VictorJuiz/thesis huggingface dataset:
Scalar and Tensorial Metasurfaces from Microwaves to Optics
Keywords: Chiral metasurfaces
Huygens' metasurfaces
Impedance surfaces
Metasrfaces
Reflectarrays
Transmitarrays

This thesis explores engineering of the scattered wavefronts, from microwaves to optics, with metasurfaces comprising arrays of polarizable, subwavelength-sized particles. The scalar and tensorial aspects of wavefront manipulation are considered based on four novel metasurfaces. The aim of the scalar wavefront manipulation is to achieve complete control over the reflected wavefront without inducing unwanted spurious fields, while the aim of the tensorial metasurfaces is to realize chiral polarization control. For the scalar wavefront engineering, an optical Huygens' metasurface and a vanadium-dioxide metasurface have been devised that respectively leverage the Schelkunoff's equivalence principle and the theory of holography. A detailed analysis on an optical Huygens' metasurface is presented whereby surface losses, which have heretofore been considered merely as an undesirable feature, have been discovered to play a critical role in suppressing unwanted excitations. An investigation has also been conducted on reconfigurable scalar metasurfaces through the demonstration of a vanadium-dioxide metasurface in which the reconfigurability is attained via a large refractive index change enabled in vanadium dioxide. Instead of relying on surface losses, however, the proposed vanadium-dioxide metasurface judiciously assigns unwanted fields in the `invisible region' such that only the desired reflected fields are excited in the far-field zone. In a departure from scalar wavefront engineering, this thesis also presents optical and microwave tensorial metasurfaces for chiral polarization manipulation. For this purpose, a highly efficient optical circular polarization selective surface is demonstrated by cascading rotated silicon nanorods. The design methodology, which employs multi-conductor transmission line theory, is discussed. In the microwave regime, dual-band tensorial metasurfaces are presented. The analysis involves combining a semi-analytical method with a nonlinear optimization technique. Their physical realization is also discussed along with numerical and experimental verifications at microwaves.
Protecting Persistent Data with Run-time Invariant Checking
Keywords: atomicity
consistency
data corruption
integrity checking
operating systems
storage systems

This thesis describes how we use run-time invariant checking to protect data from corruption originating at high levels in the storage stack. In concert with existing techniques for protection against corruption in the lower levels of the storage stack, we make guarantees of data structure consistency in file systems and other storage applications. We address the when, what, and how of run-time invariant checking. The fundamental requirement is that the application is crash consistent, ensuring there is a suitable point in logical time when it is safe to check the invariants. The consistency point provides us a point in time when we can check invariants, and an opportunity to check the invariants before the corrupt writes take effect. Every file system, database, or other storage application has its own data structures, and hence its own consistency invariants. We emphasize checking incrementally because of the scale of data in persistent storage. Our systems check updates for consistency using differential invariants, which are derived from global invariants. Differential invariants compare the old and new states to determine precisely what needs to be checked so the global invariants are not violated by the update. They rely on the consistency of the previous state, so our checking relies on storage systems using other mechanisms to ensure checked data is preserved. In addition to consistency invariants, we also check the atomicity and durability invariants of file system crash consistency mechanisms. Our evaluation shows the overheads of incremental checking are reasonable. For the Ext3 and Btrfs file systems, the performance overhead of runtime consistency checking is largely masked by device latency. For persistent memory, we see a more substantial overhead, from 10%-50% in our Redis benchmarks. These numbers are also significantly affected by the choice of persistent memory framework adopted, and this is an opportunity for future improvement as more efficient frameworks are developed.
Interactions and Functions of the Ubiquitin Specific Protease 7 in Human Cells
Keywords: Deubiquitylation
Interactions
proteomics
Ubiquitin
USP7

The ubiquitin-specific protease 7 (USP7) is a deubiquitylating enzyme that regulates many important cellular processes and is highly studied for its contributions to cancer. Our lab has previously discovered a binding pocket in the USP7 N-terminal TRAF domain that mediates interactions with target proteins. In this thesis I demonstrate how I contributed to the identification of a second binding pocket located in the Ubl2 ubiquitin-like structure of the USP7 C-terminal domain. Furthermore, to gain a more comprehensive understanding of the interactions and functions of USP7, I used a proteomics approach to profile USP7 interactions in cancer cells. This confirmed reported associations of USP7 with USP11, PPM1G phosphatase and TRIP12 and identified novel interactions with FBXO38 and two DEAD/DEAH-box RNA helicases, DDX24 and DHX40. I show that USP11, PPM1G, DDX24, TRIP12 and FBXO38 bind USP7 through its TRAF binding pocket, while DHX40 interacts through the Ubl2 pocket. Motifs in USP11 and DDX24 that are critical for USP7 binding were also identified. Modulation of USP7 expression levels and inhibition of USP7 catalytic activity showed that USP7 consistently stabilizes DDX24, DHX40, TRIP12 and FBXO38 dependent on its catalytic activity, while USP11 and PPM1G levels were not consistently affected. Together these results better define the mechanisms of USP7 interactions and identify FBXO38, DDX24, and DHX40 as new USP7 targets. Furthermore, a BioID approach was used to profile the interactions and putative functions of FBXO38, revealing an interaction with KIF20B, a Kinesin-6 protein required for cytokinesis. I show that depletion of either FBXO38 or USP7 result in dramatic decreases in total KIF20B levels and its localization to the midbody, which were manifested in cytokinetic defects. Furthermore, cytokinetic defects associated with USP7 silencing were rescued by restoring FBXO38 or KIF20B. Therefore, I have identified novel roles for USP7 and FBXO38 in the regulation of cytokinesis.
Coarse-grained Theory and Simulation of Assemblies of Intrinsically-disordered Nucleoporins
Keywords: Intrinsically disordered proteins
Nuclear Pore Complex
Nucleoporins
Polymers

Selective import and export through the nuclear envelope in the eukaryotic cell is solely regulated by the transporter known as Nuclear Pore Complex (NPC). The transport conduit of the NPC is occupied by intrinsically-disordered nuclear pore proteins collectively known as FG nucleoporins, which confer selectivity to the pore, hindering the passage of large, neutral molecules while facilitating the translocation of cargos recognized by carriers known as transport proteins. Currently, the mechanism of selectivity and permeability behaviour of the NPC is a subject of intense research, though much of our understanding of the NPC is based on inferences from experiments on in vitro assemblies of FG nucleoporins, requiring rigorous analysis through a theoretical framework. In this thesis, employing approaches based on mean field theory and numerical simulations, I investigate the behaviours of in vitro assemblies of FG nucleoporins under conditions commonly studied in experiments. The models studied in this thesis depend on the most important interaction and geometric parameters of the system, but are capable of providing semi-quantitative descriptions of experimental results. In addition, these models provide the means to characterize the effective interactions between the FG nucleoporin assemblies and transport proteins, and translate equilibrium measurements of these interactions into the dynamics of transport. In all types of FG nucleoporin assemblies, different entropic and enthalpic effects stemming from molecular interactions determine the affinity between FG nucleoporin and transport proteins, demonstrating the physics of the in vitro assemblies that are expected to arise in the NPC.
Craft and the Contemporary Geographies of Manufacturing: Local Embeddedness, New Workspaces, and the Glamourization of Work in the Craft Brewing Sector
Keywords: Brewing
Craft
Manufacturing
Portland
Oregon

Craft forms of production have enjoyed a notable revival in recent decades and have been argued to provide a source of competitive advantage in a post-Fordist economic landscape. Craft combines physical manufacturing with creative production to produce objects imbued with notions of quality, authenticity, skill, and bespoke production. Craft elevates particular practices and processes, which has allowed it to become viewed as a more environmentally responsible and socially just way of organizing production. This dissertation explores the normative landscape of craft, emphasizing the implications it has for contemporary geographies of manufacturing. Drawing on a mixed methods approach, and an in-depth case study of the craft brewing sector in Portland, Oregon, the dissertation highlights three unique geographies associated with contemporary craft manufacturing. First, the dissertation highlights a tendency towards spatial agglomeration and a (re)localization of small-scale production in advanced economies. It traces the development of Portland’s craft brewing cluster, highlighting the significant role that place-specific institutional and material factors have played in the emergence and growth of the cluster. Second, the dissertation highlights a heightened perception and desirability of manufacturing work associated with the contemporary resurgence of craft, despite the presence of precarious working conditions in craft sectors. A key finding of the dissertation is that precarious working conditions are actually being exacerbated by the heightened status of craft brewing work. Finally, the dissertation highlights a fusion of industrial and cultural production associated with the recent craft revival and documents the ways this has transformed industrial workspaces. In particular, the dissertation emphasizes the unique spatial and locational requirements of craft breweries as well as the ways that their workspaces are enlisted to serve both production and consumption functions. It also places the material landscape of craft beer production in conversation with urban planning, revealing the ways in which craft breweries are used by policy-makers to promote gentrification, tourism and neighbourhood branding and the ways in which these policies are simultaneously benefitting and threatening the continued existence of Portland’s significant craft brewing cluster.
Early Childhood Educators' Knowledge and Self-efficacy in Foundational Literacy Instruction
Keywords: Early Childhood Educator
Knowledge
Literacy
Oral Language
Phonemic Awareness
Self-Efficacy

This thesis is comprised of two studies. The first utilizes a mixed-method approach and explores early childhood educators’ early literacy knowledge and self-efficacy for early literacy instruction. Fifty-four ECEs participated in this research, of which 29 were pre-service ECEs and 25 were in-service ECEs. Participants were assessed on their early literacy knowledge and self-efficacy for early literacy instruction. They were also assessed on their early literacy-related experiences, including assessments of their literacy-related training and practicum experiences as well as assessments of their professional experiences. Study 1 revealed significant gaps in ECEs’ early literacy knowledge, and identified differences between pre-service and in-service ECEs in their early literacy knowledge and experiences. The findings of study 1 showed that despite their varied early literacy-related experiences and training, both pre-service and in-service ECEs lacked adequate knowledge and self-efficacy in phonemic awareness and oral language instruction, two essential components of early literacy education. The second study is a mixed methods study examining the impact of a targeted professional development intervention designed to improve knowledge and self-efficacy in phonemic awareness and oral language instruction. Study 2 found that the professional development intervention was effective in improving both knowledge and self-efficacy in phonemic awareness and oral language instruction. Qualitative findings provided further insight as to specific components of the intervention that were seen as beneficial in improving the knowledge and self-efficacy of ECEs, which included opportunities to apply theoretical learning through hands-on activities and video demonstrations. Overall, the findings of this thesis provide insight into the early literacy experiences, knowledge and self-efficacy for early literacy instruction of pre-service and in-service ECEs. Furthermore, the findings suggest that ECEs can make significant improvements in knowledge and self-efficacy through a targeted professional development intervention.
Computer-aided Diagnosis for MRI Screening of the Breast in High Risk Women
Keywords: Cancer detection and diagnosis
Computer-aided diagnosis
Decision tree classifiers
Magnetic resonance imaging

Breast cancer is currently the second leading cause of death from cancer in Canadian women. Routine mammograms are considered the best screening approach for early detection in the general population but magnetic resonance imaging (MRI) is recommended in addition to mammography to women at high risk of developing breast cancer. The main reason for this recommendation is the high sensitivity attributed to the characteristic uptake of gadolinium contrast agent by cancerous lesions during T1-weighted (T1w) dynamic contrast-enhanced (DCE) imaging. Dynamic lesion characteristics such as time-course uptake, morphology, and enhancement type patterns known as mass, non-mass or foci (
Examining the Leadership Role of the Dean of Business in Ontario Colleges:Using Narrative Inquiry to Reflect Leadership Identity Journeys of Selected Deans in this Role
Keywords: competency frameworks
educational administration
leadership
learning
Ontario college system
reflection

My research study leadership journeys of selected incumbents in the role of dean of business in the Ontario College System. Using the methodology of narrative inquiry, I wanted to understand how their journeys led them to the role of dean, how they experienced the role, their perceptions of their own leader self-identity, how they approached their learning and growth while in the role, and to what extent they engaged in reflective practice. Participants engaged in two interview sessions with me, responding through dialogue to a guiding set of interview questions. A significant feature of the experience of business deans is that many of them had well-established career roles in business settings and joined the Ontario College System mid-career, most often directly assuming the role of dean. One of the contributions that I am seeking to make through my work is to integrate the stories of their personal career journeys with their leadership identity development and to understand how the Leadership Capability Framework for the Ontario College System captures or misses the requirements for the role of dean of business. Several common themes emerged: (a) they found the program development aspects of their role challenging as they tried to learn the college context that seemed at times esoteric, (b) they perceived their roles and contributions as impactful on their own institutions, (c) they expressed interest in career advancement roles in system but were unsuccessful in securing them, (d) the Leadership Capability Framework was viewed as describing generic not contextual leadership requirements, and (e) their reflective practice was very informal. These findings present implications for the Ontario College System as it seeks to attract, retain, and develop leaders in this role, and for the leadership learning that is required to support leadership development and growth.
The Functional and Clinical Consequences of TP53 Mutations in Cancer
Keywords: Bioinformatics
Cancer
Protein Oligomerization
TP53
Transcription Factor
Tumor Suppressor

The discovery of genetic variants linked to cancer have provided useful biomarkers for diagnostics, prognostics, and therapeutic targets. Mutations in the TP53 gene that encodes the p53 tumor suppressor protein are the most abundant genetic variants in human cancers, yet their clinical utility has not been fully explored. Normally, the p53 protein plays a crucial role as a barrier to cancer. Hundreds of different sporadic and germline (Li-Fraumeni syndrome) pathogenic p53 mutants have been identified; some with loss of function or partial function, and others gaining oncogenic activity. Currently, there is no clinical distinction between different p53 mutants as a biomarker despite evidence of substantial functional disparity. A greater understanding of the functional diversity between different variants will be necessary to improve the clinical utility of TP53 mutations. The central theme of this thesis was to characterize the cellular functions of different p53 mutants and translate this knowledge to the clinic as informative biomarkers. Specifically, the thesis focuses on how the oligomerization and residual transcriptional activity of p53 mutants can impact oncologic outcomes. First, I describe the preliminary study that compared the cellular activities of oligomeric p53 variants, reporting that p53 cellular activities are modulated by its oligomeric state. Second, in a follow-up study, I outline the clinical consequences of each clinically-relevant germline TP53 mutation in the oligomerization domain. A strong genotype-phenotype relationship was observed where the ability of mutant p53 to oligomerize prognosticated more favourable clinical outcomes. Lastly, I describe a functionally integrated meta-analysis that stratified cancer patients with TP53 mutations according to their mutant-specific level of residual transcriptional activity. A male-specific linkage between increased residual activity and prolonged survival was uncovered in glioma and gastric adenocarcinoma patients. This association was recapitulated in the lifetime cancer survival of Li-Fraumeni syndrome, where brain and gastric tumors are more common among men. Together, this thesis demonstrates that a wide spectrum of functionality exists between different p53 mutants that should be considered in clinical decision-making.
Molecular and Functional Heterogeneity of Cancer Associated Fibroblasts in High Grade Serous Ovarian Cancer
Keywords: Cancer Associated Fibroblasts
CD49e
FAP
Ovarian Cancer

Cancer-associated fibroblasts (CAFs) have been shown to play a role in promotion of cancer cell proliferation and invasion, and mediation of chemotherapy resistance in several cancer types. The work described in this thesis explores the role of CAFs in high-grade serous ovarian cancer (HGSOC) and their heterogeneity at the intra-tumoral and inter-tumoral levels. I demonstrate that CAFs derived from primary tumors by outgrowth in culture mediate cancer cell invasion and chemotherapy resistance. Following a high-throughput flow cytometry screen of a large panel of cell surface-specific antibodies, I have identified CD49e to be uniquely expressed on the surface of CAFs in HGSOC. I further validated and characterized CD49e+ fibroblasts through transcriptional profiling and discovered that patients stratify into two groups based on their CAF gene expression profiles. One group of patients has predominantly CD49e+Fibroblast Activation Protein (FAP)-Hi CAFs in the stroma, while the other group of patients has predominantly CD49e+FAP-Lo CAFs. The molecular signature of CD49e+FAP-Hi CAFs resembles the classical CAF phenotype in its expression of alpha-smooth muscle actin (αSMA), collagens, and growth factors. However, the CD49e+FAP-Lo subset is distinct and possesses a novel preadipocyte-like signature. The CD49e+FAP-Lo phenotype has remained largely unnoticed as it is generally outcompeted in vitro by CD49e+FAP-Hi cells when grown under classical CAF culture conditions. Subsequently, I functionally characterized the properties of each of these subsets in the context of cancer using in vitro and in vivo assays. I showed that FAP-Hi CAFs better promote cancer invasion, growth, metastasis, and chemoresistance than their FAP-Lo counterparts. Moreover, I identified transcription factor TCF21 as a candidate master regulator of the functional disparities between FAP-Hi and FAP-Lo fibroblasts. Through RNA-Seq profiling, I generated a gene signature that is unique to each subtype of CAFs. I applied the gene signature to the existing Cancer Genome Atlas (TCGA) database and showed that infiltrating fibroblasts heavily contribute to the molecular classification of HGSOC patients and their survival outcomes. Finally, I demonstrated that FAP-Hi and FAP-Lo stromal phenotypes are present in pancreatic, bladder, and esophageal carcinomas.
Storytelling of Indigenous and Racialized Women in the Academy in Toronto: Implication for Building Counternarrative Learning Spaces
Keywords: Counternarrative
Indigenous
Mentorship
Racialized
Storytelling
Women

Indigenous and racialized women utilize storytelling as a counter-hegemonic practice; a form of resistance in the academy. This research is centered within a graduate program in Social Science and Humanities, where a high volume of intellectual exchange involves sharing personal, cultural and collective experience. For Indigenous and racialized women, however, personal storytelling renders us vulnerable, especially when the stories become subject matter for research conducted within the dominant culture. However, telling our stories is profound because it helps us develop a sense of self-determination and supports cultural recovery. This project braids anti-colonial, anti-racist, and feminist theoretical frameworks. It depends on concepts developed by Indigenous elders, activists and scholars: Indigeneity, Resistance and Responsibility/Reciprocity. These discursive lenses enable me to situate my arguments about the narrative consumption of Indigenous and racialized female students in the Eurocentric academic setting. Primary data was obtained from face to face interviews as well as a group sharing circle. Two of the participants identified as Indigenous women, seven identified as racialized women, two as queer and all as cis-female. Seven of the participants were graduate students at universities in Toronto, and two of them had already graduated at the time of my interviews in 2014. There are three main findings. First, the act of narration itself enabled us to reclaim our holistic self and resist ongoing historical oppression. Second, the consumption of stories belonging to Indigenous and racialized women by white academics are not isolated experiences. Third, there is a need for mentorship essential to student success. Finding a peer support network among cohort members plays an important role in mitigating daily challenges, however, participants strongly emphasized the importance of institutional support and mentorship from faculty to center the notion of reciprocity. Finally, recommendations focus on the resource development available to Indigenous and racialized women to enhance our experience in the graduate program.