title: Why Stay: Young Independent Filmmakers in Contemporary Havana

contributor:
Lord, Susan
Cultural Studies

subject:
Cuban Studies
Latin American Studies
Film and Media Studies

abstract: Thesis (Master, Cultural Studies) -- Queen's University, 2015-10-23 15:44:22.477

abstract:
This project, containing a written thesis and documentary film, investigates contemporary film production by young Cuban filmmakers in Havana, Cuba. In the changing audiovisual landscape young filmmakers are often positioned as ‘independent’ cultural producers. Social, political and economic relationships to institutional structures have encouraged initiatives within the filmmaking community. Young filmmakers participate in these initiatives forming new spatial, social and financial relationships on and off the island. These connections are facilitated through growing access to media and technology as well as a desire for engagement with global film markets. These factors also influence the types of images young filmmakers seek to produce as well as their production methods.
The documentary film entitled Por Amor al Arte follows the experiences and films of five young filmmakers in Havana, Cuba. The documentary further addresses the question: How do young Cuban filmmakers produce films away from the Instituto Cubano del Arte e Industria Cinematográficos (ICAIC), the dominant film institute, within the contemporary Cuban context? And do they have the desire to continue to produce film in Cuba and why? Because the Cuban film industry continues to function on the centralized model established after the Cuban Revolution of 1959, the ICAIC maintains its position as the sole producer and distributor of Cuban cinema. Due to scarce resources and little economic support in the 1990s many of Cuba’s filmmakers sought alternative methods to produce their films away from the ICAIC. Today young filmmakers benefit from certain resources and approaches developed in the 1990s, while new struggles emerge within a contemporary context. Filmmakers who produce away from the ICAIC, however, do not have legal standing in the country and cannot operate as independent production companies. Furthermore, most productions are created and screened in Havana, Cuba, which privilege those who live in the city. Young filmmakers in Havana negotiate these factors and consider the possibilities of staying in Cuba to produce their work.

abstract: M.A.


title: Optimal and Suboptimal Signal Detection-On the Relationship Between Estimation and Detection Theory

contributor:
Gazor, Saeed
Electrical and Computer Engineering

rights: Queen's University's Thesis/Dissertation Non-Exclusive License for Deposit to QSpace and Library and Archives Canada

rights: ProQuest PhD and Master's Theses International Dissemination Agreement

rights: Intellectual Property Guidelines at Queen's University

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:
Detection Theory
Invariant tests
CFAR
Estimation Theory

abstract: Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2015-10-25 20:40:41.828

abstract:
In this thesis, we consider a general binary and M-ary hypothesis testing problems with unknown parameters. In a hypothesis testing problem, we assume that the probability density function (pdf) of observation is given while some unknown parameters exit in the structure of the pdf and the set of unknowns under each hypothesis is given.

In the first part of this study, for a binary composite testing, we prove that the Minimum Variance and Unbiased Estimator of a Separating Function (SF) serves as the optimal decision statistic for the Uniformly Most Powerful (UMP) unbiased test. In many problems, the UMP test does not exist. For such cases, we introduce new suboptimal SF-Estimator Tests (SFETs) which are easy to derive for many problems.

In the second part, we study the relationship between Constant False Alarm Rate (CFAR) and invariant tests. We generally show that for a family of distributions, the unknown parameters are eliminated from the distribution of the maximal invariant statistic under the Minimal Invariant Group (MIG) while the maximum information of the observed signal is preserved. We prove that any invariant test with respect to the MIG is CFAR. Then, we introduce the UMP-CFAR test as the optimal CFAR bound among all CFAR tests.

In the third part, the asymptotical optimality of the CFAR tests is studied after reduction using MIG. We show that the CFAR tests obtained after MIG reduction using the Wald test is SFET and the Generalized Likelihood Ratio Test and the Rao test are asymptotically optimal. To find an improved test, we maximize the asymptotic probability of detection of the SFET using the Maximum Likelihood Estimation (MLE). We propose a systematic method allowing to derive the Asymptotically Optimal SFET. Finally, we extend the concept of SFET to the M-ary hypothesis testing. Defining M different SFs for an M-ary problem, we show that the optimal minimum error test is achieved using the MLE of SFs. Moreover, in the case that the optimal minimum error test does not exist, the error probability of the proposed SFET tends to zero when the number of independent observations tends to infinity.

abstract: PhD


title: Estimating Body Segment Inertial Parameters of the Human Body Using a Microsoft Kinect

contributor:
Dumas, Geneviève A.
Mechanical and Materials Engineering

subject:
Body Segmentation
Microsoft Kinect V2
Point Cloud
Body Volume
3D Scanning
Biomechanics
3D Mesh
Body Segment Inertial Parameters

abstract: Thesis (Master, Mechanical and Materials Engineering) -- Queen's University, 2015-10-27 15:28:47.274

abstract:
Estimating biomechanical measures of the human body requires body segment inertial parameters (BSIP). Widely cited estimation methods (Chandler et al., 1975; Dempster, 1955) are based on an elderly population, have inherent errors (Hanavan, 1964) and may not represent subjects to which they are applied. Subject specific methods such as medical imaging or geometrical techniques can be time consuming, expensive and may require a variety of manually acquired inputs. Presented here is an alternative, subject specific approach to estimating BSIPs, requiring no manual measurements at a equipment cost of approximately $300.
A 3D scanning protocol using a single Microsoft Kinect V2 was developed. Twenty-one subjects (10 male, 11 female) were scanned 3 times with per scan durations of approximately 20-30 seconds. Each full body 3D scan was segmented in Meshlab according to a 16 segment link model defined by Zatsiorsky and Seluyanov (1983). The 3D data was analyzed in custom MATLAB software that estimated the volume, MOI, COM, length and mass of each of the link segments. Results were compared to estimates obtained using an elliptical cylinder model (ECM) (Jensen 1978) and to estimates obtained using regression equations developed from medical imaging techniques (Zatsiorsky and Seluyanov 1983).
The body volume estimates using the Kinect demonstrated high repeatability (ICC≥0.95) with a volume overestimation ranging from 0.0023 m3 (3%) for males and 0.0038m3 (5.1%) for females. The upper torso accounted for the majority of the overestimation of approximately 0.0019m3 (83%) for males and 0.002 m3 (53%) for the females. The Kinect protocol estimated COM with an average error of  <2%. Segmental mass estimates were overestimated by 3.11% for males and 5.23% for females when compared to ECM. This research established that the Kinect V2 could be used as a tool for BSIP estimation. Future work should improve on the scanning posture, scanning protocol and reducing the scan duration. Furthermore, future research should investigate on methods to eliminate the manual segmentation proposed for this protocol.

abstract: M.A.Sc.


title: Modelling and verification of predictable data flow in real-time systems

contributor:
Dingel, Juergen
Computing

subject:
model checking
predictability
real-time operating systems
schedulability

abstract: Thesis (Master, Computing) -- Queen's University, 2015-10-28 01:28:37.567

abstract:
As vehicle electronic control systems become responsible for an increasing number of functions, developers of such systems find themselves pulled in two directions: the need to perform more and more computation while at the same time reducing cost, weight and power consumption. Traditionally, safety isolation and fault containment of software tasks has been achieved through either physical or temporal segregation. This approach is reliable but inefficient in terms of processor utilization. Recently, there has been a move towards systems which achieve better processor utilization by executing all tasks together and guaranteeing safety isolation and fault containment by means of formal verification.

First, a definition for one such system was developed, based on PharOS and Giotto. The system modelled attempts to ensure observably deterministic data flow (i.e., inputs from and outputs to other systems), but allows for non-observable nondeterminism. It also allows for sporadic deadline overruns and accounts for criticality during fault handling.

Second, a method for verifying a given input system definition (system, set of tasks and fault model) for predictable data flow was developed. A stand-alone tool was made that performs this verification and displays the results graphically. The core exhaustive verification is performed by the Spin model checker.

abstract: M.Sc.


title: “I am Deliberate and Afraid of Nothing”: Using Body Mapping as a Research Tool to Explore HIV Risk Among Youth in Soweto, South Africa

contributor:
Power, Elaine
Kinesiology and Health Studies

subject:
Adolescents
South Africa
Body Mapping
HIV Risk

abstract: Thesis (Master, Kinesiology & Health Studies) -- Queen's University, 2015-10-28 12:23:02.628

abstract: In 2012, I used Body Mapping to explore personal experiences of HIV risk among 6 young men and 4 young women, ages 18-19, in Soweto, South Africa.  Using a series of arts-based exercises designed to foster participant engagement and knowledge production, and facilitated over the course of four days, participants used the power of art-making to engage in a participant-researcher dialogue about sex, HIV risk, relationships, violence, substance use, the need for trusted mentors, and more. At the end of each art-making day, the Body Mapping participants gathered to discuss their artwork. The participants conveyed that the Body Mapping experience provided a safe, non-judgmental space in which they could challenge their attitudes and understanding about difficult-to-discuss topics. Moreover, the results of the Body Mapping project suggest that HIV prevention measures are not as important as young people’s need for trusted adults with whom they can speak candidly about life’s challenges. The participants also suggested that they require sexual health information and resources based on their lived experiences. Moreover, they articulated that they most needed accessible and youth-friendly communication tools that facilitate honest, non-judgmental, and deliberate conversations about their sexuality, relationships and sexual health practices with trustworthy, reliable adults. Furthermore, the Body Mapping narratives, together with the artwork, offer an in-depth perspective of growing up in post-apartheid South Africa, one in which community leaders, educators and those who connect with youth must challenge their way of engaging with and developing HIV prevention messaging for young people. For youth to better understand HIV risk, adult mentors must be willing to listen to adolescents and young adults and provide them with a safe space in which to talk openly, honestly and without judgment about their risk-taking behavior.

abstract: The work in this thesis will be published.

abstract: M.Sc.


title: Technological Moral Proxies and the Ethical Limits of Automating Decision-Making In Robotics and Artificial Intelligence

contributor:
Sismondo, Sergio
Philosophy

subject:
human robot interaction
science and technology studies
autonomous cars
internal cardiac defibrillators
bioethics
social robotics
anthropomorphism
applied ethics
robotics governance
design ethics
robot ethics
engineering ethics
machine ethics

abstract: Thesis (Ph.D, Philosophy) -- Queen's University, 2015-10-29 14:15:46.57

abstract:
Humans have been automating increasingly sophisticated behaviours for some time now. We have machines that lift and move things, that perform complex calculations, and even machines that build other machines. More recently, technological advances have allowed us to automate increasingly sophisticated decision-making processes. We have machines that decide when and how to use lethal force, when and how to perform life-saving medical interventions, and when and how to maneuver cars in chaotic traffic. Clearly, some automated decision-making processes have serious ethical implications—we are now automating ethical decision-making. In this dissertation, I identify and explore a novel set of ethical implications that stem from automating ethical decision-making in emerging and existing technologies.
I begin the argument by setting up an analogy between moral proxies in healthcare, tasked with making ethical decisions on behalf of those who cannot, and technological moral proxies, those machines (artefacts) to which we delegate ethical decision-making. The technological moral proxy is a useful metaphor. It allows us to import the many established norms surrounding moral proxies in bioethics, to inform the ethics, design and governance of certain machines. As is the case with moral proxies in healthcare, we need norms to help guide the design and governance of machines that are making ethical decisions on behalf of their users. Importantly, I argue that we need a methodology and framework to ensure we aren’t subjecting technology users to unacceptable forms of paternalism.
Having set up the analogy, I situate the discussion within various theories in science and technology studies (STS). STS provides a rich philosophical vocabulary to help ground the particular ethical implications, including implications for designers and engineers, raised by machines that automate ethical decision-making. Thus, STS helps to frame the issues I raise as design and governance issues.
I then provide a rudimentary taxonomy of delegation to help distinguish between automated decision-making that is ethically permissible, and that which is impermissible. Finally, I combine the various pieces of the argument into a practical “tool” that could be used in design or governance contexts to help guide an ethical analysis of robots that automate ethical decision-making.

abstract: PhD


title: Assessing the biocompatibility of oligomers and amine-functionalized polymers for use in two-phase partitioning bioreactors

contributor:
Daugulis, Andrew J.
Chemical Engineering

subject:
Biochemical Engineering
Bioprocessing
Reactive polymers
Two-phase partitioning bioreactors

abstract: Thesis (Master, Chemical Engineering) -- Queen's University, 2015-10-29 14:13:13.437

abstract: Two-phase partitioning bioreactors (TPPBs) are a bioprocessing tool that limits inhibition of cell growth by toxic compounds in bioreactors by utilizing an immiscible secondary phase to sequester compounds that inhibit microbial cell growth. Early TPPBs used organic solvents as the sequestering phase despite challenges identifying solvents that were inexpensive and biocompatible, although recent efforts have utilized polymers as the sequestering phase in TPPBs. Research on the selection of polymers for use as the sequestering phase in TPPBs has focused on predicting solute uptake by first principles in order to maximize the partitioning coefficient of a target solute. Some research has shown that low molecular weight (MW) polymers have improved partitioning coefficients, although their biocompatibility is in need of further study; this thesis investigates the effect of polymer MW on microbial biocompatibility. Trends in biocompatibility were assessed for polypropylene glycol to Saccharomyces cerevisiae and Pseudomonas putida. Given that log P has been used as an important physiochemical property for predicting biocompatibility, with higher log P values associated with improved biocompatibility, experiments were performed to determine the log P of polymers. Polymers were also water-washed to shift the log P upwards by removing low MW polymer chains. Average log P determination experiments showed that as the polymer MW increased, the measured log P also increased. Biocompatibility, as measured by the change in optical density of the cultures after 24 hours of exposure to the polymers, also improved with increasing MW and log P, and that polypropylene glycols possessing MWs of 1000 and higher were all found to be biocompatible. It was also shown that water-washing noticeably improved biocompatibility by removing low MW polymer from samples. Initial research was also undertaken to examine the use of amine-functionalized reactive polymers for extracting organic acids in TPPB in terms of their efficacy and their biocompatibility. An amine functionalized polyacrylate was synthesized which was stable under acidic conditions, and did not inhibit cell growth over 24 hour exposure. It was also shown to extract 60-85% of organic acids from aqueous solution over 2 hours with polymer concentrations of 10 g/L, and acid concentrations of 2.5 g/L.

abstract: M.A.Sc.


title: Association between exercise, cardiorespiratory fitness and change in insulin sensitivity

contributor:
Ross, Robert
Kinesiology and Health Studies

subject:
Exercise
Insulin sensitivity
Cardiorespiratory fitness

abstract: Thesis (Master, Kinesiology & Health Studies) -- Queen's University, 2015-10-29 16:12:32.722

abstract:
The ability of the body to manage blood sugar is referred to as insulin sensitivity. Reduced insulin sensitivity is both a risk factor and is involved in the pathogenesis of type-2 diabetes. Cardiorespiratory fitness (CRF) is an established predictor of insulin sensitivity. Whether this association persists following control for exercise is not known. The primary objective of this study was to determine the independent associations between changes in exercise, CRF and insulin sensitivity. The influence of changes in body weight and waist circumference (WC) on these associations was examined in secondary analyses.
       Participants were 140 middle-aged, inactive, abdominally obese adults that participated in a 24-week exercise program. Exercise was performed 5 times per week for the duration of the program and was measured as Calories of energy expended, herein referred to as exercise energy expenditure (exercise EE). CRF was measured using a treadmill test to exhaustion. Body weight was measured on a Detecto scale and WC was measured at the level of the hip bone. Physical activity performed outside of the exercise sessions was measured using portable activity monitors known as accelerometers. Caloric intake was monitored using daily diet records. Following oral consumption of a 75-gram glucose drink, 2-hour insulin area under the curve was calculated as a measure of insulin sensitivity.
        Change in insulin sensitivity was associated with exercise EE, change in CRF, change in body weight and change in WC. Exercise EE was associated with change in insulin sensitivity after we adjusted for change in CRF, whereas change in CRF was not associated with change in insulin sensitivity after we adjusted for exercise EE. After further adjustment for changes in body weight and WC, neither exercise EE nor change in CRF were associated with change in insulin sensitivity. Changes in body weight and WC were associated with change in insulin sensitivity after adjustment for exercise EE and change in CRF.
      The principle finding of this study was that the link between CRF and insulin sensitivity is largely explained by variations in exercise. Further, a reduction in obesity is one of the ways in which exercise improves insulin sensitivity.

abstract: Will be submitting to a journal.

abstract: M.Sc.


title: On the Development of the Wavelength Shifter Deposition System for the DEAP-3600 Dark Matter Search Experiment

subject:
Vacuum Deposition
Wavelength Shifting
Dark Matter

abstract: Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2015-10-30 11:58:00.315

abstract: The DEAP-3600 dark matter search experiment uses 3600 kilograms of liquid argon as a target medium contained in a spherical acrylic vessel. Particle interactions in liquid argon produce vacuum ultraviolet light at a peak wavelength of 128 nanometers, which is not directly visible by the 255 inward-facing photomultiplier tubes. To make visible these interactions, the organic wavelength shifter 1,1,4,4-tetraphenyl-1,3-butadiene, with a re-emission spectrum peaked at 430 nanometers, was evaporatively deposited over the inner surface of the acrylic vessel. The several micron thick coating covers approximately 9 square meters. Application of the coating was performed under vacuum using an evaporation source deployed in the center of the vessel before filling with argon. Research and development on the deployment system for sources inside the acrylic vessel, small scale testing of the evaporation source, and data from test deposition thickness monitoring will be presented, as well as details on the development of the final source, deployment, and performance.

abstract: M.Sc.


title: A Role For Ideal Theory In Light of The Theory of Second Best

contributor:
Kymlicka, Will
Philosophy

subject:
Political Philosophy
Ideal Theory

abstract: Thesis (Master, Philosophy) -- Queen's University, 2015-10-30 13:54:57.604

abstract:
Political theorists, in increasing frequency, have focused on the application of theories of justice to concrete social issues and policy prescriptions. This so called “policy turn” has made it ever more important to reflect upon the goal of political theory. At the heart of this debate is a concern for action-guidance and a dissatisfaction with what political philosophy has offered in terms of practical relevance. The ideal guidance approach to ideal theory, best exemplified by John Rawls, holds a complementary relation between ideal and non-ideal theory, in which the former provides the goal for the latter to approximate. This approach to ideal theory, however, has been challenged by the Theory of the Second Best which undermines the assumption that simply approximating an ideal will result in the second best available option. Despite this challenge from the TOSB it will be the project of this paper to defend a more indirect role for ideal theory in political theorizing.
 My thesis is organized as follows. Chapter 2 will introduce the concept of ideal theory and fact sensitivity and provide a brief overview of how philosophers have attempted to define these concepts. I will argue that it is important to distinguish the ideal guidance approach from more epistemological approaches to theorizing about justice. In chapter 3, I will examine a unique challenge to the ideal guidance approach to ideal theory, the Theory of Second Best (TOSB). In chapter 4, I will discuss how comparative approaches to justice attempt to construct a theory of justice in light of the TOSB by rejecting the use of ideal theory for real world reform. Finally, in chapter 5, I will mount a moderate defense for the use of ideal theory in normative political theorizing.

abstract: M.A.


title: The Design and Development of an IPv6-Enabled Wireless Sensor Network and Industrial Machine Monitoring Application

contributor:
Lai, Yongjun
Mechanical and Materials Engineering

subject: Industrial Wireless Sensor Networks

subject: IPv6

subject: 6LoWPAN

subject: Wireless Sensor Networks

abstract: Thesis (Master, Mechanical and Materials Engineering) -- Queen's University, 2015-10-30 15:58:10.681

abstract:
Wireless sensor networks are becoming more and more popular in a widespread number of applications related to monitoring environments, structures, and machinery. Wired monitoring systems are currently widely adopted in industrial settings due to their reputation and history in performing to established standards. In order to explore the field of low-power wireless industrial sensor network monitoring applications, experimental work has to be done in numerous environments.
In this thesis, there is a focus on the design and development of hardware and software for such a purpose. Network coordinator devices capable of Internet connectivity over Ethernet, battery-powered sensor nodes equipped to measure acceleration and temperature, and accelerometer boards were designed and produced for the application. The software on the devices was developed as an adaptation of an open-source operating system, Contiki, and explores Internet version 6 connectivity. The goal of the work on this system is to develop a wireless sensor network platform for future research in the areas of sensor testing and industrial monitoring.
Two test networks were created with the aforementioned devices to demonstrate their functionality. One network was formed in a laboratory environment where network performance could be judged and tests could be run efficiently. The network contained nine end-nodes and one gateway, and ran for 49 days with an average packet reception rate of 98.2%. The second network was setup in a compressor room on Queen’s University campus; the topology included four end-
ii
nodes and one gateway. The network observed continuous data collection for 36 days with an average packet reception rate of 86.6%. The battery replacement cycle for the end-nodes was calculated in-laboratory to be 1.36 years; the platform would be suitable for use in a laboratory setting for future research but more work on the system is necessary to improve performance in an industrial environment.
The compressor room case study continues to run as a subject of future work. Software changes expected to improve the performance of the system will be uploaded to the devices as they are developed. Such software changes may improve the system’s efficiency and result in an improved battery replacement cycle length.

abstract: M.A.Sc.


title: Molecular Characterization of Gleason Patterns 3 and 4 Prostate Cancer Using Reverse Warburg Effect-Associated Genes

contributor:
Park, Paul
Pathology and Molecular Medicine

subject:
Gleason Pattern
Biomarkers
Stroma
Prostate Cancer
Reverse Warburg Effect
Nanostring

abstract: Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2015-11-05 15:21:10.73

abstract:
Background:
	Gleason scores (GS) 3+3 and 3+4 prostate cancers (PCa) differ greatly in their clinical courses, with Gleason pattern (GP) 4 representing a major independent risk factor for cancer progression. However, GP is not reliably ascertained by diagnostic biopsy, largely due to sampling inadequacies, subjectivity in the Gleason grading procedure, the high degree of heterogeneity of the disease, and a lack of more objective biomarker assays to stratify PCa aggressiveness. In most aggressive cancer types, the stromal microenvironment exhibits a reciprocal pro-tumourigenic metabolic phenotype consistent with the Reverse Warburg Effect (RWE). The RWE can be viewed as a physiologic response to the tumour phenotype that is both independent of tumour genotype and direct tumour sampling. This study aims to classify GP3 and GP4 based on differences in their stromal RWE-associated gene expression profiles.
Methods:
	Gene expression profiling was conducted on RNA extracted from laser-capture microdissected (LCM) stromal tissue surrounding 20 GP3 and 21 GP4 cancer foci from PCa patients with GS 3+3 and GS ≥4+3 respectively. Genes were probed using a 102 gene NanoString probe-set targeted towards biological processes associated with the RWE. Differentially expressed genes were identified from normalized data by univariate analysis. A top-scoring pair (TSP) analysis was also completed on raw gene expression values.
Results:
	Univariate analysis identified nine genes (FOXO1 (AUC: 0.884), GPD2, SPARC, HK2, COL1A2, ALDOA, MCT4, NRF2 and ATG5) that were differentially expressed between GP3 and GP4 stroma (p<0.05). However, following correction for false discovery only FOXO1 retained statistical significance at q<0.05. TSP analysis identified a significant gene pair, namely ATG5/GLUT1. Greater expression of ATG5 relative to GLUT1 correctly classified 77.4% of GP3/GP4 samples.
Conclusions:
	The stroma associated with GP3 is distinct from that associated with GP4 tumour foci by the higher expression of FOXO1 and a greater expression of ATG5 relative to GLUT1. Together, FOXO1 and the relative expression of the ATG5/GLUT1 gene pair represent RWE-based classifiers for GP3 and GP4 PCa, that have the potential to distinguish between true low-risk (GS 3+3) and false low-risk (GS 3+3 harbouring unsampled ≥GP4) patient cases.

abstract: M.Sc.


title: Differences in Abdominal and Liver Fat Accumulation Between Obesity-Matched Adults With and Without Type 2 Diabetes

subject:
liver fat
visceral adipose tissue
Type 2 Diabetes

abstract: Thesis (Master, Kinesiology & Health Studies) -- Queen's University, 2015-11-02 15:48:12.06

abstract:
Despite attempts to identify the mechanisms by which obesity leads to the development of Type 2 Diabetes (T2D), it remains unclear why some but not all adults with obesity develop T2D. Given the established associations between visceral adipose tissue (VAT) and liver fat with insulin resistance, we hypothesized that compared to age and obesity matched adults who were non-diabetic (NT2D), adults with T2D would have greater amounts of VAT and liver fat.
The International Study of Prediction of Intra-Abdominal Adiposity and Its Relationship with Cardiometabolic Risk/Intra-Abdominal Adiposity (INSPIRE ME IAA) aims to study the associations between VAT and liver fat and risk of developing T2D and cardiovascular disease. Four thousand, five hundred and four participants were initially recruited; from this, 2383 White and Asian adults were selected for this ancillary analysis. The NT2D and T2D groups were matched for age, body mass index (BMI) and waist circumference (WC). The T2D and NT2D groups were also compared to participants with either impaired fasting glucose (IFG) or impaired glucose tolerance (IGT; IFG/IGT)). Abdominal adipose tissue was measured by computed tomography; liver fat was estimated using computed tomography-derived mean attenuation. Secondary analysis determined whether differences existed between NT2D and T2D groups in VAT and liver fat accumulation within selected BMI categories for Whites and Asians.
We report across sex and race, T2D and IFG/IGT groups had elevated VAT and liver fat compared to the NT2D group (p<0.05). VAT was not different between IFG/IGT and T2D groups (p>0.05), however liver fat was greater in the T2D group compared to the IFG/IGT group in both Whites and Asians (p<0.05). Within each BMI category, the T2D group had elevated VAT and liver fat compared to the age and anthropometrically matched NT2D group in both Whites and Asians (p<0.05). With few exceptions, abdominal subcutaneous adipose tissue was not different in the T2D or IFG/IGT groups compared to the NT2D group independent of sex and race.
Compared to age and obesity-matched adults who are NT2D, we observe that White and Asian adults with T2D, and those with IFG/IGT, present with greater levels of both VAT and liver fat.

abstract: I request the thesis be restricted as I am submitting the manuscript for publication.

abstract: M.Sc.


title: Development of models to study Salmonella enterica infection of THP-1 cells pre-treated with IL-27

contributor:
Martin, Nancy L.
Microbiology and Immunology

subject:
THP-1 cells
Salmonella pathogenicity island 1
IL-27
Innate immunity
Salmonella enterica

abstract: Thesis (Master, Microbiology & Immunology) -- Queen's University, 2015-11-02 18:15:48.298

abstract: IL-27 has been shown to have important pro- and anti-inflammatory roles in the adaptive immune response.  However, its role in the innate immune response is less well characterized.  The goal of this research was to examine the role of IL-27 in the innate immune response.  Two in vitro models of Salmonella enterica serovar Typhimurium infection of the human monocytic cell line, THP-1, were developed.  S. typhimurium is an intracellular pathogen that can facilitate its own uptake into host cells where it is able to replicate, often leading to host cell death.  Based upon previous research on the role of IL-27 in innate immunity, it was hypothesized that IL-27 pre-treatment of THP-1 cells would result in an enhanced ability of THP-1 cells to fight S. typhimurium infection.  Infecting THP-1 cells with late stationary phase S. typhimurium resulted in a low level of infection whereas infection of THP-1 cells with late exponential phase S. typhimurium led to a high level of THP-1 cell infection.  Adherent THP-1 cells were stimulated with IL-27 for 16 hours prior to infection with either late stationary or late exponential phase S. typhimurium.  A gentamicin protection assay was used to quantify internalized bacteria to assess if IL-27 pre-treatment affected the initial invasion and subsequent survival of S. typhimurium in THP-1 cells.  THP-1 cells stimulated with IL-27 had the same level of internalized S. typhimurium as untreated THP-1 cells initially and over the subsequent 12 hours.  THP-1 cell viability was monitored between 1-12 hours after the addition of S. typhimurium to determine if IL-27 pre-treatment influenced THP-1 cell death.  Pre-treatment with IL-27 did not result in a difference in THP-1 cell death.  TNFα and IL-6 secretion from S. typhimurium infected THP1 cells were assayed to determine if IL-27 pre-treatment resulted in an altered cytokine response.  IL-27 stimulation resulted in significantly higher (p<0.01) levels of TNFα and IL-6 than untreated cells at 1-12 hours after the addition of S. typhimurium indicating IL-27 stimulation of THP-1 cells promotes a pro-inflammatory response.  Overall, IL-27 pre-treatment of THP-1 cells did not alter S. typhimurium infection of THP-1 cells but did enhance the pro-inflammatory response by these cells indicating IL-27 has a role in the pro-inflammatory response by innate immune system to S. typhimurium infection.  Further work is needed to explore the host-pathogen interaction that resulted in enhanced cytokine production in THP-1 cells and if this plays a significant role in immune cell survival over an extended time frame. Understanding the role of IL-27 in the innate immune response to pathogens will provide more information on how the immune system combats disease.

abstract: I wish to protect my right to commercial publication.

abstract: M.Sc.


title: The Role of Agency and Communion in Attitudes Toward Smart Drugs

contributor:
Fekken, G. Cynthia
Psychology

subject:
agency
communion
cognitive enhancement
attitudes
smart drugs

abstract: Thesis (Ph.D, Psychology) -- Queen's University, 2015-11-03 16:37:06.132

abstract: Recent advances in biotechnology have opened the door to new forms of human enhancement via smart drugs. Studies show that the decision by healthy individuals to use off-label pharmaceuticals in an attempt to self-enhance is surprisingly common in student populations. These studies investigate attitudes toward smart drug use in oneself and in others by relating enhancement decisions to key psychological variables, with a focus on the social dimensions of agency and communion. Data from three main studies and one pilot study show that people generally want to enhance any traits they feel they lack and which they see as important and negatively related to communion. Preferences toward distinctly agentic and communal traits indicate that people prefer to enhance in themselves traits that are associated with agentic themes of intelligence, efficiency, and capability more so than traits associated with communal themes of kindness, trustworthiness, and social relationships. This preference is reversed when considering self-enhancement of others, suggesting that attitudes toward smart drug use vary according to the perspective of actor or observer. Evidence from a priming study also affirms the importance of agency for the self: participants primed with agency were more willing than neutral participants to enhance agentic traits, while priming communion had no measurable effect on self-enhancement preferences.

abstract: PhD


title: Haloperidol-Environment Interaction Modulates Expression of c-Fos Proteins in the Basal Ganglia in Rats

contributor:
Beninger, Richard J.
Dumont, Eric
Neuroscience Studies

subject:
Haloperidol
Inverse incentive learning
Dopamine
c-Fos immunohistochemistry

abstract: Thesis (Master, Neuroscience Studies) -- Queen's University, 2015-11-11 09:43:09.917

abstract: Inverse incentive learning is the loss by stimuli of their ability to elicit approach and other responses. This has been shown in the horizontal bar test. Rats in the Paired group (n = 10) were injected with haloperidol (0.25 mg/kg) and initially descended almost immediately but over days descent latencies grew longer. Control rats were tested daily and received haloperidol (Unpaired group, n = 9) or saline (Saline group, n = 10) later in their home cage. Controls showed no evidence of increased descent latencies. On the final test day, all groups were tested after haloperidol and only the Paired group showed increased descent latencies. c-Fos immunohistochemistry was used to identify brain regions associated with inverse incentive learning. Expression of c-Fos positive neurons in the nucleus accumbens core and ventral pallidum was significantly lower in the Paired rats than in the Unpaired and Saline rats, even though all groups received haloperidol on the test day. Compared to the Saline group both the Paired and Unpaired groups showed evidence of lower c-Fos levels in the dorsal striatum and nucleus accumbens shell, possibly a result of daily haloperidol injections. No group differences in c-Fos expression were found in the piriform cortex, ventral hippocampus, ventral tegmental area or lateral habenula. The numbers of rats in the Saline, Paired, and Unpaired groups were: 9, 10, and 6 for the piriform cortex, dorsal striatum, nucleus accumbens and ventral pallidum; 5, 10, and 5 for the ventral hippocampus; 5, 5, and 5 for the ventral tegmental area; and 6, 6, and 7 for the lateral habenula. Results reveal brain region-specific changes in neuronal activity associated with inverse incentive learning. Results support possible underlying neuroplastic changes for learned decreases in responsivity to environmental stimuli.

abstract: Co-authors copyright form has not been submitted.

abstract: M.Sc.


title: The Social Reorganization of Polar Science: Responding to Cryospheric  Change in the International Polar Year 2007-2008 and Beyond

contributor:
Hand, Martin
Sociology

subject:
Arctic change
International Polar Year
science and technology studies
climate change

abstract: Thesis (Ph.D, Sociology) -- Queen's University, 2015-11-06 15:19:49.591

abstract:
While the natural sciences have convincingly argued for the reality of anthropogenic climate change, the social sciences have not paid sufficient attention to how knowledge of climate change becomes real through social practices. Yet investigating how climate change becomes real offers insight into the range of responses available to publics and policymakers. This dissertation addresses this gap in knowledge by studying how the sciences are being reorganized in response to cryospheric change.
The social reorganization of the polar sciences that is examined in this dissertation is informed by two main factors: (1) the recognition of the implications that anthropogenic climate change has for Indigenous populations dwelling in the Arctic, and (2) the recognition that climate change impacts in the Arctic cannot be adequately understood by examining parts of the environment in isolation from each other, but rather that a more holistic consideration is required.
To examine the social reorganization of the polar sciences, this dissertation draws upon science and technology studies, reflexive sociology, and poststructuralist ethics. The dissertation uses several qualitative methods, including in-depth interviews with key informants and participant-observation.
The central empirical foci of the dissertation are the inclusion of the “human dimension” in the International Polar Year (IPY) 2007-2008, the engagement with Indigenous knowledge in Canadian IPY projects, and the call to go “From Knowledge to Action” that concluded the IPY in 2012. I further examine the roles of uncertainty pertaining to rates of ice sheet melt, the positioning of stakeholders as mediators of complexity, and how the gap between knowledge and action is addressed in the Canadian High Arctic Research Station (CHARS) through social-ecological systems theory.
One of the main narratives this dissertation relates is the shift from reflexivity to resilience that informed the transition of Canadian science-for-policy from planning for the IPY 2007-2008 to planning for CHARS. I argue for the importance of “listening vulnerably” to human and non-human others, including the role sea ice plays as homeland for Arctic Indigenous peoples.

abstract: I conducted interviews with key informants, some of whom waived their right to anonymity. I told them they would have the opportunity to check any statements attributed to them before I publish in public a venue. At this point, not all research participant have provided feedback.

abstract: PhD


title: Indirect Co-culture of Human Adipose-Derived Stem Cells and Nucleus            Pulposus Cells for Intervertebral Disc Regeneration Using Peptide-Conjugated Hydrogels

contributor:
Amsden, Brian
Flynn, Lauren E.
Chemical Engineering

subject:
stem cell based therapy
intervertebral disc regeneration

abstract: Thesis (Master, Chemical Engineering) -- Queen's University, 2015-11-06 15:15:01.325

abstract: Intervertebral disc degeneration (IVDD) is a main cause of chronic low back pain, which results in significant economic loss to society and compromised life quality of patients. Traditional treatments of IVDD include surgical procedures, such as discectomy, and spinal fusion. However, these methods cannot preserve the biological or biomechanical functions of the intervertebral disc (IVD). Moreover, they decrease the mobility of the associated spinal motion segment and increase the load and stress on contiguous discs. Currently, artificial IVD replacements have gained interest. Although these implants are capable of preserving disc motion and disc height, they are unable to sustain compressive forces applied on the IVD due to their lack of elasticity. Therefore, there is a great need for an alternative therapeutic strategy for the treatment of IVDD. For mild or early stages of IVDD, regeneration by injecting pre-differentiated adipose-derived stem cells (ASCs) into the nucleus pulposus (NP) has been considered. This study aimed to investigate whether NP cells could direct human adipose-derived stem cells (hASCs) to differentiate into an NP cell phenotype. These cells could then serve as an alternative cell source for the treatment of intervertebral disc degeneration in the clinical setting. Interactions of ASCs and NP cells were studied via an indirect co-culture system using N-cadherin conjugated hyaluronic acid (HA) embedded within calcium alginate gels as scaffolds by evaluating the changing profiles of extracellular matrix (ECM) components, including glycosaminoglycans (GAGs) and type II collagen. NP cells showed the potential ability to induce hASC differentiation in terms of enhanced ECM production, such as collagen and GAG in an indirect co-culture system.

abstract: M.A.Sc.


title: Rhodium-Catalyzed Carbocyclizations of Alkylidenecyclopropanes with Allenes and Carbon Monoxide: Stereoselective Construction of Six- and Seven-Membered Rings

contributor:
Evans, P. Andrew
Chemistry

subject:
rhodium-catalyzed carbocyclizations
alkylidenecyclopropanes

abstract: Thesis (Ph.D, Chemistry) -- Queen's University, 2015-11-23 15:12:49.624

abstract:
This thesis is divided in the following manner:  Chapter 1 offers a short introduction, Chapter 2 describes the higher-order rhodium-catalyzed semi-intermolecular [(3+2)+2] carbocyclizations of alkylidenecyclopropanes (ACPs) with allenes, Chapter 3 highlights our results with respect to the rhodium-catalyzed semi-intermolecular [(3+2)+1] carbocyclizations of ACPs and carbon monoxide, while Chapter 4 covers the conclusions and future recommendations.
Section 2.1 provides an introduction into the metal-catalyzed carbocyclizations, followed by a description of three-carbon synthon utilized in higher-order carbocyclizations.  Section 2.2 particularly focuses on the reactivity of ACPs towards different transition metals to provide three-carbon surrogates in this type of cycloadditions.  Section 2.3 describes the metal-catalyzed cycloaddition reactions that employ allenes as exogenous two-carbon π-components, and concomitantly highlight the challenges associated with controlling chemo-, regio- and stereoselectivity for these processes.  The development of the rhodium-catalyzed [(3+2)+2] carbocyclization of alkyne-tethered ACPs is discussed in Section 2.4, which includes the optimization studies, the scope with respect to both substrates and also a plausible reaction mechanism, which accounts for the exclusive formation a single geometrical and regioisomer.  Section 2.5 describes the isolation of the key rhodacycle intermediate and its application towards the development of a highly enantioselective [(3+2)+2] carbocyclization of alkene-tethered ACPs and allenes.  We were able to isolate the corresponding cyclic adduct in 90:10 enantiomeric ratio and excellent regio- and diastereoselectivity.

Chapter 3 commences with an introduction to the Pauson–Khand reaction (PKR) and continues with the description of the intra- and intermolecular [3+2+1] carbocyclization reactions (Section 3.1).  The following section details our efforts towards the development of the diastereoselective rhodium-catalyzed [(3+2)+1] carbocyclization of alkenylidenecyclopropanes and carbon monoxide.  In collaboration with Prof. M.-H. Baik’s group, we employed high-level DFT calculations, which were supported by experimental studies, in order to construct a reliable hypothesis and demonstrate the scope for this reaction.  All reactions afforded the six-membered bicycles in excellent yield and diastereoselectivity.  Finally, Section 3.3 describes an extension of this [(3+2)+1] carbocyclization reaction by employing alkyne-tethered ACPs to construct substituted bicyclic phenols.  Overall, the methodologies described in this thesis have the potential of being utilized as key steps in the synthesis of important natural products (e.g. guaianolides).

abstract: To prevent competitors from getting an unfair advantage on all aspects of the work outlined therein

abstract: PhD


title: Validation of the Self-BAT (Self-Administered Bleeding Assessment Tool) and Evaluation of Determinants of Health in Hemophilia Carriers

contributor:
James, Paula
Pathology and Molecular Medicine

subject:
Hemophilia Carriers
Quality of Life
X-Inactivation
FVIII
FIX
Bleeding Assessment Tool

abstract: Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2015-11-17 14:21:27.992

abstract:
Hemophilia A and B are X-linked deficiencies of coagulation factor VIII and IX respectively.  Males are affected, while females are carriers of the disease. Recently, it has become clear that more than a third of hemophilia carriers (HC) are symptomatic. Carriers may experience prolonged bleeding postpartum, following trauma and surgery as well as menorrhagia.  This is the first research to incorporate both a bleeding assessment tool, to assist in objectively quantifying severity of bleeding symptoms, as well as a validated quality of life (QoL) questionnaire to facilitate an understanding of the relationship between bleeding symptoms and QoL.
 The objectives for this study are to validate a self-administered bleeding assessment tool (Self-BAT) as a screening tool to accurately identify HC with low factor levels (FL) and abnormal bleeding symptoms, to measure QoL of HC using the SF-36v2 and describe its relationship to bleeding severity and FL, and to investigate variability in FL.
To date, 59 HC have been enrolled.  A positive or abnormal Self-BAT bleeding score (≥6) has a sensitivity of 83%, specificity of 42%, a positive predictive value (PPV) of 0.48 and a negative predictive value (NPV) of 0.79 for the identification of HC with low FL. Analysis of QoL data shows an inverse correlation between QoL and BS (r=-0.52, p<0.0001).  No significant relationship is observed between QoL and FL. This study found skewed X-inactivation ratio (XIR) to be significantly more prevalent in this population than has been observed in the general population.  This suggests that determination of XIR may be useful in predicting risk of deficient FL.
This study validates the Self-BAT as an effective tool to identify HC with low FL and/or abnormal bleeding symptoms. For HC, Self-BAT BS is a more accurate measure of bleeding severity and resultant QoL than FL. HC will benefit from treatment strategies aimed at controlling bleeding symptoms which will facilitate improvements in the management of these patients overall.

abstract: M.Sc.


title: A New Robust Scenario Approach to Supply Chain Optimization under Bounded Uncertainty

contributor:
Li, Xiang
Chemical Engineering

subject:
Supply Chain Optimization
p-Norm
Generalized Benders Decomposition
Uncertainty

abstract: Thesis (Master, Chemical Engineering) -- Queen's University, 2015-11-19 16:46:06.148

abstract:
Supply Chain Optimization (SCO) problem under uncertainty can be modeled as two-stage optimization problem where first-stage decisions are associated with design and development of facilities and second-stage decisions are associated with operation of the supply chain network. Recently, a robust scenario approach combing the traditional scenario or robust approach has been developed to better address uncertainties in SCO problems, and it can ensure solution feasibility and better expected objective value. But this approach can only address uncertainties bounded with the infinity-norm.

This thesis proposes a modified robust scenario approach, which can be used to address uncertainty region bounded with the p-norm in SCO. In this case, after the normalization of the uncertainty region, the smallest box uncertainty region, that covers the normalized uncertainty region, can be partitioned into a number of box uncertainty subregions. Following some screening criteria, two subsets of the subregions that over-estimates and under-estimates the original uncertainty region can be selected. When the number of scenarios increases, the optimal objective values of the two robust scenario formulations converge to a constant, which is a good estimate of the true optimal value. This new robust scenario approach is then extended for any bounded uncertainty regions, in the context of robust optimization.

In many industrial problem, the historical realizations of uncertain parameters are known. This thesis gives a preliminary discussion on a data driven robust scenario approach, where the available data are normalized and a reference box that covers the data with a certain confidence is constructed. Then, the reference box is partitioned into box-shaped uncertainty subregions.

The benefits of the proposed robust scenario approach are demonstrated through some simple examples as well as an industrial SCO problem. The approach requires the solution of large-scale optimization problems when the number of scenarios is large, and these large-scale problems have a decomposable structure that can be exploited for efficient solution via decomposition-based optimization. A computational study demonstrates that, when the large-scale optimization problem is a second-order cone programming problem, generalized Benders decomposition is much faster than a state-of-the-art optimization solver.

abstract: M.A.Sc.


title: Functional Characterization of Human ADCK3 and ADCK4, Mitochondrial Atypical Kinases

contributor:
Jia, Zongchao
Biomedical and Molecular Sciences

subject:
ADCK4
mitochondria
atypical
kinase
coenzyme Q
ADCK3

abstract: Thesis (Master, Biomedical & Molecular Sciences) -- Queen's University, 2015-11-20 12:47:27.947

abstract: AarF domain containing kinases 3 and 4 (ADCK3 and ADCK4, respectively) are paralogous human mitochondrial proteins, co-orthologs of the yeast protein Coq8 and bacterial protein UbiB. These proteins are required in the biosynthesis of coenzyme Q, a lipid-soluble electron carrier well known for its role in energy metabolism, more specifically in the electron transport chain. Patients with mutations in ADCK3 experience an onset of neurological disorders from childhood, including cerebellar ataxia and exercise intolerance. Mutations in ADCK4 cause steroid-resistant nephrotic syndrome, and are also associated with coenzyme Q deficiency. Aside from this minimal characterization at the biochemical level, the precise biological functions of both ADCK3 and ADCK4 remain poorly understood. After extensive screening for soluble recombinant protein expression, N-terminal fusions with maltose-binding protein were found to facilitate the overexpression of human ADCK3 and ADCK4 truncations in Escherichia coli as soluble and biologically active entities. For the first time, our work revealed Mg2+-dependent ATPase activity of ADCK3, providing strong support for the theoretical prediction of these proteins being functional atypical kinases. Subsequent experimentation confirmed protein kinase activity for both ADCK3 and ADCK4. This observed kinase activity was inhibited by the presence of an atypical N-terminal extension – containing an invariant KxGQ motif – found within the kinase domains of these proteins, suggesting an autoinhibitory role for this motif. Additionally, ADCK3 was shown, through radiometric kinase assays, to phosphorylate a peptide corresponding to a potential phosphorylation site in ATP synthase F0 subunit 8, providing insight into a potential role of this atypical kinase family.

abstract: M.Sc.


title: Reinterpretation of the Ambient Paleoenvironmental Redox Conditions and Timing of Mineralization at SEDEX Zn-Pb Deposits in the Howard’s Pass District, Yukon

contributor: Geological Sciences and Geological Engineering

subject:
SIMS
SEDEX
Phosphorite
REE-Y
Sediment-Hosted Zn-Pb
Pyrite
LA-ICP-MS

abstract: Thesis (Ph.D, Geological Sciences & Geological Engineering) -- Queen's University, 2015-11-24 10:25:54.617

abstract:
The Howard’s Pass district (HPD) of sedimentary exhalative (SEDEX) Zn-Pb deposits is located in the Selwyn basin, Yukon, and comprises 14 Zn-Pb deposits that contain an estimated 28 Mt of Zn+Pb metals. Semi-massive to massive sulfide mineralization is hosted in carbonaceous and calcareous to siliceous mudstones. Host rocks to these deposits lack visual and chemical evidence of hydrothermal alteration and mineralogical haloes and, accordingly, several aspects regarding mineral deposit genesis in the HPD are poorly constrained or unconstrained. Detailed petrographic and combined electron probe microanalysis (EPMA), laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and secondary ion mass spectrometry (SIMS) studies were done on pyrite and apatite to better understand the mineralizing process(es), source(s) and pathways of sulfur and the ambient marine paleoenvironment at the time of mineralization.
Pyrite is a minor, but ubiquitous component of the host rocks and mineralization. Individual crystals or crystal aggregates of pyrite are texturally complex and show multi-stage growth. Growth stages range from syngenetic to earliest diagenesis, to early to late diagenesis, through to metamorphism; LA-ICP-MS and SIMS analyses reveal that pyrite of different textures possesses different trace element and sulfur isotope compositional ranges. Moreover, these data support a predominantly diagenetic origin for base-metal sulfide mineralization, formed from thermochemically-reduced sulfate below, or at, the sediment-water interface.
In places, the host rocks also contain abundant apatite that occurs as fine-grained layers stratigraphically above, within, and below the SEDEX deposits. EPMA and LA-ICP-MS reveal that apatite major, minor, trace and rare earth element-yttrium (REE-Y) compositions are remarkably similar throughout the stratigraphic succession. Several REE-Y proxies for depositional conditions and comparisons among apatites with diverse origins indicate that apatite from the HPD is hydrogenous rather than hydrothermal in origin. Previous workers concluded that sustained euxinic conditions were requisite in the formation and preservation of SEDEX deposits in the HPD, but the data presented in this thesis contradict this. These data include uniformly negative Ce anomalies in apatite (i.e., suboxic phosphogenic conditions) and extremely negative sulfur isotope values in framboidal pyrite (i.e., incremental depletion of seawater sulfate in the water column did not occur). Collectively, the current research presented here has redefined the ambient environmental and genetic models for the HPD.

abstract: PhD


title: Pattern Analysis of TXL Programs

contributor:
Cordy, James R.
Computing

subject:
programming languages
pattern detection
feature recommendation
clone detection

abstract: Thesis (Master, Computing) -- Queen's University, 2015-11-25 13:43:16.259

abstract: All programming languages need to be updated regularly by adding new features that fill programming needs. Existing approaches to determine new language features are completely manual and are based on language developers' experience, source code analysis, feature requests, and programmer interviews. Although these are acceptable practises, they are time-consuming and require a lot of brainstorming tasks, such as preparing interview questions, understanding ambiguous ideas, finding the common requirements, etc. No research, to our knowledge, has attempted to make the task of language feature identification easier. Through our research, we propose a systematic approach for identifying language features with the help of pattern and clone detection tools that work on source code. It semi-automates the task of feature identification, works quickly, and reduces the effort involved in existing practises. We identify features for the TXL language by implementing our idea and enabling the NiCAD clone detector to perform clone analysis on TXL source code, and developing a pattern detector. After detecting code patterns with the pattern detector and analyzing them, we propose eleven new features that can help improve the feature set of TXL.

abstract: M.Sc.


title: Improving the Problem Solving Performance of Struggling Learners in Mathematics

contributor:
Berg, Derek
Education

subject:
Students with Mathematics Difficulties
Cognitive Strategy Instruction
Graphic Organizers
Intervention Research
Mathematics Education
Mathematical Problem Solving

abstract: Thesis (Master, Education) -- Queen's University, 2015-11-25 14:34:30.385

abstract:
This study investigated the effectiveness of an intervention approach called Cognitive Strategy Instruction (CSI) that was supported with the use of graphic organizers (GOs). The intention of the research was to determine if CSI with the use of GOs could help improve the word problem solving performance of Grade 8 students experiencing difficulties in mathematics. The CSI approach incorporated instructional elements and guidelines from a Cognitive Strategy program called Solve it! (Montague, 2003). This study was conducted over 18-weeks. Three, female students participated in a 13-week group instruction. Field observations were collected during instruction to examine students’ mannerisms, such as their positive and negative responses, as well as their understanding of the material. Data were also collected from pre- and post- measures to examine students’: (a) feelings toward math problem solving; (b) knowledge, use, and control of the seven cognitive strategies and processes; and (c) performance in solving math word problems. The students participated in pre- and post- individual interviews (based on the modified MPSA-SF; Montague, 1996), as well as a pre- and post-math word problem solving quiz (based on Grade 6 EQAO assessments).
The results indicated that students’ participation on CSI training with the support of GOs may provide potential benefits to students who struggle in math. Two of the three students improved their performance in solving one-step math word problems on the post-intervention quiz. There was also a general improvement in students’ feelings toward math problem solving and an overall improvement in their knowledge and application of the problem solving strategies. In addition, the field observations provided insight about students’ positive and negative responses during instruction, such as their engagement and motivation. This study provides educators with an instructional program to help struggling students succeed in Ontario’s math classrooms. Future research is recommended to gain further insights about the perceived benefits of CSI training with the support of GOs.

abstract: M.Ed.


title: Thermal Evidence for Surface and Subsurface Water Contributions to Baseflow in a High Arctic River

contributor:
Lamoureux, Scott F.
Geography

subject:
Surface flow
Subsurface flow
Arctic
Baseflow
Hydrology
Canadian
Thermal evidence
Thermal regime
Cape Bounty
Longitudinal survey
Channel snow
Lateral inflow
Temperature
Isotope
Deuterium
Enrichment
Discharge
Depletion
Heat exchange

abstract: Thesis (Master, Geography) -- Queen's University, 2015-11-25 20:36:12.681

abstract:
Changes in river temperatures are caused by thermal energy exchanges at the interface between water and the atmosphere and between water, the streambed, and subsurface water. In permafrost regions, deeper active layer formation due to a warming climate can affect ground and channel bed thermal regimes and subsurface flow pathways. The main hypothesis is that within cold region landscapes, stream inflows into rivers provide relatively warm sources of water, while subsurface sources of water such as soil water contribute relatively cold water sources which alter the thermal and isotopic composition of the river, and as such, downstream temperature measurements can identify these sources in space and time.
In this study, river water temperature patterns were used as primary indicators of slope water exchanges along the West River at the Cape Bounty Arctic Watershed Observatory (CBAWO), Melville Island, Nunavut, Canada (75º N, 109º W). Water temperature data was collected through detailed longitudinal surveys along the river during the 2014 recession and baseflow periods to locate surface and subsurface lateral inflows. Limited water stable isotope sampling was also undertaken at fixed stations to determine possible mixing from different water sources.
Atmospheric factors and channel snow were found to be the main contributors to thermal variance in the river during the 2014 Summer season, with tributary inflow discharge also being a strong factor. The longitudinal temperature profiles indicate clear localized downstream changes in the thermal conditions of the river at multiple locations, and are interpreted to be indicative of subsurface and surface water exchange through inputs of cooler or warmer water. River temperature increased downstream and stable isotopic composition show progressive downstream enrichment in the two study reaches during the majority of the baseflow period, which is indicative of a culmination of localized surface flow inputs along both reaches.
These results demonstrate some key processes that influence the thermal regime of a High Arctic river and will contribute to a greater understanding of how surface, subsurface and other water exchanges influence stream hydrology, ecology and biogeochemistry.

abstract: M.Sc.


title: Microstructural Evaluation and Thermal Creep Behavior of Zr-Excel

contributor:
Daymond, Mark R.
Mechanical and Materials Engineering

subject:
Zr-Excel pressure tube
heat-treatment
texture
anisotropy
line-broadening
dislocations
thermal creep
creep anisotropy

abstract: Thesis (Ph.D, Mechanical and Materials Engineering) -- Queen's University, 2015-11-26 16:15:21.68

abstract: Dual phase (α-β) Zr-Excel Pressure Tube (PT) material has been heat treated in the (α+β) or β-phase regime to generate variable microstructures. These heat-treated microstructures revealed significant modification in the inital microstructure. The microstructural changes by heat-treatment will have a profound influence on their deformation behavior; characterizing those properties is the main goal of this study. In this dissertation, the experimental results are presented in a manuscript format, which is divided in three technical chapters. Chapter 3 discusses the effect of heat treatment on texture modification; where, as received (ASR) PT materials were heated to a range of temperatures and cooled either in water or in air. It has been observed that due to the orientation relationship between α and β-phase, the ASR microstructure has been significantly altered during heating and cooling. The extent of this alteration strongly depends on the solution temperature and cooling rate. Although, variant selection is observed during texture modification, significant randomization is noticed in the room temperature texture. In Chapter 4, line profile analysis technique has been used to quantitatively analyze the microstructural details of the heat-treated materials. Diffraction pattern analyses demonstrated significant peak broadening in the heat-treated material; which is attributed due to the increase of volume fraction of martensitic α and alteration in the dislocation structures. Line profile analyses also revealed that primary α consists with large sub-grains and correlated dislocations but the martensitic α are highly dislocated. Finally in Chapter 5, thermal creep behavior of the heat treated materials has been studied. Microstructural analyses were also conducted in the pre- and post-creep materials to understand the creep mechanism. Creep anisotropy of the heat treated materials has been investigated by correlating the experimental creep data with their associated texture. The ASR PT material shows very anisotropic creep behavior due to the strong texture. However, the water-quenched-895 treatment substantially decreased the anisotropy by creating a balance between the texture and microstructure. Nevertheless, texture randomization at higher solution temperatures might have changed this balance and made the material being anisotropic again.

abstract: PhD


title: Geological models and their influence on geotechnical investigation

rights: Creative Commons - Attribution-Non-commercial-No Derivate Works - CC BY-NC-ND

subject:
Geotechnical Models
Geological Maps
Conceptual Geologic Models
Geological Models
Geological Patterns
Uncertainty

abstract: Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2015-11-30 10:48:12.703

abstract:
Geological models, including maps and 3D models, are used in geotechnical site investigation in order to contribute to the evaluation of an area.  A geological map is constructed through a complex, subjective interpretation process and represents both a data set and a conceptual geological model.  Uncertainty is associated with the data set, but also with the conceptual geological model.  This uncertainty can be considered as potential change to a set of discrete geological interpretations, here called patterns.
Similar to the conceptual abstractions used in architecture and software engineering, geological patterns provide a means of using, organizing and transmitting information.  It is possible to recover a set of permissible patterns, a representation of a conceptual geological model, from a geological map alone.  The connections between aspects of the geological patterns called parameters and the geotechnical evaluation function can be made explicit.  The result can be used to construct a map of the relative uncertainty of the geotechnical evaluation, as a function of the uncertainty associated with the conceptual geological model.  It can also be used to map the relative effectiveness of different observation modes for constraining the geological and thus the geotechnical model.
The analysis described here allows unprecedented consideration of where geotechnical models are uncertain and how that uncertainty can be resolved.  The generalization of geotechnical evaluation as an evaluation function allows the adaptation of this workflow to other fields of geological decision-making, such as mineral exploration and land use planning.

abstract: M.A.Sc.


title: The Effect of Polymer Chain Mobility on Protein Adsorption and Subsequent Cell Behavior

contributor:
Amsden, Brian
Chemical Engineering

subject:
Protein Adsorption
Polymer Chain Mobility

abstract: Thesis (Ph.D, Chemical Engineering) -- Queen's University, 2015-11-27 14:33:17.291

abstract: Many cell types are known to respond to the stiffness of polymeric biomaterial substrates. However, the mechanism by which cells sense this stiffness is still under investigation. Cell response to a material is believed to be mediated by the composition and/or configuration of the protein layers that adsorb to the biomaterial surfaces prior to cell contact. It is, therefore, hypothesized that polymer stiffness, and specifically, the flexibility of the polymer chains at the polymer aqueous interface, affects the composition and configuration of the adsorbed protein layer, which is responsible for influencing cell response. In this thesis, two biomaterials known to induce stiffness dependent cell responses are used as model systems to determine whether polymer chain flexibility influences cell behavior via differences in the protein adsorption. The first is an elastomer formed from an acrylated star-poly(D,L-lactide-co-ϵ-caprolactone) (ELAS) which has been shown to support higher NIH3T3 fibroblast proliferation on a less stiff version of the elastomer despite minimal differences in surface chemistry. The second is poly(trimethylene carbonate) (PTMC) which has been shown to degrade in vivo via macrophage mediated erosion at molecular weights higher than 100 kg/mol, but does not degrade at molecular weights of less than 70 kg/mol, despite no difference in surface chemistry. Quantity and viscoelastic properties of protein layers adsorbed from individual solutions of albumin, immunoglobulin G, fibronectin and vitronectin, as well as fetal serum and adult plasma supplemented environments were compared on different stiffnesses of these materials to determine whether polymer chain flexibility affects protein adsorption. Polymer stiffness was found to affect quantity and conformation of individually adsorbed protein layers as well as the composition of protein layers adsorbed from serum and plasma supplemented media. Surface adsorbed fetuin A and vitronectin were identified and proposed to be responsible for influencing fibroblast proliferation and macrophage behavior, respectively. It was concluded that the flexibility of the polymer chains at the polymer-aqueous interface affects the arrangement of water molecules at the interface and alters the entropic gain associated with protein adsorption, thus favoring the adsorption of different types and adsorbed conformation of proteins which influences the subsequent cell response to the biomaterial.

abstract: PhD


title: Sleep Well, Work Well: Three Studies

contributor:
Barling, Julian
Management

subject:
Sleep Apnea
Work Withdrawal
Work
Work stress
Leadership behaviors
Sleep

abstract: Thesis (Ph.D, Management) -- Queen's University, 2015-11-28 10:06:51.658

abstract:
My dissertation explores the relationship between sleep and work, with attention to how sleep impacts work-related outcomes. Study 1 extended the current work stress and sleep literature by examining the reciprocal relationship between sleep and work stress within the job demands-control-social support model of work stress. The reciprocal relationship was tested using five-wave longitudinal data. This cross-lagged model was partially supported, as sleep impacted perceptions of work stress across the five wave study, whereas work stress affecting sleep was marginally significant across the five wave study.
Study 2 examined the influence of sleep on both positive (i.e., transformational leadership) and negative (i.e., abusive supervision) leadership behaviors. I hypothesized that sleep influences leadership indirectly through its effects on self-control. To examine the indirect relationship between sleep and leadership behaviors, a daily diary study methodology was used, where leaders described their daily sleep and self-control and followers rated their leaders’ leadership behaviors. A multilevel structural equation model was used to test these mediational models. There was support for sleep affecting abusive supervision through self-control across the 15 day daily study, however this relationship was not supported for transformational leadership.
Study 3 examined the impact of a common sleep disorder (obstructive sleep apnea; OSA) on work withdrawal behaviors. To examine this relationship, a sample of individuals attending an overnight sleep laboratory, with possible OSA were recruited. A within-subjects, pre-test, post-test design was used, where individuals completed a survey before and then two times after they received clinical treatment for their sleep disorder. Latent growth curve modeling was used to test this relationship. Findings show that daytime sleepiness caused by OSA effects withdrawal from work (partial absenteeism and absenteeism). Daytime sleepiness also lead to withdrawal at work (work neglect) through cognitive depletion. In addition, receiving treatment for sleep apnea decreased daytime sleepiness across time, and this improvement in daytime sleepiness resulted in decreased withdrawal from and at work over time; the indirect effects of the improvements in daytime sleepiness on withdrawal at work was mediated by improvements in cognitive depletion.
The dissertation closes with a general discussion of the contributions of these three studies.

abstract: PhD


title: RAD9A Stabilization and Destabilization Processes in Checkpoint Maintenance and Checkpoint Recovery

contributor:
Davey, Scott
Pathology and Molecular Medicine

subject:
Rad9A
Rad9A Stabilization
Chk1
Brca1
Rad9A Ubiquitination
Rad9A Phosphorylation
Positive Feed Back Loop
Rad9A Acetylation
Rad9A Accumulation

abstract: Thesis (Ph.D, Pathology & Molecular Medicine) -- Queen's University, 2015-11-27 21:05:56.396

abstract: The phosphorylation of the sensor-checkpoint Rad9A is essential for Chk1 activation in S-phase and during the G2/M checkpoints. Previous studies have demonstrated a late phosphorylation of Rad9A after DNA damage. Rad9A late phosphorylation requires the previous phosphorylation of S387, and it is not detected when Rad9A is overexpressed. Since Rad9A and TopBP1 interact through a phosphorylated S387 for ATR activation, it has been hypothesized that the late, damage-dependent phosphorylation on Rad9A is part of a positive feedback loop involved in checkpoint maintenance. This thesis shows that Rad9A is hyperphosphorylated and accumulates in cells exposed to DNA damage, and that this prevents Rad9A polyubiquitination and degradation. This work also shows that Rad9A polyubiquitination and degradation is observed in cells recovering from DNA damage, and that there are active processes regulating Rad9A degradation. This research further shows that Chk1 is required for the stabilization and accumulation of Rad9A after DNA damage, and that there is a positive feedback loop involving Rad9A and Chk1.  Rad9A acetylation is observed in conjunction with polyubiquitination, and Rad9A deacetylation following DNA damage prevents Rad9A polyubiquitination and degradation. This work also shows evidence of Brca1 and Rad9A association at the time of Rad9A polyubiquitination and degradation suggesting a Brca1 involvement in this process. In summary, this thesis shows a new positive feedback loop between Rad9A and Chk1 for checkpoint maintenance and the stabilization of Rad9A through its deacetylation following DNA damage to prevent Rad9A polyubiquitination and degradation.

abstract: PhD


title: Inline Coherent Imaging of Laser Additive Manufacturing

subject:
inline coherent imaging
laser processing
ICI
powder bed fusion
3D printing
selective laser melting
laser melting
process monitoring
melt pool morphology
additive manufacturing
laser materials processing
laser additive manufacturing

abstract: Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2015-11-29 14:37:52.655

abstract:
Metal-based laser additive manufacturing techniques such as selective laser melting offer unique capabilities in the manufacture of geometrically complex metal components. The ability of these techniques to fabricate unique part designs of high-strength metals is of great interest to advanced engineering sectors such as aerospace, automotive, biomedical, dental, and defense. Despite the advantages offered by these processes, online quality assurance and process control still remain major challenges limiting the widespread adoption of these techniques. In this thesis a low-coherence interferometric imaging technique, termed inline coherent imaging (ICI), is integrated into the selective laser melting process to monitor melt pool morphology changes and stability at 200 kHz with axial and transverse resolutions reaching 6 µm and 35 µm respectively. Powder layer, processed track, and layer quality are assessed in situ using ICI.

ICI-based imaging of single track processing of 316L stainless steel powder was investigated under a range of process parameters to determine the influence of processing conditions on melt pool morphological stability. Process parameter spaces involving 40-320 W laser powers; 50-600 mm/s scan speeds; 50-500 µm layer thicknesses; and supported and unsupported build environments were investigated. Galvanometer-based scanning of the imaging spot relative to the melt pool presented a unique perspective of the melt pool local geometry, undetectable by existing thermal-based imaging techniques. High-speed, time-resolved ICI measurements demonstrated that melt pool fluctuations and morphological stability strongly influence final track quality. Process defects resulting from poor process parameter regimes were detected and characteristic fault signatures were identified. Building on the success of ICI in monitoring single track processing, an ICI-integrated 3D-capable selective laser melting system was designed and constructed. System imaging and processing capabilities are characterized, and layer-wise ICI measurements of powder bed and processed layers taken during a 3D build are presented. Results presented throughout this work demonstrate the potential benefits ICI offers laser additive processes: layer-wise quality assurance measurements, morphology-based feedback control signals, improved parameter space optimization processes, and reductions in overall build times.

abstract: This thesis contains novel material pertaining to monitoring of laser additive manufacturing, through the technique of inline coherent imaging (ICI), which may be the framework for a patent application in the near future.

abstract: M.A.Sc.


title: Spatial-Temporal Analysis of Lyme Disease Risk due to Climate Change in Southern Ontario from 2001 to 2014

contributor:
Chen, Dongmei
Geography

subject:
Lyme Disease
Black-Legged Ticks
Modeling
Population Model
Climate Change
Ixodes Scapularis
Spatial-Temporal Analysis

abstract: Thesis (Master, Geography) -- Queen's University, 2015-11-29 14:55:44.169

abstract:
The number of Lyme disease cases in Ontario has increased in the last decade and is projected to continue to increase due to climate change.  The northern limit of Lyme disease cases in Ontario has also been progressing northward from the United States.  It is unknown whether the increase in Lyme disease cases is due to climate change, changes in host abundance, host and vector migration, or a combination of these factors.  The objective of this research is to determine if the climate has changed to increase the geographic range of areas suitable for sustaining a reproductive tick population.

Monthly air surface temperature values from the National Centers for Environmental Prediction’s North American Regional Reanalysis was used to yield positive degree days above 0 degrees Celsius from 1979 to 2013 and derive warming trends in Ontario.  Next, the average of monthly mean day and monthly mean night time land surface temperature from MODIS were fed in to a basic reproductive tick population model to determine areas with climate suitable for sustaining tick populations.   Principal components analysis was conducted to determine changing suitability patterns.  The model outputs were compared against tick surveillance data supplied by Public Health Ontario from 2002 to 2012.

Areas in Ontario were identified where Lyme disease risk has become suitable for sustaining a black-legged tick population due to climate change, particularly in 2005, and 2010 - 2012.  This study shows that climate has allowed black-legged tick populations to sustainably move northward in the past decade.  However, the vast majority of submitted ticks were collected by health practitioners in geographic locations that were already suitable for sustaining a reproductive tick population.  This suggests that most Lyme disease cases in the past decade have been due to the tick population stabilizing in areas of suitability, or increased human-tick interaction in areas already suitable, rather than progression of ticks into new geographic areas due to climate change.
This analysis supports climate change models that indicate Lyme disease risk will continue to move northward and also provides high resolution Lyme disease risk maps.

abstract: M.Sc.


title: Free Radical Polymerization studies of vinyl ester monomers using Pulsed-Lased Polymerization with Size Exclusion Chromatography (PLP-SEC)

contributor:
Hutchinson, Robin A.
Chemical Engineering

subject:
Radical Polymerization
Size Exclusion Chromatography
Viny Ester Monomers
Pulsed-Lased Polymerization (PLP)

abstract: Thesis (Master, Chemical Engineering) -- Queen's University, 2015-11-29 14:49:38.843

abstract: Polyvinyl acetate and other polyvinyl esters, and their copolymers are used in coatings, adhesives and plastics, and hence fundamental understanding of the mechanisms and polymerization kinetics is vital for process development, and production of existing and new polymer grades in an effective and safe manner. The propagation kinetics of radical homopolymerization (bulk) of vinyl acetate (VAc), vinyl pivalate (VPi) and vinyl benzoate (VBz) was studied using Pulsed-Laser Polymerization coupled with Size Exclusion Chromatography (PLP-SEC) at laser pulse repetition rate (prr) between 2 and 500 Hz, and the temperature range of 25 - 90 °C. The propagation rate coefficient, kp, determined for VAc and VPi increases significantly with prr (20 % between 200 and 500 Hz prr), with the kp value for VPi ~50 % higher than that of VAc. This significant increase in kp with prr has been explained by the head-to-head addition defects that occur during vinyl ester polymerizations. For VBz, no kp value was reported due to lack of PLP-structure, likely due to resonance stabilization of the radical. Solution polymerization of VAc and VPi was also studied by PLP-SEC using ethyl acetate (EAc) and heptane (50 % by volume) at 50 °C, with the kp values having no substantial solvent effect. The polymerization kinetics of these vinyl ester monomers were also investigated using small-scale batch polymerization at 60 °C both in bulk and in solution (using EAc). The monomer conversion profiles obtained showed the same pattern in both bulk and solution, with the rate of conversion faster for VAc than VBz, and VPi even faster, trends consistent with the kp values determined using PLP-SEC. Kinetic models were implemented in the Predici software package, and are shown to fit the experimental batch polymerization data reasonably well.

abstract: M.A.Sc.


title: Spatial and temporal patterns of net carbon exchange in the polar semi-desert vegetation type on Melville Island, Nunavut

contributor:
Treitz, Paul
Scott, Neal
Geography

subject: NEE Arctic

abstract: Thesis (Master, Geography) -- Queen's University, 2015-11-30 11:02:21.426

abstract:
While studies of mesic tundra vegetation types across latitudinal gradients have shown decreasing levels of net ecosystem exchange (NEE) of carbon dioxide at more northern sites, little work has explored the factors regulating NEE in the polar semi-desert, a vegetation type which is widely distributed across the High Arctic. In 2013, eight ADC Automated Carbon Exchange (ACE) systems were deployed at the Cape Bounty Arctic Watershed Observatory (CBAWO) to quantify the contribution of the polar semi-desert vegetation type to landscape-scale NEE. As polar semi-desert vegetation cover varies at relatively small spatial scales, the chambers were distributed between vegetated areas (18-51% cover) and bare soil. Measurements were made every 30 minutes from late May to late July. Air temperature, soil temperature, and soil moisture measurements were collected in conjunction with NEE and ecosystem respiration (Re). In July 2013, Normalized Difference Vegetation Index (NDVI) data were collected to quantify variability in vegetation cover within the polar semi-desert. NDVI varied from -0.12 to 0.31, with the highest values occurring at vegetated sites and low values occurring on bare soil. Percent vegetation cover and NDVI correlated well at peak biomass (R2 = 0.96).
NEE is driven by variability of several biophysical factors, and the factors that best predict NEE vary throughout the season. In the early season, respiration drives NEE, and air temperature is the strongest predictor (R2 = 0.23 to 0.55). During the warmer part of the season, photosynthesis is the dominant component of NEE, and photosynthetically active radiation becomes the best predictor. Results suggest that once a threshold temperature is reached photosynthesis will dominate NEE in polar semi-desert vegetation types. Therefore, longer growing seasons, if associated with higher temperatures, would enhance NEE. These relationships may be useful for quantifying NEE in polar semi-deserts using remotely-sensed data in future studies.

abstract: M.Sc.


title: Fast and Sensitive Detection of Bacteria by Means of AC Electrokinetics and Micro-Raman Spectroscopy

contributor:
Docoslis, Aristides
Chemical Engineering

rights: Creative Commons - Attribution-Non-commercial - CC BY-NC

subject:
Rapid Bacteria Detection
AC Electrokinetics

abstract: Thesis (Master, Chemical Engineering) -- Queen's University, 2015-11-30 17:39:04.603

abstract:
Rapid diagnosis of pathogens requires the ability to detect the presence of a target pathogen in a sample at as low concentrations as possible. In the present thesis, a surface-based method that can provide early and label-free detection of target microorganisms in water is presented. The method combines three key features, namely, (a) accelerated transportation to, and focusing of bacteria on, the detection surface by means of alternating current (AC) electrokinetic effects; (b) selective capture of the target microorganism using surface-immobilized antibodies; (c) sensitive detection of target bacteria with micro-Raman spectroscopy. The non-uniform electric field is created by an AC signal-driven planar, quadrupolar, gold microelectrode array that is deposited on the detection surface (oxidized silicon wafer). The combined effects of AC electroosmosis and dielectrophoresis concentrated the bacteria onto a surface within a few minutes. Bacterial detection is subsequently, accomplished through Raman spectra acquired at pre-determined locations near the electrodes after sample removal and rinsing of the capture surface. Detection was successful at concentrations as low as 102 bacteria/mL using a sample volume of 50 μL. The method is sensitive enough to detect the capture of a single bacterium.
The bacterial capture efficiency was found to be strongly dependent on the selection of the applied voltage and AC frequency values. Tests performed in the range 1-20 Vpp and 1 kHz-1 MHz showed that the most effective operating conditions was (12 Vpp, 10 kHz). Overall, high bacteria capture efficiencies were observed at low frequencies (≤10 kHz).
The mechanism of bacteria capture was investigated with the aid of numerical simulations. It was found that the capture efficiency was very high under electric field conditions that cause a strong AC electroosmotic effect. The simulations results were in qualitative agreement with the experimental observations.

abstract: M.A.Sc.


title: Modification of Alginate and Development of Polymeric Nanocarriers by Living Radical Polymerization for Controlled/Targeted Drug Delivery

contributor:
Neufeld, Ronald J.
Cunningham, Michael F.
Chemical Engineering

subject:
Living Radical Polymerization
Drug Delivery
Alginate
Biomaterials

abstract: Thesis (Ph.D, Chemical Engineering) -- Queen's University, 2015-12-01 14:50:52.955

abstract:
Alginate-based amphiphilic graft copolymers were synthesized by single electron transfer living radical polymerization (SET-LRP), forming stable micelles during polymerization induced self-assembly (PISA). First, alginate macroinitiator was prepared by partial depolymerization of native alginate, solubility modification and attachment of initiator. Then, methyl methacrylate was polymerized from the alginate macroinitiator in mixtures of water and methanol forming poly(methyl methacrylate) grafts, prior to self-assembly. PISA of the amphiphilic graft-copolymer resulted in the formation of micelles with diameters of 50-300 nm. As the first reported case of LRP from alginate, this work introduces a synthetic route to of alginate-based hybrid polymers with a precise macromolecular architecture and desired functionalities. LRP from alginate can be applied to improve alginate-based hydrogel systems such as nano- and micro-hydrogel particles, islet encapsulation materials, hydrogel implants and topical applications. Such modified alginates can also improve the function and application of native alginates in food and agricultural technologies.
Targeted drug delivery using polymeric nanostructures has been at the forefront of cancer research engineered for safer, more efficient and effective use of chemotherapy. Here, a new polymeric micelle delivery system was designed for active tumor targeting via receptor-induced endocytosis. Oseltamivir phosphate targets and inhibits Neu1 sialidase activity associated with receptor tyrosine kinases such as epidermal growth factor (EGF) receptors which are overexpressed on cancer cells. By decorating micelles with oseltamivir, it was found that micelles actively targeted human pancreatic PANC1 cancer cells. Amphiphilic block copolymers with oseltamivir conjugated at the hydrophilic end, oseltamivir-poly(polyethylene glycol methyl ether methacrylate)-block-poly(methyl methacrylate), were synthesized using reversible addition-fragmentation chain transfer (RAFT) living radical polymerization. Oseltamivir-conjugated micelles have self-assembling properties forming worm-like micellar structures. Oseltamivir-conjugated micelles dose dependently reduced the cell viability of PANC1 cells compared to micelles without oseltamivir. Oseltamivir-micelles loaded with hydrophobic dye produced internalization by PANC1. These results clearly indicate that oseltamivir-conjugated micelles show potential as an entirely new active tumor targeting drug delivery system with the ability to internalize hydrophobic chemotherapeutics by receptor-mediated endocytosis.

abstract: We are currently in the process of filing patent application on one innovation described in this thesis. We will notify Queen's University when this process is complete so the thesis can be published. Thank you

abstract: PhD


title: Non-hydrostatic modelling of nearshore wave transformation and breaking over varying beach morphology

contributor:
Mulligan, Ryan P.
Civil Engineering

subject:
shore-oblique bars
erosional hotspots
SWASH wave model
LIDAR
non-hydrostatic wave modelling

abstract: Thesis (Master, Civil Engineering) -- Queen's University, 2015-12-04 09:02:34.042

abstract:
A non-hydrostatic phase-resolving wave model is used to investigate wave transformation and energy dissipation due to wave breaking over different small and large scale morphological features.  Simulations of waves in the nearshore region of a sandy beach at the Field Research Facility (FRF) in Duck, North Carolina (NC) were conducted to evaluate the Simulating WAves til SHore (SWASH) model ability to predict wave transformation and breaking in a high resolution 3-dimensional configuration for four moderate wave events. The model is forced with directional wave spectra from an acoustic wave sensor at the boundary of the computational domain, and validated with three acoustic sensors and water surface elevation observations from a LIDAR scanner mounted on the beach dune. Results indicate the model is able to accurately predict significant wave heights, spectral evolution, and energy dissipation due to wave breaking in the nearshore. This research shows that small-scale morphological features including shore-parallel bars, rip channels, and a large-scale feature corresponding to scour depression under the pier have a strong impact on the rate of wave energy dissipation and location of breaking in the surf zone.

The validated model is applied to four additional field sites in NC to determine the influence shore-oblique bars have on wave transformation and the alongshore variability in wave energy. Two sites with shore-oblique sandbars, and two beaches with straight contours were simulated with SWASH. The results indicate that higher alongshore variability in depth due to the shore-oblique bars causes large alongshore changes in cross-shore wave energy flux. This work shows that shore-oblique bars, known to be spatially correlated with areas of high shoreline change rates, introduce high alongshore variability in nearshore wave energy that could be the primary driver of changes in sediment transport rates and induce localized erosional hotspots on the shoreline.

abstract: Body chapters and the works in this thesis are going to be submitted for publication at a later date.

abstract: M.A.Sc.


title: Planting Stories, Feeding Communities: Knowledge, Indigenous Peoples and Film

contributor:
Lovell, W. George
Geography

subject: Indigenous Film and Stories

subject: Native Studies

subject: Ontario

subject: Reporting Academic Findings to Indigenous Communities

abstract: Thesis (Ph.D, Geography) -- Queen's University, 2015-12-03 23:19:44.735

abstract:
This dissertation, a companion to the documentary film Planting Stories, Feeding Communities, explores how film can be used to transmit information generated by an Indigenous community during research and return it in a manner that most closely approximates the multi-sensorial scope of the oral tradition. Of all modern forms of communication, I argue that film is the medium that lies closest to the mode of Indigenous storytelling. My dissertation explores film as a means of reporting findings back to the Six Nations of the Grand River First Nation, whose members played key roles in the history of Native Studies in Ontario – hitherto the focus of my MA research. Throughout, the most pertinent question has remained: What are the “best practices” – under the current circumstances – that can be put in place to ensure that colonial approaches, imposition of harmful outside authority foremost of all, are not perpetuated?
Bridging the gulf between my Indigenous and European ancestry requires a leap of faith from both sides. Lee Maracle, a writer of the Stó:lō Nation, describes the dilemma as “a basket in the middle of the bridge into which each side can contribute their accumulated light and teachings” (SAGE Writing Retreat, February 22, 2014). My contribution to the basket, I trust, is acceptance of a number of best practices revealed through collaborative research, which might contribute to increased transmission of academic findings to Indigenous communities.
Procedures rooted in community-based participatory research (CBPR) offer an array of best practices that proved pivotal to maintaining a balanced relationship between the researcher and those who are researched, ensuring that (as much as possible) control of the process rests with the community. Members of Six Nations expressed their opinions on camera in (i) a Community Circle and (ii) interviews with the key subjects. Subsequently, we collaborated to create a film to tell their story. “Best practices,” therefore, highlight ways in which film as a means of pedagogy can be used to transmit information to Indigenous communities in a manner that resembles and echoes the oral tradition.

abstract: I want time to refine the documentary film, which constitutes the essence of my dissertation, before releasing it to the public.

abstract: PhD