes a meta-epidemiologic study of the frequency, setting and purposes of run-in periods in parallel randomized controlled trials of self-administered medications for chronic diseases in adults. Chapter 3 is a study within a trial of an international randomized controlled trial that compares spironolactone to placebo for the prevention of cardiovascular morbidity and mortality in dialysis. It compares the ability
of a 3-week study visit in addition to a 7-week study visit during an active-run-in period to identify and exclude participants with non-adherence. Chapter 4 is a protocol for a randomized placebo controlled crossover trial of low fixed dose pharmacologic therapy for restless legs syndrome in hemodialysis that includes a placebo run-in period for adherence and tolerability. Chapter 5 is a survey of Canadian nephrologists regarding the use of cannabinoids for symptom management in patients with kidney disease and support for their use in clinical trials.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A Formal Approach to Secure the Segmentation and Configuration of Dynamic Networks

contributor:
Ridha, Khedri
Computing and Software

abstract:
Network segmentation and layered protection are critical strategies used in building and designing secure networks. Although they are recommended by security practitioners and agencies, they are defined vaguely and lack precise formal treatment. Implementing these strategies might be achievable for a small network with few resources; however, it is nearly an impossible task for a large network with a large number of resources and complex policies. The challenge is even harder for dynamic networks, where resources frequently join and leave the network. This case requires an adaptive approach for maintaining the implementation of these strategies.

In this thesis, we provide a formalism for the strategies of layered protection and network segmentation. The formalism is based on Product Family Algebra (PFA) and guarded commands. We use this formalism to assess whether a network satisfies these strategies. Furthermore, we articulate two implementation schemes for the layered protection strategy. Moreover, based on the introduced formalism, we propose two algorithms for structuring and configuring robust and secure networks. We then extend the formalism and the algorithms to handle networks with several entry points, where each entry point is intended to give access to a certain subnetwork.  We employ the algorithms for the dynamic configuration and governance of Software Defined Networks (SDN). In addition to SDN data and control planes, we propose a  plane in charge of the configuration and governance of SDN data planes.  We call it the Dynamic Configuration and Governance (DCG) plane and it is intended to give agility to dynamic networks. Moreover, we propose and assess three architectures that use the DCG plane. The assessment results identify an architecture that is suitable for dynamic networks and another for networks that are more stable regarding changes to policy and network topology.

The formalism presented in this thesis provides an automatic and adaptive approach for the segmentation and configuration of networks. It takes into consideration the security requirements of local resources as well as the global security situation.  It constitutes a foundational framework for automated security solutions applicable to computer networks that use any type of connecting technology or topology.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Towards a theory of adoption and design for clinical decision support systems

contributor:
Archer, Norm
Sartipi, Kamran
Business Administration

subject: clinical decision support systems

abstract:
Timely and appropriate clinical decisions can be lifesaving, and decision support systems could help facilitate this. However, user adoption of clinical decision support systems (CDSS) and their impact on patient care have been disappointing. Contemporary theories in information systems and several evaluation studies have failed to explain or predict the adoption of CDSS.

To find out why I  conducted a qualitative inquiry using the constructivist grounded theory method. Guided by the theory of planned behaviour, I designed a functional clinical decision support system called DermML. Then, I used it as a stimulus to elicit responses through semi-structured interviews with doctors, a community to which I also belong. Besides the interview data, I also collected demographic data from the participants and anonymous clickstream data from DermML.

I found that the clinical community is diverse, and their knowledge needs are varied yet predictable. Using theoretical sampling, constant comparison and iterative conceptualization, I scaled my findings to a substantive theory that explains the difference in practitioners' knowledge needs and predicts adoption based on CDSS type and use context. Having designed DermML myself, the data provided me with design insights that I have articulated as prescriptive design theory. I posit that GT can generate explanatory and predictive theories and prescriptive design theories to guide action.

This study eliminates the boundaries between the developers of CDSS, study participants, future users and knowledge mobilization partners. I hope the rich data I collected and the insights I derived help improve the adoption of CDSS and save lives.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Advanced optofluidic sensing and imaging technologies

title: Advanced optofluidic sensing and imaging devices for onsite monitoring

contributor:
Fang, qiyin
Biomedical Engineering

subject:
optofludics
imaging
sensing
water quality monitoring

abstract:
Water contaminations are currently threatening ecosystems and human health on a world-wide scale. Monitoring the water quality is one of the most essential steps to provide better understanding and mitigation of water contamination. Among the water quality monitoring techniques, optofluidic technologies have created a burgeoning number of novel devices designed to test water quality in an efficient and portable format. However, current optofluidic devices have yet to be successfully translated to onsite monitoring applications due to their high cost, high maintenance and dependence on delicate laboratory instruments or bulky instruments.
In this work, we developed two optofluidic platforms for onsite water quality monitoring: a fluorescence-based optofluidic platform for chemical analysis and an imaging-based optofluidic platform for microbe detection. Several technologies associated to optical sensing modules were developed to overcome the above challenges, making the optofluidic platforms compatible with onsite monitoring applications. First, excitation coupling mechanism and frequency domain time-resolved fluorescence (TRF) were developed on the fluorescence-based optofluidic platform to improve sensing sensitivity and stability, while reducing dependence on costly instruments. Their effectiveness was demonstrated by dissolved oxygen (DO) measurements and ray-tracing simulation. Second, a low-cost and portable imaging system with dual modalities were developed on the imaging-based optofluidic platform. Thus, both morphological features and fluorescent features can be observed for microbe detection without using bulky microscope setups. The effectiveness of dual-modality imaging was demonstrated by experimental results of phytoplankton analysis. Third, a fluorescence lifetime imaging (FLIM) approach was developed under a low-cost (Complementary metal–oxide–semiconductor) CMOS format. This approach enables integrating FLIM module in portable optofluidic platforms for onsite monitoring.
These advances bring optofluidic platforms closer to realizing the requirements of onsite water quality monitoring and provide a clear picture for future improvements and research directions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: EXAMINING THE EFFECTS OF ACUTE EXERCISE ON NATURAL KILLER CELLS IN CHILDREN WITH ACUTE LYMPHOBLASTIC LEUKEMIA

title: EFFECTS OF EXERCISE ON NATURAL KILLER CELLS IN CHILDREN WITH LEUKEMIA

contributor:
Obeid, Joyce
Medical Sciences

subject: Exercise, NK cells, acute lymphoblastic leukaemia

abstract:
Children treated for acute lymphoblastic leukemia (ALL) are immunodeficient and therefore at an increased risk of infection and cancer recurrence. Natural killer (NK) cells are a subset of lymphocytes that are very efficient at combatting infections and cancer; however, children treated for ALL have impaired NK cell number and function. Exercise has the potential to bolster NK cell number and function, at least in healthy children and adults. Limited evidence suggests exercise may also have beneficial effects on NK cells in children treated for cancer. However, these previous exercise immunology studies in children with cancer have yielded low sample sizes. Therefore, the aim of this study was to assess the: 1a) feasibility, 1b) acceptability and 1c) safety of performing an exercise intervention in children with ALL. The secondary objectives were to assess the 2a) effects of acute exercise on NK cell number, function and receptor expression in children receiving maintenance therapy for ALL compared to healthy children, as well as to 2b) assess how the NK response changes over 4 months of therapy, and to 2c) assess the link between physical activity and NK cell number and function at rest in children receiving maintenance therapy for ALL.
Children undergoing maintenance therapy for ALL (n=4) were recruited from McMaster Children’s Hospital, and healthy sex and pubertal-status matched children (n=4) were recruited from the Hamilton community. ALL patients completed a total of 3 exercise visits, occurring monthly after their regularly scheduled chemotherapy session. At each exercise visit, children were asked to complete 30 minutes of continuous biking, followed by 1 hour of rest. Blood samples were drawn at rest prior to exercise (PRE), immediately after exercise (POST) and 1 hour into recovery (REC). Healthy children only completed one exercise visit. During recovery, participants were asked to complete a physical activity enjoyment scale (PACES) questionnaire and a structured interview in order to assess exercise acceptability and to gauge participant feedback on study components, respectively. Participants were outfitted with an accelerometer to track physical activity levels between visits. Feasibility was assessed by tracking recruitment statistics, study completion rates and exercise completion rates. Acceptability of accelerometer wear was assessed by tracking accelerometer wear and log rates. Safety was assessed by tracking adverse events. All parameters were reported using descriptive statistics.
We approached 22 patients to participate, and 4 children completed the study (100% completion rate) out of a goal of 15. Primary deterrents to participation were that patients and families did not want to extend time spent at the hospital or had time restrictions and that patients were uncomfortable with blood collection methods. Exercise was feasible (94% exercise completion rate), acceptable (4.2 ± 0.38 out of 5 PACES score), and safe. Accelerometer wear rates (61.9% (range 3.7-100.0%)) and log completion rates (69.0% (25.9-100.0)) were moderate.  Exercise transiently increased NK cell number and function in healthy children and some children with ALL. There were no patterns in the change of the NK cell response to acute exercise over time. We were unable to assess the link between physical activity and NK cells due to a paucity of data. This study cautiously suggests that exercise is a feasible, acceptable and safe intervention that may increase NK cell number and function in children treated for ALL.

abstract: Thesis

abstract: Master of Science in Medical Sciences (MSMS)

abstract:
Children treated for leukemia have weak immune systems, making them more susceptible to developing infections and cancer recurrence. Natural killer cells are a special immune cell that is very effective at combatting cancer and infections; however, children treated for leukemia have very low amounts of natural killer cells and they do not function well. Exercise is a simple way to boost the immune system in healthy adults and children, by increasing the number and function of natural killer cells. We don’t know what effect exercise has on natural killer cells in children with leukemia. Previous studies looking at the effects of exercise on the immune system of children with cancer have not been able to recruit enough children to participate. Therefore, it is also important to investigate why children with cancer may not want to participate in exercise studies looking at immune function. The main goals of this thesis were to assess how likely we are to recruit enough children being treated for leukemia to participate in a study looking at how exercise changes natural killer cells, if our participants enjoyed being part of this study, and how safe exercise is for children being treated for leukemia. We also wanted to learn about how natural killer cells respond to exercise in children being treated for leukemia.
We found that most of the children and families that decided not to participate in our study felt they did not have time, and the second most common reason for not participating was because the children experienced anxiety surrounding blood draws for the study. The children that decided to participate in the study enjoyed the exercise and being in the study. We also found that the exercise was safe. Finally, we saw that exercise was able to increase natural killer cell numbers and function in some, but not all, children treated for leukemia. The results of this study suggest that exercise may be a realistic and safe way to improve immune function in some children with leukemia.


title: An Agent-Based Financial Network Modeling Based on Systematic Trust

contributor:
Grasselli, Matheus
Computational Engineering and Science

subject:
Economics
Financial Mathematics
Agent-Based Models
Systematic Banking
Financial Network Modeling
Financial Economics

abstract:
In this research project, we introduced an agent-based banking system based on systematic trust. The features of the model and attributes of the agents are defined and analyzed precisely, and the results are explained. Some of this model's features include but are not limited to considering the savings system, insurance deposits, the impact of the Central Bank loans, and correlated regional shocks in a banking system. Different Scenarios are applied. The results indicate that by having the Central Bank loans in the model, the banking system experience dramatically fewer failures. Even if some correlated regional shocks occur, the system can be more stable than when the Central Bank does not exist. Moreover, the trust system establishes and forms during different financial periods based on the bank's clients’ point of view about the bank's performance as an intelligent system to attract more capital for the system by providing some information for the agents to join the more prestigious banks.
Conclusively, in the early financial periods, banks need more financial supports to support the clients’ deposits and to make their reputation for attracting more clients; hence the Central Bank is an essential parameter to help the banks to be more stable and supports the banks in their early stages of growth. The Central Bank loans would be significantly important in panic times, such as regional correlated preference shocks.

abstract: Thesis

abstract: Master of Science (MSc)


title: Alone in a Crowd: Social Isolation, Place, and Connection in Later Life

contributor:
Dunn, James
Andrews, Gavin
Ploeg, Jenny
Health and Aging

subject:
gerontology
aging
social isolation
living alone

abstract: The problem of social isolation among older people has been thoroughly documented, studied, and addressed through both policy and social services, and yet persists as a major social issue. There exist several notable gaps within the scholarly literature on isolation, particularly with respect to the role(s) of place-based risk factors, the relationship(s) between exclusion and social isolation, and best practices for isolation interventions. This thesis addresses these knowledge gaps and presents both empirical and theoretical contributions resulting from a three-part investigation. These studies are presented in three distinct papers to constitute a sandwich dissertation. The first paper examines the role of neighbourhood characteristics in shaping social isolation among older people by analyzing the Canadian Longitudinal Study on Aging (CLSA) baseline data in a series of multiple regressions. Findings indicate that the selected neighbourhood characteristics account for only a small portion of the social outcome measures of interest but raise meaningful questions about the intersection of place and social connection that warrant further study. The second paper investigates both the harmful and protective aspects of places in shaping isolation risk through a qualitative study of older people informed by a place-based exclusion lens. Interview results highlight several aspects of places that contribute risk of isolation and are used to adapt the model of known isolation risk factors. The third and final paper analyzes a sample of friendly visiting programs by conducting a realist synthesis to determine how, for whom, and under what conditions friendly visiting programs are most successful. Results of the synthesis are used to build a friendly visiting program theory to be tested in future studies. Together these three papers contribute to both the applied and theoretical literature on social isolation, and can inform the development of future research, policy, and intervention strategies.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The research reported in this thesis focuses on social isolation among older people and is organized into three papers. The first paper looks at data from the Canadian Longitudinal Study on Aging to learn more about how aspects of neighbourhoods might lead older people to become isolated. The second paper reports the major themes from in- depth, qualitative interviews with 17 older people living in Hamilton, Ontario. The third and final paper analyzes a set of articles evaluating friendly visiting programs for isolation older people and uncovers some of the characteristics and features of successful programs. The results of these three studies provide important insights into the ways in which neighbourhoods impact the social lives of older people, and how individual risk of becoming isolation might be tied to places. Results also show that friendly visiting programs for isolated older people can be very successful if they have certain key features included in their design.