VictorJuiz/thesis huggingface dataset:
Manufacture and Characterization of Micro-/Nano-fibrillated Composites and their Applications

Micro-/nano-fibrillated composites (M/NFC) are a new generation of composites containing well-dispersed, high aspect ratio polymeric fibrils. The novel composites have shown great promise as next-generation materials for construction, gas barrier packaging, and foaming applications. However, it is still not fully understood how the fibrils’ development during processing and their final morphology are impacted by the manufacturing and material parameters. Moreover, the applications of M/NFC have been limited, mainly focused on taking advantage of the mechanical properties. Therefore, this dissertation aims to show the fundamental mechanisms of the fibrils’ formation, and the practical applications of M/NFCs in thermal insulation and antistatic fields. The first part of the thesis includes in-depth analysis of some crucial parameters and their influence on the evolution of the fibrils’ morphology. Experimental results indicate that tuning the reinforcement to matrix viscosity ratio significantly impacts the fibrils’ morphology. By choosing a low viscosity ratio system, the fibrils’ diameters are refined, and continuity is enhanced, resulting in composites with improved mechanical properties. Moreover, a new method of applying coupling agent is proposed to further enhance the dispersion of the fibrils and improve the interfacial adhesion between the matrix and fibrils. The results indicate that the new method can improve the interface without damaging the fibrils’ morphology. The second part of the thesis focuses on the development of new applications of M/NFC. With the formation of the physical network of the dispersed fibrils in the polymer matrix, the viscoelastic properties and crystallization kinetics are enhanced, making the M/NFCs a great candidate for foaming. Low-density, closed cell foams are successfully manufactured from M/NFC showing ultra-low thermal conductivity (~32 mW∙m-1∙K-1). Furthermore, we demonstrated a new approach to generate electrically percolated core-sheath fibrils with low reinforcement concentrations in a polymer matrix. We first designed a completely wetted morphology where the reinforcement phase was coated with conductive layers within the polypropylene matrix. The subsequent melt spinning process transformed the dispersed, completely wet droplets into high aspect ratio core-sheath fibrils, which percolated into conductive network structures. Since the content of the matrix can be maintained at a very high level (> 90%), the resultant materials, even without compatibilization, have both good electric conductivity and excellent mechanical properties. This dissertation developed fundamental understanding and in-depth analysis of structure-property relationships and propose new manufacturing approaches of micro/nano-fibrillate composites for various applications.

Advisor: Park, Chul C
Lee, Patrick P
Molecular Cancer Subtypes and Their Associations

Molecular profiling can be a powerful tool for improving cancer classifications and patient management decisions. Breast cancer is a classic example of molecular cancer subtypes and their translational and clinical utility. Subtypes can be prognostic, which can help guide decisions on treatment intensification or deintensification. Some subtypes indicate treatment response and thereby guide treatment decisions. Cohort selection in research or for clinical trials can be aided by cancer subtypes to identify homogeneous patient criteria. Subtypes are assessed through different types of molecular features and integrative subtypes can be created by combining data types. New molecular data types are found as cancer is characterized in new ways. Datasets with increased and novel data types require novel integration methodologies for cancer subtyping.To improve integrative cancer subtypes, I took three different approaches. First, the tumour microenvironment plays an integral part of cancer development, but is not usually included in cancer subtyping with genome-wide molecular data types because of difficulties acquiring larger datasets. By deconvolving tumour adjacent cell (TAC) mRNA abundance, I created a new data type for exploring the tumour microenvironment. I investigated TAC mRNA abundance associations with survival and the well-known intrinsic subtypes in breast cancer. I discovered that somatic SNVs associate with subtype-specific TAC mRNA abundance differences. Second, I focused on localized prostate cancer, where there are significant rates of over- and under-treatment despite clinical risk classification used in treatment management. I created integrative genomic subtypes by integrating whole genome sequencing data types using a driver-based approach. Third, I expanded my subtyping beyond identified drivers and created an integrative subtype generation (iSubGen) framework that is data type agnostic. iSubGen can integrate TAC mRNA abundance with other traditional gene-based and non-traditional data types, like trinucleotide mutational signatures. Importantly, iSubGen can also accommodate missing data which is crucial for integrative subtyping of large numbers of data types. Together, this work provides a new approach to integrative subtyping with a wider range of data types.

Advisor: Boutros, Paul C
Development of Bioanalytical Platforms for the Discovery of Small Molecule-Protein Interactions in Parkinson’s Disease

Parkinson’s disease is a type of progressive neurodegenerative disease that affects the neuromotor function of the brain. The current theory suggests that its pathologies are connected with α-synuclein (α-syn) aggregation. Monomeric α-syn can cluster to form oligomers. Leading to the formation of β-sheet rich fibrils and the eventual Lewy body inclusion. The presence of biometals such as Cu(II) can drastically enhance the speed of α-syn aggregation as well as induce higher reactive oxygen species (ROS) formation. Plant extracts such as pyrroloquinoline quinone (PQQ) have been shown to contain an anti-fibrillation effect. As such it is critical to examine the rescue effect of PQQ against Cu(II) induced α-syn toxicity. In Chapter 1, a detailed discussion between α-syn in PD pathologies, biometal implications, and plant-based PD therapeutic molecules is presented. This is accompanied by a review of fundamentals of electrochemistry to highlight the advantage of electrochemical sensors. This is followed by a summary of the current available electrochemical platform that studied biometal and neurodegenerative disease-related proteins (Chapter 2). Then, the antioxidative and rescue effect of PQQ against Cu(II) α-syn was studied. Based on circular dichroism and ROS detection assay results PQQ was effective at preventing Cu(II) induced α-syn aggregation (Chapter 3). We found, binding events between α-syn and metal or small molecules occur at the primary structure. Thus, a novel sensor platform was developed to study the α-syn-Cu(II) interaction variance caused by point-mutation on the α-syn sequence (Chapter 4). This result was in agreement with our isothermal titration calorimetry, (ITC) and x-ray photoelectron spectroscopy (XPS). Furthermore, this novel platform was able to be incorporated into a flow-injection system and demonstrate the binding between α-syn and PQQ occurs at the lysine residue (Chapter 5). Finally, in Chapter 6, a ferrocene-modified α-syn peptide fragment was employed to observe Cu(II) induced early misfolding events. Cu(II) was shown to cause α-syn conformation change and PQQ was able to revert the effect. Overall, this thesis proved the feasibility of using peptide fragments as a new approach to designing biosensors. With further development, this system will become a keystone tool in the search for the cure in PD.

Keywords: Bioanalytical chemistry
Biosensor
Electrochemistry
Parkinson's disease
Pyrroloquinoline quinone
α-Synuclein
Advisor: Kerman, Kagan
Emotion-related Processes in Children: Links to Aggression and Prosociality

Emotion-related processes are considered important for how children respond to social situations. This dissertation focuses on two key emotion-related processes: emotion recognition and physiological regulation. The goal of this dissertation is to gain a better understanding of when, how, and in what contexts these processes relate to children’s socio-emotional development. Studies 1 and 2 assess emotion recognition and physiological regulation to further understand how they individually relate to children’s socio-emotional development. Study 1 focuses on relations between physiological regulation—measured via resting respiratory sinus arrhythmia (RSA)—and prosociality in children. Specifically, this study addresses whether a “Goldilocks” (i.e., curvilinear) model more appropriately matches how physiological regulation is related to prosociality in children, as opposed to a linear relation. Study 2 focuses on how negative emotion (NE) recognition is linked to aggression, as opposed to externalizing problems more generally, in children within and across time. Emotion recognition and physiological regulation are closely anatomically and theoretically related, thus study 3 assesses their potential independent and interacting contributions to overt aggression. The findings suggest that NE recognition is important for understanding overt aggression, as opposed to non-aggressive externalizing problems, in early and middle childhood. Further, NE recognition subcomponents (insensitivity and misspecifications) were differentially related to distinct forms (reactive and proactive) of children’s overt aggression within and across time. Many of these relations were buffered in children with higher resting RSA. Lastly, moderate resting RSA was associated with increased prosociality in middle, but not early, childhood. Together, these findings suggest that (1) poor NE recognition is linked to increased overt aggression in children, (2) lower resting RSA is related to difficulties with prosociality and aggression, especially when combined with other emotion processing challenges (i.e., poor NE recognition), (3) relations differed based on whether relations were assessed concurrently versus longitudinally, and (4) some relations depended on the developmental period of the child. This research suggests that the importance of emotion recognition and physiological regulation depends on the age of the child and the time span assessed. Additionally, these processes interact with one another and may differentially affect prosociality versus aggression in children.

Keywords: Aggression
Childhood
Emotion recognition
Physiological regulation
Prosociality
Respiratory sinus arrhythmia
Advisor: Malti, Tina
E3 Ubiquitin Ligase Cbl-b deficient T cells resist Treg cell-mediated suppression and enhance anti-tumor immunity

Regulatory T cells are one of the integral components of the adaptive immune system that contribute to the regulation of anti-tumor T cell responses. However, studies have suggested that alterations in T cell signaling networks can result in T cells that are resistant to the suppressive effects of Treg cells. Here, we specifically investigated the role of E3 ubiquitin ligase Cbl-b in establishing T cell resistance to Treg cell-mediated suppression. First, we found that the absence of Cbl-b, a negative regulator of multiple TCR signaling pathways, rendered CD8+ T cells impartial to Treg cell-mediated suppression. Transcriptomic analyses suggest that pathways associated with cellular proliferation and cytokine production likely contribute to the observed phenotype. In particular, hyper-secretion of IFN-γ by Cbl-b deficient CD8+ T cells served as a novel mechanism which selectively renders CD8+ T cells less sensitive to suppression by Treg cells. We recapitulated our findings in a syngeneic murine model by first confirming that adoptively transferred tumor specific CD8+ T cells are susceptible to regulation by Treg cells. Unlike the wildtype counterpart, Cbl-b deficient CD8+ T cells were resistant to the suppressive effects of Treg cells in the tumor, and the therapeutic benefit of Cbl-b deficiency was abrogated upon IFN-γ blockade. Next we examined the effect of Cbl-b deficiency in CD4+ T cell compartment. Ablation of Cbl-b rendered CD4+ T cells impartial to Treg suppression by regulating cytokine networks leading to improved anti-tumor immunity despite the presence of Treg cells in the tumor. Specifically, Cbl-b deficient CD4+ T cells hyper-produced IL-2 and together with IL-2Rα upregulation served as an essential mechanism to escape suppression by Treg cells. In summary, our data highlight the role of Cbl-b deficiency and subsequent hyper-secretion of cytokines as a key mechanism which renders T cells resistant to Treg cell-mediated suppression. Such a strategy could be potentially incorporated in adoptive T cell therapy to generate robust effector T cell responses and anti-tumor immunity.

Keywords: Cancer immunology
Immuno-oncology
Immunotherapy
Regulatory T cell
T cell
Advisor: Ohashi, Pamela S
Computational Tools for Patient-specific Surgical Planning of Tetralogy of Fallot Repair

Surgical repair of the congenital heart defect Tetralogy of Fallot (TOF) involves a series of steps to remove right ventricular outflow tract (RVOT) and pulmonary artery (PA) obstruction. However, there is a large degree of geometric variability among TOF anatomies, and the most suitable repair strategy for a given patient is unknown preoperatively. The goal of this thesis is to further our understanding of the relationships between geometry and hemodynamics in the TOF patient population, as well as the patient-specific factors that may influence the choice of surgical repair strategy, using computational methods including computational fluid dynamics (CFD) simulations and virtual surgery techniques. Four studies make up this thesis: the first study presents a methodology to evaluate geometric parameters of the RVOT and PAs and applies this methodology to 11 postoperative TOF patients. Results showed significant variability within the dataset. The second study conducts a morphometric and statistical shape analysis of 16 postoperative TOF patients, as well as computational fluid dynamics (CFD) simulations on the patient-specific geometries. Results demonstrated a negative relationship between cumulative and maximum torsion and the energy efficiency of the geometry, highlighting the importance of avoiding the introduction of torsion during surgical repair. The third study virtually induces a range of stenoses on three TOF geometries to investigate the sensitivity of the efficiency of different anatomies to geometric modification. Results found differences in the peak efficiency across the patients, motivating the pursuit of patient-specific surgical repair strategies. Finally, the fourth study applies virtual surgery techniques to a preoperative TOF anatomy, to explore the effect of different surgical repair strategies on postoperative hemodynamics and efficiency. Results revealed significant differences in the postoperative pressure gradients and energy efficiency for the range of repair strategies, and enabled selection of the optimal repair technique for the patient. Overall, this thesis underscores the utility and benefit of computational tools for patient-specific, surgical planning of TOF repair. Including computational tools in this process has the potential to enable identification of the patient’s optimal surgical repair strategy preoperatively, reducing guesswork in the operating room and improving long-term outcomes for this patient population.

Keywords: Computational fluid dynamics
Tetralogy of Fallot
Virtual surgery
Advisor: Amon, Cristina
The Virus in the Garrison: Contagious Disease in Canadian Fiction

This dissertation analyzes Canadian representations of contagious disease in novels written after the emergence of HIV/AIDS. Ultimately, I argue that contagion in literature registers distinctive fears about the fluid and changeable nature of Canadian communities in an increasingly globalized world. Most existing scholarship on contagious disease in fiction considers contagion on a global or transnational scale, often in deference to the ease with which viruses cross borders. In contrast, my project contends that purely transnational considerations of disease risk flattening key differences in how national communities—particularly the imagined national communities present in literature—shape contagious diseases both physically and metaphorically. In a Canadian context, literary engagements with contagious disease are situated in a discursively unique environment informed by legacies of colonialism, globalization, and fraught national identity. This research stands as one of the first inquiries into the representation of contagious disease in contemporary Canadian fiction.Each of the chapters attends to one of three narrative motifs common in how Canadian authors deploy contagious disease in their fiction: contact, apocalypse, and mutation. Crucially, the texts under consideration all pair representations of contagious disease as metaphor with an awareness of contagious disease as embodied reality, a connection that speaks to the intersections of imagined community with lived experience. The first chapter, which considers Lee Maracle’s Ravensong duology, attends both to traumatic colonial contact and to the conditions necessary for more equitable forms of engagement. In the apocalypse chapter, I examine how Emily St. John Mandel’s Station Eleven and Nick Cutter’s The Troop engage with the fraught process of confronting precarity. In the final chapter, which centers on mutation, I argue that Margaret Atwood’s MaddAddam trilogy deconstructs the generic conventions of plague narrative in the service of a commentary on the limitations of narrative in disease contexts. Taken together, these texts chart deep anxieties about the outcomes of confronting the porous boundaries of imagined community on both metaphorical and embodied levels. This dissertation concludes by re- engaging the key claims made in the body of this project in light of the COVID-19 pandemic, finding evidence of further narrative shifts in representations of contagion.

Keywords: Canadian literature
Health Humanities
Medicine in Literature
Advisor: Goldman, Marlene
An Organ-on-a-chip Platform for Cardiac Fibrotic Disease Modeling and Pre-clinical Drug Evaluation

Myocardial fibrosis is a severe global health problem due to its prevalence in all forms of cardiac diseases and direct role in causing heart failure. The discovery of efficient anti-fibrotic compounds has been hampered due to the lack of physiologically relevant models that can faithfully replicate disease-related phenotypes. Herein, we propose the Biowire II platform as a powerful tool for cardiac disease modeling and pre-clinical compound screening. The disease model is constructed to recapitulate contractile, biomechanical, and electrophysiological complexities of fibrotic myocardium. Additionally, we constructed a heteropolar integrated model with fibrotic and healthy cardiac tissues coupled together. The integrated model captures the regional heterogeneity of scar lesion, border zone and adjacent healthy myocardium. Through precision phosphoproteomics analysis, the Biowire disease model provides a comprehensive profile of molecular pathways and targets involved in fibrosis remodeling. To set up an analytical system for the investigation of therapeutic targets and time-dependent biological actions in disease progression, we developed another modified model to recapitulate non-genetic cardiomyopathy. The long-term tissue cultivation and real-time functional readouts enable monitoring of both acute and chronic cardiac responses to Angiotensin II (Ang II), a key mediator in cardiac physiology. Along with mapping of cytokine secretion and proteomic profiles, this model presents an opportunity to quantitatively measure the dynamic pathological changes that could not be otherwise identified in conventional animal and 2D models. A further optimized screening strategy is used to evaluate compounds that target Ang II-induced cardiac remodeling. Through assessing the effects of different compounds, the drug screening data implicated multifaceted cardioprotective effects of relaxin in restoring contractile function and reducing fibrotic remodeling. Overall, this thesis provides an engineered platform where cardiac disease remodeling can be explicitly studied over the pathological process, thereby enabling the investigation of new disease mechanisms and the discovery of potential drug candidates.

Keywords: Cardiac fibrosis
Disease modeling
Organ-on-a-chip
Tissue engineering
Advisor: Radisic, Milica
Investigating the Therapeutic Potential of Targeting Kallikrein-related Peptidases in Inflammatory Dermatoses

Kallikrein-related peptidases (KLKs) are a family of 15 serine proteases with various (patho)physiological functions in the human body. KLKs are involved in the homeostasis and establishment of skin barrier integrity in human epidermis. Among the skin KLKs, KLK5 and KLK7 carry out key processes and are highly regulated by endogenous inhibitors. Dysregulated and unconstrained KLK5 and KLK7 activity and expression in the skin is detrimental. This has been observed in several inflammatory skin disorders, with increased KLK proteolytic activity causing inflammation via activation of pro-inflammatory receptors and pathways and breakdown of the essential epidermal barrier. Therapeutics targeted at regulating the disrupted KLK5 and KLK7 in inflammatory skin disorders may enable the restoration of physiological skin KLK activity and provide improved therapeutic benefits over current treatments focused on symptom alleviation. To that end, a drug discovery screening approach was conducted aimed at identifying small molecule inhibitors of KLK5 and KLK7 activity and expression. A screen of a kinase inhibitor library yielded no compounds capable of reducing KLK5 expression in human keratinocytes. A high-throughput screen of five chemical libraries led to the identification of a naturally occurring chemical compound called, Brazilin, which was capable of inhibiting KLK5 proteolytic activity with a Ki of 6.4 μM. In addition, a screen of a kallikrein-targeted library of chemical compounds led to the characterization of a 1,2,4-triazolo[1,5-a]pyrimidine (TP) heterocycle backbone as a KLK7-specific inhibitor. These TP structures display highly favorable characteristics for further drug development. There remains a need to better understand the mechanisms by which KLK5 causes inflammation and barrier disruption in inflammatory skin disorders. This would help to determine possible effects of KLK5 inhibition in human keratinocytes. Here we use MS-based proteomics to gain insight into the molecular events and mechanism that may lead to disease occurrence in those patients with unregulated KLK5 in the epidermis. To address this aim we utilized shotgun label-free quantification (LFQ) mass spectrometry to define the protein signature of the secretome in keratinocytes treated with KLK5. Keratinocytes appear to have a mechanism through which they try to regulate KLK cascade proteolytic activity and KLK5 can downregulate this response.

Keywords: Drug Screening
Inflammation
Kallikrein
Netherton Syndrome
Skin
Therapeutics
Advisor: Diamandis, Eleftherios P