VictorJuiz/thesis huggingface dataset:
Systematic Characterization of Human 14-3-3 Paralogs Reveals Highly Similar Interaction Specificities and Uncovers their Role as Chaperone-like Molecules
Keywords: 14-3-3
Chaperones
Mass-spectrometry
Microscopy
Phase separation
Protein interactions

Human 14-3-3 proteins are a family of seven highly conserved phospho-serine/threonine binding domains. They interact with hundreds/thousands of structurally and functionally diverse protein clients, thereby acting as central hubs of many signaling networks. However, how each 14-3-3 paralog differs in client specificity is not known for most clients because interaction specificity differences have never been quantitatively assessed on a large scale for the full complement of 14-3-3 paralogs. Furthermore, due to the lack of systematic functional screens, it is not known how most client proteins are regulated by 14-3-3s. Here, I used affinity purification coupled to mass spectrometry (AP-MS), proximity biotinylation (BioID2), and LUminescence-based Mammalian IntERactome profiling (LUMIER) to generate quantitative and directly comparable interactomes of all seven human 14-3-3 paralogs. I also used a high-content immunofluorescent imaging approach to uncover the effect of disrupting 14-3-3 interactions on client protein localization. The resulting networks revealed that all paralogs, with the exception of 14-3-3σ, have extremely similar or nearly identical interaction specificities. Furthermore, I found that loss of 14-3-3 binding leads to coalescence of a large fraction of clients into discrete foci or clusters in a client-specific manner, suggesting a central chaperone-like function for 14-3-3 proteins. Consistent with this, engraftment of 14-3-3 binding motifs to non-clients suppressed their aggregation or phase separation. This is also supported by the enrichment of features in 14-3-3 interactors that promote aggregation and phase separation. Finally, I showed that 14-3-3 proteins negatively regulate the localization of the RNA-binding protein SAMD4A to cytoplasmic granules and suppress its activity as a translational repressor. Ultimately, I was able to generate the most comprehensive framework for deciphering differences in interaction preferences between 14-3-3 paralogs. Furthermore, my work was able to greatly expand on the functional consequences of 14-3-3 binding in human cells, revealing that 14-3-3 proteins have a more prominent role as chaperone-like molecules than previously thought.
Takemitsu’s Solo Guitar Music Inspired by Visual Art: Informed and Imaginative Interpretation and Performance
Keywords: extra-musical
guitar
hermeneutics
interpretation
performance
Takemitsu

The guitar music of Japanese composer Tōru Takemitsu presents a unique contribution to the solo guitar repertoire. Like much of his creative output, his guitar music features some ambiguous inspiration from extra-musical sources. The purpose of this study is to uncover information on the connection between Takemitsu’s guitar pieces and the works of visual art for which they are named; additionally, this information is incorporated into a multi-level approach to interpretation and performance. The methods include first establishing an approach to the problem from the perspective of the performer through a framework built upon hermeneutic methods, literature on the role of the performer, performer’s analysis (John Rink), analogy of score as script, and reflections on the practice-based learning process on the guitar. The suggested approach is then applied to two case studies, Takemitsu’s All in Twilight (1987), and Equinox (1993). The approach includes producing translations of pertinent Japanese texts, conducting interviews with two professional guitarists (Tanenbaum and Fukuda), and investigating the artists Klee and Miró and the works of visual art after which each piece is named. The results show that for each case the viewing experience, evocation of the title, and aesthetic of the artwork inspired Takemitsu’s creativity. This manifested in various associations and references to concepts and fascinations of the composer, including the conflation of dream and water themes, nocturnal references, the subconscious mind, transitions of nature, the end of life, and the space between dualities of day and night, life and death, and sound and silence. The composer embedded these associations in part through intertextual reference to previous works of his own and those of major influences Messiaen and Debussy, with overlapping motivic material, contours, and harmonies. The results of each case study present an informed and imaginative interpretation, rather than an authoritative reading. The information on the visual artists, artworks, and extensive reflections on the technical execution of the pieces on the guitar may be used by students and professionals as a guide toward their own interpretations of the case-study pieces and further related works by this and other composers.
Making a Beautiful Difference: How Teachers Support Students with Learning Challenges in Rural Nepal
Keywords: Development
Education
Nepal
Schools
Special Education
Teachers

The growing demand for high-level English education in south Asia has created a network of private schools, promising better results and outcomes for students than local-language government schools. This in turn creates an expectation that all children should be able to access this type of schooling, and an environment where academic achievement is prioritized for a variety of complex reasons. Typically within these systems, students who did not succeed in school were pushed out early, or held back repeatedly over multiple years. However, with the global push to ensure access to education to all of the world’s children, children who struggle academically are spending more and more years in a classroom, despite their lack of perceived success. How do teachers support students who are struggling academically within a system which emphasizes academic achievement, and which measures success based on a strict series of exams? The purpose of this research was to explore the experiences of teachers in supporting students who struggle academically in a small community in rural Nepal, and explore the process of creating a positive model of support for students at the study school. I interviewed teachers and explored ideas related to the supports and barriers they faced in supporting struggling students, the value of education to their community, and the changes they felt were needed to better support students with learning challenges. I took a qualitative case study approach based in narrative and ethnographic traditions, and collected data through individual interviews and group discussions with the participants, as well as through the analysis of field texts, including the use of reports, journals and photographs. I analyzed the data using thematic analysis and organized in relation to an initial, and then revised, conceptual framework that included a variety of influences impacting the teachers in their work. I used narrative and story throughout to contextualize and discuss the findings, and discuss implications for theory, practice and further research.
Acquiring Information from Bayesian Surprise in Cognitive Linear Gaussian Dynamic Systems
Keywords: Autonomous systems
Bayesian surprise
Cognitive linear Gaussian dynamic systems
Cognitive radar
Expectation of Bayesian surprise
Surprise-based internal rewards

The development of autonomous systems (AS) requires cognitive entities capable of acquiring information, learning, planning, and reasoning that eventually adapt to environmental uncertainties. Since surprising events encourage learning and information-seeking in biological agents, this research suggests surprise as the intrinsic motivator to design cognitive dynamic systems undergoing autonomous behavior. Amongst several definitions of surprise, this thesis proposes the Bayesian surprise to express information utility and to guide novelty acquisition from uncertain measurements by considering the impact of new data on changing prior beliefs. By adopting Gaussian noise-driven linear dynamic models to represent the environment, the Bayesian surprise drives the system to estimate future environmental states from noisy measurements and execute a decision to minimize the estimation error over time. This research implements a novel planning algorithm, where the system computes the contribution of prospective actions---which are available from a library---to state estimation and selects the one that maximizes the expectation of Bayesian surprise. Theoretical analysis shows that the action corresponding to the highest expectation of Bayesian surprise conveys the maximum information and reduces the state estimation error. Furthermore, a learning and planning algorithm is derived by intrinsically assigning novel rewards which are developed based on the expectation of Bayesian surprise. This thesis proposes reward functions inspired by credibility measures in estimation/control theory to evaluate the consequences of past actions. The performances of the proposed algorithms are compared to the state-of-the-art for numerous experiments. For a cognitive linear Gaussian dynamic application (i.e., cognitive radar), results show that the proposed planning algorithm outperforms its competitors with respect to the mean square relative error when one-step and multiple-step planning are considered. In comparison to alternative methods, the learning and planning algorithm implemented by the proposed surprise-based rewards significantly improves the state estimation performance. Also, results indicate that multiple-step planning does not necessarily lead to lower error, mainly when the environment changes abruptly.
Structural and Mechanistic Characterization of Type II-C Anti-CRISPR Proteins
Keywords: anti-CRISPR
Cas9
CRISPR-Cas

The CRISPR-Cas adaptive immune system provides bacteria with defence against phage predation.CRISPR-Cas systems use protein-RNA complexes to cleave and eliminate invading phage genomes in a sequence specific manner. Phages have evolved a countermeasure through the expression of small protein inhibitors against CRISPR-Cas called “anti-CRISPRs”. Anti-CRISPR proteins use incredibly diverse mechanisms to either bind directly to or enzymatically modify Cas proteins to prevent cleavage mediated by CRISPR-Cas. CRISPR-Cas enzymes, especially Cas9, have been repurposed in many biotechnologies including genome editing. Anti-CRISPRs have potential to be utilized as “off-switches” for CRISPRCas9 gene editing, addressing safety and ethical concerns for the technology. Since their discovery in 2013, over 90 protein families of anti-CRISPRs have been reported, with 37 being inhibitors of Cas9 specifically. However, much of the mechanistic details of the anti-CRISPR proteins are left incomplete. In this thesis work, I characterize the inhibitory mechanisms of two CRISPR-Cas9 inhibitors, AcrIIC4 and AcrIIC5, using structural biology and biochemical and biophysical assays. I demonstrate that AcrIIC4 inhibits the DNA cleavage activity of Cas9 by binding to the REC2 domain of Cas9 and preventing the conformational changes required for Cas9 to switch into the active state, while AcrIIC5 inhibits Cas9 from binding to target DNA using DNA mimicry. The inhibitory mechanisms elucidated in my thesis work can be applied to the potential development of AcrIIC4 and AcrIIC5 for biotechnological purposes. This work also expands our knowledge of the vast arsenal phages have evolved to circumvent CRISPRCas defence.
Evidence for Somatosensory Facilitation during Object Reception and Action Observation
Keywords: Action
Action Observation
Social Touch
Somatosensory
Touch

Previous research on somatosensory and tactile processing related to movement has focused on somatosensory and tactile suppression as well as the modulating factors that contribute to this suppression. However, there is a large discrepancy between the understanding of the factors that influence somatosensory and tactile suppression vs. the factors that influence somatosensory and tactile facilitation. Therefore, the aim of the dissertation was to unravel some of the factors related to the facilitation of somatosensory and tactile processing. Study 1 specifically addressed whether the expectation of tactile feedback utilization would lead to tactile facilitation during an object reception task. The results showed that tactile perception was improved as the object approached an individual’s hand and even when the individual only had the expectation of contact (i.e., when the object unexpectedly stopped short of the hand). Study 2 specifically addressed whether observed moment speed influenced tactile processing during action observation. The results showed that tactile perception was improved when observing slow reaching and grasping movements but not when observing higher movement speeds. Study 3 specifically addressed whether somatosensory processing was influenced by the speed of observed social touch interactions. The results showed that the difference in the speed of the interaction led to a greater change in somatosensory processing when observing ball-to-hand vs. ball-to-leaf-contact. Overall, the dissertation provides novel evidence for the facilitation of somatosensory and tactile processing in anticipation of tactile feedback utilization, with kinematics as a modulating factor when observing action and social touch interactions.
Talking Back: An Exploration of Negative Self-Talk in Undergraduate Voice Majors
Keywords: Meditation
Mindfulness
MPA
Music
Performance
Self-Talk

This research centers on the experience of negative self-talk in undergraduate voice majors. The research questions are (1) How prevalent is negative self-talk in individual singers? (2) Why do students experience negative self-talk? (3) How does negative self-talk impact the wellbeing of this population? And (4) Can mindfulness-based meditation serve as an effective intervention in reducing the effects of negative self-talk? To answer these questions, a multiple case study was designed alongside an eight-week mindfulness-based intervention. Five undergraduate student participants were sent an email once a week for eight weeks, which included introductions to mindfulness concepts and audio files of guided meditations, which they were to practice daily. During these eight weeks, each student participated in a series of three interviews and completed questionnaires relating to music performance anxiety, self-efficacy, and mindfulness following “high stakes” performances of their choosing. In Chapter 1 of this dissertation, I present my own experience with negative self-talk in performance, and in Chapter 2, I review the current literature on Music Performance Anxiety (MPA), self-talk, and wellbeing. I present my research design and intervention in Chapter 3 and describe the five participant case studies in Chapter 4. I provide within-case and cross-case analyses in Chapter 5. In the cross-case analysis, four themes emerged: 1) Cognitive manifestations of performance anxiety; 2) Comparison; 3) Over-analyzing; and 4) Increased mindfulness. Following the eight-week intervention, overall awareness around performance and performance process increased, a deeper connection to breath was developed, and greater overall acceptance was gained. Chapter 6 contains a discussion of limitations and future directions for this research. Given the results of this and similar studies, I suggest that music educators consider adding mindfulness practices into their curriculum to enhance both the performance experience and overall wellbeing of student musicians. This intervention took place during the COVID-19 pandemic, which is discussed throughout.
Synthesis and Characterization Of Cellulose Nanocrystal Based Rod-Like Nanoparticles For Investigation Of Surface Chemistry Effects On Cellular Internalization of Nanoparticles
Keywords: cellulose
CNC
nanoparticles
ovarian cancer
polymers

Cellulose nanocrystals (CNCs) are biocompatible, non-toxic nanoparticles with many surface hydroxyl functionalities available for chemical modification. In this thesis, I describe the modification of CNCs for applications in the investigation of how nanoparticles interact with cancer cells. I modify CNCs with benzaldehyde functionalities as reactive handles for conjugation with hydrazinonicotinamide-modified polymers via a bisarylhydrazone. I first describe the sequential epoxidation and amination of pristine CNCs and carry out analysis of the effects of the reaction conditions. I then describe the synthesis of mPEG-PGlu(DOTA)-HyNic polymers using three different lengths of mPEG. The final polymer modification I describe is that of Folate-PEG-HyNic. In a final synthetic step, I conjugate the HyNic polymers to the CNC-aldehyde in a UV-Vis quantifiable reaction generating four CNC-polymer conjugates: CNC-PEG2K, CNC-PEG3K, CNC-PEG11K, and CNC-Folate. In this thesis, I describe careful and systemic study of the many synthetic steps. My interest in synthesizing these CNC-polymer conjugates was as potential drug delivery vehicles and for a systematic investigation of the effects of nanoparticle surface chemistry on cellular internalization. Surface chemistry effects were analyzed by measuring the median fluorescent intensity by flow cytometry of cell populations incubated with fluorescein-labelled CNC-polymer conjugates. The effects of PEG length were investigated using the CNC-PEG2K, CNC-PEG3K, and CNC-PEG11K conjugates upon incubation with two ovarian cancer cell lines, SKOV3 and HeyA8. I found that cellular internalization decreased with increased PEG block length for each of the cell lines. Additionally, I was able to use the same two cell lines to investigate active vs passive targeting of nanoparticles to cells as HeyA8 has low folate receptor expression whereas SKOV3 has high folate receptor expression. I found that the amount of nanoparticles internalized by and adhered to SKOV3 was higher for the actively targeted conjugate (CNC-Folate) than for the passively targeted conjugate (CNC-PEG2K). Finally, I used trypan blue incubation experiments to distinguish CNC conjugates adhered to the cell surface from those that were internalized. The results described in this thesis add to the conversations about CNC modification and characterization as well as the requirements for effective nanomedicines.
Canada's Hot Little Prophet?: Walt Whitman, Richard Bucke, Psychiatry, and Metaphysical Religions in Nineteenth-Century Ontario
Keywords: Cosmos
History of Medicine
History of Psychiatry
Metaphysical Religion
Study of Religion

My dissertation focuses on the friendship between the Canadian psychiatrist and superintendent for the London Asylum for the Insane, Dr. Richard Maurice Bucke and the American poet, Walt Whitman. I situate their adaptation and reimagining of a Christian ideology to suit their psychiatric and poetic needs within nineteenth-century interrelatedness of Christian, medical, psychiatric, and new metaphysical religions. The physical body is known through observation and experimentation, which then creates a “neutral” body from which other bodies can be adjudicated. This “neutral body” becomes an unnecessarily complex or impractical mechanical device that is often poorly constructed and even dangerous. In other words, both Bucke and Whitman embed a sense of Christian ideology into the physical bodies of those they are either diagnosing or writing about. The first chapter of my dissertation provides a literature review including relevant literature from the study of religion in regard to new metaphysical religions, science, and the relationship between religion and the secular. I also provide an overview of the literature regarding nineteenth-century asylums as well as the relevant literature on Bucke and Whitman. My second chapter provides an overview of the relationship between the history of new metaphysical religions and psychiatry. The bulk of my analysis comes in chapters three and four where I go in-depth regarding the relationship between Bucke and Whitman, how their ideas of religion impacted each other and their own works respectively. Finally, I examine their conceptions of religion and the body through the framework of the Cosmos. Ultimately, I argue that both Whitman and Bucke create distinct (but complementary in their consequences) conceptions of Cosmos due to a shared, Christian centred, ideological framework. Further, imagining bodies as having cosmic potential like Whitman and Bucke do, allows them to maintain their positions of authority as the science and discourse revolving around gendered and racialized bodies changes.
Security Enhancement of Power Transformer Differential Protection
Keywords: adversarial training
anomaly detection
cyber-physical security
machine learning
smart grid
trustworthy machine learning

The growing use of information and communication technologies information and communication technologies (ICTs) in power grid operational environments has been essential for operators to improve the monitoring, maintenance and control of power generation, transmission and distribution, however, at the expense of an increased grid exposure to cyber threats. Information technology (IT) and operational technology (OT) convergence has incentivized hackers to trigger more attacks on cyber-physical systems in recent years. This has resulted in more global investment on cybersecurity. Moreover, the amount of data flow in such systems is beyond human supervision capabilities. Hence, data driven methods provide a wealth of opportunities to enhance cybersecurity. Of specific interest, we focus on the use of machine learning in an IT/OT converged environment for the purpose of intrusion detection, an essential step in cyber-physical grid security due to the complex nature of emerging power systems. We focus on the IEC 61850 substation environment, which lies at the heart of IT/OT convergence. This thesis first searches for the optimized models using applicable neural network architectures and compares their performances. The results of hyperparameter tuning are used to propose universal models for all types of faults for each architecture for IEC 61850 transformer protection relays. Next, an adversarial training method is proposed to enhance the security of the models. The performance of the models before and after adversarial training is compared. The results are used to propose the best model for enhancing the security of the transformer protective relays. Then, a black-box attack framework is proposed to study the capability of the attacker to conduct a successful attack without knowing the model parameters.