VictorJuiz/thesis huggingface dataset:
Control of Acoustic Waves by Locally Resonant Phononic Crystals

Locally resonant acoustic materials were proposed to control sound using structures with feature size orders of magnitude smaller than the acoustic wavelength in air. Millimeter-sized resonators over the audible frequency range typically consist of dense cores coupled to stiff shells through elastically soft material. Using a rigid core-shell approximation (RCSA), we analytically derive the frequency-dependent, effective inertial quantities for the fundamental translational and rotational resonances of such core-shell resonators. The effective inertia is expressible in closed form by elementary functions, enabling a mapping of the low-frequency physics to a simple model involving a point mass or a rod harmonically coupled to a box. We present an effective inertia-spring tensor (EIST) model for the low-frequency acoustic modes of phononic crystals with multiple, local, resonances within each unit cell and their coupling to spatially separated resonators. The EIST model is a generalization of the widely quoted point-mass-in-a-box representation of resonant acoustic metamaterials. Our model consists of an array of frequency-dependent, effective masses and moments of inertia coupled to near and distant neighbors by a wave-vector-dependent effective spring constant matrix. We demonstrate, using several two-dimensional and three-dimensional models, that our simple representation accurately describes exact phononic band structures involving coupled translational and rotational modes, in close agreements with the finite-element method. The existence and the frequency range of local resonance band gaps are predicted by the concurrence of negative effective mass and moment of inertia. A large local resonance gap may occur in spectral proximity to a distinct gap arising from Bragg scattering. Our model is generalized to complex dumbbell-shaped resonators, revealing a dense collection of flat ``slow sound'' bands near the local resonance band gap. We demonstrate that thin claddings of such locally resonant, phononic crystals, of only three to five unit cells in thickness, can effectively prevent sound transmission, by a combination of reflection and absorption, over much of the audible spectrum. Moreover, frequency-selective sound transmission can be enabled by engineering waveguide channels that transmit sound through the local resonance gap, the Bragg gap, or both. This offers a path to sound-sculpting claddings that can surround a noise-generating source.

Keywords: Acoustics
Band gap materials
Band structure
Local resonance
Metamaterials
Phononic crystals
Advisor: John, Sajeev S.J.
Biological, Clinical, and Functional Implications of Cell-Free DNA Topology in Cancer

Cells can release their DNA into the extracellular space and circulation by active mechanisms or as a product of cell death. In oncology, this cell-free DNA (cfDNA) has emerged as a promising source of cancer biomarkers because it contains actionable information about a patient’s disease and can be readily obtained via a simple blood draw. In addition to its use in biomarker applications, cfDNA may also function as a mediator of pro-inflammatory signaling in the tumour microenvironment. Despite its mounting importance both clinically and physiologically, the biological features of cfDNA remain poorly understood. In particular, the structural relationship between cfDNA and other biological macromolecules – its topology – has not been thoroughly investigated. This lack of knowledge has limited the implementation of cfDNA to its full potential as a cancer biomarker, while also hampering our understanding of how cfDNA influences intercellular communication and tumour immunity. To address this gap, I first conducted a fundamental and comprehensive characterization of cfDNA topology in pre-clinical cancer models. I implemented a novel DNA-targeted immunoprecipitation assay to demonstrate that distinct topological subsets comprising membrane-protected or accessible cfDNA had unique sub-cellular origins and mechanisms of active release. I then applied these methods to clinical cohorts and found that topological characterization enhanced the diagnostic and prognostic capabilities of mitochondrial cfDNA. Based on these findings, I proposed a series of experiments to elucidate the in vivo origins of distinct cfDNA topological subsets and discussed important considerations for future clinical studies evaluating cfDNA topology as a liquid biopsy analyte. Next, I examined the impact of topology on the ability of tumour-derived cfDNA to stimulate DNA-sensing pathways in immune cells. Through rigorous mechanistic investigations, I observed pro-inflammatory macrophage signaling in response to accessible cfDNA released from tumour cells undergoing secondary necrosis. From this in vitro model, I outlined subsequent experimental steps to determine the fate of cfDNA-induced inflammation in the tumour microenvironment, and I considered the impact of cfDNA immunogenicity on the successful implementation of DNA-sensor-targeting cancer immunotherapies. Altogether, the knowledge gained from these studies contributes to a refined model of cfDNA biology and structure, which can be leveraged both for cancer liquid biopsy applications and to bolster our overall understanding of tumour-immune interactions as they relate to patient responses to immunotherapy.

Keywords: Cell-Free DNA
cGAS-STING
Liquid Biopsy
Tumour Immunity
Advisor: Bratman, Scott V
Understanding the Preliminary Stages of Social Evolution in Western Black Widow Spiders

The transition from solitary to social living is considered one of the major evolutionary transitions. While much social evolutionary research considers costs and benefits associated with sociality, these studies are dominated by taxa with complex cooperative social behavior. Investigating species in the early stages of social evolution provides insight into evolutionary forces that underlie the initiation of sociality . I test key predictions of three hypotheses of social evolution in the western black widow spider, Latrodectus hesperus, which displays variation in sociality across its range, from solitary to facultative group living. I studied three focal populations, one facultatively group living population in British Columbia (BC), and two solitary populations, one from California (CA), and one from Texas (TX). I used an experimental approach to test patterns of kin discrimination, inbreeding depression, and aggression in two contexts across the solitary and social populations. I found that the social BC population had higher mating success with kin compared to nonkin, and did not suffer from inbreeding depression. The CA population showed the opposite pattern of higher mating success with nonkin and both solitary CA and TX populations suffered significant inbreeding depression. However, the BC population had the lowest fecundity overall, suggesting a history of inbreeding in this population. The social BC population also displayed the lowest levels of foraging aggression. However, group living individuals within BC were more aggressive than solitary living individuals. The solitary CA population was the only population that displayed ritualized escalation of agonistic behavior, suggesting an evolutionary history of high interindividual conflict. Finally, I used reduced representation sequencing to directly assess levels of inbreeding, genetic diversity, and gene flow across the three focal populations. I found that the social BC population had the highest levels of inbreeding, lowest genetic diversity, and that gene flow was restricted between all sampled populations. Together, these results suggest that an increase in relatedness and higher aggressiveness are factors that may be contributing to social group formation and continued social evolution in L. hesperus.

Keywords: Behavior
Bioinformatics
Genomics
Social Evolution
Spider
Advisor: Andrade, Maydianne CB
Fallout 250: Anishinaabe Post-Apocalypse Survivance Handbook

Welcome to the End of Anishinaabe Time and its afterwards. Here, Anishinaabeg and their Kin are trapped in the DeathWorld where there has been a mass destruction of Anishinaabe Lifeworld and continual fallout for 250 years. Throughout this process, the totalitarian regime has created belligerent systems known as the ®CMP (Racist Colonial Matrix of Power) to ensure that Anishinaabe forms of resistance cease to be intelligible acts. Anishinaabe Remnants (ARs) are all that remain. ARs are persecuted, imprisoned, and subjected to torturous forms of erasure. Some ARs have been so badly mutated that they have become a dangerous force of destruction feeding off the most vulnerable for their own benefit.But not all is lost. In the Post-Apocalypse, there are many Anishinaabe Remnants and Kin fighting to escape the DeathWorld, fighting to salvage what is left of Anishinaabe ways of being and create something new out of 250 years of indelible violence. This Handbook is part of the fight. In the far future, a series of Spirit Worlding events converge to launch the construction of an Intergalactic Aatisokaanan Docking Station where Survivance literature can be developed. The Fallout 250 Anishinaabe Post-Apocalypse Survivance Handbook is one such book that is brought back during the time of the Post-Apocalypse to be a guide for Anishinaabe Remnants and their Kin to light the 8th Fire and save the world! The Handbook is written in the literary genre of Role Playing Games (RPGs) and contains character descriptions, skills development, collectables, and a walkthrough for the main missions required in order to journey away from victimry towards a rapprochement with the non-human and human critters in the Post-Apocalypse. The Handbook works from the position that the reader must complete all missions in order to light the 8th Fire and live beyond the the Deathworld’s apocalyptic erasure. Are you ready? Because it’s time to Get Lit!

Keywords: Anishinaabe
Anishinaabemowin
Decolonization
Futurities
Indigenization
Indigenous
Advisor: Titchkosky, Tanya
DCAF1 as a Novel Therapeutic Target for Lung Cancer

Lung cancer remains a leading cause of mortality worldwide, ranking as the second most common cancer and deadliest form in Canada. Therefore, it is important to address the urgent unmet need for novel and effective lung cancer treatments. By mining the DepMap genome-wide shRNA dropout screen, we identified a strong dependency in non-small cell lung cancer (NSCLC) on the WD40 and E3 ligase DCAF1 protein. In-house experiments confirmed that knockdown of DCAF1 resulted in a significant suppression of growth in various tested NSCLC cell lines. Moreover, DCAF1 knockdown led to cell death in all tested cell lines, with a cell cycle defect preceding cell death specifically observed in p53 wild-type cell lines. In order to understand the underlying mechanisms of DCAF1 in NSCLC, unbiased approaches such as RNA sequencing and shotgun proteomics were utilized. Our findings revealed that DCAF1 knockdown led to downregulation of pathways associated with DNA damage, cell cycle regulation, translation, and rRNA processing. Our preliminary data indicate that defects in rRNA processing are more likely to precede changes in DNA damage and cell cycle progression and might be the primary cause of our observed growth suppression phenotype. Furthermore, as part of our efforts to develop therapeutic agents for NSCLC, a hit (Z1391232269) against the WD40 domain of DCAF1 with a Kd of 490 nM in SPR was discovered using an experimental DNA-encoded library followed by a machine learning approach. Z1391232269 was successfully co-crystalized with the WD40 domain of DCAF1. A series of structure activity relationship studies to optimize Z1391232269 identified OICR-38268 a more potent analogue with a Kd of 35 nM by SPR and an EC50 of 10 μM in cells. In conclusion, our study highlights the importance of DCAF1 for NSCLC growth and that targeting it might represent a novel therapeutic approach for lung cancer treatment. Lastly, the discovery of a DCAF1 ligand represents a significant step towards the development of targeted therapeutic agents for NSCLC.

Advisor: Al-awar, Rima
A Comparative Variationist Analysis of Phonetic Variation and Change in Toronto Heritage Tagalog

Heritage languages are defined as a product of language contact. In this scenario, patterns of variability are often attributed to contact with the majority language. However, variability may not necessarily or solely be due to contact; it may also be driven by language-internal processes or even identity construction. This dissertation adopts a comparative variationist approach and develops a framework for examining variable patterns of bilingual sound production and the interplay between contact-, internal-, and identity-based processes underlying variation and change. Using Tagalog spontaneous speech data from two generations of heritage speakers in Toronto, and from older and younger homeland speakers in Manila, three phonetic variables are examined: the F2 of /u/, voice onset time (VOT) of /p t k/, and the realization of /r/. Inter-group comparisons and multivariate analyses reveal distinctive patterns. Focusing on Heritage Tagalog, results demonstrate that the F2 of /u/ exhibits stable variation whereas the VOT of /p t k/ and the realization of the rhotic as an approximant show signs of change. While the change in VOT may be attributed to contact with English (the heritage speakers’ majority language), the change in the use of the approximant reflects an interplay between contact with English as well as the language-internal process of lenition. Contact-induced patterns, however, do not point to complete (phonetic) assimilation. These findings suggest that heritage speakers have acquired and maintained separate categories for Tagalog sounds, but these categories nonetheless interact with those for their similar English sounds. Furthermore, the extent to which heritage speakers are oriented towards their Filipino heritage and culture influences the linguistic conditioning of /u/ and /p t k/, suggesting that structural aspects of the phonetic system are being deployed in the construction and expression of identity. Taken together, while heritage speakers display robust phonological knowledge in Tagalog, their linguistic experiences under contact have led to some changes, reflected in phonetic differences. More broadly, this study demonstrates that patterns of variability are not attributable to only one source. This work advances theories of language contact by increasing our understanding of how linguistic, social, and contact-based factors conspire to give rise to variability and change among heritage speakers.

Keywords: bilingualism
heritage languages
language contact
phonetics
Tagalog
variationist sociolinguistics
Advisor: Nagy, Naomi
[STATIC] Desire

This thesis composition and its accompanying research paper documents the development of a personal compositional practice that involves the interaction of contemporary cinematic creativity tools, methods, and performance practices with the rigorous structures and aesthetics of contemporary music. This 'post-cinematic' practice is explored in this composition by using modern film music technology and methods to generate and develop musical material, and through engaging with filmic approaches to both musical form and performance practice.

Keywords: cinematic
cli-fi
climate
eclectic
metamodernist
post-cinematic
Advisor: Britton, Eliot
Production of Race Logic and Resistance in Education: Unveiling Racism in the Turkish Educational System through the Perspectives of Kurdish Teachers and Students

Production of Race Logic and Resistance in Education: Unveiling Racism in the Turkish Educational System through the Perspectives of Kurdish Teachers and StudentsBy Sevgi Arslan A thesis submitted in conformity with the requirementsfor the degree of Doctor of Philosophy The Department of Social Justice Education Ontario Institute for the Studies in Education University of Toronto © Copyright Sevgi Arslan 2023 This research investigates the complex processes of racism within the educational context of Turkey, focusing specifically on the perspectives of Kurdish educators and students. The present study project is grounded in a discursive anti-colonial paradigm and employs a mixed-method research methodology. The primary objective of this study is to provide a comprehensive understanding of the mechanisms by which race logic is produced and upheld inside educational institutions in Turkey. Additionally, it examines the ways in which both students and teachers negotiate, challenge, or reinforce prevailing racist narratives and behaviors. This study seeks to contribute valuable insights to the current body of information on the interrelationships among racism, education, and resistance by employing a comprehensive analysis of data obtained via photo-elicitation, quantitative surveys, and in-depth discussions. The findings suggest that the Turkish education system plays a significant role in the continuation of racist violence and oppression. The current education system reinforces a framework that is deeply entrenched in racial categorization, leading to the marginalization and subjugation of Kurdish identities and cultural manifestations in schools. This is accomplished through various levels: epistemic (consisting of knowledge systems and cultural norms), structural (including institutionalized ideology), and direct (relating to specific actions carried out by educators). The study's findings offer useful insights that can inform the development of targeted interventions and policies to promote inclusivity, social justice, and equity within Turkey's educational system.

Keywords: Anti-Colonial Theory
Kurdish
Kurdish Studies
Racism
Turkish Education System
Advisor: Dei, George
Preperiodicity in Arithmetic Dynamics

Motivated by the Uniform Boundedness Conjecture of Morton and Silverman, we prove various results related to preperiodic points of algebraic dynamical systems. Our main contribution concerns the distribution of preperiodic points in one-parameter families of rational functions $f_t$ defined over a number field $K$. We show that for all $t$ outside of a set of natural density zero, every $K$-rational preperiodic point of $f_t$ is the specialization of some $K(T)$-rational preperiodic point of $f$. Assuming a weak form of the Uniform Boundedness Conjecture, we also calculate the average number of $K$-rational preperiodic points of $f$, giving some examples where this holds unconditionally. To illustrate the theory, we give new estimates on the average number of preperiodic points for the quadratic family $f_t(z) = z^2 + t$ over the field of rational numbers. This builds on work of Le Boudec and Mavraki. Our second contribution is a new technique for constructing endomorphisms with many preperiodic points. Working over a field of characteristic 0, we use Lagrange interpolation to produce degree-$d$ polynomial maps of $\A^n$ with a finite orbit of size nearly $n$ times the naïve bound. This extends a result of Hutz. For our final contribution, we introduce a new generalization of the notion of preperiodic hypersurface and explore some of its basic ramifications. We also prove that among nonlinear endomorphisms of projective space, those with a periodic critical point are Zariski dense. This answers a question of Ingram.

Keywords: arithmetic dynamics
critical points
dynamical systems
Lagrange interpolation
number theory
rational functions
Advisor: Ingram, Patrick
Lipid Loading of Macrophages Repurposes NADPH Metabolism to Suppress Glycolysis and Inflammation

Hypercholesterolemia is a key risk factor for atherosclerosis, yet the casual relationship between lipid loading of macrophages (Mφs) and inflammation remains unclear. Past findings from in vitro studies that profiled the inflammatory responses of lipid loaded Mφs are controversial, with some supporting that lipid loading drives sterile inflammation, while others showed that it deactivates Mφs inflammatory response. Emerging in vivo studies now revealed that foamy Mφs from mouse atheroma are less inflammatory than the non-foamy ones, suggesting that lipid loading of Mφs alone is insufficient to drive inflammation in atherosclerosis. However, mechanistic evidence to support this notion is still lacking. Recent advances in the immunometabolism field have illustrated how the rewiring of metabolism, such as HIF-1α-mediated glycolytic reprogramming, is critical for Mφ inflammatory responses. Therefore, we embarked upon studies to investigate how lipid loading of Mφs impairs their response to inflammation by modulating their intracellular metabolism. Specifically, we hypothesized that lipid loading of Mφs deactivates their inflammatory response induced by LPS by suppressing their glycolytic metabolism. To test this, we used metabolomics and seahorse analyzer to confirm that lipid loading of Mφs reduced LPS-induced glycolysis. This correlated with an impairment of HIF-1α protein levels, as well as the gene and protein expression of glycolytic enzymes. We then found that Mφs that are unable to degrade HIF-1α due to their genetic deficiency of Vhl were resistant to the inhibitory effects of lipid loading on HIF1a levels, suggesting that lipid loading impairs HIF-1α stability. Further studies in cell lines that expressed various HIF-1α mutants revealed that lipid loading also reduced HIF-1α transactivation capacity. Given the importance of reactive oxygen species (ROS) in activating HIF-1 stability, we then explored a role for Nrf2, a transcription factor that mediates antioxidative responses, in suppressing HIF-1 function. Indeed, we found that lipid loading of Mφs induced a primary Nrf2 response, which was further enhanced post LPS stimulation. This secondary response increased the expression of NADPH-dependent ROS detoxification enzymes, thus repurposing NADPH consumption from ROS synthesis to its detoxification. This shift in NADPH metabolism then impaired HIF-1 function, and eventually led to the deactivated inflammatory response in lipid loaded Mφs. Mφs that are deficient in Nrf2 were resistant to the inhibitory effects of lipid loading on glycolysis and inflammation. Finally, comparisons of the transcriptomic analyses between oxLDL-loaded LPS-activated cultured PMφs with foamy aortic intimal Mφs derived from mouse and human atheroma confirmed similar inflammatory and metabolic profiles.

Advisor: Cybulsky, Myron