title: Informed Textual Practices? A Study of Dunhuang Manuscripts of Chinese Buddhist Apocryphal Scriptures with Colophons

contributor:
Benn, James
Religious Studies

abstract:
Taking Buddhist texts with colophons copied at Dunhuang (4th–10th century C.E.) as a sample, my dissertation investigates how local Buddhists used Chinese Buddhist apocrypha with respect to their contents, and whether they employed these apocrypha differently than translated Buddhist scriptures. I demonstrate that not all of the practices related to Buddhist scriptures were performed simply for merit in general or that they were conducted without awareness of scriptures’ contents. Among both lay Buddhist devotees and Buddhist professionals, and among both common patrons and highly-ranking officials in medieval Dunhuang, there were patrons and users who seem to have had effective approaches to the contents of texts, which influenced their preferences of scriptures and specific textual practices. For the patrons that my dissertation has addressed, apocryphal scriptures did not necessarily meet their needs more effectively than translated scriptures did.
     I reached these arguments through examining three sets of Buddhist scriptures copied in Dunhuang manuscripts with colophons. In Chapter One, I explore the relationships between colophons for, and the contents of, three Chinese Buddhist apocryphal scriptures. In Chapter Two, I focus on a bhikṣuṇī local to Dunhuang and her commissioning of a set of Buddhist scriptures (including both apocryphal and translated scriptures) for her aspirations to become a man, and to achieve Buddhahood. Lastly, in Chapter Three, I concentrate on a prince, who had control over Dunhuang, and his commissioning of the Scripture of Perfection of Wisdom for Humane Kings as well as other Buddhist texts at different occasions, in order to explore his rationale for invoking the Heavenly Kings by employing these Buddhist texts for his own aspirations.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: MonsterLM: A method to estimate the variance explained by genome-wide interactions with environmental factors

contributor:
Pare, Guillaume
Statistics

subject: Statistical Genetics, Linear Model, SNPs, Gene-Environment Interactions

abstract: Estimations of heritability and variance explained due to environmental exposures and interaction effects help in understanding complex diseases. Current methods to detect such interactions rely on variance component methods. These methods have been neces- sary due to the m » n problem, where the number of predictors (m) vastly outnumbers the number of observations (n). These methods are all computationally intensive, which is further exacerbated when considering gene-environment interactions, as the number of predictors increases from m to 2m+1 in the case of a single environmental exposure. Novel methods are thus needed to enable fast and unbiased calculations of the variance explained (R2) for gene-environment interactions in very large samples on multiple traits. Taking advantage of the large number of participants in contemporary genetic studies, we herein propose a novel method for continuous trait R2 estimates that are up to 20 times faster than current methods. We have devised a novel method, monsterlm, that enables multiple linear regression on large regions encompassing tens of thousands of variants in hundreds of thousands of participants. We tested monsterlm with simulations using real genotypes from the UK Biobank. During simulations we verified the properties of monsterlm to estimate the variance explained by interaction terms. Our preliminary results showcase potential interactions between blood biochemistry biomarkers such as HbA1c, Triglycerides and ApoB with an environmental factor relating to obesity-related lifestyle factor: Waist-hip Ratio (WHR). We further investigate these results to reveal that more than 50% of the interaction variance calculated can be attributed to ∼5% of the single-nucleotide polymorphisms (SNPs) interacting with the environmental trait. Lastly, we showcase the impact of interactions on improving polygenic risk scores.

abstract: Thesis

abstract: Master of Science (MSc)


title: New Delhi Metallo-beta-lactamase (NDM) plasmid predictions

contributor:
McArthur, Andrew
Biochemistry and Biomedical Sciences

subject: NDM plasmids

abstract: The complete detection and genome sequencing of resistance plasmids is required to understand the co-occurrence of resistance genes on plasmids and their transmission, which is necessary to mitigate the spread of drug resistant bacterial infections. One group of multi-drug resistance plasmids of interest are the New Delhi Metallo--lactamase (NDM) associated plasmids. Bacteria pathogens with NDM genes are resistant to a broad range of beta-lactam antibiotics, including carbapenems, a mainstay for treating bacterial infections. We sequenced clinical isolates collected from patients that failed to respond to antibiotic treatments in the Hamilton-Niagara community using Next Generation Sequencing (NGS) technology, which is the standard technique for sequencing bacterial genomes. I analyzed their assembled genomes via the development of a new resistance plasmid prediction bioinformatics pipeline: RGI:Mobilome. RGI:Mobilome predicted NDM bearing plasmids in 15 isolates, along with other resistance genes on plasmids. However, the NDM plasmid predictions of all 15 isolates were fragmented due to incomplete genome assemblies, caused by repetitive sequences within bacterial genomes and use of Illumina sequencing technology. However, plasmid predictions greatly improved when we leveraged the high nucleotide accuracy of Illumina reads and the structural resolving power of long reads generated with the Oxford Nanopore Technology (ONT) to produce ‘hybrid’ genome assemblies. From the 15 putative hybrid-assembly NDM plasmids, one plasmid was a complete match to a known pKP-NDM1 plasmid, seven plasmids were “variants” of known and well-characterized plasmids, and the remaining seven plasmids were “distant homologs” of known and well-characterized plasmids, suggesting previously undescribed NDM-associated plasmids in our community. This thesis project reveals the diversity of NDM plasmid types within the Hamilton-Niagara community, which is valuable to epidemiologists and public health practitioners to devise actionable plans required to mitigate the spread of multi-drug resistance NDM plasmids and for clinicians to treat infections caused by NDM positive strains.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The spread of antimicrobial resistance often arises from the exchange of resistance plasmids between bacterial species in their immediate environment. One resistance gene carried on plasmids is the New Delhi Metallo-beta-lactamase (NDM) gene, which confers resistance to almost all beta-lactam antibiotics. To control the spread of NDM plasmids, we need to detect them completely. Using genome sequencing, we analyzed clinical isolates from patients in hospitals within the Hamilton-Niagara community for NDM plasmids. From our results, we detected one complete match to a known NDM plasmid. We also detected seven NDM-associated plasmids that are close variants of known NDM plasmids, plus another seven NDM-associated plasmid that we classified as ‘novel’ since they are widely different from known NDM plasmids. This thesis reveals the diverse NDM plasmids within the clinics of the Hamilton-Niagara community, which should guide public health workers to develop policies to mitigate the spread of resistance NDM plasmids.


title: Sex and gender differences in psychosocial factors for exercise and risk factors for cardiovascular disease and cognitive impairment in individuals with and without stroke

contributor:
Tang, Ada
Rehabilitation Science

subject:
Sex
Exercise
Gender
Arterial Stiffness
Walking Capacity
Stroke
Exercise Self-Efficacy
Outcome Expectations for Exercise
Motivation for Exercise
Older Adults
Gender Roles
Gender Identity

abstract:
Sex and gender considerations are influential on psychosocial and physiological determinants of cardiovascular health in individuals with and without stroke. The first study of this thesis explored gender-based differences in exercise self-efficacy, outcome expectations for exercise and motivation for exercise post-stroke. Gender identity was assessed using the Bem Sex-Role Inventory-12 and a gender role index was created using established gender-related roles. The Self-Efficacy for Physical Activity Scale was used to assess self-efficacy for exercise, the Short Outcome Expectations for Exercise Scale assessed outcome expectations for exercise and a Relative Autonomy Index was calculated to assess motivation for exercise. We found that masculine gender identity was associated with highest ratings of exercise self-efficacy, whereas feminine gender identity was related to the lowest exercise self-efficacy [F(3, 9)=5.36, p<0.05]. Gender identity was not associated with outcome expectations [F(3,8)=0.86, p=0.50) nor motivation for exercise [F(3,4)=0.67, p=0.61)]. Additionally, there were no associations between gender roles and self-efficacy (n=13, r=0.10, p=0.73), outcome expectations (n=13, r=-0.13, p=0.68), or motivation for exercise (n=8, r=0.09, p=0.83).
The second study of this thesis examined the associations between global cognitive function (Montreal Cognitive Assessment, MoCA), arterial stiffness (carotid-femoral pulse wave velocity) and sex, and between global cognitive function, walking capacity (6-Minute Walk Test, 6MWT) and sex in older male and female adults with and without stroke. There was no association between global cognition and arterial stiffness, and sex did not moderate this association. However, cognitive function was positively associated with 6MWT, and with the addition of sex, Sex*6MWT, age and history of stroke, explained 21% of the variance of the MoCA score.
Our findings provide insight into the importance of sex-and gender-based considerations in clinical research and may inform future larger-scaled studies aiming to increase the generalizability of their findings to males and females and individuals of all gender identities.

abstract: Thesis

abstract: Master of Science Rehabilitation Science (MSc)

abstract: The roles that an individual undertakes, and how they see themselves and are seen by others may be related to exercise participation. In addition, a person’s biological makeup may impact their health and ability to think. In the first study of this thesis, we found that individuals with stroke seeing themselves as women had lower beliefs about their abilities to exercise, but their beliefs about the benefits of exercise or their motivation for exercise were similar to individuals who identify as men. There were no differences in beliefs about exercise abilities, outcomes, or motivation between individuals with stroke who took on masculine vs. feminine roles. In the second study, we found that walking distance, but not arterial health, was related to the ability to think in males and females. Overall, this work provides information of the importance of biological, social roles and behaviours on health.


title: Northeastern Ontario Child Welfare Workers’ Experiences of Trauma-Management and Emotional Support Provided by Agencies Following the Death of a Child Client

contributor:
La Rose, Tara
Social Work

subject:
child welfare
child maltreatment fatalities
workplace trauma
death and dying
mental health
trauma management

abstract: Although the death of a child client is among the worst work-related events that a child welfare worker can experience, the phenomenon is tremendously understudied concerning how the event impacts the staff involved and how, or if, their employing agencies supported any mental health needs that may have arisen after the death. This study investigates what types of mental health/emotional support was made available to Northeastern Ontario child welfare workers following the death of a child client, and how effective that support was in helping the worker cope with any difficulties related to the death. This study was guided by principles of Constructivist Grounded Theory and semi-structured qualitative telephone interviews were conducted with five (5) participants. My analysis found that the death of a child client can negatively impact both the mental wellbeing of involved workers as well as the organizational climate of an agency. My analysis also found that workers may delay the emotions associated with the grieving process to effectively focus on the administrative requirements resulting from the child’s death, potentially to their detriment. The different ways child welfare organizations supported staff through these events included individual and group psychological debriefings, grief counselling, and providing information regarding additional support options. Only three of the five workers engaged in the strategies provided to them by their agency, and of those three, only one found the services to be helpful with managing emotional difficulties related to the child’s death. What remained true among all five participants was that they each had very personalized ideas as to what they felt would have best helped them through this difficult event. I conclude that based on related literature and the findings of this study, child welfare organizations are recommended to invest in a thorough and embedded agency framework of trauma-management that addresses policy and procedure development as well as support coordination at the pre-trauma, immediate trauma, and post-trauma levels. Additionally, trauma-management should not be a singular standardized response and should be tailored to the individualized needs of each worker. Agencies should be well-versed in delivering different strategies of trauma-management and letting the worker lead in determining what type of support they are looking for and when would be best to receive it.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: A TRACE/PARCS Coupling, Uncertainty Propagation and Sensitivity Analysis Methodology for the IAEA ICSP on Numerical Benchmarks for Multi-Physics Simulation of Pressurized Heavy Water Reactor Transients

contributor:
Novog, David
Engineering Physics

subject:
CANDU
IAEA
Code Coupling
TRACE
PARCS
SCALE

abstract: The IAEA ICSP on Numerical Benchmarks for Multiphysics Simulation of Pressurized Heavy Water Reactor Transients was initiated in 2016 to facilitate the development of a set of open access, standardized, numerical test problems for postulated accident scenarios in a CANDU styled Reactor. The test problems include a loss of coolant accident resulting from an inlet header break, a loss of flow accident caused by a single pump trip, and a loss of regulation accident due to inadvertently withdrawn adjusters. The Benchmark was split into phases, which included stand-alone physics and thermal-hydraulics transients, coupled steady state simulations, and coupled transients. This thesis documents the results that were generated through an original TRACE/PARCS coupling methodology that was developed specifically for this work. There is a strong emphasis on development methods and step by step verification throughout the thesis, to provide a framework for future research in this area. In addition to the Benchmark results, additional studies on propagation of fundamental nuclear data uncertainty, and sensitivity analysis of coupled transients are reported in this thesis. Two Phenomena and Key Parameter Identification and Ranking Tables were generated for the loss of coolant accident scenario, to provide feedback to the Benchmark Team, and to add to the body of work on uncertainty/sensitivity analysis of CANDU style reactors. Some important results from the uncertainty analysis work relate to changes in the uncertainty of figures of merit such as integrated core power, and peak core power magnitude and time, between small and large break loss of coolant accidents. The analysis shows that the mean and standard deviation of the integrated core power and maximum integrated channel power, are very close between a 30% header break and a 60% header break, despite the peak core power being much larger in the 60% break case. Furthermore, it shows that there is a trade off between the uncertainty in the time of the peak core power, and the magnitude of the peak core power, with smaller breaks showing a smaller standard deviation in the magnitude of the peak core power, but a larger standard deviation in when this power is reached during the transient, and vice versa for larger breaks. From the results of the sensitivity analysis study, this thesis concludes that parameters related to coolant void reactivity and shutoff rod timing and effectiveness have the largest impact on loss of coolant accident progressions, while parameters that can have a large impact in other transients or reactor designs, such as fuel temperature reactivity feedback and control device incremental cross sections, are less important.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: This thesis documents McMaster’s contribution to an International Atomic Energy Agency Benchmark on Pressurized Heavy Water Reactors that closely resemble the CANDU design. The Benchmark focus is on coupling of thermal-hydraulics and neutron physics codes, and simulation of postulated accident scenarios. This thesis contains some select results from the Benchmark, comparing the results generated by McMaster to other participants. This thesis also documents additional work that was performed to propagate fundamental nuclear data uncertainty through the coupled transient calculations and obtain an estimate of the uncertainty in key figures of merit. This work was beyond the scope of the Benchmark and is a unique contribution to the open literature. Finally, sensitivity studies were performed on one of the accident scenarios defined in the Benchmark, the loss of coolant accident, to determine which input parameters have the largest contribution to the variability of key figures of merit.


title: Characterizing the effects of acute exercise on Natural Killer cell recruitment and receptor expression in pre-pubertal and post-pubertal youth

title: Effect of exercise on natural killer cells in children and adolescents

contributor:
Obeid, Joyce
Medical Sciences

subject: Exercise Immunology Pediatric

abstract: Natural Killer (NK) cells are recruited into circulation in response to physiological stress such as exercise. In adults, NK deployment and receptor expression are proportional to exercise intensity, and the cytotoxic CD56dim NK subset is preferentially deployed compared to immunoregulatory CD56bright subset. We know much less about the NK response to different exercise stimuli in children; however, pre-pubertal children are less responsive to acute exercise and recover faster than post-pubertal children and adults. The aims of this study were to (1) investigate the effects of exercise intensity and structure on NK recruitment and receptor expression, (2) compare the response among pre-pubertal and post-pubertal children, and (3) assess if factors such as fitness and physical activity were correlated with the magnitude of NK cell response. Healthy, recreationally active, pre- and post-pubertal boys and girls were recruited from the Hamilton community (N=11; 5 pre-pubertal, 6 post-pubertal). At the initial study visit, participants completed an aerobic fitness test to determine V̇O2peak and ventilatory threshold. At the subsequent visits, participants performed one of four cycling structures in a randomized, counterbalanced order, including: high-intensity continuous (HI-CONT), high-intensity intermittent (HI-INT), moderate-intensity continuous (MI-CONT), or moderate-intensity intermittent (MI-INT) exercise. Blood was collected pre-, post-exercise, 30- and 60-minutes into recovery. NK cells, CD56dim, and CD56bright NKs, activating (NKG2D and DNAM1) and inhibitory receptors (NKG2A and KIR2DL2/DL3) were quantified via flow cytometry. Participants were also outfitted with an accelerometer to measure physical activity. Three-way mixed ANOVA were used to examine effects of time, exercise and puberty on NK parameters, with Tukey’s HSD post hoc where appropriate. Pre-pubertal children showed no significant increase in the NK concentration in response to any of the exercise stimuli. Post-pubertal children, increased their NK cell concentration PRE to POST in all exercise stimuli except MI-CONT. Greater increases in NK concentration were seen POST HI-INT (124723 +/- 91596 cells/mL) and MI-INT (109644  +/- 84664 cells/mL), compared to HI-CONT (19931 +/- 1492 cells/mL) and MI-CONT (17082 +/- 9516 cells/mL), respectively (p < 0.001). Only increases in the expression of NKG2A were observed during REC1 (63.6 +/- 13.7 %), and REC2 (64.2 +/- 12.8 %) compared to PRE (57.9 +/- 13.4%) (p < 0.01).  However, the density of NKG2D, NKG2A and DNAM1 were all significantly increased at REC2 compared to PRE. Fitness (R2=  - 0.742) but not moderate-to-vigorous physical activity (R2= 0.098) or sedentary time (R2= 0.621) were significantly negatively associated with the magnitude of NK cell response. We demonstrated that an acute bout of intermittent cycling (5 min of exercise) leads to greater NK recruitment and a more immunoregulatory NK environment than continuous cycling in post-pubertal children. Contrarily, we showed that pre-pubertal children are not responsive to acute exercise of 30-minutes or shorter. Across our cohort, exercise also upregulated the density of expression of both activating and inhibitory receptors.  Future research should examine if the NK cell response to acute exercise is maintained with repeated exercise exposures or exercise training.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: This study looked at how exercise can be used to change the behavior of Natural Killer cells. These are cells that are part of the immune system and help protect people from viruses and cancer cells by quickly detecting cells that don’t belong in our bodies. They can also produce messenger chemicals to make other protective cells in the body aware of invaders. In this study children came into the lab and completed a different cycling exercise every time. In total, they completed four cycling exercises that included: 1) very hard cycling for 30 minutes; 2) very hard cycling in intervals, with 15 seconds of pedalling as hard and as fast as possible followed by a 1 minute rest, and repeating this for a total of 20 times; 3) comfortable cycling for 30 minutes; and 4) comfortable cycling in intervals. During each visit blood was collected from participants in order to count the number of natural killer cells there were before and after exercise as well as 30- and 60-minutes after the participants stopped cycling. Our study showed that in younger kids (8 to 10 years old), exercise doesn’t change how many natural killer cells are in the blood. However, in teens (14 to 18 years old) we showed that pedaling in intervals increased the number of natural killer cells in the blood more than riding a bicycle for 30 minutes straight. Our research helps us understand how exercise can be used to make our immune system stronger.


title: CLOSED-LOOP DYNAMIC REAL-TIME OPTIMIZATION WITH STABILIZING MODEL PREDICTIVE CONTROL

contributor:
Mhaskar, Prashant
Swartz, Christopher
Chemical Engineering

abstract:
Real-time optimization (RTO) is a supervisory strategy at the upper level of the industrial
process automation architecture that computes optimal set-point trajectories
that are in turn passed on to the lower-level advanced controller for tracking. In recent
times, process industries have been operating plants in an increasingly dynamic
environment thus motivating the replacement of the traditional steady-state RTO
with a dynamic RTO (DRTO). Conventionally, the DRTO problem involved computing
optimal input trajectories without incorporating the e ects of the lower-level
controller that motivated the development of a closed-loop DRTO (CL-DRTO).
A previously published CL-DRTO strategy optimizes set-point trajectories based on
an economic cost function, while including the lower-level MPC calculations with
an assumption that the process is open-loop stable. But the economic optimum,
in certain process industries, could lead to operating the plant at or around an unstable
steady-state. Therefore, the goal of this research is to develop a CL-DRTO
formulation that enables handling unstable operating points via an underlying MPC
with stability constraints. In this work, we focus on a traditional two-layer DRTO
approach due to its close ties to the industrial automation architecture.
To this end, a stabilizing MPC that handles trajectory tracking for unstable systems is
embedded within the upper-level DRTO, resulting in a multi-level dynamic optimization
problem. Subsequently, this optimization problem is reformulated by applying
a simultaneous solution approach. The economic bene ts realized by the proposed
strategy are illustrated through applications to both linearized and nonlinear dynamic
models for single-input single-output (SISO) and multi-input multi-output (MIMO)
CSTR case studies.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Health Vulnerability to Extreme Heat Events in Hamilton, Ontario

contributor:
Newbold, Bruce
Geography

subject: Extreme Heat, Climate Change, Hamilton, Health, Immigrants, Newcomers

abstract: Climate change is expected to affect Canada through extreme heat events (EHEs). Already vulnerable populations, including newcomers and immigrants, will especially be vulnerable to the health impacts associated with EHEs. This population is important to consider for a country as diverse as Canada. With a focus on Hamilton Ontario, this thesis will assess barriers that immigrants and newcomers face with coping to EHEs. Adverse impacts they face will also be discussed. Current formal and informal coping methods will also be highlighted. Quantitative analysis will also be used to explore the relationship between EHEs, air quality (as measured by the Air Quality Health Index (AQHI)), forward sortation areas and hospital admission for heat-related illnesses. The results of this study highlight that unique factors influencing heat health vulnerability among immigrants and newcomers in Hamilton. The benefits of current formal and informal coping mechanisms will also be discussed, as well as areas for improvement. Quantitative analysis also highlights that the AQHI, maximum temperature and a heat event can impact if an individual is admitted to the hospital for a heat-related illness. However, age, gender and most FSAs were not statistically significant. This thesis highlights the importance of considering the immigrant and newcomer population for EHE and general climate change adaptation efforts.

abstract: Thesis

abstract: Master of Arts (MA)


title: An Anti-Colonial Examination of How Disability is Conceptualized, Responded to and Experienced by Prisoners within the Federal Prison System of Canada

contributor:
Joseph, Ameil
Social Work

subject: disability race anti-colonial prison incarceration

abstract: This research examines how disability is conceptualized, responded to and experienced by prisoners within the federal prison system of canada , by attending to the constructs of disability and criminality as they relate to racial and colonial hierarchies. Drawing on anti-colonial theory and the concept of subalternity, this research aims to resist essentializing identity in a way that would limit ‘disability’ or ‘race’ to a particular spatial/temporal context. The constructs of race and disability will be attended to simultaneously, while engaging with how these identity categories have been co-constructed in relation to ‘criminality’, for the furthering of colonialism. Accordingly, this research contextualizes the mass-incarceration of racialized/disabled individuals within a broader, historic, colonial project of confinement and removal. I draw on 4 in-depth semi-structured interviews conducted for this study, with individuals who are living with disabilities and have been incarcerated in canadian federal prisons. Throughout this thesis, I couple my analysis of the ‘problem’ in question with attention to ‘how’ the problem is often discussed in dominant critical research and discourse, particularly attending to eurocentric articulations of race, disability and incarceration.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: Tense Misalignments: Re-Imagining Colonial Binaries in Understanding the Relationship between Sikhi and Alcohol

contributor:
Rowe, Mark
Religious Studies

subject:
Sikhism
Alcohol
Masculinity
Colonialsim
Intergenerational Trauma
Second-Generation
Sikhi
Punjabi

abstract: Exploring the relationship that second-generation Sikh-Canadians have with alcohol, this research focuses on predominant understandings of alcohol in the community. Themes include Panjabi culture, Sikh understandings of alcohol, masculinity, intergenerational trauma and colonialism.

abstract: This thesis explores the relationship that second-generation Sikh-Canadians have with alcohol. Predominant understandings of alcohol in the community argue that Panjabi culture promotes the consumption of alcohol while Sikhi prohibits it yet culture and religion cannot easily be separated or understood in such monolithic ways. Problems with alcohol are often relegated to a Panjabi issue stemming from a hypermasculine culture that emphasizes overconsumption. Simply blaming “the culture” misses the heterogeneity of the community and the impacts of intergenerational trauma and contemporary formations of masculinity, culture, and religion that are rooted in colonialism. Furthermore, stating that Sikhi is vehemently anti-alcohol fails to engage with the Guru Granth Sahib and the lived reality. The central thesis of the Guru Granth Sahib, IkOankar (1-Ness), advocates against binaries, moving away from normative and simplistic understandings of good and bad or prohibited and accepted. This is not to argue that Sikhi promotes alcohol consumption rather, depicting alcohol consumption in reductive and binary terms is against the IkOankar paradigm and fails to engage lived Sikhi. Although in mainstream understandings of Sikhi, alcohol is prohibited, this is not always what is practiced. Moving beyond simple prohibition or acceptance, alcohol consumption can be understood through the dynamic ways in which Sikh-Canadians engage with the substance.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: Predominant understandings of alcohol in the Sikh community argue that Panjabi culture promotes its consumption while Sikhi prohibits it yet culture and religion cannot easily be separated or understood in such monolithic ways. Simply blaming “the culture” misses the heterogeneity of the community and the impacts of intergenerational trauma and contemporary formations of masculinity, culture, and religion that are rooted in colonialism. Furthermore, stating that Sikhi is vehemently anti-alcohol fails to engage with the central thesis of the Guru Granth Sahib, IkOankar (1-Ness), and the lived reality.


title: Effect of elevated embryonic incubation temperature on the temperature preference of juvenile lake (Coregonus clupeaformis) and round whitefish (Prosopium cylindraceum)

contributor:
Wilson, Joanna
Biology

subject:
Whitefish
Shuttle Box
Temperature Preference
Incubation Temperature

abstract: Lake (Coregonus clupeaformis) and round (Prosopium cylindraceum) whitefish are two species of cold-adapted freshwater fish that spawn in shallow (<10m) cobble beds in the Laurentian great lakes. Developing whitefish embryos are potentially exposed to various anthropogenic sources of warming, including climate change and thermal effluents discharged in the nearshore environment. Several studies have investigated the effects of elevated incubation temperatures on whitefish embryos (particularly lake whitefish) but little work has been done to examine post-hatch effects. Thermal preferenda (temperature preference) describe the range of temperatures an organism will occupy when given a choice and are traditionally thought to be species-specific. Temperature preference can be modulated by a variety of abiotic and biotic factors including environmental temperature and is typically correlated with optimal growth temperature for a species. Assays for thermal preferenda require at least 24 hours, which includes a long tank-acclimation period that limits throughput and thus impacts replication in the study. A shuttle box thermal preference assay was optimized from 24-hours to 4-hours; length of acclimation time and trial length had no significant impact on thermal preference. Whitefish were incubated at natural and elevated temperatures until hatching; all groups were moved to common garden conditions (15°C) during the post-hatching stage.  Temperature preference was determined at 12 months of age; lake whitefish were also tested at 8 months. Round whitefish displayed a significant decrease in temperature preference when incubated at 2°C and 6°C compared to 0.5°C. Lake whitefish had similar temperature preferences regardless of age and incubation temperature. This suggests that there is a difference in thermal tolerance between these species, as round whitefish were more sensitive to elevated incubation treatments. This thesis identified a persistent effect of elevated incubation treatments on the thermal preference of juvenile round whitefish, lasting up to 12 months post-hatch, which highlights the importance of examining sub-lethal thermal effects and thermal plasticity of cold-adapted species.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Lake and round whitefish are cold-adapted freshwater species that spawn in shallow coastal water in the Laurentian great lakes. Anthropogenic warming from various sources (e.g. climate change, thermal effluent) has been shown to reduce survival of whitefish embryos, but few studies have investigated the effects of elevated embryonic incubation temperatures on surviving juveniles. Fish typically prefer a small range of temperatures (temperature preference) that they will occupy if given a choice, which can be affected by a variety of factors including early life thermal exposure. This thesis shows round whitefish incubated at elevated temperatures (2°C, 6°C) display decreased temperature preference up to 12 months post-hatch, while lake whitefish had similar temperature preference regardless of incubation temperature. Therefore, this thesis provides more evidence that round whitefish are a more thermally sensitive species.


title: Producing names with a bizarre voice does not improve memory for face–name pairs

contributor:
Milliken, Bruce
Shore, David
Psychology

subject:
face–name associations
bizarreness
vocal productions

abstract: Most social interactions require correct identification of an individual’s face and name; however, this can be a rather challenging task. The present study examined whether a mnemonic proposed by pop-culture can enhance memory for face–name associations. More specifically, we tested whether vocalizing names in an unusual voice can improve subsequent memory for an individual’s face and name. The memory literature has examples of enhanced memory for items that require bizarre mental imagery as opposed to normal mental imagery, and separate evidence of enhanced memory for items that are said aloud, as opposed to items read silently. However, it is unclear whether bizarre production of names compared to regular production of names will lead to enhanced memory for faces, names, or face–name associations. In the present study, participants studied face–name pairs while vocalizing the names in a bizarre voice or a normal voice. Memory for face–name associations was tested using cued recall tests and a recognition test. The results suggest that using a bizarre voice disrupts memory performance compared to using a normal voice. Contrary to suggestions in pop-culture, the production of a bizarre voice appears to make it harder to associate face–name pairs during learning.

abstract: Thesis

abstract: Master of Science (MSc)


title: Monitoring Spatial Distribution of Solvent Extractable Organics in Pit Lake Fluid Fine Tailings

subject:
Geochemistry
Chemistry
Analytical Chemistry
Oil Sands
Organic Biogeochemistry
Chemometrics

abstract:
The extraction of bitumen from the cretaceous oil sands ore within the Athabasca Oil Sands Region (AOSR) in Northern Alberta has generated over 1.18 trillion liters of by product in the form of Fluid Fine Tailings (FFT) and Oil Sands Process Water (OSPW)3. A reclamation strategy being investigated is water capped tailings technology (WCTT), that involves the development of Pit Lakes (PLs) by sequestering FFT below a water cap composed of both OSPW and fresh water to steadily densify these tailings over time4. A challenge that may impede this reclamation strategy is that as FFT densifies porewater containing oxygen consuming constituents (OCC) derived from anaerobic microbial degradation of labile petroleum hydrocarbons, such as gases (e.g. H2S, CH4), dissolved organic carbon (DOC) and dissolved ions (e.g. NH4+, HS-, and Fe2+), have the potential to be mobilized into to the overlying water cap.
This dissertation is focused on developing an optimized comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOFMS) methodology for analyzing the spatial distribution for a subset of identifiable solvent extractable PHCs species from FFT within Base Mine Lake (BML) the first full-scale demonstration of PL technology. The chemical “fingerprint” constructed from the concentration of each identified PHC isomer at a given depth and cosine theta (cos-Ɵ) similarity metric suggested the contribution of a singular source of PHCs within BML. Although a similar source fingerprint persisted throughout the study site, the spatial distribution for the isomers identified suggested differences in PHC input contributions across the FFT sampling platforms with the largest variation in concentration being attributed to the labile low molecular weight n-alkanes (C11 – C13) and postulated biomarker, drimane. These low molecular weight compounds, with the exception of drimane, are suspected components of residual naphtha, and the large variabilities in concentration are suggestive that these species may be linked with fluctuating inputs and/or sorption of naphtha to the organic phase of the FFT. Equally possible, the pronounced variability in the low molecular weight n-alkanes concentrations

abstract: Thesis

abstract: Master of Science (MSc)


title: Defining mechanisms underlying context-specific TCF/LEF deployment at target genes

contributor:
Doble, Brad
Biochemistry and Biomedical Sciences

subject:
Wnt
Stem Cells
Cancer
Micropatterning
Proteomics
TurboID
Drug Screening
Bookmarking

abstract:
The canonical Wnt/β-catenin signaling pathway is essential for the proper regulation of cell-fate decisions throughout embryogenesis and in adult issues. Activation of the Wnt signaling pathway allows for nuclear localization of the cell adhesion protein β-catenin, which then interacts primarily with members of the T-Cell Factor/Lymphoid Enhancer Factor (TCF/LEF) transcription factor family to modulate gene activity. The TCF/LEF family includes TCF7, TCF7L1, TCF7L2, and LEF1. While all four family members share a common DNA binding consensus sequence, their expression throughout embryogenesis and adult stem cell populations is unique, with their misexpression commonly occurring in Wnt related cancers and correlating strongly with metastasis and poor patient outcomes.
TCF/LEF exchange at target gene loci is a key feature of mediating context-specific cellular responses to Wnt signaling and can be observed to occur in a variety of populations throughout development and in adult stem cell populations. To model TCF/LEF exchange in vitro we have optimized a micropatterning fabrication and culture protocol capable of identifying and isolating discrete LEF1-only and TCF7L1-only populations during gastrulation-like processes. To characterize how complements of TCF/LEFs change during cellular divisions we have developed a novel mitotic chromatin proteomic technique. This method identifies LEF1 as the only TCF/LEF to remain associated with mitotic chromatin in Wnt-activated conditions in mouse embryonic stem cells that are transitioning out of pluripotency as a consequence of removing leukemia inhibitory factor from their culture medium. Additionally, gene targeting techniques were used to label endogenous LEF1 and TCF7L1 with different fluorescent proteins in a single mouse embryonic stem cell line, allowing us to use TCF/LEF protein expression as a reporter of Wnt/β-catenin pathway status, which we found to be capable of identifying a unique set of compounds that are undetected by traditional Wnt activity (TOP-Flash) reporter screens.
By using gene editing technology, and novel applications of proteomic and cell culture techniques, we have been able to investigate the mechanisms driving TCF/LEF expression and exchange in mouse embryonic stem cells to identify potentially clinically relevant therapeutic targets for their potential use in addressing TCF/LEF dysregulation in cancer. We have identified a novel mechanism through which TCF/LEFs maintain cell fate over cellular division; presented a novel live-cell drug screening platform capable of identifying compounds missed by existing platforms; and presented an optimized cell culture technique for the isolation of TCF/LEF exchange events. Taken together, the work in this thesis provides new insights into the mechanisms through which TCF/LEFs regulate their gene targets during cell fate transitions and throughout mitosis.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract:
Throughout development and adult life cells are in constant communication, using a variety of cell signaling pathways to maintain adult stem cell populations and to pattern tissues throughout the body. Communication between cells often requires one cell to release a protein molecule (called a ligand) that is recognized by a receptor molecule on the surface of another cell. These cell surface receptors, when bound by the signaling ligand become activated and often set of a cascade of internal cellular events that ultimately result in changes in gene transcription in the nucleus. These transcriptional changes are toggled by proteins known as sequence-specific transcription factors that are able to selectively regulate expression of target genes. The net effect of combinations of extracellular ligands binding cell surface receptors determines the selective recruitment of specific transcription factors that activate a cell’s transcriptional program, in turn defining its fate and function.
A very important developmental signaling pathway is the Wnt signaling pathway, which employs a family of secreted Wnt molecules as ligands. The Wnt pathway is critical at all stages of organismal development and plays an essential role in tissue maintenance in mature animals. However, due to its critical role in stem cell maintenance, when mutations occur in Wnt signaling components it can have dire consequences. Wnt signaling has been found to be disrupted in more than 70-80% of all cancers. One major feature among these Wnt-related cancers is the inappropriate expression and mobilization of Wnt transcription factors. While the expression and activity of Wnt transcription factors – known as T-Cell Factor/Lymphoid Enhancer Factors (TCF/LEFs) – changes throughout development and stem cell maintenance, their inappropriate expression is frequently associated with metastasis and poor patient outcomes.
We have used mouse embryonic stem cells (mESCs) as a model system with which to study the mechanisms employed by TCF/LEFs to regulate their target genes. Through a number of approaches, which include adding fluorescent tags to TCF/LEF factors to track their intercellular locations and expression levels or enzymatic tags to identify proteins that interact with individual TCF/LEFs during a snapshot of cell activity, we have gained new knowledge about how these critical transcription factors regulate Wnt-regulated transcriptional programs. We also describe a method for generating micropatterned growth surfaces for mESCs that forces clusters of cells to grow within small circular shapes with a diameter of 1 mm or less. We show that mESCs confined to circular micropatterns differentiate in a highly reproducible manner that allows us to study the cell populations undergoing differentiation with a focus on cell fate determination mechanisms.


title: Systematic Approach to Multideterminant Wavefunction Development

contributor:
Ayers, Paul
Chemistry

subject:
quantum chemistry
electronic structure theory
method development
ab initio methods
multideterminant wavefunction

abstract: Electronic structure methods aim to accurately describe the behaviour of the electrons in molecules and materials. To be applicable to arbitrary systems, these methods cannot depend on observations of specific chemical phenomena and must be derived solely from the fundamental physical constants and laws that govern all electrons. Such methods are called ab initio methods. Ab initio methods directly solve the electronic Schrödinger equation to obtain the electronic energy and wavefunction. For more than one electron, solving the electronic Schrödinger equation is impossible, so it is imperative to develop approximate methods that cater to the needs of their users, which can vary depending on the chemical systems under study, the available computational resources and time, and the desired level of accuracy. The most accessible ab initio approaches, including Hartree-Fock methods and Kohn-Sham density functional theory methods, assume that only one electronic configuration is needed to describe the system. While these single-reference methods are successful when describing systems where a single electron configuration dominates, like most closed-shell ground-state organic molecules in their equilibrium geometries, single-reference methods are unreliable for molecules in nonequilibrium geometries (e.g., transition states) and molecules containing unpaired electrons (e.g., transition metal complexes and radicals). For these types of multireference systems, accurate results can only be obtained if multiple electronic configurations are accounted for. Wavefunctions that incorporate many electronic configurations are called multideterminant wavefunctions. This thesis presents a systematic approach to developing multideterminant wavefunctions. First, we establish a framework that outlines the structural components of a multideterminant wavefunction and propose several novel wavefunction ansätze. Then, we present a software package that is designed to aid the development of new wavefunctions and algorithms. Using this approach, we develop an algorithm for evaluating the geminal wavefunctions, a class of multideterminant wavefunctions that are expressed with respect to electron pairs. Finally, we explore using machine learning to solve the Schrödinger equation by presenting a neural network wavefunction ansatz and optimizing its parameters using stochastic gradient descent.

abstract: Thesis

abstract: Doctor of Science  (PhD)


title: Objective post-concussion sleep quality: exploring the effects of concussion and determining its relationship with recovery outcomes in children and adolescents

title: Analysis of post-concussion sleep quality in youth

contributor:
Carol, DeMatteo
Catherine, Wiseman-Hakes
Joyce, Obeid
Rehabilitation Science

subject:
concussion
sleep quality
actigraphy
pediatric
recovery

abstract:
Background: Sleep is commonly disrupted following pediatric concussion. Recently, post-concussion sleep quality has been identified as a potential factor that may influence recovery length. However, few studies have examined this relationship using objective sleep measures in a pediatric population. Nor, have any studies examined the trajectory of objective sleep parameters after pediatric concussion.
Objectives: The purpose of this thesis is to: 1) Provide a review of current literature regarding pediatric concussion, healthy sleep quality, and sleep quality in the context of concussion and recovery from concussion; 2) Examine how objective sleep outcomes are affected and change post-concussion in children and adolescents; 3). Explore how post-concussion sleep quality parameters are related to length of recovery, quality of life (QOL), and depression symptomatology; and 4) Discusses the results from the two studies in the context of current literature and of each other.
Methods: Sleep quality was inferred from the outcomes of five objective sleep parameters. Sleep parameters were measured using actigraphy in children and adolescents with concussion following return to school (RTA) and return to activity (RTA) protocols. Sleep data during the initial 4 weeks of recovery was assessed as an outcome, as a predictor of recovery length, and as a correlate of quality of life (QOL) and depression symptomatology
Results: Most objective post-concussion sleep quality parameters were adversely affected by concussion but show trajectories indicating improvement throughout the initial 4 weeks of recovery. Sleep quality parameters were not associated with time to complete return to school or activity protocols. Sleep parameters were not strongly correlated with QOL or depression symptomatology outcomes.
Conclusions: These results indicate that objective post-concussion sleep quality is impaired following concussion, but these outcomes do not appear to be associated with recovery, QOL or depression symptomatology. Other factors, or improvements in sleep quality may better explain recovery outcomes.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Children and adolescents are at risk for experiencing changes in sleep following concussion that result in poor sleep quality. Given the important role of sleep in maintaining our overall health, sleep likely plays a role in recovery. However, this relationship is poorly understood. The purpose of this dissertation is to identify how sleep changes following concussion and how these changes affect sleep quality and recovery. Study results reveal that the sleep parameters in the initial 4 weeks following concussion are significantly affected by concussion, suggesting that the sleep quality of children and adolescents is poorer than healthy youth. However, sleep quality does appear to improve with time. Further analyses found sleep quality does not appear to be related to recovery length or outcomes. Thus, the sleep quality of youth may be negatively impacted by concussion, but this may not directly influence recovery.


title: Detection of Gadolinium in Liver and Kidney Phantoms Using X-Ray Fluorescence

contributor: Radiation Sciences (Medical Physics/Radiation Biology)

subject:
Medical Physics
Physics
Radiation
Gadolinium-Based Contrast Agents
Liver and Kidney
MCNP

abstract:
Gadolinium (Gd) is commonly used in contrast agents (GBCAs) to improve magnetic resonance imaging. GBCAs improve tumor imaging and were
thought to be stable and clear from the body through excretion after administration. However, they have been found to dissociate and remain in organs
such as the liver and kidneys. In these studies, a non-invasive Cd-109 based
K x-ray fluorescence (K-XRF) “Clover-Leaf” detection system to study liver
and kidney Gd levels was investigated to improve the minimum detection
limit (MDL). Two Cd-109 sources, one with a relatively low activity of 0.78
GBq and a second high activity source of 5 GBq irradiated a human torso
water phantom containing liver and kidney phantoms with Gd concentrations ranging from 0-100 ppm. The MDL was calculated from two different
time measurements 5 hours (weak source) and 30 minutes (strong source).
In addition, liver and kidney phantom measurements with overlaying tissue
thicknesses from 6-26 mm were investigated. At present, the K-XRF detection system is able to detect the Gd in each phantom with both sources.
The MDL for the liver and kidney with the weaker source is 2.95 ppm and
3.60 ppm, respectively. The MDL for the stronger source is 3.61 ppm and
3.87 ppm, respectively. The overlaying tissue thickness MDLs decreased exponentially since the thickness increased which increases the scattering and
attenuation. Simulations with MCNP successfully modelled the experiments.
MCNP simulations of the kidney with varying Gd concentrations in the cortex and medulla suggest that the XRF measurement is not sensitive to the
Gd distribution in the phantom. To conclude, this detection system can
measure Gd in liver and kidney phantoms and has low MDLs. Future work
should focus on varying the detection capabilities, measuring the effects to
the organs at risk, possible clinical trials, and improving the MCNP model
and peak extraction.

abstract: Thesis

abstract: Master of Science (MSc)


title: The role of influenza hemagglutination-inhibition antibody as a vaccine mediator in children

contributor:
Loeb, Mark
Health Research Methodology

abstract:
Background. Vaccination may protect through the humoral immune response, or cellular immune response, or most likely both. The humoral pathway can be mediated through the rise of serum hemagglutination inhibition (HAI) titers. Our objective was to investigate the proportion of protection against influenza mediated through the rise of HAI titer (indirect effect) compared to that induced through other immune mechanisms (called direct effect) for different influenza types and subtypes.
Methods. We analysed data from a cluster randomized trial where Canadian Hutterite children were vaccinated and assessed the 2008-2009 season to estimate the effect of higher HAI titer in protection against influenza. We included data from 618 children from 46 colonies, aged between 3 and 15 years with a mean age of 9.06 years who were vaccinated with inactivated trivalent influenza vaccine or hepatitis A vaccine. We used the inverse odds ratio weighting method to calculate the direct and indirect effect of vaccination against influenza A/H3N2 and influenza B/Brisbane by regressing vaccination on HAI titer.
Results. Our results show that the vaccine efficacy was 63% for influenza A (H3N2) and 28% for influenza B. The hazard ratio for the direct and indirect effect of vaccination for protection against influenza A/H3N2 was 0.38 (95% confidence interval [CI] of 0.00 to 5.47) and 0.96 (95%CI of 0.00 to 2.89) respectively. The hazard ratio for influenza B direct and indirect effect was 0.96 (95% CI of 0.00 to 12.02) and 0.75 (95%CI of 0.07 to 1) respectively.
Conclusions.  Although vaccination provided a higher protective effectiveness against influenza A in children, only 3.82% of this protection was mediated through the indirect pathway, that is through rise of hemagglutination inhibition titer. In contrast, more than 85% of the protection against influenza B occurred through rise of HAI titer.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: Multi-Subcarrier Signal Processing for Fiber Optic Communication Systems

contributor:
Kumar, Shiva
Electrical and Computer Engineering

subject:
signal processing
optical fiber
optimization
nonlinearities
multi-subcarrier
subcarriers

abstract:
Although fiber optic communication systems have enjoyed tremendous developments since their inception roughly fifty years ago, there are still improvements to be made. One such area for growth, relating more to long-haul applications of optical fibers, is the mitigation of nonlinear penalties. These nonlinear penalties appear due to the transmitted signal affecting the material properties of the fiber itself, and are more prominent when said signal has more energy in it—a conflicting effect from the traditional stance where more energy is considered beneficial. These penalties come in different forms, although they all have the same degrading effects for the system in question. Therefore, it is imperative to find new techniques that can mitigate these nonlinear penalties to ensure the optimal performance for our systems. One such technique, that we call multi-subcarrier processing, is the interest of the thesis here.
	The first section proposes a new method to compensate for the receiver side digital signal processing. More specifically, it introduces an algorithm that can remove the intermediate frequency offset that the signal acquires after passing through the system, which is necessary for coherent systems employed today. As some traditional algorithms used in the signal processing no longer work for multi-subcarrier systems, this new algorithm is necessary to compensate effectively for said offset.
	The second section introduces a new signal processing technique for the multiplexing and demultiplexing of multi-subcarrier signals. By making use of the well-known Fast Fourier Transform algorithm, the computational cost for generating said signals can be drastically reduced as the number of subcarriers grow larger. As systems continue the trend of operating at greater baud rates, the savings introduced here should be of even greater significance for commercial systems of the future.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Cycling in Hamilton, Ontario: A Mixed Methods Investigation on the Built Environment and Route Choice

contributor:
Paez, Antonio
Health Research Methodology

subject: Cycling; public health; built environment; route choice

abstract:
Cycling for transport is an increasingly popular mode of travel in Hamilton, Ontario. Between 2011 and 2016, the mode share of cycling grew from 0.6% to 1.2%. As
of 2019, 46% of the planned cycling facilities network has been built, which suggests that the city is transitioning to a cycling city. However, less is known about the built
environment factors that influence cycling trips or the routes travelled by people who
cycle in Hamilton. Drawing on the strengths of quantitative and qualitative methods, this research explores the built environment correlates of cycling and the perceptions of people who regularly cycle. First, a spatial interaction model was developed to test the level of cycling flows against various built environment attributes using trips data from the 2016 Transportation Tomorrow Survey. A novel feature of this analysis is the use of a cycle routing algorithm to infer routes as impedance factors. The most parsimonious model suggests that the shortest-path quietest routes best explain the pattern of travel by bicycle in Hamilton. To build upon these findings, objective built environment attributes were documented along select shortest-path quietest routes using environmental audits. The qualitative phase of the study then explores how well these approximated routes match where cyclists travel in Hamilton, as well as how the built environment more broadly in a growing city is perceived and experienced, by interviewing people who regularly travel by bicycle. The interviews highlight that the built environment is not yet bicycle-oriented and that cycling infrastructure influences mobility and route choice. As a result, people who cycle seek out routes that enable them to minimize interactions with cars, by incorporating quiet streets, and that have enjoyable environments. Policy implications and recommendations specific to these findings are discussed to further support the city of Hamilton’s transition to a more bikeable city.

abstract: Thesis

abstract: Master of Public Health (MPH)


title: Minding the Gap: Understanding changes in momentary intentions and physical activity behaviours during late adolescence using ecological momentary assessment

title: Variation in daily and within day intentions and the intention-behaviour gap

contributor:
Kwan, Matthew
eHealth

subject:
behaviour
physical activity

abstract: BACKGROUND: The construct of intention continues to be an important correlate and predictor of physical activity; however, a substantial intention behaviour gap continues to exist. Little literature has examined this gap on a micro-temporal scale, and none have addressed the adolescent population. PURPOSE: The purpose of this thesis is to 1) examine whether there are variations in daily and within day intentions to be physically active in the adolescent population, and 2) whether the intention -physical activity gap is reduced when assessing intention and behaviour on a micro-temporal scale using Ecological Momentary Assessment (EMA). METHODS: This thesis sample included 193 grade 11 students from a large school board in Southern Ontario. Participants responded to 5 EMA prompts for 7 days on their smartphones and wore accelerometers for the duration of the study. Each EMA prompt included a brief questionnaire assessing participant intentions to engage in physical activity. A mixed-effects logistic regression model was used to determine variability in intentions and descriptive analyses were used to examine the intention - behaviour gap. RESULTS: A mixed-effects logistic regression did not indicate differences in intentions between days of the week (coef. = -0.07 SE: 0.07, p=.27) but did indicate that likelihood of reporting intentions significantly decreases over the course of the day (coef. = -.479 SE=.05, p<.01). For daily intentions and physical activity, 89% of daily intenders engaged in subsequent physical activity while 46% of within day intenders engaged in subsequent physical activity. CONCLUSIONS: Findings suggest that there is some variation in intentions and that a micro-temporal time scale measurement serves to reduce the intention - behaviour gap. This adds to our understanding of the relationship between intentions and physical activity. In better understanding this relationship, we can begin to guide interventions that bridge the gap between intentions and physical activity in the adolescent population.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Despite the known benefits of physical activity, rates remain low amongst adolescents. Previous research has outlined the importance of intentions as a predictor of physical activity; however, an intention behaviour gap persists. The current study examined this gap by assessing variation in intentions over the course of the week and day, and by examining intentions and physical activity closer together in time through the use of a smartphone app. Significant variation was found in intentions within the day to engage in activity. Descriptively assessing intentions and physical activity by measuring them closer together in time indicated a reduction in the daily intention behaviour gap but no significant differences between intentions and behaviour measured frequently within a day. Findings suggest that the intention to behaviour gap may be reduced by assessing intentions and behaviour more frequently and closer together in time. Further research is required to quantify this reduction.


title: Enhanced Recovery After Surgery in Autologous Breast Reconstruction: A Pilot Randomized Controlled Trial

contributor:
Simunovic, Marko
Voineskos, Sophocles
Thoma, Achilleas
Health Research Methodology

abstract:
Background: Enhanced recovery after surgery (ERAS) is an approach to perioperative care shown to shorten hospital length of stay (LoS) and decrease opioid use after colorectal surgery.  There is increasing interest in applying ERAS to breast reconstruction, but the supporting evidence is limited. In this pilot study we evaluated the feasibility of conducting a randomized controlled trial (RCT) comparing ERAS to standard perioperative care among patients undergoing abdominal-based autologous breast reconstruction (AABR) for breast cancer.
Methods: We conducted a parallel two-arm pilot RCT of adult patients undergoing AABR between November 2019 and April 2020. Patients were randomly assigned to ERAS or standard perioperative care. Feasibility outcomes included patient rates of eligibility, recruitment, retention, and adherence to study protocol. The primary clinical outcome was median hospital length of stay. Secondary clinical outcomes included in-hospital opioid use, adverse events at 30-days, and quality of life questionnaires including BREAST-Q and EQ-5D-5L at 30-days.
Results: Of 22 screened patients, 21 (95.4%) were eligible for the study and 20 patients (95.2% of eligible) consented to study enrollment. Two patients did not undergo surgery due to COVID-19 related cancellations. Among the 18 randomized patients (90%) 10 received the study intervention and 8 received standard care. All patients undergoing surgery completed the trial with 30-day follow-up. There was 85.8% adherence to study protocol items in the ERAS group. The ERAS group had a slightly shorter median hospital length of stay (ERAS 4 days, IQR 3-5; Standard care 4.5 days, IQR 3.25-5.75) and lower mean total oral morphine equivalent consumed (ERAS 82.3mg, SD 66.5; Standard care 408.1mg, SD 368.6).
Conclusions: This pilot study supports the feasibility of a larger RCT evaluating effectiveness of ERAS, as demonstrated by high rates of patient recruitment, study completion, and adherence to study protocols. Effectiveness outcomes also encourage a larger RCT.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Many women with breast cancer need surgical removal of their breast. Reconstructing the breast after such surgery improves patient quality of life. The breast can be reconstructed using implants or tissue from another part of the patient’s body such as the abdomen. Patients undergoing breast reconstruction using their abdominal tissue experience longer recovery and use more pain medications compared to reconstruction using implants. We would like to test if a new approach to surgical care can improve recovery for patients having breast reconstruction using their abdominal tissue. As a first step, we would conduct a small pilot study to test if patients are willing to participate in this research, and if this approach can be delivered by the healthcare team. The results of this study will help decide if a larger study should be organized to test if we can improve recovery for patients having breast reconstruction using abdominal tissue.


title: Identifying Geographic Areas Where Children May Be At-risk of Lead Poisoning and Assessing the Need for Lead Abatement in Urban Areas: A Case Study in Hamilton, Ontario

subject:
environmental health
pediatric health
lead poisoning
hamilton

abstract:
Thirty years since the removal of lead from gasoline, lead still poses a health risk. Children are most at-risk for adverse health outcomes caused by lead toxicity due to both behavioural (e.g., hand-to-mouth behaviour) and physiological differences (i.e., increased intake of lead by body weight, higher uptake rate and a higher vulnerability to the effects of lead) compared to adults (Yeoh et al., 2009). As a result, governments must identify children that may be at-risk of lead poisoning and develop practical methods to mitigate lead exposure.
Before a government can develop a policy to help mitigate exposure of lead for children, we need to understand the spatial distribution of lead within the city. A popular spatial model used within air pollution research may allow more accurate, and more localized predictions than the most common interpolation method, kriging. Land use regression (LUR) is a technique leveraging multiple predictor variables to help estimate the spatial distribution of the dependent variable. By using historical sources of lead, LUR can be used to model soil lead levels (SLL) with localized variation. Unfortunately, spurious relationships can be the basis of a LUR model, which may lead to an overfitted spatial model resulting in a model with little generalizability and questionable ability to estimate the dependent variable at unobserved locations. Ultimately, Empirical Bayesian Kriging may be the best option for soil contamination research due to its ability to provide a smoothed prediction surface and its dependence on the spatial structure of the data to provide estimations.
The benefit to society and the return on investment (ROI) is often the justification for lead remediation. Gould (2009) estimates a $17 to $221 ROI for every dollar spent on lead hazard control. One of the main components of this estimate of ROI comes from the decrease in intelligence quotient (IQ) that a child may experience as a consequence of lead toxicity. There are three main ways that a decrease in IQ can negatively impact the economy, (i) lower potential lifetime earnings, (ii) reduced tax revenues, and (iii) higher spending on special education (Gould, 2009). Since IQ has such a significant role in the ROI estimates, chapter 3 seeks to achieve a greater understanding of the relationship between blood lead levels (BLLs) and IQ. The loss of IQ points for an increase in blood lead concentration proposed by Lanphear et al. (2005) and referenced by Gould (2009) is significantly higher than what we found in our meta-analysis. Thus, the projected ROI proposed by Gould (2009) may be much lower than previously calculated.
In the final chapter, the cost associated with permanent lead abatement is investigated based on ROI projections as a case study in Hamilton, Ontario. We show that, in most cases, permanent lead remediation is far too expensive for a municipal government. Furthermore, the capital initially invested may not be distributed back into the local economy, as the ROI suggests. We suggest that municipal governments make decisions based on need, rather than basing remediation decisions on ROI projections. Furthermore, we recommend the use of hazard quotient maps to help justify lead remediation as a more accurate representation of potential lead toxicity, instead of only looking at SLL exceedances across the city.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: The Potential of Contracting in Global Agri-Food Governance: The Pursuit of Public Interests Through Private Contracts

contributor:
Porter, Tony
Political Science

subject:
Global Governance
Private Governance
Agriculture
Private Law
Contract Farming
Private Authority
Globalization

abstract:
This dissertation contends that to appropriately address important cross-border problems and pursue public interest(s) in an increasingly globalized world, we must deal directly with the more complex, networked, interdependent and hybrid governance forms which have grown increasingly common alongside globalization. Consequently this, dissertation examines the largely unexplored possibility of commercial contracts to act as a governance tool capable of improving the ethical quality and effectiveness of global agri-food governance to address critical challenges in that sector. These include those associated with food safety, ecological sustainability and biodiversity, gender equality, access to food, poor working conditions, inequality as well as issues of representation and inclusion in decision-making.

To do so, the dissertation advances a novel conceptual framework of commercial contracting that opens up space to explore and identify features of contracting which enable it to go beyond private interests to also address public ones. To demonstrate this, the dissertation utilizes empirics from my case study, which is grounded in the transnational pineapple value chain between Ghana and Western Europe.

This dissertation makes four key contributions to knowledge. First, it has developed a novel and generalizable conceptual framework of contractual governance through which activists and policymakers can address critical global agri-food governance challenges. It has also advanced practical options to do so.  Second, this dissertation has important implications for global and private agri-food governance literatures, which have ignored the commercial contract and the influential role that it plays in the governance of food. Third, this thesis contributes to a body of existing literature indicating that “private” governance arrangements may be more capable than many often given them credit for in governing in democratically legitimate ways over issue areas of broad public interest. Finally, this thesis contributes empirical data in a field and area of study which is notoriously opaque and inaccessible.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This dissertation examines the potential of private contracts to increase the sustainable and ethical production and consumption of food. It argues that contracts are more capable of regulating over important issues that are of common concern than they are given credit for. It also argues that commercial contracts have particular features that make them well-suited to regulating long-distance relationships that span the borders of countries and include a variety of different stakeholders. This is noteworthy, because the regulation of long-distance relationships is becoming both more common and important in the world today. To demonstrate my arguments, the dissertation uses data taken from interviews with pineapple farmers and exporting companies in Ghana who produce pineapple for supermarkets in Europe. It also draws on interviews from public regulators in the European Commission, and international organizations, as well as lawyers, academics and private standard-setting bodies in agriculture such as GlobalGAP.


title: Chemiresistive Detection of Metal Cations in Water

contributor:
Kruse, Peter
Chemistry

abstract:
Metal cations serve an important physiological purpose in humans, and one of the
most abundant sources of these cations is water. Many cations beneficial to human life are
found in water. However, many cations that are deemed detrimental to health may also be
present in these water sources. Currently, many methods exist to detect, quantify, and
monitor metal cations in water ranging from simple visual tests to more elaborate lab-based
methods. The method of metal cation detection employed in this thesis relies on the use of
chemiresistive sensors. These sensors monitor the changes in the transductive portion of the
sensor, which can be observed through the changes in the current resistance of the sensor.
One example of a transducing film is graphene, which is known for its high conductivity.
Herein, chemiresistive sensors based on a few layer graphene transducing film have been
employed for the detection of metal cations, namely copper, silver, lead, and mercury. The
films were functionalized with molecules specific to each cation to ensure selectivity. Charge
transfer between the metal-molecule complex and the few layer graphene film drives the
sensing mechanism. An investigation was also made into the efficient selection of sensor
molecules to be used for functionalization by observing four different phenanthroline
derivatives. This was done to allow for a smarter way to select sensor molecules. The work
presented in this thesis suggests that the detection of metal cations using these few layer
graphene based chemiresistive sensors is a viable pathway towards cheap online water quality
monitoring.

abstract: Thesis

abstract: Master of Science (MSc)


title: “The lights are on, but is anyone home?”: Estimating dwelling distribution in rural Alberta

contributor:
Yiannakoulias, Niko
Geography

subject:
Distribution
Settlements
Geography
Spatial Analysis

abstract:
With Canada's increasing population, natural disasters such as flooding events will have
an increasing impact on human populations. The severity of these events requires that decision
makers have a clear understanding of the flood risks that communities face in order to plan for
and mitigate flood risks. One key component to understanding flood risk is flood exposure, an
element of which is the presence of structures (e.g., residences, businesses, and other buildings)
in an area that could be damaged by flooding. Presently, several resources exist at both the
national and global level that can be used to estimate the spatial distribution of structures. These
resources are typically generated at global scales and do not account for regional or local data or
processes that could enhance the accuracy and precision of exposure estimation in sparsely
populated areas. The present study investigates the feasibility of creating a region-specific
dwelling distribution model that helps improve estimation of residential structures in rural areas.
Herein, we describe a rural dwelling distribution model for the province of Alberta that can be
used to assist in the estimation of structural exposure to flood risk. The model is based on a
random forest classification algorithm and several publicly available datasets associated with
dwelling and population density. The model was validated using visually referenced data
collected from earth imagery. The resulting dwelling layer was then evaluated in its ability to
spatially disaggregate census dwelling counts, as well as predict dwelling exposure in several
scenarios. This method appears to be a useful alternative to globally scaled models, or using the
census alone, particularly for rural areas of Canada.

abstract: Thesis

abstract: Master of Science (MSc)


title: Human Commensal Microbiota That Inhibit the Growth of Respiratory Tract Pathogens

contributor:
Surette, Michael
Biochemistry and Biomedical Sciences

subject: Human Microbiome, Commensals, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus faecium, Growth Inhibition Bacteriocins

abstract: Lower respiratory tract infectious diseases are a world-wide healthcare burden with bacterial pathogens accounting for a large portion of primary and secondary infections. The human respiratory tract is home to hundreds of species of microbes that comprise the human airway microbiome. These commensals play a crucial role in human health in part by providing colonization resistance against pathogens. In a previous study from the Surette lab it was shown that specific bacterial isolates from the respiratory microbiome inhibits the growth of pathogens aerobically. This included an isolate of Staphylococcus aureus which inhibited the growth of Enterococcus faecium. This activity was further characterized in this thesis and the underlying mechanism was explored through comparative genomics. As well, this observation provided proof-of-concept for a large-scale screen for additional isolates which inhibit pathogen growth. I hypothesized that the respiratory tract microbiota included many other bacteria capable of inhibiting the growth of respiratory tract pathogens in both aerobic and anaerobic environments, and that anaerobic conditions will identify new activities not detected aerobically. To examine and identify potential beneficial bacteria, I have screened ~5000 respiratory tract bacteria from the Surette lab’s airway isolate collection against four pathogens: Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa and Klebsiella pneumoniae. The respiratory tract commensals were pinned onto the pathogen-lawn and their interaction was expressed as zones of clearing or altered growth phenotypes of the pathogen. The results of the screen showed that anti-pathogen activity was a common feature of respiratory tract commensals. In particular, S. pneumoniae was inhibited by taxonomically diverse members of the microbiota representing three phyla (Proteobacteria, Firmicutes and Actinobacteria). Many of the facultative anaerobes that inhibited S. pneumoniae expressed their activity in anerobic conditions.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The human respiratory tract harbours commensal and pathogenic bacteria, and the latter cause most of the lower respiratory tract infections. The commensal bacteria help to train the immune system and impede the growth of pathogens through colonization resistance. A previous study by the Surette lab identified bacterial isolates from the respiratory tract that inhibit the growth of select pathogens, among them, a particular strain of Staphylococcus aureus. Based on the results of the earlier study, I hypothesized that the respiratory tract bacteria is a good source of commensals that can inhibit the growth of S. aureus and other respiratory pathogens, such as Streptococcus pneumoniae, Pseudomonas aeruginosa and Klebsiella pneumoniae. To find potential therapeutic bacteria, I screened ~5000 respiratory tract isolates from the Surette lab’s strain collection for the ability to impair growth of target pathogens. Additionally, I further characterized the activity of the previously identified S. aureus strain against various Lactobacillalles strains and used comparative genomics to identify potential biosynthetic genes required for biosynthesis of molecules with antibacterial activity within the genome of S. aureus. The research reported in this thesis demonstrates that many commensal bacteria that live within our airways have the ability to inhibit the growth of bacterial pathogens. This work may provide a new source of antibiotics against respiratory infections and new strategies to reduce susceptibility to infections in vulnerable populations.


title: Decoding Adolescent Rickets: The Effects of the Environmental and Social Contexts on the Development of Rickets in Adolescents in the Netherlands from the 17th to 19th Centuries

contributor:
Brickley, Megan
Anthropology

subject:
Rickets
Adolescence
Anthropology
Biological Anthropology
Paleopathology
Vitamin D Deficiency

abstract:
Vitamin D deficiency at Middenbeemster and Hattem is the result of cultural variables that limit an individual’s exposure to sunlight. During growth spurts, such as the pubertal growth spurt, high demand for vitamin D puts individuals at an increased risk for developing conditions such as rickets. This thesis aims to determine whether adolescent rickets can be identified in archaeological skeletal remains, and how to quantify the observed changes. The current work also aims to use the prevalence of adolescent rickets to understand the underlying social changes affecting individuals in the Netherlands in the 17th to 19th centuries. Two collections of archaeological human remains from the 17th to 19th century Dutch sites of Middenbeemster (n=246) and Hattem (n=117) were evaluated using macroscopic, metric, radiographic, and micro-CT analysis of skeletal remains. Adolescent individuals were evaluated for signs of active adolescent rickets, and adults were evaluated for signs of residual adolescent rickets. Statistical analysis found that measurements quantifying shape changes at the distal ulna, medial clavicle, and sacral angle can be used to identify adolescent rickets in a skeletal sample.
	Adolescent rickets at Middenbeemster and Hattem was found to be distributed equally amongst males and females and was found to occur less frequently than rickets in infants and children from the same population. Rickets in adolescents was most likely caused by the onset of new jobs or roles resulting in individuals remaining indoors for long periods of time. Rickets may have also been caused by illness. By identifying rickets in adolescents, this thesis provides a window to view the changing roles of individuals as they begin to occupy new spaces in their transition from children into adults, thus providing a novel way to investigate the lives of adolescents.

abstract: Thesis

abstract: Master of Arts (MA)


title: The Psychometric Properties of Generic Preference-Based Measures in Amyotrophic Lateral Sclerosis

title: PSYCHOMETRICS OF MEASURES IN AMYOTROPHIC LATERAL SCLEROSIS

contributor:
Kuspinar, Ayse
Rehabilitation Science

subject:
Psychometric Properties
Health-Related Quality of Life
Amyotrophic Lateral Sclerosis
Patient Reported Outcome Measures
Economic Evaluation

abstract:
Background: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the loss of motor neurons. Preference-based measures (PBMs) of health-related quality of life (HRQL) can be utilized for cost-effectiveness analyses of interventions in individuals with ALS. However, current measures are generic (GPBMs) and the psychometric properties of these measures have not yet been evaluated in ALS.
Purpose: The purpose of this thesis was to evaluate the psychometric properties of GPBMs in ALS by 1) conducting a systematic review of the psychometric properties of GPBMs, and 2) assessing the content and convergent validity of GPBMs in ALS.
Methods: Two studies were conducted. First, a systematic review was performed, and four databases were searched to identify studies that used and reported on the psychometric properties of GPBMs in ALS. Second, participants were recruited from three clinical sites across Canada and outcome measures were administered through an online or hardcopy survey. Areas of importance to the HRQL of individuals with ALS were identified using the Patient Generated Index (PGI), mapped against GPBMs to determine their coverage and scores were compared to determine convergent validity.
Results: For the first study, the EQ-5D-3L was found to be the most commonly used GPBMs in ALS. It demonstrated convergent and known-groups validity however, significant floor effects were observed. For the second study, results indicated that the majority of GPBMs identified approximately half of the areas impacted by ALS. In addition, there were several domains not identified by GPBMs.
Conclusion: This thesis highlights the importance of complete psychometric evaluation of measures in ALS. There is the need for the development of an ALS specific preference-based measures that reflects the health concerns of individuals with ALS; as GPBMs used in ALS were evaluated and deemed to be lacking in support for their usage in ALS.

abstract: Thesis

abstract: Master of Science Rehabilitation Science (MSc)

abstract: Amyotrophic Lateral Sclerosis (ALS) is a fatal disease that causes individuals to lose their strength and eventually the ability to speak, eat, move and breathe. Questionnaires can be used to understand the health-related quality of life (HRQL) of individuals with ALS however these measures do not always reflect the experiences of these individuals. The goal of this dissertation was to identify whether measures truly capture areas important to individuals with ALS. In our studies, we found that there is little proof in the accuracy of measures used. In addition, the measures do not fully capture the areas of life important to individuals with ALS. This is important to help researchers and health care professionals understand the effects of ALS on HRQL. These results will help them determine which treatments are worthwhile and the best to use in practice and provide recommendations for future research.


title: Investigating the Transcriptional Responses of Escherichia Coli under Chemical Challenge

contributor:
Brown, Eric
Biochemistry

abstract: Bacteria live in diverse and dynamic environments that necessitate adaptation to external stimuli. Here, we probe Escherichia coli K-12 with a wide array of chemical stressors spanning several drug classes, and gauge the transcriptional responses using a promoter-GFP fusion library. Assayed with PFIboxes, the output fluorescence images are temporally resolved and data rich. When quantified as gene expression, these transcriptional responses are seemingly unique to each molecule tested, yet clear differences exist between drug classes. Promoters showing large magnitudes of differential regulation in selective conditions, such as DNA damage, oxidative stress, and cell wall stress, can be used as diagnostic reporters for primary screening assays. The transcriptional signatures generated by these experiments were used to train a 10-layer convolutional neural network in Keras for mechanism of action (MOA) predictions. This model was used to predict the mechanism of action of cefmetazole, polymyxin B, as well as cinoxacin, a compound excluded from the training set. The model predicted the identity of cefmetazole and polymyxin B with 95-100% accuracy. Cinoxacin was predicted to be enoxacin, another fluoroquinolone antibiotic, with ~80% confidence, illustrating the power of prediction MOA of unknown molecules with a large training dataset. This deep learning model predicted the MOA of an unknown compound, MAC168425, as trimethoprim. Further characterization of the compound suggests that its inhibitory activity is involved in folate-binding and utilization, and glycine cleavage. In all, this work illustrates that microbial reporter arrays generate unique patterns which can be used to make hypotheses on the MOA of unknown molecules.

abstract: Thesis

abstract: Master of Science (MSc)


title: Being-Towards-Death-and-Resurrection: An Examination of Finitude and Infinitude in the Writings of Martin Heidegger and Emmanuel Falque

contributor:
Kroeker, Travis
Religious Studies

subject: Heidegger Death Resurrection Falque Levinas

abstract: This thesis gives an account of Heidegger’s understanding of anxiety and death as it relates to the Christian theology of resurrection. It does so by investigating three primary accusations that Heidegger makes against Christianity with respect to its views on death and anxiety interpreted through a belief in an afterlife. In order to interact with Heidegger’s criticisms, Christian phenomenologist Emmanuel Falque’s work is explored for a more dialogical Heideggerian and Christian understanding of death. In doing so, this thesis picks up questions such as: can resurrection interpreted phenomenologically contribute something new to a Heideggerian view of Dasein as a Being-towards-death? as well as in what ways can Heidegger’s starting-point of finitude formulate new possibilities for interpreting Christ’s death and resurrection? Are these theological events necessary for an “authentic” understanding of death and finitude? These questions pertain to anxiety about what Heidegger calls the “to-come”, a concept mapped out in Heidegger’s own work on Christianity and then secularized in his fundamental ontology delineated in chapter one. Chapter two takes up Falque’s work on the death of Jesus and its correlations to Heideggerian views on death, while chapter three contemplates resurrection (and through this, birth) and the various modes of being that it opens up for human finitude. Chapter three concludes with a Levinasian reading of the New Testament resurrection accounts in order to consider how the Christian mode of Being-towards-resurrection can work alongside and, in a certain sense, within a Heideggerian view of human finitude as a Being-towards-death.

abstract: Thesis

abstract: Master of Arts (MA)


title: Jus Gentium & the Arab as Muselmänner: The “Islamist Winter” is the Pre-Emptive (Creative) Chaos of the “Arab Spring” Multiplying Necropolises

title: JUS GENTIUM & THE ARAB AS MUSELMÄNNER

contributor: Political Science - International Relations

subject: Jus gentium

subject: International law

subject: Positivist jurisprudence

subject: Necropolitics

subject: Biopolitics

subject: Displacement

subject: Operation Timber sycamore

subject: Arab Spring

subject: Islamist Winter

subject: Constructive Chaos

subject: Regional Refugee Resilience Program (3RP)

subject: Homo Sacer/Musulmann

subject: Arab Philosophical Theology

subject: Latin-European Philosophical Theology

abstract: While the (re)conquest of Arabia as manifest in 2003 Iraq, and 2006 Lebanon, were respectively Act I and II accenting sovereign figures exercising necropower by adjudicating (il)legal doctrines (i.e., pre-emptive defense strategy) legalizing extrajudicial techniques of violence founded on discursive technologies of racism, I argue that the “Islamist Winter” – temporarily dubbed the “Arab Spring” in 2011 – is Act III reifying similar legal doctrines (i.e., Bethlehem Legal Principles) and a (secular) linear temporal perception of time seeking to implement a New Middle East (NME) that is no longer “resistant to Latin-European modernity” but amenable to such inclusive exclusion historicist telos. The importance of “creative anarchy” as a positivist legal technique in producing chaotic developments such as carnage and a “crisis” or “emergency” of displacement – with sovereign members of jus gentium authorizing agents of terror (i.e., death squads/war-machines) – is that it reveals the deadly technologies of racism and relations of enmity inherent in sovereignty as a positivist juridical concept endowing sovereign figures with the power to formulate legal doctrines that ultimately subjugate Arab life to the power of death (necropower). Therefore, one of the main questions orbiting the writing of this dissertation is interested in deconstructing and critiquing jus gentium – by adopting a Third World Approach to International Law (TWAIL) in tandem with necropolitics and biopolitics as paradigms of analysis – to disclose that it is because jus gentium valorizes positivist jurisprudent scholastics postulating an unbridgeable cultural gap between an Athenian mode of Being as a universal sovereign subject, and a Madīnian mode of Being as the particular object denied sovereignty, that leads ratiocinative sovereign figures to legally exercise necropower on the Arab body. Therefore, the following chapters seek to go beyond the limited (post-colonial) idea asserting that the problem with international law is that it is primarily “Eurocentric” since the simple solution to such a claim would be to include the non-European body in International Law. Rather, the primary question constellating this monograph is: what are the experienced consequences of being temporally included and what are the experienced consequences of being temporally excluded from a legal regime (i.e., jus gentium) reifying a Latin-European philosophical theology universalizing a particular set of liberal-secular cultural mores as a “cultural benchmark” (i.e., purity-metric) in order to be-come imagined as temporally “inside” jus gentium?

abstract: Thesis

abstract: Doctor of Social Science


title: Microbial Communities in Septic Tank Anaerobic Digesters and Their Interactions with Digester Design and Chemical Environment

contributor:
Schellhorn, Herbert
Golding, Brian
Biology

subject:
metagenomics
wastewater
sequencing
microbial community
anaerobic digestion
septic tank
microbiology

abstract: Anaerobic digester design and operation influences the biomass degradation efficiency performed by complex and diverse microbial communities. Optimum anaerobic digester design and operational parameters in residential on-site wastewater treatment sites (OWTS) establishes physiochemical environments suitable for the growth and stability of the microbial communities responsible for organic waste degradation. A comparative study of the microbial communities and their functional profiles between different OWTS designs and operational parameters have not been done despite their functional importance in residential organic waste removal. Using whole-metagenome shotgun sequencing, microbial community compositions and functions were compared between two digester designs: conventional box septic tanks and septic tanks equipped with a novel closed-conduit tube called the InnerTubeTM. Wastewater was sampled along the length of each digester to explore the microbial community stratification during the anaerobic digestion treatment process. Additionally, the effect of effluent, aerobic recirculating-lines on the digester microbiome was also explored. Physiochemical characteristics in the form of oxygen demand, nitrogen and solids content was used as endpoints and correlated with microbial community and functional gene abundances to explore the microbes driving anaerobic digestion. Conventional digesters were characterized by syntrophic proprionate-oxidizing microbes and acetoclastic methanogens, while InnerTube™ digesters were characterized by syntrophic sulfate-reducing microbes and hydrogenotrophic methanogens. Recirculating digesters were enriched with denitrifying microbial consortia in syntrophy with hydrogenotrophic methanogens. Microbial communities were organized according to hydrolytic, acidogenic, acetogenic, and methanogenic groups along the digester treatment process. Insight into the core microbiome of OWTS can inform bioaugmentation and digester design and operation optimization strategies to improve the treatment of decentralized residential sewage sources.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Anaerobic digesters are used throughout North America to treat residential sewage. Despite their prevalence, the composition and function of the microbial communities driving sewage degradation in residential digesters has not been studied. We used DNA sequencing to compare the microbial communities and functional genes in different anaerobic digester designs across Southern Ontario. Our findings suggest there are successive microbial groups along the length of septic tanks and that different septic tank designs harbor characteristic sulfidogenic and methanogenic microbes. Characterization of these microbes could inform septic tank bioaugmentation, design and operational optimization strategies to improve sewage treatment performance.