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Applicability of Adaptive Co-Management within Indonesian Small-Scale Fisheries.
No full textSmall-Scale Fisheries (SSF) governance has historically excluded small-scale fishers from participating in decision-making processes, negatively influencing millions of livelihoods. Governance of SSF is complex due to interactions between users and the environment, both with varying influence on the system. Indonesia is of particular importance for SSF governance due to its archipelagic structure, fishing culture and the direct link between economic viability and SSF. Indonesian SSF provide livelihood, nutrition, and economic security to millions of fishers. Indonesian SSF however face, illegal and unreported fishing practices, fishing location disputes, pollution, poor living conditions, declining fish stocks and extreme volatile weather conditions. Effective governance strategies for SSF that can adapt to dynamic conditions within Indonesian SSF are critically needed. This thesis aims to explore the strength of adaptive co-management indictors present within Indonesian SSF, and how current governance of SSF can be transitioned, aiding in the transition of these fisheries from vulnerability to viability. Adaptive co-management is a governance approach that combines co-management and adaptive management, while integrating the practices of learn-by-doing, social memory and social networks into governance proceedings. This thesis indicates that adaptive co-management is an effective governance approach for complex social-ecological systems such as SSF. With adaptive co-management providing an avenue to facilitate vulnerable to viable SSF transitions. Long-term institutional support, effective capital building and social capital, were the strongest indicators of adaptive co-management, marking these critical for future development in SSF
Studying Immersive Deception: Manifestations and User Perceptions of Deceptive Design in Commercial Virtual Reality
No full textDeceptive Design (formerly “dark patterns”) refers to design practices that distort or impair users’ ability to make informed decisions, regardless of intent. As immersive technolo- gies, such as Virtual Reality (VR) and Augmented Reality (AR), transform people’s daily experiences, their immersive virtual environments unleash a highly engaging experience while enabling new opportunities for deceptive design strategies that users cannot easily recognize or resist. Consequently, ethical and privacy concerns are expanding into these environments. While previous research has examined deceptive design issues in websites, mobile apps, games, and gamification, the extent of these problems in immersive environ- ments remains largely unexplored. This thesis investigates deceptive design in immersive environments with a specific attention to VR. It identifies deceptive design that presents in VR and emerges from VR technology’s unique properties, and examines their impacts from users’ perspective.
We first conducted a systematic literature review to synthesize the state-of-the-art research on deceptive design. This review revealed potential deceptive strategies that can be employed in immersive environments, and those that can be enabled by the large amount of user data collected by these technologies. However, most of the existing literature focused on hypothetical scenarios rather than examining deceptive design as it appears in commercially available applications. Informed by the findings from this review, we surveyed experienced users about their awareness of data practices in immersive technologies, examined deceptive design in commercially available VR applications, and compared these findings with those from traditional computer platforms. To ensure consistent and comparable deceptive design analyses across these platforms, we developed a Deceptive Design Assessment Guide grounded in foundational deceptive design literature. This Assessment Guide was applied and validated in two studies that examined how deceptive practices manifest and influence user experience in exemplary computer and VR applications. Our findings show that the deceptive design in VR applications relies heavily on 2D interfaces, such as dialogue windows and checkboxes, rather than fully integrating VR-specific properties. Hypothesized scenarios from the literature, such as perception-hacking and emotional-based manipulation, were not observed in our selected VR applications. Certain VR properties (e.g., realistic simulation, virtual-physical barrier) amplified the impacts of deceptive design in users’ decision-making process but did not directly enable it. While users cannot point out specific design elements that used deceptive practices, they still expressed a general discomfort and feeling of manipulation. Nevertheless, many users felt powerless in protecting themselves or asserting their autonomy, and perceived deceptive design as a standardized industry practice with no possible escapes.
Our research has implications for future research, and immersive technology design, development, and regulation for building better industry design standards and stronger user protections. For future researchers, the findings provide guidance on fostering user awareness through effective educational strategies, expanding theoretical approaches for understanding deceptive design in immersive environments, and refining user-centered empirical approaches for identifying and evaluating deceptive practices. For designers and developers, this thesis offers a structured Assessment Guide and actionable recommendations for supporting the creation of ethical and user-centered immersive applications that respect privacy and autonomy. For immersive technology regulation, this thesis identifies the limitations of current regulations and provides practical advice for expanding and strengthening regulatory frameworks, enforcing transparent privacy communication and ethical industry design standards tailored to immersive technologies. In conclusion, this thesis advances the understanding of deceptive design in commercially available VR applications, delivers actionable strategies for identifying and mitigating deceptive practices, and establishes a foundation for cross-disciplinary collaborations to protect user well-being in immersive environments
Exploring the Dominant Negative Potential of 11 Mutants in
No full textCytochrome oxidase (COX) is the terminal enzyme of the electron transport chain and plays a crucial role in cellular respiration. As a multisubunit enzyme, COX consists of catalytic core subunits encoded by the mitochondrial genome and requires the coordinated action of more than 30 nuclear-encoded assembly factors for proper biogenesis and function. Human COX deficiencies have been associated with mutations in both nuclear and mitochondrial genes and are thus characterized by immense genetic heterogeneity and a vast spectrum of clinical phenotypes. 11 is a nuclear-encoded copper chaperone that is required for COX assembly. Beyond this well-characterized role, COX11 has an additional, uncharacterized role in cellular redox homeostasis. Caron-Godon et al. reported a patient with compound heterozygous mutations in 11, whose homologous mutations were studied in haploid yeast. When grown on non-fermentable carbon sources, one of the mutant alleles, P238T, demonstrated robust growth, indicative of respiratory competence, in contrast to the truncation mutants, Y250* and R254*, which exhibited a complete and partial respiratory deficiency, respectively. Given that COX deficiencies are inherited in an autosomal recessive manner, this finding adds an unexpected complexity to the patient’s phenotype, which may suggest the possibility of a hypomorphic or dominant negative allele.
To better recapitulate the patient’s genotype, I employed a pseudodiploid system in , which involves the stable co-expression of two mutant 11 alleles in a single haploid background. Functional assays, including growth on non-fermentable carbon and COX enzymatic activity, as well as immunoblotting of core COX subunits, demonstrated that the pseudodiploid double mutants, representative of the patient, supported robust respiration and maintained COX assembly at levels comparable to those of wild-type.
In contrast, evaluation of oxidative stress markers revealed defects in cellular redox balance. Double mutant strains, particularly P238T/R254*, exhibited significantly elevated superoxide dismutase activity, a pronounced decrease in mitochondrial aconitase activity, and increased sensitivity to hydrogen peroxide. These data indicate that the redox equilibrium is compromised even when cytochrome oxidase function is preserved
Between the Covers and Beyond the Page: Gauging Climate Fiction's Impact through Ecocriticism and Virtual Book Club Observations
No full textDespite increasing global concern about climate change, a gap persists between climate worry and action. Researchers across various disciplines and popular media suggest that narratives can motivate pro-environmental behaviour. Cli-fi novels, in particular, are believed to influence readers’ behaviours and perceptions of climate change. However, most evidence supporting these claims comes from classroom observations and traditional humanistic inquiry. In 2018, a new research methodology emerged, empirical ecocriticism, which set out to determine how general readers engage with these novels. This dissertation follows the principles of this method, namely, the combination of ecocritical analyses with empirical methods. To that end, the first part of this dissertation (Chapters 2 and 3) is an ecocritical examination of four diverse cli-fi novels published in the last decade to determine how they conveyed climate change information to their readers and how this portrayal may affect readers’ understanding of this issue. The second part of this dissertation (Chapter 4) is a report on empirical findings from a book club observation study of readers reading these same cli-fi novels.
The two interdisciplinary objectives of this dissertation were to firstly examine how cli-fi novels relate information about climate change and what aspects of climate change are emphasized to readers in these novels, and secondly to contribute to the emerging field of empirical ecocriticism by reporting on how groups of readers discussed cli-fi novels and the climate change information therein. To achieve these objectives, I: (1) interpreted of four diverse cli-fi novels using ecocritical methods and (2) designed and implemented a book club observation study of general readers reading these same novels.
Drawing on ecocriticism, climate change communication, and social sciences research, Chapter 2 introduces a new subcategory of cli-fi – ambivalent cli-fi. This subcategory is defined through an analysis of two realistic cli-fi novels Weather by Jenny Offill and Blaze Island by Catherine Bush to determine how climate change is portrayed in these novels and how their narratives might help readers explore their emotional responses to climate change. The novels were chosen due to their connections to the 2020s and the ecocritical analysis of these novels demonstrates that they can help readers sit in the uncomfortable space where the world is not yet irreversibly ruing, yet there is also no easy solution.
Chapter 3 examines Blackfish City by Sam J. Miller and The Marrow Thieves by Cherie Dimaline, two speculative cli-fi novels, whose authors claimed they wanted their readers to feel hope despite narratives that portray radically altered environments and nightmarish societies. This chapter reviews climate change communication research that points towards more inclusive messaging favouring neither hope nor despair. The ecocritical analysis of the two novels utilizes Albert Camus’ notion of the absurd to address the feelings of existential crisis evoked by the novels’ depictions of climate change. It concludes by advocating for the creation of narratives that help audiences find ways to embrace futures that are neither apocalyptic nor utopic.
Chapter 4 reports on virtual cli-fi book club sessions conducted from January to June 2022, involving 40 participants from across Canada. Participants read the same cli-fi novels discussed above in order to ascertain how ecocritical readings of these novels might differ from general readers’ interpretations. Pre- and post-survey data indicated that participants were younger than the average Canadian population (65% less than 44 years old compared to 42%), liberal, and concerned about climate change. The study identified three main themes from participant discussions: (1) the relatability of the cli-fi novels enhanced the believability of the story and climate change; (2) the presence or absence of hope was linked to whether novels included individual actions to mitigate climate change; and (3) participants experienced anxiety when they empathized with characters and scenarios. These findings suggest that readers use cli-fi novels to understand current climate issues. Results from the book club observation study also suggested that general readers in groups find solace and reach new conclusions through discussion. This discovery underscores the importance of considering reading as both an individual and social practice for empirical ecocriticism.
The conclusions drawn from the ecocritical chapters highlight how cli-fi narratives have the potential to influence reader emotions. The arguments in Chapters 2 and 3 demonstrate that the negative emotions present in each cli-fi novel are necessary for readers to engage with and learn from. Chapter 5 concludes with a comparison of these arguments with the results from the book club study (Chapter 4). This discussion reinforces research from climate change communication and the social sciences that argues audiences (and readers) do not need to be frightened with catastrophic images of climate change dystopias. Instead, what readers (and non-scholarly audiences) might need now are stories that help them learn how to live-with climate uncertainty, and spaces to do this together
Suppressing Tymovirus replication in plants using a variant of ubiquitin
No full textThis is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.RNA viruses have evolved numerous strategies to overcome host resistance and immunity, including the use of multifunctional proteases that not only cleave viral polyproteins during virus replication but also deubiquitinate cellular proteins to suppress ubiquitin (Ub)-mediated antiviral mechanisms. Here, we report an approach to attenuate the infection of Arabidopsis thaliana by Turnip Yellow Mosaic Virus (TYMV) by suppressing the polyprotein cleavage and deubiquitination activities of the TYMV protease (PRO). Performing selections using a library of phage-displayed Ub variants (UbVs) for binding to recombinant PRO yielded several UbVs that bound the viral protease with nanomolar affinities and blocked its function. The strongest binding UbV (UbV3) candidate had a EC50 of 0.3nM and inhibited both polyprotein cleavage and DUB activity of PRO in vitro. X-ray crystal structures of UbV3 in the cytosol of A. thaliana suppressed TYMV replication in planta, with the reduction in viral load being correlated to UbV3 expression level. Our results demonstrate the potential of using UbVs to protect plants from tymovirus infection, a family of viruses that contain numerous members of significant agricultural concern, as well as other plant viruses that express functionally related proteases with deubiquitinating activity.National Sciences and Engineering Council of Canada (NSERC), RGPIN-2020-05682 || NSERC, RGPAS-2020-00012 || Canadian Institutes of Health Research COVID-19 Rapid Research Funding, OV3-170346 || Canadian Institutes of Health Research Project Grant, PJT-148510 || Canada Research Chain, CRC-2022-00420 || U.S. Department of Agriculture, Agricultural Research Service grant 3060-21000-045-00D || Canada Research Chair in RNA and Protein Biophysics || NSERC CREATE Postdoctoral Fellowship || University of Manitoba Graduate Fellowship
Multi-scale Modelling of Neurosteroid-mediated Seizure Trajectories in Childhood Absence Epilepsy
No full textChildhood absence epilepsy (CAE) is a pediatric generalized epilepsy disorder characterized by brief episodes of impaired consciousness and distinctive 2.5--5 Hz spike-wave discharges (SWDs) on electroencephalography. With a well-established genetic aetiology, this condition tends to resolve spontaneously during adolescence in most cases. While several mechanisms have been proposed for remission, understanding remains insufficient to guide early intervention practices.
In this thesis, we first utilize a conductance-based thalamocortical network model that exhibits characteristic SWDs, to demonstrate that allopregnanolone---a progesterone metabolite known to enhance GABAa receptor-mediated inhibition---has an ameliorating effect on SWDs. To investigate the divergence between this finding and clinical observations, we developed an enhanced thalamocortical model that incorporates a layered cortical structure to explore regional cortical heterogeneity and frontocortical connectivity as potential resistance factors to ALLO-mediated recovery. Our results suggest that non-resolving CAE may be due not only to increased frontocortical connectivity but also to the composition of cell types within the network. Specifically, a higher proportion of bursting-type cells may prevent the therapeutic effects of allopregnanolone. We extended our investigation to examine whether these findings apply to CAE caused by different genetic mechanisms, particularly mutations in sodium channel genes by modelling their effects at the individual neuron level. Furthermore, we examined the degree to which these alterations lead to network-level pathological activity, as well as the influence of ALLO on these genetically distinct networks. Our results demonstrate that ALLO facilitates recovery from SWDs regardless of the underlying mutation type. However, enhanced frontocortical connectivity prevents recovery in some mutation types, particularly when mutation effects are severe.
Altogether, the multi-scale computational framework developed in this thesis demonstrates that CAE remission is determined by complex interactions between hormonal influences, genetic factors, and network connectivity patterns. The results suggest that certain genetic mutations may predispose individuals toward either remission or non-remission, which can be further modulated by connectivity profiles. In particular, enhanced frontocortical connectivity appears to be a significant factor in resistance to hormone-mediated remission. Additionally, this thesis develops techniques for analyzing transitions between distinct dynamical states in neural systems, incorporates genetic and hormonal factors into conductance-based models, and provides a computational framework to identify key parameters governing epileptic activity. These approaches not only advance our understanding of CAE specifically, but offer generalizable insights into the mathematical modelling of neurological conditions characterized by spontaneous shifts in brain dynamics
EV Electrical Systems for Student Teams: An Iterative Design Approach with Practical Lessons
No full textThe shift toward vehicle electrification has created an urgent need for engineering students to acquire
practical knowledge in electric vehicle (EV) systems. While industry and academia offer theoretical
instruction, student design teams often lack practical guidance, resulting in preventable errors, safety
risks, and incomplete competition vehicles. This thesis addresses that gap by identifying key lessons
to learn for building EV electrical systems and offering real-world insights through a case study of the
University of Waterloo Alternative Fuels Team (UWAFT) during the EcoCAR 5 competition.
The thesis is structured around three primary electrical domains: High Voltage (HV), Low Voltage
(LV), and Serial Communication Systems. Each chapter begins with generalized best practices, safety
procedures, and design considerations, then explores how UWAFT applied—or struggled to apply—
these concepts in practice.
In the HV domain, the thesis covers critical safety mechanisms like Isolation Monitoring Devices
(IMDs), Emergency Disconnect Systems (EDS), and Lockout/Tagout (LOTO) procedures. It
highlights common student pitfalls such as improper cable terminations and the consequences of
electromagnetic interference (EMI).
The LV section details harness design, schematic development, wire selection, and assembly
techniques essential for powering 12V components safely and reliably. Emphasis is placed on
documentation, modularity, and physical protection of circuits.
In the Serial Communication chapter, the CAN bus protocol is explained in the context of a complex
vehicle network involving autonomous driving, propulsion control, and diagnostics. The harness
assembly techniques from the LV chapter are expanded upon for the specific case of CAN cables.
Finally, UWAFT’s Serial Network Diagram (SND) serves as a practical guide to organizing and
troubleshooting communication systems.
Through a combination of foundational theory and applied case study, this thesis equips student teams
with a framework for developing safe, functional, and competition-ready EV electrical systems. It
also highlights the importance of mentorship, iterative learning, and documentation in engineering
education
Robust Methods and Model Selection for Causal Inference under Missingness of the Study Exposure
No full textThe goal of this thesis is to develop new robust methods for the estimation of the causal effect and propose a model selection algorithm when the exposure variable is not fully observed. We mainly discuss the methods using propensity score (PS) and imputation approaches to address both missingness and confounding issues in the observational dataset.
How to deal with missing data in observational studies is a common concern for causal inference. However, if the exposure is missing at random (MAR), few approaches are available, and careful adjustments on both missingness and confounding issues are required to ensure a consistent estimate of the true causal effect on the response. In Chapter 2, a new inverse probability weighting (IPW) estimator based on weighted estimating equations (WEE) is proposed to incorporate weights from both the missingness and PS models, which can reduce the joint effect of extreme weights in finite samples. Additionally, we develop a triply robust (TR) estimator via WEE to protect against the misspecification of the missingness model. The asymptotic properties of WEE estimators are shown using properties of estimating equations. Based on simulation studies, WEE methods outperform others, including imputation-based approaches, in terms of bias and variability.
Additionally, properly selecting the PS model is a popular topic and has been widely investigated in observational studies. However, there are very few studies investigating the model selection issue for estimating the causal effect when the exposure is MAR. In Chapter 3, we discuss how to select both imputation and PS models, which can result in the smallest root mean squared error (RMSE) of the estimated causal effect. Then, we provide a new criterion, called the “rank score”, for evaluating the overall performance of both models. The simulation studies show that the full imputation plus the outcome-related PS models leads to the smallest RMSE, and the newly proposed criterion is also able to pick the best models.
Compared to the MAR assumption, the missing not at random (MNAR) assumption allows for the association between the missingness and the exposure variable, which is a weaker assumption and more reasonable in some application studies. Even though many researchers have discussed how to deal with the missing outcome or confounders in observational studies, very little discussion focuses on the missing exposure under the MNAR assumption. In Chapter 4, we propose the IPW estimators using joint modelling, called “IPW-Joint'', to estimate the causal effect when the exposure is MNAR, which combines estimated weights from the missingness and PS models. Furthermore, to address the problem of model selection in the high-dimensional setting, we apply outcome-adaptive LASSO with weighted absolute mean difference (OAL-WAMD) as a new algorithm to select the outcome-related covariates when the exposure is MNAR. The simulation studies show that IPW-Joint contains more robust properties and smaller variance than the traditional IPW approach. In addition, OAL-WAMD outperforms the traditional LASSO in terms of higher true positive rates (TPR) and smaller variance in both low and high-dimensional settings.
In Chapter 5, we summarize the major findings and discuss the potential extensions. The proposed methodology can be applied to several areas, including new drug development, complex missing data problems and finding real-world evidence in observational data
Automating Construction Material Sourcing and Distribution for Circularity
No full textCircularity in the construction industry is developing, with increasing emphasis on extracting resources from existing infrastructure. Given the growing amount of resources embedded in the current housing stock, sustainability within the industry is critical. To support the large-scale reuse of Reclaimed Construction Materials (RCMs), through active reuse strategies, it is essential to develop tools and frameworks for sourcing RCMs. This study contributes to that effort by providing insights into the creation of such frameworks and emphasizing the value of material reuse within the construction sector. Although material reuse is considered an excellent circular strategy, the application of reuse across the industry still faces technical, social, and environmental limitations.
A significant drawback of material reuse is the complexity of finding RCMs that fit a design with limited alterations required for use. Furthermore, the environmental and economic cost of acquiring and reusing RCMs is taxing, compared to acquiring New Construction Materials (NCMs). Additionally, there is limited insight into other options for restoring existing building resources before replacement. Therefore, this thesis develops decision support frameworks for component level assessment of RCMs and assembly level assessment of RCMs. The component level assessment tool is designed to integrate 3D scanning, Optimization Programming Languages (OPL), Life Cycle Assessment (LCA) and Building Information Modeling (BIM) tools to create an enhanced digital supply sourcing system; whereby RCMs at secondary sources can be found with basic required information like; cost, proximity and dimensions to enable planning and implementation.
The component-level assessment framework is refined and extended through a policy assessment study, demonstrating its adaptability to diverse challenges presenting both risks and potential benefits for policy implementation. This thesis is fundamentally based on real-world data gathered from RCM stores and it challenges the current ongoing building design practices that deem material reuse as a problematic approach by enabling flexible sourcing of used and new building materials and providing an assessment framework for selecting appropriate restoration strategies. The approach alters the social perspective to consider partial integration of RCMs at varying levels of integration in new building projects
Socioeconomic Indicators and Psychopathology in Children with Chronic Physical Illness
No full textBackground: Children with a chronic physical illness (CPI) have an increased risk of developing psychopathology. The combination of chronic stress and socioeconomic disadvantage often contributes to poor mental health in this vulnerable population of children.
Research Questions: This study addresses the following questions: (1) Are neighborhood-level socioeconomic indicators worse among families of children with CPI compared to the general population? (2) Are these socioeconomic indicators associated with psychopathology among children with CPI over a 48-month period? (3) Does child stress moderate associations between socioeconomic indicators and child psychopathology over time?
Methods: Data come from the Multimorbidity in Children and Youth across the Life-course (MY LIFE) study, which followed 263 children aged 2-16 years who had been diagnosed with a CPI, for 48 months. A one-sample t-test compared mean differences in socioeconomic indices, measured by the Ontario Marginalization Index (ON-MARG), between MY LIFE and the general population. Linear mixed models (LMMs) examined associations between ON-MARG dimensions and psychopathology symptoms, as measured with the Emotional Behavioural Scales. Moderation by child HCC was investigated using a time-varying product-term interaction.
Results: At baseline, the study included 263 children with a CPI (mean age: 9.4 years, 53% male). Children in MY LIFE resided in areas characterized by greater socioeconomic disadvantage relative to the general population (M= -0.38- -0.20, p= <0.001). Material resources (β=0.13, p=0.03) and the two-way interaction between households and dwellings and time (β=0.02, p=0.04) were significantly associated with parent-reported externalizing symptoms. Households and dwellings (β=0.09, p=0.02) and the three-way interaction between age and labour force, time, and child stress (β=0.02, p=0.04) were significantly associated with child-reported externalizing symptoms. No significant associations were noted between ON-MARG dimensions and parent- and child-reported internalizing symptoms.
Conclusion: Children with CPI were more likely to live in areas of high socioeconomic disadvantage with housing and material deprivation predicting elevated psychopathology symptoms. LMMs showed that time-varying child stress may have a moderating effect on indicators of socioeconomic disadvantage, particularly related to households and dwellings and material resources. Differences between parent- and child-reported models reinforce the importance of multi-informant perspectives. Findings highlight the need for integrated, equity-informed interventions targeting both socioeconomic and physiological drivers of child psychopathology among children with CPI