VictorJuiz/thesis huggingface dataset:
The Ruins of Detroit
Keywords: Mixed Media
Urban Ruins
Orchestra
Orchestra and Soundtracks

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.
Particle Definitions and the Information Loss Paradox
Keywords: black hole
quantum field theory
information loss
curved spacetime
Hawking radiation
Unruh radiation
particles
Klein Gordon

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.
A Design Procedure for Determining the In Situ Stresses of Early Age Cemented Paste Backfill
Keywords: Paste
Backfill
Model
Cemented
Stresses

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

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.
New Synthetic Applications of Rhodium-Catalyzed Carbon-Carbon and Carbon-Heteroatom Bond Forming Reactions
Keywords: organic chemistry
transition metal
organic synthesis
heterocycle
rhodium
asymmetric catalysis
regioselective
stereoselective

This thesis is divided into four chapters that describe the new development in rhodium-catalyzed addition reactions and asymmetric ring opening (ARO) reactions of strained alkenes. Chapter 1 describes a regioselective Rh(I)-catalyzed addition reaction of arylboronic acids to unactivated alkenes - protected allylic amines and allyl sulfones. These formal hydroarylation processes have significantly advanced the substrate scope. Comprehensive studies were carried out to optimize the reaction conditions and a wide range of arylboronic acids were employed. The reaction was found to be linear-selective and a mechanism based on functional group- directing effects has been proposed. Chapter 2 discloses the discovery of Rh(I)-catalyzed addition of arylboronic acids to (benzyl- /arylsulfonyl)acetonitriles. Novel β-sulfonylvinylamine products were formed in a stereoselective fashion (Z-alkene). Upon hydrolysis, β-keto sulfones were obtained with a broad scope of aryl and sulfonyl substituents. These (Z)-β-sulfonylvinylamines were useful synthons in the synthesis of unsymmetrical polysubstituted pyridines via 1-aza-allyl anion intermediates as well as 1,4- benzothiazine derivatives via intramolecular cyclization. Chapter 3 reports the use of two new nucleophiles in Rh(I)-catalyzed ARO of oxabicyclic alkenes - water and triethylamine trihydrofluoride. In the water-induced ARO, an unprecedented domino ARO/isomerization process was discovered which led to the formation of 2-hydroxy-1- tetralones. By modifying the reaction conditions, trans-1,2-diols can be obtained in excellent enantioselectivity. Using triethylamine trihydrofluoride as a nucleophile, an aliphatic C-F bond was constructed enantioselectively in the ring-opening process which provided fluorinated building blocks containing both allylic fluoride and fluorohydrin units. Finally, Chapter 4 details the development of a one-pot synthesis of a chiral dihydrobenzofuran framework using Rh-catalyzed asymmetric ring opening and Pd-catalyzed C-O coupling. The product can be obtained in excellent enantioselectivity without isolation of intermediates. Systematic metal-ligand studies were carried out to investigate the compatibility of each catalytic system using product enantiopurity as an indicator.
Post-translational Regulations of FUSCA3 in Arabidopsis thaliana
Keywords: Development
Protein-protein interaction
Phosphorylation
Phase transition
Plant hormone
Protein degradation

Seed formation consists of two major stages: embryo pattern formation and maturation. During seed maturation, the embryo accumulates storage material, acquires desiccation tolerance, and enters a stage of dormancy. Genetic analyses have identified several master regulators that orchestrate late embryogenesis, including the B3-domain transcription factor FUSCA3 (FUS3). In Arabidopsis, FUS3 has been shown to be a central regulator of hormonal pathways; it positively regulates late embryogenesis by increasing abscisic acid (ABA) level while repressing gibberellin (GA) synthesis. In turn, FUS3 protein level is positively and negatively regulated by ABA and GA, respectively. However, the mechanism of how this regulation occurs has not been well characterized. In this study, FUS3 has been shown to be an unstable protein rapidly degraded by the proteasome through a PEST instablility motif. To further characterize the mechanisms involved in FUS3 homeostasis, FUS3-interacting proteins were identified. The SnRK1 kinase AKIN10 was shown to interact with and phosphorylate FUS3 at its N-terminus. Furthermore, overexpression of AKIN10 delays FUS3 degradation, suggesting AKIN10 positively regulates FUS3 protein accumulation. Overexpression of AKIN10 delays developmental phase transitions, and causes defects in lateral organ development. These defects were partially rescued by the loss-of-function fus3-3 mutation, suggesting FUS3 and AKIN10 genetically interact to regulate these developmental processes. SnRK1/AMPK/Snf1 kinases are regulators of energetic stress responses. Overexpression studies suggest both FUS3 and AKIN10 positively regulate ABA signaling, but differ in sugar responses during germination; AKIN10 mediates glucose sensitivity, while FUS3 regulates osmotic stress responses. Overexpression of AKIN10 and FUS3 results in glucose and osmotic stress hypersensitivities, respectively, both of which are partially dependent on de novo ABA synthesis. Thus, FUS3 and AKIN10 act in overlapping pathways and combine different environmental signals to generate a common ABA-dependent response. In summary, novel mechanisms that regulate FUS3 homeostasis and function were identified. A model explaining the interaction between FUS3 and AKIN10 during embryonic and vegetative development, and the function of these two central developmental regulators in hormonal and stress signaling pathways is discussed.
Write the Book of Your Heart: Career, Passion and Publishing in the Romance Writing Community
Keywords: romance fiction
gender
flexible labour
women writers
linguistic anthropology
creativity
Canadian writers
work

This dissertation explores how a solitary writer becomes a social writer, entering into the industrial and community relations of mass publishing. A significant part of this transformation is managed through writing organizations which mediate between the corporate world and individual writers. Despite being one of the most prolific and commercially successful book-markets in a time when both publishing and reading are perceived to be under threat, romance fiction, because of its gendered and classed status, is often neglected by the academy and patronized in the media. Researched through observation of the largest romance writers groups in Canada, which I call City Romance Writers, this dissertation explores how writers’ associations help shape would-be writers into players in the professional market, negotiating the boundaries between professional and amateur, local and global, creative and market-driven. It explores how romance writers organize to manage risk and uncertainty in the publishing industry and how they make claims to legitimacy and authority in the public sphere. Finally, it examines how structures of gender, race and class shape the communities romance writers form and the claims they make. I argue that romance writers’ discourses and practices surrounding writing and publication are a revealing terrain for the exploration of contemporary issues of media production, flexible labour, gender and community. In part because of the particular characteristics of romance writing itself, these themes are also underpinned by the constant presence of love, as a discourse, an activity and a story. While revealing the importance of affective discourses of passion and love in mobilizing writers to embrace their own flexibility, this dissertation also argues that writers’ affective relationship with their writing is not fully contained by capitalism.
Efficient Machine Learning with High Order and Combinatorial Structures
Keywords: Machine Learning

The overaching goal in this thesis is to develop the representational frameworks, the inference algorithms, and the learning methods necessary for the accurate modeling of domains that exhibit complex and non-local dependency structures. There are three parts to this thesis. In the first part, we develop a toolbox of high order potentials (HOPs) that are useful for defining interactions and constraints that would be inefficient or otherwise difficult to use within the standard graphical modeling framework. For each potential, we develop associated algorithms so that the type of interaction can be used efficiently in a variety of settings. We further show that this HOP toolbox is useful not only for defining models, but also for defining loss functions. In the second part, we look at the similarities and differences between special-purpose and general-purpose inference algorithms, with the aim of learning from the special-purpose algorithms so that we can build better general-purpose algorithms. Specifically, we show how to cast a popular special-purpose algorithm (graph cuts) in terms of the degrees of freedom available to a popular general-purpose algorithm (max-product belief propagation). After, we look at how to take the lessons learned and build a better general-purpose algorithm. Finally, we develop a class of model that allows for the discrete optimization algorithms studied in the previous sections (as well as other discrete optimization algorithms) to be used as the centerpoint of probabilistic models. This allows us to build probabilistic models that have fast exact inference procedures in domains where the standard probabilistic formulation would lead to intractability.
Neto1 and Neto2 are Auxiliary Subunits of Synaptic Kainate Receptors
Keywords: glutamate receptors
auxiliary proteins

Neto1 and Neto2 are CUB domain-containing transmembrane proteins that are expressed in the mammalian brain. Previous studies showed that Neto1 is a NMDAR-associated protein with important roles in synaptic plasticity and learning/memory (Ng et al., 2009). To establish the functions of Neto2, I first searched for its binding partners. Using yeast two-hybrid analysis, GST pull-down and co-immunoprecipitation studies, I found that Neto2 can bind to the PDZ domain-containing protein GRIP. In the brain, GRIP regulates the synaptic trafficking and stability of AMPA and kainate receptors (KARs) (Hirbec et al., 2003). To determine whether Neto2 is required for the synaptic expression of KARs and/or AMPARs, I examined whether Neto2 was associated with these receptors at the postsynaptic membrane. Coimmunoprecipitation studies showed that while Neto2 is a component of postsynaptic KAR protein complexes, it is not associated with AMPARs. In the cerebellum, Neto2-null mice showed a 44% (n=3;p<0.01) decrease in the abundance of postsynaptic KARs with no change in the level of total KARs, thus suggesting a specific deficit in KAR synaptic localization. Unexpectedly, loss of Neto2 had no effect on the abundance of hippocampal KARs (n=3; p>0.05), or on neurotransmission by them (n=12; p>0.05). To determine whether this normal KAR function might be due to compensation by Neto1, which also interacts with KARs, I examined KAR abundance in Neto1-null, and Neto1/2-double null hippocampus. Loss of Neto1 resulted in a 53% decrease in postsynaptic levels of GluK2-KARs (n=3;p<0.01). However, in double null animals, the reduction was indistinguishable from Neto1 single null mice, suggesting that Neto2 is not involved in the postsynaptic localization of hippocampal KARs. In Neto1-null mice, KAR-mediated currents showed smaller amplitude (61% of wild-type;n=14;p<0.01), and faster decay kinetics (40% of wild-type;n=14;p<0.001). Together, these findings establish both Neto1 and Neto2 as auxiliary proteins of native KARs: Neto1 regulates the synaptic abundance and kinetics of KARs in the hippocampus, while Neto2 mediates the synaptic localization of cerebellar KARs. Additionally, the results presented here, in conjunction with previous findings, reveal a unique ability of Neto1 in controlling synaptic transmission by serving as an auxiliary protein for two different classes of ionotropic glutamate receptors.
The French Wh Interrogative System: Est-ce que, Clefting?
Keywords: Canadian French
Syntax
Historical Linguistics
Wh- Interrogatives
Variation
Diglossia

This thesis revisits the variation inherent to the French wh interrogative system. In La[urentien]F[rench], there are many ways to ask wh questions, all of which are said to have the same general interpretation. By looking at different types of data, historical as well as contemporary, this thesis puts forward three main findings/proposals: i. the high degree of variation is due to the use of wh est-ce que, which appeared in Old French as an interrogative cleft (Rouquier 2003); ii. between Old and Modern French, wh est-ce que has gone through a typical cycle of grammaticalisation (as described by Roberts & Roussou 2003, van Gelderen 2008a, b), while the free relative of the Old French cleft remained unchanged; iii. today’s LaF wh system is dominated by the wh est-ce que and variants (over 98 percent of use – Elsig 2009), which lack traditional wh movement. It is proposed that wh est-ce que and variants appear in a construction containing an atrophied clefted CP adjoined to a main clause containing a wh operator, whereas the variant traditionally called wh in situ is generated in a structure in which the wh element is interpreted and spelled-out in the position of Merge. In addition to its theoretical contribution, this thesis helps to bring together theoretical and applied linguistics, since it makes use of different types of data, both historical and synchronic (oral and written corpora, experimental studies and grammaticality judgements). Moreover, the conclusions raise important questions about the realities of diglossia in the French diaspora: wh interrogative variants are divided according to fundamental structural differences; some have wh movement (high, formal register) and others do not (vernacular and neutral register). Finally, this thesis also contributes to the theories of oralité (Gadet 1992), since it sheds light on a complex system of variants found exclusively in vernacular speech.
Training Recurrent Neural Networks
Keywords: Recurrent Neural Networks
Optimization

Recurrent Neural Networks (RNNs) are powerful sequence models that were believed to be difficult to train, and as a result they were rarely used in machine learning applications. This thesis presents methods that overcome the difficulty of training RNNs, and applications of RNNs to challenging problems. We first describe a new probabilistic sequence model that combines Restricted Boltzmann Machines and RNNs. The new model is more powerful than similar models while being less difficult to train. Next, we present a new variant of the Hessian-free (HF) optimizer and show that it can train RNNs on tasks that have extreme long-range temporal dependencies, which were previously considered to be impossibly hard. We then apply HF to character-level language modelling and get excellent results. We also apply HF to optimal control and obtain RNN control laws that can successfully operate under conditions of delayed feedback and unknown disturbances. Finally, we describe a random parameter initialization scheme that allows gradient descent with momentum to train RNNs on problems with long-term dependencies. This directly contradicts widespread beliefs about the inability of first-order methods to do so, and suggests that previous attempts at training RNNs failed partly due to flaws in the random initialization.