VictorJuiz/thesis huggingface dataset:
VEPH1 Modulation of the BMP Signaling Pathway: Effects on Cadherin Levels and Cell Migration

VEPH1 is an 833-amino acid adaptor protein containing a conserved C-terminal PH domain. It has been implicated in the modulation of the TGF-β and mTOR signaling pathways, which are heavily involved in cancer progression through the promotion of EMT. EMT is a program of steps cancer cells undergo to metastasize to secondary sites, involving the downregulation of epithelial polarity and cell-cell adhesion, and upregulation of mesenchymal characteristics. A key event is the repression of the cell adhesion molecule E-cadherin by the SNAI1/2 family of transcription factors, which are, in turn, regulated post-translationally by GSK3β-mediated degradation. VEPH1 was previously shown to interact with the TGF-β type I receptor (TβRI), ALK5, and inhibit downstream SMAD2/3 signaling. VEPH1 was also predicted to interact with BMP signaling pathway members SMAD1, ALK2 and ALK6. The TGF-β/BMP superfamily regulate development, immunity and tumorigenesis through SMAD and non-SMAD pathways. The objective of my study was to investigate the impact of VEPH1 on BMP-SMAD signaling and BMP-induced changes in proliferation and migration. I hypothesized that VEPH1 modifies BMP4 canonical signaling via a physical interaction with SMAD1 and/or type 1 receptors ALK3 or ALK6. VEPH1 inhibited BMP4-induced SMAD1/5 phosphorylation and SMAD1 nuclear accumulation in HepG2, SKOV3 and ES2 cells. A positive effect on basal nuclear SMAD1 levels in SKOV3 cells suggests VEPH1 could modulate SMAD1 distribution. Cell line-specific effects of VEPH1 were observed on BMP gene target transcript and protein levels. VEPH1 decreased SNAI1 protein levels in HepG2 cells, which was consistent with N-cadherin-to-Ecadherin switching, resembling MET, and reduced migration and increased aggregation, as well as decreased GSK3β phosphorylation levels. In SKOV3 cells, VEPH1 increased AKT phosphorylation levels and SNAI2 protein levels, which correlated with a decrease in E-cadherin and augmented migration. VEPH1 also decreased basal and BMP4-induced cell culture growth in HepG2 and SKOV3 cells. Although a physical interaction of VEPH1 was not observed with either SMAD1 or ALK3, novel ALK5-mediated BMP4-SMAD1 signaling was identified for SKOV3 cells, along with ALK3 signaling. This study provided cell-specific models for a VEPH1 effect on BMP-dependent and –independent cancer progression, further highlighting its role as a modulator of cancer signaling pathways.

Keywords: BMP4
Cadherin
Cancer
EMT
SMAD1/5
VEPH1
Advisor: Brown, Theodore J.
New Results in Model Theory and Set Theory

Traditionally, the role of general topology in model theory has been mainly limited to the study of compacta that arise in first-order logic. In this context, the topology tends to be so trivial that it turns into combinatorics, motivating a widespread approach that focuses on the combinatorial component while usually hiding the topological one. This popular combinatorial approach to model theory has proved to be so useful that it had become rare to see more advanced topology in model-theoretic articles. Prof. Franklin D. Tall has led the re-introduction of general topology as a valuable tool to push the boundaries of model theory. Most of this thesis is directly influenced by and builds on this idea. The first part will answer a problem of T. Gowers on the undefinability of pathological Banach spaces such as Tsirelson space. The topological content of this chapter is centred around Grothendieck spaces. In a similar spirit, the second part will show a new connection between the notion of metastability introduced by T. Tao and the topological concept of pseudocompactness. We shall make use of this connection to show a result of X. Caicedo, E. Due˜nez, J. Iovino in a much simplified manner. The third part of the thesis will carry a higher set-theoretic content as we shall use forcing and descriptive set theory to show that the well-known theorem of M. Morley on the trichotomy concerning the number of models of a first-order countable theory is undecidable if one considers second-order countable theories instead. The only part that did not originate from model-theoretic questions will be the fourth one. We show that ZF+DC+“all Turing invariant sets of reals have the perfect set property” implies that all sets of reals have the perfect set property. We also show that this result generalizes to all countable analytic equivalence relations. This result provides evidence in favour of a long-standing conjecture asking whether Turing Determinacy implies the Axiom of Determinacy.

Advisor: Tall, Franklin D
Eye Biometrics Signal Analysis and Potential Applications in User Authentication and Affective Computing

As the adoption of biometric technologies grows, there is an escalating worry regarding the potential for bypassing, disguising, or replicating biometric data. Established biometric methods, such as facial recognition and fingerprints, are susceptible to these forms of drawbacks, undermining their core objective, which is to use physical traits for reliable deployment. This thesis proposes utilizing eye biometric signals (eye movement and pupillometry) for identifying individuals and recognizing affective states. Eye biometric signals are critical biological signals that inherently incorporate liveliness verification and resist counterfeiting due to their distinctive nature. However, utilizing eye signals as a biometric is challenging because recordings from the same person can vary due to factors like background noise, physical exertion, and emotions. While variations due to noise and physical activity can be managed through proper pre-processing and feature extraction techniques, the influence of psychological factors on eye biometric signals is more complicated to handle. This thesis deals with this problem from an affective computing point of view. First, the thesis pinpoints the psychological conditions that can influence the eye signals which, consequently, threaten the precision of its deployment in various applications. It outlines experimental arrangements purposely designed to induce active and passive arousal as well as positive and negative valence. A data-driven model serves as the foundation for detecting emotional patterns after tailoring the model for eye biometric signals. The results demonstrate the identification of psychological/affective states that affect eye biometrics to a degree that may render biometric matching unreliable. Three application scenarios are examined: a) user authentication, b) affective/emotional state recognition, and c) Post-traumatic Stress Disorder (PTSD) detection. The developed models are tailored to suit each context, and the pros and cons of each setup are explored. Additionally, to improve the utility of these emerging modalities, a multimodal framework is introduced that combines facial expressions and pupillometry. Finally, this thesis introduces a study that investigates the existence of bias with eye biometric signals and identifies the different factors that affect modality performance. Overall, this thesis endeavors to develop the necessary algorithms and practical infrastructure for effectively employing eye biometric signals in real-world biometric systems.

Keywords: Affective Computing
Biomterics
HCI
Machine Learning
User Authentication
Advisor: Hatzinakos, Dimitrios
Exploring the Potential of Software-Defined Networking for Smart Grid Automation: A Cyber-Physical Systems Approach

With the emerging concept of smart grids integrating renewable energies and the emergence of connected devices. The power grid is becoming increasingly dependent on underlying communication infrastructure. Concerns about the cybersecurity and resilience of power systems have heightened in electric utilities and regulatory agencies over the past decade mainly because of the unpredictable target, location and scale of cyberattacks and the potential severity of consequences. The cyber vulnerability of power grids is on the rise by the emergence of smart grid technologies increasingly reliant on the communication infrastructure. This underlines an imminent need for the modelling and examination of power grid vulnerabilities to cyber-physical attacks. \par This thesis provides an in-depth analysis of the operational vulnerabilities in Energy Control Systems (ECS) to cyberattacks, spanning from the fundamental protection level operating in a Local Area Network (LAN) to the advanced Supervisory Control and Data Acquisition (SCADA) level functioning within a Wide Area Network (WAN). To facilitate this analysis, a co-simulation platform bridging Information Technology (IT) and Operational Technology (OT) simulators was developed, focusing on the vulnerability assessment of communication-assisted protection schemes (CAPS) to cyberattacks. The research underscores the pressing requirement for a more resilient communication infrastructure to fortify power system protection. In response to this need, Software-Defined Networking (SDN) was incorporated into the co-simulation platform, which remarkably enhanced the resilience of CAPS against cyberattacks. As a result, the co-simulation platform was further optimized to explore the potential of SDN in strengthening the resilience of the SCADA system operating within the WAN. SDN capabilities are leveraged to propose an innovative IT/OT intrusions Detection System that improves the resilience of Telecontrol commands. Later, SDN with Genetic Algorithm is proposed as an alternative to the standard MPLS infrastructure used in Wide Area Networks. Our results demonstrated that SDN-GA significantly improves the resilience of physical systems as it can promptly respond to dynamic changes within large-scale networks. Ultimately our thesis shows that Software Defined Networking capabilities significantly improve the resilience of smart grid automation at every level of the ECS infrastructure.

Keywords: Communication networks
Cybersecurity
Smart-Grids
Advisor: Kundur, Deepa DK
Models of Elite and Equipotent Dynamics in Cellular Reprogramming and Cancer Growth

Recent advances in lineage tracking using DNA-based barcoding technologies have provided new insights into the developmental dynamics of cell populations. Understanding factors that determine the appearance and disappearance of individual lineages and their derivatives in dynamic, heterogeneous systems has broad implications for normal and aberrant tissue development, providing a new lens to understand behaviours in multicellular systems. This thesis develops models of cellular dynamics in two biological contexts: cellular reprogramming - wherein the stem-like capacity to differentiate into multiple types of cells is restored to cells that were differentiated; and cancer tumor growth during chemotherapy treatment. The reprogramming field has largely accepted the “clonal equipotency” paradigm, where somatic cells have an equal potential to attain a stem-cell like state. I use stochastic modelling to demonstrate that the equipotency hypothesis does not agree well with lineage tracking data, and propose a non-neutral model of reprogramming. In this model, an elite class of lineages with higher fitness better explains experimental data and is supported by evidence that cells differentiating from the neural crest have an increased propensity to reprogram. In the context of cancer tumor growth during chemotherapy treatment, I discuss my contributions to work where we combined cellular barcoding and mathematical modelling to better understand patient-derived colorectal cancer growth. Although mutation-driven drug tolerance can arise in cancer tumors, there is increasing evidence that non-genetic processes also drive drug tolerance. Drug tolerant persister (DTP) cells have been identified across a wide range of tumors in response to both chemotherapy and targeted agents. Some work suggests that only a subpopulation of lineages possesses the capacity to persist through. Barcode analysis revealed no loss of clonal complexity of tumors that entered the DTP state and recurred following treatment cessation. Our mathematical model demonstrates that all cancer cells, not only a small subpopulation, possess an equipotent capacity to become DTPs. I conclude with a discussion of genetic barcoding and sequencing methods, modelling the process to better quantify the limitations of accuracy introduced by different experimental parameters. I propose a lineage assignment protocol that can increase the amount of data available without compromising lineage assignment accuracy.

Advisor: Goyal, Sidhartha
Autonomous Operation and Control of a Mixed-Source Microgrid with Grid-Forming Converters

This thesis investigates the suitability of existing converter control schemes to operate a mixed source microgrid. Dynamic modeling in state space is used to demonstrate that inverse droop control is the best existing method for microgrid operation, exhibiting superior voltage and frequency quality when faced with common disturbances. This thesis subsequently proposes a new algorithm to autonomously operate a mixed-source microgrid – the remote field-oriented synchronous drive. The remote field-oriented drive operates alongside existing governor and exciter controls to rapidly damp microgrid voltage and frequency dynamics even during severe disturbances such as the line-start of a large induction motor or a three-phase grid fault. The proposed algorithm also supports a proposed supervisory control scheme which allows the mixed-source microgrid to connect to a larger transmission network and participate in various power systems operation schemes. The relative performance of existing converter control schemes as well as the proposed remote field-oriented drive is validated using a detailed hardware-in-the-loop simulation consisting of a PLECS RT-Box and external digital controllers. HiL simulations show that the proposed remote drive exhibits a near 10-fold improvement in transient frequency regulation and a near 2-fold improvement in transient voltage regulation during various loading contingencies when compared to traditional governor/exciter controls. The proposed algorithm is also shown to eliminate the subsynchronous shaft speed oscillations seen when using existing converter control schemes. Finally, the proposed algorithm is shown to allow a mixed-source microgrid to seamlessly synchronize with and subsequently operate within a larger transmission network, actively regulating the power flow between the microgrid and transmission network without requiring any structural or parametric changes to converter-side controls.

Keywords: Grid-Forming Converters
Microgrid
Mixed-Source Microgrid
Remote Drive
Synchronous Generators
Advisor: Lehn, Peter W
Neobarroco en la literatura latinoamericana del siglo XX

This research examines the baroque attributes, elements, and modes in the works of three Latin-American authors mainly, but not exclusively, from the theoretical perspective of Cuban writer and critic Severo Sarduy (1937-1993), who articulates a baroque supported, on the one hand, on affectation and parody —intertextuality and intratextuality being its main components— and on the other, on a subversive and disruptive spirit, the origins of which go back to the astronomical postulates of Johannes Kepler and the effects or resonances that they continue to produce in the history of thought, including literature. In Chapter 1, I analyze the novel La guaracha del Macho Camacho (1976) by Puerto Rican writer and playwright Luis Rafael Sánchez (1936-), using the theory Sarduy develops in his essay “The baroque and the neobaroque”, which connects the Latin-American neobaroque with affectation and parody, while also exploring the thematic and narrative decentering in the text using one of the six manifestations of the Keplerian ellipse proposed by Sarduy in his book Barroco. My goal is to locate the different ways in which this approach helps in reading Sánchez’ novel as a critique of simple or commonplace ways of interpreting Puerto Rico’s reality. Chapter 2 focuses on the 1978 novel Casa de campo by Chilean writer José Donoso (1924-96). I examine the plurality of the point of view and narrative modes in the novel, an overlooked aspect of its neobaroque aesthetic. I argue that the playfulness and plurality of points of view and narrative modes in the book constitute Donoso’s revolt against contemporary literary conventions and exemplify the rebelliousness and diversity of the neobaroque. Finally, in Chapter 3, I propose that if the retombée of the Keplerian ellipse can reach and impact any type of thought, like Sarduy claims, that would include the ethical sphere. This chapter proposes the presence of a neobaroque ethics —supported by the so-called “intelligent” emotions and what Spanish philosopher Antonio Marina labels “creative intelligence”— in the detective short story “La nota roja que no existió” (1988) by Mexican-Argentinian writer Myriam Laurini (1949-).

Keywords: Jose Donoso
Luis Rafael Sanchez
Myriam Laurini
Neobaroque
Neobarroco
Severo Sarduy
Advisor: Sarabia, Rosa
Times of Uncertainty and Future Projections for Forced Migrations: The Case of Syrian Refugee Mothers and Youths in Canada

Migration scholars have recently been focusing on temporality as a distinct phenomenon of the migratory process. In this dissertation, I produce new knowledge on the temporal dimensions of forced migration by asking: how does time work with space to shape forced migrants’ experiences after resettling in the host country? Taking the important case of Syrian refugee families in Canada, I explore —in four chapters— how mothers and teenagers experience time and uncertainty, and perceive past, present, and future following their resettlement. I draw on two waves of in-depth interviews with 41 mothers during their first year of resettlement (2016-2017) and three waves with 20 additional mothers between 2018 and 2021. I also draw on in-depth interviews with 25 teenagers. First, I demonstrate the importance of examining refugee mothers’ future projections in the first year of resettlement and considering a cultural and religious dimension of future projection. I put forward two novel concepts (“foreclosed futures” and “entangled timelines”) that capture mothers’ future perceptions during this initial period. Second, I demonstrate the ways in which mothers’ language learning process in the host country shapes their temporal experiences beyond the first year of resettlement. I analyze the different ways in which mothers find themselves “stuck” in the present, where multiple structural barriers and individual challenges significantly slow down their language acquisition process and prevent them from achieving other goals. The conflict between government expectations for the long-term future and participants’ immediate priorities underscores how language, space, and time co-construct notions of the future. Moreover, I examine how age and life stage at the time of migration shape these teenagers’ temporal experiences in the host country. I analyze two different trajectories for refugee teenagers: those who arrived as children in the earlier waves now experience a “slow present,” while recently resettled older teenagers experience a “tense present.” Lastly, I discuss two innovative methods used in my research with refugee teenagers, including “collective interviewing” and the “timeline-drawing” activity, which have allowed participants to be more creative in narrating their stories and trajectories. Ultimately, these findings suggest that scholarship on forced migration may continue to benefit from attention to how time and temporal experiences shape newcomers’ lives.

Keywords: MENA
migration
mothers
Syrian refugee crisis
temporal
youth
Advisor: Milkie, Melissa
Maghbouleh, Neda
Faculty Perspectives about the Impacts of Implementing Indigenous Content at Humber College in Ontario, Canada

This qualitative, multi-method study examined course outlines through a Qualitative Document Analysis (QDA), which then led to the Qualitative Interviews (QI) of faculty members who taught Indigenous content within their academic courses. The initial analysis focused on 180 course outlines from 8 different academic programs in the Faculty of Social and Community Services at Humber College. Degree and diploma program course outlines were included in the analysis, which was centred on locating Indigenous content within each of the 8 academic programs. The QI explored the perspectives of 12 professors in the Faculty of Social and Community Services at Humber College who had taught courses that had embedded Indigenous content. These interviews sought to understand the perspectives of professors about the challenges, success, and motivations to include Indigenous content in their curricula. Through the QDA and QI, critical themes were uncovered, and emphasized the importance of the relationships developed within the classroom setting between professors and students, and the diverse culture that each post-secondary classroom offers learners. Each academic program contained a different level of Indigenous content, and the professors offered critical insights into what content was taught and what the impacts of this learning were within the classroom. The professors who had integrated Indigenous content into their pedagogy and curricula demonstrated Culturally Responsive Teaching practices and were engaged in a variety of ways with Indigenous content and the 94 Calls to Action of the Truth and Reconciliation Commission. Professors’ approaches to teaching and learning, commitments to social justice, and interest in the decolonization and Indigenization of curricula had the most significant impacts on the implementation of Indigenous content.

Keywords: critical whiteness theory
culturally responsive teaching
faculty motivation
focused curriculum
Indigenous content
student development theory
Advisor: Waterman, Stephanie