VictorJuiz/thesis huggingface dataset:
Viral Infectivity Factors of Human Immunodeficiency Viruses: Functional Convergence Through Structural Divergence
Keywords: APOBEC
biophysics
HIV
protein-protein interactions
structural biology
viral infectivity factor

The human immunodeficiency virus (HIV) causes the acquired immunodeficiency syndrome. Both HIV type 1 (HIV-1) and HIV type 2 (HIV-2) viruses encode for a powerhouse protein named viral infectivity factor (Vif). The HIV Vif encodes for several functionalities that are collectively aimed at disarming an immunological pathway in humans. The apolipoprotein B mRNA-editing catalytic polypeptide-like 3 (APOBEC3/A3) proteins embody this immunological pathway through their nucleic acid mutator activities that inactivate viral genomes. The HIV Vif is the “annihilator” of A3 proteins, since Vif is an E3 ubiquitin ligase substrate receptor that targets A3 proteins for poly-ubiquitination and degradation. The HIV Vif mediates its functionalities through structural determinants located in N- or C-terminal domains. The Vif C-terminal domain interfaces with Elongin B-Elongin C complex (EloB-EloC), and Cullin 5 (Cul5). Vif interactions with EloB-EloC and Cul5 link Vif to the ubiquitination machinery. The Vif N-terminal domain interfaces with A3 proteins using determinants unique to each A3 protein. For a VifN-term-A3 interface to form, Vif conformations need be stabilized via interactions with another protein called core-binding factor β (CBFβ). VifN-term-CBFβ interactions enhance Vif stability and are indispensable for other Vif-protein interactions. The HIV Vif protein acts as a structural hub that nucleates protein-protein interactions required for targeting A3 proteins. The present dissertation employed biochemical, biophysical, and structural methods to study structure-function relationships of HIV-1 and HIV-2 Vif proteins. HIV-1 and HIV-2 viruses have disparate evolutionarily histories and their respective Vif proteins have divergent sequences. Functionally, HIV-1 and HIV-2 Vif have converged (since both target A3 proteins). Structurally, we have begun to discover their differences. In the present dissertation, we generated the first soluble HIV-2 Vif species suitable for in vitro and structural studies. Additionally, we studied Vif-CBFβ, Vif-A3, Vif-Cul5, Vif-[EloB-EloC] and Vif-Vif interactions for HIV-1 Vif and/or HIV-2 Vif. We attempted crystallographic and microscopic studies of various Vif species and made key advances. Notably, we have now initiated cryo-electron microscopic studies of a self-associating HIV-2 Vif-CBFβ-EloB-EloC-Cul5 pentameric complex. Collectively, our studies revealed that HIV-1 and HIV-2 Vif proteins evolved divergent structures that bring about the same ultimate outcome – eliminating human A3 proteins.
Phage Display for the Development of Synthetic Antibodies Targeting Receptor Tyrosine Kinases
Keywords: Antibody
Cancer
Immunotherapy
Phage Display
Protein Engineering
Receptor Tyrosine Kinase

Receptor tyrosine kinases (RTKs) are single-pass transmembrane receptors that drive the growth and development of human tissue from embryo to adult. Overexpressed RTK family members are present on the surface of cancer cells, making them susceptible to targeting by therapeutic IgGs, molecules that exhibit high affinity and specificity, the ability to recruit the immune system, and the ability to disrupt RTK signaling. Two RTK sub-families, the Eph and ErbB families, have previously been linked to cancer development and progression. Epidermal growth factor receptor (EGFR), the first RTK discovered and a member of the ErbB family, has been extensively validated as tumourigenic and has been the target of four approved therapeutic IgGs. Unfortunately, resistance to existing therapies is common and occurs in 70-90% of patients. Conversely, the Eph receptor family, represented by EphA2 and EphA3 in this study, has been suggested to be either oncogenic or tumour-suppressive, and lacks approved therapeutics. The goal of this project was to examine the epitope-specific effects of these receptors through targeting with high affinity IgGs. I constructed RTK-biased phage-displayed Fab libraries and utilized them to develop hundreds of antibody clones, which were screened for optimal therapeutic and research characteristics. In the first data chapter, I describe the development of anti-Eph receptor IgGs and accompanying proliferation experiments on pancreatic and ovarian tumour cell lines expressing EphA2 and EphA3. I show that cellular Eph receptor context is critical in determining the pharmacological and proliferative response to Eph receptor antagonism, where co-targeting of EphA2 and EphA3 is the most effective therapeutic modality for the treatment of cancers expressing both receptors. In the second data chapter I present the development of two anti-EGFR IgGs, one that targets the same domain as all approved IgG therapeutics, and one that targets a novel epitope. Both IgGs are effective at reducing the proliferation of EGFR-expressing cancers. Importantly, I show that the two IgGs have non-identical anti-proliferative profiles in vitro, revealing a new modality for the treatment of EGFR-positive tumours. My work demonstrates the utility of phage display for the development of IgGs and the therapeutic potential of epitope-specific targeting of RTKs.
Towards the Development of Preclinical Models and Subtype-Specific Therapeutics for Atypical Teratoid Rhabdoid Tumors
Keywords: ATRT
Drug Screening
Genetics
Mouse Models
Radiation
Synergy

Atypical Teratoid Rhabdoid Tumor (ATRT) is a rare, devastating and largely incurable pediatric brain tumor diagnosed early in childhood. Use of intensive, high-dose chemotherapy and/or craniospinal irradiation has improved short-term survival for some patients, however, long-term survival rates remain dismal with 70-75% of children succumbing to their disease. Poor survival outcomes and treatment toxicity necessitate targeted and more efficacious therapeutics for children suffering from this disease. Genetic characterization of primary tumors has revealed that in addition to SNF5 loss of function, ATRTs comprise three molecular subtypes that differ at the level of global gene expression as well as DNA methylation, and are found in distinct anatomical compartments. In this thesis we describe the generation of a genetically engineered mouse model that recapitulates the spatial pattern of human disease upon targeted loss of Snf5 to putative cells of origin using the Cre lox recombination strategy (Chapters 1-4). We have also developed a robust drug screening strategy that employs a rigorous dose assessment methodology for high throughput analysis of a library of 477 kinase inhibitors against a panel of subtyped ATRT cell lines (Chapters 5-8). Using this methodology, we identified multiple kinase inhibitors which demonstrate therapeutic benefit in Group 2a/b ATRT. Numerous kinase targets showed subtype-specific expression, among which is ERBB2 that is exclusively expressed in Group 2a and Group 2b ATRTs. More broadly, we found that ATRT cell lines are highly sensitive to PI3K and MAPK signaling blockade, and that combinatorial inhibition of these signaling pathways acts synergistically to reduce cell viability. Lastly, we combined our drug screening strategy with radiation treatment and found that the multikinase inhibitor, dasatinib and MTOR inhibitors, rapamycin, everolimus and temsirolimus are capable of sensitizing Group 2a/b cells to radiation. This thesis work advances ATRT research on two important fronts: the much-needed development of preclinical models and the identification of novel, subtype-specific therapeutics.
Women Workers Behind the AI Revolution: The Production and Reproduction of Data Annotation Platforms
Keywords: automation
data annotation
home-based work
Indian labour market
platform labour
women workers

This thesis examines women’s conditions of work and social relations within transnational data annotation platforms, focusing on the gendered and racialized dynamics in this platform work. The proliferation of the Artificial Intelligence (AI) industry and machine learning companies fundamentally rely upon human labour of data annotation. The potential of platform technologies occupies the heart of debates on digitally mediated work and the disruption of traditional norms of workplaces and employment. The study focuses on the experiences of women who form a substantial part of the data annotation workforce. The labour force for this low-wage, piece work is primarily home-based workers in Global South countries, and India has emerged as a significant location for this work. As a feminist scholar, I center my attention on women’s lives and experiences, revealing the gendered and racialized dimensions of platform work and challenging typical notions of freedom, inclusion, and an available workforce. This qualitative study draws on field visits, arts-informed methods, and semi-structured interviews with home-based women data annotators living in India. The study also draws on interviews with key informants, including union organizers, and document analysis of State policy and platform company contracts. The study examines how platforms reproduce women’s proletarianization and diminish their political power inside the family. The study contributes to debates on worker organizing in the platform economy, adding dimensions of informal organizing amongst women data annotators in India and the possibilities of expanding the organizing agenda for platform work towards a more collective working-class struggle against the capitalist political economy.
Partitioning and biodegradation of diethylenetriamine (DETA) and metal-DETA chelates, and their predicted behaviour in tailings management areas
Keywords: Biodegradation
Bioremediation
Chromatography
Diethylenetriamine
Pyrrhotite

Pyrrhotite (Po) is an unwanted mineral with low economic value which dilutes valuable mineral streams and contributes significantly to SO2 emissions during smelting. The most effective pyrrhotite rejection method is by using chelating agents, such as diethylenetriamine (DETA), during flotation. DETA improves the concentrate grade; however, its use results in stable chelates between DETA and metal ions: nickel and copper. Once in the tailings management area, DETA-metal chelates cannot be removed by hydroxide precipitation. DETA mobilizes the metal ions through the treatment area and into the environment, which is detrimental to the local flora and fauna.To effectively assess the implications of DETA in a mine tailings management area, DETA must be reliably detectable. An analytical method for DETA detection method was developed using cation exchange chromatography with conductivity detection without the need for preconcentration or derivatization. The limits of detection and quantification were 0.002 and 0.005 mM, respectively, in deionized water samples. This method also proved effective to detect DETA chelated with metals such as nickel and copper. The behaviour of DETA was modeled in a theoretical tailings management area using experimental sorption data along with geochemical modelling using OLI Studio software to 1) predict the concentration of DETA, Cu-DETA, and Ni-DETA in final effluent and 2) ascertain if copper and nickel concentrations would be expected to exceed regulated limits. Operational parameters were investigated to ascertain their influence on the model outputs. In all cases, except the case for dry stacking the DETA containing tailings, the concentration of metal in the final effluent exceeded regulated limits. These results strongly indicate the necessity for a DETA mitigation strategy. This thesis investigates the potential of biodegradation of DETA and metal-DETA chelates using a mixed bacterial culture. Cation and anion ion chromatography results were used to track the DETA degradation progress by measuring DETA, ammonium, and succinate concentrations. The biomass generated by the degradation process was observed using microscopy, quantified using qPCR, and bacteria genera were identified using 16S rRNA sequencing. Evidence of complete DETA degradation in the presence of an external energy source, succinate, was demonstrated for unchelated DETA and for Ni-DETA. DETA was demonstrated to be a nitrogen source.
Stakeholder Perspectives on Consent and Violence Prevention in Ontario K-12 Education
Keywords: consent
curriculum design
media literacy
social justice education
violence prevention

This study examines the implementation of sex and consent education in Ontario K-12 public schools by focusing on perceptions of stakeholders in education: parents, students, and teachers. The study asks: What factors inhibit and activate consent education curriculum reform in Ontario K-12 public schools? How do diverse stakeholders respond to curriculum modules pertaining to sex and consent, and what factors determine these responses? By addressing these questions, the study enriches research on sexual violence prevention in K-12 education, deepening knowledge that supports or inhibits such education. The study highlights an important gap in the literature: the role of parents/families in shaping sex-education. The study extends multiple fields: critical media literacy education, consent education, sexual violence prevention, and social justice education. The social justice education framework anchoring this study draws from critical race theory, intersectionality, and feminist standpoint theories focused on the role of social differences in sexual violence and its prevention. The study uses three qualitative approaches: (1) the design of an original media literacy curriculum module to discuss consent and non-violence with Ontario adolescents, (2) curriculum assessment of the module by diverse adult stakeholders in Ontario (n=20), collected through in-depth personal interviews to probe adult stakeholder views about sex-education; and (3) analysis of archival documents, including official curricula and media reports to map the social and cultural contexts of sex-education in Ontario. Based on stakeholders’ perceptions of the study’s curriculum module, the analysis highlights four barriers to effective sex-education in Ontario K-12 public schools: (1) rigid “consent” definitions that neglect the diverse cultures and histories of Ontario’s population; (2) “childhood innocence” narratives that do not consider research assessing adolescent needs and activism; (3) the persistence of neoliberalism that prioritizes preparation for the workplace over non-violence; (4) a lack of training and administrative support for K-12 educators. Additionally, four key factors enabling K-12 consent education were analyzed: (1) youth and parents’ intrigue with media-based pedagogies; (2) teachers’ professional development pertaining to consent; (3) educator collectives and resource-sharing groups; and (4) parent council activism and education. The study concludes by discussing future directions of the research, including piloting the module.
Applications and Effects of Halogenation on Boron Subphthalocyanines for use in Organic Electronic Devices
Keywords: Light Emitting Diodes
Organic Electronics
Photovoltaics
Solar Cells
Stability

Organic photovoltaic (OPV) research has reached the stage in development where it is ready tobegin scale up and translate the technology from the lab to the next phase. Here, the versatile macrocyclic compound known as boron subphthalocyanine (BsubPc) is the focus of this process. BsubPcs can be chemically modified with different axial and peripheral substituents most promisingly being different halogenation. Peripheral chlorination has previously been shown to deepen the BsubPc energy levels enough to allow triplet harvesting from singlet fission materials. In this thesis it was shown how triplet harvesting is not only a pathway to improve device performance but how it can also enhance outdoor stability. Fluorination of the BsubPcs has a similar influence on the energy levels but also offers some synthetic, stability, and solubility benefits so there is a desire to find applications for these materials. Initial screening in triplet harvesting devices revealed that fluorinated BsubPcs performed significantly worse as acceptor molecules. Upon further testing fluorinated BsubPcs showed promising results as OPV donor materials and in simple solution cast organic light emitting diodes (OLEDs) but remained worse than chlorinated BsubPcs as OPV acceptors. In a further attempt to improve stability chlorinated BsubPcs were incorporated into solution cast OPVs to compare architectural differences between sequential and blended active layer deposition. Although neitheriii architecture produced particularly stable devices the sequentially deposited devices did have a notable stability improvement over traditional blended devices in outdoor applications. To fully assess OPV stability common materials were also subjected to individual layer accelerated aging which revealed that the organic layers undergo different crystallization depending on the level of humidity in the environment and certain active materials can be photobleached by strong light. The adverse impact of impurities on device performance was also highlighted to evaluate what will be required when OPV technology is eventually translated beyond the lab. Specifically, unintended methyl group additions originating from the synthesis of α-sexithiophene significantly affected open circuit voltage and performance of baseline OPV devices. The conclusions outlined here serve to guide further development of halogenated BsubPcs for different organic electronic applications as well as to elucidate possible avenues for improving the outdoor stability of OPVs.
Control and Topological Solutions for Emerging Converters with Increased Capacitive Energy Storage
Keywords: Converter modeling
DC-DC converter control
Flying capacitor converter
Low-power applications
Multi-level topologies
Power supplies

Emerging Multi-Level Flying Capacitor (ML-FC) topologies have proven to be an attractive alternative to conventional dc-dc converters due to their potential to increase power density and improve efficiency in a wide range of power applications. There are, however, technical challenges to their wider adoption in dc-dc applications, regarding the balancing of the voltages of the Flying Capacitors (FC) that compose it. There are two main routes that designers take to address this issue. First is by utilizing passive balancing techniques, which often include topological and modulation solutions assuring that the FC voltages stay close, albeit unregulated, to their ideal values. The second method is to use feedback control to directly regulate the FC voltages. Both these methods have their own challenges. The first method requires the use of specific modified converter topologies, which have a limited scope of application. The second method is more universally applicable. However, the existing control techniques for ML-FC converters are either unreliable or lack a precise dynamic model for the FC voltages behavior. The goal of this thesis is to contribute to both methods. Chapter 3 presents a passive balancing technique applicable for multi-phase ML-FC converters, along with experimental validation on how it can successfully simplify multi-phase ML-FC designs. Regarding active regulation methods, Chapter 4 focuses on resolving an existing control instability issue that appears during light-load operation when attempting to control the FC voltages using duty-cycle as the control input. The solutions presented in Chapter 4 resolve the issue for the specific case of the 3L-FC converter. Finally, Chapter 5 presents a completely new way of actively regulating the FC voltages using phase-shift modulation. This new control method is general and applicable to any N-level ML-FC converter, thanks to the accurate dynamic model developed, and verified, through simulations and experiments for various converter examples.
Instrument Design and Analysis Techniques for Low-Redshift 21 cm Cosmology and Transient Detection with CHORD and CHIME
Keywords: 21 cm
baryon acoustic oscillations
cosmology
fast radio bursts
interferometry
radio astronomy

The Canadian Hydrogen Observatory and Radio-transient Detector (CHORD) is a compact, innovative “large-$N$ , small-$D$” radio interferometric array set for construction in British Columbianext to its older sibling, the Canadian Hydrogen Intensity Mapping Experiment (CHIME). With its 0.3–1.5 GHz band, sub-30 K system temperature, sub-millimeter precision dish surfaces, nearly 15,000 m$^2$ collecting area, and very broad field of view, it is designed to map the Universe’s matter distribution up to redshifts of $$ = 3.7 and boost fast radio burst (FRB) detection rate. This work emphasizes that CHORD’s array elements be located as close as possible to enhance sensitivity to lower k-modes of the matter power spectrum and minimize transient search cost. It also introduces arguments for using very deep dishes ($f/D = 0.21$) based on coupling and ground illumination considerations. Preliminary calibration results from the Deep Dish Development Array (D3A6) suggest that the signal chain’s system temperature matches specifications at lower frequencies ($\nu$ < 0.8 GHz), while further testing is required for higher frequencies. The CHORD feed, designed for the array, is inexpensive and quick to assemble, while maintaining a 30 K system temperature using ambient-temperature analog receiver hardware across the band. The design’s major novelty is an oversized backshort on an exponentially tapered (“Vivaldi”) design, adaptable to an observatory’s impedance and beam shape requirements via a simple optimization algorithm, particularly suitable for very deep dishes ($f/D ≤ 0.25$). In those dishes, the aperture efficiency remains above 50% over the band. Cosmological measurements are complicated by instrumental coupling and foregrounds. We show that coupling can be estimated from electromagnetic (EM) simulations of the array elements using a combination of their S-parameters, time-domain response, and beam shapes. Lowering the focal ratio of the dishes emerged as a powerful method to reduce coupling power. Foregrounds are typically removed from data using their spectral smoothness via a Fourier decomposition along the frequency axis; this can also be done with a singular value decomposition, and we successfully demonstrate this approach on CHIME data.