VictorJuiz/thesis huggingface dataset:
Ecological and Evolutionary Consequences of Herbivory on Plant Communities

Understanding the consequences of species interactions is central to ecological and evolutionary research. My research focused on better understanding the evolutionary ecology of plant- herbivore interactions by asking two broad questions: 1) How do herbivores shape the composition and diversity of plant populations and communities? And, 2) How does genetic variation and ongoing evolutionary dynamics in herbivores influence plant ecology? To test the first question, I utilized long-term herbivore manipulations in the grasslands of Silwood Park, England. I tested ecological and evolutionary consequences of rabbit (Oryctolagus cuniculus) grazing on plant populations by collecting seeds from rabbit exclosures ranging in age from 4 months to >20 years and growing them in common environments. I found that rabbit exclusion caused evolution of multiple plant defensive traits in three plant species and influenced the costs and benefits of a mutualistic interaction between a grass and its fungal endophyte. In another experiment at Silwood Park I investigated how multiple groups of herbivores (rabbits, insects, and mollusks) and nutrient additions shaped plant species richness and phylogenetic diversity. I found that nitrogen addition strongly reduced species richness while rabbit grazing increased plant phylogenetic diversity. To test the second question, I conducted field experiments where I manipulated the genotypic composition of green peach aphid (Myzus persicae) populations on two host plant species. I found that genetic variation in M. persicae had large impacts on plant growth, that M. persicae populations changed in genotype frequency (i.e. they evolved) over 5 generations, and that in some cases faster evolving populations had larger negative impacts on plant growth. Together these results demonstrate how herbivory can concurrently shape the ecology and evolution of plants at multiple levels of organization and that herbivore genetic variation and evolution can have important consequences on plant ecology.

Keywords: community genetics
community phylogenetics
contemporary evolution
herbivory
plant-herbivore interactions
Advisor: Marc, T J Johnson
A Narrative Perspective on the Study of Select Professional Trumpeters' Experiences: Shaping a Musical Life

Many aspiring young trumpeters the world over share the same purpose: to achieve international acclaim for their art. Each trumpeter seeking such acclaim needs to adopt those skills and characteristics necessary to achieve greatness in performance and maintain a professional career. As master musicians continue to excel in their fields, their students are privileged to learn from their expertise. My career as a performer and educator has been profoundly shaped both by the teachings of my professors and the concerts of internationally acclaimed performers. Concepts of trumpet pedagogy have changed significantly since the early twentieth century. Methods have become increasingly under examination as performance demands have grown. However, there is a lack of research on the personal professional knowledge of trumpet performers. The documentation of this specialist knowledge from the artists themselves is particularly sparse. As a result, only select students have the privilege of gaining this information. In many cases successful musicians often have a small number of protĂŠgĂŠes who receive this wisdom aurally. Although a number of studies focus on specific pedagogical techniques and philosophical ideologies, few studies exist that connect innate methods of pedagogy to the careers of trumpet performers. Moreover, a body of literature that documents the cultural impact on professional and educational development in trumpet performance is lacking. This study seeks to document the professional wisdom of four successful artists so that more students and pedagogues may benefit.This research found that the stories told by professional trumpeters suggest key elements of their success. There are similarities in their pedagogical approaches and innate qualities that are vital to that success. Their teachers have had profound influence on their development. Another common element was an early involvement with music in the family. Cultural backgrounds had some influence on the various pathways to the respective professional careers, but since many professionals aim for acclaim across the globe for their performances, it is not the culture that defines an individual's style, but the person him/herself who grows into his/her own style.

Keywords: Performance
Trumpet
Advisor: Cameron, Walter
Optical Switching in Next-generation Data Centers

This thesis presents advanced optical connectivity solutions for next-generation data centers, spanning millions of processing cores. The wavelength routing of optical packets based on arrayed waveguide gratings (AWGs), tunable wavelength converters (TWCs), and fiber delay lines (FDLs) is a disruptive technology for capacity, footprint, and flexibility requirements of massive cloud data centers. We develop a wavelength-division multiplexed (WDM) design based on Birkhoff-von Neumann architecture as a bit-rate transparent, scalable solution to switching bottlenecks in data center networks. As no mature all-optical buffering technology is currently available, central to our design is the buffering strategy that we adopt to store contending packets. Due to the limited number of FDLs, packet drops are common in optical packet switching (OPS) data centers and limit the network throughput. In a practical scenario, physical layer impairments, predominantly amplified spontaneous emission (ASE) noise and crosstalk, degrade Q-factor and lead to additional packet drops. To examine the performance of optical buffer units more accurately, we develop a unified analysis framework, integrating the network layer and the physical layer effects. Using this framework, we refine our architectures and provide guidelines for minimizing the physical layer impact. Besides, optical switch designs should not neglect the diversity of data center traffic patterns when developing connectivity solutions. Empirical studies of data center network traffic reveal that server traffic exhibits strong spatial and temporal correlations. We examine the effectiveness of an AWG-based load balancer with round-robin tuning TWCs in resolving congestion penalties in the data center network. Our cross-layer analysis suggests that the physical layer impairments due to the load balancer hardware could counteract its potential gains and lead to significant throughput degradation. To resolve this challenge, we develop a novel modular router architecture based on WDM shared recirculation buffers that integrates the functions of load balancing and routing and maximizes the optical buffering gains. The router employs a load-balancing scheduler to maximize throughput and minimize delay. Our mathematical analysis and Monte Carlo simulations show that the consolidation of optical buffer slots into WDM FDLs accompanied with internal load balancing leads to a virtually lossless router, resilient to data center traffic anomalies.

Keywords: cloud computing
data center
optical packet switching
wavelength-division multiplexing
wavelength routing
Advisor: Alberto, Leon-Garcia
Engineering of Doping and Transport for Enhanced Colloidal Quantum Dot Photovoltaics

Colloidal Quantum Dots (CQDs) are nanoscale quantum-tuned semiconductor particles suspended in solution. When deployed as optoelectronic materials, CQDs are closely packed together into thin films enabling charge transport. This also enables the formation of semiconductor junctions and contacts with other bulk semiconductor materials and metals, respectively. However, limited attention has been given to understanding the fundamental electronic behavior of these materials as bulk-like films, gaining fine control over their semiconducting properties, and then leveraging these insights to make better semiconductor devices. In this thesis, I explore two of the most fundamental concepts to CQD semiconductor device physics: charge carrier doping density and charge carrier transport. With the aid of optoelectronic simulation, I show that these are the most important paths to pursue in order to improve the photovoltaic device performance. I develop a doping density theory that I then rigorously test for the PbS CQD materials system; this theory is also applicable to other types of CQD materials. I demonstrate doping densities on the order of 1016 cm-3 to 1018 cm-3 for both p- and n-type films. My work enables a previously unavailable p-n homojunction within one CQD materials system, and furthermore allows to grade the doping within the active absorber layer to reach power conversion efficiencies (PCEs) exceeding 7%. I then study CQD size polydispersity, and use it to investigate the details of charge transport in the rough energetic landscapes inherent to these materials. Here, I find that midgap trap elimination is the most important concept in rapidly obtaining dramatic photovoltaic performance gains. By directly measuring the diffusion length in highly coupled CQD films, and combined with optoelectronic modeling, I was able to develop a new passivation strategy achieving a record 8.5% PCE. My research serves as a roadmap for future performance improvements in CQD photovoltaics.

Keywords: doping
photovoltaics
quantum dot
solar cells
transport
Advisor: Edward, H Sargent
A Health Promoting Continuous Learning Sustainable Education System

Abstract This thesis was inspired by a new, evolving vision of a health promoting, continuous learning, education system with an ecological consciousness and focus on sustainability. In health promotion we are coming to a greater understanding of what creates health and how it is created in complex living systems - individuals, organizations, communities, and our planet. The setting is a large school district in Ontario involved in transformational systems change through creating collaborative learning environments, distributed leadership, and networking - locally and internationally. The research questions were: 1) Why and how do the top three most influential system environments (leadership, a culture of continuous learning, and interrelatedness of work and life) promote the optimal health, well-being, and sustainability of individuals (teachers, principals and supervisory officers) and the school district as a whole?; 2) What are the principles, patterns, relationships, and synergies that are integral to creating a health promoting, continuous learning, sustainable system? and; 3) Is there one or possibly two system environment(s) that might be a major enabler(s) for creating a health promoting, continuous learning, sustainable system? This study was a purposive qualitative study involving sixty semi-structured interviews with teachers, principals, and district leaders. The data were analyzed using thematic analysis and an ecological, holistic systems approach, involving dialogue with experts in systems thinking, theory and change.The findings identify: (a) 12 major themes emerging from three system environments; (b) the synergy point; (c) leadership as the major enabler (d) one major pattern of increasing complexity and consciousness of health, well-being, and sustainability; (e) three sub-patterns: leadership, a culture of continuous learning, and interrelatedness of work and life; and (f) four tensions and paradoxes. This study makes five substantial contributions: * drawing on an ecological, holistic systems approach to health, well-being, and sustainability;* using a systems approach to research design and methodology;* using three knowledge lenses to draw on literature across diverse fields; *identifying 12 Principles of a Health Promoting, Continuous Learning, Sustainable System; *developing a Reflective Framework: Five Levels of Complexity and Consciousness of Health, Well-Being, and Sustainability.Recommendations and suggestions for further study are outlined.

Keywords: educational leadership and systems change
health promoting continuous learning sustainable education systems
health promotion and systems change
healthy schools
workplaces and communities
leadership and systems change
sustainable systems
Advisor: Carol, Rolheiser
FKBP14 in Notch Signalling and Drosophila Development

Presenilins (PSs) are highly conserved transmembrane proteins that form the catalytic core of the gamma-secretase complex, which cleaves a growing list of transmembrane proteins including Notch and Amyloid Precursor Protein. Autosomal dominant mutations in the genes encoding human PS have been closely linked to cases of early onset familial Alzheimer's Disease (FAD), and these FAD-linked PS mutations influence the activity of gamma-secretase. The production and maturation of gamma-secretase subunits are highly codependent, yet the mechanisms regulating assembly and activity of the complex are unclear. A screen in Drosophila identified FKBP14, an FK506-binding proteins (FKBP), as a genetic modifier of Presenilin (Psn), with FKBP14 mutants exhibiting defects typical of loss of Notch signalling. FKBPs are highly conserved and involved in a wide array of biochemical processes including protein folding, assembly, and trafficking, yet they are non-essential in yeast and their role in development of multicellular organisms remains unclear.The work presented in this thesis establishes a role for FKBP14 in multicellular development as a regulator of Notch signalling via Presenilin and the gamma-secretase complex. I show that FKBP14 mutants genetically interact with components of the Notch pathway, and that Psn-dependent gamma-secretase cleavage, a process required for Notch signalling, is reduced in FKBP14 mutants. I also identify a Notch-independent role for FKBP14 in cell viability during Drosophila development and present data establishing that both the PPIase and EF hand domains of FKBP14 are required for its function. Altogether, these data demonstrate that FKBP14 plays a critical role in development, one aspect of which includes regulating members of the Notch signalling pathway. Investigation of the role of FKBP14 in Notch signalling via its interaction with Psn, and potentially broader roles in development, may provide a greater understanding of FKBPs in multicellular signalling.

Keywords: FKBP14
Notch
Presenilin
Advisor: Gabrielle, L Boulianne
Quantum Hamiltonian Reduction of W-algebras and Category O

W-algebras are a class of non-commutative algebras related to the classical universal enveloping algebras. They can be defined as a subquotient of U(g) related to a choice of nilpotent element e and compatible nilpotent subalgebra m. This procedure constitutes a quantisation of the classical construction of Hamiltonian reduction.We define a quantum version of Hamiltonian reduction by stages and use it to construct intermediate reductions between different W-algebras U(g,e) in type A. This allows us to express the W-algebra U(g,e') as a subquotient of U(g,e) for adjacent nilpotent elements e' e.It also produces a collection of (U(g,e),U(g,e'))-bimodules analogous to the generalised Gel'fand-Graev modules used in the classical definition of the W-algebra; these can be used to obtain adjoint functors between the corresponding module categories.The category of modules over a W-algebra has a full subcategory defined in a parallel fashion to that of the BGG category O; this version of category O(e) for W-algebras is equivalent to an infinitesimal block of category O by an argument of Miličić and Soergel. We therefore construct analogues of the translation functors between the different blocks of O, in this case being functors between the categories O(e) for different W-algebras U(g,e). This follows an argument of Losev,and realises the category O(e') as equivalent to a full subcategory of the category O(e), where e' e in the refinement ordering. Future work is to use this to provide an alternate categorification of U(sl

Keywords: Category O
Poisson Geometry
Quantum Hamiltonian Reduction
W-algebras
Advisor: Joel, Kamnitzer
Proteomic Signatures of the Colorectal Cancer Desmoplastic Invasion Front

Cancer-associated fibroblasts (CAFs) comprise a proponent compartment of the tumor microenvironment and are implicated in tumor progression. Local invasion and tumor-budding formation, i.e. detachment of individual cancer cells from the tumor invasion front, are regulated by CAFs and the desmoplastic stroma. Given accumulative evidence that such cells have undergone dedifferentiation and have acquired stem-like properties, it was hypothesized that they may be subjected to epithelial-to-mesenchymal transition (EMT) in a context-dependent manner. This thesis attempts to identify and characterize the contextual signals originating from the adjacent CAF population, responsible for mediating these malignant phenomena.Colorectal cancer was opted as model system to address these questions. Co-cultures mimicking the colorectal cancer desmoplastic tumor-host cell interface were generated. Mass spectrometry-based proteomic methods and bioinformatics pipelines were deployed to draw comprehensive signatures of growth factors/mediators secreted in these cocultures, with potential of regulating EMT in neoplastic invasive margins. Given previously-established, tumor-suppressive roles of the BMP pathway, a group of bone morphogenetic protein (BMP) antagonists, namely GREM1, FST and HTRA3, demonstrated attractive candidacy as potential EMT mediators. Using in vitro assays, this thesis further provided experimental insights that antagonist-dependent disruption of the BMP pathway induces enhanced motility and triggers mesenchymal phenotype switching in colon cancer cells. Finally, this thesis provided translational impact of these results in colon cancer patients. BMP antagonists, especially HTRA3 and GREM1, were overexpressed in desmoplastic stromata with tumor budding presence, and their expression significantly correlated with increased tumor-budding score. Additionally, GREM1 was more prominently expressed in invasion fronts with nuclear versus membranous beta-catenin expression.Overall, the data provided here support a working model, whereby contextual BMP antagonism may drive EMT, local invasion and de novo formation of tumor buds from the desmoplastic invasion front. Unraveling this axis thoroughly might be critical for clarifying pharmaceutical opportunities and proposing targeted strategies to manipulate metastasis.

Keywords: Bone Morphogenetic Protein Pathway
Cancer-associated Fibroblasts
Colorectal Cancer
Epithelial-to-Mesenchymal Transition
Proteomics Bioinformtics
Tumor-Budding
Advisor: Eleftherios, P Diamandis
Boron and Phosphorus Removal from Si-Cu Alloy Using CaO-SiO2-Na2O-Al2O3 Slag

A combination of solvent refining and slag treatment was employed to investigate the possibility of removing boron and phosphorus from crude silicon to acceptable levels for solar applications. Metallurgical grade silicon (MG-Si) was alloyed with pure copper and the alloy was subjected to refining by liquid CaO-SiO2-Na2O-Al2O3 slags at 1773K (1500째C). The distribution of B and P between the slags and the alloy was measured under a range of slag compositions, varying in CaO:SiO2 and SiO2:Al2O3 ratios and the amount of Na2O. The results showed that both basicity and oxygen potential have a strong influence on the distribution of B and P. With silica affecting both parameters in these slags, a critical P_(O_2 ) could be identified that yields the highest impurity pick-up. The addition of Na2O to the slag was found to increase the distributions of boron and phosphorus into the slag. A thermodynamic evaluation of the system showed that alloying copper with MG-Si leads to substantial increase of boron distribution coefficient. The highest boron and phosphorus distributions were 47 and 1.1, respectively. Using these optimum slags to reduce boron and phosphorus in MG-Si to solar grade level, a slag mass about 0.3 times and 17 times mass of alloy would be required, respectively. The loss of Na2O and B2O3 from CaO-SiO2-Al2O3 slags containing a high content of Al2O3 and Na2O was studied in the temperature range of 1573-1773K (1300-1500째C) by thermogravimetric analysis (TGA) under isothermal conditions. Higher basicity and larger B2O3 and Na2O concentrations were also found to increase the evaporation rate. The rate appears to be controlled by chemical reaction at the surface in the beginning, followed by a mixed chemical reaction-mass transfer regime, and finally a liquid-phase mass transport step. The apparent activation energies for the evaporation reaction were calculated for different slag compositions.

Keywords: Boron removal
CaO-SiO2-Na2O-Al2O3 slag
Phosphorus removal
Slag treatment
Advisor: Torstein, Utigard
From Crying Comes Light: The Impact of Post-traumatic Stress on the Poetry of Amir Gilboa

The research starts by explaining the theoretical basis for the impact of post-traumatic stress on the poetry of Amir Gilboa, as well as on individual who have been traumatized by extreme events. The first chapter focuses on Gilboa's reconstruction of Holocaust testimonials as expressed in his poetry. This includes referring to the question of whether artistic expression is possible after Auschwitz.Chapter Two focuses on post-traumatic stress as it is reflected in Gilboa's final posthumously published book of poems entitled Amir Gilboa: The Days are Coming; Poems 1942-1946 (edited and introduced by Hagit Halperin). This book was written during the war and the Holocaust but only published in 2007. The importance of this collection of poems is that they are conducive to a fresh understanding of the poet and his oeuvre. The poems present the poet's inner-struggle regarding writing poetry during war time, and the guilt of not being able to save his family.Chapter Three delineates Gilboa's response and relationship to Jewish-national destruction. Since the descriptions of destruction in Gilboa's poetry draw upon his personal feelings of trauma, there is a convergence of the individual and the national collective in his poetry. Chapter Four deals with: The "Binding" Motif (haAkedah) as an expression of the victim and the (Holocaust) survivor's feelings, including those of second generation survivors. Chapter Five presents research regarding the revival that arises from the destruction in Gilboa's poetry. The underlying assumption is that there is a directḥ connection between destruction and lamentation and renewal and redemption. Chapters Six and Seven connect Gilboa to early Agnon, both in Yiddish and in Hebrew, as well as to Bialik's poetry, and as an innovative "young" poet alongside Amichai and Ravikovich. I demonstrate that in addition to the continuity between Bialik's poetry and Gilboa's poetry there is a strong innovative streak in his oeuvre, apparent in the development of modern structures. This comparison places Gilboa as a poet who stands between two generations.

Keywords: Hebrew Litrerature
Holocaust
Poetry
Advisor: Harry, Fox