title: Characterization of Pulse–Shape Discrimination for Background Reduction in the DEAP-1 Detector

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subject:
Dark Matter
Argon detector

abstract: Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2009-01-26 09:28:25.432

abstract:
DEAP (Dark Matter Experiment with Argon and Pulse Shape Discrimination) is
an experiment that aims to directly detect dark matter particles via nuclear recoils
in liquid argon. The experiment uses the scintillation property of liquid argon as a
means to discriminate the γ and β backgrounds from the expected signal. DEAP-1
is a 7 kg single phase liquid argon detector. It was constructed to demonstrate the
scalability for a larger (3600 kg) detector. The detector was originally operated at
Queen’s University, where the background rejection level achieved was 6.3×10−8 for
the recoil detection efficiency of 97.1%. The detector was relocated to SNOLAB,
where the background in the energy region of interest was reduced by a factor of
7.7 (from 4.61±0.17 mHz to 0.60±0.05 mHz.). The background rejection level of
9.64×10−9 (10.4 part per billion) was achieved from the combined data set (Queen’s
University and SNOLAB) for a recoil detection efficiency of 35.5 ± 1.3 %. With
the current background rate, the background rejection level required for the 3600 kg
detector (1.8×10−9 ) is projected to be achieved in 382 days at the neutron efficiency
of 9.1±0.6 %.

abstract: M.Sc.


title: MIMO-aware Medium Access Control in IEEE 802.11 Networks

contributor:
Hassanein, Hossam S.
Electrical and Computer Engineering

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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:
Wireless LANs
Medium Access Control

abstract: Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2009-01-26 10:11:16.729

abstract:
Wireless Mesh Networks (WMNs) are dynamically self-organized and self-configured, where the nodes in the network automatically establish an ad hoc network and maintain mesh connectivity. These properties make WMNs a key technology for next generation wireless networking. However, supporting Quality of Service (QoS) to enable multimedia services is still one of the major issues in next-generation WMNs.

In distributed systems like WMNs, the Medium Access Control (MAC) layer is considered very important in the IEEE 802.11-based wireless networks, as it supports many crucial operational functions. Hence, QoS support in WMNs can be enhanced through the efficient cross-layer design of MAC protocols that utilizes advanced physical layer technologies viz Multiple-Input Multiple-Output (MIMO) with its multiple spatial channels that are capable of simultaneous receive or transmit streams. MIMO has become a very attractive technology in providing support for different QoS requirements.

In this thesis we propose a novel QoS MIMO-aware MAC Protocol (QMMP). QMMP is a MAC protocol framework that exploits the MIMO system gains to boost QoS support. The proposed MAC framework includes the following components. The first component enables concurrent sharing of the increased MIMO bandwidth, i.e., instead of allocating all the spatial channels to one connection, connections can concurrently share the increase bandwidth via splitting the spatial channels. The second component reduces the medium access collisions problem. In distributed systems like WMNs, medium access collisions have a noticeably negative impact on resource (bandwidth) utilization as they leave the bandwidth unutilized for a long time. To address this problem, we propose a spatial channels sharing scheme during medium contention period. The third component boosts the bandwidth utilization during data transmission. We propose resource management schemes that adapt the physical data rate and the aggregation frame length according to the instantaneous channel quality. Then we propose a QoS-aware bandwidth provisioning mechanism that performs effective bandwidth distribution to further boost QoS support.

abstract: PhD


title: The Role of Neu1 Sialidase in Toll-Like Receptor Activation

contributor:
Szewczuk, Myron R.
Microbiology and Immunology

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subject:
Toll-Like Receptors
Neu1 Sialidase
Glycosylation

abstract: Thesis (Ph.D, Microbiology & Immunology) -- Queen's University, 2009-01-26 12:33:32.743

abstract: Receptor glycosylation is critical in receptor-ligand interactions in immune cells, but the exact role of glycosylation in receptor activation upon ligand binding has not been elucidated. In neuronal cells, we have shown that when neurotrophic factors bind their respective Trk tyrosine kinase receptors, receptor activation and subsequent neurotrophin-mediated signaling is dependent upon the induction and activity of an endogenous sialidase enzyme. In this thesis, we report that toll-like receptor (TLR) activation upon ligand binding is similarly dependent on the induction of a cellular sialidase, which we have identified as Neu1 sialidase, which specifically targets and hydrolyses alpha-2,3-linked sialic acid residues on the receptor. Blocking Neu1 sialidase activity with specific inhibitor Tamiflu detrimentally impacts ligand-induced TLR4/MyD88 interaction, NFkappaB activation and TLR-mediated effector responses like nitric oxide and pro-inflammatory cytokine production. Diminished cytokine production is also seen in vivo in Neu1-deficient mice.  We propose a mechanism for the induction of Neu1 sialidase, upon ligand binding to TLR, that involves the activation of heterotrimeric G-alpha protein-dependent G-protein coupled receptor (GPCR) signaling to activate a matrix metalloproteinase (MMP) enzyme, likely MMP-9. It is suggested that MMP-(9) targets the cell surface elastin receptor complex of Neu1/protective protein cathepsinA/elastin binding protein (EBP), which potentially catalytically activates Neu1. In addition, we report an association between Neu1 and TLR2, TLR3 and TLR4 on the plasma membrane that has not previously been described. The idea that the multiple functionality and diversity of TLRs and TLR-mediated signaling may be an immunologic paradigm capable of explaining all human disease is provocative but plausible. Certainly, the structural integrity of TLRs, their ligand interactions and activation are essential for immunological protection. Thus, understanding the molecular mechanism of Neu1 sialidase regulation of TLR activation will provide important opportunities for disease control through TLR manipulation. The future directions of this research will also open a new area of glycobiology research (the glycomics of innate immune responses) and will widen the scope for the development of novel therapeutic drugs to combat infections and inflammatory diseases.

abstract: PhD


title: Dynamic Pile-Soil Interaction in Laterally Spreading Slopes

contributor:
Take, W. Andy
Civil Engineering

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subject:
Pile-Soil interaction
Lateral Spreading
Liquefaction

abstract: Thesis (Master, Civil Engineering) -- Queen's University, 2009-01-27 10:09:43.902

abstract:
The collapse of buildings and infrastructure is an unfortunate consequence of major earthquakes (e.g., the 1964 Alaskan earthquake, the 1995 Kobe earthquake in Japan and the 2007 Pisco earthquake in Peru). Liquefaction-induced lateral spreading is known to be one cause of severe damage to deep foundation systems. However, the dynamic soil-structure interaction between liquefied soil and piles is extremely complex and further work is required to define the appropriate design pressures and to understand the mechanisms at work.
This thesis presents the findings of an experimental program carried out using the large geotechnical centrifuge at C-CORE in St John’s Newfoundland, to investigate the mechanism of lateral spreading and its implications for dynamic soil-pile interaction. Soil and pile responses were measured using accelerometers, pore pressure transducers, and digital imaging using a high speed camera. Using these images, transient profiles of slope deformation were quantitatively measured using Particle Image Velocimetry (PIV). These tests illustrate the potential for earthquake shaking to excite the natural frequency of the liquefied soil column, which can lead to increased transient lateral pressures on piles in liquefiable ground. This study recommends that this potential for “auto tuning” should be anticipated in design and proposes a new limiting pseudo-static backbone p-y curve for use in the design of piles subjected to lateral spreading ground deformation.

abstract: M.Sc.


title: A New Power Signal Processor for Converter-Interfaced Distributed Generation Systems

contributor:
Bakhshai, Alireza
Joos, Geza
Electrical and Computer Engineering

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subject:
Distributed Generation Systems
Grid Synchronization

abstract: Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2009-01-27 11:37:07.279

abstract:
Environmentally friendly renewable energy technologies such as wind and solar energy systems are among the fleet of new generating technologies driving the demand for distributed generation of electricity. Power Electronics has initiated the next tech¬nological revolution and enables the connection of distributed generation (DG) systems to the grid. The challenge is to achieve system functionality without extensive custom engineering, yet still have high system reliability and generation placement flexibility. Nowadays, it is a general trend to increase the electricity production using DG systems. If these systems are not properly controlled, their connection to the utility network can generate problems on the grid side. Therefore, considerations about power generation, safe running and grid synchronization must be done before connecting these systems to the utility network.
This thesis introduces a new grid-synchronization, or more visibly a new “power signal processor” adaptive notch filtering (ANF) tool that can potentially stimulate much interest in the field and provide improvement solutions for grid-connected operation of DG systems.  The processor is simple and offers high degree of immunity and insensitivity to power system disturbances, harmonics and other types of pollutions that exist in the grid signal. The processor is capable of decomposing three-phase quantities into symmetrical components, extracting harmonics, tracking the frequency variations, and providing means for voltage regulation and reactive power control.  In addition, this simple and powerful synchronization tool will simplify the control issues currently challenging the integration of distributed energy technologies onto the electricity grid. All converter-interfaced equipments like FACTS (flexible ac transmission systems) and Custom Power Controllers will benefit from this technique. The theoretical analysis is presented, and simulation and experimental results confirm the validity of the analytical work.

abstract: PhD


title: Origin and Geochemistry of Modern Bahamian Ooids

contributor: Geological Sciences and Geological Engineering

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subject:
Ooid
Bahamas
d18O
d13C
Mg/Ca
Sr/Ca
Radiocarbon Dating

abstract: Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2009-01-27 13:29:42.765

abstract:
The Bahamian Archipelago is one of the few locations in the world where ooid formation is actively occurring. Ooid cortices from six locations in the region were incrementally dissolved and analyzed for 14C, δ18O, δ13C, Mg/Ca and Sr/Ca ratios. Ooids were examined under SEM after each step in the incremental analyses to characterize the nature of dissolution. Radiocarbon dating indicates that surface ooids began forming across the Archipelago between 1000 and 2800 yr BP and continue to form today.
The ooids have the same pattern of microboring alteration across the region.  The surface and outer cortex of the ooids are punctuated with unfilled microborings, whereas the inner cortex contains two morphologies of aragonite cement filling the microborings. The two morphologies of cement form in association with two different species of cyanobacteria, one is Solentia sp. the other is interpreted to be Hyella sp..
The chemistry of ooids from across the region is remarkably similar. δ18O and δ13C values for all samples vary directly, having a slope of approximately 1.  The outer cortex has low δ18O and δ13C values of -3.4‰ and 0.2‰ respectively, whereas the δ18O and δ13C values of the inner cortex are high with values of 1.9‰ and 6.8‰ respectively. The presence of aragonite cement in microborings in the inner cortex increases the overall isotopic composition of both oxygen and carbon in the ooid, causing it to appear close to equilibrium with seawater. The isotopic variation in δ18O and δ13C within the cortex can be characterized as a mixing line between the low values in the unaltered ooid laminae and the aragonite cement in the microborings.
The most exterior portion of the ooid has very high Mg/Ca values and is interpreted as an amorphous calcium carbonate (ACC) coating. There are two other phases in the cortex, both being aragonite.  The outer cortex has a higher Mg/Ca ratio and lower Sr/Ca ratio than the inner cortex. This difference in chemistry is a result of the presence of aragonite cement in the inner cortex.
Stable isotopic and trace element results coupled with SEM investigations indicate that microbes do not play a role in ooid formation, but instead alter the texture and chemistry of ooids after they have formed. This alteration occurs throughout the entire shoal region. A new model of ooid formation is proposed whereby a veneer of ACC precipitates on an ooid while it is at the sediment-water interface (the active phase).  This veneer of ACC later recrystallizes to aragonite needles, possibly nucleating on organic material and a new cortex layer is formed. Observations from this study lead to a deeper understanding of the chemical processes involved in ooid genesis, which allows for a better understanding of paleoenvironments hosting ooid formation.

abstract: M.A.Sc.


title: Encoding of Streaming Peripheral Information in Video Games

contributor:
Graham, Nicholas
Stewart, James
Computing

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subject:
Streaming Peripheral Displays
Video Games

abstract: Thesis (Master, Computing) -- Queen's University, 2009-01-28 10:41:41.602

abstract:
Traditional peripheral displays rely on drawing the user's attention and gaze through alerts. These displays function best when the central task does not require the user's constant attention. For tasks that require a user to always maintain focus, alert-based displays are not appropriate. We assert that conveying information to a user
without drawing his gaze, allows the user to maintain constant focus on his primary task while still receiving additional information. In this thesis we use video games to examine streaming peripheral displays as a means of presenting information without drawing gaze.

The results of our experiments showed no significant difference between user performance using our display encoded for peripheral viewing versus an unencoded display. Additionally,
we found that players were successfully able to perceive information shown on a streaming peripheral display, however, as game difficulty increased the effectiveness of the streaming peripheral display decreased. Finally, we show that as game level increases, users adopt risk-tolerant strategies. Drawing from these results, we have suggested some additional heuristics pertaining to streaming peripheral displays. Moreover, we have suggested further situations where streaming peripheral displays may be useful.

abstract: M.Sc.


title: Formative Computer-based Assessments: The potentials and pitfalls of two formative computer-based assessments used in professional learning programs

contributor:
Shulha, Lyn
Klinger, Don A.
Education

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subject:
Formative
Assessment
Computer-Based Assessment
Computer Assisted Assessment
Professional Learning
Higher Education

abstract: Thesis (Ph.D, Education) -- Queen's University, 2009-01-28 13:55:37.823

abstract: A case study approach is used to examine two formative computer based assessments (CBAs) used in a School of Medicine and Faculty of Education at a Canadian university. Both assessments contained primarily scenario-based, multiple-choice items however the number of items and complexity was different. The formative CBAs were examined in terms of how feedback is provided to students, the effectiveness of different types of feedback, and the characteristics of items used for assessment. Feedback was channelled to students in one case, immediately following responding to an item and in the second case, at the end of a set of items. Feedback given to students immediately following an item was more effective given that the timing captured students’ construction of knowledge. The most favoured type of feedback provided additional information. Students also indicated that feedback using a live internet link to direct them to a resource would be acceptable. Although feedback that simply stated a response was correct or incorrect was previously shown to be ineffective, students from the School of Medicine indicated this type of feedback was acceptable for low cognitive items. In both case studies, students reported that more items were required and in one case study, students recommended these items be added at the higher end of the cognitive scale.

abstract: PhD


title: Fps/Fes Kinase Regulates Cytoskeletal Reorganization and Migration of Mast Cells

contributor:
Craig, Andrew W.
Biochemistry

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subject:
Fps/Fes
Mast Cells
Migration

abstract: Thesis (Master, Biochemistry) -- Queen's University, 2009-01-28 15:05:04.056

abstract: Mast cells are granulocytes that require signaling from the receptor protein-tyrosine kinase Kit and its ligand stem cell factor (SCF) for their maturation and function. In addition to providing growth and survival signals, the Kit receptor is involved in crosstalk to β1 integrins leading to mast cell adhesion, spreading, and migration on fibronectin (FN). Previous studies reported the involvement of the non-receptor protein-tyrosine kinases Fps/Fes and Fer in signaling downstream of the high affinity IgE receptor in mast cells and identified cell migration defects in Fer-deficient bone marrow-derived mast cells (BMMCs). Fps/Fes also becomes phosphorylated downstream of the Kit receptor in BMMCs, and this involves the action of the Src family kinase Fyn as an upstream activator of Fps/Fes. In this study, the Fps/Fes SH2 domain was observed to bind the phosphorylated Kit receptor in vitro, suggesting that the SH2 domain plays a role in the activation mechanism of Fps/Fes. To investigate the function of Fps/Fes in Kit signaling, BMMCs were generated from wild-type and Fps/Fes-null mice. Analysis of downstream effectors revealed that Fps/Fes is required for maximal p38 MAPK signaling. Further examination of Fps/Fes-deficient BMMCs revealed increases in adhesion, spreading, and a defect in cell polarization on full-length FN (a ligand for multiple β1 integrins), compared to wild-type BMMCs. Similar phenotypes are observed using an α5β1 integrin-specific FN fragment (9-11) as the matrix. Reduced phosphorylation of the putative Fps/Fes substrate HS1 (a cortactin homologue involved in actin regulation) is observed in Fps/Fes-deficient BMMCs, compared to control cells, and this may contribute to the observed cytoskeletal defects. Restoring Fps/Fes expression in Fps/Fes-deficient BMMCs by retroviral transduction results in a rescue of cell spreading, polarization, and chemotaxis defects to levels similar to those of wild-type cells. This thesis provides novel insights into the potential mode of Fps/Fes activation downstream of the Kit receptor, and a role for Fps/Fes in regulating crosstalk between Kit and α5β1 integrins to promote cytoskeletal reorganization and motility of mast cells.

abstract: M.Sc.


title: Picturing Public Health Surveillance: Tracing the Material Dimensions of Information in Ontario’s Public Health System

contributor:
Lyon, David
Sociology

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subject:
Sociology
Surveillance Studies

abstract: Thesis (Ph.D, Sociology) -- Queen's University, 2009-01-29 15:28:27.326

abstract:
The aim of this dissertation is to explore public health surveillance from a surveillance studies perspective.  The public health system in Ontario, Canada, provides an ideal setting for such exploration, especially because of initiatives that have been undertaken in the wake of the 2003 outbreak of Severe Acute Respiratory Syndrome (SARS).  Post-SARS, local public health practice in Ontario has been increasingly overtaken by a system-wide imperative that seeks to transform surveillance through investment in large-scale, information technology (IT).  By critiquing the dominant conception of information in social scientific, public health and medical care discourse, and by exploring the increasing integration of large-scale IT into public health surveillance practice, this dissertation considers the uncertain trade-offs involved in the contemporary movement towards large-scale, IT-mediated public health surveillance systems.  The theoretical framework that guides this line of inquiry emerges out of a Deleuzian-Latourian tradition in surveillance studies.  This framework foregrounds the material assemblages, the network of people, machines, microbes, maladies, organizations, and so on, that make public health surveillance possible.  Material assemblages tend to be submerged from view, even marginalized, by large-scale, IT-mediated surveillance systems.  Such systems strive to immaterialize information.  They are organized according to an immaterial conception of information.  This arrangement fosters the marginalization of the material dimensions of information.

In order to empirically specify the heterogeneity of the marginalized material assemblages that make public health surveillance possible, 64 semi-structured, open-ended interviews were conducted with public health professionals and patients.  The main findings of this dissertation are explained using the example of communicable-disease surveillance, and particularly HIV/AIDS surveillance.  These findings highlight the systemic nature of marginalization that accompanies the increasing automation of public health surveillance.  They suggest the need to question whether large-scale, IT-mediated surveillance is optimally configured, not merely for the challenges posed by disease, but also for the broader provision of public health services.

abstract: PhD


title: Resource Management in Multi-hop Cellular Networks

contributor:
Hassanein, Hossam S.
Akl, Selim
Computing

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subject:
Multi-Hop
TDD
CDMA
Cellular Networks
Optimal
Channel Assignment
Cell Size
Coverage
W-CDMA

abstract: Thesis (Ph.D, Computing) -- Queen's University, 2009-02-02 22:53:41.825

abstract:
In recent years, mobile communications have become affordable and popular. High cellular capacity in terms of number of users and data-rates is in need. As the available frequency spectrums for mobile communications are limited, the utilization of the radio resources to achieve high capacity without imposing high equipment cost is of utmost importance. Recently, multi-hop cellular networks (MCNs) were introduced. These networks have the potential of enhancing the cell capacity and extending the cell coverage at low extra cost. However, in a cellular network, the cell or system capacity is inversely related to the cell size. In MCNs, the cell size, the network density and topology affect the coverage of source nodes and the total demands that can be served and, thus, the system throughput. Although the cell size is an important factor, it has not been exploited for maximizing throughput. Another major issue in MCNs is the increase in packet delay because multi-hopping is involved. High packet delay affects quality of service provisioning in these networks.

In this thesis, we propose the Optimal Cell Size (OCS) and the Optimal Channel Assignment (OCA) schemes to address the cell size and packet delay issues for a time division duplex (TDD) wideband code division multiple access (W-CDMA) MCN. OCS finds the optimal cell sizes to provide an optimal balance of cell capacity and coverage to maximize the system throughput, whereas OCA assigns channels optimally in order to minimize packet relaying delay. Like many optimized schemes, OCS and OCA are computationally expensive and may not be suitable for large real-time problems. Hence, we also propose heuristics for solving the problems. For the cell size problem, we propose two heuristics: Smallest Cell Size First (SCSF) and Highest Throughput Cell Size First (HTCSF). For the channel assignment problem, we propose the Minimum Slot Waiting First (MSWF) heuristic. Simulation results show that OCS achieves high throughput compared to that of conventional (single-hop) cellular networks and OCA achieves low packet delay in MCNs. Results also show that the heuristics, SCSF, HTCSF and MSWF, provide good results compared to the optimal ones provided by OCS and OCA, respectively.

abstract: PhD


title: Assessing changes in pollen assemblage and charcoal accumulation during known changes in climate from c. 5,400 to 3,300 Years Before Present at the forest-prairie ecotone in Alberta, Canada

contributor:
Cumming, Brian F.
Biology

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subject:
Sedimentary Charcoal
Paleoecology
Fire
Sedimentary Pollen

abstract: Thesis (Master, Biology) -- Queen's University, 2009-01-29 12:15:32.137

abstract: The ecotone between aspen parkland and mixed-grass prairie in mid-eastern Alberta is a climatically-sensitive area that has been subject to periods of enhanced aridity occurring at multi-decadal to centennial-scale cycles throughout much of the last 6000 years.  To assess the ecotonal response to changes in effective moisture, as inferred by diatom-inferred salinity, temporal variations in pollen and charcoal preserved in a sediment core from Chauvin Lake were analyzed over several diatom-inferred moisture-cycles from c. 5,400 to 3,300 YBP.  Changes in landscape vegetation were inferred by variation in both the percent relative abundance and influx rates of pollen taxa found in a sediment core from Chauvin Lake.  Variation in sediment charcoal accumulation rates for both total charcoal and morphotypes, as well as the percent relative abundance of charcoal morphotypes, were used to infer changes in landscape fire regimes during these aridity cycles. One-way ANOVAs were used to determine significant differences in average accumulation rates or relative abundances between the arid and more mesic periods.  Changes in the relative abundance of Cyperaceae and Ambrosia pollen between wet and dry periods suggests a shift in the spatial arrangement of vegetation, and a decrease in the sediment influx of most taxa, suggests a decrease in production of landscape vegetation during periods of aridity.  Charcoal morphotype analysis, especially variation in Type M, Type D and Type B, suggests fewer, more intense fires during periods of drought.  Lack of change in total charcoal may be related to increased secondary sedimentation of charcoal during periods of drought due to increased soil erosion.  This study suggests that the spatial arrangement and production of landscape vegetation is dependent on climate, and fire prevalence decreases during periods of drought due to reduced fuel availability.

abstract: M.Sc.


title: Automated Capacity Planning and Support for Enterprise Applications

contributor:
Hassan, Ahmed E.
Computing

format:
1354163 bytes
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subject:
Capacity Planning
Framework
Fault Resolution
Customer Support
Event Correlation

abstract: Thesis (Master, Computing) -- Queen's University, 2009-01-29 14:14:37.235

abstract:
Capacity planning is crucial for successful development of enterprise applications. Capacity planning activities are most consequential during the verification and maintenance phases of Software Development Life Cycle. During the verification phase, analysts need to execute a large number of performance tests to build accurate performance models. Performance models help customers in capacity planning for their deployments. To build valid performance models, the performance tests must be redone for every release or build of an application. This is a time-consuming and error-prone manual process, which needs tools and techniques to speed up the process. In the maintenance phase, when customers run into performance and capacity related issues after deployment, they commonly engage the vendor of the application for troubleshooting and fine tuning of the troubled deployments. At the end of the engagement, analysts create engagement report, which contain valuable information about the observed symptoms, attempted workarounds, identified problems, and the final solutions. Engagement reports are stored in a customer engagement repository. While information stored in the engagement reports is valuable in helping analysts with future engagements, no systematic techniques exist to retrieve relevant reports from such a repository.

In this thesis we present a framework for the systematic and automated building of capacity calculators during software verification phase.  Then, we present a technique to retrieve relevant reports from a customer engagement repository. Our technique helps analyst fix performance and capacity related issues in the maintenance phase by providing easy access to information from relevant reports. We demonstrate our contributions with case studies on an open-source benchmarking application and an enterprise application.

abstract: M.Sc.


title: Hamster Oviductin Enhances Tyrosine Phosphorylation of Sperm Proteins During Capacitation

contributor:
Kan, Frederick W. K.
Anatomy and Cell Biology

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subject:
Oviductin
Tyrosine Phosphorylation

abstract: Thesis (Master, Anatomy & Cell Biology) -- Queen's University, 2009-01-30 15:38:54.594

abstract: Capacitation is essential for fertilization of ovulated oocytes. Capacitation is correlated with activation of a signal transduction pathway leading to protein tyrosine phosphorylation, an essential prerequisite for fertilization. Oviductin has been shown to bind to the acrosomal cap and the equatorial segment region of the sperm head.  In light of findings reported in previous studies, we hypothesized that estrus stage-specific oviductin (EOV) enhances tyrosine phosphorylation. Immunofluorescent detection by light and confocal microscopy and immunogold labeling by electron microscopy and surface replica techniques were used to localize tyrosine phosphorylated proteins to the equatorial segment region and midpiece after incubation in medium in the presence or absence of EOV.   In the presence of EOV, an increase in tyrosine phosphorylation in the equatorial segment region was observed as early as 5 minutes after incubation. On prolonging incubation in medium containing EOV immunostaining further increased, indicative of increased levels of tyrosine phosphorylation of sperm proteins as capacitation proceeds. Regardless of the presence or absence of EOV, phosphotyrosine expression was observed along the tail, specifically at the midpiece. However, this reactivity was enhanced in the presence of EOV. Western blot analysis of NP-40 extractable and non-extractable sperm proteins confirmed these observations. NP-40 extractable sperm proteins (25, 37, 44kDa) and non-extractable sperm proteins (70, 83, 90kDa) showed increased intensity when sperm were capacitated in the presence of EOV after 5-, 60-, 120- and 180-minutes of capacitation. Mass spectrophotometric analysis identified enolase, ATP-specific succinyl CoA, succinate CoA ligase, zona pellucida binding protein, heat shock protein 90, aconitase and hexokinase as proteins that undergo enhancement in tyrosine phosphorylation in the presence of EOV. The proteins identified are known to be involved in specific functions including cellular metabolism, molecular chaperoning and normal sperm development. In summary, the present investigation has provided new evidence showing that sperm capacitated in vitro in the presence of EOV display an enhanced expression of tyrosine phosphorylation compared to sperm incubated in capacitating medium alone. These results indicate that inclusion of oviductin in media used for in vitro fertilization (IVF) may improve success rates of IVF by enhancing the signaling pathways involved in sperm capacitation.

abstract: M.Sc.


title: Long-Term Performance of HDPE Geomembranes as Landfill Liners

contributor:
Rowe, Kerry
Civil Engineering

format:
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subject:
Antioxidant
Degradation
Diffusive Migration
Geomembrane
HDPE
Landfill
Leachate
Long-Term Performance
Service Life
Simulated Landfill Liner
Temperature
Thickness
Volatile Organic Compounds
Geoenvironmental Engineering
Geotechnical Engineering
Civil Engineering

abstract: Thesis (Ph.D, Civil Engineering) -- Queen's University, 2009-01-30 09:30:49.135

abstract: High density polyethylene (HDPE) geomembranes are normally used as part of a composite liner for waste containment facilities such as municipal solid waste (MSW) landfills and heap leach pads. Field conditions, which include physical stresses on the geomembrane, elevated operating temperatures, and contact with leachate constituents, have the potential to affect the service life of the HDPE geomembranes. This thesis examined the long-term performance of different HDPE geomembranes based on both conventional laboratory accelerated immersion tests and simulated landfill liner tests. A 1.5mm HDPE geomembrane was immersed in different synthetic leachates at different temperatures in order to evaluate the effects of leachate chemical constituents on the depletion of antioxidants. The results showed that a basic leachate with trace metals, surfactant, and a reducing agent was the most appropriate for evaluating the potential degradation of HDPE geomembranes. A similar immersion test was performed to evaluate the effects of thickness on the ageing of HDPE geomembranes. Three commercially available HDPE geomembranes having nominal thicknesses of 1.5, 2.0, and 2.5mm were immersed in a synthetic leachate at four different temperatures in this experiment. The results showed that a thicker geomembrane may have a longer service life if other things are similar. The depletion of antioxidants from a 1.5mm thick HDPE geomembrane was examined by conducting accelerated ageing tests at 55, 70, and 85oC under simulated landfill liner conditions. The results showed that the antioxidant depletion rate was consistently lower for the simulated landfill liner tests compared to the leachate immersion tests. The effectiveness of the aged HDPE geomembrane on the migration of volatile organic compounds (VOCs) was examined by conducting diffusion and partitioning tests using both unaged and aged HDPE geomembranes. The results showed that the ageing of HDPE geomembranes did not increase diffusive migration of organic contaminants, provided that the geomembrane remained intact. A new method was developed to estimate the service life of the HDPE geomembrane based on the landfill liner temperature history. The service lives of the HDPE geomembranes were calculated to be between 20 and 4700 years, depending on the geomembrane type, exposure conditions, and the time-temperature history examined.

abstract: PhD


title: Quantitative Analysis of Multihop CDMA Cellular Networks

format:
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subject:
Cellular Networks
Multihop Relay
Capacity Analysis
Energy Consumption
Multihop Cellular Networks

abstract: Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2009-01-30 09:34:39.735

abstract:
Multihop Cellular Networks (MCNs) form combined wireless paradigm that carries the advantages of both traditional cellular networks and wireless multihop relay. Cellular networks depend on a fixed infrastructure to provide wide area coverage for users with high mobility profile. Multihop relay networks depend on wireless devices inside the network to relay signals through multiple hops from source to destination. MCNs were proposed to overcome inherent drawbacks in cellular networks like congestion and dead spots. These gains build on the characteristics of multihop relay that result in increased capacity, decrease energy depletion and virtually extended coverage. But while these gains have been widely accepted and advocated, they have not been verified in rigor. A realistic need therefore exists to quantify these gains in order to realize more capable network management functionalities for this new paradigm.
In this thesis, we present an analytical framework for MCNs. We quantify the capacity and energy consumption in MCNs, while considering various call distributions, network loads and transmission power. We apply our framework to Code Division Multiple Access (CDMA) cellular networks, which are very dependent on interference levels in their performance. Our results show that capacity can be increased in CDMA cellular networks using multihop relay by increasing either the number of simultaneous calls or data rates. We also demonstrate that consumed energy is decreased in MCNs, especially in environments with high path loss. We validate that multihop relay is most rewarding when calls tend to originate near cell borders. Beyond verifying basic claims, we explore other potential gains of MCNs. We investigate the viability of congestion relief and load balancing and substantiate the benefits for congested cells neighbored by lightly loaded cells. Load balancing has also been shown to increase data rates and fairness in user allocations. Lastly, we explore enabling multimedia applications in MCNs and study the application of data rate adaptations given multiple classes of service.
A key advantage of our work is that, while applied to CDMA in this thesis, the presented analytical framework can be extended to other technologies. The framework also accommodates both mobile and fixed network relay elements, expanding its applicability to next generation cellular networks.

abstract: PhD


title: Functional Characterization of TAFI mutants Resistant to Activation by Thrombin, Thrombin-Thrombomodulin or Plasmin

contributor:
Boffa, Michael
Biochemistry

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subject: TAFI, Coagulation, Fibrinolysis, Thrombin, Plasmin, Activation Kinetics

abstract: Thesis (Master, Biochemistry) -- Queen's University, 2009-01-30 11:44:37.191

abstract: Thrombin-activatable fibrinolysis inhibitor (TAFI) is a human plasma zymogen that acts as a molecular link between the coagulation and fibrinolytic cascades. TAFI can be activated by thrombin and plasmin but the reaction is enhanced significantly when thrombin is in a complex with the endothelial cofactor thrombomodulin (TM). The in vitro properties of TAFI have been extensively characterized. Activated TAFI (TAFIa) is a thermally unstable enzyme that attenuates fibrinolysis by catalyzing the removal of basic residues from partially degraded fibrin. The in vivo role of the TAFI pathway, however, is poorly defined and very little is known about the role of different activators in regulating the TAFI pathway. In the present study, we have constructed and characterized various TAFI mutants that are resistant to activation by specific activators. Based on peptide sequence studies, these mutants were constructed by altering key amino acid residues surrounding the scissile R92-A93 bond. We measured the thermal stabilities of all our mutants and found them to be similar to wild type TAFI. We have identified that the TAFI mutants P91S, R92K, and S90P are impaired in activation by thrombin or thrombin-TM, thrombin alone, and thrombin alone or plasmin, respectively. The TAFI mutants A93V and S94V were predicted to be resistant to activation by plasmin but this was not observed. The triple mutant, DVV was not activated by any of the aforementioned activators. Finally, we have used in vitro fibrin clot lysis assays to evaluate the antifibrinolytic potential of our variants and were able to correlate their effectiveness with their respective activation kinetics. In summary, we have developed activation resistant TAFI variants that can potentially be used to explore the role of the TAFI pathway in vivo.

abstract: M.Sc.


title: The type I antifreeze protein gene family in Pleuronectidae

contributor:
Davies, Peter L.
Biochemistry

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subject:
Antifreeze Protein
Starry Flounder
Gene Family
Type I
Pleuronectidae
Gene Dosage
Platichthys stellatus

abstract: Thesis (Master, Biochemistry) -- Queen's University, 2009-01-30 13:38:08.346

abstract:
Antifreeze proteins (AFPs) protect marine teleosts from freezing in icy seawater by binding to nascent ice crystals and preventing their growth.  It has been suggested that the gene dosage for AFPs in fish reflects the degree of exposure to harsh winter climates.  The starry flounder, _Platichthys stellatus_, has been chosen to examine this relationship because it inhabits a range of the Pacific coast from California to the Arctic.  This flatfish is presumed to produce type I AFP, which is an alanine-rich, amphipathic alpha-helix.

	Genomic DNA from four starry flounder was Southern blotted and probed with a cDNA of a winter flounder liver AFP.  The hybridization signal was consistent with a gene family of approximately 40 copies.  Blots of DNA from other starry flounder indicate that California fish have far fewer gene copies whereas Alaska fish have far more. 	This analysis is complicated by the fact that there are three different type I AFP isoforms.  The first is expressed in the liver and secreted into circulation, the second is a larger hyperactive dimer also thought to be expressed in the liver, and the third is expressed in peripheral tissues.  To evaluate the contribution of these latter two isoforms to the overall gene signal on Southern blots, hybridization probes for the three isoforms were isolated from starry flounder DNA by genomic cloning.  Two clones revealed linkage of genes for different isoforms, and this was confirmed by genomic Southern blotting, where hybridization patterns indicated that the majority of genes were present in tandem repeats.

	The sequence and diversity of all three isoforms was sampled in the starry flounder genome by PCR.  All coding sequences derived for the skin and liver isoforms were consistent with the proposed structure-function relationships for this AFP, where the flat hydrophobic side of the helix is conserved for ice binding.  There was greater sequence diversity in the skin and hyperactive isoforms than in the liver isoform, suggesting that the latter evolved recently from one of the other two.  The genomic PCR primers are currently being used to sample isoform diversity in related right-eyed flounders to test this hypothesis.

abstract: M.Sc.


title: Design and Fabrication of a Nanocantilever for High-Speed Force Microscopy

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subject: physics

abstract: Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2009-01-30 14:18:19.893

abstract:
The atomic force microscope (AFM) has become an important tool in many fields ranging from materials science to biology.  The central component of the AFM is a probe consisting of a soft cantilever to which a sharp tip is attached.  By scanning the probe over the surface of a sample and measuring small deflections of the cantilever, atomic resolution images can be obtained for both conducting and non-conducting samples.  Unfortunately, the scan speed of conventional AFM is limited such that several minutes are required to obtain a high-quality image.  If the scan speed of the AFM could be increased to allow for dynamic imaging, it could be used for many new applications in materials science, life science and process control.

Much of the current work toward high-speed AFM has involved improvements to scanners and electronics.  Innovative scanner design and control has resulted in operational frequencies up to 1 MHz while specialized electronics has pushed the feedback bandwidth up to 100 MHz.  To realize the full potential of these systems, a cantilever with a resonance frequency much greater than 100 MHz is required.  Unfortunately, current microfabrication techniques used to produce AFM cantilevers limits the fundamental resonance frequency to several MHz.

The purpose of this project was to miniaturize a cantilever into the nanometer regime allowing for increased resonance frequencies.  Three modeling methods were used to design a 200 MHz silicon nitride cantilever suitable for integration into an atomic resolution, frequency-modulation AFM.  A process was developed to fabricate the cantilever coupled to an atomic point contact (APC) displacement detector.  The cantilever mask and APC electrodes were defined through electron-beam lithography and double-angle evaporation.  The cantilever pattern was transferred to the nitride layer through focused ion beam milling; a subsequent wet etch into the underlying Si substrate suspended the structure.  Then, using an active feedback system, electromigration was used to form the APC at 77 K and 10E-6 Torr.  Progress was also made toward measuring cantilever motion with the APC displacement detector through microwave reflectometry.

abstract: M.Sc.


title: All Education is Environmental Education

contributor:
Lewis, Magda Gere
Education

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subject: Environmental Education

abstract: Thesis (Master, Education) -- Queen's University, 2009-01-30 14:22:09.994

abstract:
The purpose of this study is to explore how secondary school students construct meanings for environmentalism. The study participants consisted of grade twelve students from a rural eastern Ontario secondary school. The questions guiding this research are: a) in what ways do these students develop an understanding of environmentalism; b) what factors influence these students' decisions to take, or to not take, senior level elective Environmental Education courses as part of their secondary school curriculum; and c) what are students’ perception of Environmental Education and the current curriculum in secondary schools. Using a critical theory approach, this qualitative study employed two different methodological approaches: a survey, in the form of a questionnaire, and focus groups.
Eighty-five grade twelve students participated in this study, eleven of which were also involved in three different focus group interviews. The survey was used to explore the general knowledge base and attitudes of these students towards environmentalism. The survey was conducted in May 2008, and the focus groups were conducted in June of the same year. Results were analyzed to identify, describe and compare the attitudes of students, and how they form meanings for environmentalism. Five themes emerged from the analysis of data generated from the surveys and the focus groups. Those themes were: students’ definitions of environmentalism; students’ perceptions regarding Canadian environmental concerns and these concerns within a global context; where and what students are learning about the environment; students’ perceptions of the current curriculum; and students’ attitudes, lifestyle and choices they make as a result.
The most significant finding was not only the apparent lack of direction these students perceive themselves to be receiving regarding Environmental Education in the secondary context, which in some cases leads to a deficiency in understanding and concern, but also their noting the prevalence of media as a source of information about environmentally-related issues. Suggestions for future research on other salient aspects of Environmental Education are offered to shed further light on this issue.

abstract: M.Ed.


title: Neural Processes Involved in Action Selection During a Mixed-Strategy Game

contributor:
Dorris, Michael C.
Neuroscience Studies

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subject:
decision making
mixed-strategy
superior colliculus
monkey
motor intention
reinforcement
saccade

abstract: Thesis (Master, Neuroscience Studies) -- Queen's University, 2009-01-30 17:11:21.002

abstract:
Game theory outlines optimal response strategies during mixed-strategy competitions in which available actions are selected probabilistically.  The neural processes involved in choosing individual strategic actions, however, remain poorly understood.  Here, actions need to be selected (1) in the absence of sensory instruction or reward cues and (2) independent of previous events.  This thesis examines the neural processes involved in action selection during mixed-strategy competition.  To do so, we both measured and manipulated presaccadic activity in the primate superior colliculus (SC), a structure involved in the generation of orienting saccadic eye movements, during a strategic game.
The first study tested whether the SC is involved in choosing saccades under strategic conditions. Monkeys were free to choose either of two saccade targets as they competed against a computer opponent during the mixed-strategy game ‘matching-pennies’. The accuracy with which pre-saccadic SC activity predicted upcoming choice gradually increased in the time leading up to the saccade. Probing the SC with supra-threshold stimulation demonstrated that these evolving signals were functionally involved in preparing strategic saccades. Finally, sub-threshold stimulation of the SC increased the likelihood that contralateral saccades were selected.
In the second study, we compared the influence of previous actions and rewards on updating premotor activity in the SC in the strategic condition where eliciting stochastic responses was optimal and in a non-strategic condition where stochastic responses were also elicited but through explicit instruction.  To avoid exploitation by opponents during mixed-strategy competitions one should select behaviors unpredictably, that is, independent of previous choices and their outcomes.   The iterative updating of neural processes involved in selecting actions to produce mixed-strategy behaviors, however, remain poorly understood  In both tasks, premotor activity and behavior were shaped by past actions and rewards with more recent events exerting the largest influence.  Importantly, these sequential effects were attenuated under strategic conditions suggesting that updating of selection processes is not entirely automatic but can be tailored to different decision-making contexts.  Together our results highlight the active role played by the brain in choosing strategic actions.

abstract: M.Sc.


title: Central Solar Heating Plants with Seasonal Storage for Residential Applications in Canada: A Case Study of the Drake Landing Solar Community

contributor:
Harrison, Stephen J.
Environmental Studies

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subject:
Drake Landing Solar Community
Qualitative Case Study
Central Solar Heating Plant
Canada
Solar Thermal

abstract: Thesis (Master, Environmental Studies) -- Queen's University, 2009-02-03 14:08:18.825

abstract:
In Canada, 20% of greenhouse gas (GHG) emissions result from burning fossil fuels to heat homes, buildings, and water. Solar thermal technologies convert the sun’s energy into emission-free heat. The Drake Landing Solar Community (DLSC) in Okotoks, Alberta uses a Central Solar Heating Plant (CSHP) with Seasonal Storage to achieve an astounding annual reduction of 89 % in fossil fuel consumption and more than 5 tonnes in GHG emissions per home.
	This thesis examines: (1) the role for solar thermal technologies in Canada; and (2) what social, economical, and environmental factors are critical to the implementation and ultimate success of the DLSC. The former was examined through a literature review and the latter through a qualitative case study. Data was collected from published articles, media reports, conference proceedings, and in-person interviews in Okotoks.
	International markets have shown strong solar thermal growth, yet Canada lags significantly despite its powerful solar resources and readily available technology. Europe has demonstrated that strong policies with ambitious targets have a critical role in the implementation of solar technologies. A review of recent public opinion polls demonstrates Canadians value the environment and would favour such policy developments.
	The case study sought to understand the roles and motivations of the municipality, home builder group, and homeowners. The municipality exhibited tremendous leadership when it embarked on a path towards sustainability that included controlled growth based on ecological limitations and investment in solar thermal technology for municipal buildings. The Federation of Canadian Municipalities was instrumental in exposing Okotoks and the home builder group to the CSHP successes in Europe. The flexibility and innovation of the home builder group provided conventionally-styled homes, which were able to seamlessly incorporate the technologies of the DLSC.
	For the homeowners, critical components of the success of the project included: a means to participate in environmental change, increased community cohesion due to aligned values; and price stability for their heating costs. Additionally, all of the homeowners interviewed stated that they would be willing to pay extra to support the technology, which indicates that future projects may require less subsidization.

abstract: M.E.S.


title: Copolymerization studies of ethylene and trimethylsilyl protected 1-alkenols using a Brookhart-type alpha-diimine nickel(II) dibromide precatalyst

contributor:
Baird, Michael C.
Chemistry

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subject:
M.Sc. Thesis
Polymer Chemistry

abstract: Thesis (Master, Chemistry) -- Queen's University, 2009-01-31 14:43:09.93

abstract:
There has been considerable interest over the past decade in the preparation and applications of copolymers of ethylene with functionalized polar olefins. Such copolymers are expected to exhibit a variety of potentially very useful properties such as paintability, adhesion to polar surfaces, and miscibility with polar polymers such as polyesters and polyamides, but there are limitations associated with producing copolymers of ethylene with polar monomers via Ziegler-Natta processes. Many classes of Ziegler-Natta catalysts, especially those of the early transition metals (Ti and Zr), are highly oxophilic and hence are poisoned by functionalities such as -OH groups. This problem can in principle be alleviated by implementing the use of protecting groups such as –OSiMe3, which has previously been shown to be an effective masking agent both for steric reasons and because O-Si π bonding decreases the Lewis basicity of the ether oxygen atom. One can also utilize late transition metal catalyst systems, which are generally less Lewis acidic and therefore less susceptible to poisoning by functional groups.

In this thesis the results of an investigation of the copolymerization of ethylene with CH2=CH(CH2)nOSiMe3 (n = 1, 2, 8) will be presented. We have been using MAO activated dibromo[1,4-bis(2,6-diisopropylphenyl)acenaphthenediimine]nickel(II) (D) as catalyst, as this system is known to produce reasonably linear polyethylene and hence may be expected to produce essentially LLDPE containing –(CH2)nOSiMe3 branches. The latter can be hydrolyzed to give polar –(CH2)nOH branches.

abstract: M.Sc.


title: A Defence of Thomas Pogge’s Argument for a Minimally Just Institutional Order

contributor:
Schüklenk, Udo
Philosophy

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subject:
Pogge
Global Justice
Negative Rights
Severe Poverty
Human Rights
Global Institutional Order

abstract: Thesis (Master, Philosophy) -- Queen's University, 2009-02-02 16:07:34.355

abstract:
In an attempt to illustrate that the developed world has obligations to alleviate severe poverty, Thomas Pogge created a theory driven by human rights to focus on negative rights and duties of the avoidance of harm.  His theory of global justice is developed on a minimalist account of what it means to harm.  For him, the violation of the negative duty not to harm constitutes an injustice.  This injustice is enacted against the citizens of developing nations by the global institutional order.  Citizens of the developed world are perpetuating injustice by harming individuals through the imposition of a global order that avoidably causes human rights deficits without due compensation or reform to policies.

   Many critics take issue with his definition of harm as focused on negative rights, as well as find his theory of causation troublesome.  His critics largely object to his assertion that the developed world causally contributes to severe poverty.  Critiques of Pogge attempt to demonstrate that it is not the case that the developed world is causally responsible for severe poverty. In doing so, some make reference to domestic factors within developing nations, which they claim Pogge largely neglects.  Others argue that the current global institutional order benefits developing nations.  Furthermore, some of his critics engage with the normative demands that follow from his argument.  They claim he has a minimal definition of harm and injustice that leads to unmanageable maximal obligations.  Conversely, there are claims his argument leads to normative demands that are insufficient in redressing injustices.

   I argue that Pogge’s theory of global justice has developed the foundation necessary to motivate affluent nations to establish a minimally just global institutional order that avoids the perpetuation of avoidable human rights violations.  This foundation elucidates and establishes, through the global institutional order, an overarching causal relationship between the world’s affluent nations and the severely poor.  This relationship, despite critiques, is essential in order to illustrate that developed world citizens do indeed contribute to severe poverty and so must take action to establish a minimally just institutional order.

abstract: M.A.


title: The Corinthian Lord's Supper and the Greco-Roman Banquet Tradition

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subject:
Lord's Supper
Greco-Roman Banquet
Corinthians

abstract:
Scholars now recognize that there is no clear evidence to trace the ritual meal in 1 Corinthians 11:17-33 back to the historical Jesus, or to existing Jewish meals. Similarly, evidence is lacking to prove that the ritual meal originated with Paul’s community, or any other first century community. Later church liturgies reflect a variety of forms, making it
similarly impossible to trace the ritual backwards through the various Jesus groups. Scholars now suggest that each community developed its own ritual, based upon the rituals, prayers and banquets of their immediate context.

In this thesis, the banquets of the voluntary associations are examined in order to provide a socio-cultural context for the Corinthian meal. In finding an analogy for the Corinthian Jesus-meal in the meal practices of the voluntary associations, we note similar honour/shame values typical of the Greco-Roman world. Tensions and divisions are
attributable to this code of values and occur both in the Corinthians’ behaviour and in Paul’s attempt to modify the code to reflect more Christian values. Other comparisons between the association banquets and the Corinthian banquet are explored in the expectation that the association banquet traditions may shed some light on the Corinthians’ actual meal practices. Association banquets offer useful analogies to help explain the timing, location, provisions and funding, and the ritual of the Lord’s Supper itself. The banquet rituals of the associations thus prove to be a rich tradition upon which
Paul draws in order to create a new social identity for his community, albeit one based upon Christian values.


title: Multitaper Methods for Time-Frequency Spectrum Estimation and Unaliasing of Harmonic Frequencies

contributor:
Takahara, Glen
Thomson, David J.
Mathematics and Statistics

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subject:
Time-Frequency Analysis
Nonstationary
Spectral Analysis
Aliasing

abstract: Thesis (Ph.D, Mathematics & Statistics) -- Queen's University, 2009-02-05 10:18:13.476

abstract:
This thesis is concerned with various aspects of stationary and nonstationary time series analysis.  In the nonstationary case, we study estimation of the Wold-Cram'er evolutionary spectrum, which is a time-dependent analogue of the spectrum of a stationary process.  Existing estimators of the Wold-Cram'er evolutionary spectrum suffer from several problems, including bias in boundary regions of the time-frequency plane, poor frequency resolution, and an inability to handle the presence of purely harmonic frequencies.  We propose techniques to handle all three of these problems.

We propose a new estimator of the Wold-Cram'er evolutionary spectrum
(the BCMTFSE) which mitigates the first problem. Our estimator is based on an extrapolation of the Wold-Cram'er evolutionary spectrum in time, using an estimate of its time derivative. We apply our estimator to a set of simulated nonstationary processes with known Wold-Cram'er evolutionary spectra to demonstrate its performance.

We also propose an estimator of the Wold-Cram'er evolutionary spectrum,
valid for uniformly modulated processes (UMPs). This estimator mitigates the second problem, by exploiting the structure of UMPs to improve the frequency resolution of the BCMTFSE. We apply this estimator to a simulated UMP with known Wold-Cram'er evolutionary spectrum.

To deal with the third problem, one can detect and remove purely harmonic  frequencies before applying the BCMTFSE.  Doing so requires a consideration of the aliasing problem. We propose a frequency-domain technique to detect and unalias aliased frequencies in bivariate time series, based on the observation that aliasing manifests as nonlinearity in the
phase of the complex coherency between a stationary process and a time-delayed version of itself.  To illustrate this ``unaliasing'' technique, we apply it to simulated data and a real-world example of solar noon flux data.

abstract: PhD


title: Some Advances in the Multitaper Method of Spectrum Estimation

contributor:
Thomson, David J.
Mathematics and Statistics

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subject: Time Series Analysis

subject: Statistical Signal Processing

abstract: Thesis (Ph.D, Mathematics & Statistics) -- Queen's University, 2009-02-05 18:01:45.187

abstract:
Four contributions to the multitaper method of applied spectrum estimation
 are presented.  These are a generalization of the multitaper
 method of spectrum estimation to time-series possessing irregularly
 spaced samples, a robust spectrum estimate suitable for cyclostationary,
 or quasi cyclostationary time-series, an improvement over
 the standard, multitaper spectrum estimates
 using quadratic inverse theory,
and finally a method of scan-free spectrum estimation
 using a rotational shear-interferometer.  Each of these topics forms a chapter in this thesis.

abstract: PhD


title: Ediacaran rangeomorphs in the Mistaken Point biota, Newfoundland

contributor: Geological Sciences and Geological Engineering

subject:
Ediacara
rangeomorph
Mistaken Point
Bradgatia

abstract: Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2009-02-06 09:38:13.177

abstract:
The Ediacara biota is a cosmopolitan assemblage of the first macroscopic multicellular soft-bodied fossil organisms (Late Neoproterozoic, 575 – 542 Ma).  The Avalon Peninsula of Newfoundland preserves entire communities composed of hundreds of organisms in their natural life positions on decameter- to hectometer-scale bedding plane surfaces as impressions under a layer of ash.  The communities are dominated by rangeomorphs, an extinct taxon with modular construction and fractal architecture.
	Bradgatia, a multibranched rangeomorph initially studied from 7 specimens from England, is represented by >200 specimens from 8 surfaces on the Avalon Peninsula.  The Bradgatia petalage is a radial array of up to eight rangeomorph petals with four visible orders of rangeomorph branching.  The petalage changes throughout ontogeny from juvenile I- or V-shaped organisms to larger U-shaped specimens to the largest and oldest O-shaped specimens.  Counts of the number of petals within each taphomorph suggest that a constant number of petals was maintained throughout ontogeny.  There is no significant variation in the number of frondlets with petal length suggesting that petals maintained a constant number of secondary branches throughout ontogeny.
	Culmofrondis new genus and species is a rangeomorph frond known from a single surface within the Mistaken Point Formation.  It is constructed from non-rangeomorph primary branches which are subdivided by rangeomorph secondary and tertiary branches.  The zigzagging central midline and non-rangeomorph primary branches are typical of Charnia-type branching whereas its rangeomorph secondary branches and flexible primary branches are typical of Rangea-type branching.
	Both Bradgatia and Culmofrondis were basally attached to the ocean floor by holdfasts suggesting they were sessile, epifaunal benthic organisms.  Both were oriented parallel to contour current direction and display decreasing preservation distally along specimens.  Additionally, Bradgatia overlies spindles and discs and Culmofrondis possesses a long stem further supporting an epifaunal suspension feeding lifestyle.  Bradgatia’s multiple petals and lack of a stem would have maximized the surface area available for suspension feeding whereas the elevated petalodium of Culmofrondis would have accessed nutrients in a zone higher in the water column with lower competition.

abstract: M.A.Sc.


title: Speciation and mobility of Antimony and Arsenic in mine waste and the aqueous environment in the region of the Giant mine, Yellowknife, Canada

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subject: antimony arsenic

abstract: Thesis (Ph.D, Geological Sciences & Geological Engineering) -- Queen's University, 2009-02-08 16:57:48.711

abstract:
Antimony is a potential human and ecosystem health risk, yet large gaps in the existing knowledge of the geochemical behaviour of Sb persist. At the Giant mine, an abandoned gold mine about to undergo remediation, Sb is elevated in mine waste and in downstream pond and stream sediments that have been impacted by mine waste. Gold at the Giant Mine, Yellowknife NT, is refractory, hosted in arsenopyrite (FeAsS) and pyrite (FeS2), and associated with stibnite (Sb2S3) and Sb-sulfosalts. The gold was liberated by roasting the ore which produced two arsenic (As) and antimony (Sb)-rich waste streams: calcine and electrostatic precipitator (ESP) residue. The roaster-derived As and Sb host phases, maghemite and hematite, are found in sediment, and are undergoing post-depositional transformations.
Bulk and micro- X-ray Absorption Near Edge Spectroscopy (XANES) methods, and synchrotron-based micro-X-ray fluorescence (μXRF) and micro-X-ray diffraction (μXRD), were employed to characterize the Sb-host phases and determine the solid-phase speciation of Sb in mine waste and sediment. Antimony in mine waste is largely associated with roaster-derived maghemite and is hosted as Sb(III) and Sb(V). The bulk and μXANES analyses indicate a more prominent Sb(III) composition in the ESP residue, compared to the calcine. In the surficial and deeper sediment Sb(III) and Sb(V) bound to oxygen are present, as well as Sb(III) bound to sulfur in the deeper sediment. The presence of the Sb(III) bound to sulfur phase in the deeper sediment implies that Sb associated with the roaster oxides is destabilized, but subsequently precipitates as, or adsorbs onto, a sulfide. Furthermore, the preferential attenuation of the Sb(III) species likely accounts for the dominance of Sb(V) in pore-water at all three sites, and at all depths. Co-existing with the sulfur-bound Sb phases in the deeper, relatively reducing sediment, is a compositionally significant, and finely disseminated Sb(V) bound to oxygen phase.
Antimony and As are often assumed to exhibit similar geochemical behaviour. This study offered an opportunity to compare the mobility of As and Sb since both are elevated in concentration in the environment and in mine waste. Arsenic and Sb exhibit similar geochemical behaviour in the upper 2cm, but the higher affinity of As for sorption sites results in dissimilar distribution in pore-water. Both elements undergo post-depositional reduction resulting in an increase in the mobility of As, and attenuation of Sb. Aquatic horsetails (Equisetum fluviatile) present in Baker Creek significantly reduces the mobility of both elements.

abstract: PhD


title: Molecular characterization of age-related genes in Drosophila melanogaster

contributor:
Seroude, Laurent
Biology

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subject:
Quantitative PCR
Gene Expression Analysis
Reverse Transcription Efficiency

abstract: Thesis (Master, Biology) -- Queen's University, 2009-02-09 10:59:16.871

abstract:
Aging, characterized by a time-dependent functional decline, eventually results in the death of an organism.  Unfortunately, this complex biological phenomenon is poorly understood.  In order to dissect the molecular changes associated with aging, the identification and molecular characterization of the genes that regulate this universal process is absolutely necessary.  The expectation is that the isolated genes potentially have human homologues and can be experimentally analyzed in Drosophila melanogaster in order to determine basic function.
In an attempt to find candidate genes that may influence aging, the enhancer trap technique was utilized to identify age-related regulatory elements.  The genomic regions surrounding the insertion site of the enhancer trap lines have the potential to be regulated by the characterized enhancer.  A previous screen determined the temporal pattern of 180 enhancers trap lines, known as DJ lines.  Many of these lines demonstrated an expression pattern that was associated with age.  Several of the genes within the nearby genomic regions of six sequenced DJ lines, DJ695, DJ710, DJ849, DJ767, DJ761 and DJ694, were chosen for transcript quantification.
Prior to gene quantification, reverse transcription, an essential step in the experimental procedure, was assessed for the error it incorporated into quantification.  Specifically, an exogenous molecule was used to ensure that unsuccessful reverse transcription reactions had the potential to be identified and, soon after, discarded.  This was achieved through the use of a spike RNA molecule, Luciferase.  Luciferase was shown to be a diagnostic tool that can be used in determining reverse transcription efficiency.  Eight genes were chosen from the aforementioned DJ lines and quantitative PCR revealed that the natural regulation of some genes were comparable to the, previously obtained, expression pattern of the enhancer trap line.  Although the expression of other genes did not correlate to that of the enhancer trap lines, all genes exhibited expression patterns that were age-associated.  The known functions of these candidate genes and the relevant homologues are discussed.  These findings validate the use of the enhancer trap technique in the identification of candidate genes involved in the aging process.

abstract: M.Sc.


title: Forecasting and Non-Stationarity of Surgical Demand Time Series

contributor:
Strum, David
Thomson, David J.
Mathematics and Statistics

subject:
Time Series Analysis
Sugical Demand
Holiday Variance
Multitaper
Variance Filter

abstract: Thesis (Ph.D, Mathematics & Statistics) -- Queen's University, 2009-02-09 11:55:42.494

abstract:
Surgical scheduling is complicated by naturally occurring, and human-induced variability in the demand for surgical services. We used time series methods to detect, model and forecast these behaviors in surgical demand time series to help improve the scheduling of scarce surgical resources.

With institutional approval, we studied 47,752 surgeries undertaken at a large academic medical center over a six-year time frame. Each daily sample in this time series represented the aggregate total hours of surgeries worked on a given day. Linear terms such as periodic cycles, trends, and serial correlations explained approximately 80 percent of the variance in the raw data. We used a moving variance filter to help explain away a large share of the heteroscedastic behavior mainly attributable to surgical activities on specific US holidays, which we defined as holiday variance.

In the course of this research, we made a thoughtful attempt to understand the time series structure within our surgical demand data. We also laid a foundation, for further development, of two time series techniques, the multiwindow variance filter and cyclostatogram that can be applied not only to surgical demand time series, but also to other time series problems from other disciplines. We believe that understanding the non-stationarity, in surgical demand time series, may be an important initial step in helping health care managers save critical health care dollars.

abstract: PhD


title: Modeling Trihalomethane Formation in Drinking Water With Application to Risk-Based Decision-Making

contributor:
Hall, Kevin
Civil Engineering

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subject:
Environmental Engineering
Drinking Water

abstract: Thesis (Ph.D, Civil Engineering) -- Queen's University, 2009-02-10 14:41:03.975

abstract:
A model-based methodology for risk-based decision-making of water treatment and disinfection strategies that deal with the management of trihalomethanes (THMs) has been developed. Trihalomethanes (THMs) are by-products of chlorination for drinking water and have been characterized as possible and probable human carcinogens. Among THMs, bromodichloromethane (BDCM) has a much stronger association with stillbirths and neural tube defects than the other THMs species.
The parameters affecting formation of THMs and BDCM were identified through multivariate statistical analysis of the Ontario Drinking Water Surveillance Program database and by reviewing publications. Formation of THMs is affected by chlorine dose, dissolved organic carbon, pH, temperature and reaction time; these parameters along with bromide ions have effects on brominated THMs formation in drinking water.
Two models for predicting formation of THMs and BDCM in drinking water have been developed. Controlled experimental investigations were performed in laboratory following statistical design of the experiments using synthetic water samples. Using statistically significant parameters, models have been developed. The adequacies of the models were tested using appropriate statistical diagnostics and validation experiments.
The models have been integrated into a risk-based decision making framework. Formation of THMs and BDCM were estimated by importing water quality and operational parameters into these models. The costs, technical feasibility and performances of different treatment and disinfection options were determined. Through the incorporation of multiple criteria (human health risk, cost, technical feasibility and disinfection performance), different treatment and disinfection strategies were evaluated and compared. A fuzzy logic stochastic approach has been utilized for the evaluation and tradeoff studies among different criteria.
Overall, this thesis has continued to improve the environmental decision making process. The results of this thesis have provided a clearer understanding of parameters influencing THMs and BDCM formation in a complex environmental scenario. This thesis has presented a comprehensive approach to better control water quality and associated operational parameters through the use of predictive models and to perform decision making following a holistic approach. The results of this thesis will also assist in critical decision making for possible upgrading of water supply systems, analyzing uncertainty and complying with the regulatory limitations.

abstract: PhD


title: Regulatory Domains of the Human Calpain Family

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subject:
Calpain
Calcium
Proteases
penta-EF-hand domain (PEF domain)

abstract: Thesis (Ph.D, Biochemistry) -- Queen's University, 2009-02-11 12:30:29.18

abstract:
Calpains are intracellular enzymes that merge cysteine protease and calcium sensing activities together in one molecule. They respond to Ca2+ signals and modify the activity of their targets by selective proteolysis. Calpains are involved in normal cellular process like cell migration and apoptosis. The over-activation of calpain due to disturbances in Ca2+ homeostasis or inactivation due to mutations, contribute to diseases like ischemic injury and muscular dystrophy.
	The classical calpains 1 and 2 are heterodimeric enzymes containing a large (80 kDa) subunit and a small subunit (28 kDa). Dimerization occurs through the 5th EF-hand of penta-EF-hand (PEF) domains present in both large and small subunits. In this study, I have used structural genomics approaches to explore the PEF and C2-like regulatory domains of some of the other 12 human calpain isoforms.  I have shown that recombinant PEF domain of skeletal muscle-specific calpain 3 exists as a stable homodimer when produced alone. Modelling studies suggest that there would be no barriers for dimerization of the full-length enzyme through the PEF domains which would place the protease cores at opposite ends of the dimer. Co-expression studies using small subunit were performed with PEF domains of calpains 1, 3, 8, 9, 11, 12 and 13. A differential tagging system was devised to differentiate heterodimers from homodimers. The PEF domains of calpains 1, 3, 9 and 13 co-expressed with the small subunit, while the others failed to express.  The PEF domains of calpains 1 and 9 formed heterodimers. Conversely, the PEF domain of calpain 3 formed a homodimer and that of calpain 13 predominantly formed a homodimer with a small amount of heterodimer. Homodimerization of calpains implies they are less-likely to be inhibited by the endogenous calpain inhibitor, calpastatin.
C2-like regulatory domains of calpains 5-13 were also studied. The structure of the distal C2-like domain of calpain 7 was solved. It is markedly different from canonical C2 domains and may not bind Ca2+.

abstract: Couple of chapters in the thesis are not published.

abstract: PhD


title: Stress responses in an outbred, wild-derived hamster, Phodopus campbelli: Individuality in the cortisol response to acute restraint stress and the absence of strong association with behavioural responses to acute restraint

contributor:
Wynne-Edwards, Katherine E.
Biology

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subject:
Phodopus campbelli
cortisol

abstract: Thesis (Ph.D, Biology) -- Queen's University, 2009-02-11 12:29:33.22

abstract:
Glucocorticoid reactivity is often used as a biomarker of emotional stress status in animals and man. Likewise, behavioural responses of individuals to standardized stresses are also widely used to assess the magnitude of perceived stress. Unfortunately, there is little evidence that widely used physiological measures and widely used behavioural measures yield similar, or even correlated, results. The current study provides an explicit test of the relationship between the two approaches.
Dwarf hamsters (Phodopus campbelli) were subjected to a standardized, on-back restraint in a socially subordinate position and had plasma samples drawn under brief, home-cage, isoflurane anesthesia to quantify cortisol before and after the acute stress. Individual responses were transformed into parameters describing the absolute change in cortisol, the proportional changes in cortisol, and the overall exposure to cortisol across stress and recovery. There was exceptional individual variability in cortisol responses to the standardized stressor, including monotonic declines, and cluster analysis failed to effectively partition between-individual variation by sex, age, or housing conditions, for any parameter.
Next, physiological measures, and a battery of behavioural tests routinely used to assess, anxiety, stress, and emotionality differences, as well as resistance to capture and intruder aggression, were combined in an expanded population including individuals from genetic lines selected to increase or decrease cortisol concentration. In general, dwarf hamsters showed less neophobia than is typical of laboratory mice and rats (e.g. animals quickly dropped from the elevated plus maze). In addition, results were combined to create behavioural indices by orienting each test score relative to an emotionality continuum and combining tests based on, a priori, expectations of similarity. Multivariate regression failed to detect covariation between physiological and behavioural measures, despite the large number of parameters describing those responses.
Although the experimental design did not include replication, or comparison of physiological responses to different stressors, it was clear that behavioural and physiological responses were neither interchangeable nor statistically associated. Thus, results challenge widespread assumptions about the interaction between the glucocorticoid response to stress, and the manifestation of that stress through alterations in behaviour. Additional research exploring physiology-behaviour associations in genetically diverse populations is warranted.

abstract: PhD


title: Seeking Stability Amid Deep Division: Consociationalism and Centripetalism in Comparative Perspective

contributor:
McGarry, John
Political Studies

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subject:
power-sharing
ethnic conflict management

abstract: Thesis (Ph.D, Political Studies) -- Queen's University, 2009-02-12 12:11:51.013

abstract:
For the design of power-sharing practices in deeply divided places, there are two main macro-political strategies: consociationalism, developed and defended by Arend Lijphart, and centripetalism, associated with the work of Donald L. Horowitz. In this thesis, I consider the academic debate between advocates of the two approaches and consider the extent to which either model represents a successful tool of ethnic conflict management. Two broad questions are asked: can centripetalism promote political stability in deeply divided places? Can consociationalism? I address these questions by engaging a comparative case analysis of six deeply divided places, three of which have adopted centripetal institutions (Fiji, Sri Lanka, and Nigeria’s Second Republic) and three of which have adopted consociational institutions (Bosnia and Herzegovina, Burundi, and Northern Ireland).
I present three central arguments in the thesis. First, centripetalism should not be recommended as a strategy of conflict management in deeply divided places.  Its track record in such places reveals serious weaknesses.  Indeed, it has tended to promote instability and exacerbate division rather than promote moderation. Second, consociationalism is better able to promote stability in deeply divided places. Third, consociationalism’s prospects of promoting stability are further enhanced when it is implemented in a revised and expanded form, labelled here as “comprehensive consociation.” This type of power-sharing addresses issues that go beyond concern with just political institutions, such as security sector reform, property restitution, and the return of refugees. These are the type of issues that are most likely to promote political instability if left unresolved. Failure to deal with such issues, I argue, is likely to make it more difficult for elites to agree to share power, or to maintain such arrangements.

abstract: PhD


title: Application of Cysteine Scanning Mutagenesis to the Multidrug Resistance Protein (MRP)1

contributor:
Deeley, Roger G.
Pathology and Molecular Medicine

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subject:
Multidrug Resistance
ABC Transporter
Cancer
Cysteine

abstract: Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2009-02-17 12:51:38.13

abstract: Multidrug resistance protein (MRP)1, a member of the ABCC branch of the ATP-binding cassette (ABC) superfamily of transporters, can confer resistance to a broad spectrum of chemotherapeutic agents.  In addition to the core functional unit of ABC transporters that consists of two membrane spanning domains (MSD) and two nucleotide binding domains (NBD), MRP1 contains a third MSD (MSD0) resulting in the following arrangement: NH2-MSD-(MSD-NBD)2.  In lieu of high-resolution structural information for MRP1, cysteine scanning mutagenesis (CSM) was applied to MRP1 and involves the development of a functional template devoid of cysteines into which paired cysteines can be introduced.  Previous attempts to create a functional, cys-less template of MRP1 demonstrated that cysteines in MSD0 were structurally and functional important (1;2).  However, given that MRP1 lacking MSD0 remains functional, a partially functional, cys-less MRP1 lacking this domain has been expressed in yeast (3-5).  Given these results, with the ultimate goal of applying CSM to MRP1 in its entirety, we investigated the endogenous cysteines within MSD0 and co-expressed MRP1 half-molecules and validated these potential CSM templates by transport and ATP binding/hydrolysis assays.  Mutation of cysteines within the core of MRP1 had detrimental effects on MRP1 transport activity and further mutation of cysteines by domain revealed that wild-type activity was retained in an MSD0-less MRP1 dual lacking cysteines in both NBDs.  This construct was used for introduction of cysteines on juxtaposed faces of the NBD1:NBD2 heterodimer at positions 775 and 1329; comparable residues in the related Cystic Fibrosis Transmembrane Regulator (CFTR/ABCC7) have been suggested to be evolutionarily coupled and joined by a hydrogen bond, maintained in structures of related proteins (6). Unfortunately, functional assays revealed that introduction of cysteines at these positions greatly reduced transport activity of MRP1 and diminished trapping of nucleotide at both NBDs.  Finally, alanine substitution of the seven cysteines in MSD0 was not without effect and cellular trafficking assays, co-expression studies and SDS-PAGE analysis suggested an altered conformation of this domain.  In addition, a disulfide pair of Cys7 and Cys32 was suggested by these experiments in MSD0 and further supported by examination of these mutants in full-length MRP1.

abstract: M.Sc.


title: Growth and Myosin Heavy Chain Expression in the White Muscle of Juvenile Walleye (Sander vitreus)

contributor:
Tufts, Bruce L.
Biology

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subject:
Myosin Heavy Chain
Fish

abstract: Thesis (Ph.D, Biology) -- Queen's University, 2009-02-19 12:30:51.406

abstract:
Walleye are an important recreational and commercial fish species that are distributed over an expansive geographic range across North America. However, its palatable white flesh and appeal to anglers have lead to declines in natural populations throughout Canada and the United States. These declines have prompted the idea that aquaculture may serve as a means of satisfying consumer demands and decreasing pressure on wild stocks. While culture programs exist for walleye, little is known about the growth physiology of walleye in a culture system. The goals of this thesis, therefore, were to develop a molecular marker that could be used to rapidly assess growth in juvenile walleye, and to make improvements to culture practices that will optimize growth.
To begin, we examined the relationship between growth and the expression of the myosin heavy chain gene (MyHC) in the white muscle of juvenile walleye. The coding region of MyHC from the fast skeletal muscle of walleye was amplified using a full length cDNA. Growth was then characterized using traditional measurements of growth (length, weight and condition factor), as well as MyHC protein concentration and MyHC mRNA levels. Both MyHC mRNA and protein expression were highly correlated with faster growth in juvenile walleye. Over shorter time scales, the MyHC mRNA marker was sensitive enough to detect impacts of fasting that could not be detected using traditional measurements of growth.
Next, MyHC mRNA quantification was applied to an aquaculture setting. Feed training is an important bottleneck during juvenile walleye culture that often leads to mortalities and cannibalism. These experiments showed that the brief fasting period during the diet switch from plankton to commercial pellet feed caused a significant decrease in MyHC mRNA levels. Furthermore, the success of feed training in terms of survivorship and growth potential increased significantly for larger fish.
The final section of this thesis examined how acute and chronic temperature exposure impacted MyHC mRNA and protein expression. Results showed that the nature of the heat stress can significantly affect the MyHC response. These findings are important as the temperature stresses induced in these studies are common during the summer months in southern Ontario.

abstract: PhD


title: “A Mirror of Men”: Sovereignty, Performance, and Textuality in Tudor England, 1501-1559

contributor:
Pappano, Margaret
English

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subject:
Performance
Textuality
Sovereignty
Tudor England

abstract: Thesis (Ph.D, English) -- Queen's University, 2009-02-25 22:42:18.684

abstract: Sixteenth-century England witnessed both unprecedented generic experimentation in the recording of spectacle and a shift in strategies of sovereign representation and subject formation: it is the central objective of this dissertation to argue for the reciprocal implication of these two phenomena. Henry VII, Henry VIII, and Elizabeth I used performance to legitimate their authority. Aristocratic and civic identities, in turn, were modelled on sovereign identity, which was disseminated through narratives in civic entries, tournaments, public progresses, and courtly pageantry. This dissertation investigates the relationship between ritualized social dramas (a marriage, birth, and coronation) and the mechanisms behind the recording and dissemination of these performances in courtly and civic texts in England from 1501 to 1559. Focussing on The Receyt of the Ladie Kateryne (London 1501), The Great Tournament Roll of Westminster (Westminster 1511), and The Quenes Maiesties Passage (London 1559), this project attempts to understand the role performance texts played in developing conceptions of social identity. Specifically, this dissertation seeks to demonstrate that a number of new hybrid genres emerged in Tudor England to record ritualized social dramas. I argue that each of the texts under scrutiny stands out as a unique record of performance as their authors use unprecedented narrative strategies to invest their accounts with “liveness,” situating the reader as a “spectator” of the sovereign within a performative context. An important objective of these hybrid genres was to control the audience/reader’s response to the symbology of performance. Each monarch attempted to influence social and political identities through courtly performance; however, the challenges of governing differed among reigns. While Henry VII struggled against charges of illegitimacy, Henry VIII had to consolidate the loyalties of his nobles, and Elizabeth I came to the throne amidst religious turmoil and anxieties about female rule. Strategies for the performance and recording of sovereign authority shifted, therefore, to account for the changes in England’s political structure. By examining how performance is textualized in these new genres, I attempt to expose the tensions animating the relationships among the monarch, his/her nobility, and the civic authorities.

abstract: PhD


title: Exploring the Functional Significance of the Caenorhabditis elegans VAB-1 Eph RTK and DAF-18/PTEN Tumour Suppressor Interaction

contributor:
Chin-Sang, Ian D.
Biology

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subject:
DAF-18
PTEN
C. elegans
VAB-1
Eph RTK
Protein Interaction
Tumour Suppressor

abstract: Thesis (Master, Biology) -- Queen's University, 2009-02-27 17:09:10.582

abstract: The Caenorhabditis elegans Eph RTK, VAB-1, has known roles in neuronal and epidermal morphogenesis as well as oocyte maturation through interaction with its ephrin ligands. In humans, Eph receptors are involved in nervous and vascular system development and have been implicated in cancer formation and progression. DAF-18, a C. elegans ortholog of the human tumour suppressor gene, PTEN, has been identified as an interacting partner with the Eph RTK, VAB-1.  Mutations in human PTEN have been associated with numerous cancers and in the worm, DAF-18 is a well studied member of the DAF-2/Insulin receptor-like signaling pathway which has roles in dauer formation, thermotolerance and adult longevity.  Our lab has previously shown that VAB-1/EphR binds DAF-18. To further investigate the significance of this interaction as well as offer additional function to the proteins involved, I have shown that VAB-1/EphR is a negative regulator of DAF-18/PTEN at the protein level. Western blotting reveals that endogenous expression of DAF-18/PTEN is low in wild-type animals and expression is increased in a vab-1/ephR mutant. Additionally, VAB-1/EphR and DAF-18/PTEN are expressed in head neurons, oocytes and the germline precursor cells, Z2/Z3. vab-1/ephR mutants show increases longevity and sensitivity to dauer conditions which is consistent with increased DAF-18/PTEN activity. Lastly, daf-18(ok480) is able to suppress the oocyte maturation phenotype and increased MAPK expression displayed by vab-1(dx31) animals, providing genetic evidence of an interaction. By identifying the tissues where these proteins are co-expressed and substantiating the interaction with multiple analyses, novel roles may be proposed for each: VAB-1/EphR in DAF-2/Insulin signaling and DAF-18/PTEN in oocyte maturation downstream of VAB-1/EphR signaling.  This work provides further understanding of how an organism coordinates complex developmental processes and reiterates the notion that cellular signaling is a complex network of interacting players. As many signaling pathways are evolutionarily conserved, my research in C. elegans may provide a mechanism on how Eph RTKs and PTEN are regulated in more complex organisms, including humans.

abstract: We are currently in the process of submitting a manuscript for publication based on the results of this thesis. We would like to keep the thesis restricted until the manuscript has been formally accepted.

abstract: M.Sc.


title: A Modified Genetic Algorithm and Switch-Based Neural Network Model Applied to Misuse-Based Intrusion Detection

contributor:
Akl, Selim
Feng, Wenying
Computing

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subject:
Network Security
Intrusion Detection Systems (IDS)
Data Mining
Machine Learning
Real Time Detection
Genetic Algorithm
Neural Networks

abstract: Thesis (Master, Computing) -- Queen's University, 2009-03-03 13:28:23.787

abstract:
As our reliance on the Internet continues to grow, the need for secure, reliable networks also increases. Using a modified genetic algorithm and a switch-based neural network model, this thesis outlines the creation of a powerful intrusion detection system (IDS) capable of detecting network attacks.

    The new genetic algorithm is tested against traditional and other modified genetic algorithms using common benchmark functions, and is found to produce better results in less time, and with less human interaction. The IDS is tested using the standard benchmark data collection for intrusion detection: the DARPA 98 KDD99 set. Results are found to be comparable to those achieved using ant colony optimization, and superior to those obtained with support vector machines and other genetic algorithms.

abstract: M.Sc.


title: A Sensor Network Querying Framework for Target Tracking

contributor:
Akl, Selim
Computing

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subject:
sensor networks
target tracking
heuristic algorithms
energy-awareness
sensor collaboration
routing scheme

abstract: Thesis (Master, Computing) -- Queen's University, 2009-03-04 11:18:14.392

abstract:
Successful tracking of a mobile target with a sensor network requires effective answers to the challenges of uncertainty in the measured data, small latency in acquiring and reporting the tracking information, and compliance with the stringent constraints imposed by the scarce resources available on each sensor node: limited available power, restricted availability of the inter-node communication links, relatively moderate computational power.

This thesis introduces the architecture of a hierarchical, self-organizing, two-tier, mission-specific sensor network, composed of sensors and routers, to track the trajectory and velocity of a single mobile target in a two-dimensional convex sensor field. A query-driven approach is proposed to input configuration parameters to the network, which allow sensors to self-configure into regions, and routers into tree-like structures, with the common goal of sensing and tracking the target in an energy-aware manner, and communicating this tracking data to a base station node incurring low-overhead responses, respectively.

The proposed algorithms to define and organize the sensor regions, establish the data routing scheme, and create the data stream representing the real-time location/velocity of a target, are heuristic, distributed, and represent localized node collaborations. Node behaviours have been modeled using state diagrams and inter-node collaborations have been designed using straightforward messaging schemes.

This work has attempted to establish that by using a query-driven approach to track a target, high-level knowledge can be injected to the sensor network self-organization processes and its following operation, which allows the implementation of an energy-efficient, low-overhead  tracking scheme. The resulting system, although built upon simple components and interactions, is complex in extension, and not directly available for exact evaluation. However, it provides intuitively advantageous behaviours.

abstract: M.Sc.