title: Confronting Theory with Evidence: Methods & Applications

contributor:
Hurley, Jeremiah
Racine, Jeffrey
Buckley, Neil
Mestelman, Stuart
Economics

subject:
Nonparametric Analysis
Experimental Economics
Environmental Economics
Health Economics

abstract:
Empirical economics frequently involves testing whether a theoretical proposition is evident in a data set. This thesis explores methods for confronting such theoretical propositions with evidence. Chapter 1 develops a methodological framework for assessing whether binary (`Yes'/`No') observations exhibit a discrete change, confronting a theoretical model with data from an experiment investigating the effect of introducing a private finance option into a public system of finance. Chapter 2 expands the framework to identify two discrete changes, applying the method to the evaluation of adherence to clinical practice guidelines. The framework uses a combination of existing analytical techniques and provides results which are robust and visually intuitive. The overall result is a methodology for evaluation of guideline adherence which leverages existing patient care records and is generalizable across clinical contexts. An application to a set of field data on supplemental oxygen administration decisions of volunteer medical first responders illustrates.

Chapter 3 compares the results of two mechanisms used to control industrial emissions. Cap and Trade imposes an absolute cap on emissions and any emission capacity not utilized by a firm can be sold to other firms via tradable permits. In Intensity Targets systems firms earn (owe) tradable credits for emissions below (above) a baseline implied by a relative Intensity Target. Cap and Trade is commonly believed to be superior to Intensity Targets because the relative Intensity Target subsidizes emissions. Chapter 3 reports on an experiment designed to test theoretical predictions in a long-run laboratory environment in which firms make emission abatement technology and output production decisions when demand for output is uncertain, and banking of tradable permits may or may not be permitted. Particular focus is placed on testing whether the flexibility inherent to Intensity Targets can lead them to be superior to Cap and Trade when demand is stochastic.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Borderline Personality Disorder: Examining Trajectories Of Development Among Adolescents

contributor: Clinical Epidemiology/Clinical Epidemiology & Biostatistics

subject:
adolescence
group-based trajectory modeling
borderline personality disorder

abstract:
Title: Borderline personality disorder: examining trajectories of development among adolescents

Background: Borderline personality disorder (BPD) tends to be highly comorbid with other disorders. In adolescence, information about the classification and development of BPD is in its early stages. There is limited empirical research available that investigates predictors of clinically significant symptom trajectories of the disorder using data collected in childhood. Given the enormous personal and societal costs associated with BPD, early detection and prevention is important. Clinical implications of this research include an improved understanding of risk factors and possible mechanisms for development of BPD symptomatology.

Objectives: To identify trajectories of BPD symptomatology in a Canadian sample of adolescents (N = 703) assessed at ages 13, 14, 15 and 16, while examining predictors of trajectory group membership assessed at age 12.

Methods: Data from the McMaster Teen Study was used to examine trajectories of BPD symptoms using group-based trajectory modeling. The influence of gender, depression, ADHD, family functioning and various sociodemographic variables as predictors of an individual’s group membership was tested. Chi-square, analysis of variance and multinomial logistic regression was used to analyze the data.

Results: A four-group trajectory model was most robust at describing BPD symptomatology in this age group. Univariate analyses supported female gender, depression and ADHD at baseline, parental age, marital status, education, and income as significant predictors of group membership. Female gender, depression and ADHD severity at baseline were significant predictors of group membership when adopting a multivariate approach. There is a greater prevalence of girls with higher depression and ADHD scores in the high-increasing features and BPD group.

Conclusion: Findings demonstrate four various developmental trajectories of BPD features. Results further the understanding of the factors associated with development of the disorder across time.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Information about the classification and development of borderline personality disorder (BPD) in adolescence is in its early stages. While evidence for similar construct validity to the adult disorder exists for adolescents, major gaps in knowledge regarding the stability in course of BPD symptoms and predictors of clinically significant symptom trajectories in this age group remain. As most clinicians will assess youth already having significant features of the disorder, early detection requires knowledge of the indicators that precede an unfavourable trajectory. This dissertation will help address these gaps by modeling trajectories of BPD symptoms in youth across ages 13-16, whilst examining factors influencing trajectory group membership.


title: Characterizing Binocular Rivalry Across the Lifespan

contributor:
Sekuler, Allison
Bennett, Patrick
Psychology

subject:
binocular rivalry
aging

abstract: Binocular rivalry allows for the unique examination of the neural processes associated with binocular vision by instigating a disruption of normal stereoscopic vision. Although binocular rivalry has been examined extensively in young adults, we know relatively little about its developmental trajectory across the human lifespan. This thesis provides a foundation for characterizing perceptual alternations during binocular rivalry in children and older adults, with a specific emphasis on expanding our understanding of binocular rivalry in older adults. From a theoretical perspective, my studies on aging and binocular rivalry have a specific significance, because unique changes that are known to occur with aging to certain neural mechanisms often associated with characteristics of perceptual alternations allows for the study of aging to serve as a test for many of the current models of binocular rivalry. Overall, my studies provide evidence for a significant transitional period in the binocular visual system at the age of 70 and older, and highlights the developmental trajectories of specific characteristics of binocular rivalry from childhood to senescence.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Development of a Low-Cost Incubator for Biosensor Application

contributor:
Filipe, Carlos
Chemical Engineering

abstract:
Extensive research has been conducted in the development of biosensors for the developing world in recent years. Despite the plethora of novel sensing systems and an ever increasing library of testable analytes, the implementation and use of biosensors as a commercial product has been limited thus far. This limitation is mainly economic, due to the high cost of construction of complex biosensors and short shelf lives. This research summarizes a step in the development of an ultra-low cost biosensor platform which will allow for a greatly increased flexibility in the application of biosensors throughout the developing world by allowing for complex systems to be simplified, satisfying the ASSURED criteria for an ideal biosensor.
Demonstrated in this work is the creation, characterization and testing of an ultra-low cost incubator for the purposes of PCR, bacterial cell culturing and cell lysis as an initial example of the great promise of the development of this low-cost, versatile and reliable biosensor platform.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Phosphate as an indicator of occupational intensity at shell midden sites on the central coast of British Columbia

contributor:
Cannon, Aubrey
Anthropology

subject:
phosphate
shell middens
British Columbia
archaeology

abstract: This thesis explores phosphate as an indicator of occupational intensity (i.e. as a function of scale and length of occupation) at shell midden sites on the central coast of British Columbia. Despite the prevalence of shell middens in coastal environments world-wide and the long history of elemental analysis in archaeology, shell middens are not routinely investigated for their chemical content. Ongoing research on the British Columbia central coast has shown clear associations between fish bone densities (NISP/L) and site area (m2), which have proven useful for characterizing variability among settlements in the region. This provided the opportunity and essential basis for investigating phosphate. Due to its general abundance, persistence, and established association with human activity, phosphate was expected to reflect previously inferred patterns in occupational intensity, which were based on fish bone density and site area data. Results show clear relationships between phosphate values, fish bone densities, and site area, which speaks to the utility of phosphate as an independent indicator of the relative intensity of residential activity among sites.

abstract: Thesis

abstract: Master of Arts (MA)


title: Fiber Reinforced Elastomeric Isolators for Bridge Applications

contributor:
Tait, Michael
Civil Engineering

abstract:
Bridge structures are considered a critical component in transportation systems. Bridges are divided into two main components, the superstructure and the substructure. Often the superstructure is integrated with the substructure. However, this type of integrated connection results in a direct transmission of straining actions developed within the superstructure to the substructure and vice versa. This consequently leads to a significant increase in the demand capacity of both elements. Examples of various actions that can develop in the superstructure include thermal expansion/contraction, pre-stress shortening/camber and creep. Deformation induced from ground motions during a seismic event is an example of an action that develops in the substructure. It has been proposed to isolate the superstructure and substructure by implementing bearings/isolators between these two components in order to reduce the transmission of straining actions. If the elements are used only to transfer the vertical loads as well as to accommodate the rotational and/or lateral deformations then it is referred as a bearing. However, if the bearings are also used for seismic isolation of the bridge then they are defined as isolators. Thus, isolators also act as bearings, but bearings may not be capable of acting as isolators.
Elastomeric bearings/isolators are among the most common and widely used bearing type. Traditional elastomeric bearings are comprised of elastomer layers reinforced with steel plates/shims and are called Steel Reinforced Elastomeric Isolators (SREI). However, the application of these bearings has been limited to high-importance structures. This is due to the fact that SREI are characterized by their high cost and weight. These features result from labour intensive manufacturing costs and significant weight of the steel shims and end plates. As such, it has been proposed that a reduction in weight and cost could be achieved if the steel reinforcement was replaced with another type of material having comparable mechanical properties to steel, such as fiber fabric sheets. This relatively new type of isolator is called a Fiber Reinforced Elastomeric Isolators (FREI). FREI can be constructed without thick steel end plates and are placed, unfastened, between the superstructure and the substructure. In this case, the isolator is denoted as an unbonded-FREI (U-FREI). In addition to the expected reduction in weight and potential cost, U-FREI can be manufactured and cut to the desired shape and size from large sheets using a standard band saw. Furthermore, U-FREI are able to detach from the contact supports by rollover and lift-off under excessive deformations in the lateral and rotational direction, respectively. This is due to the unbonded boundary conditions and the negligible flexural rigidity of the fiber reinforcement.
Research studies have revealed that U-FREI have desirable performance characteristics for building applications. This dissertation investigates the feasibility of extending the use of          U-FREI to bridge applications. Experimental testing was carried out to study U-FREI behaviour under a wide range of bridge loading conditions in the vertical, rotational, and lateral directions. Numerical studies were also completed to assess the resulting stress and strain state within U-FREI. Finally, the seismic performance of a bridge, equipped with a U-FREI isolation system was evaluated via non-linear time history analysis using a large suite of earthquake motions.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: The effects of a single bout of high intensity aerobic exercise on the long-term memory of younger adults

contributor:
Heisz, Jennifer
Kinesiology

subject:
High intensity aerobic exercise
Long-term memory
Younger adults
Neurobiology of stress
Academic performance
Physical fitness
Cortisol

abstract: University evaluations often reflect an individual’s ability to memorize and recall lecture material during exams. Consequently, the ability to effectively encode, store, and later retrieve information is an integral part of learning and academic success. Notably, students who are more physically active tend to have better academic performance. The neurobiology of stress is a strong candidate for the mechanism underlying this exercise-cognition interaction. Given that exercise is a physical stressor, it is hypothesized that exercise-induced adrenocortical activations increase cortisol levels. Critically, cortisol increases memory consolidation for newly learned information. One hundred twenty-eight young adults (36 males; age: M±SD =19.47±1.55 years) viewed a video lecture before exercise (n = 41), after exercise (n = 42), or after rest (n = 45). The exercise was high intensity interval training on a cycle ergometer and memory for the lecture material was assessed using a multiple-choice quiz conducted 14 minutes and 48 hours after the lecture. There was a significant positive correlation between aerobic fitness and grade point average [r(95) = 0.22, p < .05], immediate recall [r(100) = 0.39, p < .001], and delayed recall [r(98) = 0.28, p < .01]. A mixed model ANOVA found a significant main effect of group on comprehension of the lecture material, F(2, 96) = 3.34, p < .05, revealing greater memory benefits at both 14 minutes and 48 hour delays for those who exercised compared to those who did not exercise; however, pairwise comparisons found this effect specific to the exercise post group. There was also a main effect of group on cortisol levels, F(2, 107) = 3.97, p < .05; however, only the exercise prior group exhibited significantly greater levels than the control group. Thus cortisol levels collected during the experimental session did not clearly differentiate the exercise conditions or reflect the observed memory benefits for the exercise post group. This may have resulted from the gradual increase in cortisol following exercise that had time to increase when exercise was completed at the beginning of the exercise session (exercise prior) rather than at the end (exercise post). Overall, this study suggests that both physical fitness and an acute bout of aerobic exercise are associated with academic and memory performance. More research is needed to understand the mechanism.

abstract: Thesis

abstract: Master of Science (MSc)


title: The storm you cannot see: Exploring the biological and clinical effect of depressive symptoms on executive function in adolescents after concussion

title: Depressive symptoms and executive dysfunction in adolescents after concussion

contributor:
DeMatteo, Carol
Rehabilitation Science

subject:
concussion
depression
executive function
fMRI
adolescents
brain injury

abstract:
Concussions impact the cognitive abilities and emotional wellbeing of adolescents. More specifically, adolescents exhibit signs of executive dysfunction and depressive symptoms following concussion. Evidence suggests a link between cognitive performance and depressive symptoms in concussed populations; however, concussion research has focused mostly on cognitive deficits and emotional dysregulation in singularity, rather than as an integrated system. Therefore, the purpose of this thesis is to explore the clinical and biological relationship between depressive symptoms and executive dysfunction following mild traumatic brain injury (mTBI) or concussion in pediatric populations.
Chapter 1 provides an overview of the literature surrounding children and youth with concussive injury as it pertains to executive dysfunction and depressive symptoms. Chapter 2 describes the clinical nature of the relationship between depressive symptoms and executive dysfunction. The results demonstrate that individuals with elevated depressive symptoms had comparable performance to individuals with normal levels of depressive symptoms on executive function scores. This included their performance on an inhibitory control task in which emotional distractors were presented. Regardless of levels of depressive symptoms, adolescents with concussive injury displayed impaired executive functioning compared to normative data, which emphasizes the importance of evaluating executive function following concussion.
Chapter 3 involves the use of functional brain imaging to explore the physiological differences between adolescents with average and elevated depressive symptoms on emotion-mediated inhibitory control processes. The group as whole did not display activity in the frontostriatal regions that are associated with inhibitory control, which suggests a potential impairment in this network. Adolescents with elevated depressive symptoms displayed fewer areas of activity compared to adolescents with average levels of depressive symptoms. As a number of individuals (particularly those with elevated depressive symptoms) were injured in the occipital region of the skull, the coup-contrecoup impact may have resulted in frontal lobe injury.
Faces were used to evoke emotional processing throughout the inhibitory control task. The results revealed that adolescents with elevated depressive symptoms were more likely to engage in brain regions subserving evaluative processing of social interactions. This might suggest that depressive symptoms display differences in physiology when emotional stimuli are present.  These findings provide insight into the role the environment plays in contributing to the cognitive demands placed on adolescents recovering from concussion.
Chapter 4 reviews the key messages derived from these results and describes their clinical relevance. This exploration may lead to a more holistic understanding of concussion and a better approach to injury management, particularly for adolescents who express higher levels of depressive symptoms following concussion.

abstract: Thesis

abstract: Master of Science (MSc)


title: Optimization of an Image-guided Radiation Therapy Protocol for Advanced Stage Lung Cancer

contributor: Radiation Sciences (Medical Physics/Radiation Biology)

subject:
image registration
image-guided radiation therapy
lung cancer

abstract:
Image-guided radiation therapy (IGRT) provides accurate and precise tumour targeting. To ensure adequate coverage in IGRT, a planning target volume (PTV) margin is added around the target to account for treatment uncertainties. Treatment plans are designed to deliver a high percentage of the prescription dose to the PTV; thus, portions of healthy tissue are also subjected to high radiation dose.  IGRT employs dedicated devices that enable visual assessment of some treatment uncertainties, such as variations in patient set-up.  Safe and effective IGRT delivery requires adherence to disease site-specific protocols that describe process details such as imaging technique, alignment method, and corrective action levels. Protocol design is challenging since its effect on treatment accuracy is currently unknown. This thesis aims to understand the interplay between lung IGRT protocol parameters by developing a framework that quantifies geometrical accuracy.
     Deformable image registration was used to account for changes in target shape and size throughout treatment. Sufficient accuracy was considered when at least 99% of the target surface fell within the PTV. This analysis revealed that the clinical 10 mm PTV margin can be safely reduced by at least 2 mm in each direction.
     Evaluation of IGRT accuracy was extended to spinal cord alignment. Simulations were carried out with various matching strategies to correct for set-up error, including rotational off-sets. Inappropriate combinations of matching strategies and safety margins resulted in sub-optimal geometrical coverage.  Various lung IGRT protocol options were recommended to optimize accuracy and workflow efficiency. For example, an 8 mm PTV margin can be used with spinal cord alignment, a 4 mm cord margin, and up to 5° of rotational error. A more aggressive protocol involved a 6 mm PTV margin with direct target alignment, a 5 mm cord margin, and a 4° rotational tolerance.

abstract: Thesis

abstract: Master of Science (MSc)


title: Towards Generating Software Modularizations

contributor:
Carette, Jacques
Lawford, Mark
Computing and Software

abstract: Program generators are programs that produce other programs, thereby saving time and effort. Program families can be encoded in a generator to produce all members of such a family while leveraging automation and reducing duplication. Through multi-stage programming (MSP) in the form of MetaOCaml, a generator has been created for multiple partial implementations of the KeyWord in Context (KWIC) example from Parnas' seminal paper on modular decomposition. What makes this work novel is the generation of different program modularization implementations, as well as different programming paradigms (imperative or functional). This is achieved by using a common abstract internal representation of the signatures of the system components, and applying them to a single abstract representation of the commonalities of the components. Thus the work challenges commonly held perceptions of concepts such as program modularization and programming paradigm by being able to generate members of a program family that varies on both these aspects.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Exploring strategies used by older drivers during ingress and egress and their varying physical mobility

contributor:
Vrkljan, Brenda
Rehabilitation Science

subject:
older drivers
hand contact locations
physical mobility
vehicle transfer
vehicle ingress
vehicle egress
self-reported measures
objective measures
Other Rehabilitation and Therapy

abstract: The overall purpose of the present study was to examine the strategies used by older adults with regard to both foot placement and hand contact location as they enter (ingress) and exit (egress) a vehicle. A cross-sectional study was used to identify and, in turn, examine the participants’ ingress and egress strategies in relation to their physical mobility and other characteristics. All participants had a valid driver’s license and they completed the following: 1) demographic (self-report) questionnaires; 2) clinical measures of physical mobility (i.e. Timed Up and Go, Berg Balance Scale, One Legged Stance test, Rapid Pace Walk test). A physical mobility index was also developed using these clinical measures. During both ingress and egress, older drivers were more likely to use one-foot strategies, which are considered less stable. Participants who used one-foot ingress and egress strategies had better overall physical mobility. The armrest location was used by the majority of older drivers for both ingress and egress, and is used most often during one-foot strategies. Participants who used multiple hand contact locations during ingress/egress had lower physical mobility than participants who used a single hand contact location or made no contact with the vehicle. Finally, the results from this study can inform educational materials targeting this population and determining design changes to the automobile that can prevent injuries to older drivers.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: Maternal obesity remodels the maternal intestinal microbiota and is associated with altered maternal intestinal and placental function

contributor:
Sloboda, Deborah M.
Health Sciences

subject: Maternal obesity, Pregnancy, Intestinal microbiota, Placenta, Developmental origins of health and disease

abstract: The prevalence of overweight and obesity have risen to epidemic proportions. Overweight and obesity are prominent risk factors for the development of chronic disease including diabetes, cardiovascular disease and cancer. Especially pronounced in women of reproductive age and children, the obesity epidemic represents a major threat to global health. Maternal obesity is a key predictor of childhood obesity and diseases of metabolic origin in adulthood. Previous work has demonstrated that the exposure to early life adversity, in the context of maternal obesity, is associated with an increased risk of metabolic disease and obesity in the offspring later in life.  Although the mechanisms outlining the relationship between maternal and offspring obesity remain unclear, the intestinal microbiota has come forth as a promising area of research. To understand the factors involved in the maternal intestinal microbial shifts with healthy pregnancy, the preliminary study focused on investigating whether female sex-steroid hormones mediate maternal intestinal microbial shifts in non-pregnant, regularly cycling female mice. We have identified that intestinal microbial shifts are not associated with sex-steroid hormone fluctuations. The second study examined whether maternal intestinal microbial shifts that occur during obese pregnancy were associated with altered inflammatory signaling and function of the maternal intestine and placenta at a critical period of development; embryonic (E) day 14.5. Females fed a high fat diet (HFD) were significantly heavier at mating and throughout gestation compared to CON. At E14.5, High fat (HF) dams displayed increased adiposity, hyperglycemia, hyperinsulinemia, hyperleptinemia and were insulin resistant. Pregnancy and maternal obesity resulted in shifts in the maternal intestinal microbiota, where the most significant increase in microbial relative abundance was exhibited by the mucin degrading genus, Akkermansia.  At E14.5, maternal intestinal microbial shifts were associated with higher maternal intestinal NFκB activity in all sections of the maternal intestine, most notably in the maternal colon. Maternal obesity was associated with increased Muc5ac mRNA levels and a modest increase in CD3+ T cells in the maternal colon at E14.5. However, maternal intestinal permeability was unchanged between groups. In the placenta, mRNA levels of key signaling components in the pro-inflammatory toll-like receptor 4 (TLR4) pathway; TRAF6, NFκB and potent pro-inflammatory cytokine TNF-α were increased and in HF females. Maternal obesity was associated with an increase in CD3+ T cells in the junctional zone (JZ), but not in the labyrinth zone (LZ) of the placenta at E14.5. These findings were associated with increased mRNA levels of critical nutrient transporters; glucose transporter 1 (GLUT1) and sodium-coupled neutral amino acid transporter 2 (SNAT2) and a modest increase in glucose transporter 3 (GLUT3) in HF placentae compared to CON. These data identify the mechanistic signaling pathways and cell types involved in modulating the intrauterine environment, thus contributing to the current literature devoted to the investigation of the developmental origins of obesity.

abstract: Thesis

abstract: Master of Science (MSc)


title: Novel vascular risk markers in community-dwelling adults with and without stroke

contributor:
Tang, Ada
Rehabilitation Science

subject:
stroke
vascular health
rehabilitation

abstract: Stroke is the leading cause of adult neurological disability. Novel markers of vascular disease progression, such as arterial stiffness and endothelial function, may provide early and sensitive stroke risk detection. However, measurement properties of these novel vascular risk markers have not yet been established in the post-stroke population, nor has the association between these risk markers and measures of physical function. Moreover, given that subclinical vascular disease may initially manifest as a decline in cognitive function, understanding vascular disease progression in older adults with and without cognitive impairment may provide information regarding early stroke risk. This study aimed to investigate 1) test-retest reliability and between-side differences in novel vascular risk markers in individuals with stroke, 2) differences in arterial stiffness and endothelial function between older adults without cognitive impairment, with cognitive impairment, and with stroke, and 3) relationships between novel vascular risk markers and physical function in individuals with and without stroke. Participants were 50-80 years of age, able to ambulate ≥10 meters, and for those with stroke, ≥1 year post-stroke. Carotid-femoral, carotid-radial, and femoral-foot pulse wave velocity (cfPWV, crPWV, and ffPWV, respectively) were used to quantify systemic arterial stiffness, and compliance and distensibility were used to quantify local carotid arterial stiffness. Flow-mediated dilation (FMD) was used to quantify endothelial function. Findings revealed almost perfect test-retest reliability of cfPWV (ICC>0.91, P<0.0001) and substantial test-retest reliability of FMD in individuals with stroke (ICC>0.70, P<0.01). There were no between-side differences in novel vascular measures, no differences in these measures across subgroups of increasing vascular risk, and a positive correlation between cfPWV and walking speed. Findings suggest that in the post-stroke population, cfPWV and FMD may be the most appropriate measures of vascular risk progression, that it may be more clinically feasibly to assess these measures on the unaffected side.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Novel measures of arterial health, such as arterial stiffness and endothelial function, may provide early stroke risk detection. This study aimed to assess the day-to-day reliability and between-side differences of these new arterial measures in people with stroke, and to also investigate relationships between these measures and cognitive function in older adults with and without stroke. Arterial stiffness was assessed using pressure sensors that measure the speed of the pulse waves, and endothelial function was assessed using ultrasound to measure the capacity of the arteries to expand following an increase in blood flow. Results found that the most well-established measures of arterial health were reliable and there were no between-side differences in any measures. No relationships were observed between arterial measures and cognitive function. Overall, this study increases knowledge surrounding novel measures of arterial health in older adults with and without stroke.


title: Exploring microbial community dynamics: Positive selection for gain of RpoS function in Escherichia coli & microbial profiling of the Niagara Region

contributor:
Schellhorn, Herb
Golding, Brian
Morton, Richard
Biology

subject:
microbiology
microbial genetics
escherichia coli
RpoS
osmotic
salt
gain
mutation
reversion
second-site
environmental
metagenomics
diversity
community
taxonomy
water quality monitoring
Niagara
Lake Ontario
Lake Erie
16S sequencing
QIIME
indicator
OTU

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

abstract: The effect of changing environmental conditions on microbial population structure can be observed at both the species and community level. Within the Escherichia coli species, null mutations in the RpoS stationary phase regulator are commonly selected by growth on poor carbon sources. In contrast, mutations which restore RpoS function may provide a selective advantage for cells exposed to environmental stress. The loss and subsequent restoration of RpoS form a population-level switch for adaptation within poor carbon and high stress environments. To investigate selection for RpoS reversion, we exposed rpoS-deficient E. coli to high salt concentrations and assessed the phenotype of presumptive mutants. 3-9% of salt-resistant mutants contained reversion mutations within rpoS, while in 91-97% the loss of RpoS function was maintained and mutations at alternative gene loci were identified. These results show that RpoS function can be restored in deficient E. coli under selective pressure. At the community level, the application of next-generation sequencing (NGS) technology to characterize environmental microbial diversity can potentially augment traditional water quality monitoring methods. To investigate the use of NGS in identifying microbial taxa within the Niagara Region, we collected water samples from Lake Erie, Lake Ontario, and nearby areas and examined the metagenome of microbial communities. A QIIME (Quantitative Insights Into Microbial Ecology) analysis of sequence data identified significant differences in relative microbial abundance with respect to sample metadata (e.g. location and subtype), significant correlations between relative abundance and quantitative parameters (e.g. Escherichia coli counts and fecal DNA markers), and detected pathogen-containing taxa at a relative abundance of 0.1-1.5%. These results show that sequence-based analyses can be used in conjunction with traditional identification methods to profile the metagenomic community of environmental samples and predict water quality. Both within-species and community-wide analyses thus offer insight into how microbial populations respond and adapt to environmental fluctuations.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The effect of changing environmental conditions on microbial population structure can be observed at both the species and community level. Within the Escherichia coli species, we investigated reversion of loss of function mutations in the RpoS protein regulator in high salt conditions and identified RpoS restoration under selective pressure. At the community level, we examined the microbial DNA of water samples from the Niagara Region under select environmental conditions and assessed the viability of next-generation sequencing in augmenting traditional water quality monitoring methods. Both within-species and community-wide analyses offer insight into how microbial populations respond and adapt to environmental fluctuations.


title: On the origin of obesity: A critical review of biological, environmental, and cultural drivers of genetic risk among human populations

contributor:
Meyre, David
Health Research Methodology

subject:
obesity
evolution
natural selection
thrifty genotype hypothesis
pleiotropy
genetics

abstract:
Genetic predisposition to obesity presents a paradox: how do genetic variants with such a detrimental impact on human health persist through evolutionary time? Numerous hypotheses, for instance the thrifty genotype hypothesis, attempt to explain this phenomenon, yet fail to provide a satisfying answer to the modern obesity epidemic. In this critical review, I appraise existing theories explaining the evolutionary origins of obesity and explore novel biological and sociocultural agents of evolutionary change that may help explain the distribution of obesity and leanness predisposing variants in modern human populations.
Gene pleiotropy and adaptations to diverse environmental niches may explain the rise and subsequent selection of obesity risk alleles. The regulation of gene expression by epigenetic mechanisms may serve as a stochastic factor affecting the manifestation of obesity phenotypes. Finally, exposure to malnutrition and disease epidemics in the wake of colonialism, culturally mediated notions of attractiveness and desirability, and diverse mating systems – including forced copulation, consanguinity and polygamy – may play a role in shaping the human genome. In short, I posit that in order to explain ethnic variation in obesity susceptibility, we must examine the origin of physiological adaptations and understand the sociocultural experiences of individuals and populations.
As an imperative first step towards the identification of important drivers of obesity gene evolution, this review will inform empirical research focused on testing evolutionary theories by way of population genetics and mathematical modelling. Ultimately, these data will promote a better understanding of the aetiology of obesity and are expected to guide the development of targeted management, treatment, and prevention strategies.

abstract: Thesis

abstract: Master of Science (MSc)


title: INVESTIGATING THE MECHANISM OF ACTION OF GUANOSINE BY THE G1 RECEPTOR

contributor:
Jiang, Shucui
Mishra, Ram
Neuroscience

subject:
Guanosine
GPCR
G1 receptor
Binding Assay

abstract: When released extracellularly, the purine nucleoside guanosine (Guo) can exert a wide range of physiological effects in vitro and in vivo. Guo can induce the release of neurotrophic factors such as nerve growth factor (NGF) and brain derived neurotrophic factor (BDNF) and can initiate the differentiation, growth and proliferation of neurons and glia. While structural and pharmacological evidence support the existence of a putative Guo binding site in the rat brain, there is a paucity of information on the mechanism through which Guo exerts these effects. Through bioinformatic research, our lab has identified an orphan G-protein coupled receptor as the first Guo receptor (termed G1R). The aim of this dissertation is to determine the mechanism of action of Guo using radioligand binding assays. It is hypothesized here that G1R is a distinct purinergic receptor for Guo. Using the calcium phosphate (CaP) co-precipitation (co-i.p.) method, Drosophila Schneider 2 (S2) cells were stably and transiently transfected with G1R recombinant cDNA. A series of binding assays using tritiated Guo ([3H]-Guo) showed no difference in binding between CaP transfection groups and wild S2 controls that do not endogenously express G1R, suggesting that the [3H]-Guo may not have a high binding affinity for the G1R binding site. Preliminary experiments using the Lipofectamine® 3000 to transfect S2 cells showed higher G1R mRNA expression as well as increased binding affinity to Guo when compared to the CaP transfected groups. This suggests that the results in the CaP mediated groups may be due to low transfection efficiency. In conclusion, transfections using the CaP method resulted in too low of a transfection efficiency to see a difference in binding affinity between wild S2 and transfected S2 cells. Findings from this work can be used to further examine the binding relationship of Guo to the G1R and optimize transfections using S2 cells and radioligand binding assays using purine based compounds.

abstract: Thesis

abstract: Master of Science (MSc)


title: Fault Detection and Identification of Vehicle Starters and Alternators Using Machine Learning Techniques

contributor:
Habibi, Saied
Mechanical Engineering

subject:
Machine Learning
Fault Diagnosis
Fault Detection and Identification
Fault Detection
Fault Identification
Starters
Alternators
Automotive Industry
Artificial Intelligence
Deep Learning
Data classification
Data clustering
Neural Network
Support Vector Machine
Label Propagation
Unknown Faults Detection

abstract: Artificial Intelligence in Automotive Industry

abstract:
Cost reduction is one of the main concerns in industry. Companies invest considerably for better performance in end-of-line fault diagnosis systems. A common strategy is to use data obtained from existing instrumentation. This research investigates the challenge of learning from historical data that have already been collected by companies. Machine learning is basically one of the most common and powerful techniques of artificial intelligence that can learn from data and identify fault features with no need for human interaction. In this research, labeled sound and vibration measurements are processed into fault signatures for vehicle starter motors and alternators. A fault detection and identification system has been developed to identify fault types for end-of-line testing of motors.
However, labels are relatively difficult to obtain, expensive, time consuming and require experienced humans, while unlabeled samples needs less effort to collect. Thus, learning from unlabeled data together with the guidance of few labels would be a better solution. Furthermore, in this research, learning from unlabeled data with absolutely no human intervention is also implemented and discussed as well.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: MAINTENANCE OF THE ROVER SITTER POLYMORPHISM AND THE EFFECT OF MALE-MALE COMPETITION ON MATING SUCCESS IN FRUIT FLIES

title: ROVER/SITTER POLYMORPHISM & SEXUAL SELECTION IN FRUIT FLIES

contributor:
Dukas, Reuven
Psychology

subject:
Animal behaviour
Drosophila
Rover/Sitter
Courtship Interference

abstract: The fruit fly, Drosophila melanogaster is an exceptional model species for understanding both proximate and ultimate causes of variation in behaviour. Here, we have examined two behaviors: foraging and mating. We discuss these research projects in turn. Almost 40 years ago, the classic foraging behaviour polymorphism rover/sitter was first discovered. Recently, evidence has suggested that the polymorphism is maintained by negative frequency-dependent selection at the larval stage. In two separate experiments we failed to replicate negative frequency-dependence in the survival of rover and sitter larvae. However, we empirically demonstrated differences in burrowing behaviour between the rover and sitter morphs which may be a possible mechanism causing the negative frequency-dependent relationship between the morphs. Future replication of negative frequency-dependence is necessary if we are to understand the maintenance of this polymorphism in nature. We examined mating behaviour from the perspective of two mechanisms of sexual selection: female choice and male-male competition. The study of sexual selection requires careful isolation of these mechanisms. Owing to difficulties in experimental design, studies have yet to properly separate and quantify the individual effects of female choice and male-male competition in fruit flies. Here, we designed a novel arena to assess true female choice. We then used this arena to test the effect of male courtship interference on mating outcomes. However, due to an unforeseen amount of male harassment of females in the arena, we withhold any strong conclusions about the effect of male-male interference behaviour. We also attempt to demonstrate the potential for sexual selection on traits associated with interference behaviour in males.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Role of the Vasculature and Immune System in Models of Glaucoma

contributor:
Ball, Alexander K.
Neuroscience

subject:
Glaucoma
Optic Nerve Crush
Retinal Ganglion Cells
Elevated Intraocular Pressure
Vasculature
Immune System
Neurodegeneration
Glial Cells

abstract: Purpose: The purpose of this study was to investigate the role of the vasculature and immune system in models of glaucoma. Vascular changes have been implicated in glaucoma. As well there is mounting evidence that the immune system plays a role in the disease. It is my hypothesis that the vasculature and immune system play a role in the retinal response to injury in models of glaucoma. Methods: Immunohistochemistry, in vivo retinal imaging (Bright field, fluorescent, optical coherence tomography), Slit2 injections and Evan’s blue labeling were used to investigate vascular and immune changes associated with retinal ganglion cell death after optic nerve crush up to 28 days after injury. Histology, immunohistochemistry, and intravascular labeling were utilized to investigate the role of the vascular degeneration and the systemic immune response to elevated intraocular pressure in 8-16 week old AP-2β Neural Crest Cell Knockout (AP-2β NCC KO) mice. Results: The vascular and immune responses to optic nerve crush were not found to play a significant role in the response to retinal ganglion cell death. Conversely the role of vascular degeneration and immune cell recruitment to the retinas of AP-2β NCC KO mice demonstrated that these factors played a significant role in the retinal response to injury. Conclusion: The vasculature and immune system play a varied role in the response to retinal injury and neurodegeneration depending on the model being studied. The vascular and immune changes were of minimal significance in acute optic nerve crush injury. On the other hand, the chronic injury associated with elevated intraocular pressure in AP-2β NCC KO mice was associated with significant vascular degeneration and systemic immune cell infiltration.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Complex regional pain syndrome: advancing rehabilitation through better evaluation and treatment

contributor:
MacDermid, Joy C.
Rehabilitation Science

subject:
complex regional pain syndrome
outcome measurement
rehabilitation

abstract:
Introduction: Complex regional pain syndrome (CRPS) is a form of neuropathic
pain that sometimes develops after trauma or surgery. While diagnostic criteria
have been debated, there is agreement participation in rehabilitation should be
the primary management. However, there are gaps in the evidence guiding
assessment and treatment choices for individuals with CRPS. The purpose of
this thesis was to advance the rehabilitation of CRPS by 1) ongoing development
and refinement of evaluations for the specific symptoms of CRPS, and 2) to
investigate effectiveness of a new treatment (somatosensory rehabilitation)
posited to address allodynia associated with CRPS.
Methods: We conducted a series of 4 studies addressing various aspects of
CRPS assessment and the somatosensory rehabilitation method: a) a cognitive
debriefing study for content validation of the Patient-Reported Hamilton Inventory
for CRPS; b) English translation and cultural validation of the Radboud
Evaluation of Sensitivity; c) a retrospective cohort study of the effectiveness of
somatosensory rehabilitation for allodynia in the upper limb; and d) a pilot study
of the somatosensory rehabilitation method to consider the measurement
properties of the embedded evaluation tools of allodynography and the rainbow
pain scale, and to provide estimates for future controlled trials of effectiveness.
Results: The cognitive debriefing study identified potentially problematic items,
and constructs which needed enhancement in future versions of the PR-HICRPS
assessment. The second paper reported the translation and cultural
validation of the RES-E, finding support for test-retest reliability, internal
consistency, and preliminary evidence for construct validity and reproducibility.
The third paper presented preliminary evidence of a strong effect size for the
SRM in an uncontrolled consecutive cohort. Finally, the fourth paper provides an
interm analysis of the psychometric properties of allodynography and the rainbow
pain scale, and estimates large sample sizes will be required for future trials.
Discussion and Conclusion: None of the assessment tools described herein is ready for unrestricted use in clinical practice or research. Although the effect size estimates for somatosensory rehabilitation from the retrospective cohort are encouraging, the incomplete pilot data suggests large, multi-site trials and careful selection of the primary outcome measures will be required for future, rigorous trials of this method.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Complex regional pain syndrome (CRPS) is a painful collection of symptoms that can develop after trauma. Why it happens is not well understood, but most scientists and health care providers agree that rehabilitation should be the primary focus for managing the painful consequences of this condition. There is a need for simple and accurate ways to assess CRPS, as well as to treat it. Better assessment will support treatment that is more targeted to the symptoms of the individual. One of the very challenging symptoms experienced by persons with CRPS is painful sensitivity of the skin, also known as allodynia. This thesis describes the development and testing of several new patient-reported assessments for CRPS and allodynia, as well as two studies on a new method of treatment for allodynia.


title: A numerical study of cohomogeneity one manifolds

contributor:
Wang, Mckenzie
Mathematics and Statistics

subject: Differential Geometry

abstract:
This dissertation explores numerical solutions for the cohomogeneity one
Einstein and Ricci soliton equations when the principal orbits are SU(3)/T^2 and
Sp(3)/Sp(1)^3. We present new numerical evidence for steady, expanding solitons as
well as Einstein metrics with positive scalar curvature. In the case of steady solitons
we produced a one-parameter family of solutions. In the expanding case, we generated
a two-parameter family of solutions and in particular in the negative Einstein case
we generated a one-parameter family of solutions. In the compact Einstein case we
found numerical evidence for an in nite number of Einstein metrics.

abstract: Thesis

abstract: Master of Science (MSc)


title: Investigating the Role of the RNA-Binding Protein MUSASHI-2 (MSI2) in Normal Hematopoiesis and Leukemia

contributor:
Hope, Kritstin
Biochemistry

subject: RNA-Binding Protein, Musashi, Hematopoiesis

abstract:
Musashi-2 (MSI2), a member of the Musashi family of RNA-binding proteins, is thought to play a critical role in the maintenance of stem cell populations and in the formation of aggressive tumours. Multiple studies indicate that MSI2 plays an important role in the maintenance of hematopoietic stem cell (HSC) populations and recent studies in humans identify MSI2 as an independent prognostic factor for overall survival in patients with Acute Myeloid Leukemia (AML). Importantly, though correlative studies implicate MSI2 as a contributor to aggressive disease in human AML, no study to date has attempted to analyze the functional role of MSI2 in primary human AML samples. Furthermore, though MSI2 is critical for the maintenance of HSCs, the mechanisms through which MSI2 functions are unknown. The work presented in this thesis elucidates the biochemical mechanisms through which MSI2 functions and examines the functional role of MSI2 in human AML.
	Using a lentiviral-mediated shRNA knockdown of MSI2, I demonstrate that MSI2 is critical for the maintenance of human AML. A loss of MSI2 greatly impairs the ability of AML samples to maintain disease in a xenotransplantation assay.  MSI2 is an RNA binding protein that is thought to repress the translation of target mRNAs in the cytoplasm and prevent the maturation of microRNAs (miRNAs) in the nucleus. The targets of MSI2 are believed to be potent regulators of stem-ness and dysregulation of these targets could very well contribute to neoplastic transformation. Cross-linking immunoprecipitation followed by next generation sequencing (CLIP-Seq), revealed the RNA binding properties of MSI2 and the RNA targets bound by MSI2. To identify novel MSI2 protein interactors, the MSI2 locus was endogenously tagged with the promiscuous biotin ligase BirA* and subjected to BioID analysis. When compared to appropriate controls, we were able to robustly identify proteins that associate with MSI2. The analysis of one of these protein binding partners, Insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) reveals a critical role in the normal function of HSCs.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
The hematopoietic system is responsible for the production of billions of mature cells everyday. These mature cells are “differentiated”, meaning that they have gone through a process that has allowed them to become specialized to perform a very specific role. Throughout the process of differentiation, most functional cells lose their ability to proliferate. The continued production of these functional cells comes from a pool of rare, quiescent, hematopoietic stem cells (HSC). These cells maintain the production of mature cells throughout the lifetime of an organism. The Musashi-2 (MSI2) protein has been identified as a protein that is critical for the normal function of HSCs. By altering the levels of the MSI2, it is possible to greatly impair or enhance the activity of HSCs. Moreover, correlative studies implicate MSI2 as a contributor to aggressive Acute Myeloid Leukemia (AML), a disease that occurs when HSCs become dysregulated. Despite its important roles in normal and abnormal hematopoiesis, very little is known about how MSI2 functions and whether it actually has a functional role in AML. We set forth to identify mechanisms through which the MSI2 protein functions and to prove that MSI2 contributes to the maintenance of human AML.
We reveal that the MSI2 protein plays a critical role for the maintenance of human AML and identify novel pathways through which the protein functions. Importantly, MSI2 is known to interact with mRNA in order to alter post-transcriptional gene expression. We thoroughly characterize the RNA-binding characteristics of MSI2 and identify a plethora of MSI2 RNA targets. In an unbiased manner, we also identify a list of MSI2-protein interactors. We identify one MSI2 protein-binding partner, Insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) that is preferentially expressed in the most immature fraction of HSCs and is critical for the proper function of HSCs.


title: Examining the impact of rehabilitation interventions on quality of life (QoL) in people with amyotrophic lateral sclerosis (ALS)

contributor:
Letts, Lori
Rehabilitation Science

subject:
amyotrophic lateral sclerosis
rehabilitation
quality of life

abstract:
The purpose of this thesis is to examine how rehabilitation interventions, specifically physiotherapy (PT), occupational therapy (OT), and speech and language pathology (SLP) or a combination of these interventions affect quality of life (QoL) in people with amyotrophic lateral sclerosis (ALS).
The purpose of the first study (Chapter 2) was to synthesize qualitative research through a qualitative meta-synthesis on the potential of rehabilitation interventions to maintain and/or improve QoL from the perspective of people with ALS. The literature search for this study was conducted using the SPIDER strategy and five articles were included. Four themes emerged: 1) the concept of control; 2) adapting interventions to disease stage; 3) struggles with interventions; and 4) barriers between healthcare providers and patients. The evidence suggests that from the perspective of people with ALS, PT, OT, and SLP interventions, or a combination of these interventions have the potential to be beneficial in the management of people with ALS and to optimize QoL.
The systematic review (Chapter 3) aimed to determine the effectiveness of rehabilitation interventions, in particular PT, OT and SLP interventions or a combination of these interventions, on QoL in people with ALS. The PICO search strategy was used and six studies were included: three RCTs, two cohort studies, and one cross-sectional study.  A narrative synthesis of interventions was conducted as the included studies were not sufficiently similar thus data extracted were not adequate for conducting meta-analyses.  Need to briefly discuss interventions, which outcomes you included and inconsistency in results across studies.  Due to the limited evidence, it was difficult to determine the exact effects of the interventions from each rehabilitation field to affect QoL for people with ALS. The evidence suggests that more research is required; currently therapists need to rely on their clinical expertise, expert opinions, and theoretical models to select the most effective interventions to sustain or improve QoL in people with ALS. Future research needs to take into consideration the needs of people with ALS to evaluate the impact of rehabilitation interventions on QoL.

abstract: Thesis

abstract: Master of Science (MSc)


title: Mixture models for ROC curve and spatio-temporal clustering

contributor:
McNicholas, Paul D
Mathematics and Statistics

subject:
Finite mixture models
ROC curve
Spatio-temporal data
Functional data
Model-based clustering
EM algorithm

abstract:
Finite mixture models have had a profound impact on the history of statistics, contributing to modelling heterogeneous populations, generalizing distributional assumptions, and lately, presenting a convenient framework for classification and clustering.

A novel approach, via Gaussian mixture distribution, is introduced for modelling receiver operating characteristic curves. The absence of a closed-form for a functional form leads to employing the Monte Carlo method. This approach performs excellently compared to the existing methods when applied to real data.

In practice, the data are often non-normal, atypical, or skewed. It is apparent that non-Gaussian distributions be introduced in order to better fit these data. Two non-Gaussian mixtures, i.e., t distribution and skew t distribution, are proposed and applied to real data.

A novel mixture is presented to cluster spatial and temporal data. The proposed model defines each mixture component as a mixture of autoregressive polynomial with logistic links. The new model performs significantly better compared to the most well known model-based clustering techniques when applied to real data.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: An Efficient Implementation of a Robust Clustering Algorithm

contributor:
McNicholas, Paul D.
Mathematics and Statistics

subject:
clustering
classification
statistical learning
machine learning
robust
computational statistics
mixture models

abstract:
Clustering and classification are fundamental problems in statistical and machine learning, with a broad range of applications. A common approach is the Gaussian mixture model, which assumes that each cluster or class arises from a distinct Gaussian distribution. This thesis studies a robust, high-dimensional extension of the Gaussian mixture model that automatically detects outliers and noise, and a computationally efficient implementation thereof.

The contaminated Gaussian distribution is a robust elliptic distribution that allows for automatic detection of ``bad points'', and is used to make robust the usual factor analysis model. In turn, the mixtures of contaminated Gaussian factor analyzers (MCGFA) algorithm allows high-dimesional, robust clustering, classification and detection of bad points. A family of MCGFA models is created through the introduction of different constraints on the covariance structure. A new, efficient implementation of the algorithm is presented, along with an account of its development. The fast implementation permits thorough testing of the MCGFA algorithm, and its performance is compared to two natural competitors: parsimonious Gaussian mixture models (PGMM) and mixtures of modified t factor analyzers (MMtFA). The algorithms are tested systematically on simulated and real data.

abstract: Thesis

abstract: Master of Science (MSc)


title: THE EFFECTS OF ONE-ON-ONE MEDICATION TRAINING ON MEDICATION ADHERENCE IN PATIENTS WITH MOOD DISORDERS AND THE EFFECT OF ELECTROCONVULSIVE THERAPY ON COGNITIVE FUNCTIONING IN PATIENTS WITH DEPRESSION

title: TREATMENT ADHERENCE AND ADVERSE EFFECTS IN MOOD DISORDERS

contributor:
McKinnon, Margaret
Neuroscience

subject:
Mood Disorders
Medication Adherence
Depression
Cognitive Functioning
ECT

abstract:
Mood disorders (MD) are among the most common mental disorders worldwide. Low treatment adherence and treatment resistance are two of the most substantial challenges facing clinicians who treat persons with MD. This thesis examined: (1) a pilot study investigating whether a one-on-one personalized medication training program, called PIMM/SAM, improves medication adherence in persons with MD; and (2) a systematic review and meta-analysis on the effects of electroconvulsive therapy (ECT) on cognitive functioning in persons with depression.
To evaluate the impact of PIMM/SAM on medication adherence, a randomized controlled trial was launched in a mood disorders inpatient unit to compare PIMM/SAM (partnership in medication management/self-administered medication) program to standard prescribing practice (SPP). Over follow-up in the feasibility portion of the trial, participants in the PIMM/SAM group (n = 7) held fewer negative beliefs about medications and had lower depersonalization scores compared to participants in the SPP group (n = 5). Between-group differences on the Medication Adherence Rating Scale favoured the PIMM/SAM group, but were not statistically significant.
To examine the effects of bilateral versus unilateral ECT on cognitive performance in persons with TRD, 18 studies across 10 different cognitive domains were meta-analyzed. In the 8- to 30-day timeframe post-ECT, persons who received bilateral versus unilateral ECT had over double the odds of worse cognitive performance in global cognition, non-verbal memory delayed recall, verbal memory immediate and delayed recall, subjective memory, and verbal memory immediate recall.
A personalized medication training program in a mood disorders clinic may have positive implications for medication adherence. The trial to evaluate PIMM/SAM versus SPP is ongoing and further evidence about the training program is expected within the next 12 months. The systematic review and meta-analysis showed that cognitive performance was worse in persons who received bilateral versus unilateral ECT in some cognitive domains at 8 to 30 days post-treatment.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Mood disorders (MD), including major depressive disorder (MDD) and bipolar disorder, are among the most common mental disorders worldwide. Treating MD is a challenge because of long treatments, the presence of other illnesses, treatment side effects, problems with memory, attention, and decision-making, a lack of understanding about medications, or incorrect beliefs about medication (BAM). Persons with MD who do not respond to drug treatment are often given electroconvulsive therapy (ECT).
This thesis explored the challenges of treating persons with MD through: (1) a pilot study examining whether a one-on-one personalized medication training program, called PIMM/SAM, would help persons with MD take their medications as prescribed; and (2) a study of the effects of ECT on cognitive functioning in depression. Results: (1) participants randomized to PIMM/SAM group held fewer negative BAM than participants receiving standard care; (2) evidence showed worse cognitive functioning in persons who received more intense forms of ECT.


title: Examining The Perception of Emotional Facial Expressions in Early Childhood

contributor:
Rutherford, M.D.
Psychology

subject:
Face Perception
Emotions
Categorical Perception
Emotion Understanding
Child Development
Visual Development

abstract:
Adults perceive basic emotional facial expressions as discrete categories using
categorical perception. Within categorical perception, discrimination of facial emotional expressions is better for between category faces than within category faces. In this thesis, I examined the developmental trajectory of categorical perception in early childhood. I also examined the relationship between sensitivity to physical differences in facial emotional expressions and the use of emotion labels in toddlers. In Chapter 2, I found that infants before 12-months failed to discriminate between category faces along a happy-sad continuum. In contrast, evidence suggest that 9- and 12-month old infants categorically perceived faces along a happy-angry continuum. These findings suggest that categorical perception may not develop concurrently for all emotions. In Chapter 3, I found that toddlers by 26-months of age categorically perceived faces along a happy-sad continuum. These results highlight the long developmental trajectory of categorical perception of facial emotional expressions across early childhood. In Chapter 4, I found a relationship between perceptual sensitivity to physical differences between happy and sad faces, and the emotion vocabulary size in 26-month-olds. This relationship suggests that learning about emotions may utilize information from multiple domains, and that learning in one domain may influence the development of another. The perception of facial emotional expressions is an essential component of early social emotional development. Categorical perception is a mechanism that aids in organizing complex social information from faces into actionable categories. The research in this thesis advances our understanding of early social perceptual development and the process that allow us to successfully navigate in the social world.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract:
Humans are experts at reading faces. Specifically, they are capable of interpreting
complex social information from faces, including emotions, and using this information to navigate social situations. In order to organize facial emotional information, humans use a mechanism called categorical perception to quickly and efficiently sort facial emotional information into discrete categories. Inferences can be made about members within a category, which aids in the prediction and production appropriate behaviours. However, there has been limited research into the development of categorical perception in early childhood. The key goal of this thesis was to develop infant and toddler appropriate methodologies that capture the development categorical perception. In this thesis, I found that categorical perception does not develop uniformly across all ages and between different emotions. Results suggest that perceptual sensitivity to differences in facial emotional expression may be influenced by the use of emotion labels, or vice versa.


title: PLASTICITY MECHANISMS IN VISUAL CORTEX: ANIMAL MODELS AND HUMAN CORTEX

title: MECHANISMS OF REINSTATED PLASTICITY

contributor:
Murphy, Kathryn
Neuroscience

subject:
plasticity
NMDA
AMPA
glutamate
GABA
metaplasticity
Human development
fluoxetine
D-serine
Ube3A
PSD-95
silent synapses
visual cortex
vision
amblyopia

abstract:
A holy grail in neuroscience is being able to control plasticity to facilitate recovery from insult in the adult brain. Despite success in animal models, few therapies have translated from bench to bedside. This thesis is aimed at addressing 2 major stumbling blocks in translation. The first gap is in our understanding of the mechanisms of plasticity-enhancing therapies, and the second is in our understanding the relevance of those mechanisms for human development.
In chapters 2 and 3, I address the first gap by asking whether fluoxetine, a selective serotonin reuptake inhibitor, which reinstates juvenile-like plasticity in adult animals, reinstates a juvenile-like synaptic environment. We found evidence to suggest that fluoxetine is neuroprotective, as it rescued all of the MD-driven changes, but surprisingly we found no evidence that fluoxetine recreated a juvenile-like synaptic environment, with the exception of Ube3A. Ube3A is necessary for critical period plasticity, indicating that Ube3A may play a crucial in enhancing plasticity in the adult cortex.
In chapter 4, I address whether D-serine, an amino acid that has similar effects to fluoxetine in terms of both plasticity and anti-depression, shares a common neurobiological signature with fluoxetine. I found that D-serine’s effects were strikingly similar to fluoxetine, with respect to markers of the E/I balance, indicating that it may be an effective alternative to fluoxetine.
In chapter 5, I address the second gap by studying the development of 5 glutamatergic proteins in human V1. Some changes occurred early, as would be predicted from animals studies, while other changes were protracted, lasting into the 4th decade. These results will help guide the use of treatments, like fluoxetine, which effect glutamatergic proteins.
iv
Together the findings in this thesis significantly advances our understanding of the mechanisms involved in restating plasticity in the adult cortex, and their relevance to humans.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract:
Neurons change to rewire, adapt, and recover. This plasticity is greatest early in development, so much research has focused on bringing it back in adults. There has been amazing progress in animal models, but this has not translated to humans. Two reasons for this are that we do not fully understand the mechanisms of these treatments in animals or whether those mechanisms are relevant for humans. My thesis addresses this by studying how 2 treatments, fluoxetine and D-serine, affect proteins that are important for plasticity, and how those proteins develop in the humans.
I found that these treatments are neuroprotective, but do not recreate a younger state. One interesting standout is an increase in Ube3A, which is essential for juvenile plasticity. I also found that much of human development is similar to animals, but the time course for some proteins is uniquely prolonged in humans. These findings have implications for the use of plasticity-enhancing treatments at different ages.


title: Time-invariant, Databased Modeling and Control of Batch Processes

contributor:
Mhaskar, Prashant
Chemical Engineering

subject:
Batch
Control
Model Identification
Time-invariant

abstract:
Batch reactors are often used to produce high quality products because any batch that
does not meet quality speci cations can be easily discarded. However, for high-value
products, even a few wasted batches constitute substantial economic loss. Fortunately,
databases of historical data that can be exploited to improve operation are often
readily available. Motivated by these considerations, this thesis addresses the problem
of direct, data-based quality control for batch processes. Speci cally, two novel datadriven
modeling and control strategies are proposed.
The  rst approach addresses the quality modeling problem in two steps. To begin,
a partial least squares (PLS) model is developed to relate complete batch trajectories
to resulting batch qualities. Next, the so called missing-data problem, encountered
when using PLS models partway through a batch, is addressed using a data-driven,
multiple-model dynamic modeling approach relating candidate input trajectories to
future output behavior. The resulting overall model provides a causal link between
inputs and quality and is used in a model predictive control scheme for direct quality
control. Simulation results for two di erent polymerization reactors are presented
that demonstrate the e cacy of the approach.
The second strategy presented in this thesis is a state-space motivated, timeinvariant
quality modeling and control approach. In this work, subspace identi cation
methods are adapted for use with transient batch data allowing state-space dynamic
models to be identifi ed from historical data. Next, the identifi ed states are related
through an additional model to batch quality. The result is a causal, time-independent
model that relates inputs to product quality. This model is applied in a shrinking
horizon model predictive control scheme. Signi cantly, inclusion of batch duration
as a control decision variable is permitted because of the time-invariant model. Simulation
results for a polymerization reactor demonstrate the superior capability and
performance of the proposed approach.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
High-end chemical products, ranging from pharmaceuticals to specialty plastics, are
key to improving quality of life. For these products, production quality is more
important than quantity. To produce high quality products, industries use a piece
of equipment called a batch reactor. These reactors are favorable over alternatives
because if any single batch fails to meet a quality specifi cation, it can be easily discarded.
However, given the high-value nature of these products, even a small number
of discarded batches is costly.
This motivates the current work which addresses the complex topic of batch quality
control. This task is achieved in two steps:  first methods are developed to model
prior reactor behavior. These models can be applied to predict how the reactor
will behave under future operating policies. Next, these models are used to make
informed decisions that drive the reaction to the desired end product, eliminating
o -spec batches.


title: Objective Method of Quantifying Sensorineural Hearing Loss

contributor:
Becker, Sue
Trainor, Laurel
Psychology

abstract:
This master’s thesis presents results from a study evaluating several different methods of
assessing hearing loss. Twenty-seven participants with sensorineural hearing loss (SNHL)
completed a combination of clinical, psychoacoustic, and objective tests. Each test
chosen in this study yielded a measure of either inner hair cell loss (IHC) loss or outer hair
cell (OHC) loss. The goal of this thesis was to evaluate whether variance in audiometric
thresholds in patients with SNHL could be predicted based on different tests of specific
hair cell loss. The tests chosen were included because each addresses specific deficits
audiograms do not measure, such as holes in hearing and loudness growth. The tasks
were the psychophysical tuning curve (PTC) task, psychoacoustic loudness growth, and
an auditory brainstem response (ABR) loudness growth task. All tests were completed
at 1000 Hz and at 4000 Hz and used an octave-band chirp stimulus. The chirp stimulus
simultaneous increases signal to noise ratio, and decreases testing time.
It was hypothesized that audiometric thresholds could be predicted through some
combination of tests that measure IHC and OHC loss. Since the ABR loudness growth
task is an objective test, it was hypothesized that it would be a key predictor at both
frequencies. We hypothesized that the subjective tests would only be predictors of
audiometric thresholds at 1000 Hz.
We were able to significantly predict audiometric thresholds at 1000 Hz from 2 different
regressions: 1) tip frequency (from the PTC task) and loudness ranking (from
the psychoacoustic loudnesss growth task), as well as from 2) tip frequency and wave V
amplitude (from the ABR loudness growth task). None of the predictors were able to
explain audiometric threshold shifts significantly at 4000 Hz. In addition, ABR Wave V
amplitude correlated with loudness ranking at 1000 Hz but not at 4000 Hz. However,
ABR wave V amplitude correlated with stimulus intensity at both frequencies. This thesis
provides evidence that ABR loudness growth tasks provide more information about
patients compared to more subjective tasks.

abstract: Thesis

abstract: Master of Science (MSc)


title: Designing a Management and Referral Tool for Patients with Multiple Chronic Illnesses in Primary Care Settings

contributor:
McKibbon, Ann
eHealth

subject: Comorbidity, Complex Patients, Data Mining, Predictive Analytics, Association Analysis

abstract:
Some local health organizations in Ontario (e.g., Local Health Integration Network or LHINs) have put forward a strategic objective to identify patients with preventable high cost healthcare service usage (e.g., hospitalizations, emergency department [ED] visits). To attain this goal, primary care service providers, who are considered the entry point to the health system, need tools to help diagnose, treat and refer those patients identified as being potential high users of the health care system.
The goal of this study was to develop a management and referral tool to identify, manage and refer patients living with multiple comorbidities to specialized care teams such as Health Links.
Data used in this analysis were obtained from the Canadian Primary Care Sentinel Surveillance Network (CPCSSN) primary care data holdings. The dataset created for this study contained 14,004 patient records.
Data analysis techniques included use of both statistical and predictive analytic tools. The base models included four data mining classification algorithms: Decision Tree, Naïve Bayes, Neural Network and Clustering. The predictive modeling approach was complemented by an association analysis.
The one-way ANOVA analysis indicated that age and health status (number of conditions, and individual medical conditions) identified statistically significant differences in patient utilization of health services.
Results from the predictive analytics showed that patient age and patient medical conditions, as well as number of medical conditions for each patient (5 or more) could be used as criteria to develop tools (e.g. searches, reminders). Specifically, Parkinson disease, dementia and epilepsy were found to be important predictors (i.e. most frequently associated with) the top 4 most prevalent conditions (hypertension, osteoarthritis, depression and diabetes) within the population of the study. The association analysis also revealed that chronic obstructive pulmonary disease (COPD) was closely associated with the top 4 most prevalent conditions. Based on the findings of this study, Parkinson Disease, dementia, epilepsy and COPD can be used to identify patients with complex medical needs who are likely to be high users of the healthcare system and to be considered for early, personalized intervention.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


contributor: Reader Geography

abstract: Title: The Nature of Consumer Behaviour: An Investigation of the Determinants of Store Loyalty, Author: Philip C. Welsh, Location: Thode

abstract:
In recent years there has been a growing interest
regarding the nature of consumer behaviour at the retail
level. This interest is a result of a desire to understand
the movement patterns of urban dwellers by both academics
and the commercial sector of society. By using the Cardiff
Consumer Panel as a data source for investigation this
research paper examined the purchasing behaviour of
consumers in the United Kingdom. Implementation of a simple
operational model called the 'run test', indicated the
degree of store loyalty that individuals exhibited. The
results of this research identified an inconsistency between
shopping behaviour at an aggregate level and behaviour at
the individual level. In an attempt to explain this
inconsistency, further analysis was carried out and the
results suggested that store loyalty may be linked to
various aspects of household characteristics, including
vehicle ownership and life-cycle stage.

abstract: Thesis

abstract: Bachelor of Arts (BA)


contributor:
Eyles, John D.
Geography

abstract: Title: Elderly Accessibility: Should Transport and Mobility be a Major Factor in Planning Senior Housing Facilities?, Author: Ted W. Wiedener, Location: Thode

abstract:
What the following study wishes to reveal to Geographers and Gerontologists, is the extent to which the location of the elderly and the location of services, are accessible to one another.

It is the author's understanding that the relative location of elderly housing facilities, oriented towards independent forms of housing options (Group 1; Independent Living), facilitate in maintaining maximum physical community interaction and social relations.

Concern over elderly accessibility relative to the location of elderly housing facilities within urban centres are expressed. Therefore, a comparative case study between
three senior housing facilities in Hamilton Ontario was formulated to determine if one area of Hamilton is indeed more accessible in terms of services used. Downtown, East End and Mountain locational constructs were used as research sites.

A questionnaire, the 'Elderly Accessibility Questionnaire' was developed in order to focus upon the demand side of locational accessibility issues concerning accessibility to (stereotypical) services and housing location.

Descriptive statistics were used to analyze the data.

No specific area was determined to be more accessible to seniors, however, perceptions concerning a senior's immediate environment and neighbouring environments were observed to be distinctive between areas. Mountain seniors perceived themselves as the most accessible relative to the Downtown and East End locations.

Various access to services was examined. Staple and stereotypical services as the grocery store, drug store, bank, doctor's office or clinic, religious centre, recreational
centre, library, places to eat out, and parks were analyzed with respect to accessibility and residential location. Staple services as grocery stores and drug stores were frequented most often by means of walking, and distances to such facilities were perceived to be less than a one mile
journey according to seniors. Bus transportation was also observed to be highly utilized by many seniors.

Transportation and personal mobility of the elderly, in terms of accessibility to services used, should therefore be consciously considered, if not mandatory legislation in the
planning of senior housing facilities.

abstract: Thesis

abstract: Bachelor of Arts (BA)


title: Using early antipsychotic response to predict treatment outcome in patients with first-episode psychosis

contributor:
Mazurek, Michael F.
Neuroscience

subject:
antipsychotic
schizophrenia
early response
bipolar disorder

abstract: Antipsychotic medications are highly effective in the treatment of patients experiencing first-episode psychosis. However, some patients do not respond to the first antipsychotic medication they are given, and may require trials of several drugs before an effective treatment is found. While antipsychotics may take months to achieve their full effect, recent evidence suggests that it is possible to predict whether a patient will respond to a particular drug by assessing early response after as little as 2 weeks of treatment. Assessing early antipsychotic response has the potential to improve treatment strategies for psychotic patients, but there is still a great deal of uncertainty about what early response can and cannot predict, and how the predictive value of early response differs among drugs and patient populations. The work presented in this thesis addresses some of the most pressing questions about early antipsychotic response in several samples of antipsychotic-naive patients with first-episode psychosis. This work demonstrates that: (1) the appropriate time point at which to assess early response differs between antipsychotic drugs; (2) early improvement in depressive and manic symptoms predicts treatment outcome, while early improvement in anxiety symptoms may not; (3) strong early response is associated with decreased rates of extrapyramidal side-effects; (4) early antipsychotic response can predict long-term treatment outcome at least 2 years after treatment initiation; (5) the appropriate time point at which to assess early response differs in patients who receive antidepressant treatment in addition to antipsychotic treatment; (6) patients with a poor early response may benefit from being switched to another antipsychotic, particularly one with a distinct receptor binding profile. These results highlight several weaknesses of the current literature, suggesting that early antipsychotic response should be assessed differently depending on the psychiatric symptom profile of each patient and the specific medications that are being used. However, the data presented here also emphasize the potential therapeutic value of assessing early response. The ability of early response to predict treatment outcome appears to be even greater than previously thought, and understanding how to appropriately use this important assessment to guide treatment strategies may improve the efficiency and efficacy of treatment for psychotic patients.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A New Method to Estimate Light Echo Apparent Proper Motion Vectors

contributor:
Welch, Douglas L.
Physics and Astronomy

subject:
Cas A
Tycho
Supernovae
Historical supernovae
Light echoes
Apparent proper motion

abstract:
This thesis presents a new method to estimate the Apparent Proper Motion (APM)
vector and its uncertainty for supernova light echoes (LEs) and tests its usefulness in
practice on LEs due to two old Galactic supernovae (SNe) - Cas A and Tycho. Ten
instances of two-dimensional cross-correlation (2-D CC) of images containing light
echoes at diferent epochs are employed to examine how well this new method works
in practice. The images selected for this work originate from KPNO 4m Mosaic 1.1
images and were originally processed by the Pan-STARRS pipeline.
All the APM estimates reported in this thesis are within 1sigma of estimates based on
supernova distance and age provided reasonable inclinations are assumed. It was found
that several factors tend to reduce the expected precision of this method and these
include: 1) the existence of more than one LE feature for each epoch, 2) longer intervals
between the two epochs lead to a bias, and 3) the existence of dust filaments at more
than one depth along the line of sight. The results of three LE fields which were in
common with the previous studies by Rest et al. in 2008 and 2011, were compared and
a good agreement was found between them in difference-images with the same time
interval.
Since pixel values have a significant role in the introduced method, a control region
is considered to eliminate the defect of the irrelevant residuals to the LE features.
Hence, the introduced method was not straightforward. In addition, this method was
not thoroughly manual independent, as the benefits of the visual measurement from
the previous method reported by Rest et al. (2008) and (2011) were adopted for this
method. However, compared to the previous manual technique, there were much less
manual measurements were taken for the whole LE features in one frame. Considering
all the challenges, the CC method is favourable as the APM vector uncertainty can be
determined, which has not been achievable with previous method before.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Brain-Body Interface in Aneurysmal Subarachnoid Hemorrhage –  Outcome Prognostication and Creation of Decision Making Algorithm

contributor: Clinical Epidemiology/Clinical Epidemiology & Biostatistics

subject:
brain-body interactions
aneurysmal subarachnoid hemorrhage
outcome prognostication
decision making algorithm

abstract:
Background
Aneurysmal subarachnoid hemorrhage can lead to multi-organ disturbances as a result of central and autonomic nervous system injuries.  Alterations in the brain-body interface associated with this cerebrovascular disorder have significant impact on patient morbidity and mortality.  Knowledge of the most pertinent brain-body associations, as well as demographic, systemic and neurological prognostic factors on hospital admission, along with their progression during hospitalization can assist the clinician and patient family in the process of treatment decision making.

Objectives
The goals of this dissertation are to:
(1)	synthesize and critically appraise the methodologic quality of existing studies that derive clinical predictor tools and clinical predictors used to determine outcome prognosis in patients with aneurysmal subarachnoid hemorrhage (SAH),
(2)	synthesize and critically appraise the methodologic quality of existing studies that derive pathophysiologic mechanisms of brain-body associations in aneurysmal SAH,
(3)	 provide new insights into the significance of brain-body associations that are essential in influencing outcome in aneurysmal SAH, and
(4)	create a decision making algorithm for aneurysmal SAH patients that is useful in bedside prognostication and clinical treatment decision making.

Methods
Existing prospective and retrospective cohort studies and randomized controlled trials were included in the systematic review investigating prognostic factors and clinical prediction tools associated with determining the neurologic outcome in adults patients with aneurysmal SAH.  Existing prospective and retrospective cohorts were included in the systematic review investigating the pathophysiologic mechanisms of brain-body associations in patients with ruptured brain aneurysms.  The multicenter Tirilazad database (3551 patients) was used to create the aneurysmal SAH prognostic model, in order to elucidate significant brain-body associations.  Traditional binary logistic regression models were used.  The classification and regression tree analysis technique is applied to the multicenter Tirilazad database in order to create a decision making algorithm.

Results
Systematic review of the literature confirmed the most frequently retained clinical outcome predictors, namely, age, neurological grade, aneurysm size and blood clot thickness.  Systematic review of the literature clarified currently known pathophysiologic mechanisms of brain-body associations in aneurysmal SAH, specifically, sympathetic activation of the cardiopulmonary system with subsequent delayed activation of neuro-cardio-endocrinological responses as part of the secondary injury cascade in response to the primary ictus of aneurysmal SAH.  Logistic regression models found the significance of hepatic disease and hypertension in development of brain edema, and the negative consequences of seizures in those with history of myocardial infarction and post admission fever worsening neurological outcome.  A clinically useful classification and regression tree revealed prognostic subgroups with important explanatory nodes including neurological grade, age, post admission fever and post-admission stroke.

Discussion
This dissertation clarified existing information on clinical predictors and pathophysiologic mechanisms of brain-body associations in aneurysmal SAH.  It also provides novel information on brain-body associations that are essential in influencing outcome in aneurysmal SAH patients despite scarce existing literature on such important relationships.  A clinically useful classification and regression tree was generated to guide both bedside prognostication and clinical treatment decision making in aneurysmal SAH patients.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: First and Second Quantization Theories of Parastatistics

contributor:
Nogami, Y.
Physics

subject: first, second, quantization, theories, parastatistics

abstract:
 Although usually only two kinds of statistics, namely Bose-Einstein and Fermi-Dirac statistics, are considered in Quantum Mechanics and in Quantum Field Theory, other kinds of statistics, called collectively parastatistics, are conceivable. We critically review theoretical studies of parastatistics to date, point out and clarify several confusions.

 We first study the "proofs" so far proposed for the symmetrization postulate which excludes parastatistics, emphasizing their ad hoc nature. Then, after exploring in detail the structure of the quantum mechanical theory of paraparticles, we clarify some confusions concerning the compatibility of parastatistics with the so-called cluster property, which has been an issue of controversy for several years. We show, following a suggestion of Greenberg, that the quantum mechanical theory of paraparticles can be formulated in terms of density matrix compatibly with the cluster property. We also discuss such topics as selection rules for systems with variable numbers of paraparticles, the connection between statistics and permutation characters, and the classification of paraparticles.

 For the quantum field theory of paraparticles, we study discrete representations of the para-commutation relations and illustrate in detail Greenberg and Messiah's theorem concerning Green's ansatzes. Also, fundamental topics such as the spin-statistic theorem, the TCP theorem and the observability of parafields are discussed on the basis of Green's ansatzes. Finally, we point out that the so-called particle permutation operators do not always define multi-dimensional representations of the permutation group both in first and second quantization theories. This questions the validity of the correspondence between the two theories which has recently been proposed.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Photochemistry of Triphenylmethylcyclopentadiene

contributor:
Warkentin, J.
Chemistry

subject: photochemistry, direct irradiation, thermolytic isomerization

abstract: The products and mechanism of the photolytic rearrangement of the equilibrium mixture of triphenylmethylcyclopentadienes have been studied. Direct irradiation of the equilibrium mixture of triphenylmethylcyclopentadienes yields 5,6,6-triphenylbicyclo{3.1.0}hex-2-ene. Photolysis with a triplet sensitizer yields dimeric products in addition to 5,6,6-triphenylbicyclo{3.1.0}hex-2-ene. Thermolytic isomerization of 5,6,6-triphenylbicyclo{3.1.0}hex-2-ene is reported. The predominant isomer in the equilibrium mixture of triphenylmethylcyclopentadiene has been established as 2-triphenylmethylcyclopentadiene.

abstract: Thesis

abstract: Master of Science (MSc)


title: Scourge of the Empire? Ancient Pathogen Genomics and the Biosocial Context of Malaria in Imperial Period Southern Italy (1st-4th c. A.D.)

contributor:
Poinar, Hendrik N.
Anthropology

subject:
Ancient DNA
Malaria
Pathogens
Imperial period Italy

abstract: The complementarity of ancient DNA lends itself to integration with paleopathological inquiries of disease, particularly in scenarios where there is limited or conflicting historical, skeletal, and archaeological information in a given spatio-temporal context. This thesis expands on molecular approaches applied to the detection of “invisible” pathogens associated with non-catastrophic morbidity and mortality that are embedded in a unique biosocial context of the disease experience. Presented in ‘sandwich-thesis’ format, I explore the historical narrative surrounding malaria in Imperial period Italy (1st-4th c. A.D.) using a molecular approach that is integrated with an ecosocial framework, as well as addressing the methodological challenges of identifying pathogens in contexts without a priori knowledge or incongruous evidentiary sources. My research presents the first partial mitochondrial genome for P. falciparum recovered from two adults (prioritized from a subset of 58 individuals) in disparate ecological and social localities in Imperial period Italy. This provides a timestamp for this ancient protozoan parasite, with an emphasis on a multi-faceted approach to frame the human-parasite-vector-environment interactions in the studied localities. Additionally, I successfully applied an in-solution hybridization capture technique designed to detect over 1,000 human pathogens in archaeological samples, both of known and unknown pathogen constituents. This technique qualitatively and quantitatively assesses the likelihood of low abundance pathogenic targets that are present, in order to prioritize candidates to further pursue with downstream analyses, as well as beginning to explore the synergistic landscape of pathogen-pathogen interactions. In combination, the research outlined in this thesis emphasizes the molecular and biosocial experience of disease as interconnected elements in dynamic epidemiological environments of the past.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Effects of Operating Variables of Sulphide Precipitation

contributor:
Woods, D. R.
Chemical Engineering

subject: operating variables, sulphide, precipitation, concentrations, metals, yield

abstract:
 The effects of engineering operating variables in the sulphide precipitation of Cu+2, Cd+2 and Zn+2 have been examined with a statistical experimental design. The independent (operating) variables studied were 1) the level of sulphide added, 2) the level of Fe+2 added as scavenger for excess HS- ion and 3) the pH level. The dependent variables were the concentrations of dissolved, suspended and total metals in the supernatant after treatment and the zone settling velocities of the suspensions.

 The major effect of the operating variables was to yield a precipitate which was either a stable colloid or a suspension which coagulated and settled. Stable colloid formation was associated with an excess of HS- ion. For those conditions which produced coagulant suspensions, 1) ten of the thirteen correlations between dependent and independent variables were not statistically significant at the 95% confidence level, 2) for practical purposes, variations in engineering operating variables did not alter the levels of dissolved and suspended Cu+2, Cd+2 and Zn+2 .

 When the precipitates coagulated and settled, concentrations of approximately 100 mg/l of each of Cu+2, Cd+2 and Zn+2 were reduced to mean values of 0.41, 0.33 and 0.62 mg/l total metals and 0.03, 0.01 and 0.37 mg/l dissolved metals respectively.

abstract: Thesis

abstract: Master of Engineering (MEngr)