VictorJuiz/thesis huggingface dataset:
Aqueous Phase Diffusion Related Isotope Fractionation in Groundwater Systems

Aqueous phase diffusion-related isotope fractionation (DRIF) for stable carbon isotopes was investigated for common groundwater contaminants through modelling to determine under what conditions DRIF effects would be observable. This study proposes a critical dispersive enrichment factor of (‒0.32‰), above which the isotope fractionation due to different dispersion coefficients of light and heavy isotopologues may be significant. This study also reveals that the key factors constraining the observation of DRIF include the ratio of macrodispersion coefficient to effective diffusion coefficient (λv/Deff), the ratio of initial contaminant concentration to the method detection limit for isotope analysis (C0/MDL), the diffusive fractionation factor, the presence of low-permeability zones, local scale compound specific transverse mechanical dispersion, soil heterogeneity, sampling method and occurrence of biodegradation. This study provides important constraints on the conditions that would merit close investigation of carbon isotope DRIF effects. These conditions include compounds with smaller molar masses (e.g., vinyl chloride or benzene) which can lead to larger diffusive fractionation factors (father from unity) and sites with high C0/MDL ratios (i.e. > 50), low λv/Deff ratios (i.e.

Keywords: Contamination
Diffusion
Dispersion
Groundwater
Isotope fractionation
Modelling
Advisor: Sleep, Brent E.
Sherwood Lollar, Barbara
Surface-atmosphere and Gas-particle Partitioning of Ammonia: Measurements, Modelling, and Trend Analysis

Atmospheric ammonia is of interest because of its impacts on ecosystem and human health, as well as climate. Processes of surface-atmosphere and gas-particle exchange were investigated through measurements, modelling, and long-term trend analysis. A Quantum Cascade-Tuneable Infrared Laser Differential Absorption Spectrometer (QC-TILDAS) was characterised for the purposes of making direct eddy covariance (EC) flux measurements of bi-directional surface-atmosphere ammonia exchange. While this instrument has great potential, improvements are needed in both sensitivity and time response of the instrument if it is to be used to make EC flux measurements. This instrument was further used to measure vertical profiles of ammonia mixing ratios, investigating the influence of the surface on column distribution, and the variation in diurnal trends with altitude. Ammonia mixing ratios were found to increase towards the surface, with greater variability during the daytime than at night. Diurnal trends in ammonia were found to change with altitude: all heights showed a daytime maximum, and the lowest measurement height showed an additional nighttime maximum. Atmospheric ammonia is closely tied to aerosol particle composition, especially in terms of particle acidity, which can alter the health and climate impacts of such particles. A 21 year dataset of particle composition was used to determine spatial and temporal trends in particle acidity. It was found that particle acidity decreased significantly over this time period, concurrent with decreases in emissions of SO2 and NOx, with implications for air quality and atmospheric chemistry. Additionally, there is a need for greater consistency in metrics used to describe particle acidity. Finally, thermodynamic and kinetic models were used to explore the potential impacts of this particle acidity on gas-particle, and consequently surface-atmosphere exchange of ammonia, demonstrating the connection between these two equilibrium processes.

Keywords: Aerosol acidity
Ammonia
Instrument optimisation
Trend analysis
Vertical profiles
Advisor: Murphy, Jennifer
Towards a Storage Stack for the Data Center

The storage stack in a data center consists of all the hardware and software layers involved in processing and persisting data to durable storage. The shift of the world's computation to data centers is placing significant strain on the storage stack, leading to a stack that is unreliable and non-performant. This is caused in large part by a lack of understanding of the failure and performance characteristics of critical hardware components, and a lack of programmability and control over the numerous software layers in the stack. The broad goal of this thesis is to improve the storage stack by leveraging insights gained from empirical studies of real-world production systems, and by proposing a new paradigm for implementing and enhancing distributed storage functionality that enables the vertical specialization of the storage stack to a wide variety of customer and data center provider needs. The first part of this thesis studies the reliability of main memory in large-scale production systems. Our findings show that conventional wisdom about memory reliability is incorrect, and that physical hardware is in fact the main culprit for most errors in main memory in the field. As a result, existing memory error protection mechanisms are inadequate. We then use the insights gained from the empirical study to propose and evaluate a suitable error protection mechanism for future data centers. The second part of this thesis offers an empirical study of the effects of temperature on the performance and power consumption of the storage stack. Since cooling constitutes a large fraction of the total cost of ownership in a data center, increasing temperatures in a data center without sacrificing performance can have a huge impact on the power consumption and carbon footprint of data centers. The final part of this thesis proposes a new paradigm for implementing and enhancing distributed storage functionality by creating programmable APIs that allow dynamic configuration and control of the software stages along the storage stack, and designing and implementing an IO routing primitive for the storage stack.

Keywords: Data Center
Performance
Reliability
Software-Defined Storage
Storage
Advisor: Schroeder, Bianca
Incurable Invisible: Living with Advanced Disease in a Canadian Cancer Hospital

This thesis follows the lives of people who are diagnosed with a cancer that is unlikely to be cured. This means that even if patients receive one or multiple rounds of the standard treatments of chemotherapy, surgery and radiation, there is a high probability that they will still die from their disease. Incurable illness presents a particular problem due to a combination of cultural meanings and values, both within biomedicine and within society. Drawing on 17 months of ethnographic fieldwork conducted in one Canadian cancer hospital, working with patients with lung and gynaecological cancers, the dissertation answers the question: What is life like for patients with advanced cancer as they live with their disease, post-diagnosis? Although its focus is primarily on the patients, it also includes the experiences of doctors and nurses at the hospital, and patients’ family and friends. I explore some of the challenges and tensions produced from living with a diagnosis of advanced cancer. For example, patients are advised to ‘live in the moment,’ but this is a very challenging directive to follow as it is interlaced with the connotation that they are being entreated to do so because their futures are uncertain. Similarly, patients have to muster enough hope to be able to endure the emotionally and physically demanding treatments, but not so much hope that they believe that the treatments will actually cure them of their disease. These entreaties require them to straddle both the worlds of oncology and survivorship and the worlds of death, dying and palliative care, which my findings indicate is extremely difficult to withstand on a day-to-day basis. I argue that advanced cancer is a kind of ‘liminal’ space, an ambiguous territory that exists between the hope for a cure and the imminence of death. Patients’ ambiguous position is made even more challenging since contemporary cancer culture in North America tends to highlight only cancer survivors or people who have ‘lost their battles’ from cancer, rendering the struggles and experiences of patients who are living with advanced cancer but not currently dying from it, both culturally silent and invisible.

Keywords: cancer
culture
liminality
medical anthropology
oncology
palliative care
Advisor: Wardlow, Holly
Rodin, Gary
Two Results on Asymptotic Behaviour of Random Walks in Random Environment

In the first chapter of this thesis, we introduce a model of directed polymer in 1 + 1 dimensions in a product-type random environment ω(t, x) = b(t)F(x), where the fields F and b are i.i.d., with F(x) continuous, symmetric and bounded, and b(t) = ±1 with probabilty 1/2. Thus ω can be viewed as the field F oscillating in time. We consider directed last-passage percolation through this random field; namely, we investigate the behavior of the length n polymer path which maximizes the sum of the environment variables it moves through. We prove a law of large numbers for the maximal action of the path from the origin to a fixed endpoint (n,⌊αn⌋), and investigate the limiting shape function a(α). We prove that this shape function is non-linear on [0, 1], and has a corner at α = 0, thus indicating that this model does not satisfy the KPZ scaling relation, despite ω(t, x) having delta-correlations in t and x. We conjecture that this shape function has a linear piece near α = 0. With probability tending to 1, the maximizing path with free endpoint will localize on an edge with F values far from each other. Assuming a conjecture on the arrival time to this localization site, we prove that the path endpoint and the centered action of the path, both rescaled by n−2/3, converge jointly to a universal law, given by the maximizer and value of a functional on a Poisson point process. In the second chapter, we consider a class of multidimensional random walks in random environment, where the environment is of the type p0 + γξ, with p0 a deterministic, homogeneous environment with underlying drift, ξ an i.i.d. random perturbation, and γ a real number characterizing the strength of the randomness. Such environments were considered by Sabot in [31], who finds a third-order expansion in γ for the non-null velocity (which is guaranteed to exist by Sznitman and Zerner’s LLN [36]). We prove that this velocity is an analytic function of the perturbation, by applying perturbation theory techniques to the Markov operator for a certain chain in the space of perturbations.

Keywords: Probability
Random Environment
Random Walk
Statistical Physics
Advisor: Khanin, Konstantin
Non-neural and Neural Contributions of Androgen Receptors to Socio-sexual Behaviours in Mice

Sexual differentiation of the brain and behaviour is mediated in part by androgens acting on androgen receptors (AR), however it remains unclear whether differentiation is due to action on AR in neural and/or non-neural tissues. To evaluate the role of neural and non-neural AR on sexual differentiation, four experiments were conducted using two models of AR overexpression: neural versus global overexpression of AR. In Chapter 1, the theoretical framework for investigating non-neural contributions of androgens on the sexual differentiation of the nervous system and behaviour is evaluated. In Chapter 2, the transgenic models are characterized by confirming AR overexpression in neural tissue of both neural and global AR overexpression mice, and in a non-neural tissue of global, but not neural, overexpression mice. Next, transgenic mice and wildtype littermates are compared on measures of aggression, copulation and social investigation in response to a male and female stimulus animal. In Chapter 3, neural and global AR overexpression models are tested on an olfactory choice paradigm and neural activity in response to female odors is evaluated. In Chapter 4, the organizational and activational effects of sex hormones on male-typical preference for volatile and non-volatile female cues are assessed by manipulating gonadal hormones during the critical period of development and in adulthood in females. Lastly, in Chapter 5, the role of adult circulating androgens in male-typical preference for volatile and non-volatile female cues is examined in both global and neural AR overexpression males and wildtype littermates by gonadectomy and hormone replacement in adulthood. Together, results suggest that 1) there are distinct roles for both neural and non-neural AR on the organization and activation of male-typical behaviour, 2) that the underlying circuitry responsible for the activation of preference for female cues is present in females, and 3) a nonlinear relationship between AR and male-typical behaviour is proposed, such that AR signaling in either less than or in excess of the normal male range decreases male-typical behaviour.

Advisor: Monks, D. Ashley
Synthesis and Surface Reactions of Hydride Terminated Silicon Nanocrystals with Strong Quantum Size Effect

Among the variety of semiconductor quantum dots targeted for applications in optoelectronics, biological imaging and chemical sensing, silicon nanocrystals (ncSi) are drawing increasing attention because of their earth-abundance, low cost, and purported lack of toxicity. To synthesize freestanding ncSi, we employed several methods that could all yield hydride-terminated ncSi and which allow further surface functionalization and chemical reactions. Among these methods, a batch synthesis based upon the solid-state disproportionation of SiO powder has not previously drawn much attention in chemistry. We describe some remarkable effects observed in the diffraction, microscopy and spectroscopy of SiO powder upon thermal processing in the temperature range 850-1100 ℃, pinpointing that the most significant disproportionation transformations happened in the range between 900 and 950 ℃. With this know-how a high yield synthesis was developed that produced polydispersions of decyl-capped, hexane-soluble ncSi predominantly with NIR photoluminescence. The hydrosilylation reaction was carried out via both the conventional heating and the unconventional microwave heating methods, and the kinetics were studied for the first time. Using size-selective precipitation, these polydispersions were separated into monodisperse fractions, which allowed their photoluminescence absolute quantum yield to be studied as a function of ncSi size. This investigation yielded volcano-shaped plots confirming the most efficient photoluminescence wavelength for ncSi to be located at 820-830 nm, which corresponded to a size of 3.5-4.0 nm. Finally, we describe the unprecedented observation that ncSi:H can function as a single component heterogeneous reducing agent for converting gaseous CO2 selectively to CO, at an impressive rate of hundreds of micromol/h∙g. The large surface area, broadband light harvesting and reducing power of SiH surface sites together play key roles in the conversion. This thesis work provides opportunities for applications of size-selected near infrared emitting ncSi in biomedical imaging, photothermal therapy, and CO2 reduction for the production of chemicals and fuels.

Keywords: CO2 reduction
hydride
hydrosilylation
photoluminescence
quantum size effect
silicon nanocrystals
Advisor: Ozin, Geoffrey A
Exploring the Memory Advantage for Vocal Melodies

The voice is a biologically significant and spectrally rich signal that plays a critical role in communication and social engagement throughout life. Nevertheless, music cognition and perception research does not typically use vocal music as stimuli, opting instead for timbres that are easier to manipulate and control (e.g., digital instruments). The evolutionary and ontogenetic significance of the voice are among the reasons to expect distinctive and favored processing of vocal music. The single previous comparison of memory for vocal and instrumental melodies revealed superior recognition of vocal melodies and no differences among various instrumental renditions (Weiss, Trehub, Schellenberg, 2012). This dissertation explores various facets of the â vocal memory advantageâ by (1) testing additional populations of listeners (children, Brazilian musicians and nonmusicians), (2) using physiological (pupil dilation) as well as behavioral responses, (3) examining the implications of divided attention (a concurrent task), and (4) confirming the generality of the findings across male and female vocalists. Children between 7 and 11 years of age remembered vocal melodies better than instrumental renditions, but younger children had poorer overall memory and were biased to judge vocal melodies as familiar. Brazilian musicians and nonmusicians displayed a similar memory advantage for vocal melodies, and expert pianists remembered piano melodies no better than other instrumental melodies. Listeners exhibited enhanced arousal for vocal melodies relative to piano melodies and for melodies heard previously than for novel melodies, as reflected in greater pupil dilation. Conditions of divided attention revealed greater attention allocation to vocal melodies than to piano melodies, as reflected in modestly greater impairment on a concurrent visual task during vocal melody presentation. Finally, the memory advantage was comparable for the original female vocalist used in Weiss et al. (2012) and two new vocalistsâ one female, and one male. Collectively, the research in this dissertation provides definitive evidence that musical timbres are unequal in their consequences for music perception and cognition. Specifically, vocal and instrumental melodies have differential effects on arousal, attention, and memory.

Keywords: Melody
Memory
Music
Timbre
Voice
Advisor: Trehub, Sandra E.
Schellenberg, E. Glenn
Efficient Structured Prediction for Visual Scene Understanding

This thesis focuses on three topics in visual scene understanding, sorted from low level to high level: unsupervised segmentation, collision-free space detection and holistic scene understanding. All of them are modeled within the framework of probabilistic graphical models. We tackle the problem of unsupervised segmentation in the form of superpixels, with the emphasis on speed and accuracy. To this end, a real-time coarse-to-fine topologically preserving segmentation algorithm [188] is proposed. In this algorithm, we define the problem as a markov random field (MRF) which preserves the boundary in the image and the topology of superpixels. We propose a coarse to fine optimization technique that speeds up the inference dramatically without sacrificing the accuracy for both static images and stereo images. This thesis next tackles the problem of the drivable collision-free space from a monocular video [189]. In contrast to previous approaches that use stereo cameras or LIDAR, we show a method to solve this problem using a single camera. The free space estimation is reduced to an inference problem on a 1D graph, where each node represents a column in the image and its label denotes a position that separates the free space from obstacles. We exploit both spatial and temporal features to define potential functions on the 1D graph, whose parameters are learned through structured SVM. The inference on the 1D graph can be efficiently and exactly solved by dynamic programming. Lastly this thesis interprets the scene by performing scene classification, object detection and semantic segmentation. Rather than solving these problems independently, the proposed method [187] is based on a holistic model which jointly reasons about three individual problems as a whole within a conditional random field (CRF). Learning and inference in the model are efficient as we reason at the segment level instead of pixel level, and introduce auxiliary variables that allow us to decompose the inherent high-order potentials into pairwise potentials between a few variables with small number of states (at most the number of classes). The experimental results show that the joint model has better performance than solving each problem independently.

Keywords: Free Space
Markov Random Field
Object Detection
Scene Understanding
Segmentation
Advisor: Urtasun, Raquel
Illuminating Mergers of Carbon-Oxygen White Dwarfs and Their Possible Link to Thermonuclear Supernovae

The merger of two carbon-oxygen white dwarfs (CO WDs) can either create a more massive WD, lead to collapse into a neutron star, or explode spectacularly as a thermonuclear, or Type Ia, supernova (SN Ia). It has traditionally been believed that SNe Ia result only from mergers at or above the Chandrasekhar mass (MCh), as these can subsequently become dense enough to trigger runaway fusion. Recently, however, it has been proposed that the merged product, or "remnant", might instead subsequently ignite fusion from high temperatures. This opens the possibility of SNe Ia arising even from sub-MCh mergers. To investigate this, I conducted a series of hydrodynamic simulations of the merging process. I first performed simulations spanning the range of possible mergers using the smoothed-particle hydrodynamics code Gasoline, finding that remnant configurations are roughly homologous for mergers of WDs with the same difference in mass ∆M. In particular, "similar-mass" mergers with ∆M

Keywords: Computer simulations
Hydrodynamics
Stellar evolution
Supernovae
White dwarfs
Advisor: van Kerkwijk, Marten H
Towards the Development of Phospholipid-Encapsulated Gold Nanorod Chains for Enhanced Raman Scattering and the Improvement of Student Scientific Communication Skills in Undergraduate Classroom and Laboratory Settings

Depending on functionalization, nanospecies can serve effectively as Surface Enhanced Raman Scattering (SERS) probes. Their efficacy can be improved by tuning their shape and concentrating their electric field profile into smaller regions. This tuning is seen particularly well in nanorods, which concentrate such fields near the rod tips or ends, in ‘hotspots’. These hotspots can be constructively enhanced through the self-assembly of the nanospecies in question, further increasing the enhancement of Raman-active species within. When considering their potential application as SERS probes, both the separation of end-to-end assembled nanorods (gap size), as well as the degree of assembly (chain length), are factors that must be optimized to obtain maximal signal. This thesis reports on the development of robust and variable methods for assembling gold nanorod species in an end-to-end configuration, and for investigating their effectiveness as SERS probes. Using both polymers and short charged ligands with control over their locations of attachment to gold nanorods, nanorod assembly could be initiated in a longitudinal direction either through changing the solvent system or through the introduction of bridging ligands. Exploitation of the inter-rod gap ‘hotspot’ region allowed for significant Raman enhancement of species located in said gap. Using phospholipids to encapsulate the assembling nanorod allowed for significant control over the proportions of species, in terms of length of the nanorod chain. This control allowed for further optimization of the Raman signals from species of interest. This thesis also details the investigation, over a period of several academic years, of the success of the Writing Instruction and Training (WIT) program, an initiative to iteratively improve student written communication skills as they related to scientific chemical communication. In courses ranging from first to third year, undergraduates were provided with opportunities to explore their perceptions of scientific communication and receive extensive and formative feedback on all aspects of their submitted work, with an eye towards fostering improvement. Examining the impact both qualitatively and quantitatively revealed that such a program was highly successful in gradually building upon and expanding student knowledge of the traditions, styles, concepts and progressions of ideas so central to chemical communication.

Keywords: Nanoplasmonics
Nanorods
Phospholipid Encapsulation
Undergraduate Education
Writing Initatives
Advisor: Walker, Gilbert C.