VictorJuiz/thesis huggingface dataset:
A Multimodal Developmental Atlas for Cerebellar Molecular Layer Interneurons

The central nervous system is comprised of an extraordinary diversity of neuronal cell-types. Classification of neurons into types and subtypes enables systematic studies of nervous system organization and function in health and disease. Defining cell types is complicated by the need to consider multiple modalities of classification including morphology, gene expression and function. Additionally, neuronal cell types diverge from common progenitors during development through protracted and dynamic processes. Studies at maturity have shown that multimodal approaches are needed to delineate the repertoire of neuronal cell-type diversity. However, similar methods have not been extended to interrogate the steps by which neuronal progenitors are programmed to acquire their adult forms and functions. In this thesis, I present a multimodal diversification map of the cerebellar molecular layer interneurons (MLIs), a heterogeneous inhibitory interneuron population that derives from a common progenitor pool. Using genetic, histological and computational approaches, I first define the diversity of mature MLIs along morphological and transcriptional axes. My analyses reveal examples of both discrete and continuous heterogeneity within each modality. Interestingly, I did not find direct correlation between MLI morphological and transcriptional identities. Instead, I identify graded transitions in gene expression profiles between morphologically discrete neurons, as well as graded transitions in neuronal morphology within transcriptionally discrete neurons. I demonstrate that neither morphology nor gene expression alone can be used to fully annotate interneuron diversity. I further define MLI subtypes by tracking the emergence of distinct identities during development using a novel application of pseudotime trajectory inference to morphological reconstructions. MLI subtype-specific morphological phenotypes emerge early during neuronal migration within the molecular layer, challenging prevailing views that MLI subtype specification is dependent on positional cues. In a complementary approach, I use in situ single molecule RNA imaging to visualize changes in marker gene expression during the timeframe of MLI migration and maturation. I find that MLIs do not establish the full repertoire of subtype-specific expression signatures until days after the completion of neuronal migration. Altogether, these studies present a multimodal map of MLI diversification and offer a framework that is broadly applicable for defining the developmental trajectory of interneuron populations.

Keywords: Brain development
Cerebellum
Interneurons
Morphology
Pseudotime
Transcriptomics
Advisor: Lefebvre, Julie L
The Physical World of the Dog

Domestic dogs are primarily recognized for their social cognition and skillful interactions with humans, but comparatively little is known about how they make inferences about physical objects or recognize cause-and-effect relationships in the environment. How do dogs perceive the world around them and what cognitive processes are involved in playing a game of fetch or finding a ball that has rolled under the couch? While these might seem like trivial scenarios, the ability to track objects (even toys) in one’s environment and make inferences about how they will behave in object interactions are mental abilities that support a wide variety of behaviours from play to hunting to understanding social interactions. Sparse previous scholarship has probed dogs’ physical and causal cognition and findings are contradictory, resulting in a poor understanding of how dogs represent the physical world. I address this knowledge gap with empirical studies of dogs’ physical and causal cognition, examining their ability to make inferences about object interactions and recognize underlying causal structures in the world. My work expands our understanding of cognitive abilities in dogs, and sheds light on the evolutionary origins of fundamental cognitive processes by exploring how dogs view and behave with objects in their environment.

Keywords: Animal behaviour
Canine science
Comparative cognition
Domestic dog
Physical inference
Advisor: Buchsbaum, Daphna
Corbit, Laura
Building AI Enabled Note-taking Interfaces for Patient Encounters

Current clinical note-taking approaches cannot capture the entirety of information available from patient encounters and detract from patient-clinician interactions. To address those issues we investigate the feasibility and suitability of using artificial intelligence (AI) technologies and mobile devices to improve clinical note-taking workflow and develop novel AI technologies for conversational understanding. First, by surveying healthcare providers’ current note-taking practices and attitudes toward new clinical technologies, we developed a novel patient-centered paradigm for clinical note-taking that makes use of hybrid tablet/keyboard devices and AI technologies. We then developed PhenoPad, which is an intelligent clinical note-taking interface that captures free-form notes and standard phenotypic information via a variety of modalities, including speech and natural language processing (NLP) techniques, handwriting recognition and more. The output is unobtrusively presented on mobile devices to clinicians for real-time validation, and can be automatically transformed into digital formats that would be compatible with integration into electronic health record systems. Semi-structured interviews and trials in clinical settings rendered positive feedback from both clinicians and patients, demonstrating that AI-enabled clinical note-taking under our design improves ease and breadth of information captured during clinical visits without compromising patient-clinician interactions. Second, we developed novel methods for speech, NLP and few-shot learning tasks, which can potentially support the development of tools like PhenoPad. For speech processing, we propose to train speaker embedding models using a meta-learning approach and to use graph-based methods for speaker diarization with and without speaker profiles. For NLP, we propose to encode syntactic information into transformer models for intent detection and slot filling, and we propose a meta-learning approach for few-shot text classification using gradients as task representation.

Advisor: Brudno, Michael
Rudzicz, Frank
Ramsey Degree Theory of Ordered and Directed Sets

We will study various Ramsey degree problems pertaining to categories of structures under variousembedding types. Using a technique originally penned by Laver, we show that the class of Aronszajn lines ordered under the embedding relation is a better quasi-order when we assume PFA. As a corollary, we deduce one-dimensional Ramsey degrees for Aronszajn lines. We also devise a colouring algorithm to colour Borel graphs coded by better quasi-orders on countable sets. We apply our algorithm to various types of well established better quasi-orders and deduce that there is a whole class of better quasi-orders that exists without a single known constructible example. We will conclude with some results pertaining to the Kechris-Pestov-Todorcevic correspondence. This will include a categorical notion of precompact expansion, which will prove to be more versatile in computing Ramsey degrees, as well as a weaker notion of the Ramsey property which also corresponds to fixed point properties of automorphism groups of ultrahomogeneous structures. This includes an application to trees under various embedding types, including the foundational strong embedding types studied by Milliken.

Keywords: Graphs
Orders
Ramsey Theory
Set Theory
Advisor: Todorcevic, Stevo
Computational dissection of the sequence elements defining human cleavage and polyadenylation sites and their role in determining gene ends

After decades of research, significant progress towards understanding how living organisms decode their genomes has been made. Eukaryotes utilize protein factors as well as DNA sequence elements to define eukaryotic gene starts and gene ends. During 3′-end gene definition, when pre-mRNA is being produced, it has to go through several steps of maturation, including cleavage and polyadenylation (CPA), when the pre-mRNA gets cleaved and a string of ~200 adenine nucleotides gets added at 3′ end of the transcript. Mechanistically, CPA is thought to utilize five key sequence recognition elements that reside in pre-mRNA 3′-UTRs: the upstream UGUA, polyadenylation signal (PAS), U-rich sequences, the CA/UA dinucleotide where cleavage occurs, and GU-rich downstream elements (DSE). It remains contentious whether these sequences are sufficient to delineate CPA sites, however. To date, no studies have explicitly attempted to assess how well the established features differentiate CPA sites from the remainder of the genes. Furthermore, it is not clear what role these sequences play in defining human geneends. Here, I expand on previous work by dissecting the contributions of numerous individual sequence features to CPA site selection. Using classical discriminative approaches, I show that computational models can be constructed that accurately identify constitutive CPA sites, relative to the entire pre-mRNA sequence, for 41% of all genes. U1-hybridizing sequences, which have been described as one of the strong additional cryptic CPA regulators, have surprisingly little impact on model performance, suggesting their limited role in regulating human CPA. Addition of all known RBP motifs to the model, however, increases this figure to 49%, with feature scores that highlight known and suspected CPA regulators, as well as many potential new factors. Together, these results suggest that while the established features have a higher specificity in defining human CPA sites than expected, the existing knowledge of sequence elements contributing to CPA definition does not account for the full complexity of CPA regulation.

Keywords: Logistic Regression
Machine learning
mRNA
polyadenylation
Random Forest
systems biology
Advisor: Hughes, Timothy R
When Global Ideas Meet Local Contexts: The Case of Girls' Education in Urban Pakistan

Global commitments to achieve gender equality in education are promoting a convergence of educational aims, policies and practices across nation-states, including those in the developing world. This study attempts to understand ways that global-level concepts related to girls’ education are interpreted in local contexts. Its overarching question is: how are global policy scripts that promote girls’ education interpreted or “refracted” by a diverse group of urban actors and elites in a developing nation-state? Specifically, this dissertation examines how three global concepts related to girls’ education – “equality and inclusion”, “value and purpose” and “empowerment” are re-interpreted by local actors. Its conceptual framework has two components: one for understanding converging meanings, and one for diverging meanings. It draws on several theoretical frameworks: institutional pillars, institutional logics, World Society theory, concerted cultivation and Bourdieu’s concepts of field theory and habitus. Data were collected through participant observations and 26 semi-structured interviews with urban parents, non-governmental organizations and policy actors. Two Pakistani cities were chosen to conduct interviews because they are key sites for observing dialectical relations between urban families and institutions and global policy prescriptions.Findings suggest that the refraction of global policies for educating girls into local understandings are guided by the parameters set by institutions of family, religion and state, each of which has its own logic that, when combined, creates a contested terrain for attaining gender equality through education. Parents aspire to cultivate a set of legitimized schooling, professional, and behavioural goals in their daughters. Policy actors recognize that standard global prescriptions may not fit well in local contexts but collaborate with partner institutions to attain legitimacy. As a result, policy actors focus more on gender parity than girls’ actual educational experiences. The study advances understandings of the issues of ‘what works’ in comparative girls’ education without neglecting ‘how it works and for whom.’ It highlights the roles of cultural- cognitive institutions and overlapping institutional identities of actors when they enact global education policy at local levels. By focusing on gendered dimensions of class reproduction processes, it extends theories of cultural capital and concerted cultivation by applying them to non-western settings.

Keywords: Bourdieu’s field theory and habitus
Girls’ education
Global education policy
Institutional logics
Isomorphism and loose coupling
Legitimacy
Advisor: Davies, Scott
International Students' Social-emotional Experiences in Ontario Elite Boarding Schools

The current Westernized definition and approaches to understanding social-emotional experiences are insensitive to cultural differences, and individuals from diverse backgrounds—including international students—are undergoing processes of marginalization, stereotyping, identity crisis, and various forms of racism as a consequence (Castro-Olivo & Merrell, 2012; Graves et al., 2017; Khalifa, Gooden & Davis, 2016; Khawaja & Stallman, 2011; Lee & Opio, 2011; Lee & Rice, 2007; Marginson, 2012; Rodriguez-Izquierdo, 2018; Slaten et al., 2016; Smock, 2013). Thus, this critical phenomenological research aims to address the evident gap in the literature by acknowledging the complex phenomenon of international students’ social-emotional experiences within a particular context of elite institutions while creating an opportunity for the students to talk about such experiences through their own voices. As a qualitative study, the main research question asks, How do international students in Ontario elite boarding schools understand/interpret their social-emotional experiences in such schools with particular emphasis on issues of “culture” (race, ethnicity, language, values, and beliefs)? Fifteen participants who have attended and graduated from Ontario elite boarding schools as international students were interviewed and the data collected have been analyzed from a critical democratic education perspective interpreted from a social justice lens. This research is significant, as it provides a different contextualization through a newly developed ‘Holistic Model,’ which captures a comprehensive picture of international students’ experiences through three chronological phases beginning from their entry into elite boarding schools to exit and examines the correlation between the three dimensions constituting students’ social-emotional experiences: multiculturalism and diversity, relationship building, and sense of belonging. Findings demonstrate that social-emotional experiences are fluid constructs that occur amongst the intersection of two or more dimensions and that “cultural cliques” is the most important determinant leading to positive experiences. Those students who had such a support network were able to develop a bicultural identity while the others without suffered from a cultural identity crisis and went through assimilation, internalization, and/or double marginalization. Furthermore, this study analyzes the role of capitalism and neoliberalism in students’ experiences, especially regarding the commodification of education and concealment of racism, justification of categorization, and hierarchical teacher-student relationship.

Keywords: Critical Democracy
Culture
Elite Boarding School
International Students
Social Justice Education
Social-Emotional Experiences
Advisor: Portelli, John
Persuasive Strategies for Social Robots Engaged in Human-Robot Interaction

As the scope of robotic applications in our world continues to grow, the integration of robots into everyday tasks requires not only functional, but also social intelligence around human behaviours such as persuasion. This ever-present behaviour is a critical component of human interactions yet has seen minimal research in human-robot interaction (HRI). The objective of this thesis is to understand how people respond to and are influenced by a social robot’s use of a variety of persuasive strategies commonly used in human interactions. This thesis achieves this through a combination of social HRI studies designed to uncover insight about people’s interactions with persuasive robots and through the application of this knowledge into the development of an adaptive learning architecture for robot persuasion. Several studies describe the investigation of a robot’s use of common persuasive dimensions such as rationale for compliance, communication explicitness, sanction use, and authoritative locus of control. These studies highlight the efficacy of emotional persuasive strategies, the importance of less direct persuasive communication, the value of using rewards to encourage compliance, and the challenge of a persuasive robot acting authoritatively. Building upon these studies, this thesis also describes the development of a hierarchical learning architecture for adaptive persuasion in HRI. This architecture is based upon a well-established psychological framework for how people process persuasive attempts and allows for a robot to adapt its persuasive behaviour to both the static and dynamic factors of a person. The architecture uniquely separates these factors into a hierarchical learning structure, using a contextual bandit approach to optimize a top-level policy for selecting abstract actions that align to static cognitive biases and a Q-learning approach to optimize for the selection of lower-level primitive actions based on a person’s dynamic affective state. Simulated experiments show the improved learning speed and robustness of this architecture over a non-hierarchical benchmark. Between this architecture and the HRI studies performed, this thesis builds an understanding about what makes a robot persuasive and strives to create a more effective adaptive learning approach for use in persuasive HRI, allowing robots to be more effective in real-world, social interactions.

Keywords: Adaptive Learning
Human-Robot Interaction
Persuasion
Persuasive Strategies
Robotics
Social Robots
Advisor: Nejat, Goldie
Characterization of the RavA-ViaA Chaperone Complex and its Association with the Fumarate Reductase Respiratory Complex

Regulatory ATPase variant A (RavA) is a prokaryotic ATPase chaperone that plays a role in two important cellular pathways. In the model bacterium E. coli, it is linked to acid stress response and cellular respiration. However, details regarding its cellular function and mechanism of action remain elusive. RavA forms a two-gene operon which also encodes for the protein ViaA (VWA-interacting with AAA+ ATPase). ViaA contains a Von-Willebrand factor A (VWA) domain. Here, an evolutionary and functional insight into the RavA and ViaA relationship was sought. Phylogenetic analyses were used to contextualize the partnership between RavA and ViaA. The species spread for RavA and ViaA was defined using genomic data. These two proteins were shown to evolve together, across a subgroup of the Gram-negative Gammaproteobacteria. Experimentally, the E. coli proteins were used to infer the roles of RavA and ViaA. A mutational analysis was used to map the direct association between RavA and ViaA. The middle domain of ViaA was shown to enhance the ATPase activity of RavA. In searching for substrates of RavA-ViaA, the two proteins were discovered to interact with a subunit of the fumarate reductase (Frd). Frd is an enzyme of the bacterial respiratory complex that catalyzes the reduction of fumarate to succinate. The characterization for the interaction of RavA-ViaA with Frd is described. ViaA was found to act as an adaptor to mediate the association between RavA and the FrdA subunit of fumarate reductase. The VWA domain of ViaA was required for its association with FrdA. Interestingly, the enzymatic activity of Frd was inhibited in the presence of RavA-ViaA. Moreover, this RavA-ViaA-Frd association was linked to bacterial persistence under antibiotic stress. In select kanamycin treated media, the presence of the fumarate reductase enzyme was associated with increased persistence to the antibiotic. The survival was mitigated by the presence of RavA-ViaA. The novel interaction established with FrdA, and the associated antibiotic-survival phenotype, suggest that the RavA-ViaA proteins are modulators of respiratory enzymes. The discoveries made here provide an exciting insight into the functional aspects for RavA-ViaA chaperone complex.

Keywords: antibiotic persistence
ATPase
chaperone
co-evolution
respiration
VWA domain
Advisor: Houry, Walid A
The King’s Sick Body: The Spiritual and Social Implications of Arnau of Vilanova’s Regimen Sanitatis

In 1305, the physician Arnau of Vilanova composed the Regimen sanitatis ad inclytum Regem Aragonum (“Regimen of health for the sick King of Aragon”) for Jaume II, king of Aragon, who was suffering a bout of discrasia (imbalanced complexion). Arnau’s work would be rapidly translated into Catalan and become an enduring classic of the regimen sanitatis literature. In this dissertation, I aim to contextualize the composition, translation, and dissemination of Arnau’s Regimen. First, I place Arnau in the context of thirteenth-century Iberian medicine, noting his many contributions to the development of university-based medicine. I go on to discuss Arnau’s spiritual concerns, and read the Regimen sanitatis in the light of Arnau’s apocalyptic preoccupations and the theory of The King’s Two Bodies, the medieval political and legal theory which posited that the king had both a private and a public body. I then move on to discuss the important role played by Blanca of Anjou, wife of Jaume II and Queen of Aragon, who commissioned the first Catalan translation of the Regimen, in the dissemination of the text, while locating Blanca in the context of Aragonese queenship and female readership/patronage of scholarly medical texts. Finally, I discuss two Catalan translations of the Regimen, with a specific focus on what was preserved and what was lost in translation, as well as the influence of the Catalan translations on later Hebrew translations of the text. This discussion of the composition, translation, and dissemination of Arnau’s Regimen provides us with insights into the relationship between medical texts and their readers, as well as how university-based scholarly medical texts made their way to non-Latinate readers.

Keywords: Arnau of Villanova
Blanca of Anjou
Jaume II
Medieval medicine
Regimen sanitatis
Advisor: Conklin Akbari, Suzanne