VictorJuiz/thesis huggingface dataset:
Problems in Supply Chain Location and Inventory under Uncertainty

We study three problems on supply chain location and inventory under uncertainty. In Chapter 2, we study the inventory purchasing and allocation problem in a movie rental chain under demand uncertainty. We formulate this problem as a newsvendor-like problem with multiple rental opportunities. We study several demand and return forecasting models based on comparable films using iterative maximum likelihood estimation and Bayesian estimation via Markov chain Monte Carlo simulation. Test results on data from a large movie rental firm reveal systematic under-buying of movies purchased through revenue sharing contracts and over-buying of movies purchased through standard ones. For the movies considered, the model estimates an increase in the average profit per title for new movies by 15.5% and 2.5% for revenue sharing and standard titles, respectively. We discuss the implications of revenue sharing on the profitability of both the rental firm and the studio. In Chapter 3, we focus on the effect of travel time uncertainty on the location of facilities that provide service within a given coverage radius on the transportation network. Three models - expected covering, robust covering and expected p-robust covering - are studied; each appropriate for different types of facilities. Exact and approximate algorithms are developed. The models are used to analyze the location of fire stations in the city of Toronto. Using real traffic data we show that the current system design is quite far from optimality and provide recommendations for improving the performance. In Chapter 4, we continue our analysis in Chapter 3 to study the trade-off between adding new facilities versus relocating some existing facilities. We consider a multi-objective problem that aims at minimizing the number of facility relocations while maximizing expected and worst case network coverage. Exact and approximate algorithms are developed to solve three variations of the problem and find expected--worst case trade-off curves for any given number of relocations. The models are used to analyze the addition of four new fire stations to the city of Toronto. Our results suggest that the benefit of adding four new stations is achievable, at a lower cost, by relocating 4-5 stations.

Keywords: Operations Management
Supply Chain Management
Location
Inventory
Advisor: Berman, Oded
Krass, Dmitry
Milner, Joseph
The Role of Glucagon-like Peptides in Experimental Type 1 Diabetes

Type 1 diabetes mellitus (T1D) is an autoimmune disorder that targets the insulin-producing β-cells. The gut may play a role in the pathogenesis of T1D, as genetically-susceptible individuals and animal models of T1D exhibit increased intestinal permeability and improving gut barrier function can interfere with the onset of diabetes. Moreover gut-derived peptides are capable of modifying barrier function and regulate β-cell mass via effects on proliferation and apoptosis. I tested whether chronic administration of glucagon-like peptide-2 (GLP-2), a peptide which potently improves gut barrier function, modifies diabetes onset in a mouse model of T1D, the non obese diabetic (NOD) mouse. Although chronic treatment with a long-acting GLP-2 analogue was associated with improved intestinal barrier function, it failed to delay the onset of T1D. Once the autoimmune attack is initiated, pathogenic T-cells infiltrate the islets and trigger the death of β-cells. Studies in animal models have revealed that β-cells exhibit a compensatory response in the initial stages of the immune attack, which eventually fails, resulting in β-cell mass deficiency and onset of T1D. Glucagon-like peptide-1 (GLP-1) exerts both proliferative and anti-apoptotic actions on β-cells. I hypothesized that chronic activation of the GLP-1 receptor (GLP-1R) would delay or prevent the loss of functional β-cell mass in the NOD mouse. I have shown that chronic administration of the GLP-1R agonist exendin-4 significantly delayed the onset of diabetes and enhanced β-cell mass. Furthermore, GLP-1R activation was associated with a reduction of islet-infiltrating immune cells, as well as changes in lymphocyte subpopulations. Consequently, I addressed whether the GLP-1R has a role in the immune system of NOD and C57Bl/6 mice. GLP-1R mRNA transcripts were detectable in several immune subpopulations, and GLP-1R activation was associated with cAMP production in primary splenocytes and thymocytes. Furthermore I demonstrated that GLP-1R signaling controls proliferation of thymocytes and lymphocytes, and is required for maintaining peripheral regulatory T-cells. In summary, these studies establish that while GLP-2R activation is not sufficient to modify disease onset in a murine model of T1D, GLP-1R activation reduces the extent of diabetes development by exerting actions on β-cells and the immune system.

Keywords: diabetes
glucagon-like peptides
GLP-1R
GLP-2
GLP-1
NOD mouse
Advisor: Drucker, Daniel J.
Accurate Residual-distribution Schemes for Accelerated Parallel Architectures

Residual-distribution methods offer several potential benefits over classical methods, such as a means of applying upwinding in a multi-dimensional manner and a multi-dimensional positivity property. While it is apparent that residual-distribution methods also offer higher accuracy than finite-volume methods on similar meshes, few studies have directly compared the performance of the two approaches in a systematic and quantitative manner. In this study, comparisons between residual distribution and finite volume are made for steady-state smooth and discontinuous flows of gas dynamics, governed by hyperbolic conservation laws, to illustrate the strengths and deficiencies of the residual-distribution method. Deficiencies which reduce the accuracy are analyzed and a new nonlinear scheme is proposed that closely reproduces or surpasses the accuracy of the best linear residual-distribution scheme. The accuracy is further improved by extending the scheme to fourth order using established finite-element techniques. Finally, the compact stencil, arithmetic workload, and data parallelism of the fourth-order residual-distribution scheme are exploited to accelerate parallel computations on an architecture consisting of both CPU cores and a graphics processing unit. Numerical experiments are used to assess the gains to efficiency and possible monetary savings that may be provided by accelerated architectures.

Keywords: residual distribution
parallel architectures
GPGPU
heterogeneous architectures
computational fluid dynamics
CUDA
high order
partial differential equation
multi-dimensional upwind
multi-dimensional limiter
Advisor: Groth, Clinton P. T.
Discovery of Novel Ovarian Cancer Biomarkers via Proteomics and Mass Spectrometry

Proteins secreted or shed by tumors can be found in serum. Detecting these proteins by mass spectrometry (MS) is difficult, due to the wide dynamic range of protein concentrations in serum. To circumvent this issue, we mined the conditioned media of epithelial ovarian cancer (EOC) cell lines which is a less complex fluid to work with. We hypothesize that some of the proteins shed or secreted by EOC cell lines are similar to those secreted or shed by EOC tumors and that some of these proteins can be used as biomarkers. We mined the conditioned medium of four ovarian cancer cell lines (HTB75, TOV-112D, TOV-21G and RMUG-S) by two-dimensional liquid chromatography-mass spectrometry. Our study identified 1208, 1252, 885, and 463 proteins from the HTB-75, TOV-112D, TOV-21G, and RMUG-S cell lines respectively. In all, we identified 2039 proteins from which we focused on 420 extracellular and plasma membrane proteins. High abundance proteins such as albumin and immunoglobulins, which are problematic for serum proteomics, did not interfere with our study. Several known markers of EOC including CA-125, HE4, Mesothelin, and KLK6, were identified in this study. The list of 420 extracellular and membrane proteins was cross-referenced with the proteome of ascites fluid to generate a final list of 51 potential candidates. According to Ingenuity Pathway Analysis, two of the top 10 diseases associated with our list of 51 proteins were cancer and reproductive diseases. Of the 51 candidates, 10 proteins were selected for verification in sera from ovarian cancer patients and healthy individuals. Clusterin showed a significant difference between cancer patients and normal, with sera from cancer patients showing higher levels. Another protein, NPC2, did not show a difference in sera between cancer and normals. Protein expression studies using immunohistochemistry showed that NPC2 is highly expressed in ovarian cancer tissue and absent in normal ovarian surface epithelium. In summary, clusterin and NPC2 appear to play a role in ovarian cancer pathobiology and their role in EOC need to be studied further.

Keywords: Ovarian Cancer
Biomarkers
Chromatography
Mass Spectrometry
ELISA
Advisor: Diamandis, Eleftherios P.
New Routes to Pnictogen-containing Polymers

New synthetic routes to nitrogen- and phosphorus-containing polymers have been investigated. These routes rely on amine- and phosphine-containing monomers bearing pendant alkyne substituents, and subsequent hydroamination, oxidation, or hydrophosphination polymerization. A series of primary amines of the form H2NC6H2R2C≡CR’ (R = H or iPr; R’ = Ph, SiMe3, nBu, or p-C6H4Me) is reported. These amines are deprotonated with nBuLi to give lithium amides, which react with zirconocene compounds to provide amidozirconium complexes. Characterization is achieved by multinuclear NMR spectroscopy, IR spectroscopy, high-resolution mass spectrometry, elemental analysis, X ray crystallography, and DFT calculations. Three routes were attempted towards nitrogen-containing oligomers: (1) thermolysis of amidozirconium complexes to afford [2+2] cycloaddition polymers; (2) Ti(IV)-catalyzed hydroamination of H2NC6H4C≡CPh; (3) chemical oxidation of H2NC6H4C≡CPh. The latter two strategies resulted in distinct nitrogen-containing oligomers. The oligomer formed by Ti(NR2)4-catalyzed hydroamination (R = Me, Et) contains up to 15 repeat units in the chain, with both imine and enamine moieties, and is capped by a molecule of HNR2 (R = Me or Et) originating from the catalyst. The oligomer formed by chemical oxidation contains up to 9 repeat units in the chain. A series of phosphines of the form X2PC6H2R2C≡CR’ is reported (X = NEt2, Cl, H; R = Me, iPr; R’ = Ph, SiMe3). Characterization is achieved by multinuclear NMR spectroscopy, IR spectroscopy, high-resolution mass spectrometry, elemental analysis, and X-ray crystallography. The primary phosphines, H2PC6H2R2C≡CR’, are relatively “user-friendly” in that they are not particularly malodorous, they are isolated as solids or highly viscous liquids, and they are stable when stored under N2 in the solid state and in solution. The primary phosphine H2PC6H2iPr2C≡CPh serves as a precursor for a zirconium phosphinidene and for the secondary phosphines RP(H)C6H2iPr2C≡CPh (R = CH2iPr, CH2Ph). Hydrophosphination polymerization gives cyclic P(III)-containing oligomers, which are converted to P(V)-based macromolecules by treatment with sulfur. The oligomers contain ca. 5 to 10 repeat units, and heating to 800 °C gives rise to phosphorus-containing ceramics. The mechanism of hydrophosphination is discussed with the use of DFT calculations.

Keywords: inorganic chemistry
polymer
oligomer
nitrogen
phosphorus
pnictogen
hydroamination
hydrophosphination
alkyne
Advisor: Stephan, Douglas
Making the Adjustment: A Grounded Theory Study of What Works and Does Not Work in Postdivorce Parenting Relationships

This study contributes to the growing knowledge base on postdivorce parenting. Recognizing the need to facilitate a better understanding of what makes the postdivorce parenting dyad work or not work, this study explored how individuals sustain a parenting relationship with their former partners when the couple relationship ends through separation or divorce. To date, knowledge about couples’ relationships has been absent from clinical approaches to assisting postdivorce parenting relationships and consequently there has been no bridge between the theories and paradigms of the couples’ literature and those of postdivorce parenting. This exploratory study examined the experiences and perspectives of 20 individual parents in Ontario, Canada. Individual interviews were held with each of the participants. The study identified key themes illuminating an emerging understanding of postdivorce relationships. These key themes will assist to better understand the postdivorce parenting relationship. Findings suggest that practitioners should consider that: (a) the postdivorce parenting relationship is highly complex and the development of a “working” or “not working” relationship results from an interaction among a range of factors; (b) understanding couple’s research is essential to comprehending this complexity because, despite the couple relationship ending, former couples remain a dyad because they are parents; (c) even when the postdivorce parenting relationship is “not working”, men and women describe other aspects of their lives as successful. The study’s findings have implications for mental health professionals and legal professionals working with parents during and following the divorce process.

Keywords: divorce
parenting
Advisor: Mishna, Faye
Understanding Biosolids Dynamics in a Moving Bed Biofilm Reactor

Biofilm systems such as the moving bed biofilm reactor (MBBR) are finding increased application in wastewater treatment. One important process that governs MBBRs and yet is poorly understood is the rate of biofilm detachment. The detachment of cells from biofilm surfaces controls both the accumulation of biofilm and the quantity of biomass that is suspended in the bulk liquid phase. This changing balance of attached and suspended cells, in this thesis named the biosolids dynamics, can impact the efficacy of MBBRs. The goal of this research was to investigate how the biosolids dynamics are influenced by process changes relevant to applied wastewater treatment systems and suggest new routes to reactor design and optimization. To achieve this goal, the work addresses three separate but interconnected lines of inquiry. First, multivariate analysis (Principal Component Analysis, Partial Least Squares) was used to examine 2 years of historical data from an MBBR operating at a Canadian pulp mill in order to identify key process variables, perform process diagnostics, and act as a predictive tool. Secondly, the effect of calcium concentration on biofilm structure, microbiology and reactor performance was investigated in four laboratory-scale MBBRs operated at a range of calcium concentrations (1 to 300 mg/L Ca2+). It was found that above a threshold calcium concentration between 1-50 mg/L, MBBR biofilms were observed to be thicker with greater density, contain larger anoxic regions adjacent to the carrier substratum, have more proteinaceous EPS, and have altered microbial community structure. The results suggest an important role for calcium that should be considered in the design and operation of MBBRs. In the final line of inquiry, a diffusion-reaction biofilm model was adapted to represent the key processes of the MBBR. The model was found to simulate average trends observed in the lab-scale experiments allowing for quantification of the detachment rate. Transient periods of reactor starvation were also simulated by introducing a novel metabolic state function to account for down-regulation of metabolism as a result of starvation. This approach was found to accurately simulate starvation response when coupled with detachment expressions that were growth-dependant.

Keywords: Biofilm
Detachment
Moving Bed
Modeling
Multivariate
Calcium
Advisor: Allen, D. Grant
Applications of Generic Interpolants In the Investigation and Visualization of Approximate Solutions of PDEs on Coarse Unstructured Meshes

In scientific computing, it is very common to visualize the approximate solution obtained by a numerical PDE solver by drawing surface or contour plots of all or some components of the associated approximate solutions. These plots are used to investigate the behavior of the solution and to display important properties or characteristics of the approximate solutions. In this thesis, we consider techniques for drawing such contour plots for the solution of two and three dimensional PDEs. We first present three fast contouring algorithms in two dimensions over an underlying unstructured mesh. Unlike standard contouring algorithms, our algorithms do not require a fine structured approximation. We assume that the underlying PDE solver generates approximations at some scattered data points in the domain of interest. We then generate a piecewise cubic polynomial interpolant (PCI) which approximates the solution of a PDE at off-mesh points based on the DEI (Differential Equation Interpolant) approach. The DEI approach assumes that accurate approximations to the solution and first-order derivatives exist at a set of discrete mesh points. The extra information required to uniquely define the associated piecewise polynomial is determined based on almost satisfying the PDE at a set of collocation points. In the process of generating contour plots, the PCI is used whenever we need an accurate approximation at a point inside the domain. The direct extension of the both DEI-based interpolant and the contouring algorithm to three dimensions is also investigated. The use of the DEI-based interpolant we introduce for visualization can also be used to develop effective Adaptive Mesh Refinement (AMR) techniques and global error estimates. In particular, we introduce and investigate four AMR techniques along with a hybrid mesh refinement technique. Our interest is in investigating how well such a `generic' mesh selection strategy, based on properties of the problem alone, can perform compared with a special-purpose strategy that is designed for a specific PDE method. We also introduce an \`{a} posteriori global error estimator by introducing the solution of a companion PDE defined in terms of the associated PCI.

Keywords: partial differential equations
unstructured meshes
scattered data interpolation
contour lines and level sets
adaptive mesh refinement
error estimation
Advisor: Enright, Wayne
Biases in Looking Behaviour during Visual Decision Making Tasks

In four experiments we used eye-tracking to investigate biases in looking behaviour during visual decision making tasks. In Experiment 1, participants viewed arrays of images of photographic art and decided which image was preferred (from a set of either two or eight alternatives). To analyze gaze behaviour during the decision we identified dwells (where a dwell is a series of consecutive fixations on a decision alternative). This analysis revealed two forms of gaze bias in the period prior to the response. Replicating prior findings (Shimojo, Simion, Shimojo, & Scheier, 2003), just prior to the response we found an increase in the frequency of dwells on the chosen item. In addition, throughout the decision, dwells on the chosen item were longer than dwells on other items. This pattern of biases was extremely similar across preference and non-preference decision instructions, but overall the biases were more pronounced in eight alternative decisions than in two alternative decisions. In Experiment 2 we manipulated the number of decision alternatives while controlling for differences in the stimulus displays. Participants viewed displays containing six everyday items, and chose either which of two sets of three items was the most expensive (two alternative set selection task) or which of the six items was the most expensive (six alternative item selection task). Consistent with Experiment 1, participants exhibited greater selectivity in their processing of stimulus information in the six alternative decisions compared to the two alternative decisions. In Experiments 3 and 4 we manipulated stimulus exposure in order to test predictions derived from the Gaze Cascade model (Shimojo et al., 2003). In Experiment 3, participants performed an eight alternative decision in which four of the items had been pre-exposed prior to the decision. In Experiment 4, stimulus exposure was manipulated during the ongoing decision using a gaze-contingent methodology. While these manipulations of stimulus exposure had strong effects on gaze bias, the specific predictions of the model were not supported. Rather, we suggest an interpretation based on prior research, according to which the gaze bias reflects the selective processing of stimulus information according to its relevance to the decision task.

Keywords: decision making
eye movements
attention
gaze bias
Advisor: Reingold, Eyal M.
"All in the Same Boat": An Analysis of a Support Group for Children of Parents with Mental Illnesses

The effectiveness of psychoeducation and peer support programs for children of mentally ill parents is frequently measured by demonstrating children’s ability to meet program goals according to pre-defined categories determined by adults. Little is known about how children respond to these goals, whether they share them, and how, or if, their needs are met. I conducted an ethnographic study of one such group for school-aged children. I examined how specific discourses framed the content of the program manual designed to educate and support children and I observed how children responded to the program. My study is rooted in Goffman’s (1959) dramaturgical analyses of the reciprocal influence individuals have on one another in face-to-face encounters. From a critical dramaturgical perspective the participants were expected to conform to behavioural expectations of the setting, itself framed by broader arenas of interaction in which shared institutionalized meanings govern (often idealized) presentations of self. Data collection included: 1. a critical discourse analysis of the program manual; 2. participant observation of interactions during the eight-week program; and 3. children’s evaluations of the program in a separate group interview. Being identified as “as all in the same boat” was meaningful and consequential for children who were expected to learn mental health/illness information because, “knowledge is power”, and to express difficult feelings about being a child of a mentally ill parent. Children could be said to have achieved the goals of the program because they developed a mutual understanding about how to interpret and give meaning to their circumstances; “recognizing” unpredictable behaviours as signs of illness and becoming responsible for managing only how “their own story would go”. Children were not expected to care for ill parents, even when they wanted some responsibility, and were strongly discouraged from turning to friends for support. Children strategized to negotiate and resist group expectations and challenge assumptions about being “all in the same boat”. Suggestions are made for determining what constitutes “good” mental health literacy based on children’s preferences for explaining their circumstances in ways they find relevant and for supporting children’s competencies to manage relationships that are important to them.

Keywords: mental health
parental mental illness
children
adolescence
qualitative methods
critical dramaturgy
ethnography
mental health services
support group
prevention
psychiatric disability
early intervention
discourse analysis
Goffman
mental health literacy
emotion
Advisor: McKeever, Patricia
Boydell, Katherine