title: THE PROCOAGULANT ROLE OF NUCLEIC ACIDS IN THE CONTACT SYSTEM

contributor:
Weitz, Jeffrey I.
Medical Sciences

subject:
Contact system
FXII
kallikrein
prekallikrein

abstract:
Nucleic acids have been identified as procoagulant species in plasma and in vivo animal studies. It is believed that the nucleic acids act as physiological activators of the contact system. However, in order to obtain a better understanding of the role of nucleic acids in the activation of the contact system it is important to analyze and evaluate the individual proteins of the contact system that are stimulated by nucleic acids and identify accompanying proteins required to mediate the nucleic acid-stimulated activation.
Previous works suggested that nucleic acids stimulate the activation of factor XII (FXII) in the presence of prekallikrein (PK) and high molecular weight kininogen (HK). In this study we will confirm if both PK and HK are required for nucleic acid-stimulated activation of FXII. We will also study the role of nucleic acids in the activation of PK in the presence or absence of activated FXII (FXIIa) and HK. Previous works also identified that zinc (Zn2+) accelerates surface-mediated activation of FXII by PK and HK, and PK by FXIIa and HK. We will be evaluating zinc’s ability to enhance nucleic acid-stimulated activation of both FXII and PK.
We have found that nucleic acids stimulate activation of FXII in the presence of PK and this furthered upon addition of HK. Nucleic acids also stimulate the activation of PK in the presence of FXIIa and this is furthered upon addition of HK. Nucleic acids have stimulated activation of FXII and PK in a dose dependent manner in the presence of the aforementioned accompanying proteins. We have showed that Zn2+ enhances activation of the contact system. Zn2+ enhances nucleic acid-stimulated, PK/HK-mediated activation of FXII. It also enhances nucleic acid-stimulated, FXIIa/HK-mediated activation of PK. These findings enrich our understanding of the role of nucleic acids and zinc in the contact system.

abstract: Thesis

abstract: Master of Science (MSc)


title: High-Efficiency Membrane Chromatography Devices for Downstream Purification of Biopharmaceuticals: Design, Development, and Applications

contributor:
Ghosh, Raja
Chemical Engineering

subject:
Membrane Chromatography
Device
laterally-fed
LFMC
Protein purification
Downstream processing
Biopharmaceutical
Monoclonal antibody

abstract:
The biopharmaceutical industry has experienced remarkable progress in the upstream production capacity of life-saving proteins. This is while the downstream processing has failed to keep pace, including unit operations which are working close to their physical limit with no economy of scale. Column chromatography which is an integral unit in different stages of downstream purification is considered as the major bottleneck in this section. The packed-bed resin media is costly and the processes are labor-intensive and extremely time consuming. Membrane chromatography which uses a stack of adsorptive membranes as the chromatographic media is one of the most promising alternatives for conventional chromatography techniques. The performance of membrane adsorbers is consistent over a wide range of flow rates which is owing to the dominance of convective solute transport as opposed to the diffusion-based nature of mass transfer within the pores of the resin beads. This translates to much higher productivity and considerably lower buffer consumption (even as high as 95%), leading to much lower overall processing costs. The other advantages are significantly lower footprints and decreased pressure drops, both contributing to diminished capital costs. Membrane adsorbers are greatly scalable and used in a single-use manner. The latter eliminates the cleaning and validation steps and brings about much shorter processing times and higher flexibility in process development.
Due to the performance advantages of membrane chromatography, this technique is now widely used in purification of high volumes of samples in late-stage polishing. Currently available membrane adsorbers have radial-flow spiral-wound configuration with high frontal surface area to bed height ratio according to which dilute impurities are removed in a flow-through format at very high flow rates and low pressure drops. Nevertheless, they fail to give high-resolution for bind-and-elute separations which makes them unsuitable for many unit operations, highly restricting their application. Severe design deficiencies such as large dead volumes and varying membrane area over the bed height result in broad and poorly resolved peaks.
Herein, a novel device design was successfully developed which addresses the abovementioned shortcomings. The laterally-fed membrane chromatography (LFMC) devices house a stack of rectangular membrane sheets with two rectangular lateral channels on both sides of the stack as the feed and permeate channels. The design offers balanced pressure over the sides of the stack as well as even solute flow path lengths due to which the solute residence time is very uniform. Also, the small dead volumes minimize the dispersion effects. These features make the LFMC technology highly suitable for bind-and-elute applications, the improvement which is brought about by a simple design. The devices are easy to fabricate and highly scalable.
The LFMC devices containing cation-exchange (CEX) membranes with 7 mL bed volume were examined for bind-and-elute separation where they outperformed the equivalent commercially available radial-flow devices. The design was further modified to give even lower dead volumes and more cost-effective fabrication. The latest embodiment of the device gave resolutions which were comparable with the ones obtained with the commercially packed resin columns in 1 mL and 5 mL scale with consistency over wide range of flow rates. The results were all acquired using a three component model protein system. Upon the approval of suitability of the device for bind-and-elute separation, the CEX-LFMC was used for purification of monoclonal antibodies (mAbs), the largest class of biopharmaceuticals. The device showed great performance in separation of mAb charge variants when extensively shallow gradients (60 membrane bed volumes) were required. The devices offered very stable conductivity gradients at high flow rates. LFMC devices in three different preparative scales gave great performance in separation of mAb aggregates which was approved for different mAb samples. The other application studied with the CEX-LFMC devices was the single-step preparative purification of mono-PEGylated proteins which is as well very challenging due to the physicochemical similarities between the target molecules and the impurities. Collectively, the LFMC devices combine the high-resolution with high-productivity which is highly desirable in downstream purification of biological molecules with great potential to expand the application of membrane chromatography.
Finally, the LFMC devices were modified to adapt the analytical scale where they were integrated with a stack of hydrophilized PVDF membranes. The device successfully delivered ultra-fast separation of mAb aggregates in less than 1.5 minutes based on hydrophobic interaction membrane chromatography (HIMC). The assay times achieved with the HI-LFMC technique outclassed the currently available ultra-high performance chromatography (UPLC) methods at the same time with being extremely cost-effective. The application of the LFMC technology in analytical scale has great potential to offer cheap and rapid analysis in process development and quality control section of biopharmaceutical manufacturing.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Importance of Healthcare Informatics Competencies (HICs) for Service Innovation in Paramedicine: A Mixed-Methods Investigation

title: Informatics Competencies for Service Innovation in Paramedicine

contributor:
Tan, Joseph
Business Administration

subject:
healthcare
innovation
health IT
paramedicine

abstract:
Paramedicine in Canada and throughout the developed world is currently undergoing unprecedented transformation to its service delivery model, largely driven by the need to relieve healthcare systems from overcrowding, and ensure its availability for all citizens. These changes are facilitated by the ability of paramedic services to adopt a number of innovative technologies, and their ability to respond by adopting new service delivery models, which may entail the deployment of paramedics in various non-emergency roles or integration with other healthcare services.
The purpose of this dissertation is to determine how paramedic services innovate, and how that innovation is influenced by technology in particular. To fulfill this purpose, a two-phase sequential explanatory mixed-methods study is conducted, with a quantitative phase followed by a qualitative phase.
In the first phase a multilevel theoretical model consisting of constructs that measure Service Innovation Performance, Dynamic Capabilities, Information Technology (IT) Capabilities and Group-Level Healthcare Informatics Competencies was evaluated with WarpPLS 5.0. A dataset with participation from paramedic leaders of Canadian land-based paramedic services (n=43) and paramedics employed at these services (n=502) was used for this purpose. Findings from this phase indicate that the information technology related knowledge and skills possessed by paramedics have an impact on various organization level dynamic capabilities, as do various IT Capabilities that focus on the relationship between the paramedic service leadership and the IT service provider.
In the second phase, a qualitative approach was taken to explore contextual and other factors that facilitate or inhibit the ability of a paramedic service to innovate. Results from this phase suggest that Canadian paramedic services primarily undertake innovative activities with a strong focus on assuring and improving patient care. The use of an electronic patient care record (ePCR) is an important resource, as it enables activities such as the improvement of the clinical skills of paramedics, as well as facilitates the generation of business cases for equipment investment. Further, the informatics competencies of paramedics greatly facilitate the adoption of technology and equipment by individual services, as paramedics with a high amount of these competencies assist other paramedics when adopting technology, communicate innovative ideas within a service, and identify areas in need of change. The results of this dissertation underline the value of technology-related knowledge and skills for paramedics, and the importance of technology in ensuring that paramedic services provide a high and continually improving standard of patient care.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Paramedicine in Canada is currently undergoing unprecedented transformation. These changes are driven by the need to relieve emergency healthcare resources from overcrowding, the increase in number of innovative technologies adopted by paramedic services, deployment of paramedics in various non-emergency roles, and increased integration with other healthcare services. The purpose of this dissertation is to determine how paramedic services innovate, and how innovation is influenced by technology. To this end, a two-phase sequential explanatory mixed-methods study is conducted, producing a few key findings that underline the value of technology in paramedicine. First, paramedics with information technology related skillsets can better identify opportunities for improvement in service delivery, and facilitate the organizational adoption of technology. Second, electronic patient care records are a vital source for a variety of innovative activities in paramedic services, such as organization-wide improvement of clinical skills and identification of areas where patient care can be improved.


title: INVESTIGATING THE ROLES OF XIN IN SKELETAL MUSCLE AND ITS SATELLITE CELL POPULATION

title: THE ROLES OF XIN IN SKELETAL MUSCLE AND ITS SATELLITE CELLS

contributor:
Hawke, Thomas
Medical Sciences

subject: Xin, skeletal muscle, satellite cell

abstract: Skeletal muscle disease (myopathy) carries an enormous psychological, social and economic impact on the lives of the patients and their caregivers. There is also an appreciable amount of economic burden on the healthcare system and our society especially when most patients are in their childhood/adolescent lives. It is not a surprising fact that a percentage of myopathies are of undetermined cause, which makes the need to identify new genes that play a critical role in muscle health of paramount importance.  The Xin gene is designated as an indispensable component for the normal development and morphogenesis of striated muscle; however, the exact roles of Xin in skeletal muscle are still undefined. Studies to date have demonstrated that Xin is expressed in activated satellite cells and newly formed myofibers following tissue injury. When using in vitro reduction of Xin expression in skeletal muscle cells, the outcome was impairments in satellite cell function and muscle response to injury. That said, there is still a significant lack of knowledge in the literature regarding the in vivo effects of the absence of Xin on skeletal muscle structure and function. Therefore, the aim of our studies was to characterize skeletal muscles in the absence of Xin and identify the potential roles of Xin in maintaining muscle integrity and health. In our studies, we uncover a new form of muscle disease resulting from the lack of Xin in a mouse model (Xin-/- mice). Xin-/- skeletal muscles show a mild form of myopathy at the light microscopy level that is associated with ultrastructural and functional defects peculiar to the Ca2+ handling. In addition, Xin-/- muscle demonstrated features of mitochondrial dysfunction that are likely secondary to the Ca2+ defects caused by the absence of Xin. Our studies provide a platform to investigate the potential manifestation of “loss of function” mutation of Xin in skeletal muscle and its possibly related pathology in human diseases.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Skeletal muscle covers the bones, produces movements and stabilizes joints. Diseases of skeletal muscle are common. Specifically, inherited diseases of skeletal muscle can cause an inability to eat, walk, run, work and even breathe. By starting at an early age, these conditions may result in the patient being bed-ridden with severe psychological, social and financial burdens for them and their caregivers. When skeletal muscles that control breathing are involved, death can occur at a young age. A considerable proportion of skeletal muscle disease are of unknown cause, and therefore, there is a constant need to discover more factors that influence muscle health to provide treatment plans for these patients. This dissertation uncovers the role of a new factor, Xin, involved in keeping skeletal muscle healthy.  The achieved results of our studies will help physicians use this knowledge into identifying new types of muscle disease and providing targeted treatments for patients.


title: Territoriality of cooperative breeding pukeko (Porphyrio melanotus melanotus) under low and high population density conditions

contributor:
Quinn, Jim
Biology

subject:
Biology
Animal behaviour
Science
Territoriality
pukeko

abstract:
Habitat saturation, due to high population density, and predation pressure have
both demonstrated to influence the formation of some social systems. For example,
helper-at-the-nest systems are formed when offspring delay dispersal due to a
lack of suitable territory availability or high cost of dispersal. In one cooperative
avian species, the pukeko (Porphyrio melanotus melanotus), a previous comparison
between high density (North Island) and low density (South Island) populations
found that at high density, there were fewer dispersal opportunities due to habitat
saturation resulting in increased relatedness amongst group members. Climatic
variations between the North Island and the South Island could explain many of
the results previously found. The recent decimation of a large pukeko population
at a North Island site provided us with a unique opportunity to compare group
structure between two populations under similar climatic conditions to determine
whether or not individuals bred independently in a low density population. For my
thesis I aimed to answer three questions. First, how does population density affect
the dispersal of offspring from their natal territory? Second, how does population
density affect relatedness of adult group members? Third, how does density affect
territory size? In this thesis I was unable to determine whether or not dispersal
events were occurring or if there was high or low relatedness amongst group
members. Territory sizes were significantly smaller at Tawharanui over Shakespear
but they were not significantly correlated with group size. Harrier presence was
significantly different between paddocks.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Ecological constraints have been shown to influence the formation of social
groups. The decimation of a population of cooperatively breeding pukeko on the
North Island of New Zealand provided us with a unique opportunity to compare
two populations under different density conditions. I explored the effect of population
density on group composition, parentage, and territory size as a means
to understand the costs and benefits of cooperative breeding and joint-nesting.
Territory sizes were significantly larger under low density conditions. I was unable
to determine whether or not population density influenced offspring dispersal or
relatedness amongst group members.


title: TANGENTIAL FLOW ULTRAFILTRATION  AS AN ANTIFOULING STRATEGY FOR  WATER QUALITY SENSORS

contributor:
Selvaganapathy, Ravi
Mechanical Engineering

abstract:
Water quality monitoring is important for water treatment facilities, food processing industry, aquaculture and in geological surveys. Gathering reliable measurements from sensors can be challenging over extended periods of time in conditions where the biological growth occurs. This is due to biofouling, the growth of biotic matter, on the sensor surface.  This deteriorates the quality of measurements from the sensors over time.
In this thesis, membrane technology was implemented to prevent the biofouling on the sensor surface by filtering out the bacteria from the water sample. The effects of accelerated biofouling on the microfabricated pH and DO sensors were studied. A decrease of 21% in the sensitivity value is observed for the pH sensor and a decrease of 66% in the sensitivity value is noted for the DO sensor. Next, the sensors were integrated in a customized flat sheet Tangential Flow Filtration (TFF) device with an ultrafiltration membrane and placed on the permeate side of the filtration device. The decrease in the sensitivity noted for the pH and DO sensors used with TFF were 5 times lower as compared to when used without the TFF device.
In summary, the device proposed in this thesis was shown to successfully prevent the deterioration of sensitivity of the microfabricated pH & DO water monitoring sensors by preventing the formation of biofilm on the sensor surface and the grooved spacers used in the TFF helped in mitigating membrane fouling.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: SYNTHESIS AND CHARACTERIZATION OF RARE EARTH-BASED MAGNETOCALORIC PHASES

contributor:
Mozharivskyj, Yurij
Chemistry and Chemical Biology

subject:
Magnetocaloric effect
Rare earth-based alloys

abstract:
In search of novel magnetocaloric materials, a number of rare earth-based phases were designed, synthesized and investigated. These compounds were prepared by arc-melting or sintering, followed by annealing at high temperature to obtain phase-pure materials. Single crystal and powder X-ray diffraction were employed for phase identification, purity assessment, structure solution and refinement. Energy dispersive X-ray spectroscopy (EDS) was used to determine sample compositions. A Quantum Design SQUID magnetometer equipped with an alternating current (ac) transport controller (model 7100) was employed to measure magnetic data and evaluate magnetocaloric properties. The crystal structure and physical properties were analyzed via electronic structure calculations.
In this thesis work, the RE5Ga3 and RECo2 (RE = rare earth) materials were chosen as a starting point for structural modifications. Specifically, substitution of Co for Ga (and vice versa) or rare earth replacement was used to design new materials. In total, four families were investigated: Ho5Ga3-xCox (x = 0, 0.1, 0.2, 0.3, 0.4, 0.5, 1), Er5Ga3-x(Fe/Co)x (x = 0, 0.4), RE(Co0.667Ga0.333)2 (RE = Gd, Tb, Dy, Ho, and Er), and Gd(Co1-xGax)2 (x = 0, 1/6, 1/3, 1/2, 2/3, 5/6, and 1). The samples were prepared by arc-melting, wrapped in Ta foil, sealed in evacuated silica tubes and annealed at specific temperatures.
The Ho5Ga3-xCox and Er5Ga3-x(Fe/Co)x systems features a Mn5Si3-type-to-Cr5B3-type structural transformation, driven by geometric factors. On the other hand, the structural transformation in the RE(Co0.667Ga0.333)2 and Gd(Co1-xGax)2 systems appears to be controlled by the valence electron count (VEC). The RE(Co0.667Ga0.333)2 (RE = Gd, Tb, Dy, Ho, and Er) phases adopt a hexagonal MgZn2-type structure (P63/mmc). Structural and magnetic properties of the MgZn2-type RE(Co0.667Ga0.333)2 materials were investigated via single crystal and powder X-ray diffraction, powder neutron diffraction (PND), and magnetic measurements. In addition to the hexagonal MgZn2-type structure, four other structures were discovered in the Gd(Co1-xGax)2 system: cubic MgCu2- (Fd3 ̅m), orthorhombic MgSrSi- (Pnma), orthorhombic CeCu2- (Imma), and hexagonal AlB2-type structure (P6/mmm). When Ga content increases, the structure moves from a “condensed cluster-based arrangement” to a “3D Network” to a “2D Network”. Meanwhile, coordination number (CN) of Co or Ga atoms changes from 6 to 4, and then to 3.
Magnetic properties of many of the RE-based phases were evaluated via temperature- and field-dependent magnetization measurement. Materials exhibited a sharp ferromagnetic transition and their MCE in terms of the isothermal magnetic entropy change, was explored.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


contributor:
LaPierre, Ray R.
Engineering Physics

abstract: Title: Core-Shell Heterostructured Nanowires on Foreign Substrates for use in Opto-Electronic Applications, Author: Parsian K. Mohsemi, Location: Thode

abstract:
The Au nanoparticle-assisted growth of coaxially heterostructured III-V compound semiconductor nanowires (NWs) on foreign substrates, through gassource molecular beam epitaxy, was explored. The structural properties of GaP/GaAsP NW systems were characterized through extensive electron microscopy-based techniques, leading to several key findings. A core-multishell NW architecture was defined, based upon the combination of seed-mediated axial growth and sidewall diffusion-mediated radial growth regimes. The formation of undesirable stacking faults, characterized as zincblende insertions within an otherwise wurtzite crystal, was effectively eliminated through the control of seed supersaturation. Thus, a novel method for the elimination of stacking faults and achievement of phase-purity in NW heterostructures was realized. The nonuniformity of group V adatom incorporation within NW segments composed of ternary III-V compounds was also investigated. The effects of preferential Pincorporation and passivating GaP shell layers on the optical properties of GaAsP core segments were determined through spectroscopic characterization techniques. Furthermore, the growth of GaAs NWs on several foreign substrates, including single crystalline Si substrates, stainless steel foils, glass substrates with polycrystalline Si buffer layers, carbon-nanotube (CNT) composite films, and highly-ordered pyrolytic graphite (HOPG), was explored. Growth on HOPG was shown to proceed according to a Ga-assisted mechanism, for which a qualitative growth model was proposed. Au-nanoparticle mediated growth was achieved on all other surfaces. The CNT composite films were selected as the most suitable substrate for the fabrication of NW-based opto-electronic devices. Flexible photovoltaic cells were fabricated using this nano-hybrid material, demonstrating a conversion efficiency of 0.32% under mechanical flexure up to a bend radius of
12.5 mm. The GaAs NWs were confirmed to be the active light-harvesting medium, while the CNT films served as flexible substrates and back-side electrodes. This work is presented as a novel route towards the realization of lowcost, flexible NW-based opto-electronic device applications.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


contributor:
Schwarcz, Henry P.
Ford, Derek C.
Geology

abstract: Title: Stable Isotope Studies of Water Extracted from Speleothems, Author: Charles J. Yonge, Location: Thode

abstract:
Calcite speleothems, if shown to be formed under conditions
of isotopic equilibrium with their parent seepage waters,
can be used to determine relative changes in the past climates
from measurement of δ^1 ^8O of the calcite. Furthermore, if δ^1 ^8O
of the parent seepage water can be estimated and shown to be
equivalent to meteoric precipitation falling at the cave site,
then depositional temperatures can be recovered from the termperature dependent oxygen isotope fractionation of the calcitewater
pairs. Cave temperatures generally reflect mean annual
surface temperatures above the cave. Thus, should the depositional
temperature accurately record the cave temperature, then
analysis of successive growth layers in speleothems should provide
a direct measure of past temperature change at a given
site. Estimates of δ^1 ^8O of past seepage water can be made, in
principle, because speleothems incorporate seepage water within
inclusions as they grow. However, since oxygen in the fluid
inclusion water may exchange with that in the carbonate phase,
hydrogen isotopes, which cannot exchange, are measured instead.
δ^1 ^8O of the original seepage water can then be inferred from
δD, if seepage water can be shown to be equivalent to included
water, because meteoric relationships exist which link them.
Work prior to this study suggested that, following the method
outlined above, isotopic temperatures could be recovered from spleothems.

The early part of this study involved the construction
and operation of a mass spectrometer and associated extraction
line for δD analyses and some modification to existing apparatus
for δ^1 ^8O analysis.

Water samples were then analysed from a number of cave
sites, mainly in the Eastern U.S., to check the isotopic equivalence
of seepage water to meteoric precipitation and observe
seasonal isotopic variations in seepage and soil water with
respect to meteoric precipitation. The general conclusion
reached was that seepage water was equivalent to meteoric precipitation
and that no seasonal variation occurred in those
caves studied in detail. Study of an Antarctic Ice Core
showed that the δ^1 ^8O-δD relation of meteoric precipitation
during the Wisconsin Glacial Maximum was different from that
at present.

The latter part of this study was concerned with the
systematics of water extraction and the isotopic measurement
of water-calcite pairs from speleothems. A previously developed
technique, involving crushing of the sample in vacuum
prior to freezing over the liberated water, was found not to
be as reproducible as had been stated in the literature, and,
as a result, an extraction method by heating was developed to
replace it. Although great difficulty was encountered in getting
this technique to function, it was found, eventually, to save time in operation, to liberate up to 2.4 times more water
and give greater reproducibility than the crushing method.
Attempts to demonstrate the isotopic equality of the two
methods was only partially successful however, but both methods
seemed to yield water from speleothems that was isotopically
depleted with respect to their parent seepage waters.

For the latter reason, experiments were undertaken to
characterize the water within the calcite because of the possible
presence of structural, isotopically modified water.
Petrographic observations left no doubt as to the presence of
fluid inclusions from 50μm down to unresolvable dimensions but
it was questionable as to whether or not all the water lay in
these sites. IR, polarized IR and neutron diffraction spectroscopy
of powders in the 100μm range failed to reveal the presence
of oriented water in the calcite lattice although 'liquid'
water was still observed.

The isotopic depletion of calcite-bound water with respect
to parent seepage water in modern' samples was found to be
22.1 ± 3.9% in δD. This value, when applied to δD profiles of
six fossil speleothems to retrieve original seepage water δD gives
rise to calculated calcite-water paleotemperatures that
are above zero. Comparison of these modified δD and temperature
profiles with other records, such as deep sea and ice cores
suggested that paleoclimatic information can be obtained from
isotopic studies of speleothems. The mechanism(s) responsible for the isotopic fractionation of calcite-bound water as it is
incorporated into the speleothems during growth is speculated
upon as an absorption-like phenomenon but no firm conclusions
are reached.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


contributor:
Gentilcore, R.L.
Geography

abstract: Title: A Perspective on Land Tenure in Upper Canada: A Study of Elizabethan Township, 1709-1840, Author: Randy W. Widdis, Location: Thode

abstract:
Whereas most studies concerning land tenure in Upper Canada
have focussed on the acquisition and utilization of land, the principal
emphases in this study are the withholding of land through speculation
and the transfer of property, two neglected aspects of land tenure.
Land transfer and speculation patterns are reconstructed for Elizabethtown
Township during the period 1790-1840. The simultaneous identification
and analysis of transfer, persistence and mobility through time
reveals factors underlying changes in the pattern of ownership.
Important factors at the township level appear to have been distance
from market, size of holding and type of tenure. A method of identifying
speculators is developed on the basis of certain criteria
relating to land utilization and holding size and a classification of
speculators is offered. It is demonstrated that speculation is a
complex activity with many different facets. The transfer of land and
speculative activity are shown to be related.

abstract: Thesis

abstract: Master of Arts (MA)


title: Advancing the Treatment of Industrial Wastewater via Integration of PeCOD® And LC-OCD Analytical Tools

contributor:
Latulippe, David
Chemical Engineering

subject: Chemical Oxygen Demand,Industrial Wastewater, Advanced Oxidation,PeCOD®, LC-OCD,

abstract:
In 2012, mandatory effluent quality standards were established in Canada as part of the Wastewater Systems Effluent Regulations (WSER) with compliance deadlines starting in 2020. Maintaining the treatment process efficacy to meet these new stringent discharge regulations is extremely challenging at treatment facilities that treat wastewater from multiple industries due to the high variation in the composition of the incoming feed to the process. In this work, application of two new analytical tools, PeCOD® and Liquid Chromatography-Organic Carbon Detection (LC-OCD), for measurement and characterization of industrial wastewater organic pollution respectively, has been investigated.
Organic pollution is commonly measured as Chemical Oxygen Demand via the dichromate method (CODCr) which requires 2-3 hours to complete. Thus this method is not suitable for applications that require rapid and frequent pollution monitoring. The Photoelectrochemical Oxygen Demand (peCOD) is an alternative parameter of organic pollution that can be measured in approximately 15 minutes via a method that utilizes the high oxidation potential of UV-irradiated TiO2 nano-particulates. Herein peCOD suitability to replace CODCr for analysis of industrial wastewater was investigated. The results indicated that for both untreated (i.e. incoming) and treated (i.e. effluent) industrial wastewater samples, peCOD results are lower than CODCr results. However, for the effluent samples, the two methods’ results are strongly correlated. Containing hard to oxidize materials (i.e. macromolecules) and high concentrations of chloride and
nitrogenous compounds were identified as potential causes of difference between the results of the two methods.
When there is variation in the composition of the incoming wastewater to a treatment process, information about the wastewater composition is required for process optimization. Thus optimization cannot be based solely on bulk measurements of organic pollution (e.g. COD). In this study, a novel combination of LC-OCD analysis with Design-Of-Experiments (DOE) methods was used to optimize the Fenton Advanced Oxidation (AO) treatment conditions in terms of chemical reagent concentrations, to develop statistical models of the process, and to identify potential mechanisms of COD removal.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract:
Many industrial facilities do not treat their wastewater on-site and instead ship it to specialized treatment facilities. Ensuring that the treated effluent meets the stringent discharge regulations is a challenging task for such facilities as the composition of the incoming feed to the treatment process changes with each shipment. In this work, application of two new analytical tools, PeCOD® and Liquid Chromatography-Organic Carbon Detection (LC-OCD), for measurement and characterization of industrial wastewater organic pollution respectively, has been investigated.
The conventional method of measuring organic pollution, Chemical Oxygen Demand (COD), requires 2-3 hours to complete. Herein the suitability of an alternative parameter, Photoelectrochemical Oxygen Demand (peCOD), that can be measured in approximately 15 minutes for replacing COD analysis in industrial wastewater plants was investigated.
Implementation of effective treatment processes that are operated at their optimum conditions is required to meet the stringent discharge regulations. Advanced Oxidation (AO) is an effective method of industrial wastewater treatment. Herein, optimum AO treatment conditions were studied via application of the LC-OCD analysis for organic pollution characterization.


title: Aristotelian Virtue Ethics and the Self-Absorption Objection

contributor:
Johnstone, Mark
Philosophy

subject: Virtue Ethics; Aristotle; Moral Motivation

abstract: Aristotelian eudaimonism – as Daniel Russell puts it – is understood as two things at once: it is the final end for practical reasoning, and it is a good human life for the one living it.  This understanding of Aristotelian eudaimonism, on which one’s ultimate reason for doing all that one does is one’s own eudaimonia, has given rise to what I call the “self-absorption objection.” Roughly, proponents of this objection state that the main problem with neo-Aristotelian accounts of moral motivation is that they prescribe that our ultimate reason for acting virtuously is the fact that doing so is good for us. In an attempt to adequately address this objection, I break with those contemporary neo-Aristotelian accounts of moral motivation that insist that the virtuous agent ought to be understood as performing virtuous actions ultimately for the sake of her own eudaimonia (enlarged, no doubt, to include the eudaimonia of others). On the alternative neo-Aristotelian account of moral motivation I go on to defend – what I call the altruistic account of motivation – the virtuous agent’s ultimate reason for acting virtuously is based on a desire to act in accordance with her particular conception of the good life, where what makes such a conception good is not that it is good for her, but rather good, qua human goodness. More specifically, on the altruistic account of motivation I advance, the virtuous agent may be understood as being motivated by human goodness, valuing objects and persons only insofar as they participate in human goodness, and where all of the virtuous agent’s reasons, values, motivations, and justifications are cashed out in terms of human goodness – as they say – “all the way down.”

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: In this dissertation, I advance a neo-Aristotelian account of moral motivation that is immune from what I call the “self-absorption objection.” Roughly, proponents of this objection state that the main problem with neo-Aristotelian accounts of moral motivation is that they wrongly prescribe that our ultimate reason for acting virtuously is the fact that doing so is good for us. In an attempt to sidestep this objection, I offer what I call the altruistic account of motivation. On this account, the virtuous agent’s main reason for acting virtuously is based on her desire to act in accordance with a particular conception of the good life, where what makes such a conception good is not that it is good for her, but rather good, qua human goodness.


contributor:
Leduc, Ryan J.
Computing and Software

abstract: Title: Symbolic Synthesis and Verification of Hierarchical Interface-based Supervisory Control, Author: Raoguang Song, Location: Thode

abstract:
Hierarchical Interface-based Supervisory Control (HISC) is a method to alleviate
the state-explosion problem when verifying the controllable and nonblocking properties
of a large discrete event system. By decomposing a system as a number of
subsystems according to the HISC method, we can verify the subsystems separately
and the global system controllability and nonblocking property are guaranteed, so
that potentially great computation effort is saved.

In this thesis, we first present a predicate-based synthesis algorithm for each type
of subsystem and then prove the correctness of the algorithms. Then a predicatebased
verification algorithm for each type of subsystem is provided. Based on the
predicate-based algorithms, a symbolic implementation is proposed by using Binary
Decision Diagrams (BDD) and the fact that a subsystem is usually composed of a
number of components. With the symbolic implementation, we can handle a much
larger subsystem of each type.

Two large and complicated examples (with estimated worst-case state space on the order of 1030) extended from the AlP example are provided for demonstrating
the capabilities of the algorithms and the implementation. A software tool for the
synthesis and verification using our approach is also developed.

abstract: Thesis

abstract: Master of Applied Science (MASc)


contributor:
Feng, Shui
Statistics

abstract: Title: Modified Fractional Brownian Motion and Option Pricing, Author: Xingqiu Zhao, Location: Thode

abstract:
The Black-Scholes model introduced by Black and Scholes (1973) and Merton (1973)
has become synonymous with modern finance theory. It assumes that the dynamics of
stock prices is well described by exponential Brownian motion, which is not consistent
with empirical stock price returns, and then the dependence structure of stock price
returns has been at the center of intense scrutiny for the last 30 or more years. This
project studies modified fractional Brownian motions and shows that two different
classes of modified fractional Brownian motions are equivalent to Brownian motion.
We discuss option pricing under the hypothesis that the underlying asset price process
satisfies a stochastic differential equation driven by a modified fractional Brownian
motion. Parameter estimation and simulation methods are given. In particular, we
investigate the ability of the self-similarity parameter H to explain the discrepancy
between the Black-Scholes model and the reality of the market. The proposed method
is applied to a real data set. The empirical results indicate that the model is better
than the Black-Scholes model.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Thabane, Lehana
Statistics

abstract: Title: Modeling Lung Disease and Its Progression in A Chronic Obstructive Pulmonary Disease Cohort, Author: Liqin Xu, Location: Thode

abstract:
Chronic obstructive pulmonary disease (COPD) is an irreversible, slowly
progressive lung disease, usually associated with smoking and with respiratory
infections. The objective of the study was to investigate the association of lung function
and its progression with smoking, infection and inflammation. I discussed the optimal
modeling strategy by comparing results from different methods of analysis and methods
of handling missing data.

It was well documented that smoking significantly accelerated lung function decline
at a rate of 89.6 mL/year and was robust to adjustment for age, gender, height and
breathlessness. C. pneumoniae was associated with decreased lung function, but was not
statistically significant. Log MMP-9, log ratio of MMP-9 to TIMP-1 and log CRP were
strongly associated with slope change in FEV 1 and robust to covariate adjustment in
weighted least squares models. Thus, they were good biomarkers for COPD progression.

There were no significant differences among generalized estimating equations,
mixed-effects and robust random-effects models for measuring lung function at
multiple-time. Smoking was positively related to lung function, but was not robust to
covariate adjustment. C. pneumoniae was not significantly correlated with lung function.
Log MMP-9 and log ratio of MMP-9 to TIMP-1 were associated with decreased lung
function, but were not statistically significant. However, log CRP was significantly
associated with lung function and robust to covariate adjustment. Thus, log CRP was the
best biomarker for modeling lung function measured at multiple- time.

The GEE modeling results of different data sets imputed by group mean estimation,
last observation carried forward, hot-deck and multiple imputation methods were
consistent, but multiple imputation was recommended to handle the missing data.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Peng, Jiming
Computing and Software

abstract: Title: 0-1 Semidefinite Programming for Cluster Analysis with Application to Customer Segmentation, Author: Huarong Chen, Location: Thode

abstract:
In general, clustering involves partitioning a give data set into subsets
based on the closeness or similarity among the data. Clustering analysis
has been widely used in many applications arising from different disciplines,
including market analysis, image segmentation, pattern recognition and web
mining.

Recently, a new optimization model, the so called 0-1 semidefinite programming(
SDP) has been introduced by Peng and Xia in [2]. It has been
proved that several scenarios of clustering, such as classical K-means clustering,
normalized-cut clustering, balanced clustering and semi-supervised clustering
can be embedded into the 0-1 SDP model.

In this thesis, we try to extend the 0-1 SDP model to the scenario of
weighted K-means clustering, where the instances in the data set are associated
with some weights indicating the importance of the instance. We also develop
a hierarchical approach to attack the unified 0-1 SDP model, in which each
binary separation is achieved by the refined weighted K-means method in one
dimensional space. Moreover, we apply the approach developed in this thesis
to a particular industrial application, where the task is to extract a model to
predict the children information of customers based on their buying behaviors.
During the process of the model building, clustering analysis was applied as the first step to group customers with similar children information, and then
the link between the segmentation of customers and their shopping behaviors
was discovered.

Numerical results based on our approach are reported in the thesis as
well.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Smyth, William F.
Statistics

abstract: Title: Pattern-Matching Algorithms on Indeterminate Strings, Author: Shu Wang, Location: Thode

abstract:
In computing, strings are sequences of simple elements (letters) drawn from some
alphabet. A string is one of the most basic and important data structures in computer
science, it exists everywhere in computer systems. Disk files, contents of memory,
source and object code of computer programs, e-mail messages are all examples of
strings. Also in bioinformatics, nucleotides in DNA can be viewed as strings drawn
from an alphabet of four basic symbols- A, C, G and T. Algorithms that deal with
strings are correspondingly very important in the field of computer science as well as
in bioinformatics, data compression, cryptanalysis and other scientific areas.

A pattern-matching algorithm is one of the most fundamental string algorithms.
Simply speaking, it outputs the occurrences of a string (called the pattern) within
another string (called the text). Exact pattern-matching algorithms have been extensively
studied in the last three decades and many algorithms have been proposed.
Among them are two well known algorithms, the Knuth-Morris-Pratt (KMP) algorithm
[KMP77], with good worst-case performance, and the Boyer-Moore (BM) algorithm
[BM77], with good average-case performance. A recent attempt to combine
the virtues of the two algorithms results in the Franek-Jennings-Smyth (FJS) algorithm
[Jen02, FJS05b, FJS05a], which has both excellent average-case and worst-case
performance.

Indeterminate strings are a new class of strings proposed in [HS03] driven by the
increasingly common application of string algorithms on biological (DNA) sequences.
Unlike letters in a normal alphabet, an indeterminate letter matches a set of letters
(under certain constraints) rather than just one during pattern-matching. Perhaps the most straightforward example of an indeterminate letter is the don't care letter
'*', that matches all letters in the alphabet. The main purpose of an indeterminate
string is to increase the flexibility of pattern-matching. It can also be seen as a
model of a DNA sequence with a polymorphism property, which is a commonplace in
molecular biology.

An indeterminate string is a relatively new idea and not too many known algorithms
work on it, except for a particular version of the ShiftOr algorithm [WM92].
However as we will see, even this version can only handle a special case of indeterminate
pattern-matching. Faster and more general indeterminate pattern-matching
algorithms are desired. In this thesis we first give rigorous definitions of indeterminate
strings and then develop our new indeterminate pattern-matching algorithms,
adapted and modified from existing exact pattern-matching algorithms. There are
many different constraints and also different models of patten-matching. We present
our solution with all these variations in order of increasing complexity. We present
our rationale of development and investigate the possibility of developing new algorithms
from different categories of existing determinate algorithms. After describing
our algorithms we conduct comprehensive experiments and compare the results carefully.
In the last chapter we present our conclusions and point out the directions of
future research.

abstract: Thesis

abstract: Master of Science (MS)


title: Robust Capillary Electrophoresis Methods for Biomarker Discovery and Routine Measurements in Clinical and Epidemiological Applications

contributor:
Britz-McKibbin, Philip
Chemical Biology

subject:
Capillary Electrophoresis
Iodide
Strong Anions
Sulfate
Cystic Fibrosis
Biomarker
Metabolomics
Analytical Methods

abstract: Biochemical markers (i.e., biomarkers) are of key importance to guide clinical decisions and public health policies by enabling early detection, accurate diagnosis and/or prevention of human diseases. However, major challenges remain due to the limited clinical utility of many biomarkers and the lack of robust analytical methods for their reliable measurements in a routine clinical setting that is also suitable to large-scale epidemiological studies. This thesis includes two major research themes involving the analysis of known biomarkers that lack appropriate methods, and the discovery of new biomarkers for complex disease conditions. In particular, this thesis describes the (1) development and validation of robust analytical methods based on capillary electrophoresis (CE) with photometric detection for the measurement of inorganic anions in volume-restricted biofluids; and (2) characterization of the sweat metabolome in infants and identification of sweat biomarkers in asymptomatic cystic fibrosis (CF) infants using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS). Chapter II introduces a simple CE assay that is remarkably selective for the analysis of sulfate, sulfite and chloride, which was applied in a pilot study to investigate the role of urinary sulfate as a biomarker for kidney stone risk assessment in children. Chapter III introduces a novel CE method for assessing iodine nutrition, which is followed by an inter-method comparison with inductively coupled plasma-mass spectrometry as described in Chapter IV. This led to the development of a fully validated CE method for monitoring the prevalence of iodine deficiency on a population level as required for global health initiatives. Chapter V demonstrates that more than 64 endogenous and exogenous compounds are present in the sweat of screen-positive CF infants, including a panel of differentiating metabolites that are associated with CF status, as well as treatment responsivity to nutritional and/or drug intervention. In summary, this thesis has contributed novel analytical methods suitable for routine biomarker analysis, in addition to the first non-targeted characterization of the sweat metabolome from infants, which require further studies to evaluate their clinical utility as biomarkers that allow for improved diagnosis, prognosis and treatment monitoring of the highly variable CF disease spectrum.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A Common Agency Approach to Lobbying: Theory and Empirical Applications

contributor:
Han, Seungjin
Economics

subject: Lobbying, Political Economy, Minimum Wage, Taxation, Income Inequality

abstract:
This thesis explores lobbying as an important political economy dimension of policymaking. It exploits theoretical, empirical, and numerical approaches and methods to investigate the possibilities of engaging in costly lobbying and how lobbying by special interests affects the setting of minimum wage and small business tax rates.  The theoretical modeling relies on the common agency framework - a situation with multiple principals who are simultaneously and non-cooperatively interacting with a single agent - of public policy lobbying and a simpler principal agent model. Empirical analysis employs panel data regression methods in the context of Canadian provinces to identify causal relationship. Both minimum wage and small business taxation invite a considerable amount of activity from various special interest groups in Canada, which engage in lobbying for a policy stance more favorable to their members.
After providing a brief overview of lobbying issues and literature in the first chapter, in the second one I show that initial lobbying cost can be a clear entry barrier, that lobbying competition can have properties of a high-stakes game and that lobbying can take place simply to preserve the status quo and not lose ground. In the pure rivalry sense, to not allow the opponent to gain ground in the policy arena. In the third chapter, I formulate a model of minimum wage determination based on the common agency lobbying framework to evaluate how the competition for political influence between unionized workers and firm owners affects the minimum wage determination. A binding minimum wage is a function of the policymaker's political ideology, the labor demand elasticity and the skill composition of union members. Specifically, when the elasticity of labor demand is large, the benefit of lobbying against (for) an increase in the minimum wage is greater since a potential minimum wage increase has a larger negative (positive) effect on firms' (unionized workers') income. Lobbying is successful in inducing the policymaker to set the minimum wage in accordance with her political preference; a more business (labor) friendly policymaker reduces (increases) the minimum wage. However, lobbying can also induce the policymaker to go against its ideological preference. Empirical analysis on a panel data for ten Canadian provinces over the 1965-2013 period gives considerable support for theoretical predictions. Preferred panel data regression specifications, controlling for unobserved province and year effects, and various province specific, time varying factors, indicate that real minimum wage decreases in skill-adjusted union density and a measure of political ideology, and increases with technological progress. Greater labor demand elasticity reinforces the influence of political ideology in the presence of lobbying. In the fourth chapter, I focus on the issue of small business tax determination and the effect of lowering its rate on income inequality.  In Canada, where the small business income tax rate is considerably lower than the top individual rate, higher income individuals are able to reduce their personal taxes by retaining and shifting income via privately owned small businesses. Therefore, because the small business owners benefit from an increasing difference between the small business and top individual tax rates, I show using a principal-agent model that by lobbying as a special interest group they can always `buy' a lower corporate tax rate from the government. However, a lower business income tax, relative to a given personal income tax rate, is not income inequality neutral and unambiguously increases the income share of the highest earning individuals in the economy, specifically those who own small corporations.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Berge Metrics

contributor:
Deza, Antoine
Computing and Software

abstract: Title: Berge Metrics, Author: Sandra Gregov, Location: Thode

abstract:
We consider a number of generalizations of the following question originally
posed by Claude Berge in 1966. Let Sn denote the set of all strings made of [n/2]
white coins and [n/2] black coins. Berge asked what is the minimum number of
moves required to sort an alternating string of Sn by taking 2 adjacent coins to
2 adjacent vacant positions on a one-dimensional board of infinite length such
that the sorted string has all white coins immediately followed by all black
coins (or visa versa).

We survey and present results dealing with the first generalization of Berge
sorting which allows Berge k-moves, i.e., taking k adjacent coins to k adjacent
vacant positions. We then explore a further generalization which asks for any
pair of strings in Sn what is the minimum number of Berge k-moves needed
to transform one string into the other. This induces a natural metric on the
set Sn called the Berge k-metric. We examine bounds for the diameter of Sn
allowing Berge k-moves. In particular, we present lower and upper bounds
for Berge 1-metric and explore some aspects of Berge 2-metric along with
computational results.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Maibaum, Tom
Kalh, Wolfram
Software Engineering

abstract: Title: A Model for the FDA General Principles of Software Validation, Author: Marwan M. Abdeen, Location: Thode

abstract:
Several institutions and agencies around the world, from both the private and public sectors,
have adopted the practice of software validation and certification to ensure higher levels
of confidence in software. The US Food and Drug Administration (FDA) is one of these
organisations. The FDA has published several guidance documents concerning the validation
of medical device software or the validation of software used to design, develop, or produce
medical devices. In its guidance documents for both the medical software industry and FDA
staff, the FDA recommends certain activities to be undertaken and certain deliverables to
be prepared. The FDA believes that undertaking these activities as well as preparing these
deliverables will achieve higher confidence in the software quality and, accordingly, better
validation.

In this thesis, we question the clarity and practicability of the FDA approach for medical
software validation. We examine the FDA approach by evaluating the FDA guidance
documents. We base our analysis on distinguishing between product and process aspects.
By bearing in mind these two concepts, we believe that the FDA validation approach leads
to confusion in the minds of both software producers and evaluators and it may well lead to
lower quality software than desired being certified, while the FDA considers its approach as
the least burdensome. As a demonstration of our claim, we analyse "Quality Planning" as
the first activity in the FDA approach. We discuss the corresponding effort for this activity
in another product-oriented evaluation approach, the Common Criteria (CC) for Information
Technology Security Evaluation. As its main objective, the comparison aims to highlight
both the inconsistency and the vagueness of the FDA evaluation function.

The FDA guidance documents are natural language in specifying their recommendations because of the wide audience to which they are addressed and the consequent need for simplicity. However, the specification is not sufficiently explicit and precise to be able to impose a contract (obligation) between the two parties (software producers and evaluators). Having illustrated the drawbacks of the FDA approach, with comparison to the CC, as they appear in the "Quality Planning" activity, we use the Product/process (P/p) method to model this activity and all subsequent ones. Despite the application of the P/p method herein to medial device certification, a critical area of application, the P/p method takes a general systems approach. It is appropriate to a variety of areas and has proven its applicability in many field. Thus, reconsideration of these issues by the FDA will lead to a more objective evaluation function and higher confidence in the medical software, which represents the most important concern among the evaluation community and the general public.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: A Multi-Level Algorithm for Production Scheduling and Sequencing Optimization in Hot Rolling Steel Mills

contributor:
Mahalec, Vladimir
Chemical Engineering

subject:
Scheduling
Steel
Optimization
Hot Rolling
Sequencing

abstract:
The objective of the hot rolling mill is to transform slabs of steel into thin strips which conform to
specific dimensional and metallurgical customer requirements. High performance and flexibility
in the operation is required due to strict customer demands, variable market conditions, and the
drive for continuous improvement.
Historically human schedulers have performed the scheduling and sequencing tasks, however it is
not a reasonable expectation that they consider all the complex objectives required in optimal
production of a hot mill. Therefore, there are significant opportunities for improvement in this
area through the application of mathematical optimization models and solution algorithms.
This work presents a set of models and a solution algorithm for optimal scheduling and
sequencing of production within a hot rolling steel mill. The models and algorithms presented
within this thesis are specifically developed for ArcelorMittal Dofasco’s Hot Strip Mill in
Hamilton, Ontario, Canada. First, a graph theoretic representation of the production block is
developed along with an asymmetric travelling salesman formulation of the sequencing problem.
A slab transition cost function comprised of the hot rolling process objectives is formalized. The
objective of the optimization is to generate a complete block sequence which minimizes the cost
of transitions between slabs thus minimizing the overall cost of production. The Concorde exact
solver is leveraged for the sequencing problem. Second, the scheduling of slabs from inventory
into blocks is considered in addition to sequencing. A methodology for slab clustering is defined.
The novel concept of width-groups is developed and a heuristic algorithm is devised to calculate
an objective for the MILP slab scheduling model. The objective of the scheduling optimization is
to construct a set of blocks which minimize deviation from the calculated width-group design. A
revised sequencing model, updated to reflect the relaxations enabled by the width-group design, is
formulated. Industrial production and offline trials show that the proposed scheduling-sequencing
framework outperforms the human scheduler in all critical performance metrics for both
scheduling and sequencing. A conservative estimate of the reoccurring monetary benefits
available from use of the proposed scheduling-sequencing optimization framework is greater than
$1.2M CAD per year.

abstract: Thesis

abstract: Master of Applied Science (MASc)


contributor:
Wassyng, Alan
Computing and Software

abstract: Title: Developing User-Centric Software Requirements Specifications, Author: Hongqing Sun, Location: Thode

abstract:
Software systems with intensive user-computer interactions account for a fairly large
part of the total real world software applications, such as web applications, MS Windows
applications, GNOME/KDE applications etc. We call this kind of software
user-centric software, denoting a defining characteristic which is that they are usable
directly by users.

Exhibited in this thesis is a systematic approach for developing a software
requirements specification (SRS) for user-centric software. While this approach conforms
to the well-recognized software requirements engineering process model, which
contains the processes of requirements elicitation, analysis, specification and validation,
it is tailored to user-centric software. The user-centric ideas are embodied and
applied throughout our approach. In the elicitation process, the joint requirements
development (JRD) sessions (known as requirement workshops) are advocated, and
step-by-step guidance is developed leading to a natural flow from the raw problem
descriptions to user requirements - the use case model. Further, based on the various
object-oriented analysis paradigms, we build a systematic analysis process to
seek analysis classes, where domain classes are harvested from the composed data
hierarchies of all use cases, and application classes and functions are captured from
sequence diagrams. Especially, our notation of boundary classes provides considerable
flexibility in the user interface (UI) design phase. During the SRS process, functional
requirements derived from the analysis model are specified according to a class specification
template. Moreover, the three-level validation process positively involves the
user's participation facilitating assurance that the right software is built. Also, to
demonstrate the practicability of this approach, it is applied in a case study dealing
with developing the SRS of a photodynamic therapy (PDT) treatment planning
application.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: A Systematic Review and Meta-Analysis of Studies of Preoperative Aspirin on Bleeding and Cardiovascular Outcomes of Patients Undergoing Coronary Artery Bypass Surgery: A Comparison of Bayesian and Classical Approaches

subject: preoperative aspirin, bleeding, cardiovascular outcomes, patients, coronary artery bypass surgery, Bayesian, classical approaches

abstract:
 Meta-analysis is a statistical method to summarize the overall evidence of effects on intervention by systematically combining outcomes from available studies in the literature which are homogeneous in research methodology and research interest. The objective of this project is to evaluate the treatment effects of preoperative aspirin on bleeding and other
cardiovascular outcomes from 11 randomized control trials (RCT) and 19 observational (non-RCT) studies. Both Bayesian meta-analysis and classical (frequentist) meta-analysis were applied to continuous and binary outcomes, and the results were compared.

 The robustness of the Bayesian approach is assessed by examining the performances of different likelihood functions and priors. We also discuss strategies on dealing with zero-event studies for binary outcomes, and the implementation of multiple imputation (MI) technique to missing data for continuous outcomes.

 Most results of primary analysis agree between the Bayesian and classical approaches. We suggest that the final conclusion of a meta-analysis should be based on the comparison of the results from both Bayesian and
classical approaches.

abstract: Thesis

abstract: Master of Science (MSc)


contributor:
Peng, Jiming
Terlaky, Tamas
Computing and Software

abstract: Title: Data Mining Algorithms for Ranking Problems, Author: Tianshi Jiao, Location: Thode

abstract:
Classification is the process of finding (or training) a set of models (or
functions) that describe and distinguish data classes or concepts. That is for
the purpose of being able to use the models to predict the unknown class labels
of instances [12].

We deal with the ranking problem in this thesis. The ranking problem
is a special case of the classification problem, where the class labels are ranks
or ratings, represented by integers from 1 to q. The ranking problem can also
be cast as the process of training a rank-prediction model that assigns each
instance a rank that is "as close as possible" to the instance's actual rank [8].
Popular applications of the ranking problem include ranking the importance
of web pages, evaluating the financial credit of a person, and ranking the risks
of investments.

Two popular families of methods to solve ranking problems are MultiCriteria
Decision Aid (MCDA) methods and Support Vector Machines (SVMs).
The performance of successful MCDA methods, such as UTilites Additives
DIScriminantes (UTADIS) and Generalized UTilites Additives DIScriminantes
(GUTADIS) , is achieved by exploiting the background knowledge that describes
the correlations between the attributes and the ranks. Unfortunately,
the background knowledge is case-dependent, hence it is likely to be unavailable, inexact or difficult to be modeled in practice. This restricts the application
of MCDA methods. SVMs, instead, do not require any background
knowledge. Their good performance is achieved by keeping balance between
minimizing the empirical loss and maximizing the separation margin. Normally,
a multi-class Support Vector Machine Classifier is constructed by combining
several binary Support Vector Machine Classifiers. In the SVM-based
approach the ranking information is not used.

This thesis attempts to construct an efficient algorithm for ranking
problems. We compare the properties of existing algorithms for ranking problems
and propose a hybrid algorithm that combines the multi-class SVM (MSVM)
and the UTADIS model. In the new algorithm, the binary SVM classifiers
are combined into a multi-class classifier based on the fuzzy voting
technique. The optimal fuzzy voting strategy is searched by solving a Linear
Program (LP). The new algorithm is called Fuzzy Voting based Support Vector
Ranking (FVSVR) method. We also extend the idea of Fuzzy Voting from
ranking problems to generic multi-class classification problems, which leads to
a Fuzzy Voting based Support Vector Machine (FVSVM) method. The benefits
of FVSVR and FVSVM are demonstrated by experimental results based
on several databases of practical classification problems.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Tool for Automatic Index Analysis of Differential-Algebraic Equations

contributor:
Nedialkov, Ned
Qiao, Sanzheng
Computing and Software

subject: automatic index analysis, differential-algebraic equations, circuit simulation

abstract:
 Systems of differential-algebraic equations (DAEs) arise in applications such as circuit
simulation, models of chemical processes, optimal control, and multi-body dynamics. Informally, the index of a DAE is the number of differentiations needed to convert it to an ordinary differential equation. The index generally indicates the difficulty of solving a DAE problem. The higher the index of a DAE, the more difficult it is to solve it numerically.

 Structural index analysis plays a crucial role in solving DAE problems. In this thesis, we present two methods for index analysis, namely, Pryce's structural analysis (SA) and Linninger's symbolic-numeric (SN) analysis. We provide a Matlab tool implementing these two approaches: an Automatic Structural Index Analyzer (ASIA). We discuss the underlying algorithms, which include generating a signature matrix and computing SA index, computing a system Jacobian, and generating a symbolic-numeric matrix and computing SN index. We also present implementation issues and illustrate how ASIA is used.

 Numerical experiments show that ASIA can produce reliable structural information. We also show examples on which structural analysis fails, and how ASIA detects such situations.

abstract: Thesis

abstract: Master of Science (MSc)


contributor:
Smith, Spencer
Software Engineering

abstract: Title: A Program Family Approach to Developing Mesh Generators, Author: Fang Cao, Location: Thode

abstract:
This thesis presents a systematic approach for rapid development of a program family of
special-purpose 2D structured mesh generators, where a mesh is a discretization of a geometric
domain into small simple shapes, such as triangles or quadrilaterals. Mesh generators
are commonly used to produce the input files for finite element and other numerical
analysis programs that solve partial differential equations.

Despite the existence of many general-purpose mesh generators, there is a lack of research
attention on the design of special-purpose generators suitable for small and specific
meshing problems. The program family approach shown in this thesis supports reuse
and code customization by identifying the commonalities and variabilities between mesh
generators. The program family we developed accommodates variabilities in geometry,
topology, material properties, boundary conditions, system parameters and output file format.
Developing mesh generators using the program family approach results in the quality
of special purpose mesh generators being improved in terms of usability, reusability and
maintainability.

The contribution of this thesis centres on the design documentation and the system implementation.
The complete documentation of our design includes a commonality analysis,
requirements specification, and module guide. The contributions with respect to the implementation
include the use of a domain-specific language (DSL) written in XML (Extensible
Mark-up Language) to model the seed specification required to produce a mesh generator
family member, as well as applying XSL (Extensible Stylesheet Language) to allow flexible
customization of the output file(s).

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Partial Evaluation of Maple Programs

contributor:
Carette, Jacques
Computing and Software

subject: partial evaluation, maple programs, computer algebra systems

abstract:
 Partial Evaluation (PE) is a program transformation technique that generates a specialized
version of a program with respect to a subset of its inputs. PE is an automatic approach to program generation and meta-programming. This thesis presents a method of partially evaluating Maple programs using a fully online methodology.

 We present an implementation called MapleMIX, and use it towards two goals. Firstly we show how MapleMIX can be used to generate optimized versions of generic programs written in Maple. Secondly we use MapleMIX to mine symbolic computation code for residual theorems, which we present as precise solutions to parametric problems encountered in Computer Algebra Systems.

 The implementation of MapleMIX has been modularized using a high-level intermediate
language called M-form. Several syntax transformations from Maple to M-form make it an ideal representation for performing program specialization. Many specialization techniques have been explored including a novel online approach to handle partially-static data structures and an on-the-fly syntax transformation technique that propagates loop context into the body of dynamic conditionals.

abstract: Thesis

abstract: Master of Science (MSc)


contributor:
Bronsard, Lia
Mathematics

abstract: Title: Some Nice Results About Anistropic Mean Curvature Flow, Author: Amad Dailey-McIlrath, Location: Thode

abstract:
Imagine stretching out a rubber band on a flat surface and letting go suddenly.
Picture the way the rubber band contracts in slow motion and that
should give you a good idea of how mean curvature flow dictates the evolution
of plane curves. The more stretched out the rubber band, the faster it
snaps back. Just like the rubber band returns to it's original round shape no
matter how it is stretched, any smooth plane curve will evolve under mean
curvature flow to a circle. Suppose that you try to kink the rubber band, try
to force a sharp corner into it. As soon as you let go those kinks disappear.
Similarly a piecewise smooth curve will smooth out instantaneously under
mean curvature flow. Now suppose that you stretch out the rubber band and
put kinks in it, but instead of letting go completely, you hold those kinks in
place. The rest of the rubber band will still try to shrink back to it's original
circular shape. This is the major topic of this paper-how do piecewise
smooth curves behave under mean curvature flow if their kinks are held fast?
It turns out that the initial evolution of a curve in such a situation depends
completely on the number and precise angles of those kinks.

One of the earliest references on mean curvature flow is a 1956 paper [15]
which explored a specific case of piecewise smooth curves evolving by mean
curvature and found that by counting the number of sides one could determine
how the enclosed area would change (Theorem 4.1). This was a surprising
result because in the smooth case, the area enclosed is always shrinking,
but by adding some sharp corners it became possible that the area would increase
initially. Little attention seems to have been paid to piecewise smooth
curves and mean curvature flow since then, with one notable exception being
a paper by L. Bronsard and F. Reitich [5] which proved that the curves
analyzed in the 1956 paper could really exist!

The main result of this paper is Theorem 4.4 which is a generalization of the
aforementioned Theorem 4.1. The new result generalizes the original in two
ways: first it is non-specific with respect to the angles at the corners, and
second, it allows for the flow to be anisotropic; the evolution of the curve
may depend on it's orientation in the plane. Two proofs of this result are
presented. One uses ideas from the 1956 paper and is fairly intuitive. The
other proof follows the strategy of a more recent paper [10] and proves the
result as an intrinsic property of the curve. The final section of the paper
mentions some other questions and topics related to mean curvature flow
and includes a new result about the behavior of curves evolving on the unit
sphere according to a generalized version of mean curvature flow.

abstract: Thesis

abstract: Master of Science (MS)


title: Property Inference for Maple: An Application of Abstract Interpretation

subject: property inference, Maple, abstract interpretation, source code, properties, constraints

abstract:
We present a system for the inference of various static properties from source code
written in the Maple programming language. We make use of an abstract interpretation
framework in the design of these properties and define languages of constraints specific to our abstract domains which capture the desired static properties of the code. Finally we discuss the automated generation and solution of these constraints, describe a tool for doing
so, and present some results from applying this tool to several nontrivial test inputs.

abstract: Thesis

abstract: Master of Science (MSc)


title: Synthesis Method for Hierarchical Interface-Based Supervisory Control

contributor:
Leduc, Ryan J.
Software Engineering

subject: synthesis method, hierarchical, interface-based, supervisory control, discrete-event system, HISC, operators

abstract:
 Hierarchical Interface-based Supervisory Control (HISC) decomposes a discrete-event
system (DES) into a high-level subsystem which communicates with n ≥ 1 low-level subsystems, through separate interfaces which restrict the interaction of the subsystems. It provides a set of local conditions that can be used to verify global conditions such as nonblocking and controllability. As each clause of the definition can be verified using a single subsystem, the complete system model never needs to be stored in memory, offering potentially significant savings in computational resources.

 Currently, a designer must create the supervisors for a HISC system himself, and then verify that they satisfy the HISC conditions. In this thesis, we develop a synthesis method that respects the HISC hierarchical structure. We replace the supervisor for each level by a corresponding specification DES. We then do a per level synthesis to construct for each level a maximally permissive supervisor that satisfies the corresponding HISC conditions.

 We define a set of language based fixpoint operators and show that they compute the required level-wise supremal languages. We then present algorithms that implement the fixpoint operators. We present a complexity analysis for the algorithms and show that they potentially offer significant improvement over the monolithic approach.

 A large manufacturing system example (estimated worst case state space on the order of 10^22) extended from the AIP example is discussed. A software tool for synthesis and verification of HISC systems using our approach was also developed.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Numerical Investigation of One-Dimensional Storage Tank Models and the Development of Analytical Modelling Techniques

contributor:
Lightstone, Marilyn
Mechanical Engineering

subject:
Thermal Storage
One-Dimensional Model
Solar Thermal
TRNSYS

abstract:
To assess the long-term performance of a solar thermal system, mathematical models that accurately capture the effects of heat transfer within and interactions between individual components are required. For solar domestic hot water systems, the components can include the solar collectors, storage tanks, heat exchangers, pumps, and associated piping. In addition, weather data and demand profiles are also required. Simplified models for each component are needed to reduce the computational time required to run long-term simulations. The simplified models, however, must also be sufficiently accurate in order to provide meaningful system-level results.
Accurate prediction of the temperature profiles in the storage tanks of these systems is important since the temperature within the tank has a large impact on the efficiency of the entire system. TRNSYS, which is a commercial code commonly used for such simulations, contains a variety of different one-dimensional storage tank models. Previous research has indicated that these models have deficiencies in predicting experimental data. Therefore, this thesis is focussed on the analysis of the tank modelling used in TRNSYS. Results of this thesis show that the poor predictions are a result of numerical diffusion due to insufficient grid resolution. The correct theoretical profiles could be obtained by using a large number of nodes. However, this would lead to a significant increase in computational time.
Alternative modelling strategies were also developed using analytical techniques to more accurately predict the temperature profiles within a storage tank while keeping a relatively low computational cost. Different models were created which considered the different mixing mechanisms present in a storage tank, such as increasing inlet temperatures with time, heat losses to the surroundings, tank wall heat conduction, and inlet jet mixing.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Experimental Investigation of Turbulent Flow in a Pipe Bend using Particle Image Velocimetry

contributor:
Ching, Chan
Mechanical Engineering

subject: Turbulent Flow, Pipe Bend, Refractive Index Matched Particle Image Veloimetry, Swirl Switching, Proper Orthogonal Decomposition

abstract:
The turbulent flow through a 90o pipe bend is complex with secondary flow that can affect pressure drop and heat/mass transfer. The mean and unsteady flow is studied using refractive index matched two-dimensional two-component (2D2C) Particle Image Velocimetry in a single 90o bend with Rc/D = 1.5 and at Re = 34800. The measurements were performed in a closed loop using a 1-inch diameter test section that was machined out of acrylic. The flow is imaged in the symmetric plane parallel to the axial flow and at different cross sectional planes including 0.25D and 1D upstream, 10o, 20o, 70o, 80o from the bend inlet and 0.25D and 1D downstream of the bend.
	The axial flow accelerates on the inner wall at the inlet and then moves towards the outer wall at 40o-50o. A shear layer is formed between high velocity fluid near the outer wall and the slower moving fluid at the inner wall side in the second half of the bend. The axial turbulent kinetic energy ((u^2 ) ̅+(v^2 ) ̅) is found to be high in regions corresponding to high velocity gradient regions: (i) at the outer wall near the inlet that extends up to the outlet, (ii) near the inner wall at 40o-50o, and (iii) at the shear layer formed near the inner wall. In the cross sectional planes, two vortices are formed and have a maximum strength at 80o from the bend inlet. The cross sectional turbulent kinetic energy  ((v^2 ) ̅+(w^2 ) ̅) is found to be highest on the inner wall at the 80o plane.
	The snapshot Proper Orthogonal Decomposition (POD) technique is used to study the unsteady flow structures within the flow. There are long and short flow structures in the upstream pipe which can be related to Very Large Scale and Large Scale Motions. The secondary flow at 20o and further downstream cross sectional planes show evidence of unsteadiness as two vortices oscillate about the symmetry axis with low frequencies of St ~ 0.07, 0.13 and higher frequency at St ~ 0.3-0.6. The low frequency oscillations can be related to Very Large Scale Motions while high frequency oscillations are related to separation of the flow on the inner wall side. Evidence of swirl switching in the high frequency range (St ~ 0.3-0.5) is found at cross sectional plane 1D downstream.

abstract: Thesis

abstract: Master of Applied Science (MASc)


contributor:
Franek, Frantisek
Computing and Software

abstract: Title: Lecture Unit on Data Warehousing with a Case Study, Author: Kedong Lin, Location: Thode

abstract:
Data warehousing can be considered as a relatively new and still evolving technology in IT
industry. The term data warehouse was coined by Bill Inmon in the early 1990's and he
defined it as a subject-oriented, integrated, time-variant, and nonvolatile collection of data
for management's decision support systems. The main task of a data warehousing system is
to retrieve and integrate data from distributed and heterogeneous information sources, and load
the summarized data into a data warehouse for further business analysis.

Data warehousing can thus be considered the infrastructure part of the decision support
system (DSS) - it supports the information management for business decision making and enables
the online analytical processing (OLAP).

Date warehousing is not a simple system for small scale businesses - a typical data
warehousing system costs on average more than $3 millions of dollars a year for hardware,
services, and system integration, according to a survey performed in 1996. On the other hand, a
successful data warehousing project can bring in excess of 500% in return on investment. As a
result, data warehousing has become a major component of business systems since its
conception. Although the technology has more than 15 years of history, new upgrades and
products for data warehousing still appear every year.

Most people interested in data warehousing can be found in business environments. The
educational institutions just began to embark on data warehousing projects only recently. The
goal of my thesis is to describe concepts and methods of data warehousing systems in a form
of a specialized unit within an undergraduate database course. In particular I focus on data
warehouse system architecture, data models, online analytical processing (OLAP), and
warehouse data processing.

Finally, a case study is included in this thesis to help understand the implementation of a data
warehousing system in the commercial environment.

abstract: Thesis

abstract: Master of Science (MSc)


contributor:
Kahl, Wolfram
Wassyng, Alan
Software Engineering

abstract: Title: Hard Real-Time Microcontroller Code Generation from Timed Automaton Specifications, Author: Victor Bandur, Location: Thode

abstract:
A method is developed for automatically synthesizing hard real-time assembly code
for simple microcontrollers directly from timed automaton software specifications.
The method uses the microcontrollers' individual instruction execution times to approximate
as closely as possible the timing requirements indicated in the specification.
In order to accommodate this approximation, certain transitions in the specification
automaton require tolerances on timing constraints to be provided as part of the
specification. A second automaton is produced that is a model of the behaviour of
the implementation. The method is applied to the synthesis of a software metronome
device for the Microchip PIC 18F452 microcontroller.

abstract: Thesis

abstract: Bachelor of Engineering (BEng)


title: Aspects of Mesh Theory

contributor:
Nicas, Andrews
Mathematics and Statistics

abstract: Title: Aspects of Mesh Theory, Author: Daniel Hambleton, Location: Thode

abstract:
The main purpose of this paper is to give a thorough account of planar quadrilateral
and offset meshes. To this end, abstract meshes, the linear spaces
C(M), P(M), and the distance functions d*(M1 , M2 ) are defined and applied
to planar quadrilateral meshes. We then study the discrete analogue of the
Gauss map as well as the defining properties of circular and conical meshes.
The proof of the angle condition for conical meshes is given and used as motivation
for the study of Lie sphere geometry. We apply the theory of Laguerre
and Moebius transformations to conical and circular meshes respectively. All
of this theory is then applied to the creation of a planar quadrilateral mesh
with the face offset property in the context of a study project.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Kahl, Wolfram
Computer Science

abstract: Title: Proofs of Relational Semigroupoids in Isabelle/Isar, Author: Jinrong Han, Location: Thode

abstract:
The concept of relations is useful for applications in mathematics, logics and computer
science. Once an application structure is identified as a model of a particular relation-algebraic
theory, that theory becomes the preferred reasoning environment in this
application area. Examples of applications in computer science are database, graph
and games. In [Kah03], Kahl proposed using the proof assistant Isabelle/Isar to provide a
collection of theories for abstract relation-algebraic reasoning. In [DG04], De Guzman
improved and populated the theories introduced by Kahl in [Kah03]. Finite maps
or finite relations between infinite sets do not form a category since the necessary
identities are infinite. In [Kah08], Kahl presented relation-algebraic extensions of
semigroupoids where the operations that would produce infinite results in category
have been replaced with their variants that preserve finiteness, but still satisfy useful
algebraic laws. In this thesis, we will build a framework by building a hierarchy of Isabelle/Isar
theories to implement relational semigroupoid theories which are presented by Kahl
in [Kah08], focusing on the following: Since the difference between semigroupoids and categories are that no identities
are assumed in semigroupoids, category theories in [DG04] will be transferred into
our semigroupoid theories by modifying definitions, reformulating theorems, adding
theorems to help reprove theorems involving identities in their proofs. New theorems and new theories will be added to implement subidentity and range
and their properties. Then new theorems and new theories about restricted residual
and standard residual and their properties will be developed. In [Kah08], Kahl proposed
that in ordered semigroupoids with domain and range, if standard residuals
exist, then restricted residuals exist too and can be calculated via standard residuals.
A new theory will be built to prove this.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Viveros-Aguilera, Roman
Statistics

abstract: Title: Risk-Adjusted Exponentially Weighted Moving Average for Poisson Data and Application in Healthcare, Author: Hui Wang, Location: Thode

abstract:
The Risk-Adjusted Exponentially Weighted Moving Average (RA-EWMA) for Poisson
data is developed in detail. The method is useful to monitor healthcare or to
other counts that are generated dynamically over time. The approach used is motivated
by and follows closely the approach used by Grigg and Spiegelhalter (2007)
for dynamic binary outcomes. In simple terms, a Bayesian approach is applied that
uses conjugate priors (gamma in the case of Poisson data) utilized iteratively to provide
the method estimates as the posterior expected means. The main application
is counts with covariates. The thesis provides the necessary formulas to update the
method's estimates. Numerical calculations are presented to illustrate the use of the
methods and to compare it to the Standard Exponentially Weighted Moving Average
(Standard EWMA), which is a standard monitoring method used in industrial applications. The numerical evidence provided in the thesis suggests that the RA-EWMA
method is more sensitive than the Standard EWMA method to the presence of the
underlying covariates. This was shown clearly on real data, specifically in the UK's
death counts from lung diseases.

abstract: Thesis

abstract: Master of Science (MS)


abstract: Title: A Graph Transformation and Visualization Framework, Author: Scott West, Location: Thode

abstract:
The study of graph transformation has applications in many fields. The development
of visual, interactive tools that operate on graphs is a subject which has received
relatively little attention in the area of functional programming. This thesis presents
a framework for developing, visualizing, and interacting with graphs in the pure
functional programming language Haskell. Additionally, an embedded domain specific
language is developed for the purposes of graph transformation within the framework.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Kahl, Wolfram
Computing and Software

abstract: Title: An Algebraic Approach to Parameterised Loop Decomposition, Author: Shiqi Cao, Location: Thode

abstract:
Loop scheduling is to explore more possible parallelism by re-organizing the
loop body without changing its semantics; it results in more efficient utilization
of the underlying hardware. Recently, research has been shifting from well studied
instruction level parallelism to thread level parallelism (TLP) in order
to follow the trends of CPU design; parts of the COCONUT project are moving
in this direction as well. Loops are usually represented in graph-like structures,
which, without algebraic properties, can make formal verification very difficult. In this thesis, a new representation of a loop, called an extensible loop
specification, is proposed, based on the code graph and loop specification concepts
already used in the COCONUT code generator. Extensible loop specifications
are intended to be used by TLP loop scheduling algorithms; their
algebraic properties derive from those of loop specifications and code graphs. During the process of discovering a new loop representation, we use a
relational model to verify some transformations of control flow graphs where
transitions are labeled with code graphs.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Farmer, William M.
Computer Science

abstract: Title: Panoptes: An Exploration Tool for Formal Proofs, Author: Orlin Grigorov, Location: Thode

abstract:
Proof assistants aid the user in proving mathematical theorems by taking care of low-level
reasoning details. Their user interfaces often present proof information as text,
which becomes increasingly difficult to comprehend as it grows in size. Panoptes is
a software tool that enables users to explore graphical representations of the formal
proofs produced by the IMPS Interactive Mathematical Proof System. Panoptes
automatically displays an IMPS deduction graph as a visual graph that can be easily
manipulated by the user. Its facilities include target zooming, floating information
boxes, node relabeling, and proper substructure collapsing.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Canty, Angelo
Statistics

abstract: Title: Using Smoothing Splines to Select Significant Genes in Microarrays, Author: Ji Li, Location: Thode

abstract:
DNA microarray technology has been widely used in many applications such as gene
discovery, disease research and drug investigation. This thesis is based on a project
studying the genetics of Type 1 Diabetes.

In this thesis we introduce a method to use smoothing splines to select significant
genes in microarrays. This method is based on significance analysis of microarrays
(SAM). We choose upper and lower significance cut-offs based on when the numerical
derivative of the spline exceeds a threshold. We declare that any genes whose observed
statistics are less than the lower cut-off or greater than the upper cut-off to be significant.
We also explain how to use this method to calculate the number of significant
genes and estimate false discovery rates.

We use both Affymetrix and Illumina real data sets in our analysis and the results
are satisfactory. We try to use the simulation study to test our method but we have a
problem that we can not generate simulated data which is similar to the real microarray
data.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Karakostas, George
Computing and Software

abstract: Title: Game Theoretical Study on Selfish Routing with User Preferences, Author: Hao Xia, Location: Thode

abstract:
We study selfish routing with user-specific preferences. The selfish routing model
captures the selfish behaviour of users in a transportation system. Each user tries to
minimize her own travel latency by choosing the shortest route, i.e. the route with
the smallest latency, without taking other users' welfare into consideration. In this
model, users are assumed infinitesimal, in the sense that the impact of the behaviour
of any single user to the network is negligible. Under certain constraints, a steady
state is known to exist, where no user has the incentive to deviate from her current
route. This state is referred to as a traffic equilibrium.

We extend the traditional selfish routing model by incorporating user preferences.
In traditional selfish routing, one assumes that users make their routing
decisions merely based on path latencies, and furthermore all users perceive the same
latency on any single edge. We observe that in reality users may have their personal
preferences on the routes to travel on, e.g., some may be accustomed to certain routes
and feel unwilling to try out new ones; some may enjoy the wonderful views available
on some routes more than their care for the slightly longer travel time; some may be
limited to certain rules because they prefer public transportations, and so on. This
observation motivates our work. We introduce to the model a set of edgewise userspecific
preferences which come as inherent properties of each user. The disutility of
using each edge, which is the basis of a user's routing decision, is now a function of
latency and user preference.

In this work several equilibria related aspects of the extended model are studied.
Since we are working with infinitesimal users, the distinct combinations of edge
preferences among all users might be either finite or infinite. There is qualitative
difference between these two cases in terms of analysis, and both cases are discussed.
We show existence and uniqueness of equilibria, give an upper bound on the price of
anarchy, and study how taxation can help in this setting.

abstract: Thesis

abstract: Master of Science (MS)


contributor:
Balakrishnan, N.
Mathematics

abstract: Title: Inference for Simple Step-Stress Model from Log-normal Distribution Under Type-I Censoring, Author: Li Zhang, Location: Thode

abstract:
It is well known that the accelerated lift-testing (ALT), which involves analyzing
times-to-failure data of a product (system or component), is one of the testing procedures
for traditional lifetime data. The ALT allows the experimenter to obtain the
failure data at high stresses more quickly than under normal operating conditions.
In this project, we apply a simple step-stress model (a special class of ALT) to a
life-testing experiment when the times-to-failure data are assumed to be log-normal
distributed under Type-I censoring mechanism. The objective of the project is to
discuss inferential methods for the unknown parameters of the model by using the
maximum likelihood estimation method along with the cumulative exposure model.
Some numerical methods (such as, Newton-Raphson and quasi-Newton methods) for
solving the corresponding nonlinear equations are discussed. Methods of constructing
confidence intervals for the unknown parameters discussed here are those based
on (i) asymptotic normality of the maximum likelihood estimators (MLEs), and (ii)
parametric bootstrap resampling technique. A Monte Carlo simulation study as well
as a simulated data are used to verify the performance of these methods of inference.

abstract: Thesis

abstract: Master of Science (MS)