title: Multi-scale thermal and circuit analysis for nanometre-scale integrated circuits

contributor:
Shang, Li
Knobel, Robert
Electrical and Computer Engineering

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subject:
multi-scale system analysis
simulation methods
thermal analysis
circuit analysis

abstract: Thesis (Master, Electrical & Computer Engineering) -- Queen's University, 2008-09-26 13:33:12.389

abstract:
Chip temperature is increasing with continued technology scaling due to increased power density and decreased device feature sizes. Since temperature has significant impact on performance and reliability, accurate thermal and circuit analysis are of great importance. Due to the shrinking device feature size, effects occurring at the nanometre scale, such as ballistic transport of energy carriers and electron tunneling, have become increasingly important and must be considered. However, many existing thermal and circuit analysis methods are not able to consider these effects efficiently, if at all. This thesis presents methods for accurate and efficient multi-scale thermal and circuit analysis. For circuit analysis, the simulation of single-electron device circuits is specifically studied.

To target thermal analysis, in this work, ThermalScope, a multi-scale thermal analysis method for nanometre-scale IC design is developed. It unifies microscopic and macroscopic thermal physics modeling methods, i.e., the Boltzmann transport and Fourier modeling methods. Moreover, it supports adaptive multi-resolution modeling. Together, these ideas enable efficient and accurate characterization of nanometre-scale heat transport as well as chip-package level heat flow. ThermalScope is designed for full chip thermal analysis of billion-transistor nanometre-scale IC designs, with accuracy at the scale of individual devices. ThermalScope has been implemented in software and used for full chip thermal analysis and temperature-dependent leakage analysis of an IC design with more than 150 million transistors.

To target circuit analysis, in this work, SEMSIM, a multi-scale single-electron device simulator is developed with an adaptive simulation technique based on the Monte Carlo method. This technique significantly improves the time efficiency while maintaining accuracy for single-electron device and circuit simulation. It is shown that it is possible to reduce simulation time up to nearly 40 times and maintain an average propagation delay error of under 5% compared to a non-adaptive Monte Carlo method. This simulator has been used to handle large circuit benchmarks with more than 6000 junctions, showing efficiency comparable to SPICE, with much better accuracy. In addition, the simulator can characterize important secondary effects including cotunneling and Cooper pair tunneling, which are critical for device research.

abstract: M.Sc.


title: Training-induced plasticity in the visual cortex of adult rats following visual discrimination learning

contributor:
Dringenberg, Hans C.
Psychology

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rights: This publication is made available by the authority of the copyright owner solely for the purpose of private study and research and may not be copied or reproduced except as permitted by the copyright laws without written authority from the copyright owner.

subject: LTP plasticity

abstract: Thesis (Master, Psychology) -- Queen's University, 2008-09-25 12:28:27.468

abstract:
Synaptic plasticity plays a key role in processes of learning and memory. Long-term potentiation (LTP) is a relatively stable enhancement of synaptic transmission following specific patterns of electrical stimulation. Some types of learning (e.g. motor learning, fear conditioning) result in
LTP-like changes at synapses. However, no studies have examined LTP-like plasticity in the visual cortex as a result of visual discrimination learning.
A visual discrimination task was used to examine changes in LTP in the primary visual
cortex (V1) of adult rats. Rats were placed in a Y-shaped water maze and required to swim to one choice arm containing a hidden platform. Distinct visual cues indicated the presence (CS+) and absence (CS-) of the platform. Rats learned to reliably discriminate the visual cues to successfully
navigate the maze. Control rats received the same procedure, but the visual cues did not have a predictive relation with the platform. Following training, trained, control, and task-naïve rats were
anesthetized and visual evoked potentials (VEPs) in V1 were recorded in response to CS+, CS-, and novel stimuli.
Results indicate that, in both task-naïve and control animals, all visual stimuli elicit VEPs of similar (p > 0.05) amplitude. In contrast, trained animals show significantly larger amplitude VEPs to stimuli encountered during training relative to novel stimuli, regardless of whether
stimuli act as CS+ or CS-. In addition, trained animals show 71% and controls 47% potentiation (p < .05) that was induced by electrical (theta-burst) stimulation of the lateral geniculate nucleus (LGN) indicating greater plasticity of thalamocortical synapses following training. There were no
differences between controls and task-naïve animals. This facilitation of LTP was shown to allow past visual experience to influence the efficiency of encoding novel visual features.
These experiments demonstrate that visual discrimination learning might involve
stimulus-selective facilitation of neuronal responses at early stages of visual processing (LGN, V1). The effect requires that stimuli carry some significance to the animal, while exposure to stimuli with no significance does not result in the same level of neuronal enhancement. Further,
visual experience alters the plasticity properties of V1 (metaplasticity) by facilitating LTP along thalamocortical sensory fibers.

abstract: M.Sc.


title: Deformable Registration to Create Cytoarchitectonic Probability Maps for Functional Analysis of Primary Auditory Cortex

contributor:
Johnsrude, Ingrid S.
Abolmaesumi, Purang
Computing

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subject:
Computer Science
Neuroscience
Medical Image Processing
Brain
Functional Magnetic Resonance Imaging
Auditory Cortex
Region of Interest Analysis
Primate Homologies
Cytoarchitecture

abstract: Thesis (Master, Computing) -- Queen's University, 2008-09-26 19:50:54.582

abstract: A novel method is presented for analyzing fMRI data, which relies on probabilistic estimates of microanatomically defined regions in individual fMRI volunteers. Postmortem structural and cytoarchitectonic information from the Julich/Dusseldorf group in Germany is aligned to the high-resolution structural MR images of functional MRI volunteers. This is achieved using nonlinear registration, which is applied only to the region of interest. The registered postmortem datasets are then combined into probability maps for microanatomically defined regions that are tailored to the anatomy of individual fMRI volunteers. These are then used as weighted spatial filters on functional MR data. In this thesis, three regions of the primary auditory cortex (located on Heschl's gyrus) have been targeted, and the analysis method is used to explore how these three areas respond to different kinds of sound. Regions Te1.0 and Te1.2 both demonstrate pitch sensitivity, consistent with published observations of the functional response of homologous regions in nonhuman primates. Area Te1.1 displayed sensitivity to both noise and pitch, consistent with the theory that it is homologous with the microanatomically similar area CM in nonhuman primates. Furthermore, the custom probability maps are much less diffuse and anatomically more precise than previous versions generated using the same postmortem data, and therefore permit a more sensitive and anatomically precise analysis of functional activity. This method could be applied to any other microanatomically defined region that has been characterized in the Julich postmortem dataset.

abstract: M.Sc.


title: “Methinks I see in my mind a noble and puissant nation” Milton, Print, and Nationhood

contributor:
Straznicky, Marta
Sauer, Elizabeth
English

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subject:
Milton, John
Nationalism
Print culture
Political Culture

abstract: Thesis (Ph.D, English) -- Queen's University, 2008-09-25 15:22:21.28

abstract:
Abstract
     This study begins by examining the interconnections between print and nationalism in John Milton’s prose works in order to demonstrate that Milton’s interest in print—including print-related activities like reading, writing, and publishing—is not simply a byproduct of his vocation.  Instead, I argue that Milton consciously registered his reliance on and use of print in writing the nation. Further, I argue that Milton’s writing of the nation is in keeping with a modern definition of nationalism as a unifying cultural construct that wields considerable emotional poignancy despite its lack of ideological specificity.  In making this argument, I am adapting a modern definition of nationalism and arguing against scholars who see nationalism as a product of modernity.
     I organize my dissertation into two sections: the first section, chapters 2 and 3, discusses the confluence of print and nationalism while the second section, chapters 4 and 5, examines Milton’s poems, Paradise Lost and Samson Agonistes, as nation-building texts.  As chapters 2 and 3 demonstrate, Milton had an acute awareness of the role of print in the public life of the nation, and he shaped his own identity as an author based on his contribution to England’s print culture.  In chapters 4 and 5, I look at the ways Milton’s poems suggest a continuation of his commitment to nation-building although the poems were written during the Restoration: a period of time when Milton would have doubted the critical capabilities of his fellow countrymen.  Paradise Lost continues the recuperative work undertaken in prose pieces like Eikonoklastes by helping to educate the reader in political reading.  In Samson Agonistes, Milton explores the way that the individual and nation are vulnerable to the same sort of corruption which emphasizes the degree to which inward and outward servitude is linked.  Yet, neither poem gives up on “nationalism” as a source of individual liberty and positive form of community.  Instead, both poems offer an examination of nationalism that balances the nation’s potential with a consideration of the limits and possible abuses of this potential.

abstract: PhD


title: New Algorithms in Rigid-Body Registration and Estimation of Registration Accuracy

contributor:
Abolmaesumi, Purang
Electrical and Computer Engineering

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subject:
Registration
Maximum Likelihood
Kalman Filter
Inhomogeneous

abstract: Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2008-09-28 07:25:38.229

abstract:
Rigid-body registration is an important research area with major applications in computer-assisted and image-guided surgery. In these surgeries, often the relationship between the preoperative and intraoperative images taken from a patient must be established. This relationship is computed through a registration process, which finds a set of transformation parameters that maps
some point fiducials measured on a patient anatomy to a preoperative model. Due to point measurement error caused by medical measurement instruments, the estimated registration parameters are imperfect and this reduces the accuracy of the performed registrations. Medical measurement instruments often perturb the collected points from the patient anatomy by heterogeneous noise. If the noise characteristics are known, they
can be incorporated in the registration algorithm in order to more reliably and accurately estimate the registration parameters and their variances.

Current techniques employed in rigid-body registration are primarily based on the well-known Iterative Closest Points (ICP)
algorithm. Such techniques are susceptible to the existence of noise in the data sets, and are also very sensitive to the initial
alignment errors. Also, the literature offers no analytical solution on how to estimate the accuracy of the performed registrations in the presence of heterogenous noise.

In an effort to alleviate these problems, we propose and validate various novel registration techniques based on the Unscented Kalman Filter (UKF) algorithm. This filter is generally employed for analyzing nonlinear systems corrupted by additive heterogenous Gaussian noise. First, we propose a new registration algorithm to
fit two data sets in the presence of arbitrary Gaussian noise,
when the corresponding points between the two data sets are assumed to be known. Next, we extend this algorithm to perform
surface-based registration, where point correspondences are not available, but the data sets are roughly aligned. A solution to
multi-body point and surface-based registration problem is then
proposed based on the UKF algorithm.

The outputs of the proposed UKF registration algorithms are then utilized to estimate the
accuracy of the performed registration. For the first time, novel derivations are presented that can estimate the distribution of registration error at a target in the presence of an arbitrary Gaussian noise.

abstract: PhD


title: Functional and physiological measures in individuals with hip osteoarthritis

contributor:
Aiken, Alice
Rehabilitation Science

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subject: Hip Osteoarthritis

abstract: Thesis (Master, Rehabilitation Science) -- Queen's University, 2008-09-25 17:11:10.365

abstract: Background: Osteoarthritis of the hip joint causes difficulties to the elderly because it impacts their ability to conduct their normal activities of daily living, such as walking, cooking, bathing, dressing, using the toilet, and performing household chores. Moreover, the joints can become painful, stiff, and swollen. The resulting pain causes limited motion, restriction of social activities, and compromised work capacity. The interaction of these factors can affect both functional and physiological status. The normal course of action for these subjects is to be referred to an orthopedic surgeon; however, the functional and physiological impact of waiting times for hip replacement consultation or surgery on subject’s function has not been properly assessed with objective outcome measures. Objectives: The purpose of this study was to investigate the differences in objective outcome measures of functional and physiological status between subjects with hip OA who were preoperative candidates for hip surgery and those who were diagnosed with hip OA at the time of referral and time of consultation. Methods: Subjects with hip osteoarthritis were selected based on their position in the continuum of care once they had been referred to a surgeon. These groups were: referral (REF) (n=7), consultation (CON) (n=7) and pre-operatively (PREOP) (n=7). Individuals with hip OA were evaluated using functional (6MWT and TUG) and physiological (hip muscle isokinetic strength - Biodex and VO2peak) outcome measures. Results: The 6 minutes walk test (6MWT), timed up and go (TUG) and VO2peak were significantly different between the three groups (p < 0.001, p = 0.005 and p = 0.001). However, no significant difference was observed in hip flexion and extension muscle strength between groups. Post Hoc analysis revealed that the REF group walked significantly greater distances (p < 0.001) when compared to the PREOP group during the 6MWT. Both REF and CON groups showed significantly shorter times in the TUG test (p < 0.009 and p < 0.02 respectively) when compared to the PREOP group and finally the VO2peak in the REF group was significantly higher than the predicted VO2peak of the CON (p = 0.002) and the PREOP (p = 0.002) groups, respectively. Conclusion: Subjects with hip osteoarthritis who are within four weeks of surgery generally walked shorter distances, demonstrate worse mobility and balance control and a lower aerobic capacity than individuals with hip OA at the time of referral to a surgeon and at the time of consultation with the surgeon. Contrary to expectation, this study did not find differences in hip muscle strength, between those with hip osteoarthritis at the time of referral; at the time of consultation and within four weeks prior to surgery.

abstract: M.Sc.


title: Hypoxia and the metabolic phenotype of prostate cancer cells

contributor:
Moyes, Christopher D.
Biology

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subject:
Hypoxia
Prostate Cancer

abstract: Thesis (Master, Biology) -- Queen's University, 2008-09-25 17:28:13.418

abstract:
Cancer cells have the ability to survive when oxygen is limiting, and upregulate
the pathway of fatty acid synthesis, owing in part to alterations in their metabolism. I
compared the metabolic phenotypes of the prostate cancer cell lines LNCaP, DU145, and
PC3 assessing energy metabolism, and metabolic gene expression. I also explored the
plasticity of the metabolic phenotype following passage, selection and in vivo growth.
Finally, I explored the sensitivity of the fatty acid synthesis pathway to low oxygen.
LNCaP cells had a more oxidative phenotype based on oxygen consumption,
lactate production, enzyme assays, and mRNA levels. While DU145 and PC3 cells were
more glycolytic, they were unresponsive to dichloroacetate (DCA), and dinitrophenol
(DNP), stimulators of oxygen consumption. Mitochondrial dysfunction in the PC3 and
DU145 cells may explain this phenomenon, for they possessed normal cardiolipin levels
but lower mitochondrial enzyme activities (cytochrome oxidase (COX), citrate synthase
(CS)).
When LNCaP cells were subjected to high passage, with and without clonal
selection, the derived lines acquired a dysfunctional oxidative phenotype, becoming more
glycolytic. Clonal selection appeared to have the most dramatic effect on cellular
metabolism. This finding is supported by decreased oxygen consumption, increased
lactate production, and a reduction in the activity of the oxidative enzymes CS and COX
in the clonally selected LNCaP-luc cell line. Similar to the DU145 and PC3 cells, NAO
fluorescence indicates that the oxidative impairment in these LNCaP-derived lines may
be due to a reduction in mitochondrial activity. The pattern of metabolic gene expression
iii
seen in vitro was unaffected when LNCaP cells were grown as subcaspular and muscle
xenografts in immunodeficient mice, though xenografts did exhibit indications of an
hypoxic response (elevated VEGF mRNA).
Oxygen deprivation in vitro increased mRNA for HIF and responsive genes but
not SREBP responsive genes. Similarly, oxygen deprivation had no influence on
triglyceride levels in any of the lines suggesting that the SREBP axis may not be directly
modulated by oxygen levels.
Collectively these studies demonstrate differences in the metabolism of these
prostate cancer models, with important ramifications of therapeutic strategies involving
metabolic targets.

abstract: M.Sc.


title: An Examination of the Effects of Mathematics Anxiety, Modality, and Learner-Control on Teacher Candidates in Multimedia Learning Environments

contributor:
Colgan, Lynda
Kirby, John R.
Education

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subject:
Mathematics Anxiety
Modality Principle
Multimedia Learning
Cognitive Load Theory

abstract: Thesis (Master, Education) -- Queen's University, 2008-09-25 19:38:33.9

abstract: This study examined mathematics anxiety among elementary teacher candidates, and to what extent it interacted with the modality principle under various degrees of learner-control.  The experiment involved a sample of 186 elementary teacher candidates learning from eight versions of a computer program on division with fractions.  The eight versions varied in modality of presentation (diagrams with narration, or diagrams with written text), control of pacing (pacing was controlled by either the learner or the system), and control of sequence (sequence was controlled by either the learner or the system).  A pre-test, post-test, demographic questionnaire, subjective measure of mental effort, and the Abbreviated Math Anxiety Survey were also administered.    This study revealed that mathematics anxiety was significantly positively correlated with mental effort, and significantly negatively correlated with engagement, pre-test and post-test scores.  Additionally, a modality x pacing interaction was observed for both high prior knowledge and low mathematics-anxious students.  Under system-pacing, the modality effect was observed, and these students achieved higher far transfer scores when learning from the diagrams and narration modality condition.  However, under learner-pacing, the modality effect reversed, and high prior knowledge and low mathematics-anxious students performed better on far transfer scores when learning from the diagrams and written text modality condition.  Low prior knowledge, and highly mathematics-anxious students performed poorly in all treatment conditions.  Additional interactions involving sequence-control, and a four-way interaction involving prior knowledge, modality, sequence-control, and pacing were also uncovered.  The results from this study demonstrate that prior knowledge and mathematics anxiety have a complex relationship with the effectiveness of the format of instruction, and the design of instructional materials needs to take into account these individual differences.

abstract: M.Ed.


title: Mercury in Sub-Saharan Africa: Developing an Exposure Assessment Framework for Ghana and Uganda

contributor:
Campbell, Linda M.
Aronson, Kristan J.
Environmental Studies

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subject:
Sub-Saharan Africa
Exposure assessment
Mercury
Ghana
Uganda
Mercury bioaccessibility

abstract: Thesis (Master, Environmental Studies) -- Queen's University, 2008-09-25 20:05:32.606

abstract: Exposure to environmental toxins is a major contributing factor to the expected increase in chronic disease within developing countries in the next 20 years.  Due to its ubiquitous distribution and persistent nature, mercury (Hg) is an example of a toxic substance that has garnered global concern because of its known detrimental effects on human and ecosystem health.  Although fish consumption is the predominant source of Hg exposure to humans in developed nations, studies in developing countries have shown that high Hg concentrations in humans cannot be explained by fish consumption alone.  The estimated daily intake (EDI) and the relative contribution of various sources of Hg to humans differ significantly between individuals, ethnic groups, and across continents.  Health Canada is currently attempting to regulate the anthropogenic release and exposure dose of Hg to its citizens based on known EDIs, however the greatest sources of Hg exposure across sub-Saharan Africa (SSA) are still unknown, thus impeding the regulatory process.  This thesis focuses on four major sources of Hg exposure in SSA: skin-lightening cosmetics, soil geophagy, small-scale gold mining, and fish consumption.  An exposure assessment model has been developed to identify the sources of greatest concern for various age groups in Ghana and Uganda and is presented using published and unpublished data, as well as experimental Hg bioaccessibility data.  The results indicate that occupational exposure and lifestyle choices (mining and use of skin-lightening cosmetics) have the greatest contribution to overall increases in Hg toxicity in adults.  The health of infants, however, is most likely to be compromised before birth and in the first few days of life due to maternal consumption of fish with elevated Hg concentrations and the use of Hg-containing cosmetics.  It is imperative that further research of these sources be carried out to prevent the possible long-term negative social and economic consequences of chronic illness in SSA.

abstract: M.E.S.


title: Giovanni Battista Montano as Architectural Draughtsman: Recording the Past and Designing the Future

contributor:
Pierre du Prey
Art History

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subject:
G.B. Montano
Baroque
Architecture
Antiquity

abstract: Thesis (Master, Art History) -- Queen's University, 2008-09-25 21:15:35.035

abstract:
Giovanni Battista Montano (1534-1621), who was born in Milan and trained as a woodcarver, relocated permanently to Rome in the early 1570s where his interest in sculpting was replaced by intense study of the city’s antique monuments and ruins. Although Montano carried out several sculptural and architectural projects during his time in Rome, it is his surviving corpus of drawings that testifies to his passion of exploring ancient architecture through the medium of drawing. While Montano was not famous during his lifetime, a large body of his intriguing designs became celebrated and widely circulated after his death thanks to the 1624 publication of Montano’s designs by his loyal pupil, Giovanni Battista Soria.  Montano’s lifelong work differs from virtually all of his predecessors and contemporaries in its “fantastical” and ornamental nature.

This thesis explores Montano’s artistic training as it relates to his later interest in imaginatively reconstructing antique buildings, along with his disregard for archaeological or historical accuracy. The subject matter upon which Montano focused is discussed, along with his objective in creating a large corpus of half-historical, half-invented drawings. His drawing techniques are explored with specific reference to the largest group of extant Montano drawings, today housed in Sir John Soane’s Museum, London, England, and also in reference to three original Montano drawings in the Centre Canadien d’Architecture/Canadian Centre for Architecture, Montréal. Also explored is the legacy and impact of Montano’s drawings and the later publications of his designs on the works of Roman Baroque architects, specifically Borromini and Bernini. This thesis ultimately attempts to understand the impact of the intellectual and artistic environment surrounding Montano in late sixteenth and early seventeenth century Rome, his drawing techniques, his choice of subject matter, and the reception that his unique works received from contemporary artists and intellectuals, along with those of the following generation.

abstract: Master


title: Staff Nurses' Perceptions of Rapid Response Teams in Acute Care Hospitals

contributor:
Howse, Ena
Nursing

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subject:
Rapid Response
Medical Emergency Team
Mental Models
Mental Model Maintenance
Mental Model Building
Patient Deterioration

abstract: Thesis (Master, Nursing) -- Queen's University, 2008-09-25 21:27:44.682

abstract: The purpose of the present study were to (a) explore the relationship between the frequency of use of Rapid Response Teams (RRTs) by hospital staff nurses and the support received from RRTs; (b) to investigate staff nurses’ perceptions of their individual level, group level and organizational level learning as a result of single or multiple exposures to the RRT; (c) to identify predictors of learning outcomes and (d) to identify overall impressions and advantages and disadvantages of the RRT. A mail survey was used to collect data. The response responses rate was 33%, 131 registered nurses responded to the survey (pre-test = 12, study = 119). The results of Pearson r correlation suggest that a high frequency of access of RRTs was positively related to process support (r = .25, p < .01). Also, perceived content and process support from RRTs was positively related to maintenance and building of staff nurses’ mental models regarding patient deterioration pertaining to self, group and organization. Multiple regression analyses show that sociodemographic and independent variables predict organizational learning outcomes (mental model maintenance and building). Overall impressions of the RRTs were high. A content analysis of nurses’ comments indicated that there were more advantages to having the RRTs than disadvantages. This study suggests that RRTs are influential in changing nurses’ perceptions about managing patient deterioration. Training programs for RRTs should include both content and process support, which may enhance building and maintaining mental models.

abstract: MNSc.


title: Effects of low-intensity exercise on blood pressure, heart rate, rate-pressure-product and cardiac autonomic function in hypertensive women

contributor:
Brown, C. Ann
Nursing

format:
3226352 bytes
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subject: Hypertension Exercise Women

abstract: Thesis (Master, Nursing) -- Queen's University, 2008-09-25 21:46:53.32

abstract: The effects of a twelve-week low-intensity exercise conditioning program on blood pressure (BP), heart rate (HR), rate-pressure-product (RPP) and cardiac autonomic function were examined in menopausal and post menopausal women with hypertension. Eligible participants (n=50) were counterbalanced to either the exercise group or the control group. Using a pretest-posttest design, participants were tested at the beginning and the end of the 12-week study period, in which BP, HR, RPP, heart rate variability and spontaneous baroreflex sensitivity were measured at rest and during standing and low intensity steady-state exercise. The exercise group participated in a 12-week, low-intensity walking program, 5 days/week, while the comparison group continued with usual activity. The exercise group adhered to 4 walking sessions per week while the control group averaged 0.6 walking sessions per week.  Repeated measures analysis of variance (ANOVA) demonstrated a reduction in systolic and diastolic BP and RPP in hypertensive women. Additionally, the low intensity exercise conditioning program attenuated the physiological response to stress (standing, exercise). This was evidenced by decreased systolic and diastolic BP and RPP in the exercise group and increased diastolic BP in the control group. Postmenopausal women demonstrated decreased log transformed high frequency power and total power in comparison to menopausal women. However, postmenopausal women also showed decreased low frequency power in comparison to menopausal women. It was concluded that a 12-week, low-intensity exercise conditioning program reduced systolic and diastolic BP and RPP in hypertensive women while attenuating their physiological responses to stress.

abstract: MNSc.


title: Examination of Geological Influence on Machine Excavation of Highly Stressed Tunnels in Massive Hard Rock

contributor: Geological Sciences and Geological Engineering

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subject:
Rock Mechanics
Numerical Modelling
Geological Engineering
Tunnel Boring Machine
Brittle Rock
Stress
Constitutive Model
Alpine Tunnel
Geomechanical Characterisation
Tunnelling

abstract: Thesis (Ph.D, Geological Sciences & Geological Engineering) -- Queen's University, 2008-09-25 23:58:58.071

abstract:
A combined geological and rock mechanics approach to tunnel face behaviour prediction, based on improved understanding of brittle fracture processes during TBM excavation, was developed to complement empirical design and performance prediction for TBM tunnelling in hard rock geological conditions. A major challenge of this research was combining geological and engineering terminology, methods, and objectives to construct a unified Geomechanical Characterisation Scheme. The goal of this system is to describe the spalling sensitivity of hard, massive, highly stressed crystalline rock, often deformed by tectonic processes. Geological, lab strength testing and TBM machine data were used to quantify the impact of interrelated geological factors, such as mineralogy, grain size, fabric and the heterogeneity of all these factors at micro and macro scale, on spalling sensitivity and to combine these factors within a TBM advance framework. This was achieved by incorporating aspects of geology, tectonics, mineralogy, material strength theory, fracture process theory and induced stresses.
Three main approaches were used to verify and calibrate the Geomechanical Characterisation Scheme: geological and TBM data collection from tunnels in massive, highly-stressed rock, interpretation of published mineral-specific investigations of rock yielding processes, and numerical modelling the rock yielding processes in simulated strength tests and the TBM cutting process.  The TBM performance investigation was used to identify the mechanism behind the chipping processes and quantify adverse conditions for chipping, including tough rock conditions and stress induced face instability.  The literature review was used to identify the critical geological parameters for rock yielding processes and obtain strength and stiffness values for mineral-specific constitutive models.  A texture-generating algorithm was developed to create realistic rock analogues and to provide user control over geological characteristics such as mineralogy, grain size and fabric.
This methodology was applied to investigate the TBM chipping process to calibrate the Geomechanical Characterisation Scheme.  A Chipping Resistance Factor was developed to combine the quantified geological characteristic factors and laboratory strength values to predict conditions with high risk of poor chipping performance arising from tough rock.  A Stress-Related Chip Potential Factor was developed to estimate conditions with high risk of advance rate reduction arising from stress-induced face instability.

abstract: PhD


title: A la recherche du soi perdu: etude phenomenologique de La derniere bande de Samuel Beckett

contributor:
Bénard, Johanne
French

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subject:
Samuel Beckett
Paul Ricoeur
Phenomenology
La derniere bande (Krapp's Last Tape)
Memory
Time
Identity

abstract: Thesis (Master, French) -- Queen's University, 2008-09-26 09:07:19.995

abstract:
The goal of the present study is to examine the way in which Samuel Beckett, an artist whose work contributes also to philosophy, presents his metaphysical vision of the world through drama, where different plays represent different philosophical interpretations of the world.  Using Paul Ricœur’s Memory, History, Forgetting as a theoretical platform, this thesis will concentrate on the manner in which Krapp’s Last Tape presents identity as a phenomenological construction based on cumulative past experiences inserted into and spread throughout time.  Based on this assumption, to tamper with one’s conceptions of a memory-time continuum is to alter the identity which is a result of this dynamic.
	The Beckettian vision of the world does not see identity – the ever-elusive self, as many authors would say – simply as a unique and separate phenomenon that, by staying constant through time, serves as the basis for one’s phenomenological experience ; rather, in Krapp’s Last Tape the self is the sum of mnemonic experiences lived through time, which in turn impacts the identity of the individual.  This philosophical perception of identity is further complicated by other phenomenological questions which must come into play if we are to study the way in which this identity is perceived not only by the reader-spectator, but also by the subject himself.  For example, how does the ideal image that Krapp constructs of himself impact his identity ?  Does he modify memory so as to conform to the idealistic vision he has created of himself, and does this image, perceived as the desired Other, foment in him a feeling of alterity when faced with himself as he is, as opposed to the fulfillment of the desired Other by which he measures his success ?

abstract: M.A.


title: Sound As a Dollar? The Propertization of Spectrum Resources and Implications for Non-Profit Community Radio in Guatemala

contributor:
Lovell, W. George
Geography

format:
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subject:
radio spectrum policy
community radio
Guatemala
propertization
liberalization

abstract: Thesis (Master, Geography) -- Queen's University, 2008-09-26 09:24:05.497

abstract: This research analyzes Guatemala’s 1996 telecommunications reform, with an emphasis on how the introduction of private property rights in the electromagnetic spectrum has affected provision of, and access to, non-profit community radio, a critical media for the country’s indigenous Maya. The Guatemalan ‘experiment’ is the first applied test of Ronald Coase’s 1959 call for property rights in radio spectrum. To date, spectrum liberalization in most countries, including Canada, has upheld a model of resource stewardship in which the state retains ownership of the spectrum and a measure of control over frequency allocations. In Guatemala, by contrast, the state has ceded spectrum control to the private sector by auctioning off legal title to electromagnetic frequencies and allowing secondary markets in spectrum trading to develop. Formerly free under license to Guatemalan nationals only, FM frequencies sold with title under Guatemala’s revamped telecommunications law fetch as much as US$750,000 at auction. Broadcasting rights have disproportionately accrued to foreign nationals and commercial operators, while community broadcasters operating without title are accused of ‘stealing’ spectrum resources (causing interference on titled bandwidth), for which they face fines of between US$10,001 and $100,000 and up to six years in prison. Scholar-advocates and industry lobbyists credit Guatemala’s propertization regime with maximizing resource efficiency, institutionalizing justice, and offering rich and poor countries alike a practical model for spectrum reform. The Inter-American Commission on Human Rights and other critics, however, argue that the regime discriminates against those who lack the financial resources to purchase spectrum title and effectively bars non-profit community radio stations from legal access to the airwaves. This study traces the intellectual roots of (neo)liberal reform and examines parallels between geographies of inequality in Guatemala’s landscape and soundscape in order to demonstrate that the costs of enclosing and commodifying resources once held in common has consistently and disproportionately fallen on Guatemala’s indigenous population.

abstract: M.A.


title: Evaluation of RNA Quality From Formalin Fixed and Paraffin Embedded Samples: Applications and Limitations

contributor:
Feilotter, Harriet
Pathology and Molecular Medicine

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subject:
FFPE
miRNA
mRNA
Heat Treatment
Microarray
Profiling

abstract: Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2008-09-26 10:49:50.044

abstract: RNA molecules isolated from FFPE samples are highly fragmented and modified, and generally deemed unsuitable for downstream gene expression profiling. With the development of molecular biology, there has been growing interest in profiling archival FFPE samples. Successful profiling of transcripts from FFPE samples would greatly expand tissue sources for large scale gene expression studies; also it would pave the way for future applications on the type of tissue readily available in the clinical setting. So far, there is a lack of systemic studies evaluating the quality of RNA isolated from routinely processed FFPE samples, and it has remained difficult to assess how well FFPE-derived RNA mirrors the status of RNA isolated before fixation. In this project, the similarity of miRNA and mRNA profiles between matched frozen and FFPE lymphoid hyperplasia tissues (N=7 for miRNA comparison, N=4 for mRNA comparison) were evaluated. We found consistently good correlation (mean of Pearson coefficient=0.939, mean of Spearman coefficient=0.905, mean of Kendall tau=0.744) between matched frozen and FFPE-derived miRNA profiles, suggesting FFPE samples may retain miRNA expression information quite well. This has major positive implications for research using FFPE samples, as miRNA profiling becomes more prominent in bioprofiling studies. On the contrary, mRNA isolated from FFPE samples showed less correlation (Spearman coefficient less than 0.75) with its frozen counterpart on the Agilent microarray platform. With a post extraction heat treatment aimed at reversing base modifications and cross linking structures, obvious global mRNA quality improvement was observed in cases where samples appeared to be heavily cross linked, but was less effective and even detrimental in cases where cross linking was less prominent.   This research suggests that the extent of cross linking may be critical in terms of determining whether a particular FFPE tissue will become a useful source of mRNA for global profiling studies

abstract: One part of the thesis got accepted for publish in Nov 2008

abstract: M.Sc.


title: Fetal behaviour in preeclamptic compared to low-risk normotensive pregnancies

contributor:
Kisilevsky, Barbara
Nursing

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subject:
Fetal behaviour
preeclampsia

abstract: Thesis (Master, Nursing) -- Queen's University, 2008-09-26 11:06:27.498

abstract: Preeclampsia is associated with placental insufficiency and fetal growth restriction.  Fetal growth restriction is associated with an increased risk for language deficits at 2-5 years of age.  However, fetal auditory processing in pregnancies complicated by preeclampsia has not been examined and is the focus of this study.  Spontaneous and auditory elicited fetal behaviours were compared in 40 mother-fetal pairs (n=20 preclamptic and n=20 low-risk normotensive pregnancies) from 33 to 39 weeks gestational age (GA).  Spontaneous fetal heart rate, body and breathing movements and muscle tone were observed and an estimate of amniotic fluid was made.  To test if the fetuses could hear, six 2.5s trials (3, 110 dB pink noise; 3, no-sound control) were intermixed and randomly presented; fetal heart rate was recorded for 30 s following trial onset and body movements were observed for 5 s.   Finally, the mother’s voice recorded reading a children’s story was presented: 2 min of no sound, 2 min of mother’s voice (95 dB A) and 2 min of no sound.  Sounds were delivered through a speaker 10cm above the abdomen.  During the 6 min procedure, fetal heart rate was recorded continuously and body movements were video recorded.  Fetuses in the preeclamptic group were born earlier, t(37)=4.79, p<0.000.  There were no differences in birth weight at delivery.  Testing showed no differences between groups for any measure of spontaneous behaviour.  There was increased heart rate, F(1,36)=37.47, p<0.001, and number of body movements, F(1, 35)=54.04, p<0.001, in response to the pink noise compared no-sound control trials, indicating that both groups could hear external sounds.   No differences in fetal heart rate or body movement responses to the playing of the mother’s voice were found between the two groups; although, there was a suggestion that gestational age affected responding.  There were no differences found in spontaneous behaviours or auditory processing behaviours in fetuses of pregnancies complicated by mild to moderate preeclampsia compared to those in low-risk, normotensive pregnancies.  It is suggested that future studies examining fetal auditory processing in preeclamptic pregnancies employ sufficient sample size for analyses by gestational age at time of testing.

abstract: MNSc.


title: Altered Vasomotion Characteristics as a Method of Investigating Vascular Phenotypic Change

contributor:
Bennett, Brian M.
Adams, Michael A.
Pharmacology and Toxicology

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subject:
Vasomotion
Vascular
Phenotype
Gap Junctions
Connexin
Fourier Transform

abstract: Thesis (Master, Pharmacology & Toxicology) -- Queen's University, 2008-09-26 11:39:44.043

abstract:
Vasomotion is the spontaneous oscillation of vascular tone, occurring due to synchronization of internal calcium fluctuations between multiple vascular smooth muscle cells by gap junction and electrical communication. Although altered vasomotion has been observed in a variety of pathological situations, characterization of these alterations has been lacking. Using a novel method of spectral quantification, and two experimental models known to have altered vascular structure, the present thesis was designed to evaluate whether vasomotion characteristics could be correlated with altered vascular structure.
	Rats with perinatal iron deficiency (PID) have previously been shown to possess altered vascular structure. When phenylephrine-mediated contractile and acetylcholine-mediated dilatory responses were investigated in PID animals, they both displayed blunted relaxation as compared to control vessels. When vasomotion characteristics were quantified, vessels taken from PID animals exhibited a decreased power in the very low frequency window (VLF <0.2 Hz). Changing vessel oxygenation to 10% O2 from 95% O2 did not result in significant alterations of vasomotion characteristics. The primary frequency of oscillation was investigated with a peak finder, and found to be significantly different compared to control in both the aorta and renal arteries obtained from PID animals.
	To investigate the effect of antihypertensive treatment (enalapril and hydrochlorothiazide) on gap junction communication, spontaneously hypertensive rats (SHR) were subject to a 2-week intensive angiotensin converting enzyme inhibitor treatment. This treatment resulted in significant vascular structural regression. All vessels (aorta, renal, mesenteric) from treated animals had greater proportions of power in the VLF window, with both the mesenteric and renal vessels exhibiting a primary peak of oscillation around 0.2 Hz; whereas the aorta had a primary peak at 0.12 Hz. Investigating altered gap junction communication with the gap junction blocker 18-α glycyrrhetinic acid, revealed that vascular bed location was the determining factor of vasomotion response. Immunoblotting did not indicate differences in connexin 43, a major gap junction protein in the vascular smooth muscle.
	These studies suggest that vasomotion characteristics can be used as a method of vascular phenotype investigation; vasomotion characteristics were significantly different in vessels taken from PID and hypertensive animals as compared to control and antihypertensive-treated animals, respectively.

abstract: M.Sc.


title: Adobe Conservation: Evaluation of Silicone and Acrylic Consolidants

contributor:
Murray, Alison
Art Conservation

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subject: Adobe Consolidants Silicone Acrylic

abstract: Thesis (Master, Art Conservation) -- Queen's University, 2008-09-26 12:01:30.22

abstract: Since soil and water were the most accessible building materials, humans used the mixture of soil and water to fabricate mud bricks or adobe. Iran, Syria, and Iraq have numerous mud brick buildings, and Arg-e Bam, located in Iran, was one of the most famous earthen monuments in the world; it was destroyed in a massive earthquake in 2003. In this research adobe samples were fabricated and different consolidants were applied to the samples. To determine the most effective consolidant, the tests were performed on the treated adobe. The soil for this research was supplied from Godfrey, a site near Kingston, Ontario, Canada. The soil was mixed with kaolin to achieve a similar grain size distribution to that of soil found in Bam. This research used four specific consolidant materials: a 5% (w/v) solution of Paraloid B-72 in toluene; a 50% (v/v) solution of methyl trimethoxy silane (MTMOS) in ethanol; a 50% (v/v) solution of ethyl silicate (TEOS) in ethanol; and Conservare H, which is the commercial brand of ethyl silicate. The research also studied the effects of Paraloid B-72 on surfaces previously treated with methyl trimethoxy silane and ethyl silicate. The chemicals were applied to the samples by brushing. After treatment, different physical properties were measured. The tests included study of density, porosity, water absorption, depth of penetration, abrasion resistance, hardness, compressive strength, bending strength and colour changes. Chemical analysis (X-ray diffraction) was used to study the chemical components of the soil and scanning electron microscopy showed changes to the treated surfaces after application of the chemicals. This research can be used as a guide in choosing the consolidants in adobe consolidation depending on the priorities defined in each building conservation project.  Also, by applying all the same tests to samples made from the actual soil from Bam, this research can be used to evaluate how grain size distribution can affect the physical properties of the consolidated samples. By considering only the grain size of the soil used for adobe fabrication, the results from this research produced the following conclusion of consolidation of adobe from Bam; if the colour change is important, then the recommended consolidant is MTMOS or TEOS; if the colour change is not important, then the recommended consolidant is Paraloid B-72. The comparison among all the consolidants and their results, except results from failure strength, leads to the conclusion that the best consolidant is TEOS followed by a second coat of Paraloid B-72.

abstract: M.A.C.


title: Structural and functional studies of bacterial protein tyrosine kinases

contributor:
Jia, Zongchao
Biochemistry

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subject:
Bacterial Tyrosine Kinase
Protein X-Ray Crystallography
Kinase Activation
Bacterial Capsule

abstract: Thesis (Ph.D, Biochemistry) -- Queen's University, 2008-09-26 12:45:02.924

abstract: While protein tyrosine kinases (PTKs) have been extensively characterized in eukaryotes, far less is known about their emerging counterparts in prokaryotes. Studies of close to 20 homologs of bacterial protein tyrosine (BY) kinases have inaugurated a blooming new field of research, all since just the end of the last decade. These kinases are key regulators in the polymerization and exportation of the virulence-determining polysaccharides which shield the bacterial from the non-specific defenses of the host. This research is aimed at furthering our understanding of the BY kinases through the use of X-ray crystallography and various in vitro and in vivo experiments. We reported the first crystal structure of a bacterial PTK, the C-terminal kinase domain of E. coli tyrosine kinase (Etk) at 2.5Å resolution. The fold of the Etk kinase domain differs markedly from that of eukaryotic PTKs. Based on the observed structure and supporting evidences, we proposed a unique activation mechanism for BY kinases in Gram-negative bacteria. The phosphorylation of tyrosine residue Y574 at the active site and the specific interaction of P-Y574 with a previously unidentified key arginine residue, R614, unblock the Etk active site and activate the kinase. Both in vitro kinase activity and in vivo antibiotics resistance studies utilizing structure-guided mutants further support the novel activation mechanism. In addition, the level of phosphorylation of their C-terminal Tyr cluster is known to regulate the translocation of extracellular polysaccharides. Our studies have significantly clarified our understanding of how the phosphorylation status on the C-terminal tyrosine cluster of BY kinases affects the oligomerization state of the protein, which is likely the machinery of polysaccharide export regulation. In summary, this research makes a substantial contribution to the rapidly progressing research of bacterial tyrosine kinases.

abstract: PhD


title: Deep and Superficial Pelvic Floor Muscle Responses to a Pain Stimulus in Vestibulodynia

contributor:
McLean, Linda
Rehabilitation Science

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subject:
vulvodynia
pelvic floor muscles
electromyography
protective responses
pressure-pain stimulus
onset time

abstract: Thesis (Master, Rehabilitation Science) -- Queen's University, 2008-09-26 15:46:22.84

abstract: Previous studies have suggested that protective responses in the pelvic floor muscles (PFMs), described in terms of hypertonicity and over-reactivity, are associated with and may worsen the symptoms of provoked vestibulodynia (PVD, i.e., chronic vulvar pain). A recent study reported that, upon manual palpation of the PFM, hypertonicity was consistently found in the superficial but not the deep PFM layers. The goals of this study were to compare superficial and deep PFM resting tone, protective response magnitude and onset timing to moderate perceived vulvar pain between women with and without PVD. Eleven women with PVD and eleven control women Tcompleted a gynecological examination and standardized PFM electromyography (EMG) testing. Three trials of sTurface EMG activity of the PFM were recorded while a pressure-pain stimulus (PPS) was applied to the vulvar vestibule. Increasing pressure was applied to achieve a perceived pain intensity rating of 6/10 using an 11-point numerical rating scale presented visually. The women with PVD had higher resting EMG activity in their superficial PFMs (p=0.04) as compared to the control group, while no difference was found at the level of the deep PFMs (p=0.12). Participants in both groups demonstrated contractile responses to the PPS in both the superficial and the deep PFM, and these responses were significantly higher (p=0.0001) in the superficial (50.06  vs 38.69 % maximal voluntary electrical activation [MVE]) as compared to the deep (24.88 vs 22.52 %MVE) PFM layers. Women with PVD had significantly higher PFM responses at the superficial layer as compared to the control women (p<0.0005). The onset of the superficial and deep EMG PFM responses followed the PPS application in both groups. No differences were found between the deep and superficial PFM onset latency to the timing of the PPS application.The results of this study suggest that women with PVD have superficial PFMs that are more responsive to vulvar pain than those in non-affected women. The findings also suggest that superficial PFM over-reactivity, rather than deep PFM over-reactivity, is part of the PFM dysfunction reported in women with PVD.

abstract: M.Sc.


title: Credit Risk, Insurance and Banking: A Study of Moral Hazard and Asymmetric Information

contributor:
Zabojnik, Jan
Milne, Frank
Head, Allen
Economics

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subject:
Economics
Financial Economics
Information Economics
Banking
Credit Risk
Insurance

abstract: Thesis (Ph.D, Economics) -- Queen's University, 2008-09-26 13:03:32.81

abstract:
This dissertation investigates agency problems within risk transfer contracts.  We pay particular attention to the consequences of credit risk transfer in the context of banking.  The first two chapters provide an introduction and literature review. We then analyze the effect of counterparty risk on
financial insurance contracts in the following two chapters, and uncover a new moral hazard problem on the part of the insurer. If the insurer believes it is unlikely that a claim will be made, it
is advantageous for them to invest in assets which earn higher returns, but may not be readily available if needed. We find that
counterparty risk can create an incentive for the insured to reveal superior information about the risk of their "investment".  In particular, a unique separating equilibrium
may exist even in the absence of any signalling device.  This constitutes a first example in which the separation of types can
be achieved without a costly signalling device.  Our research suggests that regulators should be wary of risk being offloaded to other, possibly unstable parties, especially in financial markets
such as that of credit derivatives.

The fifth chapter models loan sales and loan insurance (e.g. credit default swaps) as two key instruments of risk transfer within the banking environment. Recent empirical evidence suggests that the asymmetric information problem is as relevant in loan
insurance as it is in loan sales. Contrary to previous literature, this paper allows for informational asymmetries in both markets.
Our results show that a well capitalized bank will tend to use loan insurance regardless of loan quality in the presence of moral
hazard and relationship banking costs of loan sales. Finally, we show that a poorly capitalized bank may be forced into the loan
sales market, even in the presence of possibly significant moral hazard and relationship banking costs that can depress the selling price.

abstract: PhD


title: Development and Characterization of Polysiloxane Polymer Films for Use in Optical Sensor Technology

contributor:
Brown, R. Stephen
Chemistry

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subject:
Polysiloxanes
Long Period Grating Sensor

abstract: Thesis (Ph.D, Chemistry) -- Queen's University, 2008-09-26 15:28:35.603

abstract:
A novel sensor using a polymer coated long-period grating (LPG) has been proposed for monitoring levels of organic contaminants in air or water systems.  The sensor operates by detecting refractive index changes in the polymer coating as analytes partition in.  Polymer coatings used must be able to reversibly and reproducibly absorb contaminants of interest from the sample and have a refractive index just below that of the fiber cladding.
The synthesis and characterization of several chemically selective polysiloxanes is described.  Pre-polymer materials are made through the catalyzed condensation of silane monomers.  Different functional groups are incorporated either through polymerizing functionalized monomers, or by post-functionalizing the polymer through a platinum-catalyzed hydrosilylation reaction.  The pre-polymer materials are crosslinked into elastomeric films using titanium(IV) tetraisopropoxide.  The polymer refractive index is controlled through altering the ratios of functional groups within the polymer or changing the loading levels of titanium.  Four polymers were made, having different functional groups and optimized refractive indices for use on the proposed sensor.
The partition coefficients for the polymers with a variety of solvents are calculated and compared.  Each polymer was found to have a slightly different chemical selectivity pattern, demonstrating that a set of polymers could be used to generate a sensor array.  Partition coefficient data was calculated from the gas phase by considering the change in polymer refractive index as the solvents partitioned into the polymer.  The Lorentz-Lorenz equation was used to model the relationship between the change in refractive index and the solvent concentration within the polymer.
Finally, polymers were applied to LPGs and used to successfully detect various solvents from the gas phase.  This was accomplished by monitoring the entire LPG spectrum, and also by considering loss at a single wavelength using fiber-loop ring-down spectroscopy.

abstract: PhD


title: On Gilded Ugliness: Donatello's Penitent Magdalen and Issues of Beauty, Sanctity, and Sexuality in Fifteenth Century Florence

contributor:
D'Elia, Una
Art History

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subject:
Mary Magdalen
Donatello
Petrarch
Beauty

abstract: Thesis (Master, Art History) -- Queen's University, 2008-09-26 21:24:46.128

abstract:
The sins of the flesh and the mortification of the flesh characterize the biography of the saint known as Mary Magdalen. The polychrome wooden sculpture by Donatello from c.1455 was described by Vasari as: “wasted away by her fastings and abstinence."  The extreme emaciation of the figure contrasts with the image of the beautiful and mournful Magdalen frequently seen at the foot of the cross in medieval crucifixion scenes.  With virtually no documentation concerning its commission, much of the scholarship on this particular piece focuses on dating and the intended installation site.

This thesis aims to examine the relationship between the emaciated style and the manner of polychromy in Donatello’s Penitent Magdalen as an example of the redeeming power of penance.  On a figure known for a life of sin and prostitution but also redemption, the gilding juxtaposed with a haggard and ugly body creates a dynamic relationship between sanctity and beauty (or the lack thereof) and demonstrates the effect of penance on the sinner.  The extreme emaciation and rough finish of the piece, in tandem with the gilding of the hair, created an effect of light that was significant to the Renaissance understanding of the saint’s character but also to a larger discourse on female sexuality and spirituality.

The multifaceted character of Mary Magdalen and Donatello’s depiction of her was understood by Quattrocento Florentines on a variety of levels. Higher social classes would readily grasp the sculpture’s affinity with Petrarchan tropes and philosophical ideas, particularly in terms of light imagery and descriptions of love.  But the average viewer would also make more prosaic associations between the figure of the Magdalen and popular preaching and prostitution.

Through an examination of the cultural climate of fifteenth century Florence, this investigation will situate Donatello’s uniquely emaciated and gilded sculpture in the visual tradition of Magdalen imagery, motifs of female spirituality in Donatello’s career, the literary tradition of describing female beauty, and societal concerns about prostitution and female sexuality.

abstract: M.A.


title: Frame Partitioning in WiMax Mesh Mode

contributor:
Hassanein, Hossam S.
Computing

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subject:
Frame Partitioning
WiMax
Wireless Broadband Communication
QoS management

abstract: Thesis (Master, Computing) -- Queen's University, 2008-10-02 18:41:36.551

abstract:
WiMax or the IEEE 802.16 standard is one of the most promising broadband wireless
technologies nowadays. It is characterized by its high data rates, large coverage area,
flexible design and QoS support. The standard defines two modes of operation: Point-to-
Multi-Point (PMP) and the Mesh Mode. In the first mode, all nodes are connected
directly to the base station and communication is not allowed amongst nodes. In the mesh mode, nodes are placed in an ad hoc manner communicating to neighbors and relaying the traffic of other nodes. The goal of this thesis is to design a partitioning scheme for the frame structure of the Mesh mode. Increasing the frame utilization would
result in better support for QoS applications and optimized resource allocation, and
thus revenue increase from the service provider’s perspective.
The mesh frame is divided into control and data, which are further divided into
centralized and distributed portions. We propose a novel and efficient scheme for partitioning the data subframe between the two schedulers. We use a Markovian model
that studies the system behavior in the long run, and provides predictions based on
analysis of previous window of frames. We further enhance the decision by tuning the
partitioning through statistical analysis of smaller windows to accommodate demand
changes. Our simulations show that the proposed scheme achieves high utilization
under different network and traffic conditions and decreases the packet overflow.

abstract: M.Sc.


title: Poésie de l'absence : le rapport à l'autre chez trois poètes haïtiennes

contributor:
Hayward, Annette
Bongie, Christopher
French

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subject:
Haitian literature
Women poets
Absence
Otherness

abstract: Thesis (Master, French) -- Queen's University, 2008-09-26 15:50:00.063

abstract:
Although many in the contemporary academic world would avoid themes such as solitude, love, and, in the context of “francophone” literature, exile, I have decided to give these all the attention they deserve based on the importance they hold in the works themselves, and based on the depth they possess. It is thus from the perspective of the renewed light they bring on these topics that the following three works will be analysed: À vol d’ombre (1966) by Jacqueline Beaugé, Transparence en bleu d’oubli (1979) by Renée Marie-Ange Jolicœur, and La Fidélité non plus… (1986) by Yanick Jean. In order to contextualize these three works, I first provide a brief history of Haitian poetry in which particular attention is given to the contributions of women writers. This overview illustrates how Jean, Jolicœur and Beaugé use very general themes such as love and solitude, but also how they manage to set themselves apart.

Indeed, their works are unparalleled in Haitian literature because they constantly play with the conventions of love poetry and redefine the notion of absence. In order to establish how every absence contains traces of presence, my analysis bases itself in part on the theories of Derrida. I also explore how, in each of the collections of poems under consideration (although for different reasons), absence stifles any possibility of contact with the other. In order to understand this problem and underscore its importance, I refer to Hegel’s conception of the relationship to the other. Based on these premises, I conclude by showing how exile is a space that is at once filled with absence and with presence, and how the staging of the act of writing, in all three works, makes poetry and absence inseparable.

abstract: M.A.


title: Calpain: Transitioning From the Use of the Protease Core to the Full-Length Enzyme for the Development of Specific Substrates and Inhibitors

contributor:
Davies, Peter L.
Biochemistry

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subject: Calpain Calpastatin

abstract: Thesis (Master, Biochemistry) -- Queen's University, 2008-09-26 15:49:17.317

abstract:
Calpains are a family of calcium-dependent cysteine proteases involved in intracellular signaling. They participate in many normal cellular processes such as cell motility and apoptosis but when over-activated they contribute to diseases ranging from ischemic injury to neurodegenerative disorders.
The major calpain isoforms µ- and m- are large heterodimeric enzymes that are subject to autoproteolysis and aggregation when activated by Ca2+. To avoid these complications the protease core (domains I and II) has been used to screen inhibitors and design substrates. Using the protease core of µ-calpain, I showed that the superior calpain substrate, PLFMER, is cut at the intended scissile bond between F and M. Alanine substitutions at each position optimized the sequence to PLFAAR, which has a 2.3-fold higher turnover rate. The set of substrates derived from this study provided a tool for profiling the activity of calpain isoforms. One disadvantage of the protease core is that it is less active than the whole enzyme. This was even more apparent with the protease cores of the tissue-specific calpains 3, 8, 9 and 15 such that it prevented their use in substrate and inhibitor screening.
The recently solved crystal structure of calcium-bound full-length m-calpain has revealed additional sites for the interaction of substrates and inhibitors in the unprimed side of the catalytic cleft provided by domain III. To sample these sites, it is necessary to prevent the full-length calpain from aggregating and precipitating upon calcium binding. I have developed a method here that uses portions of calpastatin (CAST), the natural endogenous inhibitor and stabilizer of calpain, to keep the enzyme soluble. By artificially connecting those portions of calpastatin that bind to calpain domains IV and VI, it is possible to stabilize the enzyme without blocking its active site. Of the three constructs made, 1C-2A, 2C-3A, and 3C-4A, the 3C-4A peptide was shown to completely inhibit aggregation of m-calpain at a 1:1 molar ratio, as monitored by turbidity. This mechanism of stabilization will permit the use of full-length calpains for the development of specific substrates and inhibitors.

abstract: M.Sc.


title: A Novel Role for Calpain 4 in Podosome Assembly

contributor:
Mak, Alan
Biochemistry

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subject:
Calpain 4
Calpain
Src
Podosomes
Podosome assembly
Mouse embryonic fibroblast
Dorsal ruffles
PIX

abstract: Thesis (Master, Biochemistry) -- Queen's University, 2008-09-26 16:16:00.768

abstract: Podosomes are adhesive and invasive structures which may play an important role in numerous physiological and pathological conditions including angiogenesis, atherosclerosis, and cancer metastasis.  Recently, the cysteine protease m-calpain (m-Capn) has been shown to cleave cortactin, an integral component of the podosomal F-actin core, as well as various proteins found in the peripheral adhesive region leading to the disassembly of these dynamic structures.  In this study, I investigated whether Capn plays a role in the formation of podosomes downstream of c-Src.  I show that: 1) phorbol-12, 13-dibutyrate (PDBu) as well as c-Src-Y527F expression induces podosome formation in mouse embryonic fibroblasts; 2) PDBu- and constitutively active c-Src-induced podosome formation is inhibited by the knockout of the m- and µ-Capn small regulatory subunit Capn4 in mouse embryonic fibroblasts  (Capn4-/-), but is partially restored by re-expression of Capn4; 3) Capn4 localizes to podosomes; and 4) Inhibition of m- and µ-Capn proteolytic activity by the cell permeable calpain inhibitors has little effect on the formation of podosomes downstream of active c-Src.  I conclude that Capn4 may play a role in the assembly phase of podosomes independent of calpain proteolytic activity.  Work done in collaboration to determine a possible mechanism of action for the role of Capn4 in podosome assembly indicates that a possible binding partner of Capn4, β-PIX, co-localizes with, and shows in vivo association with Capn4.  Furthermore, β-PIX and Capn4 bind directly in vitro in the presence of Ca2+.  We conclude that Capn4 plays a role in podosome assembly, and this role may be through direct interaction with β-PIX in a calcium-dependent manner.

abstract: M.Sc.


title: Investigations into the Optical Properties of Individual, Air-Suspended, Single-Walled Carbon Nanotubes

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subject:
nanotube
carbon
photoluminescence
exciton
dynamics
ultrafast
femtosecond excitation correlation
FEC
relative humidity
spectroscopy
single-molecule
saturation
single-walled
fluorescence

abstract: Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2008-09-26 16:23:40.81

abstract:
Single-walled carbon nanotubes are naturally-forming nanostructures that have attracted
considerable recent research interest due to their unique opto-electronic properties
and comparative ease of fabrication. Two-thirds of nanotube species are semiconductors
due to symmetry conditions imposed by their pseudo-one-dimensional tubular structure, and exhibit band-gap photoluminescence when isolated from their environment. Despite their elegant structural simplicity, fundamental properties of carbon nanotubes, such as their intrinsic quantum efficiency, non-linear excitonic recombination mechanisms, and the role of environmental effects, continue to be disputed in the literature.

The design of an apparatus capable of observing nanotube photoluminescence is
presented, along with conclusive proof of the observation of a single (9,8)-chirality
nanotube in the form of spectral, spatial, and polarization-dependent measurements.

The dependance of the excitation and emission spectra of a single nanotube on the
excitation intensity is explored and the emission spectra found to be described by a
Gaussian peak function, in contrast to previously-reported results.

The unexpected ability to cause redshifts in the emission spectrum via the ambient
humidity is discovered, which has consequences on experimental best practices.

Photoluminescence quantum efficiencies are measured to be 4±2% and 13±6% for two different nanotubes. This is at the high end of the range for comparable literature
results, and supports the validity of a recent literature value for the effective atomic absorption coefficient for carbon, AC=1.6×10^−3nm^2, which is ten times greater
than previous literature values.

Pulsed power dependence studies show that the PL emission undergoes ‘hard’
saturation at an excitation intensity of 0.5×10^12photons/pulse/cm2, which is at
least 100 times lower than previous reports and provides insight into non-linear decay
dynamics. A novel theoretical model is developed to explain this saturation process,
which yields an absorption co-efficient of AC=1.2±0.3×10^−3nm^2 as a fit parameter.

Time-resolved photoluminescence dynamics are explored using femtosecond excitation
correlation spectroscopy. Results suggest that the one-body decay processes
are bi-exponential, with time constants of 31±4ps and 313±61ps, but also highlight the limitations of this technique in observing the expected very rapid (~1 ps) two-body Auger recombination process.

abstract: M.Sc.


title: Values of the past and the future: cultural differences in temporal value asymmetry

contributor:
Ji, Li-Jun
Psychology

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subject:
Culture
Temporal Value Asymmetry
Temporal Orientation

abstract: Thesis (Ph.D, Psychology) -- Queen's University, 2008-09-26 16:18:09.371

abstract:
Past research has indicated that Chinese culture is more past oriented; whereas North American culture is more future oriented. Such cultural differences in temporal orientation may affect how people value future and past events. I predicted that the typical temporal asymmetry effect among European North Americans - placing more value on future events than on past ones - would be reversed among Chinese due to the cultural differences in temporal orientation.
I conducted four studies to examine how culture affects the values people attached to past and future events. Overall, the results supported my predictions. Across all four studies, I found that European Canadians attached more monetary value to an event in the future than to an identical event in the past with similar temporal distance; whereas Chinese people placed more monetary value on a past event than on an identical future event. In Study 3, I also investigated the underlying mechanisms that would account for such cultural differences. Among the three mediators believed to be affected by the past and future orientations, I found two that mediated the cultural influences on the temporal value asymmetry effect: (1) emotions associated with future and past events, and (2) mental simulations of future and past events. Specifically, European Canadians predicted stronger emotions for future events than what they recalled for past events, whereas Chinese showed an opposite trend. Emotions associated with future or past events, in turn, predicted the monetary values attached to the events. In addition, relative to Chinese Canadians, who showed clearer mental simulations for past than for future events, European Canadians had clearer mental simulations for future than for past events. Mental simulations, in turn, showed a positive association with the monetary value assigned to the events.

abstract: PhD


title: An Empirical Study of a Language - based Security Testing Technique

contributor:
Dean, Thomas R.
Computing

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subject: testing security protocol DRDA

abstract: Thesis (Master, Computing) -- Queen's University, 2008-09-26 16:31:32.565

abstract:
Application layer protocols have become sophisticated to the level that they have become languages in their own right. Security testing of network applications is indisputably an essential task that must be carried out prior to the release of software to the market. Since factors such as time-to-market constraints limit the scope or depth of the testing performed, it is difficult to carry out exhaustive testing prior to the release of the software. As a consequence, flaws may be left undiscovered by the software vendor, which may be discovered by those of malicious intent.

	We report the results of an empirical study of testing the Distributed Relational Database Architecture (DRDA®) protocol as implemented by the IBM® DB2® Database for Linux®, Unix®, and Windows® product, using a security testing approach, and a framework which implements that approach, that emerged from the joint work of the Royal Military College of Canada and Queen's University of Kingston. The previous version of the framework was used in the past to test the implementations of several network protocols. Compared to DRDA, these protocols are relatively simple, as they possess a much fewer number of structure types, messages and rules.

	From our study of the DRDA protocol, several omissions in the framework were uncovered, and were implemented as part of this work. In addition, the framework was automated, a preliminary automated test planner was created and a primitive language was created to provide the ability to describe custom-made test plans. Testing revealed two faults in the DB2 server, one of which was unknown to the vendor, prior to the testing that was carried out as part of this thesis work.

abstract: M.Sc.


title: Delamination of Oil Paints from Acrylic Grounds

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subject:
Art Conservation
Paintings

abstract: Thesis (Master, Art Conservation) -- Queen's University, 2008-09-26 16:44:35.814

abstract: Many modern artists paint in oil or oil-modified alkyd paints over acrylic grounds. In some cases the oil based paints do not remain adhered to the ground. In a set of composite samples of oil or alkyd paints, over acrylic grounds, naturally aged for nine years, some of the samples delaminated. Samples were analyzed with X-ray fluorescence (XRF), inductively coupled plasma (ICP), Fourier transform infrared - attenuated total reflectance (FTIR-ATR), scanning electron microscopy (SEM),  pyrolysis gas-chromatography mass-spectrometry (PY-GC/MS), laser desorption/ionization mass-spectrometry (LDI-MS), atomic force microscopy (AFM) and other methods, in order to find what the delaminating ones have in common. In addition, two examples of severely delaminating paintings were examined, to confirm the results from the laboratory-prepared samples. Results indicate the main cause of delamination is metal soaps in the oil paint and particularly zinc soaps. There is some evidence that metal soaps were more concentrated at the interface between the layers and this disrupted the adhesion. The ground is a minor consideration as well, rougher grounds providing better adhesion than smooth ones.

abstract: M.A.C.


title: Valuing Distributive Equality

contributor:
Kumar, Rahul
Philosophy

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subject:
Distributive equality
Rawls

abstract: Thesis (Master, Philosophy) -- Queen's University, 2008-09-26 17:06:38.455

abstract: Distributive equality can be valued in different ways, which can be rendered as definitions of ways to value distributive equality.  Those definitions can be used to investigate the value, if any, that distributive equality is held to have by particular principles which regulate distributive shares.  Distributive equality can be valued as a matter of justice in two different ways; it can be an intended consequence of a principle of justice and it can be among the grounds for a principle of justice.  The definitions of those two ways of valuing distributive equality can be used to investigate the value, if any, that distributive equality is held to have by Rawls’s interpretation of the second principle of justice.  Distributive equality can be valued for reasons relating to social relations rather than justice.  When distributive equality is valued for reasons relating to social relations, a definition of that way of valuing distributive equality can be specified by reference to the reasons provided.  When distributive equality is valued for reasons relating to social relations, the relevance and implications of that way of valuing distributive equality with regard to the prior question of how society should be organized can be investigated by reference to the reasons provided.

abstract: M.A.


title: Le regard dans "L'art du maquillage" de Sergio Kokis

contributor:
Hayward, Annette
French

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subject:
Quebec Literature
Sergio Kokis
Le regard
Le masque

abstract: Thesis (Master, French) -- Queen's University, 2008-09-26 17:50:07.53

abstract: "L’art du maquillage" (1997), a novel by Sergio Kokis, a Quebec author originally from Brazil, not only illustrates the theme of exile but also the universal theme of self discovery, making it a true bildungsroman. This thesis undertakes an analysis of the role of the regard — a concept difficult to translate that includes the idea of the gaze, the look, the eye, as well as one’s perception or point of view — in order to examine its impact on the protagonist Max’s search for identity. This is accomplished in conjunction with a study of the role of the paratext of the novel and various other themes such as counterfeiting, the role of the female figure as “other” and the question of “reality” and “truth”. By way of his encounters with Marilyn de Rosemont, Caroline, Brenda, Annette and Vera, as well as the influence of the artists imitated (notably Marc-Aurèle Fortin, René Richard, Egon Schiele and Otto Dix), Max describes his evolution as an artist and as a counterfeiter. By exploring the role played by the regard in the act of creation (lending particular attention towards the end to "Les langages de la création", an essay by Kokis himself) and in the search for self, we discover the transformative power it engenders and the fact that it is a plurality of regards that orient us in the world, in our interactions with others and in our self conceptions. This plurality of the regard is well illustrated by the combination of the written word and visual art chosen as the form of expression in this novel, resulting in a captivating example of the implications of the power of representation. The narrator’s story and the accompanying illustrations, as well as the works of art described therein, allow the reader to grasp a new understanding of the importance an individual’s point of view exerts on “reality”, and the complexity of the role the regard plays in every aspect of creation.

abstract: M.A.


title: Numerical Investigation of the Scavenging Flow in a Two-Stroke Engine with Passive Intake Valves

contributor:
Ciccarelli, Gabriel
Mechanical and Materials Engineering

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subject:
Two-Stroke
Computational Fluid Dynamics
Fluid-Structure Interaction

abstract: Thesis (Master, Mechanical and Materials Engineering) -- Queen's University, 2008-09-26 18:38:53.375

abstract: The development of a numerical model of a two-stroke engine is undertaken to study the scavenging characteristics of the engine. The engine design is unique in its use of 16 passive intake valves in the cylinder head which, along with the exhaust ports located at bottom centre (BC), give the engine a top-down uniflow-scavenged configuration. Each valve constitutes a small stainless steel platelet within a cavity in the cylinder head which reacts to the pressure difference across the cylinder head. The principle focus of this study is the transient simulation of the scavenging flow using dynamic meshing to model the piston motion and the response of the passive intake valves to the scavenging flow for varied engine speed and peak pressure. A flowbench study of the steady flow through the cylinder head into a duct is incorporated as a step in the development of the transient numerical model. Validation of the numerical predictions is undertaken by comparing results from an experimental flowbench for the steady case and using a cold-flow scavenging rig for the transient simulations. Both the steady flow through the cylinder head and the unsteady flow within the cylinder indicate the presence of a recirculation region on the cylinder axis. As a result, short-circuiting of scavenging gas becomes considerable and leads to scavenging characteristics comparable to Hopkinson’s perfect mixing one-dimensional scavenging model.

abstract: M.A.Sc.


title: Effect of Alcohol Consumption and Alcohol Dehydrogenase 1C (ADH1C) Polymorphisms on Total Plasma Homocysteine Levels

contributor:
King, Will D.
Massey, Thomas E.
Community Health and Epidemiology

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subject: ADH1C Alcohol Homocysteine

abstract: Thesis (Master, Community Health & Epidemiology) -- Queen's University, 2008-09-26 21:06:15.185

abstract:
BACKGROUND: Evidence supports that an elevated level of total plasma homocysteine (tHcy) signifies a breakdown in the methionine-homocysteine cycle.  This may result in folate deficiency, DNA methylation and oxidative stress, all of which are potential mechanisms that may lead to cancer.  Few studies examined the effects of alcohol consumption on tHcy levels. No studies considered polymorphisms in alcohol dehydrogenase 1C (ADH1C), a gene that encodes for an enzyme that metabolizes alcohol to acetaldehyde, a folate antagonist; ADH1C*1 encodes for an enzyme with a higher capacity to generate acetaldehyde than ADH1C*2.

PURPOSE: This study examined the association between alcohol intake and risk of elevated tHcy while exploring a potential gene-environment interaction with polymorphisms in ADH1C.

METHOD: This was a case-control study nested in a larger cross-sectional study funded by Canadian Institutes of Health Research.  The target population was recruited from Kingston and Halifax from 2006 to 2008 and included 100 cases and 187 controls selected from healthy male and female subjects aged 20-50 years.  Cases were defined as subjects with tHcy ≥ 10 mol/L and controls < 10 mol/L.  Alcohol consumption was categorized into three groups: ≤12.0 g/day, 12.1–24.0 g/day, and >24.0 g/day.  ADH1C was dichotomized by collapsing ADH1C*1/*2 and ADH1C*2/*2 into one group and examined against ADH1C*1/*1.

RESULTS: Compared to ≤12.0 g/day, odds ratio (OR) for 12.1-24.0 g/day was 0.53 [95% confidence interval (CI), 0.25-1.13] and for >24.0 g/day was 1.19 (95% CI, 0.60-2.24), suggesting a J-shaped trend with risk of elevated tHcy.  A reduced OR was observed for ADH1C*1/*1 (OR= 0.52, 95% CI, 0.27-1.03).  The alcohol-ADH1C interaction was not statistically significant (p-value = 0.21), though a stronger J-shape trend was suggested in ADH1C*1/*1.  Among consumers of ≤12.0 g/day, a reduced measure of effect was observed for ADH1C*1/*1 (OR= 0.44, 95% CI, 0.19-1.00).

CONCLUSION: A J-shaped trend was suspected between risk of elevated tHcy and alcohol consumption. Additionally, a nonsignificant reduced effect of ADH1C*1/*1 on risk of elevated tHcy, with a more pronounced effect in the lowest group of alcohol consumption. This suggests that ADH1C may be associated to homocysteine through factors unrelated to alcohol intake.

abstract: M.Sc.


title: Reliability-based Detection of Variable-rate Space-time Block Codes

contributor:
Yousefi, Shahram
Electrical and Computer Engineering

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subject:
Wireless Communications
Variable-Rate Space-Time Block Codes
MIMO Systems
Near-ML Detection

abstract: Thesis (Master, Electrical & Computer Engineering) -- Queen's University, 2008-09-26 23:45:07.81

abstract:
We present a new sub-optimal near-maximum-likelihood (ML) detection
method for the family of variable-rate space-time block codes
(VRSTBC). The proposed detection method is based on the concept of
symbol reliability and provides a wide range of
performance-complexity trade-offs. The reliability measures are
defined with the help of a recent generic ML metric expression.  The
error performance and complexity analysis of the method via
simulations show an achievable near-ML error performance with
significant reduction in complexity. The performance of the proposed
method is also compared with the group interference cancellation
(GIC) method which was the detection method originally applied to
VRSTBCs and the results show a significant improvement. The new
method offers various levels of error protection via a simple
parameter and hence can provide the users of a wireless network with
different performance levels according to their cost allowance.
Unequal error protection by VRSTBCs under the new detection method
was explored. Several applications integrating data with different
levels of sensitivity to error can benefit from the wide range of
possibilities that the combination of the proposed detection method
and VRSTBCs provides. To further explore these flexibilities, four
practically interesting power allocation schemes were applied to the
transmission and the behaviors were observed through case studies.

abstract: M.Sc.


title: Dynamic Analysis of a FRP Deployable Box Beam

contributor:
Green, Mark F.
Eriki, Marie-Anne
Wight, Gordon
Civil Engineering

format:
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subject: bridge dynamics FRP deployable

abstract: Thesis (Master, Civil Engineering) -- Queen's University, 2008-09-26 22:49:59.077

abstract:
Fibre reinforced polymers (FRPs) are currently being used in new bridge construction as
a feasible alternative material for corroded bridge deck replacements, footbridges, and emergency
vehicle bridges. For both military and civilian applications, there exists a need for bridges that
are lightweight and inexpensive, that can be readily transported and easily erected.
The 10 m glass FRP deployable box beam presented in this thesis was developed to aid
cross-country mobility in areas where infrastructure has been damaged by conflict or natural
disasters. The box beam represents one trackway of a dual trackway system. The quasi-static
and dynamic behaviour of the box beam was investigated under laboratory and field conditions.
Quasi-static tests were conducted to ensure the strength of the steel hinge, the hinge connection to
the base plate of the box beam, and the overall box beam would support the vehicle loads in field
testing. Data from these tests were used to validate the finite element model. Field testing was
conducted to investigate the natural frequencies of the box beam, calculate the dynamic increment
of the structure, and confirm the validity of the finite element model created in Matlab. Three
vehicles were used to evaluate the response of the box beam to different types of suspension,
loads, and number of wheels per trackway.
A finite element model was developed to predict the displacement of the bridge under
various vehicle loads. The analysis resulted in displacement contours within a reasonable amount
of error when compared to those measured in field testing. Recommendations for future research
and development of the structure are provided based on this research.

abstract: M.Sc.


title: Large-Scale Exogenous Forcing of Long-Term Pacific Salmon Production and Ecosystem Interactions in Western North America

contributor:
Smol, John P.
Biology

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subject:
Pacific Salmon
Paleolimnology
Climate Change
Climate Variability
Limnology
Fisheries Management
Stable Isotopes
Diatoms
Cladoceran Zooplankton
Solar Variability
Natural Variability

abstract: Thesis (Ph.D, Biology) -- Queen's University, 2008-09-27 02:41:54.576

abstract:
Pacific salmon (Oncorhynchus spp.) production strongly influences the ecosystems, cultures and economies of the Northeast Pacific. Historical variability in population sizes is complex, reflecting natural and human drivers. The nature and extent of such ‘exogenous’ controls on salmon and their nursery ecosystems are poorly understood, a significant impediment to sustainable fisheries management.  Novel applications of paleolimnology demonstrate that past sockeye salmon abundances and nursery system ecology can be reconstructed from lake sediments.  This thesis focuses on employing these techniques to establish the forcing mechanisms underlying salmon population and ecosystem dynamics, and determine the effects and interactions of fisheries management.

I provided the first reconstruction for a southern North American stock, which demonstrated the influences of both conspicuous (e.g. commercial fishery, main-stem damming) and uncertain human impacts (e.g. local damming) on endangered salmon declines.  By reconstructing ecological variability at multiple trophic levels, I established that rehabilitative management (e.g. fish stocking) may have permanently altered nursery lake rearing capacity, a change potentially reinforced by recent atmospheric changes.  This work highlights significant impediments to ongoing recovery efforts.

I extended my analysis of salmon management by exploring the interactive impacts of exotic salmon stocking on a remote northern lake.  I demonstrated the utility of long-term data in pre-emptively understanding the complex impacts of stocking by documenting the long-term trajectories in limnological conditions.  Integrating modeling, limnological and paleolimnological analyses, I determined that climate change and salmon introductions compound to alter chemical, physical and biological lake variables, ultimately altering ecosystem structure and functioning.

Finally I reconstructed salmon abundances over the past six millennia, the longest record and the first Canadian example to date, demonstrating salmon production is cyclical and far more variable than observed in the monitoring record.  My analyses established that North Pacific salmon production is forced by ocean-atmospheric teleconnections ultimately linked to climatic variability in the tropical Pacific. Further analyses provided the first evidence for a possible solar forcing of Holocene salmon production on both orbital and higher frequency time scales.

Cumulatively this research improves our understanding of the processes underlying variability in Pacific salmon and their natal ecosystems, important to ecologically-informed future management.

abstract: PhD


title: The Universal Similarity Metric, Applied to Contact Maps Comparison in A Two-Dimensional Space

contributor:
Glasgow, Janice I.
Computing

format:
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subject:
bioinformatics
proteomics
kolmogorov complexity
universal similarity metric
protein contact map
contact map comparison
protein structure prediction

abstract: Thesis (Master, Computing) -- Queen's University, 2008-09-27 05:53:31.988

abstract: Comparing protein structures based on their contact maps is an important problem in structural proteomics. Building a system for reconstructing protein tertiary structures from their contact maps is one of the motivations for devising novel contact map comparison algorithms. Several methods that address the contact map comparison problem have been designed which are briefly discussed in this thesis. However, they suggest scoring schemes that do not satisfy the two characteristics of “metricity” and “universality”. In this research we investigate the applicability of the Universal Similarity Metric (USM) to the contact map comparison problem. The USM is an information theoretical measure which is based on the concept of Kolmogorov complexity. The ultimate goal of this research is to use the USM in case-based reasoning system to predict protein structures from their predicted contact maps. The fact that the contact maps that will be used in such a system are the ones which are predicted from the protein sequences and are not noise-free, implies that we should investigate the noise-sensitivity of the USM. This is the first attempt to study the noise-tolerance of the USM. In this research, as the first implementation of the USM we converted the two-dimensional data structures (contact maps) to one-dimensional data structures (strings). The results of this implementation motivated us to circumvent the dimension reduction in our second attempt to implement the USM. Our suggested method in this thesis has the advantage of obtaining a measure which is noise tolerant. We assess the effectiveness of this noise tolerance by testing different USM implementation schemes against noise-contaminated versions of distinguished data-sets.

abstract: M.Sc.


title: A New paradigm for Ultrasound-Based Tissue Typing in Prostate Cancer

contributor:
Abolmaesumi, Purang
Mousavi, Parvin
Computing

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subject:
ultrasound
prostate cancer
tissue typing

abstract: Thesis (Ph.D, Computing) -- Queen's University, 2008-09-27 07:51:11.45

abstract:
Prostate cancer is the most common malignancy among men. The gold
standard clinical diagnosis method for prostate cancer is histopathologic analysis of biopsy samples acquired under ultrasound
guidance. However, most prostate tumors lack visually distinct appearances on medical images. Therefore, pathologically significant
cases of cancer can be missed during biopsy, resulting in false negative or repeated trials. The goal of our research is to augment ultrasound-guided prostate biopsy by adding tissue typing information that can be used for targeted biopsies. As a new
paradigm in tissue typing, we hypothesize and demonstrate that if a specific location in tissue undergoes sequential interactions with ultrasound, the time series of echoes, which we call radiofrequency (RF) time series, would carry ``tissue typing'' information. We provide a potential physical explanation for this phenomenon and
justify it based on computer simulations of the ultrasound probe and scattering media. We also report laboratory and animal studies that illustrate the utility of the method. We rely on a set of seven spectral and fractal features extracted from RF time series for tissue typing.

To show the clinical value of the proposed approach, we report an ex-vivo study involving 35 patients in which the utility of
RF time series features for detection of prostate tumors is confirmed. The outcomes are validated using histopathologic disease
distribution maps provided for the studied specimen. We show that the RF time series features are powerful tissue typing parameters that result in an area under receiver operating characteristic (ROC)
curve of 0.87 in 10-fold cross validation for diagnosis of prostate cancer. They are significantly more accurate and sensitive than spectral features extracted from single RF frames, and also B-scan texture features (area under ROC curve of 0.78 and 0.72,
respectively). A combination of these three categories of features results in a feature vector that provides an area under ROC curve of 0.95 in 10-fold cross-validation and 0.82 in leave-one-patient-out cross validation for diagnosis of prostate cancer. Using this hybrid feature vector and support vector machines, we create cancer distribution probability maps that highlight areas of tissue with high risk of cancer.

abstract: PhD