VictorJuiz/thesis huggingface dataset:
Acid-treated Biochar as Heterogeneous Catalyst for the Visible-light Driven Wet-peroxide Valorization of Biomass into Dicarboxylic Acids

The depolymerization of biomass into dicarboxylic acids (DCAs) presents a promising green pathway to reduce reliance on fossil fuel feedstocks. However, large-scale implementation faces challenges due to costly noble metal catalysts and harsh reaction conditions. This research investigates the use of sulfuric acid-modified pyrolysis carbons (SBC) loaded with TiO2 nanoparticles as catalysts for visible-light-driven, photo-Fenton activation of H2O2 to depolymerize biomass into DCAs under circumneutral pH conditions.We evaluate the physicochemical properties of SBCs by studying the photo-Fenton-like degradation of methyl orange (MO) as a surrogate. Two applications of SBCs are explored: depolymerization of alkali lignin and oxidation of glucose into DCAs. Factors such as pyrolysis temperature, surface acidity, and persistent free radical (PFR) concentration influence the catalytic activity of SBCs. SBCs prepared at 500°C exhibit excellent performance in MO removal and total organic carbon (TOC) reduction under photo-Fenton conditions. However, the presence of PO_4^3- inhibits MO removal by poisoning the Lewis acid sites on SBC. Electron paramagnetic resonance (EPR) studies reveal key transient species involved in the degradation process, including •OH, •O_2^-, and 1O_2. For lignin depolymerization, SBC catalysts prepared from rice straw biomass show enhanced catalytic performance in activating H2O2 under Fe-free conditions. Oxygenated surface functional groups and PFRs enable SBC to activate H2O2 and dissolved O2, generating •OH and 1O_2. The addition of the NaN3 scavenger enhances cumulative DCA yields, confirming 1O_2 as the primary reactive oxygen species. The SBC catalysts demonstrate stability and recyclability over multiple cycles, with slight decreases in lignin conversion and DCA yields. Similarly, with glucose, the SBC catalysts produce mesaconic acid, an unsaturated C4-DCA in aqueous solutions via hole-mediated oxidation. Overall, this research lays the foundation for sustainable strategies to valorize biomass. By utilizing a portion of the biomass feedstock to produce durable catalysts, the remaining biomass can be efficiently converted into industrially relevant platform chemicals. These findings advance green chemistry and offer promising avenues for the eco-friendly utilization of biomass resources.

Keywords: Advanced oxidation processes
Biochar
Biomass
Fenton
Photocatalysis
Water treatment
Advisor: Farnood, Ramin R.
Persistent Place-Making in the Ancestral Wabanaki Homeland: Washademoak Multi-coloured Chert and the Belyeas Cove Quarry

Lithic quarries are significant places for hunter-fisher-gatherers; they are persistent places which offer critical tools for survival, and their archaeology often speaks to millennia of human engagements with past landscapes. Despite this, much of quarry research has been framed through a positivist lens which de-emphasizes the ways in which stone mediates both social and economic relationships and plays important roles in the ritual lives of many groups. This thesis explores how lithic resources, and the bedrock sources for those resources, offer a space for understanding Ancestral Wabanaki place-making and how groups interacted with, and constructed their past landscapes. I focus on the known bedrock source for Washademoak Multi-coloured Chert (WMCC) at Belyeas Cove, Washademoak Lake, in the Lower Wolastoq region, New Brunswick, Canada. Using a dataset of 148 archaeological sites spanning from the Palaeoindian period through to the 18th century, I argue the procurement, preparation, distribution, and use—the circulation—of Washademoak Chert maps Ancestral Wabanaki relationships within the Maritime Peninsula and beyond. These data document trade patterns, ritual, domestic life, and the ways Wabanaki participated in and reconfigured wide-ranging cultural phenomena, particularly so during the Maritime Woodland period (3000–500 cal BP). Persistent place-making is built through mutually constituted relationships between people, their landscapes, and the things they create. The circulation of those things builds connections to, and between, places and can be thought of as a type of portable place-making. By tracking the distribution of WMCC through time and space, this research explores the relationship between past peoples and their landscapes—natural and social—how those relationships were mediated through materials like stone, and how actions like quarrying, preparing, and circulating or exchanging stone were part of persistent place-making at the Belyeas Cove quarry.

Keywords: Hunter-fisher-gatherer
Lithic quarries
Maritime Peninsula
Persistent places
Place-making
Wabanaki
Advisor: Coupland, Gary G
The SO(4) Verlinde Formula Using Real Polarization

We adapt the construction of Jeffrey and Weitsman to interpret the SO(4)Verlinde formula through a real polarization. To accomplish this objective, our study focuses on the moduli space of flat G connections on a compact, oriented two-manifold of genus g denoted as $\Sigma^g$. We explore this space for various Lie groups G and establish their relationship through a double covering map. By utilizing the Goldman flow, we identify the Hamiltonian flows with a period of 1. These period 1 Hamiltonian flows then allow us to determine the Bohr-Sommerfeld fibres. Through this process, we establish a one-to-one correspondence between the number of Bohr-Sommerfeld fibres and integer labellings of a trivalent graph derived from the pants decomposition of $\Sigma^g$ under certain conditions. The count of such labelling provides the precise dimension of the Hilbert space $\mathcal{H}$, which emerges from the geometric quantization of the moduli space.

Keywords: Geometric quantization
Goldman flow
Real polarization
Symplectic geometry
Toric manifold
Verlinde Formula
Advisor: Jeffrey, Lisa LJ
Characterization and Visualization of Most Abundant Microbes in a Methanogenic Benzene Degrading Culture

A methanogenic benzene degrading enrichment culture in our laboratory harbours two poorly characterized organisms, Desulfobacterota (ORM2) and Ca. Nealsonbacteria. This enrichment culture therefore provided a valuable opportunity to study these poorly understood microbes in a stable culture. ORM2 has previously been established as the main benzene fermenter in the culture, however had never been visualized microscopically. Ca. Nealsonbacteria is a member of the Candidate Phyla Radiation with almost no cultivated representatives. The thesis aimed to visualize these two uncultivated microbes and uncover Ca. Nealsonbacteria’s role in the methanogenic benzene-degrading enrichment culture, using combinations of various microscopic techniques and genome-enabled technologies. A specific fluorescent in situ hybridization (FISH) probe was developed for ORM2 to observe its behavior during growth. FISH analyses showed ORM2 cells as variable-length rod shapes that often associated with other cells, particularly methanogens. Microscopic and genomic analyses suggested that ORM2 may produce extracellular polymeric substances (EPS) that likely contribute to cell aggregation. EPS production might consume substantial energy, possibly explaining the lag time before the onset of ORM2 growth upon fresh medium inoculation. We observed that cell aggregation seemed to be related to benzene concentration, disappearing at higher benzene concentrations of 90-120 mg/L. Furthermore, through several enrichment assays with various substrates, we assigned a role to Ca. Nealsonbacteria as a biomass recycler in the methanogenic benzene degrading culture. Microscopic images revealed that tiny Ca. Nealsonbacteria cells were attached to archaeal Methanothrix cell filaments, suggesting an epibiont lifestyle. Metabolic predictions based on a manually curated complete genome also supported this finding. In summary, this study provided the first visualization of cells from a novel clade within the Desulfobacterota (ORM2) and a member of the Candidate Phyla Radiation (Ca. Nealsonbacteria) in methanogenic benzene degrading culture, revealing their microbial spatial organization. These results provide insights into improving the growth rate and cell density of ORM2 to aid in remediation of sites contaminated with benzene and other hydrocarbons. This study also identified a rare example of a bacterial-archaeal episymbiosis, which may be a common feature of many other Ca. Nealsonbacteria that are found in abundance in anoxic environments.

Keywords: Biomass Recycling
Candidate Phyla Radiation
Electron Microscopy
Fluorescence in situ hybridization
Genome-resolved Metagenomics
Methanogenic Benzene Degradation
Advisor: Edwards, Elizabeth A
Spatial Patterns of the Amygdala Engram

The amygdala is a key region for encoding and recall of associative memories. Neurons that are more active during fear learning form an engram which is later reactivated during recall of that event. Engram populations are essential for encoding and recalling salient experiences, but the location of these neurons within the amygdala is not well understood or characterized. To understand how endogenous engram populations are distributed in the amygdala, we imaged whole amygdala subregions in three-dimensions to capture the spatial properties of all active neurons during differently valenced events (aversive or neutral) and at different memory stages (encoding or recall). At a meso-spatial scale aversive encoding engram populations had greater ventral and posterior density in the LA, greater posterior density in the BA, and greater posterior density in the CeL. Density profiles of all subregions revealed that engram states were more similar to each other compared to baseline amygdala activity. Recall states, regardless of valence during encoding, were the most highly correlated. Spatial clustering of active neurons revealed micro-level spatial clusters in all conditions including baseline. The relative number of clusters increased during aversive and recall conditions in the LA and BA, and during aversive learning in the CeC. Network graphs were constructed from engram spatial distributions; these revealed that amygdala activity was highly clustered and assortative in all conditions. Assortativity was significantly increased in the CeC during aversive encoding, and hub node number was significantly increased in the LA during both aversive encoding and recall and in the CeC during aversive encoding. We have demonstrated that meso- and micro-level spatial patterns exist in the amygdala, and these patterns are modified during engram activation at encoding or recall. These changes may reflect modified neuron activity propagation that improves signal-to-noise for salient features.

Keywords: amygdala
cluster
engram
Advisor: Josselyn, Sheena A
Nation, Narrative and Archive: In Search of Queer Histories in Zimbabwe

This dissertation argues for a new genealogy for telling the history of queerness in Zimbabwe. State-sponsored histories have created a narrow, nationalist narrative that relegates queerness to the margins. This is a project that resides in those margins. By sinking deep into the spaces that queer bodies create for themselves in those margins, I develop a reading practice that disrupts existing narratives through the analysis of archives as cultural formations and demonstrating how changing how we constitute these formations can lead to narratives that can lead to freedom. I argue that the state’s political homophobia has an outsize role in defining the discourse on homosexuality in Zimbabwe and that this results in trauma-centred narratives or what Keguro Macharia would term negating spaces. Even when scholars focus on counter-narratives, we are still allowing the state to shape the language of the discussion and therefore limit what we can imagine. By being attentive to the myriad of ways that LGBTI Zimbabweans engage in social negotiations of identity, and the stories they tell, I theorize how LGBTI people are defining non-normative sexualities in Zimbabwe. LGBTI people are already actively engaged in the work of articulating distinctively African queer subjectivities. They are already imagining a different story. Through narrative interventions in four moments of queer history in Zimbabwe, I develop a reading practice that draws from Queer African Studies, to allow for a different Queer Zimbabwean narrative, one that centers the freedom and liberation of the marginalized. This reading practice disrupts existing narratives through the analysis of archives as cultural formations and demonstrating how changing how we constitute these formations can lead to narratives that can lead to freedom. My methods are informed by my creative writing practice as I work with storytelling as method. I also draw from indigenous oral traditions and indigenous Shona frameworks of the power of story to develop my method.

Keywords: Archives
Queer African Studies
Zimbabwe
Advisor: Cowan, T.L.
Evaluating Continuing Health Professions Education as Health Policy for the Opioid Crisis

Continuing health professions education (CHPE) has been considered an essential intervention for addressing the Canadian opioid crisis. CHPE programs are complex – they involve the actions of people and a complex chain of steps, are embedded in social systems shaped by context, and are open systems subject to change. Drawing on frameworks for evaluating complex interventions, the objectives of this thesis were to: 1) systematically assess all published evaluative reports of CHPE programs for their appropriateness as interventions to reduce opioid-related harms and improve population health; 2) conduct an implementation evaluation of the Safer Opioid Prescribing CHPE program; and 3) develop a conceptual model to support the design and evaluation of population health focused CHPE. Addressing opioid-related harms was a consistent justification for the development and delivery of the 32 opioid analgesic prescribing CHPE programs. Yet, evaluations of these programs rarely encompassed patient- or population-level outcomes, focusing primarily on self-reported performance outcomes. There was likewise little explicit use of educational or other theory reported in program development and evaluation. Implementation evaluations can support such interrogations of program theory. It was determined that the Safer Opioid Prescribing program was implemented as intended along the outcomes of reach, dose, fidelity, and participant responsiveness. This identified a promising model for using virtual continuing health professions education to reach a critical mass of prescribers to address large scale health problems. However, due to the complex and dynamic nature of the opioid crisis, scaling up of successfully implemented programs is no guarantee achieving beneficial population health outcomes. Drawing on the fields of clinical population medicine, the social determinants of health, health equity, and philosophies of population health, at least five ways of re-orienting CHPE programs towards population health were identified. These included: 1) scaling effective CME programs while evaluating at population health levels; 2) (re)interpreting evidence for program content from a population perspective; 3) incorporating social determinants of health into clinically-oriented CME activities; 4) explicitly building fluency in population health concepts and practices among health care providers and CME planners; and 5) attending to social inequity in every aspect of CME programs.

Keywords: Analgesics Opioid
Education Continuing
Health Policy
Opioid-Related Disorders
Pain
Population Health
Advisor: Upshur, Ross EG
Application and Development of Machine Learning for the Discovery of Novel Functional Materials: From Lithium Ion Battery Cathodes to Direct Band Gap Optoelectronics

Nearly every industry is seeking improvement in material performance such as strength, durability, efficiency, or cost. However, traditionally, material discovery has been a slow process and there is a large desire to speed it up. Recently, a method that has been gaining more attention for the screening of large datasets to find novel materials is machine learning (ML). In the first section of my thesis, I will review the material screening process along with fundamental concepts related to batteries, opto-electronics, and machine learning. In chapter 2, I will report on a pre-screening tool used to obtain equilibrium structures enabled by ML, and in chapters 3 and 4 I will report on ML models for the screening of cathode voltage and band gap type. To obtain accurate ML predictions, optimized equilibrium structures are needed. However, these are not known for new materials and generally need to be obtained by computationally expensive optimization methods. In chapter 2, we demonstrate an ML-based geometry optimizer, capable of minimizing the energy of perturbed structures. The model was trained on both ground-state and systematically distorted structures. This allows our enhanced model to understand the effects local and global distortions have on crystal energy. In chapter 3 we developed an ML model to predict the voltage of battery cathode materials, enabling the rapid screening of new materials. The model relied on the addition of extra data points, particularly materials with unfavorable lithium binding. We were able to identify 12 viable new cathode materials. In chapter 4 we demonstrate two machine learning models, which are capable of classifying the band gap type of inorganic materials. We were able to train a model with a 90% true positive rate. We demonstrated its utility to discover new PV and LED materials, by identifying previously known materials as direct band gaps, and by converting known indirect materials to direct, by alloying. Overall, this work demonstrates practical methods to improve the prediction of novel materials, however, several challenges remain. In chapter 5, I discuss potential applications of the presented work, along with strategies to further improve and validate the models.

Advisor: Voznyy, Oleksandr
Optimization Models for Kidney Paired Donation

Kidney paired donation is a living-donor transplantation scheme allowing patients with end-stage renal disease to get a compatible donor when their own is not a match. Compatibilities among donors and patients can be modelled in a digraph, whose vertex set represents a donor with or without a paired patient and an arc depicts compatibility between donors and patients. Kidney allocation in this context consists of finding a matching, i.e., a set of vertex-disjoint cycles and chains. Despite the broad attention that kidney paired donation has received, some questions at algorithmic, operational and managerial levels remain open. This dissertation addresses the design and analysis of more realistic matching models in settings of real-world interest. This dissertation investigates new techniques from large-scale optimization to solve existing and new research questions on kidney allocation within the scheme of kidney paired donation. The central thesis of this dissertation is that optimization methods can assist kidney paired donation in the search of equitable, policy-wise flexible, failure-aware and computationally tractable kidney allocation in static and dynamic settings. Throughout this work, we address this thesis by designing novel models and solution methodologies to decide on what actions to take, when to take them and the mechanisms to protect allocation decisions from failure. Our first project presents the first branch-and-price algorithm to successfully integrate short-long cycles and chains. Empirical evidence shows the importance of long chains in creating more matching opportunities for hard-to-match patients. The second project addresses uncertainty in a two-stage optimization framework, whose solution approach is the first to address both homogeneous and non-homogeneous failure and offers flexibility on the policies that allow a failed matching to be repaired. Our algorithms for the first two chapters outperform the state of the art in their domain on publicly available instances. The last project studies the long-term implications of selecting a deterministic and robust solution in a dynamic setting using simulation.

Keywords: Branch-and-Price
Decision Diagrams
Integer Programming
Kidney Paired Donation
Large Scale Decompositions
Robust Optimization
Advisor: Aleman, Dionne
Bodur, Merve
Advanced Microscopy to Investigate Nanoparticle Transport Mechanism

Nanoparticles are used as delivery platforms for cancer therapeutics or imaging agents to tumours. However, the translation of nanoparticle therapy is hindered by the limited understanding of the transport of nanoparticles in the body. Recent advancements have shown that cellular mechanism dictates the transport of nanoparticles. In my thesis, I examine 1) locally released platelet factor 4 in injured blood vessels leads to local uptake of nanoparticles in the endothelial cells; 2) the new mechanism of nanoparticle transport by tumour-associated macrophage migration; 3) the contribution of macrophage-mediated transport of nanoparticles over passive diffusion. The knowledge presented in this thesis will help guide future nanoparticle design and therapeutic by 1) manipulating the protein adsorption to tune the uptake in cells and 2) utilizing the different mechanisms of transport to improve nanoparticle distribution in the tumour microenvironment.

Keywords: Nanoparticle delivery
Nanotechnology
Protein corona
Tumour-associated macrophage
Advisor: Chan, Warren C.W.
Frankenbike Re-imagined for Percussion Quartet and Electronics

Frankenbike re-imagined is an audio-visual installation of instruments built from re-purposed scrap metal bike frames and parts. This interactive installation explores the points of control on a bike and uses them in a tactile way to generate sound. The main components of the installation are the rotation of the drivetrain system and its counterparts, the tension of the cable and spoke systems, and engaging with the external components as percussive found sounds. It modifies them to enhance the sounds they naturally produce, creating a sonic landscape from mechanical gestures. The installation contains a main structure of two bike frames balancing on each other, and two additional mechanic stands holding suspended resonant objects. The installation uses a combination of contact, close, and external microphones for amplification, pedal effects for signal processing, and stereo output. Frankenbike re-imagined can be presented in two versions—in a concert setting with an accompanying score for percussion quartet, or in a gallery space as an interactive installation. Urban bike culture has its roots in living sustainably and economically. Bike commuting has gained popularity as a low-cost and ecological alternative to driving or taking public transportation. Connecting to these themes, Frankenbike re-imagined was built entirely from re-purposed parts—all materials used were either damaged or not suitable for reuse. The installation seeks to give them a life other than being discarded as scrap metal, existing beyond the purpose for which they were intended. Do-It-Yourself culture is also prevalent amongst city bike riders as an affordable option for bike repair, as well as to learn the skills necessary to do your own bike maintenance. Refurbishing older bikes, as well as building bikes entirely from used parts, are also low budget options. Currently I work as a mechanic in a bike repair shop where I am constantly listening to these mechanical sounds when I work. I often consider the relationship of these sounds to their functions—a sound often signifies a problem in the system that needs to be corrected, and a quiet bike usually indicates a well functioning bike. Through this project I seek to embrace these imperfections and re-imagine my mechanical skills for creative applications.

Keywords: bicycle
percussion
sound installation
Advisor: Suzuki, Kotoka
Newsome, Gregory