VictorJuiz/thesis huggingface dataset:
Proximity to Potential Sources and Mountain Cold-trapping of Semi-volatile Organic Contaminants

If sufficiently persistent, semi-volatile organic contaminants (SVOCs) can travel long distances through the atmosphere from their points of release and become concentrated in cold, remote regions. As air is sampled for SVOCs to establish both their presence and the success of emission reduction efforts, it becomes helpful to determine sampling site proximity to sources and the origin of the sampled air masses. Comparing three increasingly sophisticated methods for quantifying source proximity of sampling locations, it was judged necessary to account for the actual history of the sampled air through construction of an airshed, especially if wind is highly directional and population distribution is very non-uniform. The airshed concept was improved upon by introducing a ‘geodesic’ grid of equally spaced cells, rather than a simple latitude/longitude grid, to avoid distortion near Earth’s poles and to allow for the comparison of airshed shapes. Assuming that a perfectly round airshed reveals no information about sources allows the significance of each cell of an airshed to be judged based on its departure from roundness. Combining air-mass histories with a 2 year-long series of SVOC air concentrations at Little Fox Lake in Canada’s Yukon Territory did not identify distinct source regions for most analytes, although γ-hexachlorocyclohexane appears to originate broadly in north-eastern Russia and/or Alaska. Based on this remoteness from sources, the site is judged to be well suited to monitor changes in the hemispheric background concentrations of SVOCs. A model-based exploration revealed wet-gaseous deposition as the dominant process responsible for cold-trapping SVOCs in mountain soils. Such cold trapping is particularly effective if precipitation rate increases with altitude and if temperature differences along the mountain are large. Considerable sensitivity of the modeled extent of cold-trapping to parameters as diverse as scale, mean temperature, atmospheric particle concentration and time relative to emission maxima is consistent with the wide variety of observed enrichment behaviour. Concentration gradients of polycyclic aromatic hydrocarbons and polychlorinated biphenyls in air and soil measured on four Western Canadian mountains with variable distance from sources revealed source proximity as the main driver of concentrations at both the whole-mountain scale and along individual mountain transects.

Keywords: semi-volatile
contaminants
airshed
trajectory
mountain
cold-trapping
pertingency
receptor model
back-trajectory
polycyclic aromatic hydrocarbon
polychlorinated biphenyl
box model
brominated flame retardant
BFR
PCB
PAH
SVOC
geodesic
trajectory statistic
Advisor: Wania, Frank
Digitally Controlled DC-DC Converters with Fast and Smooth Load Transient Response

Modern switch-mode power supplies (SMPS) used for point-of-load (PoL) applications need to meet increasingly stringent requirements on voltage regulation, while minimizing physical volume and optimizing conversion efficiency. The focus of this thesis is the voltage regulation capability of low-power PoL converters during load transients. The main objective is to investigate converter topologies and control techniques that can achieve fast and smooth transient performance without significant penalty in volume and efficiency. The digital control method is used due to its ability to implement sophisticated control algorithms. The first part of this thesis investigates a dual output stages converter, with a small auxiliary output stage connected in parallel with the main output stage. While the main output stage is responsible for steady-state operation and designed to achieve optimum efficiency, the auxiliary stage is activated when a load transient occurs, to help suppress voltage deviation. Experimental results on a 6 V-to-1 V, 3W buck converter shows 35% improvement in peak transient voltage deviation while maintaining the same efficiency profile, compared to an equivalent buck converter. The second part of this thesis introduces a flyback-transformer based buck (FTBB) converter. In this topology, the conventional buck inductor is replaced with the primary winding of the flyback transformer, an extra switch, and a set of small auxiliary switches on the secondary side. During heavy-to-light load transients the inductor current is steered away from the output capacitor to the input port, achieving both energy recycling and savings due to reduced voltage overshoots. The light-to-heavy transient response is improved by reducing the equivalent inductance of the primary transformer winding to its leakage value. Compared to an equivalent buck converter, experiment results on a 6 V-to-1 V, 3 W prototype show three times smaller maximum output voltage deviation during load transients and, for frequently changing loads, about 7% decrease in power losses.

Keywords: dc-dc converter
digital control
switch mode power supply
efficiency
transient response
Advisor: Ng, Wai Tung
Prodic, Aleksandar
The Nature of Variation in Mutational Properties: Context-dependent Changes in Mutation Rates and Mutational Fitness Effects

Evaluating the evolutionary role of mutations depends on an understanding of their major properties, including their rate of origin, U, and the distribution of their fitness effects, f(s). While substantial effort has been put into measuring these properties, most studies have only examined their distributions in a single context. In nature, spontaneous mutations are likely to experience heterogeneity in genetic and environmental context, and this could lead to variation in both U and f(s). My thesis investigates the changes in U and f(s) with different genetic and environmental factors in Drosophila melanogaster, in order to elucidate the nature of context-associated variation in mutational properties. Examination of condition-dependent variation in DNA repair showed that high and low conditioned individuals differ in the use of alternative repair pathways. This could ultimately lead to variance in their heritable mutation rates. However, the assumption that condition dependence in repair arises solely due to a presumed trade-off between accuracy and the energetic costs associated with different repair pathways is too simplistic. Instead, physiological considerations appear to mediate condition-dependent changes in DNA repair. Measurements of selection on individual mutations across different genetic and environment contexts showed that context-associated changes in mutational fitness effects are common. I found that heterogeneity in fitness effects across different environments result in changes to the overall mean and variance of f(s). This does not, however, seem attributable to the degree of ‘adaptedness’ of a population to a particular environment (a prediction generated by previous theoretical analysis). On the other hand, f(s) appears to be relatively robust to differences among genotypes, with epistasis averaging close to zero. This finding suggests that genetic and environmental perturbations may affect mutations differently. Overall, my thesis represents the most rigorous empirical investigation to date of the conceptual and theoretical predictions regarding the nature of context-dependent heterogeneity in U and f(s) for multicellular eukaryotes.

Keywords: Mutations, Epistasis, DNA Repair, Drosophila melanogaster, Selection, Mutation Rate
Advisor: Agrawal, Aneil
Structural Characterization and Membrane Interactions of the Amyloid Peptide PrP(106-126)

The formation of amyloid fibrils is a key characteristic of many neurodegenerative diseases including Alzheimer’s and Parkinson’s diseases. Similarly prion diseases, those associated with the prion protein, are neurodegenerative disorders with characteristic protein aggregates accumulating in the brain of affected individuals. While fibrillar deposits of these disorders have long been associated with end-stage disease pathology, it is currently hypothesized that protein oligomers are the cytotoxic structural form of these systems. Residues 106-126 of the human prion protein have been found to form both amyloid fibrils, as well as toxic amyloid oligomers and thus provide a suitable model system. This thesis aims to describe the structures of the amyloid fibrils and oligomers formed by PrP(106-126), how they are interrelated as well as interaction with model membranes and cytotoxicity. Amyloid fibrils of PrP(106-126) contain long, unbranched filaments that contain β-sheet secondary structure and bind the amyloid-indicating dye, thioflavin-T. These fibrils are comprised of parallel β-sheets, stacked in an antiparallel fashion. The non-fibrillar amyloid oligomers are large, spherical structures that contain β-sheets but do not bind thioflavin-T. It was determined that these oligomers contain parallel β-sheets as well as the same intersheet packing as fibrils of PrP(106-126). Finally, the interaction of PrP(106-126) with lipid bilayers and cells was examined. Oligomers of PrP(106-126) were shown to affect model membranes; with anionic lipids losing integrity and cholesterol-containing lipid mixtures losing domain structure upon peptide addition. Additionally, amyloid oligomers of PrP(106-126) cause cell death across a number of cell lines as well as rat cerebellar slices. Overall, these results indicate that the conversion of oligomers to fibrils may be facilitated due to structural similarities between the two. Additionally, the toxicity of PrP(106-126) oligomers may be attributed to a loss of cholesterol domain structure causing subsequent cell death.

Keywords: Amyloid
Structural Biology
Advisor: Sharpe, Simon
Machine Learning Methods and Models for Ranking

Ranking problems are ubiquitous and occur in a variety of domains that include social choice, information retrieval, computational biology and many others. Recent advancements in information technology have opened new data processing possibilities and signi cantly increased the complexity of computationally feasible methods. Through these advancements ranking models are now beginning to be applied to many new and diverse problems. Across these problems data, which ranges from gene expressions to images and web-documents, has vastly di erent properties and is often not human generated. This makes it challenging to apply many of the existing models for ranking which primarily originate in social choice and are typically designed for human generated preference data. As the field continues to evolve a new trend has recently emerged where machine learning methods are being used to automatically learn the ranking models. While these methods typically lack the theoretical support of the social choice models they often show excellent empirical performance and are able to handle large and diverse data placing virtually no restrictions on the data type. These model have now been successfully applied to many diverse ranking problems including image retrieval, protein selection, machine translation and many others. Inspired by these promising results the work presented in this thesis aims to advance machine methods for ranking and develop new techniques to allow e ective modeling of existing and future problems. The presented work concentrates on three di erent but related domains: information retrieval, preference aggregation and collaborative ltering. In each domain we develop new models together with learning and inference methods and empirically verify our models on real-life data.

Keywords: Applied Sciences
Artificial Intelligence
Machine Learning
Advisor: Zemel, Richard S.
A Global Mapping of Protein Complexes in S. cerevisiae

Systematic identification of protein-protein interactions (PPIs) on a genome scale has become an important focus of biology, as the majority of cellular functions are mediated by these interactions. Several high throughput experimental techniques have emerged as effective tools for querying the protein-protein interactome and can be broadly categorized into those that detect direct, physical protein-protein interactions and those that yield information on the composition of protein complexes. Tandem affinity purification followed by mass spectrometry (TAP/MS) is an example of the latter that identifies proteins that co-purify with a given tagged query (bait) protein. Though TAP/MS enables these co-complexed associations to be identified on a proteome scale, the amount of data generated by the systematic querying of thousands of proteins can be extremely large. Data from multiple purifications are combined to form a very large network of proteins linked by edges whenever the corresponding pairs might form an association. Only a fraction of these pairwise associations correspond to physical interactions, however, and further computational analysis is necessary to filter out non-specific associations. This thesis examines how differing computational procedures for the analysis of TAP/MS data can affect the final PPI network, and outlines a procedure to accurately identify protein complexes from data consolidated from multiple proteome-scale TAP/MS experiments in the budding yeast \textit{Saccharomyces cerevisiae}. In collaboration with the Greenblatt and Emili laboratories at the University of Toronto, this methodology was extended to yeast membrane proteins to derive a comprehensive network of 13,343 PPIs and 720 protein complexes spanning both membrane and non-membrane proteins.

Keywords: Proteomics
Bioinformatics
Advisor: Wodak, Shoshana J.
The Ruins of Detroit

The Ruins of Detroit (2013) is a twenty-four minute orchestral work for string orchestra, string octet, celesta, harp, two vibraphones, four horns, two trumpets, two trombones, two bassoons, two clarinets, two oboes, two flutes, and pre-recorded audio soundtracks. The focal point of the work is the conceptual exploration of urban decay found throughout the city of Detroit, Michigan, in 2012. Urban ruins are visible symbols, and landmarks of our society and its changes. Perhaps no other city has been affected more by post-industrialization than Detroit, whose plight has become symbolic of the shift away from manufacturing. This concept not only manifests itself though the utilization of archival recordings and electroacoustic elements in the work, but also throughout the acoustic material as well. Structurally, the work shifts through a series of seven “atmospheres,” which are comprised of pitch collections based on all white notes that descend from A through G. The syntax is anchored in the organization of musical material into foreground (solo violin,) middle-ground (harp, celeste, string octet, piano, percussion, woodwinds, brass) and background (string orchestra, soundtracks). The central theme to this work is intended to be the wholeness of music, and challenges the listener to step inside of it, and experience it not as a representation of place, but as a place in itself: The Ruins of Detroit.

Keywords: Mixed Media
Urban Ruins
Orchestra
Orchestra and Soundtracks
Advisor: Hatzis, Christos
Particle Definitions and the Information Loss Paradox

An investigation of information loss in black hole spacetimes is performed. We demon- strate that the definition of particles as energy levels of the Harmonic oscillator will not have physical significance in general and is thus not a good instrument to study the ra- diation of black holes. This is due to the ambiguity of the choice of coordinates on the phase space of the quantum field. We demonstrate how to identify quantum states in the functional Schr ̈dinger picture. o We demonstrate that information is truly lost in the case of a Vaidya black hole (a black hole formed from null dust) if we neglect back reaction. This is done by quantizing the constrained classical system of a Klein-Gordon field in a Vaidya background. The interaction picture of quantum mechanics can be applied to this system. We find a physically well motivated vacuum state for a spherically symmetric space- time with an extra conformal Killing vector. We also demonstrate how to calculate the response of a particle detector in the a LeMaitre-Tolman-Bondi spacetime with a self- similarity. Finally, some of the claims and confusion surrounding Unruh radiation, Hawking radiation and the equivalence principle are investigated and shown to be false.

Keywords: black hole
quantum field theory
information loss
curved spacetime
Hawking radiation
Unruh radiation
particles
Klein Gordon
Advisor: Dyer, Charles C.
A Design Procedure for Determining the In Situ Stresses of Early Age Cemented Paste Backfill

Underground mining can be summarized as the removal of economically viable volumes of rock which creates underground voids. In order to optimize ore extraction, a material is used to backfill these openings prior to creating any adjacent openings. The use of cemented paste backfill (CPB), a mixture of mine tails, water, and cement binder, has gained prominence as it not only provides a material that has engineered strength and can be deployed rapidly, but also decreases the surface storage volume of the mine tails. There is limited knowledge about the behavior of the stresses within the CPB during the filling of an underground opening, particularly during the early curing ages of the hydrating CPB which is critical to the design of fill barricades. This thesis presents a design procedure which can be used to determine the in situ stresses within the CPB. Three methodologies were used in the development of this design procedure. The first was to develop a laboratory testing method that determined the time-dependent consolidation characteristics and strength parameters of the hydrating cemented paste material. The second was to collect several field-data sets. The third methodology was to numerically model the CPB using Itasca’s FLAC3D, which incorporated the underground void’s geometry, backfilling strategy, and time-dependent backfill parameters in order to determine the in situ stresses of the CBP. This simulation allowed for the prediction of both total and effective stress throughout the stope. The model and the laboratory results were used to model the stresses in several test stopes so that a comprehensive comparison could be made between the model and field instrumentation results. Four case studies were examined using a total of six different field instrumentation datasets. The results from these case studies showed that the modeling approach, given some model calibration, is capable of quantitatively representing the important geomechanical aspects of paste filling and curing.

Keywords: Paste
Backfill
Model
Cemented
Stresses
Advisor: Grabinsky, Murray
Bawden, William
Nonlinear Microscopy for Histology

Histology has long recognized the intimate link between structure and function. Over centuries histologists have utilized an assortment of optical microscopy techniques to elucidate functional attributes of tissues through investigating tissue architecture. This thesis includes developments in the field of nonlinear optical microscopy for use in histology and pathology. The main contributions focused on the study of fibrillar collagen in the extracellular matrix (ECM) with polarization-dependent second harmonic generation (P-SHG) microscopy and the study of harmonophore-stained cellular nuclei with third harmonic generation (THG) microscopy. The P-SHG microscopy technique, “polarization-in, polarization-out” (PIPO), was developed to accurately determine the second-order polarization properties of thin tissue sections. The polarization instrumentation was implemented into a nonlinear optical microscope and a custom fitting algorithm extracted ratios of the second-order nonlinear susceptibility elements at every pixel of an obtained image. Hierarchical organization, at every level of structure, can contribute significantly to the macroscopic second-order polarization properties of fibrillar collagen in the ECM and quantifiable differences between the various tissue architectures were observed. A framework was developed, based on the collagen hierarchical organization, to interpret the submicron polarization properties of various tissues. Complimentary to the P-SHG study of connective tissue, the structure of hematoxylin and eosin (H&E) stained nuclei was revealed by THG microscopy. Imaging the 3D organization of nuclei was possible using the inherent optical sectioning provided by nonlinear microscopy. The origin of THG was investigated with spectrally- and temporally-resolved measurements, as well as the THG ratio method. A rather complex situation involving multiple dye complexes was revealed. The structure of dye aggregates was investigated with THG PIPO microscopy. The techniques of PIPO and harmonophore-stained harmonic generation microscopy show great potential for ultimately furthering understanding of tissue structure and function. H&E stained tissue investigations with THG microscopy has applications as a tool for cancer diagnostics. PIPO can elucidate the symmetry and organization of materials beyond tissues, including starch, nanowires, and protein crystals. In pathology, the developed collagen framework has strong implications, as collagen is recognized as playing a more active role in a number of diseases including idiopathic pulmonary fibrosis, wound repair, and tumour development and progression.

Keywords: Nonlinear Optical Microscopy
Collagen
H&E
Polarization
Third harmonic generation
Second harmonic generation
Nonlinear Optics
Histology
Advisor: Barzda, Virginijus
Defining Nucleosome Occupancy and Positioning: Evolution and the Role of Trans-acting Factors

The fundamental repeating unit of all eukaryotic chromatin is the 147bp DNA:histone complex known as the nucleosome. Genome-wide studies have demonstrated that nucleosomes are organized with the 5&rsquo; promoter being nucleosome depleted and the transcribed region is occupied by a periodic array of positioned nucleosomes. While this organization is well described, the determinants, particularly trans-acting factors that contribute to this architecture are only partly described with gene expression, however, while the connection between chromatin and the various facets of gene expression regulation, especially in evolution, is apparent the detailed mechanisms remain to be described. In this thesis, I describe 1) The role of nucleosomes in gene expression evolution in closely related yeast species 2) The role of trans-acting factors (particularly transcription factors and co-factors) in determining the nucleosome depleted region of promoters and 3) The role of trans-acting factors in nucleosome spacing within genes.

Keywords: Chromatin
Nucleosome
Advisor: Giaever, Guri
Nislow, Corey