VictorJuiz/thesis huggingface dataset:
Novel Gene Therapy Platforms and a Mouse Model for Lysosomal Storage Disorders

Cell and gene therapies are the epitome of personalized medicine for inherited disorders. Lysosomal storage disorders (LSDs) are particularly amenable to treatment by such therapies, as overexpression in some cells may suffice to treat the deficiency in uncorrected cells by “cross-correction”. The hematopoietic system is an accessible compartment of cells that can be readily and safely transduced with lentivirus (LV) ex vivo. Hematopoietic stem and progenitor cells (HSPCs) from patients with LSDs can be engineered with LV to overexpress the deficient enzyme and transplanted back into patients. This strategy is under clinical investigation for some LSDs, including Fabry disease. Results from such clinical trials highlight areas of improvement.We aimed to leverage the potential of lymphocytes as more specific target cells for gene therapy. T and B cells are abundant in peripheral blood. Unlike HSPCs, T cells can be expanded ex vivo without loss of function. We first tested LV-modified rapamycin-conditioned T cells (T-Rapa) as alternative long-lived hematopoietic cells for treatment of LSDs. We demonstrated enzyme secretion from LV-modified T-Rapa cells in vitro, and reduction of accumulated substrate in vivo. Next, we tested a strategy to enrich for transduced T and B cell progeny in response to mycophenolic acid (MPA) following HSPC-directed gene therapy. Resistance to MPA was engineered by co-expression of mutated inosine-5’-monophosphate dehydrogenase 2 (IMPDH2IY) with therapeutic transgenes using a dual-promoter vector. In vitro testing with cell lines and primary T cells revealed enrichment of IMPDH2IY-expressing cells was possible with extended low-dose MPA treatment. We also established two in vivo models to test enrichment using this platform. In addition, we aimed to establish a murine model of acid ceramidase deficiency with spinal muscular atrophy-like phenotypes. Adequate animal models are needed to test efficacy of novel therapeutic platforms, including those described in this thesis. We modified a previously established mouse model of Farber disease by excision of intronic elements. We characterized spinal cord pathology in this new derivative strain which includes wide-spread demyelination in the white matter and sphingolipid accumulation. Together, our work provides the framework for novel gene therapy platforms and describes tools for testing them.

Keywords: Enrichment
Gene therapy
Lentivirus
Lysosomal storage disorder
SMA-PME
T-Rapa
Advisor: Medin, Jeffrey A
Generalization in Planning

The ability to generalize from past experiences in order to address new situations is one of the cornerstones of human intelligence. As such, the design of artificial intelligence systems must---at some point---consider the issues involved in generalization. In automated planning, where the objectives are to design systems that are capable of finding courses of action to achieve specific goals given a formal description of their environment, we can say that a system exhibits generalization capabilities if it can leverage its previous solution-finding efforts when addressing new problems. The pervasive use of automation in modern industries signifies that this type of generalization---generalization in planning---is a fundamental requirement for the integration of artificial intelligence techniques into real-world applications. This dissertation aims to provide a generic high-level approach that can be used when confronted with sequential decision-making problems where generalization is important. Overall, the approach works by reformulating the problems into abstract representations, finding solutions for these abstract problems, and attempting to directly use the resulting abstract solutions in the concrete problems. This satisfies the generalization requirements when multiple concrete problems can be represented in one single abstract problem, or when the insights gathered when solving one abstract problem can be transferred towards solving related problems. We instantiate this approach in three different classes of planning problems. First, we address planning problems that have propositional and numeric state variables, including problems with nonlinear numeric constraints. We then address a type of generalized planning where a family of multiple planning problems is described through the use of first-order logic quantification, obtaining a single policy that can be applied on any of the problems. Finally, we show how we can solve reinforcement learning problems where multiple different tasks must be solved in a single environment. As with all reinforcement learning problems, the exact domain dynamics are initially unknown, and solutions must be obtained by repeatedly interacting with the environment. We prove the soundness of all our approaches and present empirical results that demonstrate their efficacy across various different domains. In many cases, we see orders of magnitude improvements in overall time efficiency.

Keywords: Abstraction
Automated Planning
Generalized Planning
Hierarchical Reinforcement Learning
Numeric Planning
Reinforcement Learning
Advisor: McIlraith, Sheila Ann
Fish Community Dynamics and Spatial Overlap in Lakes Across Ontario, Canada

Inland fisheries are an important source of employment, nutrition, and recreation around the world that are often overshadowed by their marine counterparts. Given the importance of these fisheries, observational and modelling approaches are constantly being refined to improve monitoring and management approaches. Multi-species size spectrum models, which are size-structured models that take species interactions into account, have been increasingly used in marine systems to address important fisheries questions; however, they have yet to be applied to freshwater systems. In this thesis, I develop, to my knowledge, the first multi-species size spectrum model for a freshwater fishery and determine if this approach can be used to enhance the ecosystem-based fisheries management of inland fisheries. Through sensitivity analyses, I show that size and growth parameters of large predators have a strong influence on size-spectrum model output, and model uncertainty may be reduced by paying special attention to the estimation of these parameters. Further, this work highlights the possibility of simplifying multi-species size spectrum models by grouping less influential species into guilds. My calibrated model of the Lake Nipissing fishery demonstrates that multi-species spectrum models are an appropriate method to apply ecosystem-based fisheries management to inland fisheries and highlights the importance of considering species interactions under different management scenarios. In order to better understand how to simplify future analyses, I reviewed the methods and data required to partition fish communities into guilds and created a step-by-step guide to facilitate these analyses by others. Lastly, I explored patterns of spatial overlap among thermal guilds within lakes across Ontario, Canada. My findings suggest that temperature and lake depth are strong drivers of spatial overlap patterns and these patterns can be used to inform future size spectrum models. Altogether, my thesis has demonstrated the potential for multi-species size spectrum model usage in freshwater systems and highlighted approaches that could further increase the applicability of these models for temperate lakes.

Advisor: Jackson, Donald
Chu, Cindy
DNA Replication, Repair, and Chromatin Accessibility at Disease-associated Repeat Sequences

DNA repeat expansions are the cause of greater than forty untreatable neurodegenerative and neuromuscular diseases. Intergenerational repeat expansions cause genetic anticipation of disease, whereas somatic expansions drive disease progression. Alternative nucleic acid structures (slip-outs, G-quadruplexes, R-loops) that form in repeat tracts are strongly implicated in the expansion process and disease pathogenesis. Further, the epigenetic chromatin environment of expanded disease-associated repeats is well-documented to be altered from corresponding wild type alleles, with chromatin modifying enzymes and epigenetic marks contributing to repeat instability. My thesis is a three-part exploration of these factors contributing to repeat instability. First, I examine the role of Bloom’s helicase on in vitro replication and repair processing of expanded (CAG)•(CTG) repeats, which are associated with >18 neurodegenerative and neurological disorders. Next, building upon knowledge of R-loops at (CAG)•(CTG) repeats, I examine the expanded C9orf72 repeat, which is the leading genetic cause of ALS/FTD, for its ability to form R-loops, and the effect of R-loop processing on instability. Finally, I characterize chromatin structure at C9orf72 loci in cell lines derived from individuals carrying the repeat expansion, with particular interest in the effect of repeat size, disease status, and methylation status on chromatin accessibility. This work is then extended to female fragile X patient cell lines. Altogether, my work addresses gaps in our knowledge of the numerous factors thought to contribute to the mechanism of repeat instability, furthering knowledge of these complex sequences, and providing clear future research directions important for addressing these fatal diseases.

Keywords: amyotrophic lateral sclerosis
Bloom helicase
C9orf72
DNA structures
fragile X syndrome
repeat-associated disease
Advisor: Pearson, Christopher E
Emergence of a Smooth Interface between Cytoskeleton Materials Explained by Mathematical Modeling

Structures and machines require smoothening of raw materials. Self-organized smoothening guides cell and tissue morphogenesis and is relevant to advanced manufacturing. Across the syncytial Drosophila embryo surface, smooth interfaces form between expanding Arp2/ 3-based actin caps and surrounding actomyosin networks, demarcating the circumferences of nascent dome-like compartments used for forming pseudocleavage furrows between dividing nuclei. We found that forming a smooth and circular boundary of the surrounding actomyosin domain requires Arp2/3 in vivo. To dissect the physical basis of this requirement, we reconstituted the interacting networks using node-based models. In simulations of actomyosin networks with local clearances in place of Arp2/3 domains, rough boundaries persisted when myosin contractility was low. With addition of expanding Arp2/3 network domains, myosin domain boundaries failed to smoothen, but accumulated myosin nodes and tension. After incorporating actomyosin mechanosensitivity, Arp2/3 network growth locally induced a surrounding contractile actomyosin ring that smoothened the interface between the cytoskeletal domains, an effect also evident in vivo. In this way, a smooth structure can emerge from the lateral interaction of irregular active materials.

Advisor: Harris, Tony
Black Mothering: A Study of Anti-Black Racism and a Theory and Practice for Educational Futurity

This study examined Black mothers’ conceptualizations of systemic racism in schooling, the impacts of anti-Black racism, and resistance strategies employed to combat anti-Black racism. The study offers a praxis of Black mothering that in turn provides lessons on the complexity of anti-Black racism and engages the idea of educational futurity. Racial injustices faced by Black students in Kindergarten to Grade 12 (K12) has been well-documented; in the Canadian context, scholars have researched barriers faced by Black students, such as: higher rates of suspensions and expulsions (James & Turner, 2017); a shortage of Black teachers (Ontario Alliance of Black School Educators, 2015); a lack of Black history and curriculum (Henry, 1968); educational streaming into lower and limited pathways (Curtis, 2014; James, 2012); and overall lower expectations (James, 2012) and the “push out” (Dei et al., 1997) of Black student learners. This study engages the idea of parenting for survival and looks specifically at the role and intervention strategies of Black mothers who navigate these complex anti-Black systems. Through Black feminism (Collins, 1990, 2000; Crenshaw, 1989; Giddings, 1986; hooks, 1995, 2015; Rodgers, 2017), Black Canadian feminism (Wane, 2004, 2009, 2013; Wane et al., 2002), and African feminisms (Ogundipe, 1987; Steady, 1981; Tamale, 2008; Wane et al., 2002), the study examined how Black women’s social-political identities can help mobilize Black student learners. Findings revealed the ongoing forms of anti-Black racism faced by Black student learners; the negotiations of the raced, gendered, classed, and other forms of oppression faced by their mothers; and a continuation of historical injustices faced by Black families in the lived realities of Black mothers. Findings also revealed a theory and practice of Black mothering that engages principles of othermothering (Rodriguez, 2016; Wane et al., 2002), survival parenting (Davis, 1981), principles of African mothering (Dove, 2002), understanding and navigating complex systems through community rights, and strategies to bolster community-oriented change. The study offers a new orientation to understanding the nuances and complexity of Black mothering from a community-oriented and strength-based approach.

Keywords: African womanhood
Anti-Black racism
Anti-racist education
Black feminism
Black studies
Mothering
Advisor: Dei, George JS
Fixed and Scannable Pencil Beam Antennas using Metasurfaces and Metamaterial Structures

Emerging technologies such as 5G/6G communication systems, autonomous vehicles and satellite Internet have led to a renewed interest in simple and low cost pencil beam antennas, that are capable of generating fixed/scannable pencil beams. Although traditional active phased arrays are technologically suitable for these applications, there are cases where other alternatives are more attractive, especially if they are simpler and less costly to design and fabricate. The main goal of this thesis is to investigate and propose simple antenna designs that are capable of generating fixed and electronically tunable broadside and tilted pencil beams. Both metasurfaces and metamaterial periodic structures are considered attractive candidates in this thesis, and antenna designs based on both structures are proposed. In addition, there are some metasurfaces research problems that are investigated such as the modeling of omega bianisotropic Huygens' metasurfaces, studying their bandwidth capabilities and developing a framework for realizing wave transformations that do not satisfy local power conservation. Furthermore, a center-fed transmission-line grid antenna design is proposed, which is capable of generating a high aperture illumination efficiency broadside pencil beam with a decent bandwidth. A peripherally-excited antenna array architecture is also proposed, which is capable of generating highly directive tilted and broadside pencil beams, with a significant reduction in the number of sources used compared with traditional phased arrays. The proposed peripherally-excited antenna array architecture is practically realized and experimentally validated, confirming its versatility, as it can be potentially useful in MIMO and duplex antenna systems. The proposed designs are considered attractive candidates for the aforementioned emerging technologies, and can be scaled to higher millimeter-wave and terahertz frequencies with relative ease.

Keywords: Metamaterials
Metasurfaces
Pencil Beam Antennas
Peripherally-Excited Arrays
Phased Arrays
Wideband Impedance Matching
Advisor: Eleftheriades, George V
Construction of Orogenic Plateaus: Geomorphology and Geodynamics of the Puna Plateau, Central Andes

The Puna Plateau of the Central Andes provides an ideal setting to explore how tectonics and an arid climate interact to shape Earth’s surface in orogenic plateaus. This thesis combines geologic mapping, eolian geomorphology, and apatite fission track (AFT) thermochronology of the Southern Puna Plateau with numerical modelling to understand the geodynamics of plateau deformation and uplift. Mapping and AFT data of the Antofalla region suggests that the region was uplifted in the Early Eocene (~50 Ma) before being integrated into the Andean orogenic wedge during the Late Oligocene–Miocene (from 29 to 15.5 Ma). Mapping of the Salina del Fraile, a 300 km² topographic depression, suggests that its surface was lowered by wind erosion along fold hinges after this latter phase of shortening. Structural cross-sections across the Antofalla region show that Late Miocene and younger strata were deposited in a half-graben hanging-wall basin that developed on what had previously been a topographic high when roughly E-W extension reactivated the Antofalla Fault. U–Pb zircon ages from folded strata suggest that the region resumed E-W shortening in the Late Pliocene to Quaternary. The relatively low magnitude of shortening implied by cross-sections suggests that deep-seated geodynamic processes such as lithospheric dripping may be partially responsible for crustal thickening. Lithospheric dripping has been inferred in 26 locations on Earth, but its diverse effects on topography and upper-crustal strain are poorly understood. This thesis develops a lithospheric dripping framework based on relative crustal strength, where a weak crust yields upper-crustal extension and surface uplift, the opposite response of a strong crust. Numerical models presented here suggest that weak-crust dripping can explain the observed kinematics of upper-crustal deformation in Puna Plateau. The models explain Oligo–Miocene shortening as the result of eclogite production and Mio–Pliocene extension due to lithospheric dripping.

Keywords: eolian processess
geodynamics
lithospheric dripping
orogenesis
structural geology
tectonics
Advisor: Schoenbohm, Lindsay M
L2 Processing of the Spanish Article System

Recent work in L2 processing offers several explanations for why it might continue to diverge from native speaker processing, even in advanced learners. Previous proposals, such as the Shallow Structures Hypothesis (Clahsen & Felser, 2006a/b, 2018) and the Reduced Ability to Generate Expectations Hypothesis (Grüter & Rohde, 2013), have proposed that L2 processing divergence corresponds to areas of high processing cost (syntax and predictive processing, respectively). In this thesis, I develop an analysis of L2 processing in terms of an additional factor that may play a role in L2 processing, namely the L2 learning process. As the L2 interlanguage grammar development takes time, while L2 learners are developing their L2, they must process input in their L2 with incomplete grammars, resulting in encountering input that is often incompatible with some feature of the interlanguage L2 representations. This results in an overreliance on making repairs (i.e., setting aside some aspects of the input that do not fit the underlying grammar and then attempting to interpret the sentence without these aspects, using other cues such as preceding context). This hypothesis is termed Repairs as an Adaptive Mechanism for Processing with Incomplete Grammars (RAMPInG). In this thesis, I propose that the overuse of repairs as a strategy by L2 learners can explain previously reported variability in L2 processing that cannot be accounted for by previously proposed hypotheses alone. This dissertation compares results from offline judgements and online processing of article semantics and the use of article semantics to predictively process syntactic ambiguities, allowing direct comparison of previous accounts of L2 processing with the proposal in this thesis. The results of an advanced L1 English L2 Spanish group attest to native-like judgements applied to the Spanish article system. As such, a representation difference is excluded as an explanation for any divergence in processing strategies. Results from two processing tasks indicate that L2 learners process largely as native speakers both in integrating article semantics and in using article semantics to disambiguate temporarily ambiguous prepositional phrases predictively. These advanced L2 learners seemed to diverge from native speakers only when the task required a repair but not a reanalysis. The results indicate that L2 learners are more highly practiced at making repairs, which I interpret as evidence for the RAMPInG Hypothesis.

Keywords: Article Semantics
Second Language Acquisition
Second Language Processing
Spanish
Advisor: Pérez-Leroux, Ana T
Cuervo, M. Cristina
Microaggressions, Blame, and Moral Responsibility

Microaggressions—small stereotypical slights that can accumulate into serious damage when repeated—capture a common experience of marginalized groups, yet skeptics raise significant worries about how to recognize and respond to them. Are microaggressions a unified type or a hodgepodge of discrete examples? Can perpetrators be blamed, especially if their microaggressions are unintentional and only become harmful when repeated by other agents? My dissertation engages with both these debates: it presents an account that unifies different types of microaggressions and demonstrates that blame is warranted. First, I clarify what’s aggressive and micro about microaggressions by positioning microaggressions and hate speech on a spectrum of escalating linguistic violence. I specify the similarities and differences between racial microaggressions and racist hate speech by building upon the work of legal critical race theorists Richard Delgado and Mari Matsuda. I then offer a new taxonomy of microaggressions. Psychologist Derald Wing Sue theorized two types of microaggression, microinsult and microinvalidation, but failed to clearly explain the distinction between them. I offer a new way to draw this boundary: microinsults perpetuate constrictive stereotypes, while microinvalidations risk reigniting dangerous associations that have in the past been used to justify violence. Having answered the descriptive challenges, I turn to normative questions. First, I counter the growing trend of comparing microaggressions to collective harm problems, like climate change. While I agree that microaggressions contribute to collective harm, I demonstrate that microaggressions are also individually wrongful, and thus collective harm models do not fully capture moral responsibility for microaggressions. Second, I introduce my own account of moral responsibility for microaggressions, based on concepts drawn from tort law. Just as I can object to incursions onto my property, so too can I object to microinsults that threaten my mental capacities, and just as I can object when I am harmed because a business failed to take sufficient safety precautions, I can object to perpetrators of microinvalidations who failed to foresee the harm their careless words could cause. These comparisons to tort law help us to capture the relational wrong committed by microaggressors, and also points us towards the appropriate remedy: apology.

Keywords: Blame
Critical Race Theory
Feminism
Microaggressions
Moral Responsibility
Tort Law
Advisor: Mullin, Amy