VictorJuiz/thesis huggingface dataset:
The Function and Evolution of C2H2 Zinc Finger Proteins and Transposons
Keywords: Ancestral sequence reconstruction
Computational biology
Genomics
Proteomics
Transcription factors
Transposons

Transcription factors (TFs) confer specificity to transcriptional regulation by binding specific DNA sequences and ultimately affecting the ability of RNA polymerase to transcribe a locus. The C2H2 zinc finger proteins (C2H2 ZFPs) are a TF class with the unique ability to diversify their DNA-binding specificities in a short evolutionary time. C2H2 ZFPs comprise the largest class of TFs in Mammalian genomes, including nearly half of all Human TFs (747/1,639). Positive selection on the DNA-binding specificities of C2H2 ZFPs is explained by an evolutionary arms race with endogenous retroelements (EREs; copy-and-paste transposable elements), where the C2H2 ZFPs containing a KRAB repressor domain (KZFPs; 344/747 Human C2H2 ZFPs) are thought to diversify to bind new EREs and repress deleterious transposition events. However, evidence of the gain and loss of KZFP binding sites on the ERE sequence is sparse due to poor resolution of ERE sequence evolution, despite the recent publication of binding preferences for 242/344 Human KZFPs. The goal of my doctoral work has been to characterize the Human C2H2 ZFPs, with specific interest in their evolutionary history, functional diversity, and coevolution with LINE EREs. I contributed to the expert curation of the full complement of 1,639 Human TFs and used the results to quantitatively compare their evolutionary history and tissue specificities to all other Human TFs. I analyzed protein-protein interaction (PPI) data for 118 DNA-binding C2H2 ZFPs and found extremely diverse interactions with nuclear factors despite paradoxically few dedicated PPI domains, revealing a new and unexplained dimension of functional diversity in addition to DNA-binding specificity diversity. Finally, I pioneered a computational technique to reconstruct extinct LINE L1 sequences and showed that they can be used to anchor the integration of KZFP genomic binding data and binding specificities for a complete picture of dynamic KZFP-ERE sequence specificity relationships. Together, my results paint a detailed picture of the diverse functionality and rapid evolution of Human C2H2 ZFPs, contribute to ongoing theorization on KZFP-ERE coevolution, and provide parallel datasets to power future investigations.
Unacknowledged Permissivism
Keywords: belief
disagreement
evidence
permissivism
rational
rationality

Permissivism is the view that a single body of evidence can sometimes rationalize incompatible doxastic attitudes – for example, suspension of judgment and belief – toward some hypothesis. Impermissivism, by contrast, is the view that there is at most one rational doxastic response to the evidence. This dissertation argues that rationality is permissive, but in an unexpected way: cases in which a body of evidence rationalizes multiple, incompatible responses are possible, but subjects who are in such a case can never rationally believe that they are. This view has sometimes been referred to as unacknowledged permissivism. Unacknowledged permissivism is often said to be implausible. The orthodox view is that it is an unmotivated view, in part because it is said to break ties with the core motivation for defending permissivism in the first place – namely, our intuitions about cases describing disagreement between peers. I challenge the dominant view, arguing that, contrary to what has been assumed, our intuitions about these cases are compatible with unacknowledged permissivism. I also provide a positive argument for unacknowledged permissivism. I argue for a requirement of rationality that prohibits a subject from believing some proposition P while also believing that an incompatible attitude toward P is rational, given his or her evidence. A subject who believes such a conjunction is committed to a kind of intrapersonal incoherence that, in other cases, is obviously rationally problematic. If this is correct, there is a compelling case for the conclusion that believing one is in a permissive case is rationally prohibited. This, combined with the theoretical implausibility of impermissivism, constitutes a strong case for unacknowledged permissivism.
Ecology of Vector-borne Diseases at the Interface of Theory and Data
Keywords: Computational biology
Dengue
Disease ecology
Malaria
Vector-borne disease

Infectious diseases continue to impact human lives. However, surprisingly little is known about the fundamental biology of disease-causing organisms and their interactions with the host. This thesis focuses on vector-borne diseases which account for 17% of all known human infections and put more than half of the global population at risk of infection. An overarching focus of the work presented is heterogeneity within species, which is ubiquitous and fundamental to biology, yet has often been neglected outside of evolutionary biology. In infectious disease biology, a better understanding of individual heterogeneity is needed across scales. At the within-host level, infection dynamics and health outcomes are highly variable between hosts. Therefore, a single clinical intervention strategy will likely not achieve the desired cure in all individuals infected with the same parasite. At the between-host level, it is important to map the consequences of heterogeneity because a small fraction of the host population contributes disproportionately to disease transmission and determines the fate of an epidemic. By combining mathematical modelling and empirical data, this thesis develops conceptual and methodological frameworks that are rooted in ecology, but shift away from the strict focus on the average often found in biological sciences, dubbed the “tyranny of the golden mean”. This thesis uncovers within-host origins, and explores the between-host consequences, of heterogeneities in vector-borne diseases. In the first half, I outline how differences in within-host ecological processes generate variation in parasite population dynamics and health outcomes of malaria infection across inoculum sizes and host genetic backgrounds. In the latter half, I present host population-level consequences of variation generated by tri-trophic interactions be- tween parasites, hosts, and arthropod disease vectors, and of temperature-dependent heterogeneity in within-vector processes that govern the timing of infectivity. Overall, this thesis showcases the synergistic benefit of combining mathematical and computational modelling with empirical data to achieve better understanding and management of infectious diseases.
Machine Learning in Algorithmic Trading leading to Reinforced Deep Kalman Filters
Keywords: Algorithmic Trading
Artificial Inteligence
Finance
Machine Learning
Reinforcement Learning
Statistics

In this thesis, we develop machine learning frameworks that are suitable for algorithmic trading, where environments are volatile, heteroscedastic, and driven by latent factors. The thesis contains two main parts increasing in the complexity of the frameworks we develop. In the first part, we model the dynamics of ask-bid prices using and Hidden Markov Models (HMM) and compare its performance against First Order Markov Models (MM). A supervised learning method is developed for making binary (buy or sell) market order predictions using Restricted Boltzmann Machines (RBMs). The RBMs are adapted to Gaussian-Bernoulli (GB-RBM), and later to discriminative GB-RBMs (DGB-RBM). The algorithm's performance is compared to predictions made using the industry standard of naive bid-ask depth imbalances. We demonstrate that the DGB-RBM outperforms the industry standard by up to 18% increment in the area under the receiver operating characteristic curve (AUC). In the second part, we use traditional reinforcement learning (RL) algorithms to solve an optimal execution problem – where an agent seeks to optimally sell stocks to simultaneously mitigate the risk of price movements and price impact in a stochastic environment. We develop optimal policies using variants of Q-Learning, DynaQ-ARIMA and DynaQ-LSTM algorithms, which are used as benchmarks. The analysis shows that idiosyncrasies of the optimal execution problem require delicate treatment of data inefficiency and model bias issues, which we address next. We propose a model-based RL approach, coined Reinforced Deep Kalman Filter (RDKF), designed to integrate desirable properties of a reinforcement learning algorithm acting as an automatic trading system. The network architecture allows for the possibility that market dynamics are partially visible and are modified by the agent's actions. The RDKF filters incomplete and noisy data to create better-behaved input data for RL planning. The policy search optimisation also properly accounts for state uncertainty. We perform ablation studies to understand the contributions of individual components of the RDKF. The experiments show that the RDKF is data-efficient and provides financial gains compared to the benchmarks in the optimal execution problem using real data sets from the limit order book of Facebook, Intel, Vodafone and Microsoft.
The Law Society of Ontario’s Assessment of Capacity in Relation to Mental Illness: A Critical Analysis
Keywords: Capacity
Illness
Licensee
Mental
Regulatory
Society

Over the past 20 years, a number of studies across the globe have found that mental health issues—including substance abuse, depression, anxiety, and other forms of psychopathology—are especially acute in the legal profession. The Law Society of Ontario (“Law Society”), the regulator of the legal professions in the province, has a role to play in addressing these issues, particularly due to its statutory jurisdiction over the capacity of lawyers and paralegals (“licensees”). In this paper, I review in depth the Law Society’s current approach to licensee capacity concerns in its applications before the Law Society Tribunal. My critical examination of the current coercive processes is informed by their impacts on the autonomy interests of licensees. Ultimately, I argue that in light of these impacts, the Law Society’s authority with respect to licensee capacity must be strictly and narrowly interpreted, to the greatest benefit of the individuals at issue.
Anatomical Study of the Knee and Shoulder Joint Capsules: Innervation to Innovative Interventions
Keywords: Anatomy
Joint Innervation
Peripheral Nerve Block
Radiofrequency Ablation
Regional Anesthesia

The number of individuals diagnosed with osteoarthritis (OA) is expected to rise to more than 10 million by 2034. Treatment options for painful knee and shoulder joints related to OA include physiotherapy, prescription opioids and joint replacement. Image-guided peripheral nerve blocks (PNB) and radiofrequency ablation (RFA) have emerged as an alternative intervention to manage acute and chronic joint pain respectively. PNB consist of local injections that temporarily block sensory nerves from transmitting pain from the joint to the brain. More prolonged pain relief is provided by RFA which uses heat to stop sensory nerves from functioning. Currently, x-ray (FL) and ultrasound (US) imaging are used for guiding PNB and RFA procedures. To successfully use FL and/or US to guide PNB and RFA, clinicians need to know the location and course of sensory nerves, supplying the joint, in relation to surrounding bones, muscles and blood vessels. To date, there is a lack of research focusing on the anatomy of the sensory nerves and their relationship to landmarks visible with FL and/or US. Without this information, it is challenging to successfully target sensory nerves and manage pain using PNB and RFA. Therefore, the purpose of this thesis was to investigate and document the relationship of sensory nerves supplying the knee and shoulder joints, to bony and soft tissue landmarks visible with FL and/or US. This thesis involves cadaveric dissections and three-dimensional mapping of the fine sensory nerves supplying the capsule of the knee and shoulder joints in relation to bony and soft tissue landmarks. The anatomical findings will improve the management of joint pain by providing the basis to evaluate current and develop new PNB and RFA procedures that better target sensory nerves supplying the knee, and shoulder joints. More effective PNB and RFA protocols will provide improved pain management and quality of life for patients living with symptomatic knee and shoulder joint OA.
Belief-revision in Children and Adults
Keywords: belief-revision
categorical knowledge
updating

Our beliefs about the world are prone to change as we encounter information that is incompatible with existing knowledge. Prior research has dominantly focused on children’s deference to new information, when this information defies their existing perceptions and intuitions. However, the differential weight children attribute to various beliefs in their knowledge set when the new information calls for revision has been underexplored. This dissertation aims to expand our understanding of the reasoning process underlying children’s belief-revision. Do some beliefs have privileged status in children’s representation of the world, therefore making them more resistant to revision than others? Findings presented in Chapter 2 showed that 5-, 7-year-old children and adults were equally likely to revise beliefs based on generalizations (e.g., All of Sophia’s balls are dotted) and beliefs based on observations (e.g., Sophia brings a ball from her box to the table) about a particular entity when faced with inconsistent evidence (e.g., The ball on the table is striped). These results failed to replicate earlier findings showing a robust preference among 7-year-old children and adults to retain generalizations (e.g., All knights of King William wear a white hat) and instead to revise particular observations (e.g., This knight wears a black hat). In Chapter 3 I addressed the possibility that category generalizations have a privileged status specifically when they convey essential, non-accidental aspects of the category rather than non-essential, accidental aspects. The results from Chapter 3 provided partial support for the differential weight 4- to 7-year-old children assign to essential and non-essential beliefs about a novel category. Overall, children revised their beliefs randomly. However, an analysis of performance by trial showed that children did not readily revise their initial beliefs based on the essential property of the novel exemplar in the first trial. Taken together, these studies suggest that when incorporating new information into their existing knowledge, adults, and children between the ages of 4 to 7 years do not attribute a privileged status to their beliefs about category generalizations, not even when these are based on essential properties. Possible implications of children’s flexibility in revising existing beliefs are discussed.
The Utility of Zooplankton Size Spectrum Parameters as Ecological Indicators
Keywords: body size
environmental change
indicator
invasive species
size spectrum
zooplankton

The overarching goal of this thesis is to assess the sensitivity of the zooplankton community size spectrum to ecosystem change in lakes. This was accomplished using two large-scale datasets to investigate the temporal and spatial patterns of the zooplankton normalized abundance size spectrum (NASS). First, using a 30-year time series from eight lakes (Dorset lakes) I characterized the range of variability in the zooplankton NASS associated with among-lake differences and long-term environmental change and documented its common seasonal pattern. The slope (relative abundance of small and large organisms) was a relatively stable feature of the zooplankton community compared with the height (total abundance). I detected a relatively strong seasonal signal in both the slope and the height, with an overall decline in height and increase in slope over the ice-free season. Second, I used the Dorset lake dataset to investigate the among-lake and among-year drivers of variability in the zooplankton NASS and its responsiveness to invasion by Bythotrephes, a spiny water flea. Morphometric characteristics were the best predictors of both the slope and the height. Temporal variability in the slope was related to changes in lake phosphorus levels, while in the height it was related to dissolved organic carbon and ice duration. The NASS changed in both central tendency and variability after Bythotrephes invaded, demonstrating its usefulness as an indicator of a top-down perturbation. Last, I used a diverse group of Ontario lakes to better understand the drivers of among-lake variability in the zooplankton NASS. Consistent with previous results, morphometry was a strong driver of variability. Additionally, there was a strong spatial signal in the slope and seasonal signal in the height. Once these factors were controlled for, I was able to detect an influence of the fish community and anthropogenic stressors. Taken together, the zooplankton size spectrum is responsive to both bottom-up and top-down factors, with unusual size spectrum slope values potentially indicating a strong perturbation. I have offered some recommendations for continued development of the zooplankton community size spectrum as a universal tool for lake monitoring.
Les symptômes du manger : Troubles et conduites alimentaires dans la littérature réaliste et naturaliste du XIXe siècle
Keywords: Alimentation
Épistémocritique
Littérature
Naturalisme
Réalisme
Sociocritique

Cette thèse analyse la représentation des objets et des conduites alimentaires dans neuf œuvres réalistes et naturalistes du XIXe siècle. La question est surtout abordée dans une perspective sociocritique (Duchet, Amossy) et épistémocritique (Pierssens, Dahan-Gaida). L’analyse se concentre sur la présence des objets de discours alimentaire, tels que les mets et les restaurants, ainsi que les choix lexicaux et narratifs qui invoquent ce même discours. Le premier chapitre délimite l’approche théorique et explore le « discours alimentaire » tel qu’il se configure au XIXe siècle. Les deux chapitres qui suivent s’appliquent, respectivement, à l’analyse d’un corpus balzacien réaliste et du naturalisme de Zola et Maupassant. L’étude du Médecin de campagne (Balzac, 1833) suggère un modèle d’alimentation normative dont les atouts se ressentent au niveau personnel et national. À l’inverse, Eugénie Grandet (Balzac, 1833) nous permet de prendre la mesure des conséquences d’une conduite alimentaire mésadaptée. Le cousin Pons (Balzac, 1847) permet une méditation sur la question du « goût » et de ses mutations au long du siècle. Enfin, Illusions perdues (Balzac, 1837) situe le parcours narratif de son protagoniste autour des tables parisiennes, où les choix alimentaires sont investis de conséquences importantes. Le troisième chapitre quitte le réalisme balzacien, en commençant par l’analyse de Nana (Zola, 1880), roman qui s’articule autour d’une « mangeuse d’hommes ». Les autres romans zoliens analysés prennent également appui sur des stéréotypes et mythes de la dévoration : L’assommoir (1877) dépeint une surconsommation ouvrière à travers des personnages « mangeurs » et « mangés » ; Le ventre de Paris (1873) véhicule un drame politique autour de la dynamique du « gras » et du « maigre » ; enfin, Pot-bouille (1882) accuse les fausses apparences des manières bourgeoises par des scènes de dévoration économique et sexuelle. Pour compléter l’analyse du naturalisme, Boule de Suif (Maupassant, 1880) démontrera que la métaphorique alimentaire, non exclusive à Zola, peut appuyer des perspectives diverses à partir des mêmes éléments discursifs. Au fil de ces analyses, nous interrogerons la question de l’alimentation troublée, non dans son sens « officiel », mais plutôt dans son sens populaire et conflictuel.
Dynamics of Auditory Reflective Attention in Speech-in-noise Perception
Keywords: Attention
Auditory
Speech-in-noise

The ability to listen to speech in noisy environments is supported not only by mechanisms of sound segregation and auditory streaming, but also by higher-order cognitive functions such as semantics, attention, and memory. Major strides have been made to understand how each of these cognitive functions contributes to comprehension of incoming speech signals, leading to the emergence of predictive models of speech comprehension in noise. Whereas most studies have focused on the effects of prior contextual information on speech-in-noise (SIN) processing, less is understood about the mechanisms involved in the effects of subsequent contextual information, in which a noisy signal is followed by context. This dissertation characterizes the involvement of subsequent semantic contextual information across three studies, informed by an auditory attention to memory (AtoM) approach. Study 1 first directly compared the effects of prior and subsequent semantic context on identification of a word in noise, and found that a subsequent cue word that was related to a target word in noise could boost identification of the target, although not as well as presenting it prior to the target. Study 2 built on Study 1 by comparing the neural mechanisms underlying prior and subsequent semantic context using electroencephalography (EEG), with results suggesting different temporal dynamics underlying performance. Finally, Study 3 incorporated multiple words in noise as targets and manipulated the participants’ instruction of cue usage, finding dissociable effects of instruction, relatedness among the targets, and relatedness of a subsequent cue to targets. These findings are discussed in the context of models of SIN processing, semantic priming, and AtoM.
Artistic Identity and Space: The Journey of a Group of Graduates from an Arts High School
Keywords: Art Education
Artistic Identity
Arts High School
Identity
Space

While there is an abundance of information about how the arts are used to express and explore identity among at-risk or underprivileged youth, the relationship between school contexts and artistic identity is not well documented. This study aims to address this gap by investigating how artistic identity is shaped through the experiences students encounter in school settings. This narrative research examines the ways in which the notion of artist is conceptualized and explores how artistic identity is constructed in the discourse of participants. Through in-depth, semi-structured interviews, I explored the perception of the schooling experiences of 24 graduates from one arts high school in Toronto to better understand how these graduates, with the distance of time, perceive this experience in the context of their lives. The descriptive accounts provided in the graduates’ narratives unearthed the artistic identities that emerged from their early childhood experiences, in addition to revealing a sense of belonging they fostered at school that helped to shape their artistic identity. A major finding of this research is the process by which participants began to understand themselves as artists in relation to others, and within the social milieu of the arts high school. The research findings showed that the school shaped and reinforced the very concept of what it means to be an artist. Understanding the various paths that students take after graduation will shed light on the role of the arts in schools, and provide further understandings of the drives and motivations of the graduates who choose a career in art (or not) and how these factors challenge preconceived notions about what it means to be an artist.