VictorJuiz/thesis huggingface dataset:
Controlling Cell Density by Micropatterning Regulates Smad Signalling and Mesendoderm Differentiation of Human Embryonic Stem Cells
Keywords: Pluripotent Stem Cells
Mesendoderm
Hematopoiesis
Micropatterning

Human embryonic stem cells (hESC) present a potentially unlimited supply of hematopoietic progenitors for cell-based therapies. However, current protocols for generating these progenitors typically also generate undesired cell types due to imprecise control of the hESC microenvironment and poor understanding of the signalling networks regulating mesoderm differentiation (the germ layer from which hematopoietic cells emerge). This report demonstrates that activation of the downstream effectors of Activin/Nodal and bone morphogenetic protein (BMP) signalling (Smad2 (composite of Sma (smaller) and Mad (mothers against decapentaplegic) and Smad1, respectively) are both required for mesoderm differentiation. It is further shown that microcontact printing-mediated control of hESC colony size creates local microenvironments that guide differentiation, via a Smad1-dependent mechanism, preferentially towards the mesoderm lineage. These findings demonstrate the need for precise control of the microenvironment in order to effectively guide hESC differentiation to produce specific cell types for potential therapeutic applications.
Analysis of Naked in the Canonical Wnt Pathway
Keywords: Naked
Wnt

Wnt signalling is involved throughout development and is inappropriately activated in a variety of human cancers. In the canonical pathway, secreted Wnt proteins induce the stabilization of b-catenin. Drosophila Naked (Nkd), or Nkd1 and Nkd2 in vertebrates, is believed to antagonize canonical Wnt signalling through an interaction with Dishevelled (Dvl). Analysis of a high-throughput protein-protein interaction screen conducted in our lab led to the identification of novel Nkd1 interacting proteins, including Nkd1/2 and Axin1. Mapping of Nkd1 regions required for these novel interactions and functional studies, including transcriptional and siRNA mediated knockdown assays, were performed to examine the role of Nkd1 in canonical Wnt signalling. Previous work suggests that Nkd1 functions only through Dvl, but this work suggests that Nkd1 acts via a more complex mechanism. In addition to serving as an antagonist to regulate the canonical Wnt pathway, we propose that Nkd1 may also act positively to promote signalling.
Access to Dental Care for Persons with Disabilities in Ontario: A Focus on Persons with Developmental Disabilities
Keywords: access
dentistry
special needs
disability
Canada
dental care

This study was undertaken to determine if persons with disabilities encounter difficulties in accessing dental care in Ontario, to identify barriers to accessing dental care and to determine if persons with disabilities and caregivers value oral health. Community organizations providing supports for persons with disabilities were recruited to circulate a questionnaire to their members via mail or internet. Fourteen community organizations mailed out 1755 paper questionnaires. A response rate of 23.9% was calculated from original surveys returned. In total, 634 paper and internet surveys were deemed valid. Data analysis was conducted using the chi square test and logistic regression. Most (73.2%) persons with disabilities, primarily developmental disabilities, were able to access dental services in Ontario. Personal internal factors were more likely to act as barriers to dental care than external factors. The majority of caregivers and persons with disabilities believe that oral health is an important part of overall health.
Efficient, Stable Infrared Photovoltaics based on Solution-Cast PbSe Colloidal Quantum Dots
Keywords: Nanocrystals
Infrared Photovoltaics

Half of the sun’s power lies in the infrared. As a result, the optimal bandgaps for solar cells in both the single-junction and even the tandem architectures lie beyond 850 nm. However, progress in low-cost, large-area, physically-flexible solar cells has instead been made in organic and polymer materials possessing absorption onsets in the visible. Recent advances have been achieved in solution-cast infrared photovoltaics through the use of colloidal quantum dots. Here we report stable solution-processed photovoltaic devices having 3.6% power conversion efficiency in the infrared. The use of a strongly-bound bidentate linker, benzenedithiol, ensures device stability over weeks. We investigate in detail the physical mechanisms underlying the operation of this class of device. We find that diffusion of electrons and holes over hundreds of nanometers through our PbSe colloidal quantum dot solid is chiefly responsible for the high external quantum efficiencies obtained in this new class of devices.
Near-infrared Spectroscopy as an Access Channel: Prefrontal Cortex Inhibition During an Auditory Go-no-go Task
Keywords: Near-infrared Spectroscopy
access pathway
access channel
brain-computer interface
Go-No-Go Task
Prefrontal Cortex
inhibition
Change-point Detection
access technology

The purpose of this thesis was to explore the potential of near-infrared spectroscopy (NIRS) as an access channel by establishing reliable signal detection to verify the existence of signal differences associated with changes in activity. This thesis focused on using NIRS to measure brain activity from the prefrontal cortex during an auditory Go-No-Go task. A singular spectrum analysis change-point detection algorithm was applied to identify transition points where the NIRS signal properties varied from previous data points in the signal, indicating a change in brain activity. With this algorithm, latency values for change-points detected ranged from 6.44 s to 9.34 s. The averaged positive predictive values over all runs were modest (from 49.41% to 67.73%), with the corresponding negative predictive values being generally higher (48.66% to 78.80%). However, positive and negative predictive values up to 97.22% and 95.14%, respectively, were achieved for individual runs. No hemispheric differences were found.
Interactive Effects of Hypoxia and Cocaine Treatment on Ventilatory Chemoreflexes and Locomotor Sensitisation
Keywords: hypoxia
cocaine
ventilatory acclimatisation to hypoxia
ventilatory chemoreflexes
locomotor sensitisation

This study investigated two hypotheses. First, that chronic cocaine treatment would mimic the changes in breathing that are associated with ventilatory acclimatisation to chronic hypoxia (VAH). Second, that pre-treatment with a hypoxic stressor would bring about cross-sensitisation to cocaine. To address the first hypothesis, rats were exposed to either chronically hypoxic or chronically normoxic conditions and treated with either cocaine or saline for a 14 day period. Following this period, acute breathing trials were performed to measure resting ventilation and ventilatory chemoreflexes. The results demonstrated that chronic cocaine treatment did not induce the changes in breathing associated with VAH. To address the second hypothesis rats were exposed to a hypoxic stressor for 10 days (either intermittent hypoxia or chronic hypoxia) after which cocaine sensitisation was measured via locomotor sensitisation trials. The results demonstrated that cross-sensitisation between a hypoxic stress and cocaine was observed for intermittent but not chronic hypoxia.
Defining a Model of Classical Activation in Microglia
Keywords: Neuroinflammation
Microglia
Cytokine
cAMP Response Element Binding Protein

Microglia, the resident immune cells of the central nervous system, can become activated following injury, disease, or infection. In vitro, they can be activated by stimuli, which determine the inflammatory phenotype they will develop. In this thesis, stimulating microglia with tumor necrosis factor- and interferon- resulted in classical activation, characterized by proliferation, increased transcription of complement receptor 3 and major histocompatibility class II molecules, and elevated production and transcription of interleukin-1 and nitric oxide. Stimulation with TNF and IFN also changed the intensity of phosphorylated (activated) cyclic adenosine monophosphate response element binding protein immunoreactivity in microglia. Specifically, cells differentiated into populations with high or low pCREB intensity. This was the first example of such a response in microglia and was representative of what occurred in vivo, after ICH. Thus, the characterization of this model will be useful for future studies of this and other intracellular pathways of classically activated microglia.
Antisaccades: A Probe into the Dorsolateral Prefrontal Cortex in Alzheimer's Disease
Keywords: Antisaccades
Alzheimer's Disease

The number of people living with Alzheimer’s Disease (AD) is projected to increase dramatically over the next few decades, making the search for treatments and tools to measure the progression of AD increasingly urgent. The antisaccade task, a hands- and language-free metric, may provide a functional index of the Dorsolateral Prefrontal Cortex (DLPFC), which is damaged in the later stages of AD. Patients with AD make significantly more antisaccade errors than controls, however, performance in mild AD has remained unexplored. We hypothesized that mild patients will make more errors than controls. Thirty AD patients and 31 age-match controls completed both laptop-based and clinical versions of the antisaccade task. Two thirds of patients with AD made significantly more errors and corrected less of their errors than age-matched controls. Our findings indicate that antisaccade impairments exist in mild AD, suggesting DLPFC pathology may be present earlier than suggested by previous studies.
Searching for Radiosensitizers: Development of a Novel Assay and High-throughput Screening
Keywords: Radiosensitizer
High-Throughput Screening
Colony Formation Assay

The colony formation assay (CFA) is the gold standard for measuring cytotoxic effects on cells. To increase efficiency, the CFA was converted to a 96-well format using an automated colony counting algorithm. The 96-well CFA was validated using ionizing radiation (IR) on the FaDu and A549 cancer cell lines. Its ability to evaluate combination therapies was investigated using cisplatin and IR. The 96-well CFA was transferred to a robotic platform for evaluation as a high-throughput screen (HTS) readout for the discovery of novel anti-cancer compounds, and radiosensitizers. Screening yielded eight putative anti-cancer hits, and five putative radiosensitizing hits. Secondary screening confirmed 6/8 anti-cancer compounds, and 0/5 radiosensitizing compounds. Thus, the 96-well CFA can be adopted as an alternative assay to the 6-well CFA in the evaluation of cytotoxicity in vitro, providing a possible readout to be utilized in HTS for discovering anti-cancer compounds, but with limited applicability in discovering radiosensitizers.
Space for Healthy Communities: An Exploration of the Social Pathways between Public Space and Health
Keywords: public space
place attachment
place-based identity
neighbourhood health

This thesis investigates the relationship between access to public gathering spaces and self-reported health with indicators of community life as the intervening variables. This study was undertaken to investigate the relationship between the access to public space and self-rated health status in multicultural communities. A survey of 785 randomly-selected households was conducted across four low-income Toronto neighbourhoods. The investigation is framed by the 'production of healthy public space' model, which conceptualizes the pathways between the lived experience of space and health as impacting an individual’s likelihood of establishing place attachment. The results support the hypothesis that there is a relationship between the lived dimension of space and health. Mental health appears to be the outcome most affected by indicators of place attachment. Several of the aforementioned relationships were found more commonly in the densest of the four neighbourhoods and variations were found between foreign- and Canadian-born subpopulations.
Design of an Adaptive System for Upper-limb Stroke Rehabilitation
Keywords: rehabilitation
robotics
artificial intelligence
POMDP
stroke
upper-limb

Stroke is the primary cause of adult disability. To support this large population in recovery, robotic technologies are being developed to assist in the delivery of rehabilitation. A partially observable Markov decision process (POMDP) system was designed for a rehabilitation robotic device that guides stroke patients through an upper-limb reaching task. The performance of the POMDP system was evaluated by comparing the decisions made by the POMDP system with those of a human therapist. Overall, the therapist agreed with the POMDP decisions approximately 65% of the time. The therapist thought the POMDP decisions were believable and could envision this system being used in both the clinic and home. The patient would use this system as the primary method of rehabilitation. Limitations of the current system have been identified which require improvement in future research stages. This research has shown that POMDPs have promising potential to facilitate upper extremity rehabilitation.
The Relationship Between Adult Hippocampal Neurogenesis and Spatial Learning and Memory in Natural Populations of Food-storing Red Squirrels (Tamiasciurus hudsonicus).
Keywords: adult neurogenesis
hippocampus
dentate gyrus
spatial learning and memory
red squirrels
food-storing
immunohistochemistry
Ki-67
DCX
NeuN

Previous research on the relationship between spatial memory and adult hippocampal neurogenesis has been controversial. In the present study, neurogenesis was compared between two natural populations of the same species that differ in their reliance on spatial memory to cache and retrieve stored food. Western red squirrels store food in a single site whereas eastern red squirrels store food in multiple sites. Neurogenesis was assessed using endogenous markers of the number of proliferating cells (Ki-67) and the number of immature neurons (DCX), and neuronal recruitment was determined by measuring the area of the dentate gyrus of the hippocampus. The number of proliferating cells, immature neurons and neuronal recruitment were enhanced in the eastern compared to the western red squirrels, reflecting the food storing strategies used by the squirrels. This suggests that there is a positive correlation between adult hippocampal neurogenesis and spatial learning and memory.
Designing a Matrix Metalloproteinase-7-activated Quantum Dot Nanobeacon for Cancer Detection Imaging
Keywords: Quantum dot
Matrix metalloproteinase
Cancer detection
Optical imaging
Protease sensor
Nanotechnology

Quantum Dot (QD) nanobeacons distinguish themselves from molecular beacons with the promise of non-linear activation, tunability, and multi-functionality. These unique features make them highly attractive for cancer detection imaging with opportunities for increased signal-to-background ratio and tunable sensitivity. In this thesis, a nanobeacon was designed to target matrix metalloproteinase-7 (MMP-7), known to be over-expressed by a wide array of tumours. The nanobeacon is normally dark until specifically activated by MMP-7. The overall design strategy links single QDs to multiple energy acceptors by GPLGLARK peptides that can be cleaved specifically by MMP-7. However, design details such as the choice of energy acceptor and conjugation method was found to drastically alter the function of the nanobeacon. Studies of nanobeacons synthesized with Black Hole Quencher-1 or Rhodamine Red by either covalent conjugation or electrostatic self-assembly revealed that peptide conformation and bonding flexibility are both important considerations in nanobeacon design due to QD sterics.
Fluid Coke Derived Activated Carbon as Electrode Material for Electrochemical double Layer Capacitor
Keywords: fluid coke
activated carbon
electrochemical double layer capacitor
capacitance
cyclic voltammetry
constant current charge/discharge

An electrochemical double-layer capacitor (EDLC) is a potential buffer for current power and energy supply. In this work, activated carbon derived from fluid coke as a brand new electrode material was studied due to its high specific surface area (SSA) and large portion of mesopores. A suitable electrode material formula, current collector, and cell configuration were investigated to fabricate a testable system and ensure the reproducibility of measurements. Cyclic voltammetry (CV) and constant current charge/discharge (CD) techniques were used to characterize the performance of the electrode material, as well as to study its fundamental behaviour. A new procedure was established for quantifying the capacitance (Cc) of EDLC from CV which isolates the effect of internal resistance on the measured capacitance (CM). The specific capacitance of single electrode made of activated carbon (~1900 m2/g) with approximately 80% mesopores and macropores was able to reach 180 F/g at scan rate of 0.5mV/s.
Wang An Shi and the Balance of Form and Function
Keywords: Wang Anshi
Song ci

The reform-minded aspect of Wang's writing is frequently emphasized while its rhetorical component is overlooked. Similarly, in texts which appear poetic in nature the underlying subject matter of reform fails to be recognized. Both rhetoric and its antithesis function in tandem in all of Wang's texts, the one serving to balance the other; stylistic writing serves to soften political discourse. When Wang writes poetically, the problem of reform is served through allusion. In contrast, when direct terminology is employed, this is balanced by rhetorical analogy (often citing the past to prove the present, jie gu yu jin). Because his subject matter is predominantly political, Wang's memorials and prose texts are well known, while his poetry has remained in relative obscurity. Nevertheless, even the memorials rely on the balance of rhetoric and aesthetics, which he describes in his best known text "Shang Ren Zong Huang Di Yan Shi Shu".
On the Generation of Subthreshold Membrane Potential Fluctuations in Hippocampal CA1 Interneurons
Keywords: hippocampus
theta frequency oscillations

A class of hippocampal interneurons in CA1, bordering the lacunosum-moleculare and radiatum hippocampal layers (the LM/R cell), has been shown to exhibit membrane potential oscillations (MPOs) subthreshold to action potential generation. MPOs occur at theta frequency (4-12 Hz) and are of interest because of their putative role in promoting network level theta activity. MPOs arise without synaptic input suggesting that they originate through interactions in the cell’s repertoire of currents. To investigate the generation of MPOs we develop a single compartment model of the cell based on the physiological characterization of its currents. The model includes both deterministic current models and white noise. Our analysis allows for a complete characterization of the cell’s dynamics over the subthreshold range and shows that MPOs arise through the interaction between current dynamics and system noise. We find that MPOs show a particular dependency on the A-type potassium and persistent sodium current magnitudes.
Reliable Broadcast of Safety Messages in Vehicular Ad hoc Networks
Keywords: Communication networks
Wireless ad hoc networks
vehicular commuincations
vehicular safety systems

Broadcast communications is critically important in vehicular networks. Many safety applications need safety warning messages to be broadcast to all vehicles present in an area. In this thesis, we propose a novel repetition-based broadcast protocol based on ``optical orthogonal codes.'' Optical orthogonal codes are used because of their ability to reduce the possibility of collision. We present a detailed mathematical analysis for obtaining the probability of success and the average delay. Furthermore, we propose to use coding to increase network throughput, and ``adaptive elimination'' of potentially colliding transmissions to further increase reliability. We show, by analysis and simulations, that the proposed protocol outperforms existing repetition-based ones and provides reliable broadcast communications and can reliably deliver safety messages under load conditions deemed to be common in vehicular environments. We also show that the proposed protocol is able to provide different levels of quality of service.
Investigating the Correlation between Swallow Accelerometry Signal Parameters and Anthropometric and Demographic Characteristics of Healthy Adults
Keywords: aspiration
accelerometry
anthropometric
canonical correlation
segmentation algorithm

Thesis studied correlations between swallowing accelerometry parameters and anthropometrics in 50 healthy participants. Anthropometrics include: age, gender, weight, height, body fat percent, neck circumference and mandibular length. Dual-axis swallowing signals, from a biaxial accelerometer were obtained for 5-saliva and 10-water (5-wet and 5-wet chin-tuck) swallows per participant. Two patient-independent automatic segmentation algorithms using discrete wavelet transforms of swallowing sequences segmented: 1) saliva/wet swallows and 2) wet chin-tuck swallows. Extraction of swallows hinged on dynamic thresholding based on signal statistics. Canonical correlation analysis was performed on sets of anthropometric and swallowing signal variables including: variance, skewness, kurtosis, autocorrelation decay time, energy, scale and peak-amplitude. For wet swallows, significant linear relationships were found between signal and anthropometric variables. In superior-inferior directions, correlations linked weight, age and gender to skewness and signal-memory. In anterior-posterior directions, age was correlated with kurtosis and signal-memory. No significant relationship was observed for dry and wet chin-tuck swallowing
Methodologies in Digital Watermarking: Robust and Reversible Watermarking Techniques for Authentication, Security and Privacy Protection
Keywords: Digital Watermarking
Image Authentication
Privacy Protection
Security

The advances in recording, editing and broadcasting multimedia content in digital form motivate the protection of digital information against illegal use, manipulation and distribution. This thesis work focuses on one aspect of digital rights management (DRM), namely digital watermarking. Specifically, we study its use in copy protection, tamper detection and information hiding. We introduce three application-specific digital watermarking techniques. The first two algorithms, based on embedding film grain like noise and signal dependent watermarks, respectively, are designed for authentication applications. The advantage is that they are able to detect malicious tampering while being robust against content-preserving processes such as compression, filtering and additive noise. The third method, a reversible watermarking technique, is designed so that sensitive personal information can be embedded in medical images. Simulation results show that our proposed method outperforms other approaches in the available literature in terms of image quality and computational complexity.