title: In arms: Exploring the effects of military sexual trauma on intimate partner relationships

title: Military sexual trauma and intimate partner relationships

contributor:
McKinnon, Margaret
Tam-Seto, Linna
Psychology

subject:
military sexual trauma
intimate partner relationships

abstract:
Introduction: Sexual misconduct is a pervasive and deleterious issue within military contexts. Commonly cited psychological sequelae of sexual assault include anxiety, depression, suicidality, posttraumatic stress disorder (PTSD), as well as interpersonal relationship functioning issues. The experience of military sexual trauma (MST) is unique in that the environment in which the harm occurs, the culture, plays a significant role in the impact of the harm on survivors. MST is often also related to feelings of institutional betrayal and moral injury. While clinical treatment of interpersonal trauma history is common, there is a lack of research regarding the development and efficacy of clinical interventions used with couples affected by MST. The objective of the thesis is to examine how dimensions and impacts of MST affect intimate partner relationships. Methods: A multi-method qualitative approach was taken in the thesis, including a scoping review and two narrative reviews, contextualized using primary qualitative data in the conclusion chapter.
Results: MST affects dimensions of intimate partner relationships including communication, trust and attachment, intimacy, conflict, aggression, as well as sexual function and satisfaction. The present work highlights the unique considerations for those affected by MST, suggesting that the relationship between adverse psychological outcomes, such as PTSD, and relationship distress appears to be greater for military than among civilian populations. While clinical work aims to amplify positive outcomes within couple relationships, and reduce individual symptomatology, there exists a lack of interventions tailored to meet the needs of couples affected by MST specifically.
Discussion: The present thesis contributes to the growing understanding of how MST affects intimate partner relationships, as researchers and clinicians continue to seek to improve supports available for military members. The work is an appropriate start to inspire and inform future research, identifying existing gaps in the literature spurring on forthcoming work that aims to improve the wellbeing of military-connected intimate partner relationships.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The present thesis explores how military sexual trauma may affect intimate partner relationships. The work highlights how the literature discusses and describes the link between sexual assault that occurs in the military, posttraumatic stress disorder, and intimate partner relationships. In addition, the work explores concepts related to the experience of sexual assault in the military, such as betrayal, guilt, shame, as well as military culture. The thesis also identifies and summarizes information about therapeutic interventions being used with couples who are affected by military sexual trauma. The present body of work contributes to the growing understanding of how military sexual trauma affects intimate relationships and survivors, while also informing research, clinical services, and policymakers who are making meaningful change in the health and wellbeing of military members and their partners.


title: Treatment of Open Wound Infections Using Drug-Impregnated Polymer Hydrogels: A Dual Approach

contributor:
Coombes, Brian
Chemistry and Chemical Biology

abstract: The skin is the body’s largest organ and serves a variety of essential functional and aesthetic purposes. Wounds, burns, and other abrasions to the skin can have consequential effects on the rest of the body if not properly managed. Open wounds are often a breeding ground for bacterial infections and can pose a severe threat to individuals with compromised immune systems and other at-risk groups. Antibiotic- resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), thrive in these polymicrobial environments and are often difficult to treat. In tandem, bottlenecks in the drug discovery pipeline lead to slow development of novel compounds and routes of administration. One such challenge is the inherent issue of solubility of antibiotic compounds. Otherwise promising drug candidates face challenges in administration in critical cases, such as open wounds, due to their poor aqueous solubility. These barriers highlight the need for unconventional approaches to drug discovery and the delivery of therapeutics. In collaboration with an Edmonton-based biotechnology company and other research groups at McMaster University, we performed a comparative analysis of two novel hydrogels loaded with antibiotics of interest to address the aforementioned challenges in treating infected wounds. Utilizing patented technology and an optimized excisional murine wound model, the two proposed routes of antibiotic administration show promise in delivering drugs with inherently low water solubility and offer several other advantages in the development of efficient drug delivery vehicles.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Open wounds are breeding grounds for infection and can pose severe threats to individuals with compromised immune systems and other at-risk groups. Antibiotic- resistant bacteria thrive in these polymicrobial environments and are often difficult to treat. In tandem, challenges in the drug discovery pipeline lead to slow development of new antibiotics and routes of administration. One such challenge is the issue of solubility of drug compounds. Otherwise promising drugs face hurdles in administration due to their poor water solubility. These barriers highlight the need for unconventional approaches to drug discovery and the delivery of therapeutics. In collaboration with an Edmonton-based biotechnology company and other research groups at McMaster University, we studied two novel hydrogels loaded with antibiotics of interest to address the aforementioned challenges in treating infected wounds. Utilizing patented technology and pre-clinical animal models, the two proposed routes of antibiotic administration show promise in delivering drugs with inherently low water solubility and offer several other advantages in the development of efficient drug delivery vehicles.


title: Understanding the assessment of language comprehension in children with severe motor and speech impairments due to cerebral palsy

contributor:
Gorter, Jan Willem
Health Sciences

subject:
cerebral palsy
outcome measurement
family-centred care
language comprehension
implementation

abstract:
Children with cerebral palsy (CP) and severe motor and speech impairments face problems in communication. Their capacities may vary across all domains of functioning, including mobility, selfcare and communication, which means these should be assessed independently, using valid and reliable instruments. The assessment of an unobservable construct like language comprehension skills is complicated because the completion of commonly available tests requires speech and motor skills. Using such tests with children with severe motor and speech impairments does not yield a valid, reliable, or representative result. To fill the gap in language assessment instruments, the Computer-Based instrument for Low motor Language Testing (C-BiLLT) was developed in the Netherlands between 2009 and 2014, and introduced intro clinical care in 2015. This test provides an accessible alternative to traditional language tests, allowing participation of children who cannot speak, finger point, or manipulate small objects.
The overarching goal of the work in this thesis was to bring the C-BiLLT to Canada and to improve our understanding of the use of the C-BiLLT from a clinician and family perspective. To achieve this goal, the research described in this dissertation addressed objectives related to: 1) the cultural and linguistic adaptation of the test; 2) the psychometric properties of the new version; 3) the implementation of the test; and 4) the concept of family-centred care in relation to the C-BiLLT assessment.
Three empirical studies were completed. The adaptation processes (including a validation study) that resulted in the Canadian English version of the C-BiLLT (C-BiLLT CAN) are described in Chapters 2 and 3. To understand the unique implementation attributes of the C-BiLLT, Chapter 5 describes a survey among users about their C-BiLLT use, and Chapter 6 describes an interview study in which clinician behaviours are explored into more detail. Finally, Chapter 7 describes the protocol for a qualitative study using interpretive description to understand parents’ experiences of the C-BiLLT assessment for their child with cerebral palsy and severe motor and speech impairments.
The process to develop the C-BiLLT CAN comprised many phases, to ensure the linguistic and conceptual equivalence between the original C-BiLLT and the newly developed version. The benefits of a thorough cross-cultural adaptation process were confirmed by the results of the validity and reliability assessment of the C-BiLLT CAN in typically developing Canadian children. While future research is needed to confirm the feasibility and validity of the test for Canadian children with CP, our study showed that the new version is a robust instrument to assess spoken language comprehension and is available for use in clinical practice.

The C-BiLLT CAN is a scientific innovation. How scientific innovations can be best implemented into clinical practice is studied by implementation science. An implementation science lens was applied to the current use of the C-BiLLT in three countries where the test is currently available in clinical practice: The Netherlands, Belgium, and Norway. The survey study described in Chapter 5 demonstrated that clinicians use the test with children with CP (the C-BiLLT’s target population), but also with children who have other diagnoses, including Down’s syndrome and autism spectrum disorder. This study also reported on the barriers and facilitators related to use of the C-BiLLT. We categorized the reported barriers and facilitators into four groups: 1) factors inherent to the C-BiLLT (i.e., its hardware, software, and content); 2) factors related to the child; 3) factors related to the clinician; and 4) factors related to the environment.
To gain a better understanding of clinicians’ implementation behaviour and what is needed to facilitate behaviour change, fifteen survey respondents were interviewed individually. The COM-B model (Capability, Opportunity, Motivation – Behaviour) of behaviour change was the theoretical foundation for this study. This model describes how capability, opportunity, and motivation play a role in people’s behaviour. This study taught us how these components of behaviour interacted for clinicians who use, or attempt to use the C-BiLLT in clinical practice. The study highlights the need for support for the clinicians who use the C-BiLLT with children with severe motor and speech impairments. Compared to clinicians who use it with children with other disabilities, this group of clinicians faces more and more complex barriers. The studies described in Chapters 5 and 6 underline the importance of appropriately addressing barriers to C-BiLLT use.
The growing emphasis on family-centred care in pediatric rehabilitation services inspired the conceptualization of the concluding study of this thesis, of which the protocol is described in Chapter 7. The aim of the described study is to advance Speech-Language Pathology (SLP) disciplinary knowledge around family-centred assessment for children with CP and severe motor and speech impairments. The protocol describes how we would like to address this aim by collecting parent experiences of their child’s C-BiLLT assessment.
This thesis approached the C-BiLLT from the angles of cross-cultural adaptation, psychometrics, implementation, and family-centred care. The development of the C-BiLLT CAN provides the foundation for standardized and accessible assessment of spoken language comprehension for children with CP in Canada. Theory-informed knowledge translation strategies are suggested that align with real-world practice. Finally, suggestions for incorporating parents’ perspectives into the assessment process help to increase the value of the assessment for children, their families, and clinicians alike.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract:
Cerebral palsy (CP) is the most common cause of physical disability in children. CP is the result of an injury to the brain before, during, or after birth and before the age of one year. While effects of the brain injury are different for each child, for many children with CP the main effect is difficulty with voluntary movement, including fine movements of the lips and tongue to make speech. Some children with speech difficulties can communicate by pointing or making gestures, but others have such severe movement difficulties that they cannot make those gestures either. These children with severe difficulties might understand what others are saying, but tests of understanding usually require the child to respond with some type of movement, so those tests do not work for children with severe movement limitations.
The C-BiLLT, which is short for Computer-Based instrument for Low Motor Language Testing was developed to assess language comprehension in Dutch-speaking children with CP. The child who is being tested does not need to speak or to use other fine movements to respond. Instead, the child can respond using gross motor movements on a touch screen, input switches operated with anybody part, partner-assisted scanning and/or their own access method(s). The C-BiLLT could be useful for many children with CP around the world, but at present it is only available in Dutch and Norwegian.
The aim of this study was to make the C-BiLLT suitable for children in Canada. We translated the items from Dutch to English, and replaced some items of the Dutch version so that they were familiar to Canadian children. Our study told us that this new Canadian version of the test worked as well as the Dutch test. We also learned that clinicians liked the test, and used it for children with other disabilities as well. Some clinicians had difficulties using the test, and said they needed more practice. In the future we need to make sure there are opportunities for clinicians to get more training, so they have the skills to give the test to any child who would benefit.
One question we still have is how families feel when their child is being tested with the C-BiLLT. Language testing should not be scary or stressful for families or children, and we need to make sure families feel comfortable with any test. Thus, as the last step of this thesis, we designed a future study to ask parents questions about their experiences. We will use results of that study to make the C-BiLLT even more child- and family-friendly.


title: Investigating the effects of goal conflict and trait self-control on the intention-behaviour relationship in emerging adulthood

contributor:
Bray, Steven
Kinesiology

subject:
Intention-Behaviour Gap
Physical Activity
Emerging Adulthood
Moderation

abstract:
Background: The transition into emerging adulthood is a major developmental period in one’s life in which rapid declines in physical activity (PA) are documented. While many emerging adults possess intentions to engage in regular PA, evidence suggests acting on these intentions represents a significant challenge. Obtaining a deeper understanding of the factors associated with the process of translating emerging adult’s PA intentions into action may be integral in building a healthier adult population. The purpose of the study was to investigate the effects of two potential moderators of the PA intention-behaviour relationship: goal conflict and trait self-control, in a sample of emerging adults.
Methods: The study sample was comprised of 132 participants (Mage = 17.80 ± 0.46; 64% female) drawn from a larger prospective cohort study (ADAPT Study). All participants completed two online questionnaires, approximately four weeks apart. Measures of PA intention strength, goal conflict and trait self-control were assessed at time 1. At time 2, participants completed a measure of self-reported moderate-to-vigorous physical activity (MVPA) engagement. Four moderation analyses were performed to assess the independent and combined effects of goal conflict and trait self-control on the PA intention-behaviour relationship.
Results: Across all moderation analyses, the main effect of intention strength was significant (p < 0.001), providing support for the necessary role it plays in PA behaviour. However, the main effects of goal-conflict and trait self-control were not found to be significant, along with all interaction effects tested. Correlational analyses revealed intention strength (r = 0.346, p < .001) and goal-conflict (r = -0.236, p < 0.05) were significantly correlated with MVPA, however trait self-control (r = 0.048) was not.
Conclusion: Although results showed a modest intention-PA relationship, the hypothesized moderating effects of goal conflict and self-control were not supported. While the subjective perception of one’s self-control ability did not moderate the intention-behaviour relationship, future research should explore the interaction between goal conflict and self-control further using more objective measures, or in combination with self-regulation strategies such as action and coping planning. Additionally, goal prioritization may be an important factor to consider when investigating the effect of goal conflict on PA and the intention-PA relationship.

abstract: Thesis

abstract: Master of Science (MSc)


title: Three Essays on Continuity of Care in Canada: From Predictions to Decisions

contributor:
Zargoush, Manaf
Health Management

subject:
Continuity of Care
predictive prescriptive analytics

abstract: Continuity of care (COC) refers to the delivery of seamless services, continuous caring relationships, and information sharing across care providers. A disruption in COC—that is, care fragmentation (CF)—is an important cause of inefficiency in the Canadian healthcare system; such disruption leads to increased healthcare costs and reduced quality of care. Addressing this issue is particularly challenging among older adults, who often have medically complex needs; such patients can require many care transitions across multiple care settings. An effective strategy for COC improvements is to optimize discharge planning among older adults. However, this is hampered by the imperfect understanding of older patients’ needs, which are associated with their health complexity. Therefore, making early predictions about the patients’ health complexity and incorporating this information into discharge planning decisions can potentially improve COC. In this thesis, I develop data-driven predictive–prescriptive analytics frameworks that leverage machine learning (ML) approaches and a rich, massive set of longitudinal data collected over a decade. The first essay in this dissertation studies the early prediction of older patients’ complexity in hospital pathways using ML. It also examines whether we can conduct accurate prognostics with current information on patient complexity. The second study examines how two common measures of patient complexity—multimorbidity and frailty—concurrently affect post-discharge readmission and mortality among older patients. It also investigates the dependency of the outcomes on other essential socio-demographic factors. Finally, the third study examines the feasibility of predicting patients at risk of fragmented readmission—that is, readmission to a different hospital than the initial one. It uses this predictive information to derive optimal policies for preventing CF while addressing disparities in the decision-making process. The findings highlight the feasibility, utility, and performance of predicting patient complexity and important adverse outcomes, potentially undermining COC. This thesis shows that advanced knowledge and explicit utilization of this information could support decision-making and resource planning toward a targeted allocation at the system level; moreover, it informs actions that affect patient-centered care transition at the service level to optimize patient outcomes and facilitate upstream discharge processes, thereby improving COC.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The aging population in Canada is growing significantly relative to the population as a whole, and several challenges are involved in providing aging people with proper healthcare services. One of these challenges is disruptions in continuity of care. Older adults are often medically complex or frail; they may have multiple diseases and require many care transitions across healthcare settings. Poor continuity of care among these patients leads to health deterioration during care trajectories, resulting in reduced quality of care and increased healthcare costs and inefficiencies. This thesis includes three essays that provide practical insights and solutions regarding the issue of continuity of care disruptions, spanning from predicting the issue to strategies to prevent it in a data-driven manner.


title: Measuring and Characterizing Moral Injury in Vulnerable Populations

contributor:
McKinnon, Margaret
Losier, Bruno
Psychology

subject:
Moral Injury
Instrument Development

abstract:
Moral injury is a relatively new psychological syndrome characterized by profound emotional, cognitive, and social pain following perceived moral violations. Though often overlapping, moral violations can involve either the perpetration of a moral transgression (via action or inaction) or the experience of a moral betrayal by a trusted other. In each case, symptoms of moral injury may include guilt, shame, anger, loss of trust and meaning, and social withdrawal.
To date, the study of moral injury has remained nearly exclusive to the military arena. In turn, the aim of this thesis is to highlight the relevance of moral injury to other populations vulnerable to its effects. These include: 1) justice-involved individuals found Not Criminally Responsible on Account of Mental Disorder who may experience moral injury after regaining insight into their offending behaviour; and 2) Public Safety Personnel who are often exposed to morally ambiguous situations while under high levels of social responsibility.
To appreciate the impact of moral injury for these populations, adequate tools must first be developed to measure and assess it. The three studies included in this dissertation outline the key steps to instrument development using a mixed-method approach: first, a qualitative investigation with justice-involved individuals explores the unique emotional consequences following a criminal offence that will inform subsequent phases of instrument development; second, quantitative inquiries are taken to construct, evaluate, and employ a new moral injury assessment for Public Safety Personnel to uncover important causes and consequences of moral injury in this group. This dissertation serves as a strong indicator that moral injury is a unique and costly health outcome relevant across societal groups.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Moral injury is a new psychological syndrome developed to understand an individual’s response to a moral trauma. As with other traumatic stress disorders, some people may develop a moral injury after experiencing a situation or event that violates deeply held moral standards. These morally injurious events may be moral violations perpetrated by the individual and result in deep feelings of shame and guilt, or may be moral betrayals by a trusted other and result in feelings of anger and loss of trust. To better understand the causes, symptoms, and consequences of moral injury, we must first develop tools to measure and assess it. This thesis outlines the key steps involved in developing new moral injury assessments in two groups who have an elevated risk of experiencing morally injurious events and so may be more likely to develop a moral injury: justice-involved individuals found Not Criminally Responsible and Public Safety Personnel.


title: Optimization of Large-Scale Single Machine and Parallel Machine Scheduling

title: Large-Scale Single Machine and Parallel Machine Scheduling in the Steel Industry with Sequence-Dependent Changeover Costs

contributor:
Swartz, Christopher
Chemical Engineering

subject:
single machine scheduling
parallel machine scheduling
mixed-integer programming
metaheuristics
variable neighborhood descent

abstract:
Hundreds of steel products need to be scheduled on a single or parallel machine in a steel plant every week. A good feasible schedule may save the company millions of dollars compared to a bad one. Single and parallel machine scheduling are also encountered often in many other industries, making it a crucial research topic for both the process system engineering and operations research communities.

Single or parallel machine scheduling can be a challenging combinatorial optimization problem when a large number of jobs are to be scheduled. Each job has unique job characteristics, resulting in different setup times/costs depending on the processing sequence. They also have specific release dates to follow and due dates to meet.

This work presents both an exact method using mixed-integer quadratic programming, and an approximate method with metaheuristics to solve real-world large-scale single/parallel machine scheduling problems faced in a steel plant. More than 1000 or 350 jobs are to be scheduled within a one-hour time limit in the single or parallel machine problem, respectively. The objective of the single machine scheduling is to minimize a combined total changeover, total earliness, and total tardiness cost, whereas the objective of the parallel machine scheduling is to minimize an objective function comprising the gaps between jobs before a critical time in a schedule, the total changeover cost, and the total tardiness cost. The exact method is developed to benchmark computation time for a small-scale single machine problem, but is not practical for solving the actual large-scale problem. A metaheuristic algorithm centered on variable neighborhood descent is developed to address the large-scale single machine scheduling with a sliding-window decomposition strategy. The algorithm is extended and modified to solve the large-scale parallel machine problem. Statistical tests, including Student's t-test and ANOVA, are conducted to determine efficient solution strategies and good parameters to be used in the metaheuristics.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Thermoelectric Studies of the Zinc-Antimony Phases

contributor:
Mozharivskyj, Yurij
Chemistry

subject:
Thermoelectrics
Crystallography
Semiconductor Physics
Solid State Chemistry

abstract:
This dissertation is dedicated to investigating the thermoelectric properties of the
Zn – Sb phases and particularly the Zn13Sb10 material, which was shown to achieve a high
ZT (1.3 at 670K) in 1997. The Zn13Sb10 material (known as “Zn4Sb3”) was then
extensively studied as a potential thermoelectric material. The Zn13Sb10 materials,
however, were not widely adapted in thermoelectric applications.
A new synthetic procedure was developed to synthesize phase-pure Zn13Sb10
materials in this thesis, thus allowing a robust characterization of the Zn13Sb10-based
materials. This work aims to improve the thermoelectric performance of the Zn13Sb10-
based materials by substituting foreign elements into the structure of the Zn13Sb10 phase,
at the same time characterize and navigate the synthesis-property-composition
relationship of the doped Zn13Sb10 materials.
On the other hand, some relative Zn–Sb phases such as the α- and β-Zn3Sb2 were
also studied in attempt to complete the characterizations of all Zn–Sb phases stable at
room temperatures. The ZnSb phase, another well-studied Zn–Sb material, was
investigated in coherence with the Zn13Sb10 materials to understand the effects to
transport properties brought by the same atom replacement in the two systems. This was
realized in the form of a comparison between the (Zn,Cd)Sb and (Zn,Cd)13Sb10 solid
solution series.
Materials studied in this work were mostly made using the melt and solidification
method. Powder and single-crystal X-ray diffractions were employed to characterize
samples’ purity and structure determination. Energy-dispersive X-ray Spectroscopy (EDS)
was used to determine sample compositions, especially to confirm the presence(s) of
dopants in materials in small quantities. Physical properties of materials were measured to
evaluate the thermoelectric performances of materials. Computational methods, such as
the linear muffin-tin orbital (LMTO) method was used to help understand the transport
properties of materials and the electron localization function (ELF) method to analyze the
bonding natures between atoms.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Thermoelectric materials are incorporated into thermoelectric devices to generate
electricity from heat sources. As there are environmental concerns and increasing demand
of energy supplies in the society, thermoelectricity may relieve some of the pressure by
waste heat recovery, from internal combustion engines for example.
This work is dedicated to studying the zinc–antimony (Zn–Sb) materials and a
focus on the Zn13Sb10 material for thermoelectric applications. This work aims to improve
the thermoelectric efficiency of the Zn13Sb10 material, at the same time understand the
changes on the physical properties brought by the structural and the compositional
differences of the material. The relative Zn–Sb phases, such as ZnSb and Zn3Sb2, were
also characterized to compare their structures with their physical properties.


title: Measuring and valuing glaucoma health states

contributor:
Xie, Feng
Health Research Methodology

subject:
Glaucoma
Health Utility
Multi-attribute disutility
Psychometric validation
Systematic Review
Cost utility analysis

abstract:
Cost-utility is a method that integrates clinical factors of disease progression with cost and
consequence to patient’s overall health state. Cost-utility analyses describe the trade-offs that
are consequences of interventions and are commonly used to support health policy decision
making. Well constructed cost-utility analyses can improve access patients have to effective
interventions and move past ineffective or exceedingly costly interventions. The methods
employed to assess incremental effectiveness of glaucoma interventions have advanced over
time, where investigators have adapted to standards for reporting and modeling strategies.
However, most cost-utility analyses use a restrictive set of utility values from foundational,
but outdated work. Glaucoma cost-utility analyses combine utility values from patient
preferences, on multiple scales of measurement. These methodological flaws in the use
and reporting of utility values limit the internal validity of the study and external validity in
generalizing the results to broader populations. Common generic preference-based measures
of health utility, including the EuroQol 5 Dimension 3/5 Level (EQ-5D-3/5L), lack the
sensitivity to detect health state changes in patients with glaucoma.
The three main investigations of this dissertation aimed to describe the current methodological issues in glaucoma cost-utility investigations, validate a condition-specific preferencebased measure (HUG-5) in a sample of patients with various stages of glaucoma, and
generate a preference-based weighting algorithm for glaucoma health states for US general
population. A systematic review of cost-utility analyses in the literature revealed that most
all cost-utility analyses failed to document rationale for including health utility estimates or
conduct a review of appropriate utilities for relevant health states. Most authors of cost-utility
analyses did not recognize or describe the limitations of combining utilities from multiple
scales of measurement and from different preference sources. In a psychometric validation
of the HUG-5, a sample of patients with glaucoma completed the NEI-VFQ-25, the HUG-5,
and the EQ-5D-5L to describe their quality of life and health state. The HUG-5 dimensions
described similar dimensions measured by National Eye Institute Visual Function Questionnaire (NEI-VFQ-25) scales and differentiated from unrelated dimensions with adequate
test-retest reliability on 3 month follow up. To model utility values to HUG-5 health states,
a multi-attribute disutility function (MADUF) was estimated from the preferences of the
US general population. A preference-weighting algorithm assigned utility values to the
3125 health states measured by the HUG-5. In validating the MADUF with directly elicited
marker health states, the MADUF performed similar in mean absolute error relative to other
related studies for the Health Utilities Index Mark 3 (HUI-3) and Patient-Oriented Prostate
Utility Scale (PORPUS).
This work has significant implications for investigators evaluating glaucoma interventions
with cost-utility comparisons, providing an alternative measure of utility on the policy scale
with a condition-specific preference-based measure.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
Cost-utility is a method used to support decision making for which treatments are available
and how much they should cost. Utility is a value that reflects the severity of a health state
and the preferences of a population for that health state. Patients with glaucoma lose their
vision over time, resulting in worse health states and eventually blindness. It is difficult
to measure the additional value of treatments in glaucoma because the usual measures
of health state do not capture changes in health experienced by patients with glaucoma.
Previous cost-utility studies use a variety of sources to estimate the utility of preferences.
The objective of this dissertation was to describe the use and application of a preferencebased glaucoma-specific measure of utility (HUG-5), validate the measure with glaucoma
patients, and develop an algorithm that assigns preference weights to the measure. This work
identifies common issues in cost-utility studies of glaucoma interventions, describes the
properties of the HUG-5 in a sample of glaucoma patients and reports a preference-weighted
algorithm for converting HUG-5 health states to utilities that describe the preferences of the
US general population.


title: Impacts of wastewater on aquatic biota in summer and winter

contributor:
Balshine, Sigal
Psychology

abstract: Municipal wastewater treatment plant (WWTP) effluents are a substantial source of aquatic pollution, continuously introducing complex mixtures of contaminants into aquatic environments. While the effects of wastewater effluents have been observed across all levels of biological organization, the impacts on populations and communities remain relatively understudied. Additionally, despite the ubiquity of wastewater effluents and their continuous year-long release, their impacts have rarely been studied during winter. In my thesis, I examined the effects of municipal wastewaters on fish communities (Chapter 2), benthic macroinvertebrate communities (Chapter 3), and zooplankton communities (Chapter 4) along the effluent gradients of the Dundas and Woodward WWTPs in summer and winter. Furthermore, I examined the effects of wastewater exposure on the physiology and behaviour of fathead minnow (Pimephales promelas) under simulated summer (20C) and winter (4C) conditions (Chapter 5). In Chapter 2, I showed that fish abundance, species richness, and species diversity were generally highest at sites closest to the WWTP outfalls, but only during winter. I also showed that fish community compositions differed greatly along the effluent gradients of both WWTPs and in both seasons, with community divergence being highest in sites closets and farthest from the WWTP outfalls. In Chapter 3, I demonstrated that the effects of wastewater are not generalizable across different WWTPs and are likely dependent on the effluent-receiving environments. I found that at the larger WWTP (Woodward) with its more industrial/urban receiving environment, benthic macroinvertebrate abundance was higher and diversity was lower at sites downstream of the outflow compared to upstream sites in both seasons; whereas the opposite was true for the smaller WWTP (Dundas) with its wetland receiving environment. Community composition differed significantly along the effluent gradients of both WWTPs and in both seasons, with sites closest and farthest from the outfalls being the most dissimilar. In Chapter 4, I showed that zooplankton communities were numerically dominated by rotifers in both summer and winter. Furthermore, rotifer abundance was highest near the outfalls of both WWTPs, especially during winter. At the Woodward WWTP, macrozooplankton abundance, richness, and diversity all increased with distance from the outfall in the summer; while in the winter, the opposite trends were observed for abundance and richness. At the Dundas WWTP, only macrozooplankton richness increased with distance from the outfall, and this was observed only during winter. Similar to fish and benthic macroinvertebrate communities, zooplankton community composition differed along the effluent gradients of both WWTPs, with communities closest and farthest from the outfalls being the most distinct. In Chapter 5, I demonstrated that temperature plays a key role in modulating the effects of wastewater exposure on fathead minnow physiology and behaviour. Wastewater exposure at 20C was associated with increased standard metabolic rate, increased haematocrit, and reduced boldness. Whereas exposure to wastewater at 4C was only associated with reduced sociability. Altogether, my findings suggest that wastewater plumes are a significant source of nutrient enrichment and thermal pollution, particularly in winter. These factors likely make wastewater outfalls an ecological trap for fishes and other aquatic organisms in winter, where the deceptively favourable and attractive conditions are quickly outweighed by the costs of exposure to the various contaminants found in wastewater. I believe this thesis highlights the importance of conducting ecotoxicological research in winter, as it can reveal ecological surprises that would have otherwise been left uncovered.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Toric Ideals of Finite Simple Graphs

contributor:
Van Tuyl, Adam
Mathematics and Statistics

subject:
Commutative Algebra
Algebra
Combinatorics
Combinatorial Commutative Algebra
Toric Ideals
Finite Simple Graphs
Algebraic Topology
Fundamental Group
Syzygies
Graded Betti Numbers
Betti Numbers
Graph Theory

abstract:
This thesis deals with toric ideals associated with finite simple graphs. In particular we
establish some results pertaining to the nature of the generators and syzygies of toric
ideals associated with finite simple graphs.
The first result dealt with in this thesis expands upon work by Favacchio, Hofscheier,
Keiper, and Van Tuyl which states that for G, a graph obtained by
"gluing" a graph H1 to a graph H2 along an induced subgraph, we can obtain the toric ideal associated to G from the toric ideals associated to H1 and H2 by taking their sum as ideals in the larger ring and saturating by a particular monomial f. Our contribution is to
sharpen the result and show that instead of a saturation by f, we need only examine the colon ideal with f^2.
The second result treated by this thesis pertains to graded Betti numbers of toric
ideals of complete bipartite graphs. We show that by counting specific subgraphs one
can explicitly compute a minimal set of generators for the corresponding toric ideals as well as minimal generating sets for the first two syzygy modules. Additionally we provide formulas for
some of the graded Betti numbers.
The final topic treated pertains to a relationship between the fundamental group
the finite simple graph G and the associated toric ideal to G. It was shown by
Villareal as well as Hibi and Ohsugi that the generators of a toric ideal associated to a finite simple graph correspond to the closed even walks of the graph G, thus linking algebraic properties to combinatorial ones. Therefore it is a natural question whether there is a relationship between the toric ideal associated to the graph G and the fundamental group of the graph G. We show, under the assumption that G is a bipartite graph with some additional assumptions, one can conceive of the set of binomials in the toric ideal with coprime terms, B(IG), as a group with an appropriately chosen operation ⋆ and establish a group isomorphism (B(IG), ⋆) ∼= π1(G)/H where H is a normal subgroup. We exploit this relationship further to obtain information about the generators of IG as well as bounds on the Betti numbers. We are also able to characterise all regular sequences and hence compute the depth of the toric ideal of G. We also use the framework to prove that IG = (⟨G⟩ : (e1 · · · em)^∞) where G is a set of binomials which correspond to a generating set of π1(G).

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Predicting the Occurrence of River Ice Breakup Events in Canada using Machine Learning and Hybrid Modelling

contributor:
Li, Zoe
Civil Engineering

subject:
River Ice
Machine Learning
Ontology
Hybrid Modelling
Ice Jams
Hydrology
Ensemble Modelling
Flooding

abstract: River ice breakup is a vital process to the morphology and hydrology of many rivers in Canada, often governing peak flows of the river. These events can occur through multiple mechanisms, with the potential for volatile or early breakup events that can have severe impacts to the river. Ice jam flooding can be a potentially devastating result of river ice breakup while early breakup of ice cover in a mid-winter breakup can be unpredictable and greatly alter the remaining ice season. These events are growing increasingly common as a result of climate change, and as a result there is a need to develop prediction tools for these events to aid in decision making support. Past investigations into developing such tools, especially from a data-driven modelling perspective, are challenged by the availability and complexity of the data related to these rare and dangerous to measure events. Therefore, the goal of this dissertation was to develop and apply methods to address the historical challenges and shortcomings in predicting these events through the use of data-driven modelling techniques. This includes: i) development of a stacking ensemble modelling framework for the prediction of ice jam presence during the spring breakup season of a river, utilising variable selection and rare-event forecasting techniques in combination with a comprehensive selection of machine-learning algorithms; ii) return period and trend analysis of mid-winter breakups in conjunction with comprehensive input analysis techniques to identify the key drivers of these events’ severity and develop a means of classifying the flood risk based on hydroclimatic traits; iii) the development of a two-level modelling system for the prediction of the occurrence and timing of mid-winter breakups on a national scale utilising rare event forecasting techniques and imbalanced learning; and iv) development of a novel hybrid semantic and machine learning modelling system in which an ontology is used in conjunction with network analysis techniques to select variables for machine learning models, which is used on a national case study of the prediction of spring breakup timing in Canada. The results of each study in application to their respective case studies demonstrate the effectiveness of the proposed techniques, which are shown to be easily adaptable to other regions or locations. These techniques can form the backbone of decision-making support for communities on rivers that are affected by the unpredictable and oftentimes volatile nature of river ice breakup.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: River ice breakup is a key event to the hydrology of rivers throughout Canada, playing a major role in their physical and ecological characteristics. The timing and mechanism of these events can, however, be unpredictable and volatile, with the effects of climate change only exacerbating these risks. This dissertation focuses on addressing these potential issues through the application of machine learning and hybrid modeling in the prediction of river ice breakup events. Advanced data driven techniques coupled with novel applications of other analytical methods are used to: i) predict the presence of ice jams through the application of stacking ensemble modelling; ii) predict the severity of mid-winter breakups through application of trend and variable analysis; iii) predict the occurrence and timing of mid-winter breakups using rare-event forecasting techniques; and iv) develop a novel hybrid modelling scheme coupling ontology-based semantic modelling and machine learning to predict spring breakup timing. Detailed case studies for each application are provided demonstrating the effectiveness of the discussed techniques.


title: The Circulation of Greek Federal Coinage

contributor:
Pope, Spencer
Classics

subject:
Numismatics
Greek History
Ancient Economics
Greek Federations

abstract:
The aim of this discussion is to examine the coins from a selection of both Classical and Hellenistic Greek federal states in order to identify potential patterns in how the coins were used. This is done through an in-depth analysis of coin hoard data, focusing on hoards which contain the coins from a league alongside coins from poleis within that league, taking into account hoard contents, approximate deposit date, and the hoard findspot. This data is then compared to the data from hoards containing coins from the poleis of a league, regardless of whether the hoards contained coins from the league or not.
       The study finds that, while each league examined is unique, certain patterns can be identified. The leagues typically mint coins not just to the same standard as their poleis, but in the same denominations, such as the triobols of the Achaean League and her member-poleis. The hoards containing coins issued from a league show a strong preference for regional circulation, which is highlighted when juxtaposed with the hoards containing the civic coinage, which have findspots across the ancient Mediterranean world. This shows that the coins minted by the leagues served a separate and more regional purpose than the coins the poleis were minting.

abstract: Thesis

abstract: Master of Arts (MA)


title: Verbal Agreement in Kanyen'keha

title: Verbal Agreement in Kanyen'keha: A catalogue of the transitive paradigm, and a proposal for subject-object agreement by one probe with multiple agree

contributor:
Kucerova, Ivona
Cognitive Science of Language

subject:
direct-inverse agreement
verbal agreement
Mohawk
Indigenous language
multiple agree
subject-object agreement

abstract:
This work catalogues the verbal agreement paradigm of Kanyen'keha in greater detail than has previously been done. The cataloguing includes the complete intransitive, transitive, and reflexive paradigms, and description of all argumental contrasts to which the verbal agreement is sensitive. It also describes in detail the contexts where feature sensitivity is blunted, and the patterns of syncretism in the verbal agreement. Based off of this descriptive work, this work evaluates the accuracy with which previous analyses treat verbal agreement in Kanyen'keha. Finding room for improvement in these analyses, this work proposes a new analysis of Kanyen'keha, which claims all verbal agreement in transitive contexts to be realized from one agreement probe, which enters into Multiple Agree with subjects and objects. This style of analysis allows for many aspects of the agreement to be accounted
for, including person hierarchy effects, distribution of portmanteau morphology, and complex
dependency between the multiple morphemes which comprise the agreement

abstract: Thesis

abstract: Master of Science (MSc)

abstract: This thesis describes the verbal agreement of Kayen'keha in greater detail than has previously been done. This thesis also evaluates the claims of previous work done on verbal agreement of Kanyen'keha, describing where such work accurately accounts for the agreement and where it does not. Finally, this  thesis proposes a novel analysis of Kanyen'keha verbal agreement.


title: Epitope-Targeted Strategies for Inhibiting Pathogenic Immune Complex Formation in Heparin-Induced Thrombocytopenia

contributor:
Nazy, Ishac
Biochemistry and Biomedical Sciences

abstract:
Heparin-induced thrombocytopenia (HIT) is an immune-mediated adverse drug reaction to the anticoagulant heparin.1,2 HIT is characterized by pathogenic antibodies that form immune complexes with platelet factor 4 (PF4) and heparin, which can cause platelet activation and thrombosis.1,3-6 Prompt diagnosis is crucial because HIT patients experience a 5-10% daily increased risk of thrombotic episodes, which are fatal in up to 30% of patients.2,6-10 The immune response in HIT is polyspecific, resulting in the production of anti-PF4/heparin antibodies that either can (pathogenic) and/or cannot (non-pathogenic) activate platelets.10-12 Differentiating between pathogenic and non-pathogenic antibodies remains a significant diagnostic challenge in HIT, exacerbated by the low specificity and limited availability of current laboratory assays.10,14,15
Previously it was shown that platelet-activating immune complexes form when pathogenic antibodies bind PF4 at a localized region that is distinct from non-pathogenic antibodies.13 In this work, high affinity inhibitors of pathogenic anti-PF4/heparin antibodies were designed using a murine monoclonal antibody (named KKO) that binds to a region on PF4 overlapping with pathogenic antibodies.16 These inhibitors were used to develop a novel diagnostic assay that can detect pathogenic antibodies with improved specificity compared to most standard tests for HIT (specificity ~50-70%).2,15 Enzyme immunoassays (EIAs) are widely used for HIT diagnosis, but have high false-positive rates because they cannot differentiate between pathogenic and non-pathogenic antibodies.10,14,15 This study found that incorporating inhibitors to block clinically significant antibody binding sites on PF4 improved the specificity (90%) of a diagnostic EIA for HIT without sacrificing sensitivity (90-100%). Unlike most high-sensitivity and -specificity diagnostic tests for HIT, such as platelet-activation assays, this EIA can also be performed with technical ease in non-specialized laboratories.

abstract: Thesis

abstract: Master of Science (MSc)


title:
Some Aspects of Gogol's Early Humour
Gogol's Early Humour

contributor:
Rickwood, T
Russian

subject:
Gogol
Gogol's humour
Evenings on a Farm Near Dikanka
Nineteenth century literature
Russian history
Mirgorod

abstract: An analysis of the comic techniques used by Gogol in his early works, Evenings on a Farm Near Dikanka and Mirgorod, to illustrate the transition from mere aesthetic laughter to mature humour. In addition, an examination is made of his purpose as a satirist.

abstract: Thesis

abstract: Candidate in Philosophy


title: Genomic Enzymology Study of the Aminoglycoside Antibiotic Acetyltransferases

contributor:
Wright, Gerry
Biochemistry

subject: antibiotic resistance

abstract:
Since their discovery over 40 years ago, considerable knowledge has been obtained on the diversity, and structure-function relationships of aminoglycoside acetyltransferases (AACs), responsible for antibiotic resistance among priority clinical pathogens. In recent years, investigations have expanded to biochemical characterizations of AACs found in environmental reservoirs. The successful design of next-generation aminoglycosides (AGs) depends on an up-to-date understanding of the broader AG resistome.
Towards this goal, I present the first structural analysis for the unique apramycin modifying enzyme, ApmA. Apramycin is a veterinary antibiotic that is in development for clinical use. The atypical chemical scaffold provides inherent protection from many clinically relevant resistance mechanisms. Prior to the work presented herein, apmA was an uncharacterized apramycin resistance element among environmental species. I heterologously expressed and subsequently purified ApmA to characterize the nature of resistance towards this unique aminoglycoside. The results report the first acetyltransferase of the left-handed β-helix (LβH) superfamily involved in AG detoxification.
Secondly, I completed a comprehensive characterization of ApmA utilizing a structurally diverse panel of AGs for susceptibility testing, protein engineering, steady-state kinetics, and x-ray crystallography. Through these approaches, I establish the structural and functional features that define ApmA’s place within the LβH superfamily and set it apart from other known AACs. The biochemical data presented describes a chemical mechanism dependent on the substrate specificity. Furthermore, I describe the molecular determinants behind AG-modification of clinically relevant AGs.
Lastly, I describe the first comprehensive structural and functional study of clinical and environmental Antibiotic_NAT (A_NAT) inactivating enzymes. A pan-family antibiogram was obtained and mapped to the reconstructed phylogeny for the A_NAT family. Crystallographic analysis of representatives from each clade was completed with our collaborators from the University of Toronto. Through the analysis of several ligand-bound A_NAT complexes, I contributed to the elucidation of structural features responsible for substrate specificity.
The collective findings from these chapters have extended the protein landscape involved in AG-acetylation from one commonly used fold to three distinct architectures, each unique in underlying chemical mechanism and dissemination.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Pathogens continue to learn new ways to protect themselves from antibiotics. With the discovery of new antibiotics becoming more challenging, global antibiotic resistance has the potential to become the next global pandemic. One solution is to redesign traditional antibiotics to escape resistance. A reliable, effective class of antibiotics currently under development are aminoglycosides. There is considerable knowledge into the sequence-structure-function relationships of proteins traditionally regarded as the sole contributors to a form of aminoglycoside resistance. My work describes the use of computational and biochemical techniques to investigate resistant elements beyond what we know is prevalent in clinical pathogens. Through these efforts I uncover structurally, and mechanistically distinct proteins capable of broad-spectrum, high-level aminoglycoside resistance produced by bacteria in various environments. These results are invaluable for the informed design of less-resistance prone aminoglycosides and antibiotic stewardship programs to limit these forms of resistance from becoming clinically prevalent.


title: Investigating the effects of attention on afferent inhibition via transcranial magnetic stimulation

contributor:
Nelson, Aimee
Kinesiology

subject:
TMS
Afferent Inhibition
Reliability
Attention
Peripheral Nerve Stimulation

abstract: Evidence indicates attention can alter afferent inhibition, a Transcranial Magnetic Stimulation (TMS) evoked measure of cortical inhibition following somatosensory input.  This measure is emerging as a valuable tool for clinical assessment of sensorimotor function.  However, the reliability of the measure remains relatively low.  Further, attention is capable of modifying the magnitude of afferent inhibition. Therefore, for afferent inhibition to become an assessment with translation within and beyond the research lab, the reliability of the measure must be improved.  Controlling the focus of attention may be one method to improve the reliability of afferent inhibition. In the present study, two experiments were conducted. One to assess the biological effects of attention on SAI and LAI, and the other to address whether the reliability of SAI and LAI are altered in the presence of varying attentional demands. The magnitude of short- and long-latency afferent inhibition (SAI and LAI, respectively) was assessed under four conditions with varying attentional demands focused on the somatosensory input that mediates SAI and LAI circuits.  Further, the reliability of SAI and LAI was assessed with and without directed attention to the relevant somatosensory input to explore whether attention to the tactile stimulation can improve intrasession and intersession reliability of these measures.  Thirty individuals participated in four conditions; three conditions were identical in their physical parameters and varied only in the focus of directed attention (visual attend, tactile attend, non- directed attend) and one condition consisted of no external physical parameters (no stimulation). Reliability was measured by repeating conditions at three time points to assess intrasession and intersession reliability. Results indicate the magnitude of SAI and LAI were not modulated by varied attention. Reliability assessments demonstrated that the attention manipulations increased intrasession and intersession reliability of SAI and LAI compared to the no stimulation condition. This research exposes the influence of attention, and its impact on the reliability of afferent inhibition.  By quantifying these influences, this research has identified new information to inform the design of TMS research in sensorimotor integration.

abstract: Thesis

abstract: Master of Science in Kinesiology

abstract: Attention can alter transcranial magnetic stimulation (TMS) evoked afferent inhibition. Measures of afferent inhibition are emerging as valuable tools for clinical assessments of sensorimotor function. However, the reliability of afferent inhibition remains relatively low, limiting its value in the clinic. Afferent inhibition is increased when the one’s attention is focused on the peripheral nerve stimulation used to elicit afferent inhibition. However, it is unknown whether afferent inhibition, with attention directed to somatosensory input, will improve the reliability of these measures.  This is important as it suggests that changes to the methodology used to acquire afferent inhibition can improve the reliability of this measure, thereby increasing the opportunity for translation to the clinic. The goal of this study was to assess the influence of attention on afferent inhibition circuits, short afferent inhibition (SAI) and long afferent inhibition (LAI) and determine whether attention modulation would increase the reliability of afferent inhibition.


title: EXAMINING CHANGES IN MATERNAL MENTAL HEALTH AND INFANT BEHAVIOUR AFTER PEER-DELIVERED TREATMENT FOR POSTPARTUM DEPRESSION

contributor:
Van Lieshout, Ryan
Neuroscience

subject:
postpartum depression
cognitive behavioural therapy
peer-administered intervention

abstract:
Background: Postpartum depression (PPD) affects up to 20% of mothers and birthing parents, yet only 1 in 10 receive evidence-based treatment. Left untreated, PPD increases the risk of future depressive episodes, familial disharmony, and offspring problems. This study sought to determine if an online 9-week group cognitive-behavioural therapy (CBT) intervention delivered by mothers who have recovered from postpartum depression (i.e., peers) can effectively improve PPD, anxiety, social support, the mother-infant relationship, and infant temperament in those with PPD.
Methodology: During the COVID-19 pandemic, 183 participants were randomized into experimental (received intervention at baseline plus treatment as usual (TAU)) and waitlist control (TAU plus the intervention after a 9-week wait) groups. Participants were ≥18 years of age, had an infant <12 months old, were fluent in English and scored ≥10 on the Edinburgh Postnatal Depression Scale. Depression, anxiety, social support, mother-infant bonding, and infant behaviour were reported by all mothers at enrollment and 9-weeks later, and three months after that in the experimental group.
Results: Participants in the experimental group experienced clinically and statistically significant improvements in PPD and anxiety post-treatment and three months later. Perceptions of social support, infant-focused anxiety, and negative emotionality in infants also improved immediately post-intervention and remained stable three months later in the experimental group.
Conclusion: Online peer-delivered group CBT for PPD can effectively treat PPD and anxiety, as well as improve social support, the mother-infant relationship, and infant temperament. Online Peer-Delivered Group CBT for PPD is a novel approach to service delivery that can increase treatment uptake, providing mothers experiencing PPD with access to a credible and engaging source of help, and has the potential to revolutionize the treatment of PPD in Canada and around the world.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Postpartum Depression (PPD) affects up to 20% of mothers and birthing parents and can have profound negative effects on them and their families. However, just one in ten individuals with PPD receive evidence-based treatment. The objective of this work was to determine if an online 9-week group cognitive behavioural therapy (CBT; a type of talking therapy) program delivered by mothers who have recovered from PPD (i.e., peers) can improve PPD. The results of this thesis suggest that those who received this peer-delivered intervention experienced improvements in PPD, anxiety, social support, mother-infant bonding, and infant temperament. Recovered peers can be an effective means of treating PPD, and this peer-delivery model represents a special opportunity to increase treatment uptake, foster a sense of community, and an important step toward improving PPD for mothers and their families.


title: Data-Driven Modeling and Model Predictive Control of Monoclonal Antibody Process

contributor:
Mhaskar, Prashant
Chemical Engineering

abstract:
This thesis focuses on data-driven modeling and model predictive control for a monoclonal
antibody process. The process uses live cell cultures such as Chinese Hamster
Ovary (CHO) cells and thus needs special consideration. With the trend in the industry
to move towards perfusion processes which are continuous allowing better productivity,
advanced process control would play a vital role. Model Predictive Control
(MPC) requires a suitable model to optimally control the process. First principles
models for such live cell processes are complex and unsuitable for direct use in MPC.
In this work, we focus on data-driven modeling given its suitability for use in control.
The data-driven model is eventually also incorporated with some first principles
knowledge for better performance and robustness.
Data-driven modelling requires some input perturbation and data generation methods
such as Pseudo-Random Binary Sequence (PRBS) inputs. By themselves, these
methods are unsuitable for live cells as they can shock the system. To account for this,
a suitable, intensified design of experiments (DOE) approach is used to perturb the
data frequently enough to build a model of reasonable accuracy without significantly
impacting live cells. This method is general enough to be used to identify appropriate
input perturbation and data generation for many bioprocesses, and for our particular
process of study it identified an input perturbation frequency of once per three days.
The data-driven model is used in a model predictive control (MPC) scheme which respects
biological constraints and can meet desired objectives. Further improvement in
model robustness are made possible by incorporating first principles knowledge into
the data-driven model. The methods are demonstrated on an advanced simulator
developed by Sartorius with significant improvement over current industry standard.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract:
Biopharma processes involving live cells are utilised to produce several critical products
such as monoclonal antibodies which are state-of-the-art cancer therapeutics.
Improving productivity for these would require advanced process control methods
which in turn would require good models. This thesis focuses on introducing a method
to build control relevant data driven models by using input perturbation and data
generation suitable for live cell systems. The data driven model is utilised in a model
predictive control scheme which meets control objectives while respecting biological
constraints with better performance than industrial standards. Further improvement
is made by incorporating first principles knowledge into the data driven model through
a novel implementation of constrained subspace identification. The approaches are
showcased on an advanced simulator test bed created by Sartorius.


title: Transforming the Ontario Midwifery Education Program through social justice curriculum: a modified Delphi study

contributor:
Darling, Elizabeth K
Health Science Education

subject:
Social Justice
Curriculum

abstract:
Introduction: Social justice education aims for transformative, liberatory, democratic classrooms and curriculum. From inception, the Ontario Midwifery Education Program (OMEP) has included curriculum that reinforced key principles of Ontario midwifery, including informed choice, continuity of care and choice of birthplace. Despite the social justice underpinnings of these principles, the OMEP has not formally defined social justice in the context of midwifery education or formalized a social justice-based curriculum linked to the Canadian Midwifery Competencies (CMCs) set out by the Canadian Midwifery Regulators Council (CMRC).

Methods:  A modified Delphi design was utilized that involved focus groups, interviews, two rounds of surveys and a member checking session. Participants were recruited through purposeful and snowball sampling. Open coding was used to analyse qualitative data and identify themes, and quantitative data was analyzed using descriptive statistics.

Results: Three key findings were elicited. First, qualitative data was used to articulate a definition of ‘social justice’ in the context of midwifery education based on the OMEP’s social justice values, goals, and actions. Second, 86 social justice-based elements (grouped in three thematic areas) and 32 social justice-related CMCs were identified which gave way to 26 corresponding learning outcomes and 6 program level learning outcomes. Third, it was noted that the thematic categories, ‘legal and economic structures’, and ‘policy and health service structures’, were not captured in any of the 32 CMCs suggesting the need for a paradigmatic shift in social justice education in midwifery.

Conclusion: Recommendations to the OMEP are: 1. develop social justice curriculum using constructive alignment and social justice education pedagogies, 2. incorporate social justice curriculum throughout the program to be a global exemplar, and 3. add additional competencies to the existing CMRC’s roles-based framework to support structural competency education. Future work could involve the development of a Canadian midwifery education framework that centres social justice pedagogies and curriculum.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
This study aimed to define ‘social justice’ in the context of Canadian midwifery education, determine specific social justice content to be included in Ontario Midwifery Education Program (OMEP) curriculum, and identify social justice-based Canadian midwifery competencies (CMCs) set out by the Canadian Midwifery Regulators Council (CMRC). This work was completed through consensus-building methodology that included focus groups, interviews, and surveys.

A definition that aligned participants' interpretations of the term social justice was developed. A key finding was that participant-identified social justice content that dealt with ‘legal and economic structures’, and ‘policy and health service structures’ did not have any corresponding CMCs, suggesting that those respective structural competency categories may be underdeveloped in Canadian midwifery curricula. These findings suggest that the OMEP is undergoing a shift in its understanding of social justice knowledge and praxis. It is recommended that the OMEP adopt innovative social justice teaching methods and concordant curriculum to propel the program into novel territory for health professions education.


title: Overcoming Data Scarcity in IMU-based Human Motion Analysis

contributor:
Zheng, Rong
Computing and Software

subject:
human activity recognition
wearable sensor
mobile computing
machine learning

abstract:
Deep learning techniques enable the automatic analysis and interpretation of human motion from wearable sensor. However, despite extensive research efforts, the absence of vast cleanly labeled human motion sensor data in free-living setting still hindered the applications of deep models in the real world.
Human motion data is known to have a large variance among subjects and devices. As the result, there is a significant performance gap between models trained with and without part of test subjects' data. In addition, due to the difficulty in labeling wearable sensor data post hoc, existing public datasets are either collected from scripted activities under controlled settings or contain severe label noises when collected through crowdsourcing. Moreover, since collecting motion data from frail populations such as older adults with impaired mobility can be physically demanding or even cause safety concerns, the data scarcity problem becomes more severe. In this dissertation, we aim to address these challenges through a multi-pronged approach.

First, we investigate domain adaptation techniques to handle the subject variance and device diversity in wearable sensor-based human activity recognition (HAR). We propose an invariant feature learning framework (IFLF) that extracts common information shared across subjects and devices. It incorporates two learning paradigms: 1) meta-learning to capture robust features across multiple source domains and adapt trained model to a target domain with similarity-based data selection; and 2) multi-task learning to deal with data shortage and enhance overall performance via knowledge sharing among different domains. Experimental results demonstrate that IFLF is effective in handling both subject and device variations across popular open datasets and an in-house dataset from older adults.

 Inertial measurement units (IMU) datasets collected in naturalistic settings are often fraught with labeling noise due to misaligned onsets, the presence of concurrent activities, unpredictable terrains or human errors. However, state-of-the-art learning with label noise (LNL) approaches fail to converge due to the presence of subject variations. As a second contribution, we propose VALERIAN, an invariant feature learning for in-the-wild domain adaptation method for wearable sensor-based HAR. It consists of three components: self-supervised pre-training, invariant feature learning with noisy labels, and fast adaptation to new subjects. By training a multi-task model with separate task-specific layers for each subject, VALERIAN allows noisy labels to be dealt with individually for each subject while benefiting from shared feature representation across subjects. Experimental results show that VALERIAN significantly outperforms baseline approaches.

Simulating IMU data from other input modalities offers an alternative way to mitigate the wearable data scarcity problem. As a third contribution, we design CROMOSim, a cross-modality sensor simulator that synthesizes high fidelity virtual IMU data from data collected with motion capture systems or monocular RGB cameras. It utilizes a skinned multi-person linear model for 3D body pose and shape representations to enable simulating motions from arbitrary on-body positions. A deep learning model is used to learn the functional mapping from imperfect trajectory estimations in a 3D body tri-mesh representation to IMU data. Extensive empirical evidence demonstrates the high fidelity and utility of CROMOSim simulated data in downstream human motion analysis tasks include HAR and human pose estimation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: FRIENDS OR FOES? ACUTE MYELOID LEUKEMIA AND THE BONE MARROW MICROENVIRONMENT

contributor:
Berg, Tobias
Biochemistry and Biomedical Sciences

subject:
Leukemia
Adipocytes
Bone marrow microenvironment

abstract: Acute myeloid leukemia (AML) is an aggressive cancer of the blood and bone marrow, affecting 1,100 Canadians annually. Older patients make up 75% of cases yet have the lowest survival rates due to the lack of tolerable treatments. Recently, the combination of Venetoclax and Azacitidine (Ven/Aza) has shown great therapeutic promise, however, chemoresistance has become a growing concern. Current evidence points towards a chemoprotective role from the bone marrow (BM) microenvironment, specifically by BM-derived mesenchymal stromal cells (BMSCs) and adipocytes. AML cells can manipulate BMSCs and adipocytes to create a niche that supports its own growth and evades chemotherapy. However, the role of the microenvironment in Ven/Aza chemoresistance has yet to be studied. Our objective was to study the ability of the microenvironment cells to induce AML chemoresistance to Ven/Aza. We employed a 2-dimensional direct contact co-culture system between MOLM-13 AML cells and BMSCs or adipocytes in both the absence and presence of Ven/Aza to determine the effects on the AML cells. In the absence of Ven/Aza, adipocyte co-cultured AML cells showed a 47% reduction in proliferation, 10% reduction in viability, yet a 1.7-fold increase in Maximal respiration when compared to the monocultured cells. In the presence of Ven/Aza, adipocyte co-cultured AML cells showed a significant increase in both proliferation and viability. Preliminary work investigating the mechanism of action of this support points toward an anti-apoptotic mechanism mediated by the upregulation of MCL-1 upon co-culture with adipocytes. Combination of Venetoclax and Tapotoclax, an MCL-1 inhibitor, abrogated the chemoprotection provided by BMSCs and adipocytes. Overall, our data suggests a dual role of adipocytes, where their inhibition or support of AML is context dependent. Therapeutic targeting of mechanisms for adipocyte chemoprotection such as MCL-1 upregulation may re-sensitize AML cells to Ven/Aza, thereby improving patient outcomes.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Acute myeloid leukemia (AML) is an aggressive cancer of the blood and bone marrow, affecting 1,100 Canadians annually. Older patients make up 75% of cases yet have the lowest survival rates due to the lack of tolerable treatments. A novel combination of Venetoclax and Azacitidine (Ven/Aza) has shown great therapeutic promise, however, chemoresistance remains an important concern. Previous studies have implicated fat cells, or adipocytes, in AML chemoresistance, however, their role in Ven/Aza treatment has yet to be studied. Here, we show that adipocytes reduce growth of AML cells, yet enhance their metabolism. In the presence of Ven/Aza, adipocytes induce chemoresistance. We show preliminary data that this chemoprotection may be mediated by the upregulation of mitochondrial MCL-1 protein as inhibition of this protein neutralized the protection. By understanding the relationship between adipocytes and AML chemoresistance, we can target this and re-sensitize AML to Ven/Aza, thereby improving older patient outcomes.


title: TARGET ANALYTE-ASSISTED SENSITIVE ELECTROCHEMICAL DETECTION OF COCAINE USING SCREEN PRINTED ELECTRODES

title: ELECTROCHEMICAL DETECTION OF COCAINE ON SCREEN PRINTED ELECTRODES

contributor:
Srinivasan, Seshasai
Rajabzadeh, Amin Reza
Mechanical Engineering

subject:
electrochemistry
cocaine
sensors
cyclic voltammetry
illicit substances

abstract: Cocaine is one of the most abused drugs worldwide, with over 20 million users in 2019. The use of cocaine leads to various health conditions and death due to overconsumption. Existing detection technologies fall short of meeting the guidelines set by organizations regarding a practical roadside cocaine detection device. Herein, a novel electrochemical cocaine detection method is presented using the electroactive characteristics of the cocaine molecule that does not require any biomolecules or chemicals for detection. This research implements the cocaine-modified carbon working electrodes to detect cocaine using Cyclic Voltammetry in phosphate buffer solution and human saliva. The affinity of the cocaine samples to the cocaine-modified screen printed electrodes is demonstrated with the support and implementation of machine learning. The proposed cocaine detection was used to detect concentrations from 10 to 1000 ng/mL. Furthermore, the successful detection of cocaine in the presence of various interfering substances revealed that the present study is highly specific and promising for developing a roadside oral fluid cocaine detection kit.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Cocaine is one of the most abused drugs worldwide causing various health complications and death due to overconsumption. The detection of cocaine in biological fluid or hair is often a complicated and expensive procedure that is time-consuming. The use of electrochemical techniques allows for the rapid detection of cocaine. By focusing on using saliva, the process is facilitated given that it is the easiest fluid to collect from individuals. In this thesis, a new method of cocaine detection in saliva is presented using electrochemistry and modification of the device to detect very low concentrations of the illicit substance. The combined use of electrochemical techniques and machine learning resulted in the successful development of a method to detect very low concentrations of cocaine in saliva.


title: EFFECTS OF CANNABIS CONSTITUENTS ON OVARIAN HEALTH AND  FUNCTION: A FOCUS ON PRENATAL EXPOSURE

contributor:
Holloway, Alison
Health Sciences

subject: Cannabis

subject: Developmental and reproductive toxicology

subject: THC

subject: Ovarian health and function

abstract:
This thesis is prepared in the “sandwich” format as outlined in the “Guide for the
preparation of Master’s and Doctoral Theses” available through the School of
Graduate Studies at McMaster University. Chapter 1 consists of a general
introduction for the entire body of work. Sections of this chapter have been published
in a review article (doi.org/10.3390/ijms22168576). Chapters 2, 3 and 4 consist of
reprints of original research articles, all published at the time of thesis submission.
Chapter 5 includes a general discussion, limitations and future directions of this
research project. The author of this thesis is also the first author of all four published
articles included.

abstract:
As cannabis use increases, it is important to understand its impact on human health.
Particularly, the effect of cannabis constituents on female reproductive health and the
long-term effects on the offspring, when used during pregnancy, are not fully understood.
The goal of this thesis was to address this knowledge gap by evaluating the impact of
delta-9-tetrahydrocannabinol (THC), the psychoactive component of cannabis, on
ovarian health and function, focusing on the long-term effects of prenatal exposure and
the underlying mechanisms. Gestational THC exposure resulted in altered follicle
dynamics, decreased vascularization and increased follicular apoptosis in the adult rat
ovary. These alterations were associated with changes in ovarian miRNA and mRNA
expression, as well as altered protein levels of important regulating factors. Specifically,
prenatal THC exposure increased the expression of miR-122-5p and decreased the
expression of its target gene insulin-like growth factor 1 receptor (IGF-1R), involved in the
regulation of folliculogenesis, angiogenesis, and granulosa cell proliferation and
apoptosis. Reduced vascularization in THC-exposed ovaries was also associated with
decreased expression of the angiogenic factor vascular endothelial growth factor (VEGF)
and its receptor (VEGFR-2), as well as increased expression of the antiangiogenic factor
thrombospondin 1 (TSP-1). The differential expression of these important factors, along
with the decreased vascularization and increased follicular apoptosis may partially explain
the follicle dynamics observed in prenatally THC-exposed rats at 6 months of age, as they
had accelerated folliculogenesis with follicular development arrest, which could lead to
premature reproductive senescence. The direct impact of THC on rat ovarian explants
and granulosa cells was also evaluated, revealing similarities and differences between the in utero, ex vivo and in vitro models. Taken together, our results indicate that
cannabis constituents have the ability to alter key pathways in the developing ovary
that may lead to detrimental effects on female reproductive health and fertility.

abstract: Thesis

abstract: Doctor of Philosophy (Medical Science)

abstract:
The use of cannabis by pregnant women and women of reproductive age has
increased considerably during the past decades, particularly in developed countries.
This thesis evaluated the impact of delta-9-tetrahydrocannabinol (THC), the
psychoactive component of cannabis, on ovarian health and function, with a focus
on gestational exposure. Our results suggest that cannabis use during pregnancy
may have detrimental effects on the offspring’s reproductive health, as prenatal THC
exposure resulted in altered ovarian follicle dynamics, decreased vascularization
and increased follicular apoptosis that could lead to subfertility or premature
reproductive senescence. These alterations were associated with changes in
epigenetic mechanisms that regulate important growth factors in the ovary. In
addition, cannabis use during adulthood may be involved in the progression of
gynaecological disorders such as ovarian hyperstimulation syndrome, polycystic
ovary syndrome and ovarian cancer. More studies are necessary in order to fully
understand the effects of cannabis on female reproductive health.


title: Processing of Unexpected Stimulus Timing in Linguistic and Non-Linguistic Sequences

contributor:
Service, Elisabet
Connolly, John
Cognitive Science of Language

subject:
timing
linguistics
prosody
neurolinguistics
mismatch negativity (MMN)
electroencephalography

abstract:
Timing, and ergo rhythm, are intrinsic features of language that help facilitate real-time speech comprehension. However, work exploring how variable timing is processed in speech is limited. This dissertation addresses this gap in literature by exploring the tenets of how temporal variability is cognitively processed, particularly in the context of real-time stimulus processing. This research is one of the first works to examine temporal variations in linguistic and other acoustically complex contexts.
Using electroencephalography (EEG) and behavioural methods, participants were tested on their perception of temporal variations within a continuous stream of either simple tones, complex waves, or syllables. Two timing deviants were presented that occurred early or late compared to other stimuli in the sequence. Event-related potentials (ERPs) were recorded for each stimulus type across three experiments. A fourth experiment tested participant recognition memory for syllable order.
Results showed differential processing between the two timing deviants. Unexpectedly earlier tokens elicited larger pre-attentive responses compared to late, suggesting a saliency for the earlier tokens that was not present for the delayed ones. This pattern was observed across all three levels of acoustic and linguistic complexity. Compared to sequences with no timing deviants or an early timing deviant, unexpectedly late tokens were more detrimental to memory, suggesting a negative impact of delays on verbal recognition. Thus, not only were early and late timing variations processed differently, but delays in continuous sequences were also more cognitively taxing for working memory.
The results reported in this dissertation contribute to existing knowledge by enriching our understanding of the fundamentals of how aspects of prosodic timing may affect attention and memory. Additionally, it provides new insights into how speech synthesis can be used in neurolinguistic research by tracking how neurophysiological responses change with increasing acoustic complexity and linguistic familiarity.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This thesis examines how unexpectedly shorter or longer pauses in speech may affect speech comprehension. Specifically, the research reported here examined how stimuli that are presented unexpectedly early or unexpectedly late in a steady-rate sequence impact a listener’s attention and memory. Although the speed at which we speak has been studied previously, work on unexpected changes in its timing has been limited. This research begins to explore this aspect of speech processing. It contributes to our understanding of how speech timing is processed in two important ways. First, we found that unexpected delays in both non-linguistic sounds and syllables were less noticeable than unexpectedly early presentations, when participants were not required to pay attention to them. Second, we found that unexpected delays made recognition memory for stimulus order worse. Overall, the results of these studies indicate that unexpected delays in the rhythm of speech make it more difficult to understand.


title: Investigating The Suitability of Electrified Powertrain Alternatives for Refuse Trucks with Emphasis in The City of Hamilton

contributor:
Emadi, Ali
Mechanical Engineering

subject:
Refuse Truck
Battery Electric Refuse Truck
Range Extended Electric Refuse Truck
On-Board Diagnostics
Duty Cycle
Drive Cycle
Matlab
Simulink
SAE J1939
CANedge
City of Hamilton
Well-to-Wheel Emissions
McMaster Automotive Resource Centre
Mass Cycle
Power Cycle
Road Grade

abstract:
Refuse trucks, commonly referred to as garbage trucks are a critical component of a municipality’s waste management industry. Their primary purpose is to collect, transport and deposit waste from households or businesses to designated transfer sites or dumps. Historically, refuse trucks have been powered by diesel fuel. The consumption of diesel fuel paired with the frequent accelerations or decelerations between each residential household along a route attribute to high amounts of tailpipe emissions and noise pollution within neighbourhoods. There is significant opportunity to explore avenues of powertrain electrification in refuse trucks to reduce their emissions and improve energy efficiency.
To rapidly test promising powertrains, vehicle software models were developed. To accurately model the energy usage and power requirements of refuse trucks, environments for the models to operate were created. The environments were created using on-board diagnostic and positional data collected from refuse trucks in the City of Hamilton in Ontario, Canada. The data collection was done under a research collaboration between the City of Hamilton and the McMaster Automotive Resource Centre. The approaches used to develop the drive and duty cycles for the vehicle models offer some innovative approaches without the need for invasive devices to be installed.
The powertrains that were modelled includes an all-electric, ranged extended electric and conventional refuse trucks. A comparative analysis of the pump-to-wheel powertrain efficiencies were completed looking at metrics such as fuel economy, payload capacity and fuel costs. Lastly, a look at truck emissions from a well-to-wheel perspective were completed to investigate the impact of each powertrain on greenhouse gasses and the effect on air quality of their immediate surroundings.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Replication of Genes in Rolling Circles

title: encoding functions in circular replicators at the origin of life

contributor:
Higgs, Paul
Physics and Astronomy

subject: Origin of Life

abstract: A MSc thesis which describes a theoretical model for gene replication on circular RNA under prebiotic conditions

abstract: The origin of life is one of the most captivating and difficult questions that science has yet to answer. Several different questions remain, including how genetic replication may have begun. Replication is a fundamental property of life that allows for evolution and the long-term survival of life. Non-enzymatic replication should have been present at the origin of life. The RNA world theory proposes that because it can act as both an enzyme and gene, RNA could have performed the function of a replicator at the origin of life. Abiotic chemistry for RNA nucleotides is known, as well as mechanisms for simple but random RNA sequence synthesis. However non-enzymatic replication of RNA sequences which might hold functions, has only achieved mild success. This is in no small part because of replication infidelity between RNA bases, and product inhibition during template directed replication. The rolling circle mechanism found in viroids and some RNA viruses, is a likely way to avoid these issues in the RNA World. Here we present a summary of key topics to origins of life and the RNA world, a deterministic model for rolling circle replication, followed by an original computational model for gene fixation in rolling circle replication. In these simulations we observe the dynamics of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. Selection for speed of replication tends to reduce circles to a minimum length. However, errors provide a natural doubling mechanism that creates strands multiple times the length of the minimal sequence. We show that if a beneficial gene appears in this new space, the longer sequence with the beneficial function can be selected, even though it replicates more slowly. This provides a route for the evolution of longer circles encoding multiple genes.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The origin of life is a topic that many people are inherently curious about. However, science is only just making progress towards an answer. The first organisms must have been able to replicate. Modern organisms use proteins, DNA, and RNA to do this, however it is unlikely these three molecules could have co-ordinated at the origin of life. A simpler model for replication uses only RNA, which can be both a gene and a catalyst. Here we propose some computational models which study RNA replication. These models simulates strands undergoing rolling circle replication, a method of replication some viruses use which has been suggested to be sustainable at the origin of life. We show that rolling circle replication can create long strands which can have new helpful sequences of RNA. This mechanism could have helped the first organisms achieve better replication and evolution, which is a key characteristic of life.


title: The Phenomenology of Incest Abuse

contributor:
Steizinger, Johannes
Philosophy

abstract: Beginning with a brief examination of the dominant psychological perspective, I will demonstrate how the ideology espoused in the current Diagnostic and Statistical Manual insufficiently captures the reality of incest abuse. Founded upon the dogmatic assumption that there exists in each individual body an isolated psyche turned inwards, this tradition fails to recognize consciousness as an externally directed manner of relating to others. The implications of these assumptions are significant to the exploration of incest trauma, as this form of abuse is fundamentally based upon the child's relations with others. This dominant psychological and philosophical tradition influences our current understandings of trauma, yet runs counter to the experience and perspectives of those it directly impacts. For this reason, through the lens of Merleau-Ponty's phenomenology, I will argue that incest trauma ought be reduced to a series of causal events nor psychological reactions to external stimuli. I will explore Merleau-Ponty's theory of perception and provide reasoning as to why his theory of embodiment better captures the practical orientation we, as organisms, take up towards the world. I will address his understanding of the postural schema as primary consciousness, the specular image as a new horizon, and the way in which these affect the body’s primordial powers of perspective and habit. Using these terms, I will then better clarify the infant’s relations with others and how these relations give rise to a particular style of embodied existence. Lastly, I will describe the sense of attunement that may exists between the child and the caregiver, and demonstrate both the impact of its presence and its absence. Rather than solely relying upon co-morbid conditions to explain the impact of incest abuse, this relational trauma must be captured using language that directly reflect the experience of survivors.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: Using Merleau-Ponty’s phenomenology, I will explore the way in which incest abuse affects one’s development, one’s perception, and one’s relations with others. I will argue that the dominant psychological perspective, as depicted in the DSM-5, insufficiently captures the reality of incest as an ongoing relational trauma, as it is founded upon a dogmatic assumption, namely that there exists in each individual body an isolated psyche turned inwards. Dualistic in nature, this ideology fails to recognize consciousness as an externally directed manner of relating to others. The implications of these assumptions are significant to the exploration of incest trauma, as this form of abuse is fundamentally based upon the child's relations to others. As I will demonstrate, incest trauma cannot be reduced to a series of causal events nor psychological reactions to external stimuli, for these accounts fail to acknowledge the organic act of perception which organizes one's experience and relations to others.