title: Essays on Skills and Labour Market Outcomes of Immigrants and the Canadian Born

contributor:
Sweetman, Arthur
Spencer, Byron
DeCicca, Philip
Mueller, Richard
Economics

abstract:
Inequalities in basic skills and labour market outcomes between immigrants (by admission category) and the Canadian-born, and the underrepresentation of women in the information and communication technology (ICT) sector, are examined using Statistics Canada’s 2012 Survey of Adult Skills, a product of the Organisation for Economic Cooperation and Development’s Programme for the International Assessment of Adult Competencies.
	Differences in basic ICT skills, and the rates of return to these skills in the Canadian labour market, between immigrants and Canadian non-immigrants, are the focus of the first chapter. Immigrants, especially men, are observed to be disproportionately employed in ICT industries and occupations. A measure of basic ICT skills is employed to document differences in skill levels and labour market earnings across immigration classes and categories of Canadians at birth. Adult immigrants, including those assessed by the points system, are found to have lower average ICT scores than Canadians at birth, although the rate of return to ICT skills is not statistically different between the two groups. Immigrants who arrived as children, and the Canadian-born children of immigrants, have similar outcomes to the children of Canadian-born parents.
	Chapter 2 explores differences in literacy and numeracy skills, and the economic returns to these skills, for immigrants to Canada in different admission classes and their Canadian-born counterparts. First, respondents are grouped into three broad categories – adult and young immigrants, and the Canadian-born. Then, these individuals are classified into nine population subgroups: adult economic immigrants, adult refugees, adult family reunification, other adult immigrants, adult temporary residents, young refugees, young non-refugee immigrants, and second- and third-generation Canadian-born individuals. The analysis suggests that both adult and young immigrants (those who arrived in Canada at age 13 or younger) do not perform as well on literacy and numeracy tests conducted in English or French as those born in Canada, although young immigrants have higher test scores than adult immigrants. Similar results are found for wages. Among immigrants, it is observed that economic immigrants tend to have the highest test scores and hourly wages, with refugees having the lowest. The wage returns to these basic skills are economically significant at the 25th, 50th, and 75th quantiles of log hourly wages and the Canadian labour market rewards immigrants and the Canadian-born equally for their literacy and numeracy skills.
	Chapter 3 explores why the proportion of women in Canada’s ICT sector is well below their percentages in other science, technology, engineering, and mathematics (STEM) fields. A measure of basic ICT skills is used to study the skills gap and differences in returns to these skills between men and women. After controlling for appropriate covariates, Canadian women on average score higher than their male counterparts in basic ICT skills. However, women with the same ICT test scores are less likely than men to be employed in ICT occupations. Hourly wages in ICT occupations are lower for women, but the earnings gap in these occupations is not higher than those in the general labour market. Given the current and projected shortages of ICT professionals, women represent a large, yet untapped, pool of talent for this sector.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Representation of Tones and Vowels in a Biophysically Detailed Model of Ventral Cochlear Nucleus

contributor:
Bruce, Ian C.
Electrical and Computer Engineering

subject: Biophysically detailed neural network models, ventral cochlear nucleus, computational neuroscience

abstract:
Biophysically detailed representations of neural network models provide substantial insight to underlying neural processing mechanisms in the  auditory systems of the brain. For simple biological systems the behavior can be represented by simple equations or flow charts. But for complex systems, more detailed descriptions of individual neurons and their synaptic connectivity are typically required. Creating extensive network models allows us to test hypotheses, apply specific manipulations that cannot be done experimentally and provide supporting evidence for experimental results. Several studies have been made on establishing realistic models of the cochlear nucleus (Manis and Campagnola, 2018; Eager et al., 2004), the part of the brainstem where sound signals enter the brain, both on individual neuron and networked structure levels. These models are based on both in vitro and in vivo physiological data, and they successfully demonstrate certain aspects of the neural processing of sound signals. Even though these models have been tested with tone bursts and isolated phonemes, the representation of speech in the cochlear nucleus and how it may support robust speech intelligibility remains to be explored with these detailed biophysical models.

In this study, the basis of creating a biophysically detailed model of microcircuits in the cochlear nucleus is formed following the approach of Manis and Campagnola
(2018). The focus of this thesis is more on bushy cell microcircuits. We have updated Manis and Campagnola (2018) model to take inputs from the new phenomenological auditory periphery model of Bruce et al. (2018). Different cell types in the cochlear nucleus are modelled by detailed cell models of Rothman and Manis (2003c) and updated Manis and Campagnola (2018) cell models. Networked structures are built out of them according to published anatomical and physiological data. The outputs of these networked structures are used to create post-stimulus-time-histograms (PSTH) and response maps to investigate the representation of tone bursts and average localized synchronized rate (ALSR) of phoneme 'e' and are compared to published physiological data (Blackburn and Sachs, 1990).

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Integration of Eddy Covariance Fluxes, Tree Ring Records and Stable Isotope Compositions to Study Environmental Controls on Growth in Different-Age Pine Plantation Forests

contributor:
Arain, Altaf
Earth and Environmental Sciences

subject:
forest
biogeosciences
tree ring
eddy covariance
carbon isotopes
southern Ontario

abstract:
Global warming and extreme weather events have impacted the ability of Earth’s forest ecosystems to sequester atmospheric carbon dioxide. The full effects of these events on forest productivity, vulnerability, and the carbon cycle have not yet been fully assessed. One potentially fruitful approach is to explore past climate and forest growth patterns through tree ring records. These records may be used to explore how past environmental events may have impacted tree growth and provide insight into the functioning of forest ecosystems in the future. The stable isotope ratios (e.g. 13C to 12C) of tree ring material also provide additional information about tree growth trajectories and environmental stressors that may not be recognized in radial growth. In this study, tree ring and stable isotope records were measured and constructed to explore the dynamics of growth over the lifespan of plantation pine stands in southern Ontario.
Tree ring growth records were used to determine the effects of climate and other environmental changes on radial growth. These records were constructed from two white pine (Pinus strobus L.) plantations established in 1939 (TP39) and 1974 (TP74) and one red pine plantation established in 1931 (TP31). Air temperature, precipitation, and drought indices were analyzed at monthly combinations to determine controls on growth. Temperature was consistently negatively correlated to growth, while precipitation and Palmer Drought Severity Index (PDSI) were consistently positively correlated to growth. The effectiveness of each climate variable to control ring growth differed between sites which may be related to stand age, stand density, and management factors.
In both white pine plantations, inter-annual eddy-flux quantifications of gross ecosystem productivity (GEP) was found to be significantly related to tree ring growth over the overlapping period from 2003 to 2017. These relationships enabled an inter-annual estimate of GEP to be constructed for both growth chronologies over the period 1942 to 2017 for TP39 and 1981 to 2017 for TP74). Additionally, growth rings from three specimens in two different-age (14- and 77-year old) white pine plantation forests were analyzed for stable carbon isotope ratios to identify both short- and long-term variations in the physiological response to changing environmental conditions. Variations in δ13C time series from whole wood samples provided a potential record of intrinsic water use efficiency (iWUE) for these three trees. These iWUE records were compared to climate records and inter-annual eddy-flux quantifications of GEP and evapotranspiration (ET). Long-term iWUE was found to increase by 50 μmol mol–1 yr–1, with nearly all of the increase occurring as the tree shifted into active homeostasis of stomatal control in the late 1960s. Changes in time series of internal and external concentration of CO2 (ratio) also displayed a significant shift from first increasing and then decreasing trend. In the three wood samples, air temperature, ET, and GEP were found to be significantly, but inconsistently related to iWUE.
The work of this thesis shows that tree ring properties are strongly related to key environmental variables such as temperature and drought stress in pine plantation forests in southern Ontario, Canada. Results also suggest that dendrochronology and isotope tracers are useful tools to be used to evaluate historical environmental impacts on growth in these different-age plantation stands. The background knowledge of climate drivers acting on tree ring growth and ring isotopic compositions over the forests’ history may be used to make informed management decisions to promote tree productivity in a changing climate in Eastern North America.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The full effect of water availability and environmental factors on forest productivity, vulnerability, and the carbon cycle has not been fully assessed. Tree ring chronologies offer one approach to explore past climate and forest growth patterns. These records may be used to identify past environmental events may have impacted tree growth and provide insight into the functioning of forest ecosystems in the future. Additionally, stable carbon isotope ratios (δ13C, or 13C to 12C) of tree ring material provide information about tree intrinsic water use efficiency (iWUE) which is not captured in radial width measurements. Lastly, inter-annual eddy-flux quantifications record stand-level dynamics of ecosystem productivity. In this study, tree ring, stable isotopes, and eddy-flux records were measured and constructed to explore the dynamics of growth over the lifespan of plantation pine stands in southern Ontario. In all three techniques, records were constructed from three white pine (Pinus strobus L.) plantations established in 1939 (TP39), 1974 (TP74) and 2002 (TP02). Air temperature, precipitation, and drought indices were analyzed at monthly resolution to determine controls on water use and productivity. Temperature was consistently negatively correlated to growth, while precipitation and PDSI were consistently positively correlated to growth. Variations in the δ13C time series from whole wood samples also provided a record of iWUE. Long-term iWUE was found to increase by 50 μmol mol–1 yr–1, with nearly all of the increase occurring as the tree shifted into active homeostasis of stomatal control in the late 1960s. In all three white pine plantations, inter-annual eddy-flux quantifications ecosystem productivity were found to be significantly related to tree ring growth over the overlapping period from 2003 to 2017. These relationships enabled an inter-annual estimate of tree ring-inferred fluxes to be constructed for all three growth chronologies. These results suggest that dendrochronology and isotope tracers are useful tools to be used to evaluate historical environmental impacts on growth in these different-age plantation stands. The interrelationships of tree ring growth, ring isotopic compositions, and eddy-flux quantifications found here serve as useful background knowledge on which to base additional studies of forest climate change impacts.


title: Addressing the Downstream Processing Challenges Within Manufacturing of Oncolytic Rhabdoviruses

contributor:
Latulippe, David R.
Chemical Engineering

subject:
Downstream Processing
Oncolytic Viruses
Manufacturing of Viruses
Chromatography
Sterile Filtration
Rhabdovirus

abstract:
Oncolytic viruses (OVs) are a class of cancer therapy that is currently undergoing clinical trials on its way to full regulatory approval. At present, the downstream processing of OVs relies on a combination of chromatography and membrane-based processes to remove process-related (e.g. host-cell proteins and nucleic acids) and product-related impurities (e.g. aggregated virus particles). This thesis explores various methods that can potentially be used to address the challenges associated with downstream processing during the production of OVs. To this end, the Rhabdoviral vector, which is currently undergoing clinical trials (phase I/II) for use in treating advanced or metastatic solid tumors, was selected as a promising oncolytic virus.
     One potential improvement in the downstream process that was investigated was the use of monolithic column chromatography for Rhabdovirus purification. Two monolithic anion-exchange columns (2 and 6 µm pore size) and one hydrophobic interaction column (6 µm pore size) were used to examine how column pore size affects virus recovery and contaminant removal. This investigation ultimately inspired the development of a purification process based on monolithic hydrophobic interaction column chromatography. Furthermore, this work is also the first to investigate how additives, namely glycerol, impact the hydrophobic interaction chromatography of virus particles. The developed process could be readily implemented for the scaled-up purification of the Rhabdoviral vector.
     Another challenge associated with the downstream processing of OVs is membrane fouling, which is characterized by a dramatic rise in transmembrane pressure (TMP) and low virus recovery. Indeed, membrane fouling poses a significant challenge, as some recent studies have reported that it can result in viral vector titer losses of over 80%. One critical use of membranes in downstream processing is for the sterile filtration of OVs, which is a required final step that is conducted right before vialing and involves passing the virus particles through a validated sterile filter. One of the main objectives of this thesis was to develop a fundamental understanding of the sterile filtration process and to optimize it in order to achieve higher throughput and lower losses, which are both essential to the large-scale production of OVs. To this end, a dead-end sterile filtration setup was designed, and various commercially available filters were evaluated to examine how membrane morphology affects fouling and product recovery. The results of these tests showed that double-layered composite filters enabled higher virus recovery and filtration capacity compared to single-layered sterile filters.
     Another cause of membrane fouling is the aggregation of virus particles, which is mediated by various interactions in the solution. To study this, the above-described setup was re-designed to create an effective procedure that utilizes minimal volumes of virus solution, while also enabling the rapid assessment of microscale filtration performance and a comprehensive understanding of virus-virus and virus-membrane interactions. This setup was used to study how different additives, including various proteins (bovine serum albumin and α-lactalbumin) and polymers (polyethylene glycol and polyvinylpyrrolidone), affect the microfiltration of the Rhabdoviral vector and, consequently, the TMP profile. Furthermore, the correlation between the membrane fouling rate (via TMP profiles) and virus recovery was also investigated. This investigation revealed that proteins significantly increase virus transmission and that polymers are incapable of mimicking the effects of the proteins.
    To explain this phenomenon, a theory based on the biophysical structure of proteins, mainly heterogenicity in charge distribution, was proposed. Moreover, membrane surface modification tests were conducted using bovine serum albumin, with the results indicating that this approach has considerable potential for enhancing virus transmission. Due to the similarities between the test setup and actual downstream processing unit operations, the results from this part of the thesis could be easily and accurately applied to process optimization.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: There is considerable interest in the development of oncolytic viruses for cancer immunotherapy. Indeed, at the time of this thesis’ writing, a Canadian team of researchers is conducting the world’s first clinical trial using a combination of two viruses to kill cancer cells and stimulate an immune response. The process of manufacturing oncolytic viruses is generally divided into two major steps: upstream processing and downstream processing. While upstream processing focuses on virus propagation, downstream processing aims at removing process-related and product-related impurities. However, research into downstream process design and optimization has largely been neglected in favour of a focus on upstream processing, aimed at increasing bioreactor yields and achieving high viral titers. Consequently, downstream processing has become the main bottleneck in virus manufacturing processes, accounting for as much as 70% production costs. This thesis aims to identify and develop a fundamental understanding of the main challenges associated with the downstream processing of oncolytic viruses and to investigate methods for addressing them. Specifically, the present work focuses on the purification and final sterile filtration steps in the manufacturing of oncolytic Rhabdoviral vectors.


title: Rack-based Data Center Temperature Regulation Using Data-driven Model Predictive Control

contributor:
Yan, Fengjun
Mechanical Engineering

subject:
Data Center
Temperature Control
Data-driven Model
MPC controller

abstract: Due to the rapid and prosperous development of information technology, data centers are widely used in every aspect of social life, such as industry, economy or even our daily life. This work considers the idea of developing a data-driven model based model predictive control (MPC) to regulate temperature for a class of single-rack data centers (DCs). An auto-regressive exogenous (ARX) model is identified for our DC system using partial least square (PLS) to predict the behavior of multi-inputs-single-output (MISO) thermal system. Then an MPC controller is designed to control the temperature inside IT rack based on the identified ARX model. Moreover, fuzzy c-means (FCM) is employed to cluster the measured data set. Based on the clustered data sets, PLS is adopted to identify multiple locally linear ARX models which will be combined by appropriate weights in order to capture the nonlinear behavior of the highly-nonlinear thermal system inside the IT rack. The effectiveness of the proposed method is illustrated through experiments on our single-rack DC and it is also compared with proportional-integral (PI) control.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Variation of the Carbon Isotope Composition in Some Natural Processes

contributor:
Thode, H. G.
Chemistry

subject:
isotope
carbon
Texas
cap rock
sulphur wells
Louisiana
mass spectrometer
decarboxylation

abstract: The variation in the carbon isotope composition of the cap rock of Texas and Louisiana sulphur wells was investigated by means of a simultaneous collection mass spectrometer. These rocks showed anomalously large depletions in C-13. The isotope depletion in the decarboxylation of pyruvic acid, both by chemical means and by bacteria, was measured and the isotope composition of the carbon dioxide released was found to be similar to that of the cap rock. The hypothesis is advanced that the carbonate of the cap rock may have originated by the precipitation of carbon dioxide released in the bacterial decarboxylation of an organic substrate.

abstract: Thesis

abstract: Master of Science (MSc)


title: Application of Spectral Decomposition Analysis to In Vivo Quantification of Aluminum

title: In Vivo Quantification of Aluminum

contributor:
Prestwich, William
Medical Physics

subject:
spectral decomposition
in vivo
aluminum

abstract:
Aluminum is a non-essential trace element that accumulates in human bone tissue (Nayak, 2002). Its toxic effects are cumulative and result in painful forms of renal osteodystrophy, most notably a dynamic bone disease and osteomalacia, but also other forms of disease (Yokel, 2001; Cannata-Andia, 2002). Presently, histological tests of bone biopsies are the only approach for the diagnosis of aluminum-related pathologies (Malluche, 2002). Neutron Activation Analysis was proposed as an alternative method for quantifying aluminum. The Trace Element Group at McMaster University has developed an in vivo procedure for detecting aluminum levels in the bones of the hand, exploiting an accelerator-based approach. A minimum detectable limit (MDL) of 1.14mg of aluminum could be distinguished for a local dose to the hand of 48mSv (Pejovic-Milic, 2001). For the procedure to be clinically effective, the MDL should be comparable to the levels normally contained in healthy subjects (0.3-0.4 mg AI). Further refining of the method is therefore necessary. This dissertation presents an improved algorithm for data analysis, based on Spectral Decomposition. Following phantom measurements, a new MDL of(0.7±0.1)mg AI was reached for a local dose of (20±1)mSv, representing an improvement by a factor of 1.60±0.04. In addition, a time-dependent variant of this algorithm was proposed.
The study also addresses the feasibility of a new data acquisition technique, the electronic rejection of the coincident events detected by the Nai(Tl) system. It is expected that the application of this technique, together with Spectral Decomposition Analysis, would provide an acceptable MDL for the method to be valuable in a clinical setting.

abstract: Thesis

abstract: Master of Science (MS)


title: Dopamine Metabolism Quantified in the Human Brain: Tracer Kinetic Analysis of Positron Tomographic Studies

title: Tracer Kinetic Analysis of Position Tomographic Studies

contributor:
Nahmias, C.
Physics

subject:
dopamine
metabolism
human brain
positron tomographic studies
tracer kinetic data

abstract: Mathematical models are used to estimate physiological parameters which are otherwise inaccessible to measurement. When applied to tracer kinetic data obtained in positron tomographic studies, these methods allow for the quantitative analysis of regional metabolic rates in the human brain during life. Dopamine, a neurotransmitter in the mammalian central nervous system, is synthesized by the action of aromatic amino acid decarboxylase on L-dihydroxyphenylalanine (L-dopa). A fluorinated analogue of L-dopa, 6-[18F]fluoro-L-dopa, is used as a tracer in positron tomography to study the nigrostriatal dopaminergic system. Although this tracer has been in use in man for over ten years, a definitive method of quantitative analysis has not yet emerged. The comparison of quantitative results obtained by this approach has been confounded by the diversity of mathematical modelling techniques employed. These techniques range from simple graphical analyses, which yield a single rate constant for the entire system, to complex compartmental approaches, which may not present a unique solution. The goal of this research has been to develop an approach to quantitative analysis which is both informative and mathematically justifiable. Compartmental models of increasing complexity have been evaluated by statistical methods (F-test) to determine the simplest model which adequately fits the data. This strict methodological approach indicates that a two-compartment, three-parameter model produces the best fit, in a statistical sense, to the measured data. This data has also been analyzed by a simple graphical method to yield an influx constant for the system. The influx constant has also been calculated, for comparison, from the results of the compartmental analysis. The two methods were found to be in excellent agreement; both responded predictably to physiological perturbations of the system. While the compartmental method yielded a more informative analysis of the system, the graphically determined influx constant was found to be less sensitive to measurement errors. It is recommended that these two methods be applied in parallel, such that the comparison of results may serve as an internal measure of the integrity of the analysis.

abstract: Thesis

abstract: Master of Science (MS)


title: An Accelerator Based In Vivo Measurement of Aluminum in Human Bone by Neutron Activation Analysis

contributor:
Chettle, David
Medical Physics

subject:
in vivo
aluminum
human bone
neutron activation

abstract:
Aluminum is a neurotoxin and has been recognized as a causative agent for dialysis encephalopathy and renal osteodystrophy, as well as possibly being related to Alzheimer's disease. General public exposures to aluminum have increased in the modern, industrial age stimulating scientists to inquire into the degree of risk associated with such widespread use of aluminum. Aluminum is thought to be stored in bone, therefore, development of an in vivo method for the determination of aluminum a in human bone, suitable for routine monitoring of patients and population is the goal of this study. Using neutron activation analysis, low-energy neutrons are produced on the KN accelerator inducing the 27Al(n,y)28AI reaction in an irradiated site. Two different shapes (cylindrical and flat) of aluminum doped tissue equivalent phantoms, simulating both bone and soft tissue, have been built. Calibration lines, detection limits and doses delivered with the different shapes of phantom have been discussed, and compared to the previously published results. Two detection systems. an assembly of two large Nal{Tl) detectors and a hyperpure germani Jm detector, have been compared as well.
The results achieved suggest that this technique may provide an alternative choice to painful bone biopsy for the in vivo monitoring of aluminum intoxication from long-term exposure.

abstract: Thesis

abstract: Master of Science (MS)


title: "Sometime We Stir Up a Hornet's Nest" Practitioners and Paradigms of Genetic Counselling

contributor:
Counts, David
Anthropology

subject: genetics, genetic counselling, paradigms of genetic counselling, practitioners of genetic counselling

abstract:
The central investigative concern of this thesis is the culture of
genetic counselling in Canada--a specialized health service providing information and assistance to families at risk from genetic disorders. In particular, this study describes the variability that exists in the way in which genetic counsellors view their profession and explores the factors that contribute to this variability. The genetic counsellors' training, division of roles, view of their responsibility toward clients, and the historical and contemporary context in which they practise contribute to understanding the "individuals' versions of the culture of [genetic counselling]'' (Hahn 1985:53). Three means of inquiry are utilized: extensive library research, responses from a Canada-wide questionnaire sent to genetic counsellors, and ethnographic interviews. The history of genetic counselling has been described as a series of changes from research to medicine to psychosocial concerns. Current definitions of adequate genetic care, however, stress attention to both the medical genetic and psychosocial aspects of genetic disorders suggesting that both a medical and
a psychosocial paradigm now exist in genetic counselling. I argue that the association between these two paradigms is unclear, thus producing tension and ambiguity for practitioners. Genetic counsellors divide themselves into three groups--MD/MD-PhDs who are the central caregivers, PhD geneticists who are primarily involved in research, and nonMDs/nonPhDs such as nurses, social workers and master's level genetic associates who are often doing clinic-oriented clerical jobs. Nevertheless, indicative of the uneasy relationship between the
paradigms of genetic counselling, considerable debate exists in the field about who should be providing genetic counselling. A further example of this paradigmatic tension concerns the implementation of genetic counselling goals, especially for physician geneticists, the central caregivers. In particular, genetic counsellors face the problematic task of "doing something" for their clients, making them aware of their options, without influencing the client's decision making. The contemporary context of genetic counselling is predominantly a medical one; although psychosocial concerns are acknowledged as important for adequate genetic care, the means for dealing with them are not clear. I suggest that the response to the underlying tensions in genetic counselling is ultimately an individually-constructed response, based on the individual practitioner's experience, interpretation of the facts, and notion of the boundaries of their responsibility in medicine.

abstract: Thesis

abstract: Master of Arts (MA)


title: Role of the Paraventricular Nucleus in TNB-Induced Anorexia

title: Role of the PVN in TBN Anorexia

contributor:
Weingarten, H.P.
Psychology

subject: PVN, paraventricular nucleus, anorexia, TBn-induced anorexia, TBN anorexia

abstract:
Inflammatory Bowel Disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract, often associated with reduced food intake (anorexia) and weight loss. The anorexia manifest following gastrointestinal inflammation can only be expressed if appropriate signals are communicated from the inflamed segment to the brain. Yet, the nature of these signals, and the identity of the brain sites processing these anorexigenic signals, are unknown. The present experiment evaluates the contribution of the paraventricular nucleus (PVN), a brain site rich in corticotropin releasing factor (CRF) receptors and known to be involved in the control of food intake, in the anorexia associated with experimental colitis. Colitis was induced, by trinitrobenzenesulfonic acid (TNB) treatment, in animals in which the PVN was ablated or in rats with sham brain surgeries. Results indicated clearly that the expression of the anorexia following TNB treatment is fully expressed even in the absence of the PVN. This result indicates that the integrity of the PVN is not necessary for the reduction of eating associated with intestinal inflammation, thus suggesting that CRF is also not critical to colitis-induced anorexia.
inflammatory bowel disease (IBD); feeding; anorexia; gut-brain communication; paraventricular nucleus (PVN); interleukin-1 (IL-l); corticotropin-releasing-factor (CRF); neuroimmunology

abstract: Thesis

abstract: Master of Science (MS)


title: Pilot Studies for In Vivo Bone Aluminum Measurements

contributor:
Chettle, Dr. D.R.
Medical Physics

subject:
pilot studies
in vivo
bone
aluminum

abstract:
Excess aluminum has been linked to such diseases as dialysis encephalopathy syndrome and osteodystrophy, in renal dialysis patients. Though the causality relation has not yet been confirmed, aluminum has also been associated with Alzheimer's disease.
Aluminum is thought to be stored in bones, and a measure of its deposition should correlate with its total bioaccumulation. To date, only bone biopsies and desferrioxamine tests are available for such measurements. Neutron activation analysis (NAA) has been studied as a non-invasive technique for measuring bone aluminum. Two neutron beam ports from the McMaster nuclear reactor and the KN accelerator have been compared as possible thermal neutron sources. Resin-based phantoms, physiologically resembling a hand, were irradiated using the reactor based neutron source. From the results, a minimum detection limit (MDL) of aluminum in bone was obtained. An Andersson-Braun remmeter measured the dose delivered to the phantoms, due to the radiation exposure. The hand dose equivalent combined with the MDL, in this study, are compared to the results of previous NAA studies. The goal of this study is to measure low aluminum stores In Vivo, while delivering a low dose with respect to natural background levels.

abstract: Thesis

abstract: Master of Science (MS)


title: Work and Mental Health - An Analysis of Canadian Community Health Survey

contributor:
Shannon, Dr. Harry
Statistics

subject:
mental health
canadian
health survey
community

abstract: Workplace mental health is a major concern in Canada. The primary objective of this research is to describe the relationship between work and mental health, paying particular attention to work stressors and further explore moderators and mediators of any relationships, that might be targeted in future intervention strategies. The source of the data is the two cycles of the Canadian Community Health Survey conducted by Statistics Canada. All estimates produced from the data were weighted to represent the target Ontario population using the weights provided by Statistics Canada. Estimates of the prevalence of the mental disorders and substance dependence and mean scores of work stressors, according to different groups of workers, were calculated. To examine health care use, we treated consultation with a mental health professional, use of medication-antidepressants and utilization of any resource as dependent variables. Bivariate relationships between mental health disorders and other variables explored the correlates of mental health disorders. Logistic regression was used to examine moderators and mediators of work stressors in relation to mental health disorders by including some socio-demographic variables and behavioral variables as covariates and we also included terms of their interactions with work stressors. Since the level of work stressors varied by occupation and was likely determined in part by occupation, we did not include both variables in regression analyses. Further regressions with health care utilization as the dependent variable were conducted with work stressors and occupation as independent variables and other variables as covariates and in interaction terms for people with mental health disorders. The results of the study suggest that there is strong association between work and mental health problems. The findings regarding work stressors and occupation as predictors of mental health problems suggest that work health and safety practitioners must continue to pay attention to the psychosocial conditions of work. We also explored what factors predicted whether people consulted a mental health professional (CCHSl.l) or whether they used any resource available to deal with their problem (CCHS1.2).

abstract: Thesis

abstract: Master of Science (MS)


title: Beta Dosimetry: The Scaling Method for Beta-Ray Dose Distributions Applied to Layered Media

contributor:
Prestwich, W. V.
Physics

subject:
scaling method
beta-ray
dose distribution
radioimmunotherapy
radiation
cancer

abstract: Radioimmunotherapy consists in the use of beta radioactive labeled monoclonal antibodies as selective carriers of radiation to tumors. Internal spatially distributed sources created at the disease sites would deliver high radiation doses to tumors while the normal tissues would not be exposed to the intense radiation as in conventional forms of cancer treatments. A rapid and accurate estimation of the spatial dose distribution from nonuniform sources is essential for the optimization of this form of cancer therapy. The method used for such calculations is based on the knowledge of dose distributions around a unit source, quantities referred to as dose kernels. Thus far, the Monte Carlo technique is the most accurate way of the dose kernel determinations. However, for routine dosimetry simpler and less time consuming methods of adequate accuracy may appear more preferable. The "scaling factor" method is used to determine the depth dose distribution in a medium based on data about the dose distribution in an arbitrary reference medium (e.g. air, water). The transformation of the dose distribution curves from the reference medium to the desired new medium is done using a constant, known as scaling factor or relative dose attenuation, and a closely related renormalization factor imposed by the energy conservation. This work investigates the accuracy of the scaling factor method using a statistical approach (generalized chi-squared test), focusing on a particular case of potential practical interest, the scaling factor water to bone. The work also investigates a procedure for extending the applicability of the scaling factor method to dosimetry in dissimilar media, as a first step, a planar interface.

abstract: Thesis

abstract: Master of Science (MS)


title: Plasma Induced Grafting Polymerization of 2-Methacryloyloxyethyl Phosphorycholine Onto Silicone Hydrogels to Reduce Surface Hydrophobicity and Protein Adsorption

contributor:
Sheardown, Heather
Biomedical Engineering

subject:
Ophthalmic Biomaterials
Contact Lenses

abstract:
Silicone hydrogels haves been widely utilized in many in ophthalmic and other biomedical applications due to the its comfort of hydrogels, their excellent biocompatibility, high oxygen permeability and transparency. For use as a contact lens, the silicone hydrogel with interacts with the tear film, cornea, and eyelid;, thus surface properties of the gel are crucial to be considered. The highly oxygen permeabilitye performance of the silicone hydrogel contact lens materials mainly relies on the incorporationng of the siloxane functional groups., Hhowever these groups are extremely mobile and surface active, which can result in an increase in the of lens surface hydrophobicity, as well as protein and lipid deposition. Therefore, there is a need for surface modification of silicone hydrogel contact lenses.  Otherwise users may might have to choose to decrease the frequency and length of wearing duration of silicone contact lenses due to dryness or bio-fouling related issues.

A novel biomimetic methacrylate monomer which contains a phosphorylcholine group, 2-mMethacryloyloxyethyl pPhosphorycholine (MPC) is was grafted onto the surface of novel silicone hydrogel materials surface to create a thick hydration layer in order to enhance the protein resistance and surface wettability. Low temperature air plasma has beenwas chosen to initiate grafting polymerization of MPC monomers onto silicone hydrogel substrates. Hydrogels were treated with plasma and exposed to air flow to yield hydroperoxides on the surface; the, and peroxides group acted as a photo-initiators for further thermal MPC grafting polymerization.

After surface modification, the silicone hydrogels were characterized by XPS and ATR-FTIR to confirm the structure and elemental composition. A significant amount of phosphorus element was found shown on the XPS spectra of the modified materialsum,, demonstrating that so the MPC monomers were successfully grafted onto the gel surface. According to water contact measurement results, the modified samples possessed very hydrophilic surfaces, with advancing angles of about 27°, while compared the unmodified samples at around 110°. After surface grafting, between a around 20% and to 50%’s reduction in protein deposition was also observed, which aligned with water contact angle results. Other properties such as oxygen permeability, transparency, water equilibrium, and elastic modulus remained unchanged after the air plasma exposure and thermal MPC polymerization.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: A Structural Equation Modeling Approach to the Impact of Re-Engineering on the Staff of a Large Teaching Hospital

contributor:
Shannon, Harry
Statistics

subject:
equation modeling approach
impact of re-engineering
teaching hospital
hospital

abstract: In this project we used structural equation method to analyze the data collected during the period of re-engineering in hospitals in Ontario 1995 to 1997. We want to understand how organizational change affect the well being of the staff of large teaching hospital. Two main models were considered in this project: cross-sectional models and longitudinal models for the data collected in 1995 and 1997. We tested six models for each year's data in cross-sectional model, effect-indicator, cause-indicator and mixed-indicator were used in both standard and non-standard models. We explored standard model with effect-indicators in our longitudinal case. The study was carried by SAS software program. We demonstrated an important association of job stressors with psychological outcomes of hospital staff directly and indirectly via interference. Decision-making capacity was associated with psychological outcomes in the opposite direction. Similar results were concluded from longitudinal model. The limitation was discussed.

abstract: Thesis

abstract: Master of Science (MS)


title: The Effects of Manipulating the Degree of Belief in a Diagnostic Hypothesis on Feature Detection

title: Belief in a Diagnostic Hypothesis and Feature Detection

contributor:
Brooks, Lee, R.
Psychology

subject: degree of belief, diagnostic hypothesis, feature detection

abstract:
In Experiment 1, the degree of belief in a focal hypothesis was manipulated
using priming as well as the principle of unpacking of Tversky and Koehler (1994).
The effects of these manipulations on feature detection was measured. It was found that
regardless of the degree of belief in the focal hypothesis, novice diagnosticians who
have it in mind will call more of its features than those who do not have it in mind. It is
believed that this is due to the fact that having a diagnosis in mind seems to focus the
attention of diagnosticians to the relevant features. Also, our manipulation of
suggesting alternatives to the diagnosticians did not have the effect of decreasing the
diagnosticians' belief in the focal hypothesis, contrary to what is predicted by Tversky
and Koehler's unpacking principle (1994). The results from Experiment 1 suggest, and
those from Experiment 2 confirm the hypothesis that in order to decrease the degree of
belief in the focal hypothesis when it is presented with alternatives, the alternatives
must be plausible. If the focal hypothesis is extremely dominant over the alternatives, a
reversal of the unpacking principle will occur.

abstract: Thesis

abstract: Master of Science (MS)


title: An Appraisal of the MACSIM Simulation Routine In Its Application to an Alkylation Plant

contributor:
Hoffman, T. W.
Chemical Engineering

subject:
simulation
modeling
operating costs
technical feasibility
alkylation plant
Bronte, Ontario
case studies

abstract: The legibility of the digitized copy is limited due to the quality of the original document. McMaster Digitization Centre. March 26, 2019.

abstract: The object of the program was to develop general guidelines for the art of simulation, and then to show how simulation could be used in practice.  A digital computer simulation was assembled to describe the operation of the Shell alkylation plant at Bronte, Ontario. The solution of the steady-state mass and energy balances provided a working simulation on which to demonstrate the modeling and simulation techniques which are presented.  The simulation was used to predict the operating costs and to asses the technical feasibility of five plant case studies.

abstract: Thesis

abstract: Master of Engineering (ME)


title: Optimization of Septa Shadowing in Pet Scanners with Retractable Septa Using Monte Carlo Techniques

contributor:
Nahmias, C
Physics

subject: septa shadowing, pet scanners, pet, scanners, retractable septa, septa, monte carlo, monte carlo techniques

abstract:
Scatter and random coincidences are of significant concern in Positron Tomography because they lead to the misrepresentation of the activity distribution in the final image. In this regard, interplane septa have long been used in ring positron tomographs to suppress the acquisition of
photons oblique to the scan planes. The septa extend from the face of the detector array to the edge of the field of view. Not only do the septa block photons scattered oblique to the scan planes and singles originating in different planes, but they also result in a decreased count rate sensitivity
of the tomograph to true coincidence photons.
In this work, the Monte Carlo technique has been employed to study the effect of "septa shadowing" with respect to septa length in order to determine an optimal septa length. Sensitivity parameters have been derived by the use of Noise Equivalent Count (NEC) Rate Analysis, as well
as count rate sensitivity analysis in order to balance the counting and imaging performance of the system. In addition, energy spectra, sinogram profiles and scatter fraction results are presented to quantify the effects of septa length on the trues, scatter and randoms contributions of the data
collected by the scanner.
It is concluded that the highest NEC rate is achieved with positron tomographs with no septa and operating in 3D mode.

abstract: Thesis

abstract: Master of Science (MS)


title: Influence of Strength Training on Postural Control in the Older Adult

title: Strength Training on Postural Control in Older Adults

contributor:
Riach, Cindy
Human Biodynamics

subject:
strength training
postural control
exercise
adult
older adult

abstract: The present study was designed to investigate the effects of a progressive strength training program on quiet postural sway and stability limits in healthy males (n=8) and females (n=12) aged 60-80 years. The ability of the subjects to utilize visual information (eyes open vs. eyes closed) to improve quiet postural sway and stability limits was also examined. Vision, was found to significantly improve quiet postural sway (lat and a-p) and stability limits (a-p). Vision improved stability limits (lat) for the male subjects but not for the female subjects. The strength training did not significantly improve any of the balance measures but a gender by training interaction was found for quiet postural sway (normalized to stability limits) in the a-p direction. The male subjects quiet postural sway decreased after the strength training and their stability limits increased, The greatest improvements in balance were noted for the subjects who had substantially higher baseline levels to begin with. Exercise was found to improve muscle strength and this increase may have contributed to the improvements in balance noted.

abstract: Thesis

abstract: Master of Science (MS)


title: Photodynamic Therapy Dosimetry Through Measurement of Fluorescence Decrease Due to Photobleaching

title: Fluorescence and Photobleaching in Photodynamic Therapy

contributor:
Farrell, T. J.
Medical Physics

subject:
photodynamic therapy
dosimetry
fluorescence
photobleaching

abstract: The phenomenon of photobleaching of a photosensitizer during photodynamic therapy (PDT) is well known. For second generation photosensitizers it may be possible to exploit this effect to enhance the volume of damaged tissue and improve the efficacy of PDT. In addition, as a consequence of photobleaching, the fluorescence emitted by the photosensitizer will decrease during PDT. Mathematical models were developed which describe fluorescence emission, photobleaching and tissue necrosis resulting from the irradiation of tissue containing photosensitizer using an appropriate light source. Diffusion theory was used to model bleaching in a semi-infinite medium caused by broad-beam irradiation, and both pencil and broad-beam fluorescence excitation of the photosensitizer. In addition, models were developed for an isotropic point source imbedded in an infinite medium. Based on the relationship between the decreasing fluorescence signal and the increasing volume of tissue damage, these models allow the extent of necrosis achieved during treatment to be monitored. By analysing spatially resolved fluorescence measurements predictions about necrosis depth that are insensitive to treatment parameters such as photosensitizer concentration, tissue optical properties and bleach rate are possible. Tissue simulating optical phantoms that allow for relatively simple and accurate alteration to optical properties were developed. Photosensitizers which still undergo fluorescence and photobleaching in the solid medium were also added. Using these phantoms, treatment was simulated and spatially resolved fluorescence was measured as a function of time for a wide range of initial treatment parameters. Photobleaching of the photosensitizers was observed to occur through a decrease in fluorescence emission. Also, spatially resolved measurements provided information about the average photosensitizer depth, which was seen to increase with time, with little knowledge of initial treatment parameters. These experimental results were then compared with predictions from the mathematical theory, illustrating the validity of the models. The value and feasibility of this technique for photodynamic therapy dosimetry are discussed, along with planned improvements.

abstract: Thesis

abstract: Master of Science (MS)


title: Hospitals Under Pressure: Administrative Responses to Fiscal Restraint Between 1977 and 1984

title: Hospitals Under Pressure

contributor:
Carroll, Barbara
Political Science

subject: hospitals, pressure, fiscal restraint, 1977, 1984, administrative responses

abstract:
In this thesis, we examine the administrative responses
by Ontario hospitals to fiscal restraint between 1977 and
1984. Using the conceptual 'model' of organizational change
developed in James Thompson's Organizations in Action
[1967], we predict that the most significant adaptations
occurred in hospitals' administrative components, while
"core" activities such as medical procedures remained
relatively inflexible. More importantly, the observed
changes in administrative tasks and activities can be
accounted for by the role played by administrators in
maintaining internal order and dealing with external
contingencies. Accordingly, the greatest adaptations will
be in how the administrative component assesses the
performance cf "core" activities and communicates this to an
external funding agency (i.e. Ministry of Health).
We find that the empirical data collected is consistent
with our predictions. As a result, we conclude that
hospital adaptation during this time period was explicitly
related to renewing the political conditions necessary for
organizational growth. Moreover, we suggest that the
organizational logic of fiscal restraint does not affect how
hospitals perform medical activities, but rather, further
entrenches this technology through the adoption of
standardized funding formulae.

abstract: Thesis

abstract: Master of Arts (MA)


title: The Role of Nutritional Supplementation Following Resistance Exercise in Humans

contributor:
Tarnopolsky, M.A.
Human Biodynamics

subject: nutrition, nutritional supplementation, resistance exercise, exercise, human

abstract:
The purpose of this thesis was to investigate the effects of nutritional
supplementation following resistance exercise on protein metabolism, muscle glycogen resynthesis rate, hormonal responses and training status through two unique investigations. The purpose of the first investigation was to determine the effect of post-resistance exercise glucose supplementation upon skeletal muscle fractional synthetic rate (FSR), urinary urea excretion, and whole body and myofibrillar protein degradation (WBPD and MPD, respectively). Eight healthy young males performed unilateral knee extensor resistance exercise(8sets/~1 0reps/~85% 1 RM) such that the non-exercised limb served as a control. They received a carbohydrate (CHO) supplement (1g/kg) or placebo
(PL) immediately (t=Oh) and 1 h (t=+1 h) following exercise. FSR was determined for both exercised (EX) and control (CON) limbs by incremental L-[1-13C]leucine enrichment of biopsy samples of vastus lateralis over -10 hours post-exercise. Plasma insulin and glucose were determined at t= -1.5, 0, 0.25, 0.5, 0.75, 1, 1.25, 1.5, 1.75, 2, 2.25, 2.5, -10, and -10.5h post-exercise. MPD and WBPD were estimated from 24 hr urinary 3-methylhistidine (3-MH) and L-[1-13C]leucine flux, respectively, and whole body net protein balance was estimated from 24 hr
urinary urea excretion. Plasma insulin concentration was greater (p<0.01) at 0.5, 0.75, 1.25, 1.5, 1.75 and 2 h in the CHO compared to PL condition, as was plasma glucose at 0.5 and 0. 75 h (p<0.05). FSR was 36.1% greater in the CHO/EX leg than in the CHO/CON leg (p=N.S.) and 6.3% greater in the PUEX leg than in the PUCON leg(p=N.S.). 3-MH excretion was lower in the CHO (110.43 ± 3.62 J μmol/g creatinine) than PL condition (120.14 ± 5.82)(p<0.05) as was urinary urea nitrogen(8.60 ± 0.66 g/g creat vs. 12.28 ± 1.84)(p<0.05). These findings suggest that CHO supplementation (1g/kg) immediately and 1h following resistance exercise can significantly decrease myofibrillar protein breakdown and
urinary urea excretion, thus resulting in a more positive muscle and whole body protein balance.
The purpose of the second investigation was to determine the effect of various nutritional supplements upon whole body protein synthesis, urinary urea excretion, and whole body and myofibrillar protein degradation (WBPD and MPD respectively). Ten healthy young male resistance athletes performed a whole body circuit set workout (9 exercises/3 sets/80% 1 Repitition Maximum). Exercises for the legs were performed unilaterally so that the non-exercised leg served as a control They received a carbohydrate (CHO) supplement (1g/kg), a mixed CHO/PRO/FAT supplement (isoenergetic to CHO supplement)(68% CHO,
22% PRO, 10% FAT) or placebo (PL) immediately (t=Oh) and 1 h (t=+1h)
following exercise. Immediately following exercise muscle glycogen was
significantly lower (p<0.05) in vastus lateralis of the exercised leg than in the control leg immediately post-exercise in all three conditions. Both the CHO and CHO/PRO/FAT supplements resulted in significantly greater increases (p<0.05) in plasma insulin and glucose post-exercise than PL. The CHO and CHO/PRO/FAT also resulted in significantly greater(p<0.05) rates of muscle glycogen resynthesis vs. Placebo. No significant differences were observed between the three conditions for plasma testosterone and cortisol concentration post-exercise. Similarly, no differences were observed between the three conditions for urinary creatinine, and 3-MH and urea nitrogen excretion. Thus,
nutritional supplements do not appear to decrease myofibrillar protein
degradation as indicated by 3-MH and urea nitrogen excretion in highly trained resistance athletes. Taken together, the two studies suggest that highly trained resistance athletes and untrained individuals both benefit from nutritional supplementation following resistance exercise, but may do so through different mechanisms.

abstract: Thesis

abstract: Master of Science (MS)


title: Attenuation Correction in Positron Emission Tomography Using Single Photon Transmission Measurement

subject: pet, positron emission tomography, single photon transmission measurement, attenuation correction

abstract:
Accurate attenuation correction is essential for quantitative positron emission
tomography. Typically, this correction is based on a coincidence transmission
measurement using an external source of positron emitter, which is positioned close to
the detectors. This technique suffers from poor statistical quality and high dead time
losses, especially with a high transmission source strength.
We have proposed and tested the use of single photon transmission measurement
with a rotating rod source, to measure the attenuation correction factors (ACFs). The
singles projections are resampled into the coincidence geometry using the detector
positions and the r,)d source location. A nonparalyzable dead time correction algorithm
was developed for the block detectors used in the McMaster PET scanner.
Transaxial resolution is approximately 6 mm, which is comparable to emission
scanning performance. Axial resolution is about 25 mm, with only crude source
collimation. ACFs are underestimated by approximately 10% due to increased crossplane
scatter, compared to coincidence transmission scanning. Effective source
collimation is necessary to obtain suitable axial resolution and improved accuracy. The
response of the correction factors to object density is linear to within 15%, when
comparing singles transmission measurement to current coincidence transmission
measurement.
The major advantage of using singles transmission measurement IS a
dramatically increased count rate. A factor of seven increase in count rate over
coincidence scanning is possible with a 2 mCi transmission rod source. There are no
randoms counted in singles transmission scans, which makes the measured count rate
nearly linearly proportional with source activity. Singles detector dead time is
approximately 6% in the detectors opposite a 2 mCi rod source.
Present hardware and software precludes the application of this technique in a
clinical environment. We anticipate that real time acquisition of detector singles can
reduce the transmission scanning time to under 2 minutes, and produce attenuation
coefficient images with under 2% noise. This is a significant improvement compared
to the current coincidence transmission technique.

abstract: Thesis

abstract: Master of Science (MS)


title: A study on lane detection methods for autonomous driving

contributor:
von Mohrenschildt, Martin
Computing and Software

subject:
lane detection
computer vision
autonomous driving
self-driving cars
perception
artificial intelligence

abstract:
Machine perception is a key element for the research on autonomous driving vehicles. In particular, we focus on the problem of lane detection with a single camera. Many lane detection systems have been developed and many algorithms have been published over the years. However, while they are already commercially available to deliver lane departure warnings, their reliability is still unsatisfactory for fully autonomous scenarios.
In this work, we questioned the reasons for such limitations. After examining the state of the art and the relevant literature, we identified the key methodologies adopted. We present a self-standing discussion of bird’s eye view (BEV) warping and common image preprocessing techniques, followed by gradient-based and color-based feature extraction and selection. Line fitting algorithms are then described, including least squares methods, Hough transform and random sample consensus (RANSAC). Polynomial and spline models are considered. As a result, a general processing pipeline emerged. We further analyzed each key technique by implementing it and performing experiments using data we previously collected. At the end of our evaluation, we designed and developed an overall system, finally studying its behavior.
This analysis allowed us on one hand to gain insight into the reasons holding back present systems, and on the other to propose future developments in those directions.

abstract: Thesis

abstract: Master of Science (MSc)


title: Chronic Illness and Conceptions of Self in Later Life: Continuity or Change?

contributor:
Rosenthal, Carolyn
Sociology

subject: illness, chronic illness, conceptions of self, self in later life, continuity, change

abstract:
This thesis examines the processes by which the self-concept is shaped by chronic
illness in later life. This study contributes to our understanding of the development of the
self in later life by examining patterns of continuity and change. Twenty-four women
diagnosed with osteoarthritis (0A) were interviewed. The participants were community dwelling females, aged between 67 to 85 years. They were selected to reflect a range of
OA, from mild to severe forms of the disease. A qualitative approach, more specifically,
the grounded theory method was adopted for this study.
The findings illustrate that OA in later life presents a source of change for the self concept.
However, the influence of these processes of change vary considerably. In
particular, the significance of change for the self-concept is shaped by the individual's
perception of the impact of chronic illness for the self. These are shaped by several
factors. The impact of OA on the self is influenced by the ways in which the person's
multiple identities are affected. And, the person's perception of continuity and change for
her "overall" or global sense of self must be considered. Finally, the type of process
mechanisms that are drawn upon shape the person's perception of continuity and change.
Such processes include: shifting and non-shifting prominence hierarchies, the ability to
adjust and accommodate to one's limitations and the extent to which interactions and
valued identities are modified, social comparison, reflected appraisal, and the dialogue
between the past, the present, and the future self.
The data show that older people do reflect some of the same issues that have
previously been revealed by studies of chronic illness which do not focus on later life.
However, experiences of chronic illness in later life also present unique variations.

abstract: Thesis

abstract: Master of Arts (MA)


title: DRIVER BEHAVIOUR PREDICTION MODELS USING ARTIFICIAL INTELLIGENCE ALGORITHMS AND STATISTICAL MODELING

contributor:
Yan, Fengjun
Mechanical Engineering

subject:
DRIVER BEHAVIOUR PREDICTION MODELS
ARTIFICIAL INTELLIGENCE ALGORITHMS

abstract:
To improve the safety and comfort of intelligent vehicles, advanced driver models offer promising solutions. However, several shortcomings of these models prevent them from being widely applied in reality. To address these shortcomings, advanced artificial intelligence algorithms in conjunction with the sufficient driving environmental factors are proposed based on real-life driving data. More specifically, three typical problems will be addressed in this thesis: Mandatory Lane Changing (MLC) suggestion at the highway entrance; Discretionary Lane Changing (DLC) intention prediction; Car-Following gap model considering the effect of cuts-in from the adjacent lanes.
For the MLC suggestion system, in which the main challenges are efficient decision making and high prediction accuracy of both non-merge and merge events, an additional gated branch neural network (GBNN) is proposed. The proposed GBNN algorithm not only achieves the highest accuracy among conventional binary classifiers in terms of great performance on the non-merge accuracy, the merge accuracy, and receiver operating characteristic score but also takes less time.
For the DLC, we propose a recurrent neural network (RNN)-based time series classifier with a gated recurrent units (GRU) architecture to predict the surrounding vehicles’ intention. It can predict the surrounding vehicles’ lane changing maneuver 0.8 s in advance at a recall and precision of 99.5% and 98.7%, respectively, which outperforms conventional algorithms such as the Hidden Markov Model (HMM).
Finally, drivers are typically faced with two competing challenges when following a preceding vehicle. A method is proposed to address the problem through an overall objective function of car-following gap and velocity. Based on this, seeking the strategic car-following gap translates to finding the optimal solution that minimizes the overall objective function. With the support of field data, the method along with concrete models are instantiated and the application of the method is elaborated.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Lane changing and car following are the two most frequently encountered driving behaviours for intelligent vehicles. Substantial research has been carried out and several prototypes have been developed by universities as well as companies. However, the low accuracy and high computational cost prevent the existing lane changing models from providing safer and more reliable decisions for intelligent vehicles. In the existing car-following models, there are also few models that consider the effects of cut-ins from adjacent lanes which may result in their poor accuracy and efficiency. To address these obstacles, advanced artificial intelligence algorithms combined with sufficient driving environmental factors are proposed due to their promise of providing accurate, efficient, and robust lane changing and car-following models. The main part of this thesis is composed of three journal papers. Paper 1 proposed a gated branch neural network for a mandatory lane changing suggestion system at the on-ramps of highways; paper 2 developed a recurrent neural network time-series algorithm to predict the surrounding vehicles’ discretionary lane changing intention in advance; paper 3 researched the strategic car-following gap model considering the effect of cut-ins from adjacent lanes.


title: Transillumination for Detection of Early Breast Cancer - Experimental and Computer Models

title: Breast Transillumination - Experimental and Computer Models

contributor:
Patterson, Michael S.
Health and Radiation Physics

subject:
transillumination
breast cancer
computer model

abstract:
Breast transillumination has received renewed interest as a noninvasive diagnostic method. However, it is still considered an experimental technique. Many aspects of the physics involved in transillumination have not yet been studied.
In this project transillumination was simulated by experiments with a simple breast phantom of realistic dimensions. The light source used was a HeNe laser. From the experiments we found how the contrast of images of a spherical inhomogeneity (simulating a lesion e.g. tumor or cyst) depended on its size and position. The contrast was also measured as a function of the scattering and absorption coefficients of the inhomogeneity.
The contrast of the image is shown to fit very well to the curve A(1-exp(-d(Σ^inh_eff – Σ_eff))), where a simple analytical model is developed, where A is identified to (1+B)^-1, B being a build-up factor depending on the surrounding medium and on the position of the inhomogeneity in the medium and d is identified as an effective optical diameter of the inhomogeneity.
A three dimensional numerical diffusion program was developed to model the transillumination situation. It was found that diffusion theory gave accurate predictions of the contrast within the constraints of the mathematical model. The three dimensional diffusion approximation and its limitations are discussed in some detail.

abstract: Thesis

abstract: Master of Science (MSc)


title: Mucopolysaccharidosis Type VII Evaluation of Bone Marrow Transplantation and Non-Autologous Somatic Cell Gene Therapy

title: Mucopolysaccharidosis Type VII

contributor:
Chang, P.L.
Biology

subject: gene therapy, cell gene therapy, non-autologous somatic cell, bone marrow transplant, bone marrow transplantation, mucopolysaccharidosis type vii, mucopolysaccharidosis

abstract:
Deficiency in β-glucuronidase activity (EC 3.2.1.31) leads to the lysosomal storage
disease mucopolysaccharidosis type VII not only in humans but also in a recently discovered
murine mutant, the gus^mps/gus^mps mouse. Clinical and pathologic abnormalities common to the human and mouse phenotypes include shortened life span, dwarfism, dysmorphic facial
features, skeletal deformities, corneal clouding, mental retardation and abnormal lysosomal
storage material in the brain and peripheral organs. In the first part of this thesis, neonatal
gus^mps/gus^mps mice and their normal littermates were transplanted with syngeneic normal bone marrow. Neurological function was then evaluated with two behavioral tests: the grooming test, a developmentally regulated and genetically based activity, and the Morris water maze test, which assessed spatial learning abilities. The results of these tests indicated that the behavioral deficits in the mutant mice were not restored to normal. Treated normal mice also showed significant functional deterioration, indicating the detrimental consequence of this therapy in the neonatal period. The second part of this thesis focused on a novel
approach to somatic gene therapy using microcapsules. A non-autologous fibroblast cell line
engineered to secrete high levels of β-glucuronidase was enclosed in perm-selective and
immuno- protective microcapsules and implanted into the peritoneal cavity of gus^mps/gus^mps mice. During the 4 weeks of therapy, the biochemical and histological abnormalities of the mutant mice had significantly improved. β-Glucuronidase activity was restored to >50% of normal in the plasma and 11.3%-65.8% in the kidney, liver and spleen. No significant activity was found in the brain. As well, the secondary elevations of other lysosomal enzymes such as β-hexosaminidase and α-galactosidase had decreased in the kidney, liver, and spleen. Urinary glycosaminoglycan content had decreased in the treated mutants indicating that the β-glucuronidase was exerting a therapeutic effect. However, after three and a half weeks of therapy, the treated mutants became severely ill and developed haemorrhagic ascites. Since normal mice treated with similar microcapsules showed no adverse effects, we hypothesized that an immune response had been generated against the foreign protein (β-glucuronidase) by the mutants, leading to the high morbidity. Thus in spite of the biochemical and histological correction observed after bone marrow transplantation and somatic cell gene therapy, the long term efficacy of these treatments needs to be further evaluated.

abstract: Thesis

abstract: Master of Science (MS)


title: Canonical Correlation and Clustering for High Dimensional Data

contributor:
Canty, Angelo
Mathematics and Statistics

subject: Machine Learning

subject: Correlation Clustering

subject: Sparse Canonical Correlation Analysis

subject: Regularized Canonical Correlation Analysis

subject: Skin Intrinsic Fluorescence

subject: Multi-view dataset

subject: Lasso

subject: Dimensionality reduction

subject: PrediXcan

subject: High dimensional data

abstract:
Multi-view datasets arise naturally in statistical genetics when the genetic
and trait profile of an individual is portrayed by two feature vectors.
A motivating problem concerning the Skin Intrinsic Fluorescence (SIF)
study on the Diabetes Control and Complications Trial (DCCT) subjects
is presented. A widely applied quantitative method to explore the correlation
structure between two domains of a multi-view dataset is the
Canonical Correlation Analysis (CCA), which seeks the canonical loading
vectors such that the transformed canonical covariates are maximally
correlated. In the high dimensional case, regularization of the dataset is
required before CCA can be applied. Furthermore, the nature of genetic
research suggests that sparse output is more desirable. In this thesis, two
regularized CCA (rCCA) methods and a sparse CCA (sCCA) method
are presented. When correlation sub-structure exists, stand-alone CCA
method will not perform well. To tackle this limitation, a mixture of
local CCA models can be employed. In this thesis, I review a correlation
clustering algorithm proposed by Fern, Brodley and Friedl (2005),
which seeks to group subjects into clusters such that features are identically
correlated within each cluster. An evaluation study is performed
to assess the effectiveness of CCA and correlation clustering algorithms
using artificial multi-view datasets. Both sCCA and sCCA-based correlation
clustering exhibited superior performance compare to the rCCA and
rCCA-based correlation clustering. The sCCA and the sCCA-clustering
are applied to the multi-view dataset consisted of PrediXcan imputed gene
expression and SIF measurements of DCCT subjects. The stand-alone
sparse CCA method identified 193 among 11538 genes being correlated
with SIF#7. Further investigation of these 193 genes with simple linear
regression and t-test revealed that only two genes, ENSG00000100281.9
and ENSG00000112787.8, were significance in association with SIF#7. No
plausible clustering scheme was detected by the sCCA based correlation
clustering method.

abstract: Thesis

abstract: Master of Science (MSc)


title: An Examination of Sensitivity of Photodynamic Therapy-Resistant HT29 Cells to Ultraviolet Radiation and Cisplatin

contributor:
Rainbow, A.J.
Biology

subject: photodynamic therapy-resistant HT29 cells

subject: ultraviolet radiation

subject: cisplatin

subject: sensitivity

abstract:
Photodynamic therapy (PDT) is a form of cancer treatment involving light, a
photosensitizer and oxygen, whereby the photosensitizer is preferentially taken up by
tumour cells, excited when exposed to light of the appropriate wavelength, and generates
cytotoxic excited singlet oxygen that damages and destroys cells. Photofrin is the only
approved photosensitizer for clinical use in treating esophageal and early and late lung
cancers in the U.S., Canada and several other countries. Despite its effectiveness in
treating some tumour types, Photofrin use has some limitations and thus photosensitizers
are continuously being studied to find more efficient ways of killing tumour cells. Previous reports have described the isolation of photodynamic therapy resistant human colon carcinoma HT29 cells. HT29/P14, HT29/All and HT29/N8 were isolated by repeated in vitro PDT treatment to the 1-10% survival level followed by regrowth of
single surviving colonies using the photosensitizers Photofrin, Aluminium
Phthalocyanine Tetrasulphonate (AlPcS4) and Nile Blue A respectively. These PDT
resistant HT29 variants all display increased levels of BNip3, Bcl-2 and the heat shock
protein 27 (Hsp 27), but decreased levels of Bax and the mutant HT29 p53 protein. Since
mutant p53 and increased expression of Hsp27 and Bcl-2 and have been associated with
resistance to various chemotherapeutic agents in some tumour cells, whereas Bax and
BNip3 are potent inducers of apoptosis, it was considered of interest to examine the
sensitivity of these PDT resistant HT29 variants to other cytotoxic agents. Cell sensitivity
to ultraviolet (UV) A radiation (UV A), a mixture of UV A and UVB (UV AlB), UVC, or cisplatin was determined by a comparison of the D37 values for clonogenic survival in
the variants compared to that in parental HT29 cells.
The HT29 PDT resistant variants were not cross-resistant to cisplatin or UVC. In
contrast, HT29/P14, HT29/All and HT29/N8 all showed a significant increase in
cisplatin sensitivity, while HT29/All cells also showed a significant increase in UVC
sensitivity. HT29/N8, and HT29/P14 both showed a significant increase in UVA
resistance compared to HT29 cells whereas HT29/All did not. HT29/P14 was the only
POT-resistant cell line significantly cross-resistant to UVA/B relative to HT29. While
HT29/P14 and HT29/All both showed a slight increase in resistance to Photofrinmediated
PDT compared to HT29/Parental, this increase was only significant for
HT29/All. However, HT29/N8 was significantly more sensitive to Photofrin-mediated
PDT than HT29/Parental. To complicate matters, clonogenic variability was observed
amongst the two HT29 sources examined, since one of the original HT29 cell lines
showed a significantly higher resistance to Photofrin-mediated PDT compared to the
other parental HT29 cells that were used to derive the PDT -resistant cell lines. To examine if the differences in sensitivity of the PDT-resistant cell lines compared to parental HT29 cells in response to cisplatin and UV radiation were due to
differences in DNA repair, host cell reactivation (HCR) experiments were performed
with a UVC damaged B-galactosidase reporter gene from the adenovirus
Ad5HCMVSp1LacZ. HCR ofthe UV-damaged reporter gene was reduced in HT29/All
(the cell line most sensitive to UVC) compared to the parental HT29 cells at high
multiplicities of infection of the virus. This suggests the possibility of a decreased DNA repair capacity for HT29/ A 11 cells. However, due to differences in cellular morphology
between HT29 and HT29/All cells, as well as possible differences in expression of the
reporter gene, it was inconclusive that the difference in HCR reflects a true difference in
DNA repair between HT29 and HT29/All cells.  Hsp27 over expression alone was not responsible for the increased cisplatin
sensitivity of the HT29 PDT resistant variants since there was no correlation of Hsp27
protein expression levels to l/D37 (used as a measure of sensitivity), for the cisplatin
colony survival assays. In addition, Hsp27 protein expression levels did not correlate
with UVC, cisplatin or UV A sensitivity suggesting that Hsp27 may be uniquely involved
in making cells more resistant to PDT. p53 but not BNip3 protein levels correlated with
sensitivity of cells to UV A, whereas no correlation was observed between p53 or Hsp27
protein expression levels and UVC sensitivity. p53 and p21 protein levels were not
altered in either parental HT29 or the HT29/P14 POT-resistant variant following UVC
and cisplatin exposure, respectively. In addition, introduction of wild-type p53 (using
infection of a replication deficient adenovirus vector encoding the wild-type p53 gene),
into parental HT29 or the PDT -resistant HT29/P 14 variant, had no effect on cisplatin
sensitivity compared to cells infected with a control adenovirus vector expressing the
LacZ gene. Taken together, these results suggest that the increased sensitivity of the PDT
resistant variants to cisplatin did not result from differences in p53-dependent cisplatininduced
cell cycle arrest. A strong correlation of cellular cisplatin sensitivity to the ratio of BNip3 to p53
protein levels, suggests that alterations in the expression of several different genes,
including a reduced expression of the mutant HT29 p53 protein and an increased
expression of BNip3, contribute to the increased cisplatin sensitivity of the HT29 PDT
resistant variants. It has been reported previously that apoptosis induced by BNip3 is
significantly inhibited by both wild type and mutated p53. Since pro-apoptotic BNip3 is
over expressed in all three PDT-resistant HT29 cell lines, and BNip3/p53 protein
expression levels were correlated to cisplatin sensitivity, this suggests that cisplatin kills
HT29 cells through a BNip3-mediated apoptotic pathway.

abstract: Thesis

abstract: Master of Science (MS)


title: Safe-AV: A Fault Tolerant Safety Architecture for Autonomous Vehicles

contributor:
Lawford, Mark
Wassyng, Alan
Computing and Software

subject: Safe-AV

subject: Functional Safety of Autonomous Vehicles

subject: STPA

subject: Systems-Theoretic Process Analysis

subject: Autonomous Vehicle Safety Architecture

subject: Autonomous Vehicle Hazard Analysis

abstract: Autonomous Vehicles (AVs) should result in tremendous benefits to safe human transportation. Recent reports indicate a global average of 3,287 road crash related fatalities a day with the blame, in most cases, assigned to the human driver. By replacing the main cause, AVs are predicted to significantly reduce road accidents -- some claiming up to a 90% reduction on US roads. However, achieving these numbers is not simple. AVs are expected to assume tasks that human drivers perform both consciously and unconsciously -- in some instances, with Machine Learning. AVs incur new levels of complexity that, if handled incorrectly, can result in failures that cause loss of human life and damage to the environment. Accidents involving SAE Level 2 vehicles have highlighted such failures and demonstrated that AVs have a long way to go. The path towards safe AVs includes system architectures that provide effective failure monitoring, detection and mitigation. These architectures must produce AVs that degrade gracefully and remain sufficiently operational in the presence of failures. We introduce Safe-AV, a fault tolerant safety architecture for AVs that is based on the commonly adopted E-Gas 3 Level Monitoring Concept, the Simplex Architecture and guided by a thorough hazard analysis in the form of Systems-Theoretic Process Analysis (STPA). We commenced the architecture design with a review of some modern AV accidents which helped identify the types of failures AVs can present and acted as a first step to our STPA. The hazard analysis was applied to an initial AV architecture (without safety mechanisms) consisting of components that should be present in a typical AV (based on the literature and our ideas). Our STPA identified the system level accidents, hazards and corresponding loss scenarios that led to well-founded safety requirements which, in turn, evolved the initial architecture into Safe-AV.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Structured Conductive Probes for Mass Spectrometry

contributor:
Moran-Mirabal, Jose M.
Chemistry

subject:
mass spectrometry
ambient ionization
probe ionization
biaxial wrinkling
polystyrene

abstract:
The introduction of ionization under ambient conditions has greatly simplified mass spectrometric analysis. Over past decade, ambient ionization mass spectrometry (MS) methods have revolutionized the way complex samples are analyzed under environmental conditions without requiring, in most cases, any sample pretreatment. Ambient ionization MS gained popularity among other analytical techniques due to its simplicity and its suitability for analysis of small and large molecules. However, ambient ionization methods can suffer from low accuracy and sensitivity due to matrix effects and interferences within complex samples, as well as from poor ionization efficiency. Matrix effects in ambient ionization are usually caused by ion suppression and may depend on different factors, e.g. matrix-to-analyte concentration ratios, proton affinities of analyte and matrix species.
To overcome these challenges, in this thesis we present a new approach where a probe is used both as a direct sampling device and as an efficient ambient ionization source. This approach leverages high surface area gold electrodes, fabricated through low-cost bench-top fabrication methods and functionalized using self-assembled alkyl thiol monolayers, as functional conductive sampling probes (FCSPs) for the extraction and concentration of analytes from a sample solution. FCSPs loaded with the targeted analytes were then used to demonstrate a new and highly efficient ionization approach, called Primary Ion Mass Spectrometry Source (PIMSS). In this approach, following capture, the bound analytes are directly desorbed into the mass spectrometer, where ionization is achieved solely through the extraction voltage applied to the probe. 3D-printing was used to design an interface to couple FCSPs to the mass spectrometer. In this work, we discuss a detailed method development and optimization stage and present capabilities of the proposed assay.

abstract: Thesis

abstract: Master of Science (MSc)


title: CHARACTERIZATION OF INCIDENT SENIOR HIGH-COST HEALTHCARE USERS IN ONTARIO: POLICY AND RESEARCH IMPLICATIONS

contributor:
Tarride, Jean-Eric
Health Research Methodology

subject:
senior
high healthcare users

abstract:
Background and Objectives: High-cost health care users (HCU) represent a minority of patients who consume a large proportion of health care resources. Due to their high burden on the healthcare system and internal heterogeneity, a better understanding of various segments of the HCU population is needed. The general objective was to advance our understanding of incident senior HCUs in the Canadian context so that we can advise health policy makers on potential strategies to prevent seniors transitioning to HCU and to identify priorities for further investigation.
Methods: A retrospective population-based matched cohort study was conducted using province-wide linked administrative data. The research employed a spectrum of advanced methods to accomplish the general objective, including the method of recycled predictions, random intercept two-part multi-level models, and stratified logistic regression.
Results: Total costs attributable to incident senior HCU status accounted for almost one-tenth of the provincial healthcare budget, with prolonged hospitalizations making a major contribution. Unplanned first (index) hospitalizations (IHs) in the incident year were considerably more common among HCUs, with ten conditions accounting for one third of their total costs. A lower risk of IH among HCUs was associated with residence in long-term care (LTC), attachment to a primary care provider, and recent consultation by a geriatrician. Although there was little variation in costs incurred by Ontario seniors for healthcare services they receive, access to the healthcare services varied greatly. The traditional drivers of costs and mortality (e.g., age, sex, health status) played little role in driving the observed variation in HCUs’ outcomes.
Conclusions: By answering research questions, this thesis advances our knowledge of the HCU population in Canada. Further exploration of the nature and quality of care that may be associated with HCU conversion and investigation of the regional variation in accessing specific healthcare services is warranted.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: A small group of patients that use the most of healthcare resources are called high-cost users (HCU). HCUs are often seniors. Policy makers need a better understanding of new senior HCUs to be able to prevent seniors from becoming HCU. This study used administrative data and advanced statistical methods. We found that almost one-tenth of the 2013 provincial healthcare budget was spent on new senior HCUs, mainly because of lengthy unplanned hospitalizations. Patients who lived in long-term care, had a primary care provider, or recently visited a geriatrician were less likely to have an unplanned hospitalization. Overall, healthcare costs were distributed equally to Ontario seniors, but access to healthcare services varied greatly. This variation could not be explained by differences in age, sex, or health status. This thesis advances our knowledge of HCUs in Canada. Additional research is needed into care associated with becoming HCU and provincial variation in accessing healthcare.


title: UNDERSTANDING THE ROLE OF VALUES IN LATIN AMERICAN HEALTH SYSTEMS

title: THE ROLES OF VALUES IN HEALTH SYSTEMS

contributor:
Wilson, Michael G.
Health Research Methodology

subject: values, health system financing, policy decision-making, Latin American Countries, LMIC, Chile, Colombia, AUGE plan, Ricarte Soto, T-760, Ley estatutaria, CIS, discourse analysis, case study

abstract:
It is often not clear how values are incorporated into policy decision-making about health systems. This is perhaps not surprising given the complexity of decision-making about health systems, the wide range of values prioritized (and advocated for) by different stakeholders, the broad array of sources for or mechanisms available to identify values, and the many ways in which values can drive policy decisions, as well as the reality that policymakers often do not want to be explicit about the values used in policy decision-making process. Using synthesis and qualitative research methods, this dissertation investigates the role of values in policy decision-making about health system financing in Latin America and contributes to the understanding of this field by providing insights for policy and research. The dissertation moves from a general and descriptive focus to a specific and explanatory focus.  First, a critical interpretive synthesis was used to develop a theoretical framework that identifies how and under what conditions values inform policy decision-making about health system financing in Latin American countries. In chapters 3 and 4, the focus narrows by using an embedded multiple-case study design that analyzes two specific decisions in each of Chile and Colombia. Frameworks that explain government agenda setting and policy development and the theoretical framework developed in chapter 2, are used to analyze these decisions. The second study (chapter 3) is a discourse analysis which qualitatively assess how declared values inform the four decisions in Chile and Colombia. The third study (chapter 4), draws on in-depth qualitative interviews to understand how and why policymakers and stakeholders use declared and undeclared values in those four decisions in Chile and Colombia.
The research chapters build on each other and make substantive, methodological and theoretical contributions. The dissertation provides a rich understanding of the roles of values in health system financing decisions through a critical interpretive synthesis and two qualitative studies, adding to the evidence base that stakeholders and policymakers can draw from when making or shaping policy decisions. These studies collectively build an understanding about what values inform the health policy process in Latin America, how those values work, under what conditions they come to be influential, how they are applied in real decisions, and why policymakers and stakeholders perceive that values play a role in real decisions. All of this evidence has contributed to the development a new theoretical framework about the roles of values in health systems.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Values are important at all stages of the policy process. However, it is often not clear how they are incorporated into policy decision-making about health systems. In Latin America, the study of the role of values and how they inform the prioritization, development, and implementation of policies in different contexts, is an emerging field.  This dissertation addresses key gaps in understanding by: 1) developing a framework, which can be used as a tool by policymakers and stakeholders to identify which values support or compete with their initiatives, how to make initiatives more socially supported, and how to focus policies according to the goals of the government and the health system; 2) analyzing how, based on media reports and governmental and non-governmental documents, values have informed two health system financing decisions in each of Chile and Colombia; and 3) examining the views and experiences of policymakers and stakeholders about how and why values were used in decision-making processes related to the same two policy decisions in each of Chile and Colombia.


title: DEPENDENCY-PRESERVING GENERALIZATION FOR DATA PUBLISHING

contributor:
Chiang, Fei
Computing and Software

abstract:
A vast amount of microdata about individuals and entities are collected and published for different purposes, such as demographic and public health research. However, data in its original form contains sensitive information about the individuals and publishing such data violates individuals privacy. To resolve this problem, privacy-preserving data publishing (PPDP) proposes many approaches to generate a public version of data that is practically useful and an individual’s privacy is protected. k-anonymity has emerged as an efficient approach to protect
the individual’s privacy by generalizing and/or suppressing portions of the data to make individuals indistinguishable in the released data.
Existing generalization algorithms focus on minimizing the information loss during generalization of attribute values. Any data dependencies defined over the data may be lost during this generalization step. A data dependency is a formal concept which is used to describe patterns in data. These patterns are employed during data analysis and data cleaning. A typical data dependency in a database is a Functional Dependency (FD): X -> Y expresses that the values of attribute X uniquely determine the values of attribute Y e.g. postal code -> province means
the value of postal code uniquely determines the value of province.                                        In this thesis, we study the problem of publishing data with two objectives. First, protecting the identity of the individuals in the published data through k-anonymity. Second, to provide high utility by preserving the instances of the data dependencies in the released data. We introduce dependency loss as a penalty measure for the anonymized public data. We define and study the problem of dependency-preserving generalization for finding a public database instance that guarantees privacy through k-anonymity and has minimum dependency loss. We present two clustering-based generalization algorithms that find such a database instance and we run experiments to show the comparable performance and improved utility in preserving data dependencies of our algorithms.

abstract: Thesis

abstract: Master of Science (MSc)


title: Analytic 3D Scatter Correction in Pet Using the Klein-Nishna Equation

contributor:
Nahmias, C
Physics

subject: 3d, 3d scatter correction, scatter correction, positron tomography, klein-nishina equation, klein nishina,

abstract:
In order to perform quantitative 3D positron tomography, it is essential that an accurate means of correcting for the effects of Compton scattered photons be developed. The two main approaches to compensate for scattered radiation rely on energy considerations or on filtering operations. Energy based scatter correction methods exploit the reduced energy of scattered photons to differentiate them from unscattered photons.
Filtered scatter correction methods require the measurement of scatter point spread functions to be used for convolution with the acquired emission data set. Neither approach has demonstrated sufficient accuracy to be applied in a clinical environment.
In this thesis, I have developed the theoretical framework for generating the scatter point spread functions for the general case of any source position within any nonuniform attenuation object. This calculation is based on a first principles approach using the Klein-Nishina differential cross section for Compton scattering to describe the angular distribution of scatter annihilation photons. The attenuation correction factors from transmission scans are included within the theory as inputs describing the distribution of matter in the object being imaged.
The theory has been tested by comparison with experimental scatter profiles of point sources which are either centered, or off-center in water-filled cylinders. Monte Carlo simulations have been used to identify the detector energy threshold where the single scatter assumption employed by the theory is most satisfied. The validity of a mean scatter position assumption, used in the development of the theory, is tested using analytic calculations of a non-uniform attenuation phantom. The physical effects most responsible for determining the shape of the scatter profiles, as well as the assumptions employed by several common scatter correction methods, are revealed using the analytic scatter correction theory.

abstract: Thesis

abstract: Master of Science (MS)


title: DNA Haplotypes Determination for Members of Families with Phenylketonuria (PKU)

title: DNA Haplotypes Determination

contributor:
Janicki, R.
Chang, P.
Computation

subject:
dna haplotypes
families
phenylketonuria

abstract: Phenylalanine hydroxylase deficiency causes phenylketonuria (PKU) in humans. PKU is a recessive genetic disease that affects 1 in 10000 births among the Caucasian population. Its gene locus is highly polymorphic in its DNA sequence among different individuals and patients with PKU. DNA polymorphisms at the PAH gene locus are used to obtain haplotypes through restriction enzyme analysis. So far forty-six distinct RFLP haplotypes have been discovered in the human population. In theory, 384 distinct RFLP haplotypes can exist. This project is to develop a program to assist the geneticists by obtaining haplotypes for each member of the PKU family. It uses information obtained from digestion of the DNA samples from the family members with the restriction enzymes. The restriction enzymes employed for this purpose are Pvuii, Bglii, EcoRI, Mspi, Xmni, Hindiii, and EcoRV. The program "PKU" generates all possible haplotypes for each member of the PKU family. The generated haplotypes may include haplotypes from the forty-six defined haplotypes list or from the 338 other haplotypes that may fit the description from the restriction enzyme analysis. The program then carries out an elimination phase during which the "extra" haplotypes that had been generated for the family members but whose presence was not supported by the data from the other family members are eliminated from the individuals' haplotype lists. The remaining haplotypes are then used to determine a sibling's carrier status of the PKU disease, i.e., whether or not a sibling is a carrier of the PKU disease.

abstract: Thesis

abstract: Master of Science (MS)