title: A POWER ANALYSIS OF THE COMBINED INPUT AND CROSSPOINT QUEUED SWITCH

contributor:
Szymanski, T. H.
Electrical and Computer Engineering

abstract:
Crossbar switches are fundamental building blocks of digital networks, such as the
Internet. An Input-Queued (IQ) switch with a set of queues at the input side is the most widely used crossbar switch due to the scalability and low design complexity. While IQ switches are used in commercial routers, the schedulers are relatively complex. An alternative switch design is to insert a FIFO queue in each crosspoint of an IQ switch. This architecture is named the Combined Input and Crosspoint Queued switch, denoted as CIXQ. The use of crosspoint queues simplifies the scheduling of traffic through the switch, at the cost of adding N2 FIFO queues to the switch fabric.
In recent years, considerable research has been made to study the capability and
flexibility of the CIXQ switch over high-speed networks. In this thesis, we will review the CIXQ switch by focusing on the switching performance, design implementation and
power consumption. The switching performance is first evaluated using MATLAB. The
analysis results show that the CIXQ switch with a simple Round Robin scheduling can
achieve a high performance under various traffic patterns. In an attempt to analyze the
power consumption, a CIXQ switch is then implemented in VHDL based on a broadcastand-select architecture and a DEMUX-MUX architecture. The designs are tested and simulated on Altera Cyclone II FPGAs. The simulation results illustrate that the switches are operational correctly as specified in Chapter 4. As power has become a critical design issue, a power analysis for IQ and CIXQ switches is finally presented. Analytic power models for the switches in an FPGA environment are developed. As the major contribution of this thesis, we are the first to develop power models for the CIXQ switch. The power models allow the designers to explore the power efficiency of various crossbar switches in the early stages of design process. The verification indicates that the power models are quite accurate with an average error of less than 10%. The analysis also shows that a CIXQ switch with N 2 crosspoint queues consumes about three times as much power as the IQ switch for modest size switches (4x4, 8x8, and 16xl6) in an FPGA environment.
In conclusion, we present an analysis of the design implementation and power
consumption of the CIXQ switch. The discussions illustrate a fact that the CIXQ switch
with a FIFO queue in each crosspoint increases the cost and hardware complexity even
though it will simplify the scheduling problem. The designers must analyze this trade-off
when making architectural design decisions.

abstract: Master of Applied Science (MASc)


title: NUMERICAL AND PHYSICAL MODELS FOR MICROWAVE BREAST IMAGING

contributor:
Nikolova, Natalia K.
Noseworthy, Michael D.
Electrical and Computer Engineering

subject:
Electrical and Computer Engineering
Electrical and Computer Engineering

abstract:
Breast cancer is a serious health problem that severely affects the society. Science and engineering communities are looking to find more advanced and new cures to contain this deadly disease. There has been considerable success in increasing the efficacy of conventional imaging techniques for breast cancer detection such as mammography. However, the use of ionizing radiation, the incidence of patient discomfort and the low specificity are some of the negative aspects of mammography. Also, the chances to successfully cure breast cancer can increase manifold with early detection of the malignant tumors. Magnetic Resonance Imaging (MRI) is successful with its highly clear and detailed images, but it is considered too expensive for wide screening. Its low specificity is another disadvantage.

Microwave imaging of the breast, which uses non-ionizing radiation, is a
very active research area of recent times. It is hoped that once developed, it can override the negative aspects of the existing imaging modalities. The idea is to detect malignant lesions in the breast based on their electrical-property contrast with healthy breast tissues.

The electrical properties of biological tissues in the microwave region are described by their complex permittivity. Previous studies claimed that malignant tumors have very high permittivity and high loss compared to the surrounding healthy tissue. It was assumed that the modality exploiting this contrast can easily detect sub-centimeter tumors. Hence, very simple models with high permittivity and loss tumor models embedded in low permittivity homogenous models were employed to show the detection capabilities of microwave imaging techniques. The examples were fairly amateurish and claimed unrealistic performance of the rather simplistic microwave imaging techniques.

Recent studies have shown that the breast is not as simple an electromagnetic medium as was thought previously. It is a complex heterogeneous environment with high permittivity and high loss healthy tissues (such as glandular tissue) and low permittivity and low loss healthy tissues (such as fat). The internal tissue distribution and volume varies significantly from woman to woman. Thus, simple models made with hemispheres, cylinders, etc., filled with water or oil cannot mimic the reality of the breast in imaging experiments and simulations.

This is why there is a considerable demand of representing breasts as realistic physical and numerical models. Physical models are required to experimentally verify the imaging scanning systems with antennas. The numerical models are required for electromagnetic (EM) simulations that are indispensable in designing and testing image reconstruction algorithms.

The work in this thesis mainly deals with the construction and representation of breast models both in experiments and in simulations. This is impoliant work toward making microwave imaging a practical stand-alone detection system.

abstract: Master of Applied Science (MASc)


title: SEARCHING FOR GALAXY GROUPS IN PHOTOMETRIC DATA FROM THE CFHT LEGACY SURVEY

contributor:
Harris, William E.
Parker, Laura C.

subject:
Astrophysics and Astronomy
Astrophysics and Astronomy

abstract: Most galaxies in the universe live in galaxy groups, and we can use them to learn a lot about t he influence of environment on galaxy evolution. Historically, galaxy groups have been ident ified by painstakingly obtaining many spectra and finding associated gala-'{ies, however, much larger samples could be found if we had a reliable method of finding groups using photometry. We follow a variation of the Probability Friends of Friends algorithm suggested by Li & Vee (2008) to find galaxy groups in photometric redshift data. Our approach employs a continuous friends-of-friends search in t he t ransverse direction and uses the redshift probability density in redshift space. We use t his method to find galaxy groups in the 4 Canada-France-Hawaii Telescope Legacy Survey Deep Fields, and compare it to a 5th Nearest Neighbor galaxy density search algorithm applied to the same four fields. To fur ther assess our Probability Friends of Friends method, we test it on light cones from the Millennium Simulation. We found that less t han 20% of the Probability Friends of Friends groups with 12 or more members were interlopers. The average density of groups of 12 or more members is ~ 54 per square degree. Our final sample of groups in t he Canada-France-Hawaii Telescope Legacy Survey Deep Fields contains 33 ,279 groups with three or more members, 218 of which have 12 or more members.

abstract: Master of Science (MS)


title: MODELING THE EFFECTS OF HEARING LOSS ON NEURAL RESPONSES IN THE COCHLEAR NUCLEUS

contributor:
Bruce, Ian C.
Electrical and Computer Engineering

abstract:
Physiological studies of neurons in the dorsal cochlear nucleus (DC ) and ventral cochlear nucleus (VCN) performed by Ma and Young (2006) and Cai et al. (2008) ,respectively, showed the changes in response properties that arise following acoustic trauma. A model of the auditory periphery by Zilany and Bruce (2007) , capable of modeling the effects of acoustic trauma on auditory nerve (AN) fiber responses, was used to simulate inputs to computational models of DCI and VCI cells in order to determine if the changes shown by Cai et al. (2008) and Ma and Young (2006) could be fully explained by changes in the auditory periphery.

DCN cells simulated using the Zheng and Voigt (2006) DCN model receiving AN inputs from an impaired auditory periphery were able to reproduce many of t he types of responses shown by Ma and Young (2006) . Providing impaired AN inputs with compound action potential (CAP) threshold shifts beginning just above DCN cell best frequency (BF) were able to reproduce the tail responses reported by Ma and Young (2006). Type III DCN cells showed class A tail responses whereas, type IV and IV-T DCN cells showed class B tail responses as a result of impaired inputs from the auditory periphery. Type IV-T cells also showed class B-like tails in responses to CAP threshold shifts beginning well below BF. A similar study was performed with VCN cells modeled using the Rothman and Manis (2006c) model. Modeled VCI cells receiving impaired inputs from the auditory periphery did not show most of the behaviors reported by Cai et al. (2008) indicating that the changes in VCN cell reponses following acoustic t rauma are the result of either plastic changes in the brainstem or of features of normal VCI cell responses that are not currently captured by the model.

abstract: Master of Applied Science (MASc)


title: THERMAL ANALYSIS OF COMPACT SEALED COMPUTERS

contributor:
Cotton, J. S.
Mechanical Engineering

subject:
Mechanical Engineering
Mechanical Engineering

abstract:
Thermal performance of a cooling system for a small sea led computer is investigated. The cooling system consisted of a heat pipe unit which transfers heat from the CPU and northbridge chip to the case wall which had vertical fin channels mounted on the outside. Natural convection and radi at ion moved the heat from the fin plate to the surroundings. An initial benchmarking experiment determined the temperature drop across each component in the system and identi fied th e areas of focus for further research.

The heat pipe unit was se lected for initial analysis based on the benchmarking experiment. Heat pipes with sintered wick and grooved wick structures were tested at different orientations with respect to gravity. Gravity was found to cause failure of the groove wick heat pipe in certain orientations while the sintered wick was able to function adequately in any orientation.

Carbon foam is a new material with the potential for very high thermal conductivity, 2-3 times that of copper. Based on the variable performance of heat pipes, carbon foam was investigated as a possible solution. Investigations determined carbon foam had thermal conductivity in the range 30-130 W/mK, but it had high specific thermal conductivity, over fo ur times that of copper which means it could be useful in applications that are weight sensitive.

Literature research was conducted on the topic of rectangular channel fin perfo rmance and an analytical model was found to estimate performance for different fin geometries. A radiation shape factor equation for rectangular channel fins was also found. Together the models were used to estimate the best fin geometry to maximize natural convection and radiation heat transfer. Heat spreading in the fin plate was investigated using numerical simulation validated by the analytical models and previous studies of similar geometries.

A system model is developed to combine the temperature drops of all components of the system to quickly determine the affect of changing one parameter on the temperature of the CPU. Notable results include the highest power CPU that can be used in the current system, the highest surrounding temperature that a 35 W CPU can run in and the size of fin plate needed to run a 65 W CPU in a 40°C environment.

abstract: Master of Applied Science (MASc)


title: CROSS-DOMAIN MESSAGE ORIENTED INTEROPERABILITY FRAMEWORK

contributor:
Sartipi, Kamran
Computing and Software

subject:
Other Computer Engineering
Other Computer Engineering

abstract:
The variety and heterogeneity of information communication standards in different application domains are the main sources of complexity in interoperability provision among those application domains. The maturity of application domains can be assessed by the ease of communication of terms between different stakeholders in the same domain, which is central in defining standards for communication of information among organizatiuns. Currently. most research activities are focused towards standardization and illteroperabiliry among information systems within the same domain.

However. an emerging challenge is to address the exchange of information among heterogeneous applications in different domains, such as healthcare and insurance. This requires data extraction to obtain common subsets of information in the collaborating domains. The second step would be to provide intra-domain and inter-domain semantic interoperability through proprietary and shared ontology systems.

In this context, we address the above challenges through description of a framework that employs healthcare standard development frameworks and clinical terminology systems to achieve semantic interoperability between distributed systems among different application domains. A real world case study, which addresses message-oriented integration of business processes between healthcare and insurance is demonstrated.

abstract: Master of Applied Science (MASc)


title: Unequal Erasure Protection Techniques for Scalable Multi-Streams

contributor:
Dumitrescu, Sorina
Shirani, Shahram
Electrical and Computer Engineering

abstract: This thesis presents a novel unequal erasure protection (UEP) strategy for the transmission of scalable data, formed by interleaving independently decodable and scalable streams, over packet erasure networks. The technique, termed multi-stream unequal erasure protection (M-UEP) differs from UEP by placing separate streams in separate packets to establish independence and using permuted systematic Reed-Solomon codes to enhance the distribution of message symbols amongst the packets. M-UEP improves upon UEP by ensuring that all received source symbols are decoded. The R-D optimal redundancy allocation problem for M-UEP is formulated and its globally optimal solution is shown to have a time complexity of O(2^N N(L+1)^(N+1)), where N is the number of packets and L is the packet length. To address the high complexity of the globally optimal solution, an efficient sub-optimal algorithm which runs in O(N^2 L^2) time is formulated. The additional side information necessary for M-UEP at the decoder is discussed and an upper bound on the amount of side information is derived. To mitigate the necessary side information, a technique termed (FM-UEP) is presented. A constrained optimal algorithm for generating N substreams from P primary substreams (P > N) is formulated, where the placement of primary substreams into N groups is constrained to a fixed-order. Four possible fixed-orders are proposed: raster scan, zig-zag scan, dispersed dot dithered and subband dispersed. Experiments performed on SPIRT coded images (with appropriate grouping of wavelet coefficient) validate the superiority of M-UEP and FM-UEP over UEP, with peak improvements of 0.6 and 0.5 dB, respectively. Additionally, our tests reveal that M-UEP is more robust than UEP in adverse, unpredictable and varying channel conditions.

abstract: Master of Applied Science (MASc)


title: Computer Analysis of Gastroduodenal Electrical and Mechanical Signals

contributor:
Kitai, R.
Sarna, S.K.
Electrical Engineering

subject:
Electrical and Electronics
Electrical and Electronics

abstract:
The gastroduodenal junction coordination was studied by conducting experiments on six dogs. The electrical and mechanical signals in the gastroduodenal area were recorded by surgically implanting electrodes and strain gauges. Recordings were made on an analog tape recorder for about 30 minutes in the fasted state and for about 45 minuted after food or with intravenous infusion of pentagastrin. The recorded signals were later fed into Data General Nova 830 Minicomputer for subsequent analysis. In analysing these signals frequency is of prime importance as interaction could result in the argumentation of the proximal duodenal electrical/mechanical signal at antral frequency. The application of spectral analysis techniques for this purpose is described. The programs are developed for the following purposes:

1) To accept the analog data and convert them into discrete digital data.

2) To display any segment of data for visual observation of recorded signals.

3) To compute the auto and cross power spectral density.

The results of the analysis are presented in the form of tables. It is concluded that there exists a coordination. The possible mechanism could be myogenic, since coordination in the electrical activity is evident when atropine was given.

abstract: Master of Engineering (ME)


title: DEVELOPMENT OF A PORTION OF A THEORY LIBRARY FOR MECHANIZED MATHEMATICS SYSTEMS

contributor:
Farmer, William M
Computing and Software

subject:
Computational Engineering
Computer Engineering
Software Engineering
Computational Engineering

abstract: A theory library for a mechanized mathematics system (MMS) is a collection of mathematical theories which serves as a database of mathematics. A powerful library plays a significant role in making an MMS useful. This thesis demonstrates some of the techniques needed for generating a large theory library for an MMS, that has capability of both computation and deduction, by developing a small portion of a theory library. In the theory library presented in this thesis, the module system Mei, a (lamda)-calculus style module system that supports higher-order functors, is employed to manage mathematical theories. Chiron, a logic derived from von-Neumann-Bernays-Godel set theory, is used as the underlying logic of the system, and biform theories, which can include both formulas and algorithms as axioms, are used to present mathematical theories. The theory library given in this thesis is based on the branch of mathematics called calculus.

abstract: Master of Science (MS)


title: MECHANISMS OF ELECTROHYDRODYNAMIC TWO-PHASE FLOW STRUCTURES AND THE INFLUENCE ON HEAT TRANSFER AND PRESSURE DROP

contributor:
Cotton, J.S.
Mechanical Engineering

abstract:
The objectives of this research is to determine the mechanisms involved in the development of electrohydrodynamic (EHD) flow structures, such as twisted liquid cones, twisted liquid columns and entrained liquid droplets, in a two-phase flow and to determine their impact on convective condensation heat transfer. EHD involves the application of high voltage to a dielectric fluid flow to induce electric forces that can create additional convection currents in single-phase and two-phase flows and also the redistribution of the different phases within the channel in a two-phase flow. The EHD phenomenon was investigated inside a smooth horizontal tube with a concentric rod electrode used to apply high voltage to a flow of refrigerant R-134a.

The EHD flow structures were initially observed to be a transient phenomenon that appeared during the initial step input of high voltage and were not present after steady state. Investigations to sustain the EHD two-phase flow structures using various ±8kV pulse width modulated waveforms (PWM) are performed for a range of mass flux between 45 to 110 kg/m^2 s and a quality of 50%, conditions which correspond to a stratified/stratified wavy flow pattern. The effect of sustaining flow patterns consisting of these flow structures on condensation heat transfer and pressure drop is measured. The purpose of this research is to evaluate the potential of sustaining specific EHD two-phase flow patterns as a means of enhancement and control of heat transfer and pressure drop for industrial heat exchange applications.

An evaluation of the mechanisms involved in the development of the EHD flow structures was first performed by determining the effect of applying positive and negative polarity high voltage to a single-phase flow to determine the mechanisms of charge injection in this particular geometry. A negative polarity high voltage applied to the concentric rod electrode was found to result in a larger heat transfer enhancement due to the charge injection occurring at the center electrode, whereas a positive polarity high voltage applied to the rod electrode resulted in negative charge injection at the grounded tube wall. This method of charge injection was used to explain the difference in the development of the twisted liquid cone and twisted liquid column flow structures that arise due to an applied positive and negative voltage respectively.

An analysis of the development and sustainability of the EHD two-phase flow structures using various PWM waveforms was investigated using a high speed camera to visualize the flow. An image analysis of these high speed videos determined the suitable pulse width, duty cycle and voltage polarity conditions for the development of the twisted liquid cones/columns and in sustaining the structures during the pulse ON period. The sustainability of these flow structures were determined to be mainly influenced by the charge distribution within the flow and a means to sustain these flow structures for a range of duty cycles between 10%-90% was found using waveforms consisting of both positive and negative high voltage pulses. For duty cycles of 100%, an inverse annular flow pattern was observed, where liquid is extracted and encircles the concentric rod electrode. For the entrained droplets produced using EHD, the required high voltage pulse conditions for the production of the droplets was determined and the effect of EHD on the coalescence of droplets was also observed.

Experiments were performed to measure the condensation heat transfer and pressure drop performance of flow patterns consisting of EHD flow structures. The results show that flow patterns consisting of different EHD flow structures exhibit different heat transfer and pressure drop characteristics. The heat transfer enhancement was determined to be a result of the extraction of liquid from the heat transfer surface and into the central core, the increase in convection within the phases and a disruption of the thermal boundary layer. The increase in pressure drop is due to the increase in frictional pressure drop between the liquid and electrode surfaces and an increase in the interfacial area resulting in greater liquid-vapour shear. The maximum enhancement of heat transfer and the maximum increase of pressure drop by using the EHD technique were determined to be 2.9-fold and 5.0-fold respectively. The results also indicate that EHD can be used to independently control the heat transfer and pressure drop as it was shown that for a fixed heat transfer or pressure drop performance, a range of corresponding pressure drop or heat transfer conditions can be achieved depending on the flow pattern established using PWM waveforms. The findings in this study show the promise in utilizing the EHD technique as an effective means of enhancement and control of heat transfer and pressure drop performance in advanced heat exchange systems.

abstract: Master of Applied Science (MASc)


title: KINETIC DEGRADATION OF SALICYLIC ACID BY HYDROXYL RADICAL CREATION USING A HYBRID IRON OXIDE-OZONATION NANOPARTICLE SYSTEM

contributor:
Masten, Susan J.
Civil Engineering

subject:
Civil Engineering
Civil Engineering

abstract:
No Abstract available

Master of Applied Science (MASc)


title: STAP WITH ADAPTIVE STATE ESTIMATION IN NON-STATIONARY HETEROGENEOUS SYSTElVIS.

contributor:
Kirubarajan, Thia
Electrical and Computer Engineering

abstract:
In radar signal processing, the vulnerability of the desired signal to homogeneous and heterogeneous interferences increases as the communication traffic increases. The principal challenge in the radar system then is to mitigate the effects of cold (homogeneous) clutter, severe dynamic (heterogeneous) hot clutter and jamming interferences while estimating the states of targets under track. Space-Time Adaptive Processing (STAP) enhances the capability of radar systems to overcome this challenge. However, it is a sample-based system where the adaptive processing is sensitive to the underlying assumptions as well as the diversity of potential interferences. Hence, the performance of STAP deteriorates when basic assumptions are violated due to errors in receiver array elements, non-stationary nature of interferences, inadequate Independent and Identically Distributed (i.i.d.) sample data, and target like-signal in the training data set.

This thesis proposes an Adaptive State Estimation (ASE) approach to characterize STAP used simultaneously in spatial and Doppler domains for non-stationary, homogeneous and heterogeneous systems. The contributions presented here are based on the adjustment of the weight vector and the update of associated interference covariance matrix by ASE to minimize the output noise power while maximizing Signal to Interference-plus-Noise Ratio (SINR) in the Mean Squared Error (MSE) sense. The integration of STAP principle with sequential state estimation in order to decode the target signal while rejecting the interferences due to non-stationary heterogeneous clutter and jammer effects without degrading performance is the key contribution of this paper. The Proposed STAP-ASE algorithm is shown to outperform its counterparts in terms of efficiency, IF-improvement factor, Signal to Interference-plus-Noise Ratio (SINR) convergence rate and target detection. Simulation results are presented to illustrate the performance of the proposed technique.

abstract: Master of Applied Science (MASc)


title: LOCALIZATION OF SODIUM CALCIUM EXCHANGER & SARCO/ENDOPLASMIC RETICULUM CALCIUM PUMP IN PORCINE CORONARY ARTERY SMOOTH MUSCLE

contributor:
Grover, A.K.
Biology

subject: Biology Biology

abstract: Calcium (Ca2+) is an important signaling molecule hence its movement across cell membranes must be tightly regulated. Ca2+ transporters play a key role in this regulation. The sarco/endoplasmic reticulum (SER) Ca2+ pump (SERCA) and plasma membrane Ca2+ pump (PMCA) keep [Ca2+]i levels low. The sodium calcium exchanger (NCX) may work to expel Ca2+ or bring it into the cell. NCX has been proposed to playa role in refilling the SER Ca2+ pool. We recently reported a functional linkage between CXl and SERCA2 in smooth musc le cells cultured from pig coronary artery. The membrane invaginations termed caveolae (lipid rafts containing caveolin) may also playa role in directing Ca2+ movements during cell signalling. The overall objective of this thesis was to determine whether NCX, SERCA and caveolin proteins were spatially linked (colocalized) in pig coronary artery smooth muscle. This was investigated by examining their co-migration in detergent treated microsomal membranes upon sucrose density gradient fractionation. The fractions were analyzed for the abundance of NCX1, SERCA2, caveolin-1 , lipid raft markers, and cytoskeletal proteins. Then, the Pearson's and Spearman' s correlation coefficient between each proteins distribution was determined. The results indicate there was a significant correlation in the distribution of NCXl and SERCA2, NCXl and caveolin-1 , and SERCA2 and caveolin-1 in the flotation; however the migration was not perfect. In conclusion, NCXl and SERCA2 co-migrate to similar types of membrane domains in pig coronary artery smooth muscle. These domains are rich in lipid rafts and include caveolae. The results also indicate that although a spatial interaction exists, co-localization may not always be present. Thus, CXl may contribute to the SER refilling but it may not be solely responsible for this process. The partial association of NCXl and caveolin-1 suggests the role of caveolae in some Ca2+ signalling pathways but not others.

abstract: Master of Science (MS)


title: Thermal Tuning of Planar Bragg Gratings in Silicon-on-Insulator Rib Waveguides

contributor:
Jessop, P.E.
Knights, A.P.
Engineering Physics

subject:
Engineering Physics
Engineering Physics

abstract:
Thermally tunable planar Bragg gratings in silicon-on-insulator (SOl) rib waveguides with external and integrated heaters were simulated, fabricated, and measured. Planar Bragg gratings were fabricated using selective silicon self-implantation at a dose of 2 x 10^15 ions/cm^2 to amorphize and increase the refractive index by 0.3 due to the induced damage. External heating resulted in a positive shift of 0.080 nm/degree in a good agreement with the 0.082 nm/degree predicted by theory. This demonstrated the tunability of planar Bragg gratings in SOl rib waveguides and motivated the fabrication of integrated heaters on waveguides. The planar surface of implanted Bragg gratings makes it desirable for subsequent processing such as surface bonding and its tunability makes it applicable as an active device.

Simulations performed with the heat transfer module of COMSOL in conjunction with beam propagation method (BPM) simulations predicted that application of 200 mA current to 100 nm thick aluminum strips is sufficient to generate a 10 degree temperature increase in a waveguide and that a minimum thickness of 300 nm of oxide layer is required to prevent mode loss in a waveguide due to the presence of the metal layer on top. Due to temperature restrictions on implanted damage and high temperatures involved in growth of oxide, non-cured spin-on-glass was used as the insulating layer between the rib waveguide and metal strips. Although, the combination of spin-on-glass (SOG) and aluminum worked on the test samples, it was unsuccessful on the device samples, such that the integrated heaters failed and the deposited aluminum affected the propagation optical mode.

The use of Bragg gratings to couple a broad spectrum of surface illuminating light to a multimode SOl slab waveguide was also demonstrated. This has potential applications in enhancing the long wavelength performance of solar cells. The addition of Bragg gratings on top of slab waveguides promotes light coupling, trapping reflected light and also increasing the optical path length of the incident beam, which increases the efficiency of the solar cells. Bragg gratings with a pitch of 500 nm were fabricated on part of the surface of a multimode planar SOl waveguide and the coupling of light into waveguides with and without Bragg gratings were measured. The measurements and the simulations were in good agreement, confirming that broadband Bragg grating couplers are a good candidate for coupling in more light with higher efficiencies.

abstract: Master of Applied Science (MASc)


title: COMMUNITY RESEARCHERS' EXPERIENCES WITH COMMUNITY-BASED RESEARCH

contributor:
Greene, Saara
Social Work

subject:
Social Work
Social Work

abstract: Within Canada, the HIV/AIDS community is an extensively researched population where people living with HIV/AIDS (PHA) are minimally included in the research process. Community-based research (CBR) has become a widely recognized framework with which to engage in HIV/AIDS research in a response to the need for research frameworks that promote equitable collaboration between community members and community researchers. Coupled with a CBR approach, the Greater Involvement of People Living with HIV/AIDS (GIPA) principle can be incorporated into the research process so that the research is reflective of and responsive to community needs. Drawing on the experiences of five HIV/AIDS community researchers, this study seeks to better understand the tensions and challenges community researchers experience when facilitating CBR with participants with whom they identify with based on race, gender, sexual orientation, immigration status, and HIV status. Within the findings, several themes were explored by participants. The concept of multiple identities was predominately explored as well as the complexities regarding insider and outsider status. Participants also explored the tensions associated with maintaining confidentiality as well as discussing coping and self care practices. Expectations of community members and the research team were highlighted, and participants provided advice or recommendations based on their reflections of their personal experiences of engaging the CBR process. The themes explored by this particular group of community researchers demonstrate the complexities associated with their unique positioning within the research process. As the CBR approach is increasingly being utilized and recognized as an effective tool within a community research context, it is important as practitioners to be mindful of the challenges and benefits of facilitating CBR.

abstract: Doctor of Social Work (DSW)


title: ENDOCRINE DISRUPTION IN ROUND GOBY (NEOGOBIUS MELANOSTOMUS) FROM HAMILTON HARBOUR

contributor:
Wilson, J. Y.
Biology

subject: Biology Biology

abstract:
The occurrence of endocrine disruption in aquatic species is of growing concern in the Great Lakes region. Feminized male white perch (Morone americana) and round goby (Neogobius melanostomus) have been observed in Hamilton Harbour, a heavily polluted embayment of Lake Ontario. The harbour is impacted by wastewater effluent, containing pharmaceuticals and natural steroid hormones, as well as sediment-bound industrial contaminants including polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs). This study investigated the severity of endocrine disruption in Hamilton Harbour in an attempt to identify which areas of the harbour are most heavily impacted and thereby, which contaminants are the most potent endocrine disrupting chemicals (EDCs). The round goby, an invasive species found throughout the Great Lakes region, was used as the model species. Three biological endpoints in male fish were observed: intersex (the presence of oocytes in male gonads), feminization of secondary sexual characteristics, and vitellogenin (Vtg) gene upregulation. Vtg is an egg yolk precursor protein normally highly expressed in reproductively active females. Vtg qPCR assays were developed and tested using an in vivo lab exposure to estradiol, a known Vtg-inducing compound. Field studies looked for site differences and revealed that there were significant differences among sites in all three biological endpoints. More heavily impacted sites had high signals from each endpoint while moderately impacted sites displayed Vtg upregulation and feminization of secondary sexual characteristics, but not intersex. As expected, reference sites were not impacted by endocrine disruption. Sites influenced primarily by wastewater effluent were moderately impacted, suggesting that wastewater effluent is not the dominant endocrine dismpting agent in the harbour. Sites that were most heavily impacted were those characterized by high sediment PAH and/or PCB levels. PAHs and PCB appear to be the most potent EDCs in the Hamilton
Harbour.

abstract: Master of Science (MS)


title: Growth and Phospholipid Analysis of Thellungiella salsuginea Exposed to Varying Environmental Phosphate

contributor:
Weretilnyk, Elizabeth A.
Biology

subject: Biology Biology

abstract:
In global soils phosphorus is both the most abundant yet the least available essential macronutrient for plants. Phosphorus is a component of nucleic acids, some signalling molecules, membrane lipids and, as ATP, for metabolic control and energy transfer. Consequently, a phosphorus deficiency impacts many aspects of growth and development leading to plants that are smaller in stature, develop slowly and yield less than plants with sufficient phosphate.

Diversity among native plants with respect to phosphorus use can allow researchers to identify traits meriting consideration for crop improvement. Thus the objective of this thesis research was to study the response of a native crucifer found in the Yukon Territory, Thellungiella salsuginea, to various concentrations of external phosphate. Seedlings were grown on nutrient medium containing O.OS , 0.1 , 0.2 or 0.5 mM phosphate. No significant differences were found with respect to root elongation rates for concentrations below 0.2 mM phosphate but root elongation was 1.4-fold faster for seedlings grown on 0.5 mM phosphate. Thellungiella seedlings grown on low (0.05 mM) phosphate medium showed a 2.5-fold increased biomass allocation to roots when compared to plants on high (0.5 mM) phosphate medium consistent with an increased allocation to root mass under low phosphate seen with plants optimizing foraging for limiting nutrients. Even at the lowest external Pi content no seedlings showed the classic phosphate starvation response typified by short primary roots with many lateral branches.

The lack of a starvation phenotype raised questions of how Thellungiella allocates phosphate to major sinks, one being phospholipids. Therefore, a 31p_NMR profiling strategy was developed for leaf phospholipids. This approach required more tissue than was available from seedlings so rosette leaves were harvested from five-week-old plants grown in PromixBX and watered weekly with a low (0.05 mM) or high (1.0 mM) phosphate solution. Shoot fresh weight was not significantly different between treatments and visual inspection revealed no overt phenotypic differences. Shoot tissue was solventextracted to yield polar and non-polar phases. The polar phase of plants grown under low phosphate conditions contained significantly less (1.3-fold) inorganic phosphate (Pi) than plants watered with 1.0 mM phosphate (P < 0.05). Non-polar phases dissolved in 5% (w/v) sodium cholate produced high resolution spectra by 31 p-NMR. Spectra from low and high phosphate-treated plant samples usually showed five peaks tentatively identified as free Pi, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylcholine. Statistical analysis indicated that only the putative phosphatidylinositol peak showed treatment-related differences, with low phosphate plants showing about 50% of the lipid species relative to high phosphate plants.

Use of the Electronic Reference To Access In Vivo Concentrations (ERETIC) method was tested on a limited number of extracts and results show this to be a promising approach for quantifying phospholipid species profiled by 31 p_NMR. Moreover, this profiling protocol was successfully extended to Arabidopsis tissue producing spectra with a signal-to-noise comparable to those from Thellungiella samples despite using 2-fold less tissue. In the case of Arabidopsis, only four distinct peaks were identified with the one attributed to phosphatidylinositol apparently absent or below the detection limits. The difference in spectra found between Thellungiella and Arabidopsis plants warrants further investigation.

abstract: Master of Science (MS)


title: CHARACTERIZATION OF THE MENIN AND TIP60 INTERACTION IN DROSOPHILA MELANOGASTER

contributor:
Bedard, Andre
Biology

subject: Biology Biology

abstract:
Drosophila melanogaster (fruit fly) has been used as a model organism for almost a century. Drosophila shares key molecular pathways and regulatory proteins with humans, making it a useful organism to study human diseases. The disruption of these pathways often leads to similar defects in flies and humans. For example, the Fragile X mental retardation syndrome is caused by the disruption of FMR1, leading to intellectual and physical impairment from defects in synaptic transmission . Flies lacking dfmrl show behavioural defects similar to humans, and also have impaired motor control. The Ras pathway is also well studied using the Drosophila model system and mutations in Ras1 show defects in cell proliferation in flies and humans. Multiple endocrine neoplasia type 1 is another syndrome that can be studied using Drosophila as a model organism.

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant cancer syndrome predominantly characterized by tumour formation in various endocrine glands. Heterozygous patients for MENl develop the disease following a loss of the wild type allele (loss of heterozygosity). Menin is encoded by MEN1, and has no obvious sequence homology to other proteins. In order to gain some insight on the role of menin, several studies have looked for proteins interacting with menin. Using a yeast two-hybrid screen, our laboratory identified Enhancer of Polycomb E(Pc), a component of the Tip60 histone acetyltransferase complex as a candidate, novel menin interacting protein. Closer investigation revealed dTip60 as an interacting partner of Menin in Drosophila S2 cells.

Menin was found to interact with dTip60 in S2 cells under optimal growing conditions and after lhr of heat shock. However, co-immunoprecipitation after stress by Alfa-irradiation did not reveal an interaction. Additionally, the pattern of expression and role of dTip60 was examined in wild type Oregon R flies and in flies expressing RNAi against dTip60. Heat shock lethality experiments were conducted to compare Tip60 RNAi flies to controls . dTip60 did not appear to playa role in the stress response at the larval developmental stages. The Tip60 RNAi flies showed robust expression of dTip60 throughout embryogenesis; therefore the maternal contribution of dTip60 was also investigated. The maternal contribution of dTip60 was significantly reduced in embryos from females harbouring the UAS-dTip60 RNAi and daGAL4 constructs. This can be a valuable tool for future experiments with embryos into the function of dTip60.

Further experiments must be conducted to determine whether a dynamic interaction occurs after v-irradiation using closer kinetics in S2 cells. Also, experiments using wild type flies showed that dTip60 is developmentally regulated . dTip60 is required for development since Tip60 RNAi flies do not survive past the pupal stage. Increased lethality is not seen in Tip60 RNAi flies compared to controls when subjected to heat shock, suggesting that dTip60 does not playa role in stress response at this time. A v-irradiation lethality experiment should be conducted to determine if a complex containing menin and dTip60 is required for DNA damage repair. Lastly, to determine whether menin and dTip60 have a role in the same pathway, stress experiments must be conducted using Mnnr1^(-/-) flies as a comparison to phenotypes seen in Tip60 RNAi flies.

abstract: Master of Science (MS)


title: Non-Isothermal Polymerization of Styrene

contributor:
Hamielec, A.E.
Chemical Engineering

subject:
Chemical Engineering
Chemical Engineering

abstract: The non-isothermal polymerization of styrene under runaway chemically initiated reactions was studied. A system of multiple initiators was used. The experiments were performed in an insulated batch reactor. Experimental temperature and pressure profiles with respect to time were obtained and used to evaluate a mathematical model at high temperatures. Molecular weights and conversion measured by gel-permeation chromatography (GPC) provided further evidence about the adequacy of the model. The behaviour of a non-isothermal polymerization if fully discussed, including such phenomena as depropagation, gel-effect and dead-end polymerization.

abstract: Master of Engineering (ME)


title: USING SUFFIX ARRAYS FOR LEMPEL-ZIV DATA COMPRESSION

contributor:
Smyth, William F.
Computing and Software

subject:
Other Computer Engineering
Software Engineering
Other Computer Engineering

abstract:
In the 1970s, Abraham Lempel and Jacob Ziv developed the first dictionary-based compression methods (LZ77 and LZ78). Their ideas have been a wellspring of inspiration to many researchers , who generalized, improved and combined them with run-length encoding (RLE) and statistical methods to form many commonly used lossless compression methods for text, image and sounds.

The proposed methods factor a string x into substrings (factors) in such a way as to facilitate encoding the string into a compressed form (lossless text compression). This LZ factorization , as it is commonly called today, became a fundamental data structure in string processing, especially valuable for string compression. Recently, it found applications in computing various "regularities" in strings.

The main principle of LZ methods is to use a portion of the previously seen input string as the dictionary. LZ77 and LZ78 encoders differ in two aspects. The first aspect is that LZ77 uses a sliding window unlike LZ78 which uses the entire string for building the dictionary. The use of a sliding window in LZ77 makes its decoder much simpler and faster than the LZ78 decoder. This implies that LZ77 is valuable in cases where a file is compressed once (or just a few times) and is decompressed often. A rarely used archive of compressed files is a superb example. The other aspect is the format of the codewords. LZ77 codewords consist of three parts: position, length and first non-matching symbol, while LZ78 removes the need for the length of the match in the codeword since it is implied in the dictionary.

A whole family of algorithms has stemmed out of the original LZ algorithms (LZ77 and LZ78). This was a result of an effort to improve upon the LZ encoding algorithm in terms of speed and compression ratio. Some of these variants involved the use of sophisticated data structures (e.g. suffix trees, binary search trees, etc) to hold the dictionary in order to boost the search time. The problem with such data structures is that the amount of memory required is variable and cannot be known in advance. Furthermore, some of these data structures require a substantial amount of memory. LZ is the basis of the gzip (Unix) , winzip and pkzip compression techniques.

In the testing for [1], we scaled up an LZSS implementation due to Haruhiko Okumura [37] so as to be useful for regularities (N = n , the length of the whole input string, and F equal to the full length of the unfactored suffix). We found that the binary tree approach becomes uncompetitive with algorithms that use the suffix array (SA) approach for the LZ factorization of the whole string. This observation triggered us to scale down the SA approach.

The main contribution of this thesis is a novel LZ77 variant (LZAS) that uses a suffix array (SA) to perform the searches. The SA is augmented with a very simple and efficient algorithm that alternates between searching left and right in SA to find the longest match. Suffix arrays have gained the attention of researchers in recent years due to their simplicity and low memory requirements. They solve the sub-string problem as efficiently as suffix trees, using less memory. One notable advantage of using SA in an LZ encoder is that the amount of memory is independent of the text to be searched and can be defined a priori. The low and predictable memory requirement of this approach makes it suitable for memory-critical applications such as embedded systems. Moreover, our experiments show that the processing time per letter is almost stable and hence we can predict the processing time for a file given its size. Our proposed algorithm can additionally be used for forward/ backward substring search.

In this thesis we investigate three variants of the LZAS algorithm. The first two of these variants (i.e. LZAS1 and LZAS2) use a dynamic suffix array DSA. DSA is a suffix array that can be updated whenever a letter or a factor is edited (i.e. deleted/ inserted/substituted by another letter or factor) in the original string. The suffix array of a sliding window changes whenever the window slides. Hence, we use the DSA to make sure that t he suffix array is up to date. T he DSA can be compressed using a sampling technique; therefore we decided to experiment with both sampled and non-sampled DSA. The third variant (i. e. LZAS3) re-computes the suffix array instead of updating it. We use an implementation of a suffix array construction algorithm (SACA) that requires supralinear time [28] but performs well in practice. We tested these variants against each other in terms of time and space. We further experimented with various window sizes and noticed that re-computing SA becomes better than updating it using DSA when the window size is small (i .e. hundreds of bytes compared to thousands of bytes).

abstract: Master of Science (MS)


title: POWER-AWARE SCHEDULING FOR SERVER CLUSTERS

contributor:
Down, Douglas G.
Software Engineering

subject:
Software Engineering
Software Engineering

abstract:
For the past few years, research in the area of computer clusters has been a hot topic. The main focus has been towards on how to achieve the best performance in such systems. While this problem has been well studied, many of the solutions maximize performance at the expense of increasing the amount of power consumed by the cluster and consequently raising the cost of power usage. Therefore, power management (PM) in such systems has become necessary. Many PM policies are proposed in the literature to achieve this goal for both homogeneous and heterogeneous clusters.

In this work, in the case of homogeneous clusters, we review two applicable policies that have been proposed in the literature for reducing power consumption. We also propose a power saving policy, that uses queueing theory formulas, which attempts to minimize power consumption while satisfying given performance constraints. We evaluate this policy by using simulation and compare it to other applicable policies.

Our main contribution is for heterogeneous clusters. We suggest a task distribution policy in order to reduce power consumption. Our suggested policy requires solving two linear programming problems (LPs). Our simulation experiments show that our proposed policy is successful in terms of achieving a significant power savings in comparison to other distribution policies, especially in the case of highly heterogeneous clusters.

abstract: Master of Applied Science (MASc)


title: A VLSI ARCHITECTURE AND THE FPGA IMPLEMENTATION FOR MULTI-RATE LDPC DECODING

contributor:
Nicolici, Nicola
Electrical and Computer Engineering

abstract:
Low density parity check (LOPC) codes are utilized frequently in practice as a means of forward error control or error detection. This thesis intends to provide a very large scale integration (VLSI) architecture and corresponding field programmable gate array (FPGA) based implementation for a multi-rate LDPC code.

Utilizing inherent properties in the quasi-cyclic parity check matrix construction for multiple rates, a nested node situation is exploited. This exploitation produces an architecture that, for this thesis' case study of 802.15-3c, has area savings in the check node update calculation block of roughly half the design that would support multiple rates via parallel instantiation of nodes inside the check node update calculation block.

abstract: Master of Applied Science (MASc)


title: Performance Simulation with the Coconut 1ulticore Framework for the Cell/B.E.

contributor:
Anand, Christopher
Computing and Software

subject:
Computing and Software
Computer Engineering
Computer Engineering

abstract:
The multicore revolution in chip design has fundamentally altered the demands placed on developers. Thread-level parallelism is critical to optimizing software performance on multicore chips. However thread-level parallelism presents challenges with respect to optimization, safety and program representation. Program models and compiler technologies must act as a bridge from applications to efficient hardware usage.

Coconut (COde CONstructing User Tool) is an ongoing project at McMaster to develop a platform for experimenting with novel ideas in reliable and high performance code generation, currently targeting the Cell/B.E.. The Coconut Multicore Framework uses a virtual machine abstraction layer to model multicore layer parallelism on the Cell/B.E.. The abstraction creates a correspondence between ILP and multicore layers of parallelism. The abstraction also allows us to perform efficient static analysis of virtual machine programs; with this ability we have developed a tool to automatically check for parallel bugs in linear time with respect to the atomic virtual machine instructions.

In this thesis we will discuss the creation of a performance simulation tool developed to simulate the execution of our virtual machine instructions on a Cell/B.E.. The tool has scalability to future many-core architectures, due to its linearly bounded runtime complexity. The tool allows for Coconut developers to contrast the performance of different scheduling algorithms. It provides meaningful feedback as to optimization opportunities by identifying data transfer latencies which cause execution to stall. The design and performance testing results of the performance simulation tool are presented.

abstract: Master of Science (MS)


title: THE IMPACT OF INDUCED DROUGHT ON TRANSPIRATION AND GROWTH IN A TEMPERATE PINE PLANTATION FOREST

contributor:
Arain, M. Altaf
Earth and Environmental Sciences

subject:
Environmental Sciences
Environmental Sciences

abstract:
A study evaluating the response of canopy transpiration (Ec) and growth rates to reduced water input, was conducted in a managed 70-year old planted temperate white pine (Pinus strobus L.) forest, in Southern Ontario, Canada from January to December 2009. In order to induce the drought, a 20m x 20m throughfall exclusion setup was established using interlocking aluminum troughs at a 3-inch slope. Throughfall was excluded from April 1st until July 3rd. During this period, 270mm of rainfall occurred (27% of annual precipitation) of which 90% was excluded. Sap flow velocity, soil moisture and soil temperature (at multiple depths) were measured continuously in both reference and drought plots. Dendrometer bands were also installed on all instrumented trees. Prior to enforced drought, adjacent plots showed slight variability in soil moisture while tree diameter and soil temperature did not show significant variability. Daily values of Ec from each plot ranged from 0 to 1.6 mm d-1 over the growing season (March-November) for the drought and reference plot respectively. The impact of the rainfall exclusion did not affect Ec until early June, 60 days after the drought was in place. Normalized values of Ec showed a 20% decrease from the drought trees compared to the reference. Cumulative growth rates between the two plots showed a net decrease in the drought trees of 42% from the reference and earlier termination of growth. However, the growing season Ec values were 174 mm y-l and 171 mm y-l for the drought and reference plot respectively. Currently, the effects of extreme drought
events on carbon and water balances in conifer forests are poorly understood, due
to their sporadic occurrence in natural ecosystems. The findings of this study help
to establish the impacts drought may have on these ecosystems and evaluate their
potential responses under predicted future climate regimes.

abstract: Master of Science (MS)


title: Modelling, Estimation and Control of Product Properties in a Gas Phase Polyethylene Reactor

contributor:
MacGregor, John F.
Chemical Engineering

abstract:
The focus of this thesis is the modelling and control of product propelties in gas phase polyethylene reactors. The main product properties of concern are melt index (MI) and density (p), which are related to the molecular weight and composition of the ethylene/a(alpha)-olefm copolymer. A kinetic model is developed which accounts for the effects of gas composition, reactor temperature, and active site distribution of the Ziegler-Natta catalyst on the MI and p of the polymer product. The model predicts the behaviour of MI and p in an industrial reactor , as well as broadened molecular weight distribution and bimodal composition distributions, which are typical for commercial linear polyethylenes.

Because measurements of MI and p are not available on-line, a methodology is developed to infer product properties from available measurements. Simple, theoretically-based models are derived which relate MI and p to reactor operating conditions. Parameters in the models are adjusted using off-line measurements, providing an effective means for inferring both MI and p.

In a series of three product grade changeovers, dynamic optimization is used to determine optimal profiles for: hydrogen and butene feed rates, the reactor temperature setpoint, the gas bleed flow, the catalyst feed rate, and the bed level setpoint. It is shown that large transitions in MI are hampered by slow hydrogen dynamics, and that the time required for such a transition can be reduced by manipulation of the temperature setpoint and the bleed stream flow. Reduction of the bed level and catalyst feed rates during transitions can significantly decrease the quantity of off-specification polymer produced. In the absence of feedback control, disturbances and model mismatch can result in product property trajectories which differ significantly from the nominal optimal trajectory.

A novel nonlinear model-based strategy is developed for on-line product property control. This feedforward/feedback control scheme is capable of both regulating product quality about a given target and of implementing optimal transition policies with feedback. The simplified mass balance model used in the controller design contains four adjustable parameters which are updated using an extended Kalman filter (EKF). The controller and EKF provide excellent regulatory and grade transition control for the range of poleythylene products simulated. The nonlinear controller is superior to an analogous linear time-invariant internal model control (IMC) design. The control system developed in the thesis is both simple and effective, and it has great potential for improving product quality in the polymer industry.

abstract: Doctor of Philosophy (PhD)


title: A MODIFIED SPLIT-STEP FOURIER SCHEME FOR FIBER-OPTIC COMMUNICATION SYSTEMAND ITS APPLICATION TO FORWARD AND BACKWARD PROPAGATION

contributor:
Kumar, Shiva
Electrical and Computer Engineering

abstract:
In the passed half century, great improvements have been achieved to make fiber-optic communication systems overweigh other traditional transmission systems such as coaxial systems in many applications. However, the physical features including optic fiber losses, group velocity dispersion (GVD) and nonlinear effects lead to significant system impairments in fiber-optic communications. The nonlinear Schrödinger equation (NLSE) governs the pulse propagation in the nonlinear dispersive media such as an optical fiber. A large number of analytical and numerical techniques can be used to solve this nonlinear partial differential equation (PDE). One of theses techniques that has been extensively used is split-step Fourier scheme (SSFS) which employs the fast Fourier transform (FFT) algorithm to increase the computational speed.
In this thesis, we propose a novel lossless SSF scheme in which the fast decay of the optical field due to fiber losses is separated out using a suitable transformation and the resulting lossless NLSE is solved using the symmetric SSF scheme with some approximations. The various symmetric SSF schemes in terms of accuracy for the
given computational cost are compared. Our results show that the proposed scheme could lead to one or two orders of magnitude reduction in error as compared to the
conventional symmetric SSFS when the computational cost is fixed. The proposed
scheme can be also used as an effective algorithm for digital backward propagation
(BP) too. Our numerical simulation of quadrature amplitude modulation-16 (QAM-16)
coherent fiber-optic transmission system with digital BP has shown that the bit error
rate (BER) obtained using the proposed scheme is much lower than that obtained
using the conventional SSF schemes.

abstract: Master of Applied Science (MASc)


title: TESTING EVOLUTIONARY DEVELOPMENTAL HYPOTHESES WITH SEA URCHINS: A STUDY OF PLASTICITY AND HOMOLOGY

contributor:
Stone, J. R.
Biology

subject: Biology Biology

abstract:
Sea urchins traditionally have been considered as model organisms for developmental studies, as they transform from bilaterally symmetric larvae to pentaradially symmetric adults. They are classified universally as members in the phylum Echinodermata, but skeletal homologies between the class in which sea urchins are contained and other echinoderm classes remain contested. And, culturally, the high demand for sea urchin sushi, a delicacy known as uni, has spiked interest in sea urchin farming and how to capitalize on making a commercially more-desirable food product for human consumption.
In this thesis, experiments were conducted to test evolutionary developmental hypotheses about sea urchin life history plasticity, skeleton homologies, and reproductive energetics. I found that sea urchin rudiments can be resorbed, exhibiting extreme plasticity and, thereby, functioning as capacitors for ensuring metamorphose in favourable conditions; sea urchin primary podia may be considered as nonhomologous with sea cucumber ambulacral podia, in accordance with the extra-axial theory; and gravid sea urchins fed a carrot-only diet produced gonads that were more desirable commercially than were gonads produced by sea urchins fed a seaweed and carrot diet.

abstract: Master of Science (MS)


title: THE ENGLISH PRIVY COUNCIL AND RELIEF OF DISABLED SOLDIERS, circa 1558-1625

contributor:
Alsop, J.D.
History

subject: History History

abstract:
This thesis investigates the response on the part of the government of early modern England to a new social problem. In the late sixteenth century large numbers of disabled ex-servicemen were returning to an England in which they could no longer rely on traditional patrons and methods of relief for charity. The Privy Council's reaction to this phenomenon, from its initial response of moral suasion and the use of the royal prerogative to its ultimate response - sponsoring and attempting to enforce legislation, is examined for the period 1558-1625.

Unlike other poor relief legislation the relief of maimed veterans in this period has received no comprehensive treatment by historians. This study contributes to an enhanced understanding of poverty and poor relief measures. It sheds light on the social dynamics of the period, particularly what the Privy Council and soldiers perceived as the proper functioning of the social order. In addition, our grasp of the Council's role in the development and administration of social policy is improved. This examination of the Privy Council's involvement in the relief of disabled soldiers also illuminates the nature of its political relations with Parliament, and, more significantly, with local county authorities.

The study of the origins of legislated veteran's benefits is an important step towards a more comprehensive discussion of the relatively overlooked social and political impact of demobilization on early modern England.

abstract: Master of Arts (MA)


title: The 'New Eugenics:' Psychiatry and Mental Health in Post-World War II Canada

contributor:
Wright, D.
History

subject: History History

abstract: Master of Arts (MA)


title: Biosynthesis of the Pyrrolidine Ring in Plants

contributor:
Spenser, Ian D.
Chemistry

subject: Chemistry Chemistry

abstract: DL-[5-³H,5-¹⁴C]ornithine and DL-[2-³H,5-¹⁴C]ornithine were administered to intact tobacco plants (Nicotiana tabacum) in separate experiments. Proline, ornithine and nicotine were isolated. The ³H:¹⁴C ratio in proline derived from DL-[5-³H,5-¹⁴C]ornithine was the same as that in the reisolated ornithine, whereas proline derived from DL-[2-³H,5-¹⁴C]ornithine contained ¹⁴C but lost almost all tritium relative to ¹⁴C. This evidence definitely excludes 5-oxo-2-aminopentanoic acid and Δ¹-pyrroline-5-carboxylic acid as intermediates on the route from ornithine to proline. These results together with earlier work are interpreted to show that proline is derived from ornithine via 2-oxo-5-aminopentanoic acid and Δ¹-pyrroline-2-carboxylic acid. The ³H:¹⁴C ratios found in nicotine samples isolated from experiments using DL-[5-³H,5-¹⁴C]ornithine and DL-[2-³H,5-¹⁴C]ornithine are consistent with the accepted route from ornithine via 1,4-diaminobutane, mono-N-methyl-1,4-diaminobutane, 4-methylaminobutanal, and N-methylpyrrolinium ion. The ³H:¹⁴C ratio found in nicotine derived from DL-[5-³H,5-¹⁴C]ornithine is interpreted as showing that oxidation of mono-N-methyl-1,4-diaminobutane to 4-methylaminobutanal proceeds with loss of the 4(S)-hydrogen.

abstract: Master of Science (MS)


title: INKJET PRINTED CONDUCTIVE INKS FOR THE FABRICATION OF ORGANIC THIN FILM TRANSISTORS

contributor:
Zhu, Shiping
Wu, Yiliang
Chemical Engineering

abstract:
In recent years, there has been a strong interest in the use of drop-on-demand inkjet printing for the fabrication of organic thin-film transistors (OTFTs). This method would allow for roll-to-roll fabrication of low-end, disposable, and large-area electronics such as RFID tags, sensors, and flexible displays at a small fraction of the current costs. A great deal of research has already yielded new materials which are solution processable and have demonstrated excellent perfonnance when incorporated into OTFTs. One of the largest obstacles to the commercialization of this technology is the development of a successful strategy for the inkjet printing process. In order for this printing process to be successful, it must be able to deposit the components of the OTFTs such that they have sufficient resolution, excellent film thickness unifonnity and excellent perfonnance.

Here a strategy is developed which allows for high resolution printing of source and drain electrodes with excellent film uniformity. By simultaneously optimizing dot-to-dot spacing and solvent composition, near-perfect film uniformity and very high resolution can be obtained. Resolution is further improved via increasing the viscosity of the ink and decreasing the surface roughness of the substrate.

The inkjet printing system is further investigated and optimized for printing with silver nanoparticle ink. By using the design of experiments method, we detennined the independent influence of silver nanoparticle mass fraction, solvent composition, substrate surface energy, substrate temperature and dot-to-dot spacing on printed line width, line thickness and film uniformity. Furthennore, this method also allowed for the detennination of the influence of variable interaction, allowing a complete understanding of the system to be developed. This knowledge was used to develop a non-linear computer optimization program such that optimal variable settings could be detennined. As a result of this study, highly conductive silver lines with excellent resolution and film uniformity were inkjet printed and incorporated in high perfonnance OTFTs.

A novel method for printing source and drain electrodes with a very small channel length was also developed. A silver nanoparticle ink with a large concentration of free alkylamine stabilizer was used in this study. The excess alkylamine formed a hydrophobic boundary around printed silver features, which repelled any ink subsequently deposited near the original feature. This allowed for source and drain electrodes to be printed with very narrow channel length with no need for any intelmediate processing steps. Furthennore, the self-alignment nature of this technique allowed the process to automatically correct for slight printing errors, resulting in transistor arrays with very narrow channel length distributions.

abstract: Master of Applied Science (MASc)


title: THE SPINAL CORD INJURY ACTIVE LIVING GUIDE: USEFUL AND DESIRED CONTENT TO ENCOURAGE A HEALTHY AND ACTIVE LIFESTYLE

contributor:
Martin Ginis, Kathleen A.
Kinesiology

subject: Kinesiology Kinesiology

abstract:
Regular physical activity for people with spinal cord injury (SCI) has been related to numerous benefits, yet half of this population remains inactive (Martin Ginis et aI.,2010). The SCI community desires useful physical activity infonnation (Boyd & Bardak, 2004). It has been suggested that Canada's Physical Activity Guide for Adults Living with SCI (CPAG-SCI) be created (Martin Ginis & Hicks, 2007). This study sought to detemline what people with SCI would find useful in CP AG-SCI and to establish effective means for providing infonnation to maximize thoughts about being physically active. Firstly, 78 people with SCI (M(age)=45.06) were asked what content to include in CPAG-SCI and how to present it. Participants indicated that physical activity knowledge, motivational infonnation, safety and health infonnation, sources of infonnation and social support, and self-regulation infonnation were desired. CPAG-SCI as a booklet or interactive website was preferred (both 43.6%), text with pictures (83.3%), photographs (57.7%), bright colours (48.7%), simple messages (61.5%), and a calendar pull-out (70.5%). Secondly, the effectiveness of an experimental vignette aimed at changing physical activity social cognitions was explored. Based on the Health Action Process Approach (Schwarzer, 1992; 2004), participants were classified as in the motivational (n=32, M(age)=45.31) or volitional phase (n=47, M(age)=43.36), and then randomly assigned to an experimental or control vignette exposure condition. Social cognitions were measured one-week before, and immediately following, exposure to the vignette. Repeated measures ANOVAs showed that social cognitions generally decreased in those exposed to the experimental vignette, with coping plans approaching a significant decrease among those in the motivational phase (t(17) =2.10, p<.05). Exploratory analyses suggest that perceived similarity to the vignette character may be a key variable contributing to the ineffectiveness of the experimental vignette. Overall, it is suggested that physical activity vignettes in CPAG-SCI not target social cognition change.

Keywords: spinal cord injury, physical activity, vignette, perceived similarity, social cognitions

abstract: Master of Science (MS)


title: ALL-FIBER VIBRATION SENSORS FOR STEEL INDUSTRY

contributor:
Xu, Chang-qing
Engineering Physics

subject:
Engineering Physics
Engineering Physics

abstract:
This thesis explores the design, fabrication, and experimental application of a variety of all-fiber vibration sensors, based upon a Michelson interferometer design. These sensors can be used to detect vibration in the low frequency regime. It also provides motivation for its use as an inexpensive yet rugged sensor for use in the harsh environment of a steel hot mill as part of an overall preventative/predictive maintenance program since commercially available piezoelectric sensors currently in use have significant reliability problems.

While this work did result in a device that could withstand the steel hot mill surroundings and detect low frequency vibrations, higher sensitivities are expected from further optimized devices.

abstract: Master of Applied Science (MASc)


title: COMPARISONS BETWEEN ALGORITHMS TO CONSTRUCT THE RECEIVER OPERATING CHARACTERISTIC (ROC) CURVE FOR MULTIPLE SCREENING/DIAGNOSTIC TESTS

contributor:
Walter, Stephen D.
Statistics

subject:
Statistics and Probability
Statistics and Probability

abstract: Cancer can be an extremely aggressive disease, with a poor survival rate among the patients that are in the advanced stages of the disease. Early intervention can significantly affect the outcome of the disease. The requirement of early intervention necessitates a reliable cancer screening. Regular use of screening, followed by timely treatment when cancer is diagnosed, can help decrease the chances of occurrence of death due to cancer. There are several tests available for the early detection and diagnosis of cancer. When multiple diagnostic tests are performed on an individual or multiple disease markers are available it may be possible to combine the information to diagnose disease. By combining multiple tests we can optimize diagnostic accuracy. The combination of ultrasound and mammography as markers for cancer diagnosis could be useful for early intervention. Selecting a statistical tool capable of assessing the performance of a combination of different diagnostic tests is important in selecting the most suitable diagnostic standard. One way of determining the performance of any combination of diagnostic tests is through the use of the receiver operating characteristic (ROC) curve. Baker (2000) proposed three ranking algorithms that optimize the ROC curve. The objective of this study was to develop and select the ranking algorithm which provides the optimal area under the ROC curve to differentiate cancer from benign. Statistically, unordered algorithms proved to be the best among the three algorithms giving average AUCs of 0.96510, followed by Jagged Ordered Algorithm and Rectangular Ordered Algorithm giving average AUCs of 0.96396 and 0.94314 respectively. Clinically, ordered algorithms seem to be the better choice due to their convenience.

abstract: Master of Science (MS)


title: TOOL-ASSISTED KNOWLEDGE TO HL7 v3 MESSAGE TRANSLATION

contributor:
Sartipi, Kamran
Computing and Software

abstract:
Healthcare System Integration is an area of utmost importance in the overall eHealth
strategy of Ontarios provincial government as well as the federal government of Canada. A large body of researchers from various governmental and non-governmental
organizations are actively engaged in delivering solutions to integrate disparate healthcare information systems. The overall goal of these efforts is to provide a provincewide and nation-wide unified view of clinical information to healthcare practitioners, thereby enabling them to deliver accurate and timely services to the general public in a cost-efficient manner.
While the need for health information integration is clear, due to inherent complexities
of the healthcare domain as well as health information standards such as Health Level 7 (HL7), completion of such projects within budget and time is not an easy task. The goal of this study is to understand and analyze the information architecture behind HL7 version 3 (HL7 v3) with the aim of simplifying healthcare system integration process. In this thesis, we present a novel framework for extracting HL7 v3 messages to represent healthcare transactions that take place in an integration scenario. We have developed a prototype tool based on semantic web (SW) technologies to support our approach. We also present three healthcare case studies to demonstrate our solution.

abstract: Master of Applied Science (MASc)


title: EXACT QUANTUM DYNAMICS OF SPIN SYSTEMS USING THE POSITIVE-P REPRESENTATION

contributor:
Sörensen, Erik
Physics and Astronomy

subject:
Physics and Astronomy
Astrophysics and Astronomy
Physics
Astrophysics and Astronomy

abstract: In this thesis, we discuss a scheme for simulating the real time quantum quench dynamics of interacting quantum spin systems within the positive-P formalism. As model systems we study the transverse field Ising model as well as the Heisenberg model undergoing a quench away from the classical ferromagnetic ordered state. The connection to the positive-P formalism, as it is used in quantum optics, is established by mapping the spin operators on to Scwhwinger bosons. In doing so, the dynamics of the interacting quantum spin system is mapped onto a set of stochastic differential equations (SDEs) the number of which scales linearly with the number of spins, N, compared to an exact solution through diagonalization that in the case of the Heisenberg model would require matrices exponentially large in N. This mapping is exact and can be extended to higher dimensional interacting systems as well as to systems with an explicit coupling to the environment.

abstract: Master of Science (MS)


title: Vision-based Resource Constrained Event Detection for Medical Smart Homes

contributor:
Shirani, Shahram
Deen, Jamal M.
Electrical and Computer Engineering

abstract:
As the number of elderly persons as well as their fraction of the total population
continues to rise, especially in the developed countries, providing an appropriate living
environment for them using smart home technology is rapidly gaining attention. Two
important tasks of a smart home technology are monitoring the daily activities and
the vital signs of the elderly to improve their quality of life and to monitor existing
or the onset of health abnormalities. In this thesis, we focus on the monitoring of
taking medicine by the elderly person using vision sensors (low-cost cameras). This
task is important since it helps both the person and the doctor in the treatment
of illnesses of elderly persons. The allocated resources of communication bandwidth
between the sensor nodes and the computational power, used for this task, affect
the implementation cost. Therefore, it is desired to develop an effective scheme
which efficiently allocates bandwidth and computational resources to achieve a high
reliability (detection performance) at low cost.
In this thesis, we have proposed two different approaches to solve this detection
and monitoring problem. As the input data are video frames, captured by cameras
from the same scene, the frames have inter-view redundancy. Taking advantage of
this inter-view redundancy, we proposed a video coding classification scheme based
on separate encoding and joint decoding, and have obtained significant compression
improvement compared to existing techniques. In the second approach, we studied
different parts of the detection and monitoring system to find an efficient design
for distribution of different event detection parts between the nodes and the central
processing unit so that the allocated resources are reduced. In this scheme, the
useful information of the frames are extracted in the form of their main features
such that decision making based on these features is the same as decision making
based on the raw frames. As a result, we could propose a new scheme which requires
significantly less bandwidth and computational resources while achieving the same
detection performance.

abstract: Master of Applied Science (MASc)


title: A Multiple-FPGA Parallel Computing Architecture for Real-time Simulation of Deformable Objects

contributor:
Sirouspour, Shahin
Electrical and Computer Engineering

abstract:
In recent years there has been a growing interest in computer-based surgical planning,
virtual-reality enabled training of medical procedures, and computer gaming all involving non-rigid deformable objects. High-fidelity simulations of haptic interaction with deformable objects is computationally demanding. The Finite Element Method (FEM) is known to produce relatively accurate solution for continuum mechanics-based models of soft-object deformation. Linear elastic FE models require solving a large sparse system of equations. The solution accuracy can be improved by increasing the resolution of the finite element mesh resulting in a larger number of equations and hence greater computational complexity. Depending on the mechanical characteristics of the soft-object, to maintain stability and high fidelity in haptic interaction, the update rate should be in the range of 1001000Hz. This, for example, means that for a moderately-sized three-dimensional mesh of 6000 nodes, a set of 18000 linear equations must be solved within 1-10ms.

In this thesis, hardware-based parallel computing is proposed for finite-element
(FE) analysis of soft-object deformation models. In particular, a distributed implementation of the (CG) algorithms on .\' Field Programmable Gate Array (FPGA)
devices connected in a ring configuration is developed. This Parallel architecture
can be utilized to solve the large system of equations arising from FE models at high update rates required for stable haptic interaction. Massive parallelization of the computations is achieved by customizing the hardware architecture to the problem at hand and employing a large number of adaptive fixed-point computing units in parallel. The proposed hardware architecture satisfies three important criteria: (i) it meets the haptic rendering timing constraint by enabling an update rate of 400Hz; (ii) it attempts to simulate as many nodes as possible, given the available resources on the FPGA devices employed in this work and (iii) it is scalable both within an FPGA and also across multiple FPGA devices.
This research builds upon our group's earlier work in [1]. In that paper a novel highly parallelized single-FPGA architecture was proposed for solving system of equations arising from FEM using Conjugate gradient method. In this thesis, a multiple-FPGA architecture based on that design has been proposed. The contributions in the new multiple-FPGA design can be summarized as follows.

abstract: Master of Applied Science (MASc)


title: A Theoretical Calculation of Quasiparticle Properties in Aluminum

contributor:
Carbotte, J.P.
Physics

subject: Physics Physics

abstract:
Theoretical calculations of the renormalization of the electron mass and the quasiparticle lifetime due to the electron-phonon interaction are performed in aluminum as a function of position on the Fermi surface. The computations are carried out at finite temperature, and, in the case of the relaxation time, for finite energy above the Fermi surface.

We present a formal development of expressions for the mass renormalization parameter and lifetime at finite temperature to second order in the electron-phonon interaction using a perturbation-theory approach, which is mathematically simpler, if less elegant, than the usual Greensfunction method. The behaviour of the resulting integrals is discussed briefly with reference to their numerical evaluation.

Our results for the electron mass renormalization at finite temperature agree qualitatively with the expected variation of the electron wavefunctions on the Fermi surface. In terms of the results, the approximate requirements for experimental observation of the calculated increase in electronic effective mass and its anisotropy are discussed.

A comparison of the calculated temperature dependence of the quasiparticle lifetime with experiment and with other theoretical work has important implications for the accuracy of electron phonon numerical calculations in the low-frequency region.

abstract: Master of Science (MS)


title: NONLINEAR MODEL PREDICTIVE CONTROL DESIGN AND APPLICATIONS

contributor:
Mhaskar, Prashant
Chemical Engineering

abstract:
This thesis considers the problem of nonlinear predictive control design and applications. A predictive control formulation is presented which expands on the set of initial conditions for which closed-loop stability can be achieved. The key idea in this control design is to utilize control-law independent characterization of the process dynamics subject to constraints via model predicative controllers. An application of this idea is presented to the case of linear process systems for which characterizations of the null controllable region (the set of initial conditions from where closed-loop stability can be achieved subject to input constraints) are available. A predictive controller is designed that achieves closed-loop stability for every initial condition in the null controllable region. For nonlinear process systems, the constraints within the predictive controller are formulated to require the process to evolve within the region from where continued decay of the Lyapunov function value is achievable and incorporated in the predictive control design, thereby expanding on the set of initial conditions from where closed-loop stability can be achieved. The proposed method is illustrated using a chemical reactor example, and the robustness with respect to parametric uncertainty and disturbances demonstrated via application to a styrene polymerization process.

In addition, we also consider the application of the predictive control design to the problem of handling actuator faults in nonlinear continuous-time processes and transport-reaction systems. Specifically, we consider faults that preclude the possibility of continued operating at the nominal equilibrium point using the existing robust or reconfiguration-based fault-tolerant control approaches. The key consideration is to operate the plant using the depleted control action at an appropriate safe-park point to prevent onset of hazardous situations as well as enable smooth resumption of nominal operation upon fault-repair. For the case of continuous-time nonlinear process systems we consider the presence of input constraints, uncertainty, and availability of limited measurements. First a Lyapunov-based predictive controller with an explicitly characterized stability region is developed to handle the aforementioned conditions. This control design is then subsequently used to develop a safe-parking framework in the presence of uncertainty, and availability of limited measurements. The proposed framework is illustrated using a chemical reactor example and demonstrated on a styrene polymerization process. Finally, we consider the problem of model predictive control and handling actuator faults in transport-reaction processes described by quasi-linear parabolic partial differential equations (PDEs) subject to input constraints. A Lyapunov-based model predictive controller is designed which accounts for the distributed nature of transport-reaction processes and provides an explicit characterization of the set of initial conditions from where closed-loop stability of the parabolic PDE system is guaranteed. Similar to the continuous time case, this control design is then subsequently used to develop a safe-parking framework for handling actuator faults in transport-reaction processes. The proposed framework is illustrated on a diffusion-reaction process

abstract: Master of Applied Science (MASc)


title: Echo Planar Spectroscopic Imaging and 31P In Vivo Spectroscopy

contributor: Charles Cunningham, Ph.D and Michael Patterson, Ph.D

subject:
mri
nmr
spectroscopic imaging
phosphorus spectroscopy
Biological and Chemical Physics
Biomedical devices and instrumentation
Radiology
Biological and Chemical Physics

abstract:
The work in this thesis deals with pre-clinical development of rapid in vivo 31P mag- netic resonance spectroscopy (MRS) techniques. Current MRI literature of 31P spec- troscopy presents evidence of increased concentrations of phosphomonoesters (PME), and phosphodiester (PDE) as well as inorganic phosphate concentrations in tumor tissue. Human breast cancer studies have demonstrated correlation between disease progression and both PME and PDE peaks. Furthermore, 31P MRS can be used to detect, grade tumours and monitor response to chemo and radiation therapy.
Tumor measurements are typically static (i.e. single measurement per scan). In other experiments, on muscle for example, dynamic measures are required the purpose of which is to assess temporal function and recovery. In all 31P acquisitions there are problems surrounding RF coil design, pulse sequence speed, localization and system calibration. The work presented here focused on improving all these aspects and provide easy and reliable work flow to use 31P MRS in a clinical setting.
One of the aspects of this thesis lies in designing and construction of an RF coil that is well suited for integration with a clinical MRI breast imaging and biopsy system. The designed coil was tuned for simultaneous operation at 31P (51.73 MHz) and 1H (127.88MHz) Larmor frequencies. This design has advantages in the fact that complex pulse sequences with heteronuclear decoupling could be performed easily. The additional features of the coil design is that it is possible to swap it into the breast imaging system without moving the patient. Along with the designed coil, custom software was written to assist with transmit gain calibration of 31P RF pulses, to ensure maximum MR signal. The automated prescan ensures easy work flow and minimizes the operator variability and patient time inside the MR scanner.
Another aspect of this thesis deals with rapid pulse sequence development, to further speed up the 31P MRS data acquisition. Echo planar spectroscopic imaging (EPSI) with a fly–back gradient trajectory is currently one of the most reliable and robust techniques for speeding up chemical shift imaging (CSI) acquisitions. A 31P EPSI sequence was written to acquire spectroscopic imaging data at 1, 2 and 2.6 cm spatial resolution and spectral bandwidth of 3125 Hz. The sequence showed an ability to speed up data acquisition up to 16 times, where SNR permits.
Phantom studies were used to verify the double tuned coil and EPSI sequence en- suring proper and safe operation. In vivo measurements of an exercising muscle demonstrated the ability of 31P EPSI to play an important role in rapidly acquiring spatially localized 31P spectroscopic data.
With these preclinical developments in place a clinical trial is possible using 31P MRS rapidly and efficiently. Furthermore the increased usability of 31P MRS provided by the tools developed in this thesis can prove to be beneficial by integrating 31P MRS into existing clinical protocols.

abstract: Doctor of Science  (PhD)


title: A Tabular Expression Toolbox for Matlab/Simulink

contributor:
Lawford, Mark
Computing and Software

subject:
software engineering
formal methods
tabular exressions
model-based design
simulink
Software Engineering
Software Engineering

abstract:
Model based design has had a large impact on the process of software development in many different industries. A lack of formality in these environments can lead to incorrect software and does not facilitate the formal analysis of created models. A formal tool known as tabular expressions have been successfully used in developing safety critical systems, however insufficient tool support has hampered their wider adoption. To address this shortfall we have developed the Tabular Expression Toolbox for Matlab/Simulink.

We have developed an intuitive user interface that allows users to easily create, modify and check the completeness and disjointness of tabular expressions using the theorem prover PVS or SMT solver CVC3. The tabular expressions are translated to m-functions allowing their seamless use with Matlab's simulation and code generation. We present a method of generating counter examples for incorrect tables and a means of effectively displaying this information to the user. We provide support for modelling inputs as floating point numbers, through subtyping a user can show the properness of a table using a more concrete representation of data. The developed tools and processes have been used in the modelling of a nuclear shutdown system as a case study of the practicality and usefulness of the tools.

abstract: Master of Applied Science (MASc)


title: Development of Paper-based Devices for Diagnostics and Biosensing

contributor:
Filipe, Carlos
Pelton, Robert
Dr. Todd Hoare and Dr. Emily Cranston
Chemical Engineering

subject:
Paper-based devices
microfluidics
biosensors
diagnostics
Other Chemical Engineering
Other Chemical Engineering

abstract:
Research in paper-based analytical devices has been increasing rapidly in recent years. Manyof these devices are used as low-cost alternatives for diagnostics and biosensing. In this work,two novel paper-based technologies were developed.

The first paper-based technology achieved was measuring streaming potential on paper-based microfluidic devices. The streaming potential measurements were able to detect the presence of adsorbed polyvinylamine or potassium polyvinylsulfate in paper-based microfluidic channels.

The measured streaming potential ranged from -80 mV to 80 mV and the polarity was sensitive to the adsorbed polymer. Furthermore, the measured streaming potential on paper treated with BSA showed a polarity switch when the pH was changed from below the pKa to above the pKa of BSA. Lastly, streaming potential measurements may provide an electronic interface for paperbased sensors.

The second technology developed was a paper-based chromatographic pre-concentration device for biological and chemical applications. The device successfully concentrated a protein, streptavidin, via biotinylated microgels immobilized onto a selected area of the filter paper. The device was able to process a large volume of fluid with the incorporation of a passive pump made of superabsorbent polymer. The concentration factor achieved by the device was over 3000-fold. The flow dynamics through the paper was modeled using Darcy’s law. This technology could be an excellent low-cost alternative for biochemical analysis for samples thatrequire preconcentration, especially for the analysis of trace compounds in wastewater and drinking water.

abstract: Master of Applied Science (MASc)


title: Statistical Issues in a Meta-analysis of Studies of Integrated Treatment Programs for Women with Substance Use Problems and Their Children

contributor:
Thabane, Lehana
Statistics

abstract:
Meta-analysis is a statistical technique for combining findings from independent studies. A meta-analysis was performed to evaluate the effectiveness of integrated treatment programs for women with substance use issues and their children. Primary outcomes included substance use, maternal and child well-being, length of treatment, and parenting. A total of 9 randomized controlled trials (RCTs) and 84 observational studies were included in the final analysis. The p-value and capture re-capture method, were used to combine studies using different measures of treatment effect and evaluate the completeness of the literature search, respectively. Modified weights incorporating study quality were used to assess the impact of study quality on treatment effects. We also conducted a sensitivity analysis of correlation coefficients on combined estimates as a method for handling missing data.

Study quality adjusted weighting and traditional inverse variance weights provided different results for combined estimates of birth weight outcomes measured by standardized mean difference. The results from weighting by study quality provided a statistically significant result with a combined estimate of 0.2644 (95% CI: 0.0860, 0.4428), while the traditional method gave a non-significant combined estimate of 0.3032 with (95% CI: -0.0725,0.6788). The sensitivity analysis of correlation coefficients (r) on combined estimates of maternal depression effects were similar, with confidence intervals that narrowed as r increased. Values ofr = 0.2, 0.5, 0.65, 0.75, and 0.85 gave corresponding results (with 95% CI) of 0.67 (-0.10, 1.45), 0.67 (0.04, 1.3), 0.67 (0.12, 1.2),0.67 (0.18, 1.15), and 0.66 (0.25, 1.07). Robustness of the sensitivity analysis for study quality weighting and choice of correlation coefficient on combined estimates revealed benefits of integrated treatment programs for birth weight outcomes and maternal depression.

Evidence of benefit for at least some of the clients was apparent for parenting attitude measured by the Adult-Adolescent Parenting Inventory (AAPI). Results for each subscale of the AAPI were reported by timing of assessments (=< 4,5-8, => 9 months). Combined p-values were 0.0006, <0.0001, <<0.0001 for Inappropriate Expectations, 0.1938, 0.1656, <<0.0001 for Lack of Empathy, 0.0007, <0.0001 <<0.0001 for Corporal Punishment, 0.0352, 0.0002, <<0.0001 for Role Reversal, and 0.5178 (5-8 months) for Power Independence. There was insufficient evidence for concluding a significant effect of treatment on neonatal behavioural assessments measured by Apgar scores. Combined p-values of 0.6980 and 0.3294 were obtained for the 1-minute and 5-minute Apgar, respectively.

The number of missing articles estimated by the capture recapture method was 8 (95% CI: 2,24), which suggests a 90% capture rate of all relevant world literature. This result indicates that a sufficient amount of studies were retrieved to avoid bias in the results of the meta-analysis.

Conclusions regarding the effectiveness of integrated treatment programs were limited by poor quality evidence from individual studies. We suggest the use of statistical methods such as the p-value, capture re-capture, study quality weighting, and sensitivity analysis of correlation coefficients to handle missing data to address meta-analytic research questions and direct higher quality research in the future.

abstract: Master of Science (MS)


title: THE HYDROLOGICAL EFFECTS OF FRACTIONAL WETTABILITY AND CONTACT ANGLE DYNAMICS IN WATER REPELLENT POROUS MEDIA

contributor:
Smith, James E.
Earth and Environmental Sciences

subject:
Earth and Environmental Sciences
Other Environmental Sciences
Other Environmental Sciences

abstract:
Soil water repellency is a spatially and temporally variable near surface phenomenon most often associated with reduced or impeded infiltration into porous media. In recent years, soil water repellency (hydrophobicity) has garnered much attention in the literature due to its detrimental effects on soil water processes and its widespread observance allover the world in both rural and urban settings. While previous work has developed our understanding of these inherently complex systems, insight into their dynamic and variable nature is still lacking. Having utilized existing technologies in a new way, in this study we present a series of systematic field and laboratory based investigations that clarify the roles of fractional wetting and contact angle dynamics on soil water processes using hydrophobic materials found at a wildfire site approximately 1.5 years post-fire. The robust and fundamental approach taken in investigating
water repellency in these materials provided the foundation to develop two conceptual models based on our observations and with respect to existing and emerging theory. These models better explain soil water behaviour in hydrophobic systems than is currently afforded by the literature. We found that wetting and infiltration processes are contingent upon the functional relationship between wettable fractions of materials and the rate of contact angle change in non-wettable fractions.

abstract: Master of Science (MS)