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Recent Submissions
TECTONIC EVOLUTION OF THE BAIE VERTE MARGIN, NEWFOUNDLAND
(University of Waterloo, 2025-01-17) Scorsolini, Ludovico
Located along the Early Paleozoic Laurentian continental margin in Newfoundland, the Baie Verte Margin tectonistratigraphy and tectono-metamorphic evolution have been controversial for decades. Here, the results of a detailed field, petrological and geochronological study are presented, where Baie Verte Margin is subdivided into three tectono-metamorphic units separated by tectonic contacts: the East Pond Metamorphic Suite (EPMS) basement, EPMS cover, and the Fleur de Lys Supergroup (FdLS). Each unit exhibits a distinct metamorphic and structural evolution recorded during the subduction, exhumation, and post-collisional history of this ancient margin. The combination of thermodynamic modelling, petrochronology, and structural analysis provided insights into the P-T-t-d paths of the studied units, allowing a better understanding of their role during the evolution of the Taconic subduction system. High-pressure (HP) to ultra-high-pressure (UHP) conditions were reached between 483 and 475 Ma during the D1 phase, with the EPMS cover recording eclogite-facies metamorphism at ~2.8 GPa and 620°C. Subsequent decompression resulted in a β-shaped pressure-temperature-time (P-T-t) path, with near-isothermal decompression to ~2 GPa and heating to 860°C during exhumation. A multi-stage exhumation model is proposed for the EPMS eclogites: 1) buoyant rise through a low-density mantle wedge and 2) subsequent ascent at shallower crustal levels, facilitated by external tectonic forces and slab break-off, as evidenced by Late Taconic magmatism.
While the EPMS cover re-equilibrated at UHP conditions, the EPMS basement and FdLS experienced decompression and Barrovian metamorphism during late-D1, indicating decoupling of the units during this stage. Coupling between the units occurred along a D2 shear zone during retrograde metamorphism, spanning 475–452 Ma.
Two exhumation scenarios are proposed to explain the tectonic evolution of the margin: (i) Following late D1 detachment, the EPMS basement and FdLS were exhumed to crustal levels while the EPMS cover was subducted deeper into the mantle. Tectonic extrusion along D2 shear zones, potentially aided by melt weakening, then emplaced the EPMS cover between the two units. (ii) Alternatively, sequential detachment occurred from the top to the bottom of the slab, resulting in deeper subduction of lower units, followed by their exhumation through back-folding and crustal wedge thrusting.
The Silurian F3 folding deforms both D1-2 structures in each unit and the D2 shear zones that bound them, suggesting that the continental wedges, which recorded different tectono-metamorphic paths after early D1, were juxtaposed before the onset of deformation associated with the Salinic Orogeny. Later deformation phases, D4 and D5, are probably related to tectono-metamorphic activity related to the Acadian and Neo-Acadian orogenies.
This research improves our understanding of the dynamic tectono-metamorphic evolution of the Baie Verte Margin, emphasizing the role of fluids, thermal perturbations, and deformation in driving metamorphic reactions, and exhumation. The findings contribute to understanding the mechanisms controlling HP-UHP terrain evolution in subduction zones and highlight the complex interactions between subduction, exhumation, collision, and magmatism throughout the Taconic orogeny.
Code Generation and Testing in the Era of AI-Native Software Engineering
(University of Waterloo, 2025-01-17) Mathews, Noble Saji
Large Language Models (LLMs) like GPT-4 and Llama 3 are transforming software development by automating code generation and test case creation. This thesis investigates two pivotal aspects of LLM-assisted development: the integration of Test-Driven Development (TDD) principles into code generation workflows and the limitations of LLM-based test-generation tools in detecting bugs.
LLMs have demonstrated significant capabilities in generating code snippets directly from problem statements. This increasingly automated process mirrors traditional human-led software development, where code is often written in response to a requirement. Historically, Test-Driven Development (TDD) has proven its merit, requiring developers to write tests before the functional code, ensuring alignment with the initial problem statements. Applying TDD principles to LLM-based code generation offers one distinct benefit: it enables developers to verify the correctness of generated code against predefined tests. This paper investigates if and how TDD can be incorporated into AI-assisted code-generation processes. We experimentally evaluate our hypothesis that providing LLMs like GPT-4 and Llama 3 with tests in addition to the problem statements enhances code generation outcomes. We experimented with established function-level code generation benchmarks such as MBPP and HumanEval. Our results consistently demonstrate that including test cases leads to higher success in solving programming challenges. We assert that TDD is a promising paradigm for helping ensure that the code generated by LLMs effectively captures the requirements.
As we progress toward AI-native software engineering, a logical follow-up question arises: Why not allow LLMs to generate these tests as well?
An increasing amount of research and commercial tools now focus on automated test case generation using LLMs.
However, a concerning trend is that these tools often generate tests by inferring requirements from code, which is counterintuitive to the principles of TDD and raises questions about their behaviour when the flawed assumption of the code under test being correct is violated.
Thus we set out to critically examine whether recent LLM-based test generation tools, such as Codium CoverAgent and CoverUp, can effectively find bugs or unintentionally validate faulty code.
Considering bugs are only exposed by failing test cases, we explore the question: can these tools truly achieve the intended objectives of software testing when their test oracles are designed to pass?
Using real human-written buggy code as input, we evaluate these tools, showing how LLM-generated tests can fail to detect bugs and, more alarmingly, how their design can worsen the situation by validating bugs in the generated test suite and rejecting bug-revealing tests.
These findings raise important questions about the validity of the design behind LLM-based test generation tools and their impact on software quality and test suite reliability.
Together, these studies provide critical insights into the promise and pitfalls of integrating LLMs into software development processes, offering guidelines for improving their reliability and impact on software quality.
Police Militarization in Canada: Examining Racial Disparities in Use of Force and Understanding the Consequences of Citizen-Police Encounters Using a Mixed-Methods Investigation
(University of Waterloo, 2025-01-17) Sidhu, Tandeep
Despite being a critical issue in the contemporary discussion on police reform in Canada, the research investigating tactical units is still in its infancy. The existing research in this area primarily focuses on the proliferation of police militarization and its argued incursion into more general elements of patrol policing. Absent from this discussion is an analysis of use of force, racial disparities in use of force outcomes, and lived experiences of encounters with tactical units. This dissertation addresses these gaps in the literature by applying a mixed-methods approach to investigate (a) the intersections between tactical unit use of force and race and (b) the social, economic, and psychosocial challenges facing individuals who have encountered these militarized policing elements.
The quantitative aspect of the research relies on the use of freedom of information requests to collect use of force reports submitted by tactical units between January 1, 2020 and December 31, 2022. The study employs the racial disproportionality and disparity index mandated by Ontario’s Anti-Racism Act. Furthermore, the quantitative aspect of this research applies a series of univariate, bivariate, and multivariate statistical analyses to develop a knowledge base in this area and find what, if any, variables are statistically significant predictors of use of force. The qualitative aspect of this research relies on semi-structured interviews with 25 individuals who have, directly or vicariously, encountered a police tactical unit and asks a series of questions concerning the nature of the encounter and its consequences for the individual and, if relevant, their family unit.
The findings of the quantitative research demonstrate that Black people are grossly overrepresented in use of force incidents involving tactical units. Unlike their White counterparts, Black people are less frequently armed in these incidents and more likely to encounter tactical units in proactive (planned) deployments. The multivariate analysis also finds that, when controlling for a range of other variables, Black people are statistically more likely to have a firearm pointed at them. Beyond the findings central to this research, the dissertation also finds evidence suggesting significant and systemic underreporting of use of force. I argue that the reporting framework is not intended to address systemic discrimination but functions to legitimize police use of force and expand militarized policing. I argue that race-based data collection functions as a form of racialized knowledge construction rather than a mechanism through which systemic racism may be addressed.
The qualitative research findings demonstrate the wide-ranging social, economic, and psychological consequences of encounters with police tactical units. The results indicate that individuals and families face various financial challenges, such as the destruction and loss of personal property, damage to their residence, and loss of access to social housing. Some participants experience theft, and others report having to pay to repair financial costs sustained. Experiences of violence are also common among these interactions with police, as are social stigma and a range of psychological outcomes owing to the traumatic nature of these incidents. Black participants also draw on the idea of communal trauma and suggest these encounters with tactical units can be further contextualized as a tool of racialized social control directed against the Black community. The qualitative accounts also demonstrate the absence of formal institutional support and the reliance on informal support networks to manage these challenges. Finally, the accounts indicate a significant disruption to the family unit, including a loss of housing and disruptions in familial relationships.
This research relies on the use of critical race perspectives to contextualize the use of tactical units as a colourblind form of social control disproportionately applied against the Black community. The institution maintains the veneer of race neutrality by making appeals to crime control and public safety, which facilitates the expansion of aggressive policing practices and exacerbates existing racial and socioeconomic inequalities. The dissertation also offers a series of recommendations.
High-Dimensional Statistical Inference and False Discovery Rate Control with Covariates
(University of Waterloo, 2025-01-17) Zheng, Liyuan
In this thesis, we focus on three statistical problems. First, we consider graph-based tests for differences of two high-dimensional distributions. Second, we investigate the estimation of multiple large covariance matrices and the application to high-dimensional quadratic discriminant analysis. Lastly, we focus on controlling the false discovery rate while incorporating complex auxiliary information.
Testing whether two samples are from a common distribution is an important problem in statistics. Friedman & Rafsky (1979) proposed a non-parametric multivariate distribution test based on the minimal spanning tree (MST). Recently, this test has been extended under various scenarios. However, as demonstrated in Chapter 2, these extensions are not sensitive to sparse alternatives. To address this, we propose a two-step testing procedure, IM-MST. Specifically, IM-MST incorporates marginal screening while accounting for the dependence structure via energy distance, followed by MST-based tests. IM-MST combines the strength of both non-parametric screening and MST-based tests. Simulation studies and real data applications are conducted to evaluate the numerical performance of the two-step procedure, demonstrating that IM-MST exhibits substantial power gains.
When estimating covariance matrices for data from two related categories, it is reasonable to assume that these covariance matrices share certain structural components. As a result, the precision matrix (the inverse of the covariance matrix) for each category can be decomposed into three parts: a common diagonal component, a common low-rank component, and a category-specific low-rank component. This decomposition can be motivated by a factor model, where some latent factors are common across two categories while others are specific to individual categories. In Chapter 3, we propose a consistent joint estimation method for two precision matrices building on the work of Wu (2017). Furthermore, these estimators are applied to formulate a high-dimensional quadratic discriminant analysis (QDA) rule, for which we derive the convergence rate for the classification error.
In many genetic multiple testing applications, the signs of the test statistics provide important directional information. For example, in RNA-seq data analysis, a negative sign could suggest that the expression of the corresponding gene is potentially suppressed, while a positive sign could indicate a potentially elevated expression level. However, most existing procedures that control the false discovery rate (FDR) ignore such valuable information. In Chapter 4, we extend the covariate and direction adaptive knockoff procedure (Tian 2020) by implementing powerful predictive functions. Through simulation studies and real data analysis, we show that our procedures are competitive to existing covariate-adaptive methods. The companion R package Codak is available.
Discovery and characterization of novel biofilm-associated proteins in Pseudoalteromonas tunicata
(University of Waterloo, 2025-01-17) Ali, Sura
Pseudoalteromonas tunicata is a marine bacterium that is a useful model for studying mechanisms of biofilm development due to its ability to form, colonize, and inhibit growth of other microorganisms in marine and eukaryotic host-associated biofilms. However, the pathways responsible for P. tunicata biofilm formation are still incompletely understood, in part due to a lack of functional information for a large proportion of its proteome. In this thesis, I use comparative shotgun proteomics to explore P. tunicata biofilm development from the planktonic phase to three stages (early, middle, late) of biofilm development. Proteomic analysis identified 232 proteins that were up regulated during different stages of biofilm development, including proteins known to be important for P. tunicata biofilm development (e.g., autocidal enzyme AlpP, violacein proteins, and various pili proteins) as well as many hypothetical proteins of unknown function. I then characterized two novel, biofilm-associated hypothetical proteins, labeled EAR28894 and EAR30327.
Functional characterization of EAR28894 revealed that it is the major S-layer protein of P. tunicata. Bioinformatic methods predicted a beta-helical structure for EAR28894 similar to the Caulobacter S-layer protein, RsaA, despite sharing less than 20% sequence identity. Transmission electron microscopy revealed that purified EAR28894 protein assembled into paracrystalline sheets with a unique square lattice symmetry and a unit cell spacing of ~9.1 nm. An S-layer was found surrounding the outer membrane in wild-type cells and completely removed from cells in an EAR28894 deletion mutant. S-layer material also appeared to be “shed” from wild-type cells and was highly abundant in the extracellular matrix where it is associated with outer membrane vesicles and other matrix components. EAR28894 and its homologs form a new family of S-layer proteins that are widely distributed in Gammaproteobacteria including species of Pseudoalteromonas and Vibrio and found exclusively in marine metagenomes. This novel protein family was given the name Slr4.
Functional investigation of the uncharacterized protein, EAR30327, revealed its function as a novel biofilm adhesin. This protein, which I designated as BapP, was the top identified biofilm-associated protein by proteomic analysis. BapP showed partial homology to outer membrane adhesins containing repeats of bacterial cadherin-like and immunoglobulin (Ig) domains. A ΔbapP mutant strain was unable to form proper pellicle biofilms in liquid media. The Δ bapP mutant also had a significantly reduced ability to form biofilms in crystal violet assays, which was rescued by re-insertion of the bapP gene into the genome. As predicted by the identification of putative Ca2+-binding motifs in BapP, biofilm formation in the wild-type strain was demonstrated to be Ca2+-dependent, which was significantly reduced in the ΔbapP mutant. This study provides a unique proteomic dataset of biofilm development and identifies BapP as a Ca2+-dependent adhesin responsible for biofilm formation in P. tunicata. The occurrence of BapP-related homologs in other species suggests that this protein family represents a broadly conserved mechanism for biofilm adhesion in marine Gammaproteobacteria species.
This thesis research establishes a proteomics-based pipeline for biofilm protein discovery and new directions for biofilm research in P. tunicata and related bacteria, and offers insights into potential targets for biofilm management and control.