title: Feminist Philosophy of Religion in Eisler and Archaic Greece

subject: Presocratic Feminism Nietzsche Religion

abstract: The neglect of women’s perspectives by presocratic scholarship since its inception, as well as the misunderstanding of the beginning of western philosophy by feminists which has resulted from this neglect, have prevented many from appreciating both that Nietzsche’s discovery of the presocratics was a significant contribution to feminism and that contemporary feminists can, in turn, contribute to Nietzsche’s vision of the philosopher as a cultural physician by discovering at the dawn of western culture a form of religion that is the inverted image of the patriarchal dogmatism that most people associate with institutional religion, a female-centered religious tradition grounded in the love of learning … a.k.a. democracy.

abstract: PhD


title: Acoustic Signals of Closely Related Bird Species Differ More in Sympatry Than in Allopatry - But Not If They Are Learned

contributor:
Martin, Paul
Biology

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.

rights: Attribution-NonCommercial-ShareAlike 3.0 United States

subject:
Sympatry
Acoustic signals
Character displacement
Species sorting
differential fusion

abstract: Closely related species often have similar mating signals because of their shared recent ancestry, which can affect their reproductive isolation and ability to live together when they overlap in range. Similar mating signals can result in costs of co-occurrence (e.g., maladaptive hybridization, aggression), and we expect signals to diverge to reduce these costs where species overlap in range. However, other pressures (e.g., shared habitats) can lead to signal convergence instead, and it is unclear whether acoustic signals more often diverge or converge when species overlap in range. Here, we applied a comparative framework that controls for phylogeny and evolutionary time to determine whether acoustic signals of sympatric bird species are more different or similar compared to acoustic signals of allopatric species. Our holistic measures of signal differences suggest that acoustic signals of sympatric species differ more than those of allopatric species, but only if species do not learn their signals. We also found that, regardless of whether species learn their signals or not, sympatric species tended to differ more than allopatric species for three of eight frequency and time variables, with greater sympatric divergence occurring in different contexts for each variable. In contrast, sympatric species were more similar in frequency bandwidth compared to allopatric species, but only if signals were not learned, while four of eight variables showed no difference in divergence between sympatry and allopatry. Overall, our results suggest that learning may influence patterns of signal divergence in sympatry, that different selective pressures likely act on different aspects of acoustic signals, and that the methods we use to compare signals may impact which patterns we detect.

abstract: M.Sc.


title: (Re)storying the More-than-human City: Urban Coyotes in Canada

contributor:
Hovorka, Alice
Geography and Planning

rights: Attribution-NonCommercial-NoDerivs 3.0 United States

subject:
Animal geographies
More-than-human geography
Coyote
Canis latrans
Urban wildlife
Multispecies city
Urban geography
Wildlife management

abstract: The urban is most often constructed in our imaginaries, policies, and practices as a human space, understood in dualistic opposition to ‘nature’, ‘wilderness’, or the ‘rural’. This thesis aims to (re)story the city as a place of more-than-human belonging in three registers: theoretically, methodologically, and in practice. It does so using a case study of urban coyotes in Ontario as a point of entry, mobilizing ‘hybrid’ socio-ecological methods including: participant observation with Coyote Watch Canada, document review, semi-structured interviews, secondary analyses of GPS collar data, field investigations, and trail cameras. First, it (re)stories the city in urban theory by advancing a more-than-human everyday urbanism as a useful analytic for articulating a less anthropocentric reading of the city. It first performs a rhythmanalysis, demonstrating the importance of linear and cyclical rhythms in the spacetimes of human-coyote encounters. It then delves into coyote sensory worlds, illustrating the acoustic and olfactory ecologies which shape urban atmospheres, navigations, and inhabitations. Everyday urbanism shifts the focus from spectacular moments of conflict with wildlife, to a consideration of more-than-human place-making, resituating urban animals as neighbours rather than invaders. Second, this thesis (re)stories the city through a methodological focus on individual animals’ geographies. It relays narratives of two urban coyotes and their kin, Urban10 and Blondie, whose unique experiences are gleaned through hybrid socio-ecological research methods. Their stories become ones of synanthropy and cynanthropy – of animals learning to thrive in ‘human-dominated’ environments, and of the imaginative exercises of ‘becoming coyote’ required of multispecies researchers endeavouring to generate knowledge collaboratively with other-than-humans. Third, it (re)stories coyotes within urban wildlife management scholarship and practice by advancing a set of best practices for aversion conditioning (humane hazing) to mitigate human-coyote conflicts in urban areas. It challenges traditional language, characterizations of behaviours, and policy options, enabling an alternate set of compassionate responses that do not presume coyotes as incongruous with urban life, or the inevitability of animal death for human convenience. Overall, this thesis contributes to emerging dialogues at the intersection of more-than-human, animal, and urban geographies, as well as wildlife management, (re)storying the city towards livable multispecies futures.

abstract: PhD


title: A Contextual Analysis of Hotman’s Francogallia

contributor:
Jainchill, Andrew
History

subject:
history
french history
wars of religion
francogallia

abstract: This thesis analyzes Francogallia, a sixteenth century text which claimed that the historical foundations of France could be traced back to the sixth century with the union of the Franks and Gauls. Composed during the French Wars of Religion, Francogallia was largely shaped by the events of the Saint Bartholomew’s Day Massacre, which set French Protestants against the French monarchy. Through this pseudohistorical account of French history, the author, François Hotman, constructed the idea of a distinct Franco-Gallic identity as the source of a distinctly nationalistic form of sovereignty, discrediting the claims of French kings to rule on the bases of divine right and Roman law. Much of Francogallia’s argument sought to assert the primacy of national custom over what the author regarded as foreign influences, condemning the sway of the Papacy over French affairs and labelling institutions like the parlements as subversive cultural imports. Despite Francogallia’s attempts to claim the people as the source of sovereignty in France, Hotman’s reliance on historical record to make his case exhibited critical weaknesses which undermine his argument and render it less convincing than those advanced by his Catholic opponents.

abstract: M.A.


title: Methyl Acrylate and Tertiary-butyl acrylamide Solution Radical Polymerization Kinetics

contributor:
Hutchinson, Robin
Chemical Engineering

subject: Polymerization Kinetics

abstract: Acrylate-acrylamide copolymers are used in a variety of applications, including for wastewater treatment and in pharmaceuticals, cosmetics, and hair-care products. These materials are synthesized by radical copolymerization in polar media, with an increased emphasis on conducting reactions in water or alcohol/water mixtures. Under these reaction conditions, both the monomer to solvent ratio and the solvent composition are known to influence the polymerization kinetics. In this study, the copolymerization propagation kinetics of tertiary butyl acrylamide (tBuAAm) and methyl acrylate (MA), a system of commercial interest, are systematically studied using the pulsed laser polymerization-size exclusion chromatography (PLP-SEC) technique. The Mark-Houwink(M-H) calibration parameters required for molecular weight analysis of poly(tBuAAm) in THF are determined using both triple detector and dual detector SEC setups, as no values have been reported previously in the literature. The influence of temperature (30-60 oC), monomer weight fraction (5-50 %) and ethanol/water solvent composition (varying from 100% EtOH to 100% H2O) on the propagation kinetics of MA and tBuAAm was determined. The homopropagation (kp) values for 10 wt% monomer in a 75/25 EtOH/H2O mixture at 30 oC are 41,900 L·mol-1·s-1 and 13,800 L·mol-1·s-1 for MA and tBuAAm, respectively. The rate coefficients were found to increase substantially as the fraction of water in the solvent mixtures is increased, and as the monomer to solvent ratio is decreased, such that the value for 5 wt% MA in water (close to its miscibility limits) is 16 times higher than its bulk value. Experimental measurement of copolymer kp values indicate that while the terminal model predictions are successful in describing the kinetics for solvent mixtures with low water content, it fails to describe the kinetics for mixtures with 50 wt% water or greater. The large influence of solvent choice and composition on the chain-growth rates of these two monomers must be considered for both product and process design.

abstract: M.A.Sc.


title: STEREOSPECIFIC SUZUKI-MIYAURA CROSS-COUPLING OF CHIRAL BENZYLIC BORONIC ESTERS AND VINYL BROMIDES

contributor:
Crudden, Cathleen
Chemistry

subject: cross-coupling catalysis Suzuki-Miyaura

abstract: The Suzuki-Miyaura cross-coupling reaction is a powerful method for the construction of carbon-carbon bonds in academia and industry. Despite extensive research in this area and the significance of the reaction, it is most often employed to prepare flat, Csp2-Csp2 bonds between two aryl groups.  Since most bioactive compounds contain several 3-D or chiral centers, it is more desirable to make bonds between sp2-sp3 and sp3-sp3 carbon centers. However, when dealing with sp3 carbons in cross-coupling chemistry, new challenges arise such as β-hydride elimination, an undesirable side reaction. In 2009, our group reported the first example of a stereospecific coupling between chiral secondary boronic esters and aryl iodides. In this thesis, we report our investigations towards expanding the scope of our established Csp2-Csp3 coupling reaction with chiral boronic esters. By employing vinyl halides as electrophiles, we can stereospecifically prepare alkene-containing products—a useful handle for further functionalization.

abstract: M.Sc.


title: Deep Learning-Driven Identification of Atrial Fibrillation in the ICU

contributor:
Mousavi, Parvin
Maslove, David
Computing

subject:
Deep Learning
Machine Learning
Precision Medicine
ICU
Atrial Fibrillation
ECG

abstract:
The modern digitized intensive care unit (ICU) is an environment that relies on many sources of high frequency, continuously streaming sources of data for monitoring and decision making purposes.
One of the richest and most abundant sources is telemetry data from bedside monitors, and specifically electrocardiogram (ECG) waveform data.
Biosignals such as ECG hold a great deal of promise for precision medicine developments like predictive modelling or scientific discovery, especially of cardiopulmonary conditions.

One major condition of interest in the ICU is atrial fibrillation (AF) and in particular new-onset atrial fibrillation (NOAF).
AF is the most common arrhythmia among ICU patients and has been associated with a multitude of adverse outcomes.
Despite this, our understanding of the true burden of AF, how it manifests in an ICU context and how best to intervene in its treatment remain limited.

ECGs are an excellent way to identify AF, and ECG telemetry is very common in the ICU.
However, the majority of this ECG data is unlabelled, noisy and not as clean as the static, 12 lead diagnostic ECG that pervades most literature on machine learning with biosignals.
Although deep learning models have been shown to have state of the art performance in this domain, they require large quantities of labelled and more often than not clean data to effectively classify rhythms such as AF.
In this thesis, we describe three contributions to scale up AF detection in the absence of such data that cover the life cycle of a machine learning project.
Firstly, we create an annotator to speed up manual labelling with low effort to bootstrap the annotation process.
We then leverage deep learning models on noisily labelled data to classify AF, incorporating both noisy label generation methods and weakly supervised learning techniques to reduce the impact of noise.
Lastly, we look into quantifying the uncertainty of models trained and evaluated on our weak and human labelled ground truth data respectively to explore how such models might be interfaced with during deployment.
We conclude by discussing limitations of our approaches, as well as future work around proper clinical deployment for trials, real time monitoring and eventually prediction

abstract: M.Sc.


title: Polymer Light-Emitting Electrochemical Cells Enhanced with Bipolar Electrode Arrays: In Situ Doping and Formation of Multiple p-n Junctions

contributor: Physics, Engineering Physics and Astronomy

subject: Bipolar Electrode

subject: Bipolar Electrochemistry

subject: p-n Junction

subject: Doping

abstract:
Polymer light-emitting electrochemical cells (PLECs) are organic solid-state light-emitting devices operating on in situ electrochemical doping and p-n junction formation in a mixed conductor active layer. PLECs have been extensively researched for their attractive device characteristics and potential in low-cost lighting and display technologies. The majority of PLECs, however, contain only a single light-emitting junction that is very narrow and highly inefficient. Adding bipolar electrodes (BPEs) into the active material of planar PLECs dramatically changes the doping process and improves the device performance in terms of response speed and efficiency. My research focuses on the study of how various BPEs and BPE arrays affect the doping and electroluminescence (EL) of PLECs. Using arrays of metal BPE disks, we demonstrate for the first time wireless EL in a PLEC, and we show that the BPE arrays can be used to assess both the metals' ability to inject charges and the redox properties of the PLEC polymer. By constructing a large, closed BPE array, we present bulk homojunction PLECs that exhibit vastly improved EL output from over a thousand highly emissive light-emitting junctions. The clear doping and light-emission patterns greatly improve our understanding of the fundamental operation processes of the PLECs, and demonstrate that bipolar electrochemistry, realized with metallic wireless BPE, is an efficient way to engineer next-generation high performance PLECs.

Towards more practical devices, we investigate the stability and degradation mechanisms of sandwich PLECs. The conventional approach to realize long-lasting PLECs is to have a very low electrolyte content in the active layer. Such PLECs are slow to activate and plagued by black spots. We discover that PLECs made with silver triflate salt and ultralow salt concentration, can avoid the trade-off between device lifetime and response speed. Moreover, the devices exhibit a record peak luminance, a long lifetime, and a high efficiency. The high performance is attributed to the partial chemical doping of the light-emitting polymer by the silver cations and the high ionic conductivity of the electrolyte. This finding opens up new avenues for designing high performance PLECs and potentially other solid-state electrochemical devices.

abstract: PhD


title: MEDIA ROUNDTABLE PROJECT EXPLAINED

contributor: Film and Media (Screen Cultures and Curatorial Studies)

subject:
media roundtable
installation
analog
film
videotape
smartphone
CRT monitor
live feed
remediation
media archeology
active audience
affect
authenticity

abstract:
Media Roundtable is an open-ended installation project. It is designed as a physical construction, aiming to bring modern digital media formats together with analog ones, acting as a means to make the intangible tangible and vice versa. It consists of five components: a 16 mm film projection, a videotape camera with a CRT (Cathode Ray Tube) monitor, a computer with a built-in webcam, a smartphone, and an empty station lit with spotlights for the audience to join the circle or to appreciate the incompleteness. Each displayed medium is displaying a live feed of their technological predecessor, leaving the 16 mm projector as the only device projecting pre-made content, which is a film loop of scraps and countdown leaders. The hope is to invite the audience into the "roundtable" and involve them in conversations with media technology. Each audience interprets the installation based on their unique background and knowledge, while the media technologies reflect and remediate the human image. As the cameras mediate each other, the audience is the ultimate mediator, completing the installation and interpreting the narrative. At the same time, the audience is the original subject being watched since they will pass through the cameras and displays, and see their images mirrored onto them.
I was inspired by various other media artists while designing Media Roundtable, among which the most notable being Nam June Paik's TV Buddha and Alvin and Mary Lucier's I Am Sitting In A Room. Originating from affect theory, trying to bring the tangible and intangible together, Media Roundtable also showcases the correlation between remediation and hypermediacy. It can be seen as a short demonstration of media archeology and history in a circle, showing the relation of media, message, technology, and observer.

abstract: M.A.


title: Religious Refusals: A Distinctive Manifestation of Religious Freedom

contributor:
Webber, Grégoire
Law

subject:
Religious freedom
Religious objection
Human Rights
Religious Refusals
Constitui
Constitutional Law Canada/US

abstract:
My thesis examines whether religious refusals differ from affirmative religious actions. Mainly, my thesis studies the structure and properties of religious refusals and explores whether the Supreme Courts of Canada and of the United States, as well as lower courts from both jurisdictions, have been sensitive to this distinction so as to inform the adjudication process of the religious freedom claim at stake. In particular, my thesis explores how courts understand and interpret the substantiality of the burden in religious refusals. For such purpose, it relies on religious actions and examines them to determine whether the courts under study have applied the standard consistently.
My thesis proposes that religious refusals differ from religious actions and that religious refusals elicit certain properties in discussing religious freedom claims. Given the relevance of the structure and properties of religious refusals, courts should consider both in their adjudication process. Even so, my thesis is not focused on whether religious refusals should be granted or denied. My focus is only the recognition of refusals as a distinct religious instantiation. Therefore, whether courts should ultimately accept or reject religious refusals and how claims of refusals should be balanced against other rights at stake is not the focus of my research.
My analysis draws on the constitutional law of Canada and the United States. By exploring case law from both jurisdictions, my thesis breaks down the properties of religious refusals, particularly the conceptualization and application of the substantiality of the burden. I argue that because courts have not been sensitive to the distinction between affirmative religious actions and religious refusals, their approach to the substantiality of the burden is more consistent with one specific type of religious instantiation, i.e., an action.

abstract: PhD


title: Regression Testing of Distributed Real-Time Embedded Systems in the Context of Model-Driven Development

contributor:
Dingel, Juergen
Computing

subject:
Distributed Systems
Software Engineering
Regression Testing
MDE
MDD

abstract:
Modern Distributed Real-Time Embedded (DRTE) systems are composed of largescale, heterogeneous networks of software systems that constitute the backbone of
many applications we rely on day-to-day. DRTE systems may evolve over time due
to new requirements and technology improvements. Each revision requires regression
testing to ensure that existing functionality is not affected by such changes. Despite
recent progress in regression testing techniques and tools, it turns out they are inadequate for testing distributed systems. As such, a typical distributed system with
a few nodes can produce a large amount of (possibly out of order) traces only after
a few minutes of execution. Therefore, effective replay-based regression testing for
distributed systems may require efficient mechanisms for generating compact traces,
as well as reordering and replaying.
Model-driven Development (MDD) is a software development approach that advocates the use of models as the primary software development artifacts. Essentially,
MDD leverages abstraction and automation in order to simplify design of a software
system in terms of communication and activities.
In this work, we provide evidence that modeling can facilitate the ordering and
replay of execution traces collected from of a distributed system, and thus regression
testing. Concretely, we show how the use of communicating state machines to describe a distributed system obviates the need for timestamps and can be also leveraged for
significant reduction in the amount of runtime information collected at reasonable
cost.
As the first step of this work we present a novel trace reordering and replay
technique and its tool support called MReplayer. MReplayer takes advantage of
existing techniques and tools for model transformation and static analysis. MReplayer
relies on access to the descriptions of the behaviours of each component for static
analysis and replay.
For the second step of this work, we present MRegTest, an efficient replay-based
regression testing approach for distributed systems at the model level. MRegTest
builds on our reordering approach and inherits from it a reduction in the number and
size of traces required compared to standard, timestamp-based approaches.

abstract: PhD


title: Towards Softwarized Drone Networks

contributor:
Taha, Abd-Elhamid
Hassanein, Hossam
Computing

subject:
Network Softwarization
Software Defined Networks
Network Function Virtualization
Drone/UAV Networks

abstract:
Drones, or Unmanned Aerial Vehicles (UAVs), are considered essential tools in search and rescue, disaster relief, remote sensing, aerial surveillance and security.  Drone-assisted communication networks are gaining considerable attention as a cost-effective and flexible network infrastructure offering new capabilities and opportunities. In addition to enabling connectivity for complex multi-drone tasks, drone networks can be deployed to facilitate connectivity in remote areas and extreme environments and supplement and extend the coverage of mobile networks in response to variable demands. However, utilizing such flexibility requires dealing with the inherent dynamics of drone networks, characterized by a high level of mobility and limited resources. Network softwarization using Software Defined Networking (SDN) and Network Functions Virtualization (NFV) enables flexible and adaptive control and reconfigurability in drone networks through centralized programmability and virtualized network functions.

In this thesis, we investigate drone network softwarization by identifying potential gains from the flexibility offered by softwarization not investigated previously in the context of drone networks. To enable the utilization of SDN and NFV in drone networks, we propose and describe an architecture for softwarized drone networks.  Furthermore, we address an important challenge relating to SDN control, a key element in SDN architectures, allowing the programmability of the network through an interface between logically centralized controllers and the programmable network nodes. To adapt to the network mobility and connectivity constraints, we propose schemes for deploying and assigning SDN controllers embedded in drones, allowing for continuous operation of control functions with changing network topology and possible unavailability of ground infrastructure. We also utilize the flexibility offered by NFV. New deployment and orchestration schemes are needed to efficiently deploy and manage drone networks defined by Virtual Network Functions (VNFs) implementing task and  network functionalities. To this end, we describe the applicable use cases that benefit from this flexibility and propose schemes that efficiently deploy and manage NFV-based drone networks.

abstract: PhD


title: Quantifying species-level responses to urbanization in North American birds

contributor:
Bonier, Frances
Martin, Paul R
Biology

subject:
urban responses
birds
urban habitat
phylogenetic signal
urbanization
breeding range
open access data

abstract: Species vary in their responses to urbanization – most species avoid urban habitats, some tolerate these environments, and very few thrive in them. To better characterize the extent to which species vary in their responses to urbanization (hereafter urban responses), we developed several methods to quantify these responses at a continental scale across all birds. Using open access community science-derived data from the eBird Status and Trends Products and two different types of high-resolution geospatial data that quantify urbanization of landscapes, we calculated urban response indices for 476 species with breeding ranges that overlap large cities in Canada or the United States. We used six different calculations to characterize species-level urban response indices, allowing us to assess how each species’ relative abundance during the breeding season varied with estimates of urbanization. We assessed correlations among these six indices, then compressed them into a single principal component (multivariate urban response index) that captured variation in urban responses among species. We demonstrated the accuracy of our multivariate urban response index using 24 species that are well characterized in their tolerance or avoidance of urban habitat, as well as with previously published, independent urban response estimates for 99 species. We found a significant phylogenetic signal in the multivariate urban response index for younger lineages but not among deeper lineages, suggesting that traits associated with urban responses are not highly conserved. Our study provides some of the most precise estimates of species' responses to urbanization to date.

abstract: M.Sc.


title: Nurses’ Experiences with Activating Rapid Response Teams: A Qualitative Study

contributor:
Duhn, Lenora
Nursing

subject:
Rapid Response Team
Nurses

abstract:
Patient clinical deterioration is a major safety concern. One strategy implemented for healthcare
providers to help improve the timely recognition and response to patient deterioration is the
Rapid Response Team (RRT). Despite this resource, patient deterioration still occurs and delayed
activation of the RRT is one contributing factor. Little is known about the perspectives and
experiences of unit-level (also termed “ward”) nurses related to RRT activation, which is
problematic given they are the ones who are primarily responsible for that process. The purpose
of this study was to understand the experiences of nurses practising on general adult inpatient
medicine units and their activation of the RRT. The research question was addressed with a
descriptive, exploratory qualitative study. Nurses working on a medicine unit at an Ontario
hospital study site were purposively recruited to participate. Semi-structured interviews with the
six participants were held online and audio-video recorded. Inductive, thematic analysis was
used. Eleven themes about the barriers and facilitators to RRT activation, and one overarching
theme—The Self-Imposed Complexity of Deciding to Activate the RRT—resulted in relation to
the nuanced, multi-factorial decision-making process unit-level nurses undertake when
considering activation. This information will inform practice changes surrounding RRT policies,
nursing education about the RRT, and be incentive for future research on optimizing strategies
for RRTs and deteriorating patients.

abstract: MNSc.


title: REINCARNATE: Reimagining Touch, Contact, and Communication In The Context Of  Isolation and Distancing

subject:
Contact Improvisation
Social Distancing
Interactive Performance Installation
System-based Performance
Contemporary Dance

abstract: REINCARNATE is a performance installation and an experiment that attempts to engage in the study of contact in the age of global fear and stigmatization over the idea of relationship-building and bodily interaction. In this project, I incorporated a system-based performance technique coupled with the concept of contemporary dance, while negotiating the implications of contact improvisation in the age of social distancing. The performance system is based on a semi-closed set of physical movements derived from a combination of pedestrian gestures and dance moves. The performer completes instant composition on stage through the interactions with her past virtual self. By extrapolating and transporting a dancer’s movements into virtual space and having the dancer interact with and improvise to her past movements in real-time, the boundary between our material world and the virtual world becomes more nuanced. The music to which the dancer performs is also a responsive system that is organically developed by the dancer’s raising of arms and kicking of legs. The music is played by an interactive instrument built in Max/Msp platform; the different frequencies of the dancer’s movements become the input that triggers a MIDI keyboard which outputs as MIDI sounds that undergo delays and transposition. At the same time, the music that is composed in the process of the performance also stimulates the dancer’s improvisation. The purpose is to form a conversation between the dancer in the material dimension, her form in the virtual space, and the music. An audience expects to see both the dancer’s live performance and her interaction with her past self in virtual space projected onto a screen. The audience is invited to interpret the dynamics among the physical presence of the dancer, the digital figure embodying her virtual existence, and the resulting composition comprising of both audios and visuals.

abstract: M.A.


title: Probing the Probabilistic Reasoning and Belief Change Abilities of Preschool-Age Children

contributor:
Sabbagh, Mark
Psychology

subject:
Psychology
Development
Children
Preschool
Cognitive Development
Developmental Psychology
Belief Change

abstract: Research on cognitive development has challenged the assumption that children are passive participants in their own learning. Far from ‘passive sponges’, children are active participants in their learning process who select sources of evidence, actively weigh the strength and validity of the evidence they glean, and use those determinations to build and dynamically revise their beliefs. Past literature has generally investigated the belief change abilities of children using deterministic, experimenter-generated evidence in the lab (e.g., Bonawitz et al., 2019; Kimura & Gopnik, 2019; Macris & Sobel, 2017). Little is known about how children might use self-selected, probabilistic evidence to revise their beliefs over time. The current study investigated the ability of 3- to 5-year-old children to revise their beliefs on a novel ‘fishing’ game. Thirty-two children were induced with a belief about which of two possible ponds was most likely to result in catching a fish versus seaweed. After belief induction, children then continued to fish from the ponds in one of two conditions. In the “belief-consistent” condition, the pond that contained fish during the belief-induction phase continued to be advantageous for catching fish. In the “belief-inconsistent” condition, the opposite was true. Importantly, in both conditions, the advantageous ponds only resulted in catching fish 75% of the time, and thus was probabilistic. Results demonstrated that children in both conditions of the study used the self-generated, probabilistic evidence to either maintain or revise their beliefs. Children also showed sensitivity to the probability values of the two ponds, and showed evidence of  probability matching behaviour when making their pond selections. Exploratory modelling analyses illuminated the potential impact of time on children’s pond selections, revealing that children in the inconsistent condition of the study experienced a period of lability in their pond selections before stabilizing on a revised belief. These findings are interpreted with respect to theory-theory approaches to cognitive development that emphasize children’s self-directed learning from experience. Future work in this area may expand on this work by investigating neural mechanisms of belief revision and the impact of reward-learning on children’s pond selections during the testing phase of the experiment.

abstract: M.Sc.


title: The Quest for Inclusion and Overcoming Stigma: A Constructivist Grounded Theory Study with Children with Physical Disabilities in Ethiopia

contributor:
Ghahari, Setareh
Lysaght, Rosemary
Rehabilitation Science

subject: Children with physical disabilities,  grounded theory, educational participation, stigma

abstract:
Children with physical disabilities, particularly in low-income settings, have limited access to education. Even if they go to school, they lack support and are excluded from formal and informal learning platforms, mainly due to stigma and its effects. However, information on disability stigma is scarce in low-and middle-income countries like Ethiopia. This study, therefore, aimed to explore and understand stigma in educational contexts from the perspectives of children and other relevant stakeholders. Furthermore, the study addressed the knowledge gap regarding the sociocultural-contextual factors, lived experiences, and effects of stigma on educational participation among children with physical disabilities in northwest Ethiopia.
The inquiry was guided by the following research questions: a) What are the contextual factors of stigma? b) What are children with physical disabilities’ lived experiences of stigma? c) What are the effects of stigma on their educational participation? d) How do children cope with stigma and its effects? The study used a constructivist grounded theory approach to gather and analyze data.
Data were gathered through observations, in-depth interviews with children, and key informant interviews, allowing capture of participants' subjective experiences, essential meanings, and multiple realities. Inductive and iterative grounded theory technique was used to code and categorize data through constant comparative methods. Data analysis resulted in four major categories: (1) Conceptions of disability and stigma, (2) Lived experiences of stigma and intersectionality, (3) Effects of stigma on educational participation, and (4) Managing stigma. Exploring the interrelationships between these categories allowed the study’s conceptual construct to develop, i.e., The Quest for Inclusion and Overcoming Stigma.
The findings showed that children with physical disabilities struggle with stigma, live in fear, and are socially excluded. As a result, they have low participation in their socio-educational activities. This study makes theoretical and practical contributions to understanding and addressing disability stigma and can help to introduce inclusive education policy, school practice, and disability advocacy. Based on the findings, recommendations were made for a knowledge translation plan to raise disability awareness programs and inform disability policy and practice. Disability stigma research, including applying, expanding, or testing the study’s conceptual construct, is recommended.

abstract: Ph.D.


title: Security Enhancement of Vehicle Software Systems

contributor:
Zulkernine, Mohammad
Computing

subject:
Automotive Systems Cybersecurity
Vulnerability Identification
Vehicle Software Engineering
Fuzz Testing
Concolic Testing
Security Risk Assessment

abstract:
In an era of connectivity and automation, the vehicle industry is adopting various technologies to transfer driver-centric vehicles to intelligent mechanical devices driven by software components. However, software integration and network connectivity inherit numerous security issues. This thesis offers methods and tools that collaboratively enhance vehicle software security, making vehicles more resilient to cyber incidents. The uniqueness of  Connected Autonomous Vehicles (CAVs) invites challenges for Vehicle Software Engineering (VSE) that render traditional software development models and practical solutions less effective for automotive software development.
This research presents a Secure Vehicle Software Engineering (SVSE) lifecycle that ensures security-by-design, devoting security considerations throughout all phases of the vehicle software development process. We also introduce novel security enhancement techniques to be employed during the SVSE lifecycle. We propose security vulnerability metrics tailored to identify complexity within vehicle software systems that open the door for malicious behavior. These metrics are utilized with grey-box fuzzing to offer a vulnerability-oriented fuzz testing (VulFuzz) framework explicitly designed to address vehicle security testing challenges. Using the vulnerability scores, VulFuzz systematically directs and prioritizes the fuzz testing toward the most vulnerable components. Depending on the component under test, fuzz testing may not be sufficient to assure a reliable system. Fuzz testing blindness prevents it from exploring the deep paths of the system, which is critical to evaluate for safety-critical components.  As a result, we present a hybrid fuzz testing framework (VulFuzz++) that unites the efficiency of fuzzing and the precision of concolic execution to provide the automotive industry a reliable security testing tool. VulFuzz++ utilizes a tailored, targeted concolic engine that limits the symbolic exploration to only specific functions. While security testing can identify many vulnerabilities and enhance security, vehicles' resilience against attacks might change during their operational lifespan. We introduce a security decay assessment framework that monitors vehicles' security risks and recognizes security failure. We have implemented and evaluated the security enhancement techniques on OpenPilot, an automotive Autopilot system. The results show the effectiveness of the proposed techniques in strengthening vehicles' resilience by identifying vulnerabilities at an early stage.

abstract: PhD


title: Computational Methods to Process and Analyze High-dimensional Imaging Mass Cytometry Datasets in Pathological Tissue Samples

subject:
imaging mass cytometry
IMC
computing

abstract:
Highly multiplexed imaging methodologies generate high-dimensional images which allows for in situ spatial assessment of several protein markers in pathological tissue samples. Computational analyses of these images produce information of unprecedented depth and breadth that has been shown to correlate with disease progression and patient prognoses, thus proving valuable in basic science and clinical research. However, processing of such images presents many challenges, in particular the high dimensionality of the data, the presence of tightly clustered cells often difficult to segment, and the identification of cell populations which requires expert knowledge and specialized computational methods.

In this thesis, state-of-the-art computational methods for every step of the processing of high-dimensional imaging mass cytometry (IMC) images were employed. Spillover compensation was implemented to improve data quality, cell segmentation delineated single cells in the images, cell phenotyping allowed the identification of cell types and states, and lastly, neighborhood and spatial analysis provided information about spatial organization and cellular interactions. This processing pipeline was applied to two multiplexed IMC datasets acquired from Hunner lesions and pancreatic ductal adenocarcinoma tissue samples. This study represents the first application of multiplexed images to interrogate Hunner lesions to date and provides a novel perspective into the cellular immune microenvironment of these lesions. Following the processing pipeline, the results were individually presented and the outputs from the two datasets were compared for assessing the generalizability of the computational methods. Altogether, our results show that the algorithms were able to effectively extract a depth of biological information from the images and generalize to both datasets.

abstract: M.Sc.


title: Chromite Exploration and Deformation Monitoring Through PSInSAR

contributor: Geological Sciences and Geological Engineering

subject:
PSInSAR
Chromite
Mineral Exploration
SAR
InSAR

abstract:
This thesis consists of two independent studies, i) the exploration for chromite in the Quesnel terrain, British Columbia, using terrestrial geophysics, and ii) urban deformation monitoring in the Dallas Forth Worth Metroplex using PSInSAR. Chromium is a critical mineral, essential in industry, being necessary to produce stainless steel. British Columbia hosts a range of podiform chromite occurrences throughout the Quesnel Terrane. One such occurrence was investigated using ground based magnetic surveys and rock sample analysis. The results of the ground based magnetic survey allowed for a precise delineation of the serpentinized ultramafic unit, and the identification of a conjugate fault set interpreted to be related to the regional NS dextral shear system. The improved knowledge of the serpentinized zone will improve the targeting of future exploration of the chromite pods hosted in ultramafic bodies, while the identification of the shear system provided targets for the exploration of hydrothermal deposits. The analysis of the rock samples resulted in the interpretation of the relative chronology of the alteration and deformation of the chromite.

Non-linear surface deformation is a common phenomenon with numerous causes which can have significant impacts on local infrastructure in urban environments. The temporal and spatial coverage of the Sentinel-1 satellite mission acquisitions make it suitable to test the capability of persistent scatterer interferometry to sample non-linear deformation such as seasonal changes. Ninety-seven scenes from Sentinel-1 were acquired over the Dallas-Fort Worth Metroplex and were processed using the StaMPS algorithm. The PS time series results were compared with permanent GNSS station time series within the SAR footprint using wavelet analysis. The derived global wavelet spectrum and scalogram provided the power of the frequency contributions of deformation processes over time. The GNSS station positions and persistent scatterers in the surrounding areas were interpreted and compared for seasonal deformation. Most GNSS stations analyzed exhibited similar annual deformation to the persistent scatterers located nearby, with 7 out of 19 showing the same peak frequency. Results demonstrate the utility of these observations and the processing strategy for the interpretation of non-linear deformations from PSI analysis of Sentinel-1 data.

abstract: M.A.Sc.


title: Finding Patterns In Mass Spectrometry Images

contributor:
Ellis, Randy
Computing

subject:
Mass Spectrometry
Machine Learning
High-Dimensional Data
Cancer
Biomedical Computing
Computing
Breast Cancer

abstract:
Analysis of mass spectrometry (MS) images could have many applications including aiding a pathologist in diagnosis of tissue samples, guiding a surgeon during tumor removal procedures, and discovering biomarkers of disease. MS is an analytical chemistry technique that can provide insight into metabolite patterns of tissue. MS imaging (MSI) produces mappings of MS information across a tissue sample. The processing and visualization of MS images is challenging due to their high dimensionality. In this work we used MS images obtained from breast conserving surgery (BCS), a common treatment for breast cancer. Margin analysis of removed tissue from BCS has been associated with factors such as decrease in local recurrence and is commonly performed post-operatively by a pathologist. Pathologic diagnosis has reported inter-observer and intra-observer variability. The lack of high quality intraoperative analysis has led to high rates of reexcision. Analysis of tissue samples could enhance efficacy of surgical procedures such as BCS. We hypothesize that application of proposed computational methods will enable multivariate visualization of MS images with strong correspondence to gold standard annotated histology images.

For this dissertation we had access to 9 tissue samples obtained from BCS with a diagnosis of invasive ductal carcinoma. We proposed a series of computations including dimensionality reduction and graph clustering for automatic foreground segmentation and foreground clustering; affine spaces, or flats, to represent metabolite patterns of tissue types from across samples; and distance maps for novel multivariate visualization of MS images. We compared our results to conventional forms of visualization and to conventional processing methods.

Our computations achieved untargeted multivariate processing and visualization of MS images. Distance maps showed strong correspondence to annotated histology images and were superior to conventional visualization techniques. The affine spaces identified biologically relevant ions that could be associated with fatty acids, which are precursors to energy cycles that are enhanced in malignant cells. Our proposed computations were statistically significantly different than conventional methods. The proposed computations could be applied to BCS to provide surgical guidance and be used in conjunction with gold standard pathology analysis to increase speed of diagnosis.

abstract: M.Sc.


title: Biological and Chemical Oxidation of Sulfidic Minerals at Alkaline pH

contributor:
Ghahreman, Ahmad
Mining Engineering

subject:
Biooxidation
Chemical Oxidation
Pyrite
Gold Recovery

abstract: The oxidation of sulfidic minerals to liberate gold is currently performed with the utilization of microorganisms and chemical reagents. Biooxidation is a hydrometallurgical oxidation method which can be a pre-treatment method for gold recovery. Iron- and sulfur-oxidizing microorganisms with varying physiological characteristics liberate sulfide matrices by using reduced sulfur compounds for growth, which exposes minerals such as gold to lixiviants. Compared to conventional methods, biooxidation is an environmentally friendly and more economic pre-treatment method. The chemical oxidation of sulfide minerals has been performed in all pH ranges. However, operating in higher pH environments can decrease operating and material costs. The aim of this investigation is to test the oxidative capabilities of alkaline bacteria and chemical reagents in three pyrite concentrates. Two alkaliphilic, halo-tolerant, and chemolithoautotrophic bacteria Thiomicrospira aerophila (DSMZ 13739) and Thioalkalivibrio versutus (DSMZ 13738) were used for this study. For chemical oxidation, the carbonate effect which occurs due to the presence of sodium carbonate and bicarbonate was evaluated. Various parameters such as pH, temperature, pulp density, time, and changes in media were altered to determine the optimal oxidative parameters. Investigations with bacteria suggest that iron precipitates produced during oxidation passivated onto the particles, preventing them from attaching to the particle surface. This resulted in all experiments without the inoculation of bacteria oxidizing more pyrite than the experiments with bacteria. Therefore, chemical oxidation via the carbonate effect was investigated. Complete oxidation of the sample was observed at 11 days using 20 g/L Na2CO3 and 10 g/L NaHCO3 with parameters of 80 °C, air supplied at 0.1 L/min, 20% pulp density, and stirred at 500 rpm. Further, qualitative, and quantitative analysis were performed on the oxidized samples to investigate physical and chemical changes in the samples. Gold leaching tests with conventional cyanidation techniques were performed on oxidized samples to determine the relationship between oxidation and gold recovery.

abstract: M.A.Sc.


title: Nonlinear dynamics and mathematical programming with neuromorphic integrated silicon photonic circuits in Verilog-A

subject:
photonics
Neuromorphic Photonics
Artificial Neural Networks
optics
Computing architectures
Verilog-A
Nonlinear dynamics
Optimization

abstract:
The rise in machine learning applications and the availability of larger datasets has motivated the investigation of new application-specific integrated circuits (ASICs), that can solely be dedicated to performing complex calculations at a much higher speed than conventional computers. Recent advances in integrated photonic neuromorphic architectures promise to deliver computations with higher speed than electronics by exploiting the parallel nature of light through wavelength-division multiplexing (WDM) and the passive nature of optical waveguides.

In particular, photonic implementation of continuous-time recurrent networks (CTRNNs) have a potential to solve problems related to nonlinear optimization, model predictive control, and scientific computing. In recent developments, the dynamical behaviour of the photonic recurrent neural networks has been demonstrated using a combination of on-chip and off-chip components. One of the major challenges in an entirely on-chip implementation of neuromorphic photonic CTRNNs is the lack of sufficient tools to simulate fully integrated large-scale photonic integrated circuits. It is very crucial to perform simulations on a single platform to capture the behaviour of the circuit in the presence of both optical and electrical components. In this work, we have adopted a Verilog-A based approach to model photonic neuromorphic circuits. We developed Verilog-A models for the primary photonic devices (lasers, phase shifters, couplers, photodetector, and waveguide), which are the building blocks of photonic neural networks. The physical parameters of the devices are extracted from the experimental data and implemented in the Verilog-A models. The device simulations are also validated by comparing the measured and simulation results.

Subsequently, we showed the dynamical isomorphism between the fully integrated silicon photonic recurrent neural circuit and the CTRNN model by simulating dynamical bifurcations and winner-takes-all algorithm. We have also demonstrated the application of the photonic CTRNNs by simulating a 4-node recurrent neural network to solve a quadratic programming (QP) problem, which has enormous applications in optimization, and model predictive control. The work done in this thesis would significantly increase the capability of optical-electrical co-simulation that would improve the efficiency of optimizing the devices and provide an accurate simulation of the circuit performance before fabrication.

abstract: M.Sc.


title: Assessing fetal topoisomerase IIα as a mechanism of in utero benzene toxicity in generating double-stranded DNA damage in CD-1 mice

contributor:
Winn, Louise M.
Biomedical and Molecular Sciences

subject: Benzene, Fetal, Topoisomerase IIα, DNA repair

abstract: Benzene is a known human leukemogen and environmental pollutant. Recent epidemiological evidence has shown that benzene exposure during pregnancy is associated with increased infant leukemias after birth. It is hypothesized that these leukemias are being initiated in utero by benzene exposure during pregnancy. The metabolite 1,4-benzoquinone (BQ) specifically inhibits the critical DNA repair enzyme topoisomerase IIα (topo IIα) and is hypothesized to initiate leukemias through the generation of double stranded DNA (dsDNA) breaks in hematopoietic cells. My research examines the role of topo IIα as a target of benzene toxicity to generate dsDNA breaks using complementary in vitro and in vivo mouse models. We hypothesize that benzene exposure in utero will increase dsDNA breaks by perturbing topo IIα, and cause leukemia. First, using a primary cell culture derived from gestational day (GD) 14 fetal livers, exposure to BQ for 24 hours showed a concentration-dependent decrease in topo IIα activity, which was not protected by treatment with N-acetylcysteine. BQ exposure (12.5 µM) is sufficient to increase topo IIα-DNA adducts, alter the population of c-kit+Lin—Sca-1—Il7rα— cells and increases 4-hydroxynonenal (4-HNE). Levels of γH2AX, a marker of dsDNA breaks are also increased in fetal liver cell culture following 12.5 µM BQ exposure. Next, using an in vivo CD-1 mouse model of transplacental benzene carcinogenesis which previously showed that 200 mg/kg IP of benzene increases leukemia in offspring in a sex-dependent manner, topo IIα activity, DNA damage, and DNA repair gene expression were assessed and stratified by sex. Topo IIα activity was not altered in GD14 fetal livers following maternal benzene exposure, but DNA damage was increased differentially by sex. In utero benzene exposure alters fetal DNA repair gene expression for genes involved in non-homologous end joining (NHEJ) and homologous recombination (HR). Overall, this research provides evidence that benzene can induce damage in the developing fetus and supports the hypothesis that childhood leukemias is caused by maternal exposure to benzene.

abstract: PhD


title: Planar Multilayer Thin Film Coatings for Passive Winter Thermal Management

contributor:
Alam, Muhammad
Electrical and Computer Engineering

subject:
Nanophotonics
Passive heating
Zero energy building

abstract: Buildings are responsible for 40% of global energy consumption. 76% of that energy is spent on comfort control including heating, cooling and ventilation. This large energy consumption results in significant greenhouse gas emission, which adversely affects the global climate. The high cost of fossil fuel also causes widespread energy poverty. Adoption of passive heating schemes which utilize solar energy for indoor heating can greatly reduce the energy requirement of buildings in the cold climate. Currently available passive heating schemes often require significant investment and they cannot be easily retrofitted to existing buildings. Windows are a major source of heat loss in a typical building in the cold climate. Development of transparent solar energy harvesting coatings for windows can play a major role in reducing energy consumption and fuel costs. In recent years, there has been a great research effort towards designing transparent solar absorber coatings using nanophotonic structures for passive heating of windows. These coatings are highly efficient and can be retrofitted to existing windows. However, the nanophotonic designs proposed so far either require expensive materials for their implementation or require expensive fabrication processes, which are difficult to scale up. The objective of this thesis is to explore designs of transparent solar absorber coatings for windows which will overcome the limitations of previously reported nanophotonic designs. We investigate the applicability of planar multilayer thin films consisting of low cost materials for this purpose. Our study led to the proposals of two designs that predict temperature rise of 21 K and 25 K, while maintaining mean visible transmittance over 60%. We experimentally observed 6.9 K rise in temperature under sunlight for our design, which compares favorably against previously reported designs which are significantly more expensive and difficult to implement. The performance of our designs is expected to improve significantly if the fabrication process is optimized. These results illustrate the great promise that nanophotonics holds for the reduction of energy consumption of buildings, which will be a significant step towards helping the environment and improving the quality of life of people in many countries around the world.

abstract: M.A.Sc.


title: Task Offloading with Service Replication for Scalable Mobile Edge Computing

contributor:
Hassanein, Hossam
Sorour, Sameh
Computing

subject:
Mobile Edge Computing
Task Offloading
Service Replication

abstract:
Mobile Edge Computing (MEC) is a network architecture model designed to provide the end-user with fast and powerful computing. MEC accomplishes this by enabling context-aware applications over cloud computing services within the radio access network (RAN) at the edge of the network thus, closer to the mobile subscribers resulting in better performance of delay-sensitive applications. However, the number of individuals and groups of users offloading independent and inter-related computational tasks to MEC servers is rapidly increasing, thus overloading the servers, consequently increasing the risk of service interruptions.
This dissertation investigates how reactive service replication can enable individuals and groups of users to access services from remote edge servers, thus guaranteeing system scalability. We propose a task offloading and service replication scheme to improve the scalability of edge services in MEC systems from various perspectives. In particular, we dynamically manage task offloading for groups of users requesting to perform inter-related computations on local and remote MEC servers managed by the same home service provider. Our proposed scheme minimizes the average response time of all users while satisfying the delay requirements of user groups in traffic-heavy and multimedia-intensive applications (e.g., group AV/AR, multimedia conferencing). Furthermore, we propose a task offloading and resource allocation scheme using reactive service replication between multiple service providers considering prior information of available resources and pricing for each service provider. Our goal is to minimize the average response time and the cost to the underloaded service providers while satisfying the delay requirements. We also design a cost management scheme based on offloaded tasks, computing resources, and foreign service providers’ reputations to maximize the social welfare of the home service providers and the foreign service providers. Simulation results demonstrate the merits of our proposed scheme: Utilizing reactive service replication to improve the scalability of MEC system services.

abstract: PhD


title: THE INFLUENCE OF SEDIMENT CONCENTRATION AND INTERSTITIAL FLUID DENSITY ON THE LOFTING POINT OF EXPERIMENTAL HYPERPYCNAL CURRENTS

subject:
Hyperpycnal Current
Lofting
Experimental Sedimentology

abstract: Density Currents are gravity driven currents that propagate downslope when gravity pulls a dense fluid underneath a lighter fluid. Turbidity currents are an important type of density current that occur when this density difference is due to a high concentration of sediment, which is suspended in the current by turbulent forces. Turbidity currents can be initiated by many mechanisms, including slope failure, tidal forces, wave action, and by discharge from rivers. When a turbidity current is initiated by river discharge it is commonly referred to as a hyperpycnal current. Hyperpycnal currents in the ocean are unique amongst density currents because they carry fresh water and they are only more dense than ambient salt water due to their very high sediment concentration. As a hyperpycnal current propagates into a basin, if the rate of sediment deposition exceeds the rates of fluid mixing and salt diffusion, the current can become sufficiently less dense to undergo buoyancy reversal and loft into a tall, sediment-laden plume. Experimental analogs of these lofting currents were used to explore the initial flow conditions that either encourage or discourage lofting. Findings indicate that currents with interstitial fluid even slightly less dense than the ambient fluid within a basin exhibit some degree of lofting behaviour. Within currents with light interstitial fluid, sediment concentration has a larger impact on the time and distance the current travels before it lofts than changes in fluid density. The findings of this project challenge the assumption of end-member behavior, in which currents either remain entirely-ground hugging or lofting dominates the evolution of the current, and instead suggests a significant subset of currents that exist between these two extremes.

abstract: M.Sc.


title: A Computational Analysis Pipeline for Imaging Mass Cytometry Data for Cancer Research

contributor:
Mousavi, Parvin
Computing

subject:
imaging mass cytometry
analysis pipeline
phenotyping
deep learning
multiplex imaging
high dimensional data

abstract:
With recent technological advancements in tissue imaging, biologists are now able to obtain a deeper look at tissues at the cell level. Imaging mass cytometry (IMC) is a new advancement in tissue imaging that is quickly gaining wider usage since its recent launch. It improves upon immunofluorescence by quantifying up to 36 discrete signals with the use of metal-tagged antibodies. As a result, the data output of this technology is extensive and complex. The current methods of analysis for these data are provided by the manufacturer and are fairly preliminary, requiring the use of multiple independent software. Studies using this data are typically bounded to simple statistical analyses since the target audience of this technology is biologists with limited computational knowledge.
In this thesis, we propose and demonstrate various analysis methodologies with respect to IMC data. First, we develop a software TITAN that is a culmination of the functionalities provided in the current IMC analysis software. TITAN is an improvement on the current methods in efficiency and user-friendliness, as it allows all processing and simple analysis functions to occur within a single environment. Next, we propose an application of machine learning to the analysis pipeline of IMC data, specifically towards cancer research and predicting a clinical outcome. We demonstrate the feasibility of using the proposed framework to identify prognostic features, which is an important foundation for further clinical research. As well, we address the importance of cell phenotyping in relation to IMC analyses and present an automated cell annotation method using deep learning, specifically a convolutional autoencoder with joint classification. We demonstrate the use of these methodologies using a muscle invasive bladder cancer patient cohort. The dataset consists of MIBC patients' transurethral resection of bladder tumour tissues along with their matched cystectomy samples. In addition to demonstrating these methodologies, we also complete a qualitative analysis of this dataset. We compare the TURBT and cystectomy samples qualitatively using a deep autoencoder network and identify similarities between the two that would allow for a pathologist to use TURBT samples as a surrogate for cystectomy samples. Through this work, we demonstrate the potential of using machine learning with IMC data and illustrate its use for cancer research.

abstract: M.Sc.


title: Enforcing Security on Autonomous Vehicle Searches Through the Quantification of Opacity

contributor:
Rudie, Karen
Electrical and Computer Engineering

subject:
Discrete Event Systems
Opacity
Security
Autonomous Vehicles

abstract: Recently, topics of security have been explored in the field of discrete-event systems (DES). By modelling these systems with DES, the evolution of the processes can be captured, allowing for different vulnerabilities to be noticed. The DES field also provides a different set of tools which can generate new strategies to tackle the security problems in these systems. The motivating problem that this work focuses on is a group of autonomous vehicles traversing some terrain while trying to cooperatively complete a task such as searching for a target. This work shows that strategies can be employed that remove the need for communication under certain conditions. When no such strategy can be developed, it can be useful to have a tool to classify a system’s security. In DES, this has traditionally been captured by the notion of opacity. Unfortunately, this framework has many limitations. Opacity can only be applied to systems with a specific secret and it cannot tell you how obscured a system is. To address these failings, this work develops the concept of degree of opacity. This framework can measure the degree to which a system is secure based on a supplied criterion. It also can be applied to systems as a whole eliminating the dependency on a specific secret. Degree of opacity is a more general version of opacity and can be handled in similar ways. Degree of opacity can be enforced using supervisory control to produce a minimally restrictive supervisor. Alternatively, what is communicated to a vehicle or observed by a vehicle can be controlled, rather than restricting the vehicle’s movements. Unfortunately, non-monotonicity of observability means that it cannot be easily used to enforce degree of opacity like controllability was. To combat this, a strategy called transition pairing is developed which allows monotonicity to be achieved. This strategy is applied to construct an algorithm to pick which communications can be communicated to achieve a target degree of opacity.

abstract: M.A.Sc.


title: Mechanisms of wollastonite weathering and applications to CO2 storage

subject:
Wollastonite
Enhanced weathering
Silicon isotopes
CO2 Storage
Silicate weathering
Incongruent dissolution

abstract:
The mechanisms of wollastonite dissolution and its potential applications in Enhanced Rock Weathering (ERW) initiatives that sequester atmospheric CO2 were investigated in two sets of experiments. Mixed flow reactor experiments, carried out from pH 2.0 to 9.5, revealed close to stoichiometric dissolution at neutral to alkaline pH but non-stoichiometric dissolution at pH 2.0, where Ca was released to solution and most Si was retained within an amorphous silica surface layer. At pH 2.0, the Si isotope composition of the fluid become progressively isotopically lighter during wollastonite dissolution over time. The Δ30Sisolid-fluid values between the bulk reacted solid and the pH 2.0 solution are 2.49 to 2.61 ± 0.28 ‰. These values indicate a greater magnitude of enrichment of the solid in Si isotopes of heavier mass relative to the fluid than has previously been documented during precipitation of amorphous silica. Condensation reactions within a retained amorphous silica layer could lead the more polymerized layer to become increasingly refractory, favoring the release of Si isotopes of lighter mass. The pH dependence of wollastonite dissolution stoichiometry and the behaviour of Si isotopes at pH 2.0 are thus not consistent with a coupled dissolution-precipitation process as the mechanism governing incongruent dissolution of wollastonite under acidic conditions.
Column experiments that contained wollastonite, soil, and soil-wollastonite mixtures were irrigated with H2O or K3PO4 solutions. Experiments showed substantially greater dissolution of wollastonite and greater carbon capture in soil-wollastonite mixtures compared to wollastonite-only columns, but P exerted little influence on wollastonite dissolution. Adsorption to soils resulted in rapid removal of P, limiting its ability to catalyze the dissolution of wollastonite. Adsorption also significantly retarded Ca, making Ca concentrations unreliable as a means of estimating wollastonite dissolution rates. Mixed column effluent concentrations of HCO3- increased by up to 2.48 mM over time, suggesting that the presence of wollastonite resulted in retention of microbially generated CO2. These results emphasize the importance of site-specific characterization of mineral-soil mixtures. In such complex systems, silicon and other isotopic systems may be a valuable tool for gaining greater insight into weathering processes.

abstract: M.Sc.


title: The Influence of PHEMA Hydrogel Compressive Modulus and Chemistry on Lens Epithelial and Neutrophil-Like Cell Behaviours Associated with Posterior Capsular Opacification

contributor:
Wells, Laura
Chemical Engineering

subject:
PHEMA
hydrogel
lens epithelial cell
neutrophil
posterior capsular opacification
modulus
chemical functionalization
biomaterials
cataracts
epithelial to mesenchymal transition
NETosis
intraocular lens

abstract:
During cataract surgery, the impaired lens is removed and replaced with an artificial intraocular lens (IOL). Patients can experience a complication called posterior capsular opacification (PCO) that is corrected through surgery which has increased costs and can damage the retina and the IOL. PCO develops when lens epithelial cells (LECs) proliferate, migrate and undergo epithelial to mesenchymal transition (EMT). Neutrophils involved in the immune response triggered during implantation impact LEC behaviour and produce damaging neutrophil extracellular traps (NETs). Previous studies with rigid, hydrophobic acrylic materials demonstrated that stiffness and surface chemistry influence cellular responses. This project investigated neutrophil and LEC responses, simultaneously, to the material properties of a foldable, hydrophilic IOL material, poly(2-hydroxyethyl methacrylate) (PHEMA).
PHEMA-based disks were synthesized with varying amounts of comonomer (HEMA with 0, 2, and 12 mol% MMA) and functionalized with carboxyl and amine groups, yielding nine different hydrogels. Material and chemical properties of the disks were characterized, and neutrophil-like HL60 cells and B3 LECs were incubated with the disks. HL60 cell behaviour was assessed by evaluating viability and visualizing adhered and citrullinated histone H3 (cit-H3) positive cells, indicating NETosis. B3 LEC behaviour was assessed by evaluating viability and visualizing adhered cells and alpha-smooth muscle actin (alpha-SMA) expression, a marker of EMT. The influence of NETs on LECs was examined by culturing B3 LECs with disks pre-treated with NETs isolated from HL60 cells and evaluating behaviour using the previously described methods.
HL60 cell behaviour was more strongly influenced by chemical functionalization than by mechanical properties. This was demonstrated by significant increases in adherence and in cit-H3 visualization with functionalized disks and through principal component analysis (PCA). Conversely, B3 LECs behaviour and viability were more strongly influenced by mechanical properties. This was demonstrated by increases in cell adhesion and alpha-SMA expression with increasing compressive moduli of the disks and through PCA.
Moreover, B3 LECs demonstrated decreased viability and increased alpha-SMA expression when cultured with NET-pre-treated disks. The notable influence of NETs on B3 LEC behaviour suggests that, when both immune responses and LEC responses are considered, the PHEMA12-based hydrogels are the most promising for future PCO-prevention studies.

abstract: M.A.Sc.


title: Experimental setup and analysis method for the KDK ground state electron capture measurement of K-40

contributor: Physics, Engineering Physics and Astronomy

subject:
MTAS
KDK
Potassium
Dark Matter
Geochronology

abstract:
Potassium-40 is a long-lived, naturally occurring radioactive isotope. The decay products are prominent backgrounds for many rare event searches, especially those involving NaI-based scintillators (ex. ANAIS-112, COSINE-100, COSINUS, DAMA/LIBRA, SABRE,  etc.). The branching ratio of the electron capture directly to the ground state of Argon-40 has never been measured and presents an unknown background directly in the 2-6 keV energy region. This is the same region where the DAMA/LIBRA experiment observes their unique annual modulation. Knowledge of this branching ratio can place constraints on the allowed modulation fraction observed by the DAMA experiment. This branching ratio also has important implications for nuclear physics and geochronology.

KDK (Potassium (K) Decay (DK)) is an international collaboration dedicated to the measurement of this branching ratio. This thesis details an experiment that is performed using a silicon drift detector with a thermally deposited, enriched K-40 source inside the Modular Total Absorption Spectrometer (MTAS, Oak Ridge National Laboratory). MTAS is a large NaI detector whose high gamma-ray efficiency enables the proper discrimination between ground and excited state electron capture events.

Here we present the characterization of the KDK detector setup in terms of energy calibration, dead time,  gamma tagging efficiency and false negatives and positives. The analysis of a blinded, 44-day experimental run is also shown. Finally, a comprehensive Monte Carlo program is developed for simulating the KDK experiment and evaluating its sensitivity. We find that the KDK experiment will allow a successful ground state branching ratio measurement, with a p-value greater than 10e-7, if the true value is greater than 0.1%.

abstract: PhD


title: Delineating the Roles of Kinesin and Dynein Motor Proteins During Mitotic Spindle Assembly and Function in the Fungal Pathogen Candida albicans

contributor:
Allingham, John
Biomedical and Molecular Sciences

subject:
Fungal pathogens
Kinesin
Dynein
Motor proteins
Candida albicans
Budding yeast
Cell Biology
Microbiology
Antifungal Drug Resistance

abstract:
During cell division, cells must accurately orchestrate and execute DNA segregation to daughter cells. To do this, eukaryotes assemble a dynamic macromolecular structure called the mitotic spindle, which undergoes a series of conformational changes to attach, orient, and separate sister chromatids. These dynamic events depend on the correct localization and activation of structurally and functionally diverse teams of microtubule-associated motor proteins. Kinesins and dyneins are the main families of motors involved in orienting and moving the microtubule arrays that compose, or are attached to, the mitotic spindle. Many of these motor proteins' roles and molecular mechanisms have been extensively studied in several model systems. These studies have led to the broad perception that some motor functions have been evolutionarily conserved. One example is that bipolar spindle assembly ubiquitously requires kinesin-5 family members and thus these motors are essential for cell viability. However, we discovered that the human fungal pathogen, Candida albicans, relies heavily on the kinesin-14 motor, Kar3Cik1, for bipolar spindle assembly, rather than its kinesin-5, Kip1. This suggests that C. albicans uses force-producing motors differently than other eukaryotes and even related yeasts.

The studies detailed in this thesis's first two experimental chapters have delineated the roles of Kip1 and dynein (Dyn1) in C. albicans mitosis. Chapter 3 demonstrates that cells lacking Kip1 can undergo all mitotic processes, albeit with subpar integrity. Kip1-deficient cells have shorter metaphase spindles and longer and more numerous astral microtubules. Interestingly, Kip1 mutants are delayed in their entry into anaphase but execute anaphase at the same rate as wild-type cells. Furthermore, simultaneous loss of function of Kip1 and Kar3Cik1 is lethal. Chapter 4 provides evidence that Kip1 works collaboratively with Dyn1 in spindle elongation and that either motor can partially compensate for the loss of the other. The final experimental chapter, Chapter 5, investigates the curious phenotype that some spindles in Kip1 mutants disintegrate and form duplicated bipolar spindles within the same cell compartment. Evidence is provided that subsequent division of these spindles leads to the generation of random aneuploidies that can provide a growth advantage compared to wild-type cells when exposed to the antifungal drug fluconazole. Transcriptomic analysis of fluconazole-treated cells showed altered expression patterns of several genes involved in mitosis, including KIP1. This finding suggests that C. albicans cells may actively regulate mitotic kinesins under stress to promote spindle errors that foster aneuploidy and act as a driver of adaptive genome plasticity.

abstract: PhD


title: AN INVESTIGATION OF NINETEENTH-CENTURY ARCHAEOLOGICAL EVIDENCE FOR ROMAN BRITAIN AND ITS CONTEMPORARY RECEPTION WITHIN BRITISH SOCIETY

contributor:
Zaccagnino, Cristiana
Classics

subject:
roman britain
classical reception
classical studies
British classical reception
nineteenth century
archaeology
roman british archaeology
British archaeology
imperial studies

abstract: This project will analyze nineteenth-century archaeological records for Roman-British sites and policies involving artefacts and museums. I will use findings to form connections between archaeological activity during the Victorian period and contemporary British thought on Britain’s past, racial hierarchies, and imperialism. Particularly pertinent to this study is the way in which Britons used their perceived Roman past to justify the expansion and maintenance of their empire. This period of archaeological excavation was a unique time in which science and storytelling intermingled to create a picture of Britain’s past. The sudden increase in finding the remains of Roman Britain was attributed to the demands of urbanization during the nineteenth century. Thus far, Victoria Hoselitz’s work Imagining Roman Britain: Victorian responses to a Roman past (2007) is the only study I have come across to utilize a similar approach to that of my project in order to draw conclusions about British culture during the Victorian period. In order to complete my research, I have consulted nineteenth-century excavation reports by various British antiquarians. In addition, rare, published works and physical remains at various institutions, including the British Library and the British Museum, have been consulted.

abstract: M.A.


title: Towards Efficient Hydraulic Manipulator Control using Learning-Based Model Predictive Control

contributor:
Marshall, Joshua
Electrical and Computer Engineering

subject:
Model Predictive Control
Feedback Linearization
Manipulator Control
Hydraulic Manipulator Control
Optimal Control
Gaussian Process Regression

abstract:
Large-scale hydraulic manipulators are notoriously difficult to control due to the prevalent nonlinear and complex dynamics. As a result, automation and control of such machines has only proceeded as far as tele-operation. Recently, research has explored the use of Gaussian Process Regression (GPR) to enhance the modelling of manipulator dynamics, ultimately enabling more accurate control. Most control solutions have employed reactive control techniques, such as Inverse Dynamics controllers, for manipulator controllers. More recently, Model Predictive Controllers (MPC) have been explored for their foresight and constraint handling. Unfortunately, nonlinear Model Predictive Controllers pose a large computational burden, rendering these solutions infeasible for real-time applications.
This work presents a learning-based MPC methodology incorporating nonlinear predictions with robotics applications in mind. In particular, MPC is combined with feedback linearization for computational efficiency and GPR is used to model unknown system dynamics and nonlinearities. In this method, MPC predicts future states by leveraging a GPR model and optimizes a sequence of inputs over feedback linearized states. This controller was tested in simulation by using a two-link planar robot in the presence of model uncertainty. With respect to trajectory-tracking error, the proposed controller outperformed a conventional Proportional-Derivative (PD) Inverse Dynamics (ID) controller and a GPR-augmented ID controller. Although a fully nonlinear MPC formulation achieved slightly better performance, the proposed controller had an average control calculation time that was 82x faster.
With the intent of controller validation, control infrastructure was developed for a hydraulically actuated Kubota R520S robotic loader. Field trials were performed for dynamics regression and controller testing. A cascade control system was developed, with an outer-loop position controller and inner-loop torque controller. The torque controller was validated on the system, though hardware constraints limited the controller bandwidth. Differential evolution algorithm was leveraged to optimize a dynamics regression trajectory. A PD feedback controller was employed for dynamics parameter regression trial trajectory tracking. The dynamics parameters were regressed, resulting in a torque estimation root-mean-square percentage error of 41%. Finally, a PD ID controller was developed, tested, and validated on the robotic system.

abstract: M.A.Sc.


title: Biosynthesis of the Pseudomonas aeruginosa Common Polysaccharide Antigen by D-Rhamnosyltransferases WbpX and WbpY

contributor:
Brockhausen, Inka
Capicciotti, Chantelle
Biomedical and Molecular Sciences

subject:
Pseudomonas aeruginosa
Lipopolysaccharide
O antigen
Glycosyltransferase
D-Rhamnose
D-Rhamnosyltransferase
Common Polysaccharide Antigen
Polymerization
Glycobiology

abstract: The Gram-negative bacterium Pseudomonas aeruginosa is responsible for chronic and antibiotic-resistant infection in cystic fibrosis patients and immunocompromised individuals and is one of the leading organisms associated with nosocomial infection. Unlike other species, P. aeruginosa simultaneously expresses two glycoforms of lipopolysaccharide (LPS), differing in their O antigens, the most distal outer membrane polysaccharides. While the O-specific antigen (OSA) is variable in composition, the common polysaccharide antigen (CPA) is highly conserved and is composed of a homopolymer of D-rhamnose (D-Rha) in trisaccharide repeating units [D-Rhaα1-2-D-Rhaα1-3- D-Rhaα1-3]n. It has previously been established that D-Rha-transferase WbpZ adds the first D-Rha residue to the natural acceptor analogue GlcNAcα-PO3-PO3-(CH2)11-O-phenyl. Genes encoding two more D-Rha- transferases are found in the CPA biosynthesis gene cluster (wbpX and wbpY). This research seeks to biochemically characterize these two glycosyltransferases and understand their functions in the assembly of CPA. These studies show that WbpX and WbpY differ in their donor and acceptor specificities and have properties of GT-B folded enzymes of the GT4 glycosyltransferase family. Using mass spectrometry, we showed that recombinant His6-tagged WbpX and WbpY individually transferred a single D-Rha residue to the WbpZ product D-Rhaα1-3GlcNAcα-PO3-PO3-(CH2)11-O-phenyl. However, the mixture of WbpX and WbpY was able to catalyze the synthesis of longer D-Rha polymers. Furthermore, WbpX was found to possess polymerase activity in isolation under certain conditions. Nuclear magnetic resonance (NMR) analysis of the WbpX and WbpY D-Rha products revealed that WbpY is an α1-3-D-Rha-transferase, adding a single D-Rha residue to the WbpZ product. In contrast, WbpX adds several D-Rha residues to synthetic acceptor D-Rhaα-benzyl, forming both α1-2 and α1-3 linkages. Since CPA, and O antigens in general, are important virulence factors in bacterial infection, these findings open the door to advancing technology for antibacterial drug discovery and vaccine development against P. aeruginosa and other D-Rha-harbouring pathogenic bacteria.

abstract: M.Sc.


title: Topology optimization with additive manufacturing size constraints

contributor:
Kim, Il Yong
Mechanical and Materials Engineering

subject:
Topology optimization
Moving morphable components
Additive manufacturing
Build volume constraint

abstract:
Structures re-designed with topology optimization (TO) for additive manufacturing (AM) are restrained to the maximum build volume of the machine. Existing work addressing this limitation is the multi-component topology optimization for additive manufacturing (MTO-A) framework that uses an element-wise design variable (DV) method to simultaneously optimize the material layout and design of components to fit inside an AM machine. The scalability and practicality of this approach is limited in that the computational cost is directly related to the number of elements in each design field and joints required for re-assembly are not accounted for.
This work proposes a novel mathematical method that sequentially solves two subproblems to obtain the optimal material layout of a structure and the optimal decomposition points of a multi-component design satisfying the AM size constraints. Presented as decomposition optimization, the latter subproblem adopts the moving morphable components (MMC) framework to introduce AM size constraints to the optimization scheme with few design variables to enhance scalability of the problem. Joints are integrated by an MMC, referred to as partitioning rectangles, to obtain their optimal distribution in the design with the goal of minimizing the compliance for a completely decomposed structure. The AM size constraint is directly introduced in the geometry description of the MMC so that the components that fall within a partitioning rectangle are not bigger than the size of the AM machine. Additionally, an incomplete decomposition fraction constraint is introduced to limit the amount of structural material that exists outside of a partitioning rectangle. The proposed methodology is tested on three numerical examples to demonstrate its capabilities and limitations.

abstract: M.A.Sc.


title: ON THE PERFORMANCE OF DEEP LEARNING MODELS IN ENHANCED C-V2X COMMUNICATION

contributor:
Sorour, Sameh
Hossam, Hassanein
Computing

subject:
C-V2X
Deep-Learning
wireless communication

abstract:
Autonomous vehicles (AVs) are an essential component of future intelligent transportation systems (ITS). AVs promise an increase in driving comfort, greater safety, and improved fuel consumption. These benefits are attributed to AVs ability to leverage vehicle-to-everything (V2X) communication to coordinate driving, e.g., sharing maneuver intention and acquiring updated road maps. Cellular based V2X (C-V2X) had been popularized as one of the leading technologies at the forefront of ITS. C-V2X technology is already capable of supporting a basic set of AVs’ uses cases, e.g. warning messages for collision avoidance. In contrast, support for advanced use cases, e.g. cooperative lane change, is still an obstacle. Advanced AV use cases require a network able to support up to 10ms end-to-end (E2E) latency and 99.99% packet delivery rate. These stringent service requirements pose a challenge for 4G LTE and 5G New Radio (NR).
In this work, we build a simulation environment to study the feasibility of 5G NR in supporting advanced use cases in AVs and propose deep learning-based solutions to enhance its performance further. First, we propose deep leaning models to perform uplink channel state information (CSI) prediction in dynamic vehicular environments. The models are based on a combination of convolutional and recurrent neural networks (CNN-RNN), so as to suit the mobility factor in vehicular environments. Next, we propose a novel scheme based on deep learning prediction to enhance the uplink resource allocation process in 5G C-V2X. The proposed scheme enables the base station to predict vehicle maneuvers, subsequently, assign it the required resource in advance without the need for scheduling request and resource granting process. We show that this scheme improves the ability of 5G NR to support cooperative driving requirements. Moreover, we compare to traditional schemes discussing issues that arise from the introduction of prediction models and possible approaches for further enhancements in the future.

abstract: M.Sc.


title: Measuring the efficiency of the bioremediation of cyanobacterial harmful algal blooms using Viviparus georgianus

contributor:
Lefebvre, Daniel
Wang, Yuxiang
Biology

subject:
CHABs
Bioremediation
Viviparus georgianus
Cyanobacterial harmful algal blooms

abstract: With rising global temperatures, cyanobacterial harmful algal blooms (CHABs) have been increasing in size and frequency for several decades. These blooms produce toxins while severely reducing the oxygen levels of marine and freshwater ecosystems, resulting in large scale mortality events of aquatic life. A key element in a proactive approach to controlling CHABs may be bioremediation, the use of naturally occurring organisms to consume environmental pollutants. However, an optimal species for CHABs bioremediation has yet to be identified. Viviparus georgianus, the banded mystery snail, is ubiquitous to freshwaters, naturally occurs in high densities, and possesses gastropod relatives shown to be able to consume cyanobacteria with rapid detoxification effects, making them an ideal potential candidate. Despite this, little is known about their rate of consumption of CHABs, and how that may be affected by density of snails as well as affected by the species of cyanobacteria. I placed V. georgianus in microcosms with varying species of cyanobacteria or green algae, as well as varying densities of snails and then measured cyanobacteria ingested via the quantity of chlorophyll-a remaining in the water. My results demonstrated that snails in 200 mL of high cyanobacterial concentrations were able to decrease cyanobacteria by 60-70% within an hour of exposure, regardless of the presence of toxic cyanobacteria species. Over 24-hours, optimal snail density for cyanobacteria consumption occurred with 1-3 g of snails in 0.2 L microcosms, with increasing density of snails having diminishing efficacy returns.  By understanding how to optimize V. georgianus’ consumption of cyanobacteria, we can make use of a widespread and highly populous species for efficient and effective inhibition of CHAB blooms.

abstract: M.Sc.


title: Assessing the potential of shallow mesocosms to facilitate the consumption of cyanobacteria by the snail Viviparus georgianus

subject:
Cyanobacteria
Viviparus georgianus
Bioremediation
Mesocosm
cyanoHABs
cHABs
Fresh water snails
Banded mystery snail
Bloom forming cyanobacteria
Chlorophyll-a
Blue-green algae
Gastropods

abstract:
Background:
In a rapidly warming world, cyanobacterial harmful algal blooms (cyanoHABs) are becoming a pressing issue on a global scale. Pelagic cyanoHABs’ toxic effects on the well-being of ecosystems and detrimental impact on animal and human health demand economical, environmentally friendly solutions. Viviparus georgianus is a benthic snail ubiquitous to many eutrophicated Canadian bodies of water that can consume the cyanobacterium Microcystis aeruginosa. Although V. georgianus are already in the lakes where cyanoHABs are present, there is still the problem of how to overlap the interaction between these benthic snails and pelagic cyanobacteria. In our study, we assessed if V. georgianus could ingest naturally occurring, bloom-forming, multi-species cyanobacteria and discussed the necessary conditions to successfully implement shallow mesocosms to facilitate the snails’ consumption.
Methods:
We created two types of shallow mesocosms: in the first set, we placed equal biomasses of snails as well as equal volumes and concentrations of cyanobacteria but varied the depth to evaluate: 1. consumption, 2. the efficiency of consumption by small vs. large snails and 3. depth at which snails have a greater consumption. In the second set, we kept the volumes, depths, and concentrations of cyanobacteria constant but varied the snail biomass to evaluate the amount required to reduce cyanobacteria concentrations from high to moderate.
Results:
Mesocosms with snails had significantly stronger declines in cyanobacteria than mesocosms with no snails (F1,30 = 81.97, P < 0.0001) indicating that the snails consumed substantial amounts of cyanobacteria during the 48 hrs trial. Using equal snail biomass, large and small snails consumed similar amounts of cyanobacteria (F1,18 = 0.064, P = 0.804) indicating that snail size does not have an effect on consumption. The rate at which cyanobacteria concentration declined over time was similar at all depths (F16,60 = 1.509, P = 0.13). The minimum biomass of snails needed to reduce the concentration of cyanobacteria from high to moderate is 20 g of snails per litre.
Conclusions:
V. georgianus consume naturally occurring, bloom-forming cyanobacteria in relatively short periods of time in aquaria, indicating the potential for its use as a bioremediation method for in-situ studies. Within the range that we tested, depth does not have a significant impact on the snails’ consumption nor do differences in size. Future research is required to test their effectiveness in a natural setting.

abstract: M.Sc.


title: BIJECTIVE ILLUMINATION COLLECTION IMAGING: HIGHRE-SOLUTION TOMOGRAPHY IN THREE DIMENSIONS

subject:
Metasurface
High-resolution
Imaging
Depth of focus
OCT

abstract:
High-resolution optical imaging in three imensions from sub-surface of the issues enables numerous biological studies and clinical applications. High-resolution images are conventionally achieved by tight focusing of light into one point. Dictated by diffraction, tightly focused light spreads rapidly away from the focal point, hampering acquisition of high-resolution information in a relatively large depth range. As a result, microscopic imaging systems are often capable of capturing images with no depth information.
This thesis presents a solution to vercome this fundamental limitation in optical imaging through a particular architecture of illumination and collection light paths, liberating optical imaging from the restrictions imposed by diffraction. This technique, termed bijective illumination collection imaging (BICI), decouples lateral resolution from depth of focus by establishing a one-to-one correspondence (bijection) along a focal line between the illumination and collection light paths.
Unlike the traditional approach of imaging from a single focal point, BICI allows simultaneous acquisition of high-resolution images from a focal line along which lateral resolution is maintained. This approach addresses the fundamental question of how light intensity should be distributed to obtain high-resolution imaging in three-dimensions within a large depth range.

BICI uses the latest nano-optic technology, namely, metasurfaces, to shape the illumination and collection light paths. Implemented in optical coherence tomography (OCT), BICI’s impact on resolution of imaging is assessed. We demonstrate tissue imaging at 1.3 μm wavelength with approximately 3.2 μm lateral resolution maintained nearly intact over 1.25 mm depth of focus, 12- fold larger imaging depth of focus compared to that obtained using an ideal Gaussian beam with the same lateral resolution. A one-to-one comparison of tissue images obtained from BICI and the conventional OCT approach proves the former’s ability to accomplish high-resolution images within a large depth range.

The presented approach, BICI, entails no additional acquisition or computational burden and can be implemented across various wavelength ranges as its working principle remains unaltered with a wavelength change. Using metasurfaces, BICI can be feasibly miniaturized into endoscopic devices for high-resolution imaging in clinical settings. Demonstrated through OCT imaging, this approach serves as a foundation for high-resolution volumetric imaging which might be also adapted across the other existing optical modalities to capture high-resolution depth-resolved images.

abstract: PhD