VictorJuiz/thesis huggingface dataset:
Factors Affecting Liquefaction Assessment of Granular Soils through Laboratory Testing

In practice, liquefaction assessment is largely driven by case histories, but the case history database is limited and there are huge gaps in the information available in each case. As a result, laboratory tests have continued to play a key role in determining how various factors influence liquefaction susceptibility and consequences. Eventually, a mechanics-based liquefaction assessment method which can differentiate among soils depending on their intrinsic properties will help geotechnical engineers better manage liquefaction risk especially in non-conventional materials such as tailings.This dissertation presents an investigation into how factors such as particle size, particle size distribution, and specimen preparation method influence the liquefaction response of a natural soil and a tailings material. Twelve particle size distributions ranging from pure silt to fine gravel and their various mixtures were studied in detail. The results are viewed through the critical state framework by first quantifying how these factors influence the critical state loci. Liquefaction response established through cyclic and monotonic simple shear testing was then compared to a large body of work from the literature to understand how the choice of testing method influenced the outcomes of these assessments. Cyclic liquefaction triggering and its relation to the number of cycles applied, as well as post-cyclic and monotonic residual strengths were reviewed.

Keywords: Critical State Line
Laboratory testing
Liquefaction Triggering
Natural soils
Residual strength
Tailings
Advisor: Ghafghazi, Mason MG
How the Food Environment, Time Use, and Household Labour Division Influence Dietary Activities: A Case Study of Two Neighbourhoods in Toronto

The dietary transition from home-prepared meals to increased reliance on food prepared away from home has led researchers to study the factors influencing participation in various food-related activities. While exposure to food environments, a key factor impacting what food people purchase, has been extensively studied, the dynamic spatiotemporal contexts for food retail exposure remain underexplored. Time use also plays a role in what people eat. However, most studies have neglected the division of household labour, a factor that can help explain the ways coupled partners spend time on food activities. Furthermore, in food environment research, the prevailing reductionist view conceals compositional and contextual complexities of household food-provisioning practice. To address these research gaps, this dissertation aims to develop conceptualizations and methods to better understand how the food environment, time use, and household labour coordination collectively influence dietary behaviours, using a case study of two neighbourhoods in Toronto. Chapter 2 proposes a novel application of multi-channel sequence analysis in food environment research based on time use diaries and GPS trajectories concurrently collected. This method offers an effective way to assess how food exposure in varying spatiotemporal contexts is associated with food activities. Chapter 3 expands the individual-level time use analysis of in-home food chores to the household level by examining time use diaries of coupled men and women. The results suggest possible gender differences in responsiveness to partners’ time allocations, highlighting a need to account for potential impacts of intra-household dynamics on food behaviours. Chapter 4 proposes to conceptualize the interconnected food-provisioning activities undertaken by household members using the time-geographic concept of the project. The applicability of this conceptualization is demonstrated through a test case on coupled adults’ activities for providing dinner. Chapter 5 summarizes this dissertation and discusses how the three chapters above contribute to advancing the current research. Ultimately, these chapters substantially improve our understanding of the various ways in which the food environment, time use, and household labour division influence food behaviours and expand the conceptual and methodological approaches that are geared toward a more holistic understanding of food behaviours in the built environmental and social contexts.

Keywords: diet
food environment
gendered division of labour
sequence analysis
time geography
time use
Advisor: Widener, Michael MW
Evaluating Others’ Relevance: Dimensions, Levels, and Interdependence

Humans seek to determine what other people are like and use others’ characteristics—such as their age, gender, and attractiveness—to assess others’ relevance to their own goals. The resulting appraisals of others’ opportunity and threat shape social judgments and behavior. My thesis accomplishes three broad aims. With Studies 1 and 2, I demonstrate that appraisals of who threatens and who facilitates one’s goals are independent dimensions of social judgment (Lassetter et al., 2021). People can be evaluated as (a) facilitating a goal, (b) threatening a goal, (c) both facilitating and threatening a goal, or (d) neither facilitating nor threatening a goal. I term this two-dimensional model the Relevance Appraisal Matrix. Relevance appraisals shift dynamically with perceiver goals: For example, a person may be appraised as facilitating a mate-seeking goal, but as neither facilitating nor threatening a self-protection goal (Lassetter et al., 2021). Further, relevance appraisals are distinct from stereotypes of group attributes and likely act as a mechanism between stereotypes of others and downstream outcomes. With Studies 3 and 4, I show that the Relevance Appraisal Matrix describes appraisals of individual targets (e.g., a nurse, a man, a close friend) and groups (e.g., medical professionals, men). Thus, in addition to appraising whether individual targets—including close and known others—pose opportunity and/or threat, relevance appraisals function as group-level phenomena that influence evaluations of broader groups. With Studies 5 and 6, I examine the link between relevance and interpersonal closeness. Close others may be especially likely to influence decisions and goal pursuit—and possibly, more likely to both facilitate and threaten goals. I show that threat and opportunity appraisals negatively and positively relate to perceived closeness, respectively. In sum, I propose a framework for understanding the structure of relevance, test how that framework applies to individual- and group-level social perception, and examine the link between relevance and closeness. Relevance appraisals are central and consequential to social perception. My thesis illuminates the structure of these appraisals and lays the foundation for future research examining how relevance shapes attention, emotions, and behavior.

Advisor: Neel, Rebecca
Joint Influence of Human Activities and Indoor Microenvironments on Contaminant Exposure: A Mass-Balance Modeling Investigation

Human populations globally are exposed to a wide variety of contaminants in indoor “microenvironments” (e.g., homes and workplaces). Such exposures are important contributors to the global burden of disease. Measurements reveal that human occupants dynamically influence indoor environmental quality (IEQ) through their presence and activities. However, measured data of IEQ are difficult to generalize, which can be addressed by computational modeling. This dissertation investigated the joint influence of time-dependent human activities and indoor microenvironments on contaminant exposure through modeling. Accordingly, I developed a novel modeling framework, Activity-Based Indoor Contaminant Assessment model (ABICAM). This framework leverages the principle of mass balance including fundamental processes of contaminant emission, transport, and fate, while accounting for the dynamic influence of human occupants and their activities on such processes. I applied ABICAM to address two general research questions: (1) What are the important drivers of contaminant exposure variability in North American human populations? (2) How can clothing influence the transport and fate of airborne contaminants, and accordingly, human exposure? First, indoor chemical emissions drive exposures, with rates typical for a North American home spanning ~4 orders of magnitude from 1.7 (BDE-28) to 18,300 (DEP) [ng·(h·home)-1]. Time-dependent human activities (e.g., cooking) and location are important contributors to intraindividual and interindividual exposure variability. Inherent physical human attributes influence interindividual exposure variability. Specifically, a toddler’s exposures to three ortho-phthalates can be 3-4 times those of an adult just due to a higher normalized respiration rate and skin surface area; activities (e.g., showering) can triple such exposure differences. Second, clothing influences IEQ and associated human exposure as follows: (1) Clothing readily accumulates various airborne contaminants; (2) clothing can effectively minimize transdermal uptake of such contaminants; (3) cotton clothing can effectively inactivate pathogens; (4) clothing can transport airborne contaminants between indoor microenvironments and be a source of secondary exposure; (5) textile washing transports such contaminants to outdoors, depending on physical-chemical properties. Overall, this research emphasizes the importance of reducing indoor contaminant emissions, highlights vulnerable individuals (e.g., toddlers), and supports the role of clothing in minimizing human exposure while noting the trade-off between this role and increased ecosystem exposure through laundering.

Keywords: Clothing
Human exposure
Indoor air
SARS-CoV-2
Semi-volatile organic compounds (SVOC)
Transdermal uptake
Advisor: Diamond, Miriam L
Cohen Hubal, Elaine
Trait Variation and Ecological Function in Diseased Agroforestry Systems

Biodiverse agroecosystems, including agroforestry, are characterized by complicated multispecies interactions, and it is this complexity that can be exploited for crop protection against pathogens and disease management practices. However, the effectiveness of biodiverse agroecosystems in minimizing disease depends on a range of biotic and abiotic interactions, thus requiring deep understanding of the multifunctionality within these systems. Using a functional trait-based approach, my PhD thesis aims to establish a link between multispecies functional traits in agroforestry systems and disease dynamics. As a model system, I use an economically significant crop, Coffea arabica var. Caturra (coffee), grown in biodiverse agroforestry systems, and one of its equally significant foliar pathogens Hemileia vastatrix, causal agent of Coffee Leaf Rust. I found that shade tree leaf and canopy traits in these agroforestry systems are significantly related to microclimate modifications that uniquely impact pathogens and disease incidence, highlighting the nuances between agroforestry systems. Similarly, coffee leaf functional trait trade-offs show significant shifts in diseased systems. However, disease incidence does not impact the root functional trait expression of coffee. From a theoretical perspective, this research enhances our understanding of multispecies functional traits and ecosystem processes in diseased systems, opening a new dimension for functional trait research. From an applied perspective, this research demonstrates how the multifunctionality of biodiverse agroforestry systems can be optimized for crop protection and integrated into disease management practices. I provide novel information to better inform biodiverse farm design and management, as well further promote the adoption of agrobiodiversity into our agricultural landscapes.

Keywords: Agroforestry
Coffee (Coffea arabica)
Coffee Leaf Rust (Hemileia vastatrix)
Foliar disease
Functional trait ecology
Advisor: Isaac, Marney
Group Collaboration in Global Online Learning Environments

This case study seeks to better understand online collaboration in a global secondary school classroom context. Given the widespread promotion of collaborative learning as a crucial skill, coupled with a significant increase in online learning, this study aims to grow research evidence and offer practical recommendations specific to K-12 global online collaboration. This study encompasses an intervention activity designed to introduce a group film production assignment in a global online International Baccalaureate (IB) secondary level film class with no prior collaborative activity. The study provides a detailed account and interpretive analysis of behaviours amongst groups using a theory-driven coding scheme to further identify and interpret the complex interactions and exchanges. Finally, student reflections and post-activity comments provide insight into students' perceptions and attitudes about online collaboration. This study reveals the challenges groups faced with prescribed online tools, Internet connectivity, technical issues, uneven participation, and time zone differences. The learning management system, Canvas, was perceived as a location to retrieve assignments and less as a space to collaborate. Given these challenges, groups eventually transitioned to social media instant messaging (IM) to enhance interactions. The study reveals IM was the most effective for fostering frequency of communications, sustained interaction, and was found to have the widest range of collaborative behaviours. For groups, IM became an effective digital backchannel and a space to enhancegroup cohesion and connection. Students demonstrated preference for lean media affordances of IM such as speediness of responses, ease of use, informal nature of interactions and accessibility. Given the culturally and globally diverse students body, the study identifies a need to foster intercultural competences for students and educators. Technology access and Internet connectivity continue to be an equity issue for students globally. Considering a recent IB initiative to pilot more online courses across centres worldwide, this study makes four recommendations for current online IB film and other global centres endeavouring to promote online collaboration. Recommendations include the development of an IB global media repository to promote a culture of participatory media production, an increase of opportunities for intercultural collaboration, and further recommendations to improve instructional design for online collaboration.

Keywords: Film Education
Intercultural competences
International Baccalaureate
K-12 online learning
Media Education
Online collaboration
Advisor: Cooper, Karyn
CRISPR/Cas9 Screens Reveal the Consequences of Genome Stability Factor Inhibition by Small Molecules

Multiplex genome editing using CRISPR/Cas9 enables highly penetrant loss-of-function screening in an unbiased, genome-wide manner in human cells. Genome stability factors maintain the fidelity of DNA replication and chromosome segregation (mitosis). Therefore, their activity is highly relevant to physiological and disease states. Accordingly, small molecule inhibitors developed against these factors may be applied to study the consequences of their loss. In my primary research objective, I employed positive and negative selection chemical screens to search for novel determinants of WEE1 kinase and MRE11 nuclease inhibitor sensitivity. Firstly, I found unexpected but robust genetic interactions between WEE1 kinase inhibition by the clinical inhibitor adavosertib (AZD-1775), the eIF2 alpha kinase GCN2, and the ribosome quality control (RQC) machinery in human cells. Loss of the RQC protein ZNF598 sensitizes cells to adavosertib. Moreover, I show that a GCN2-dependent integrated stress response orchestrated by the ATF4 transcription factor is necessary to drive cellular toxicity upon adavosertib treatment. Consequently, GCN2 or ATF4 loss is associated with resistance to adavosertib. I provide evidence that GCN2 activation is a common but until now unrecognized outcome of WEE1 kinase inhibition. Secondly, I found novel sensitizing relationships with the MRE11 nuclease inhibitor mirin and two derivatives (PFM01 and PFM39). I show that defective mitochondrial gene expression is an unexpected hallmark of PFM01 sensitivity. My work cautions against off-target activities that may confound the interpretation of phenotypes elicited by MRE11 inhibitors. Together, the work presented in this thesis illustrates the potential of chemical genetic CRISPR screens to uncover novel genetic interactions and mechanisms of drug action. In my second research objective, I studied the regulation of DNA double-strand break repair during mitosis. I found that end resection is minimally inhibited by targeting of the CtIP/RBBP8 protein, which blocks MRE11 nuclease activity. My work suggests that supplemental mechanisms to inhibit CtIP/MRE11 exist in cells and that unscheduled end resection in mitosis can alter the fate of daughter cells. Finally, I characterized a mitotic DNA damage tolerance complex composed of MDC1, TOPBP1, and CIP2A, the loss of which is selectively deleterious to BRCA-mutated cells and potentially BRCA-mutated breast and ovarian cancers.

Keywords: CRISPR/Cas9
Functional genomics
Genome editing
Mitosis
MRE11 nuclease inhibitor
WEE1 kinase inhibitor
Advisor: Durocher, Daniel
Artist Friendly Tools For Facial 3D Modeling and Animation

One of the most powerful tools in social communication is the face, from which observers can quickly make several emotional inferences. Humans are extremely sensitive to unrealistic facial expressions and develop a sense of unease and disgust when robotic or digital depiction doesn't meet their high standards. Developing artist-friendly tools for creating and animating digital faces is challenging because the face can be thought of as comprising a high-dimensional, dynamic information space. This inherently led to modern 3D tools for faces to be complex and have a high barrier of entry. The goal of this thesis is to address the problem of designing artist-friendly 3D tools and systems for digital face modeling and animation. We focus on exploring novel digital data representations that, in turn, inspire interactive tools that significantly reduce the time and effort it takes to produce believable faces. First, we introduce a novel tool for creating muscle geometry using a volumetric representation. Second, we propose a new representation for facial expressions that enables the creation of intelligent user interfaces for posing faces. Finally, we introduce a system to produce a stylized stop-motion effect of the input animation that can be further used to bring animations into physical realms via 3D printing. While developing tools and systems, we identify key issues that hinder user experience, build novel digital representations, and confirm our design choices by various informal evaluations and comparisons.

Keywords: Animation
Character
Face
Geometry
Graphics
Interface
Advisor: Singh, Karan K
The Role of Phosphoinositides During Phagosome Formation and Resolution

Phagocytosis, the process by which cells internalize particles greater than 0.5µm into membrane-bound vacuoles (phagosomes), is key for innate immunity and tissue homeostasis. Phagocytosis can be carried out by myeloid cells such as macrophages, neutrophils, and dendritic cells. These cells, known as professional phagocytes, constitute the first line of defense against invading microorganisms and are key for the development of adaptive immunity. Furthermore, phagocytosis is essential for the clearance of the apoptotic debris produced from the daily turnover of cells. Clearance of apoptotic bodies can be carried out also by non-professional phagocytes such as fibroblasts, epithelial, mesenchymal, and endothelial cells. Phagocytosis can be divided into three main stages, phagosome formation, maturation, and resolution. Firstly, phagosome formation consists of probing for potential targets through ruffling, followed by target binding, pseudopod extension, and scission of the phagosome from the plasma membrane. Secondly, during the maturation stage nascent phagosomes convert into early phagosomes, subsequently into late phagosomes and then into phagolysosomes. Finally, the resolution of phagolysosomes consists of their shrinkage and recycling of membrane and luminal components. Phosphoinositides, specialized signaling lipid molecules in the cytosolic leaflet of the phagosomal and plasma membrane orchestrate the changes in membrane composition and actin cytoskeleton during each stage of phagocytosis. This dissertation aims to characterize the roles for two largely understudied phosphoinositides, PtdIns(3,4)P2 and PtdIns(4)P, during phagosome formation and phagolysosome resolution respectively. Specifically, I focus on describing the distribution, dynamics, metabolism, and functions of these phosphoinositides during phagocytosis. In chapter I, I review the background on phosphoinositides and their previously known involvement during phagocytosis. Chapter 2 defines the aims and hypothesis of my work. The methodology used in this work is described in Chapter 3. In Chapter 4, I describe the role of PtdIns(3,4)P2 during phagosome formation. Chapter 5 focuses on PtdIns(4)P, how its levels are regulated by the endoplasmic reticulum and its involvement during phagolysosome resolution. Finally, I discuss the importance of these events to phagosome formation and phagolysosome resolution. This work highlights the relevance of PtdIns(3,4)P2 and PtdIns(4)P for the phagocytic process and the importance of a fine-tuned regulation of these lipids.

Keywords: Cytoskeleton
Innate Immunity
Lipids
Macrophages
Phagocytosis
Phosphoinositides
Advisor: Grinstein, Sergio