VictorJuiz/thesis huggingface dataset:
"Flobject" Analysis: Learning about Static Images from Motion
Keywords: Machine Learning
Computer Vision
Object Recognition
Flobjects

A critical practical problem in the field of object recognition is an insufficient number of labeled training images, as manually labeling images is a time consuming task. For this reason, unsupervised learning techniques are used to take advantage of unlabeled training images to extract image representations that are useful for classification. However, unsupervised learning is in general difficult. We propose simplifying the unsupervised training problem considerably by taking the advance of motion information. The output of our method is a model that can generate a vector representation from any static image. However, the model is trained using images with additional motion information. To demonstrate the flobject analysis framework, we extend the latent Dirichlet allocation model to account for word-specific flow vectors. We show that the static image representations extracted using our model achieve higher classification rates and better generalization than standard topic models, spatial pyramid matching, and Gist descriptors.
Men1-dependent Increase in RPeD1 Excitability is Required for Long Term Memory Consolidation after Aversive Operant Conditioning in Lymnaea stagnalis.
Keywords: memory
Lymnaea stagnalis
Men1
plasticity

Long term memory (LTM) formation is a complex process involving signalling cascades, new protein synthesis and gene regulation. Increasing evidence demonstrates a role of intrinsic plasticity in memory formation, but the underlying molecular mechanisms remain relatively unknown. LTM was established using an aversive operant conditioning model in Lymnaea stagnalis. Using intracellular electrophysiology in an isolated preparation, increased gain of firing frequency was observed in the RPeD1 neuron after LTM. This provides the first demonstration of intrinsic plasticity after operant conditioning in RPeD1, a neuron required for the conditioned behaviour and LTM. I also determined the contribution of the transcription factor men1 to plasticity. Using in vivo RNAi silencing, I found that men1 is required for LTM and increasing RPeD1 excitability during consolidation, demonstrating men1-mediated intrinsic plasticity is critical for LTM. I propose a new model of memory formation in which men1-dependent increase of excitability during consolidation is required for LTM.
Mechanism of eIF2α Kinase Inhibition by Viral Pseudokinase PK2
Keywords: eIF2α kinase regulation
Viral pseudokinase PK2
Enzyme catalytic switching
Translation regulation

Phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) is a conserved eukaryotic mechanism to limit protein synthesis under stress conditions. Baculovirus PK2, which resembles the C-terminal half of a protein kinase domain, inhibits eIF2α family kinases in vivo, thereby increasing viral fitness in the face of host immunological and stress responses. The mechanism by which PK2 modulates eIF2α stress response signaling remains unknown. To address this issue, a combination of biochemical, biophysical and in vivo approaches were employed to probe the mechanism of PK2 inhibition on a prototypical human eIF2α kinase, the RNA-dependent protein kinase (PKR). We discovered that PK2 inhibits PKR catalytic activity by directly binding its kinase domain. This direct interaction requires both the kinase-like C-lobe fold of PK2 and a critical 22 residue N-terminal extension that precedes it. We further show that the PK2 N-terminal extension is required but not sufficient for the ability of PK2 function.
The Effect of Acute Eccentric Treadmill Running on NF-κB Activation and HSP72 Content in Skeletal Muscle from Late Middle-aged Rats
Keywords: aging
exercise
muscle

Eccentric exercise causes skeletal muscle damage, yet the acute cellular responses post-exercise have yet to be fully elucidated. To better understand the post-exercise response, heat shock protein (HSP) 72 content and nuclear factor-κB (NF-κB) activation where examined in Adult (A; 6 month) and Late middle-aged (LMA; 24 month) Fischer 344xBrown Norway rats. Animals were randomly divided into five groups (n=6): non-exercising controls (C), level (L) or eccentric (ECC) (-16°) running at 16m.m-1 and killed immediately post-exercise (0), 48 hours post-exercise (48). Following ECC, vastus intermedius (VI) from A and LMA showed more damage compared to L exercise. Neither age-group had significantly increased VI HSP72 content compared to C. Pooled results founded increased HSP72 content in ECC-48 compared to C (p<0.02). NF-κB activation in the VI was lower in LMA (p<0.001) and unchanged in WG when compared to AC. These findings suggest HSP72 is increased following eccentric exercise in the VI.
Multiple Modality Optical Neural Imaging with VCSELs
Keywords: Neuroimaging
Lasers

I investigate the use of vertical cavity surface emitting lasers (VCSELs) for portable optical neural imaging. In particular, I attempt to use one laser source to produce the different illumination needed for three techniques, imaging flow, oxygenation, and fluorescence. Our group's goal is to combine these techniques using a single source in a simple imaging format, which can be modified for portable use in awake animals. We exploit tuning properties of VCSELs to implement two distinct operation schemes with different illumination characteristics. Single mode operation provides high speckle contrasts, used to map flow speeds in laser speckle contrast imaging (LSCI). Sweep operation provides low noise, allowing us to image small signal changes with intrinsic optical signal imaging (IOSI), which relate to blood oxygenation. Finally, we use our VCSEL devices for on-chip integrated fluorescence sensing. Future work aims to develop a fully portable format, using CMOS detectors and integrated circuit control.
Targeting Tumour Metabolism through HIF-1 Inhibition Enhances Radiation Response in Cervix and Head and Neck Xenograft Tumours
Keywords: cancer
radiation
hypoxia
metabolism
HIF-1
lactate

Increased glucose metabolism may occur in malignant tumours due to altered gene expression or a response to hypoxia. It has been shown that tumours with high levels of glycolysis, indicated by elevated lactate, are less responsive to radiotherapy. It is not clear whether this effect is caused by lactate itself or rather that high lactate is a surrogate for a radioresistant property such as hypoxia. Furthermore, we are not aware of studies that examine the manipulation of lactate production in tumours to alter radiation response. We propose a novel approach of metabolic targeting of HIF-1 to address these issues. HIF-1 is a major regulator of glycolysis and its inhibition would decrease malignant cell metabolism and could lead to a decrease in lactate production. The goal of this pre-clinical study was to evaluate metabolic targeting as a strategy of enhancing radiation response by inhibiting the HIF-1 transcription factor.
Simulated Shrub Encroachment Impacts Function of Arctic Spider Communities
Keywords: spiders
Arctic
shrub encroachment
ecosystem functioning
arthropods
phenology
snow cover
snow fences
overwintering

The projected increase of shrubs across the Arctic is expected to alter patterns of snow cover, which may affect the phenology and survival of arthropods such as spiders. In this study, we simulated shrub encroachment on a series of tundra plots and examined the effects on the spider assemblages during the following growing season. Our simulated shrub treatment did not affect the abundance or composition of spider communities over the season; however, adults from the dominant genus Pardosa (Lycosidae) had significantly higher body mass on treatment plots. This difference in mass was observed following snow melt and persisted until halfway through the growing season. Given the importance of spiders as arthropod predators and as food sources for breeding birds, such a change in summer body mass could represent a shift in spiders’ functional contributions to Arctic ecosystems.
Insight into the Cargo Recognition Mechanism of Kinesin Light Chain 1
Keywords: Kinesin
Mechanism of Interaction
KLC
JNK-interacting protein (JIP)
Alcadein
Axonal Transport

Kinesin-1 transports various cargos along the axon, while the light chain subunits play a role in selecting the types of cargos to transport. However, the mechanisms of cargo recognition and interaction have yet to be characterized. Both c-Jun kinase-interacting protein-1 (JIP1) and alcadein-1 (ALC1) are kinesin-1 cargos and compete with each other for the axonal transport machinery. I identified two polar patches of KLC1 that play a role in the interactions with JIP1 and ALC1, respectively. The main components of these two polar patches are asparagine “clamps” surrounded by positively charged lysines. Consistent with this finding, negatively charged residues of JIP1 and ALC1 are required to interact with KLC1. By structural modeling, I narrowed down the possible key residues of KLC1 that are required for interaction with c-Jun kinase interacting protein-3 (JIP3). Together, these findings reveal the versatility of KLC in the mode of interaction with many different cargos.
Stochastic Modelling of a Collection of Correlated Sparse Signals and its Recovery via Belief Propagation Methods
Keywords: Compressive Sensing
Belief Propagation

The field of compressive sensing deals with the recovery of a sparse signal from a small set of measurements or linear projections of the signal. In this thesis, we introduce a stochastic framework that allows a collection of correlated sparse signals to be recovered by exploiting both intra and inter signal correlation. Our approach differs from others by not assuming that the collection of sparse signals have a common support or a common component; in some cases, this assumption does not hold true. Imagine a simplified cognitive radio problem, where users can send a single tone (sine-wave) in a finite number of frequencies; it is desired to find the used frequencies over a large area (creation of a radio map). This is a sparse problem; however, as we move spatially, the occuppied frequencies change, thus voiding the assumption of a common support/component. Our solution to multi sparse signal recovery addresses this problem, where signals that are close geographically are highly correlated and their support gradually changes as the distance between signals grow. Our approach consists of the creation of a probabilistic model that accounts for inter and intra signal correlation and then using belief propagation to calculate the posterior distribution of the signals and perform recovery.
High Dynamic Range Image Compression of Color Filter Array Data for the Digital Camera Pipeline
Keywords: high dynamic range imaging
color filter array
compression
lossy
lossless
digital camera

Typical consumer digital cameras capture the scene by generating a mosaic-like grayscale image, known as a color filter array (CFA) image. One obvious challenge in digital photography is the storage of image, which requires the development of an efficient compression solution. This issue has become more significant due to a growing demand for high dynamic range (HDR) imaging technology, which requires increased bandwidth to allow realistic presentation of visual scene. This thesis proposes two digital camera pipelines, efficiently encoding CFA image data represented in HDR format. Firstly, a lossless compression scheme exploiting a predictive coding followed by a JPEG XR encoding module is introduced. It achieves efficient data reduction without loss of quality. Secondly, a lossy compression scheme that consists of a series of processing operations and a JPEG XR encoding module is introduced. Performance evaluation indicates that the proposed method delivers high quality images at low computational costs.
Satellite and In Situ Measurement of NO2
Keywords: no2
atmospheric chemistry
atmospheric physics
remote sensing

A novel method was developed for producing high-resolution (∼ 11km) maps of surface NO2 concentrations by combining satellite retrieved NO2 columns from OMI with in situ measurements made by permanent monitoring networks. Field data from the BAQS-met field campaign in the Windsor area during 2007 was used to validate this method and explore the uncertainties and biases in the inferred values. Good correlation with the network of passive monitors was found (R = 0.69). Interference of NOz in traditional NO2 measurements was found to be small (0.9 ppb) when considered for 24-hr averages. The inference method was extended to qualitatively analyze long-term trends in Windsor. Comparison against a land-use regression model in Toronto showed similar overall trends, but the downtown core was underestimated considerably by the OMI-inferred map. While the presented inference method can simplify and increase the utility of OMI NO2 data, limitations remain as to the spatial and temporal resolution achievable.
Correlative Fiduciary Liability
Keywords: Private Law
Fiduciary

The ultimate aim of this thesis is to demonstrate that the effect of applying a corrective structure to fiduciary obligations is edifying. Corrective justice is a bipolar relationship where each of the poles refers to individuals conceptually linked through the legal relationship between them. Because corrective justice is bipolar, the upshot of such an approach ought to result in the promise of greater integrity and clarity flowing from a renewed interest in the relationship between fiduciary and principal. Underlying this polishing of the fiduciary relationship is the long-held ambition for the fiduciary relationship not to suffer from ambiguity as a symptom of its expansion beyond the sphere of trusts.
Effects of Very Preterm Birth on Brain Structure in Mid-childhood
Keywords: preterm
brain structure
MRI
cortical thickness

Children born prematurely exhibit a broad range of neuroanatomical abnormalities. The aim of this study was to investigate the long-term effects of very preterm birth on brain volume (cortical and subcortical), cortical thickness and surface area. The participants were 25 children born very preterm (<32 weeks gestational age) without significant post-natal medical sequelae and 32 term-born children between 7 and 10 years of age. Neuroanatomical measures were derived from an automated pipeline. The results suggest a pattern of decreased brain volume, surface area and cortical thickness for children born preterm and the relation between subcortical gray volume and total brain volume differed between groups. The cortex was significantly thinner for children born preterm than term-born children in focal regions of the parietal and temporal lobes. Therefore, even without significant postnatal medical sequelae, very preterm children still exhibit structural differences that persist into middle childhood.
Nonrigid Registration of Dynamic Contrast-enhanced MRI Data using Motion Informed Intensity Corrections
Keywords: image registration
contrast-enhanced imaging
DCE-MRI
kidney

Effective early detection and monitoring of patient response to cancer therapy is important for improved patient outcomes, avoiding unnecessary procedures and their associated toxicities, as well as the development of new therapies. Dynamic contrast-enhanced magnetic resonance imaging shows promise as a way to evaluate tumour vasculature and assess the efficacy of new anti-angiogenic drugs. However, unavoidable patient motion can decrease the accuracy of subsequent analyses rendering the data unusable. Motion correction algorithms are challenging to develop for contrast-enhanced data since intensity changes due to contrast-enhancement and patient motion must somehow be differentiated from one another. A novel method is presented that employs a motion-informed intensity correction in order to facilitate the registration of contrast enhanced data. The intensity correction simulates the presence or absence of contrast agent in the image volumes to be registered in an attempt to emulate the level of contrast-enhancement present in a single reference image volume.
Rhodium-catalyzed Addition of Arylboronic Acids to Nitriles: Application in the Synthesis of Unsymmetrical Polysubstituted Pyridines
Keywords: rhodium
nitrile
pyridine
unsymmetrical
1-aza-allyl anion
β-keto sulfone
β-sulfonylvinylamine

Investigations pertaining to the rhodium(I)-catalyzed addition of arylboronic acids to (arylsulfonyl)acetonitriles were undertaken. The resulting carbon-carbon bond forming reaction has led to the efficient synthesis of novel stereoselective (Z)-β-sulfonylvinylamines, which upon acidic hydrolysis, afford useful β-keto sulfones possessing a diverse range of aryl and sulfonyl substituents. The synthetic utility of these (Z)-β-sulfonylvinylamines was subsequently explored by generating the corresponding 1-aza-allyl anion equivalents under basic conditions. This interesting anionic intermediate was then introduced to various α,β-unsaturated systems to produce a diverse array of functionalized pyridine derivatives including unsymmetrical polysubstituted pyridines.
Visual Odometry Aided by a Sun Sensor and an Inclinometer
Keywords: Aerospace
Robotics
Visual Odometry
Sun Sensor

Due to the absence of any satellite-based global positioning system on Mars, the Mars Exploration Rovers commonly track position changes of the vehicle using a technique called visual odometry (VO), where updated rover poses are determined by tracking keypoints between stereo image pairs. Unfortunately, the error of VO grows super-linearly with the distance traveled, primarily due to the contribution of orientation error. This thesis outlines a novel approach incorporating sun sensor and inclinometer measurements directly into the VO pipeline, utilizing absolute orientation information to reduce the error growth of the motion estimate. These additional measurements have very low computation, power, and mass requirements, providing a localization improvement at nearly negligible cost. The mathematical formulation of this approach is described in detail, and extensive results are presented from experimental trials utilizing data collected during a 10 kilometre traversal of a Mars analogue site on Devon Island in the Canadian High Arctic.
Online Music Knowledge: The Case of the Non-musician
Keywords: self-directed learning
music information retrieval
information practice
user study
music knowledge
system design
music library
digital library

Five cases of ‘non-musicians’ learning how to make music were used to explore the information practice of users in the domain of music to support the design of music information systems and platforms. In all five cases, the use of online music knowledge was situated within a larger process of self-directed learning, as well as the larger socio-musical world of the non-musicians. Effective access to and use of available resources is paradoxically predicated on a non-musician’s ability to articulate their information needs using terms with which they are not yet familiar. The findings articulate the information practice of non-musicians as being characterized by the emergent nature of their information needs and the exploratory nature of their information practice. In particular, the user’s socio-musical world, learning or knowledge trajectories, as well as their modes of learning offer an innovative approach to understanding and anticipating music information needs.
Predicting Kinase Substrates using Conservation of Local Motif Density
Keywords: phosphorylation
cdk1

Short linear motifs (SLM) play critical roles in cell signaling and are associated with important biochemical events such as phosphorylation, glycosylation, and other post translational modifications. The primary aim of this thesis is to develop a new computational method (“ConDens”) to predict kinase substrates by assessing the evolution of phosphorylation SLM’s in a novel manner. This method could predict yeast Cdc28 kinase substrates that were not confidently detected by several other prediction methods published in literature and was demonstrated to be generalizable to other kinases. Genome-wide predictions experiments with this method also revealed potentially interesting novel substrates of Mec1, Prk1, PKA, and CKII.
Aerodynamic Shape Optimization of a Blended-wing-body Aircraft Configuration
Keywords: aerodynamic shape optimization
blended-wing-body
computational fluid dynamics
computational aerodynamics
aerodynamics

Increasing environmental concerns and fuel prices motivate the study of alternative, unconventional aircraft configurations. One such example is the blended-wing-body configuration, which has been shown to have several advantages over the conventional tube-and-wing aircraft configuration. In this thesis, a blended-wing-body aircraft is studied and optimized aerodynamically using a high-fidelity Euler-based flow solver, integrated geometry parameterization and mesh movement, adjoint-based gradient evaluation, and a sequential quadratic programming algorithm. Specifically, the aircraft is optimized at transonic conditions to minimize the sum of induced and wave drag. These optimizations are carried out with both fixed and varying airfoil sections. With varying airfoil sections and increased freedom, up to 52% drag reduction relative to the baseline geometry was achieved: at the target lift coefficient of 0.357, a drag coefficient of 0.01313 and an inviscid lift-to-drag ratio of 27.2 were obtained.
Criminalization of Marital Rape in Kenya
Keywords: Marital Rape
Kenya
Criminalization

Marital rape is not a criminal offence in Kenya. This thesis argues that criminalization of marital rape in Kenya is a necessary but insufficient means of addressing marital rape. I shall analyze the Kenyan legal framework and the international framework. The analysis of the international framework shall be focused on the Convention on the Elimination of all forms of Discrimination against Women (CEDAW). I shall undertake a comparative analysis of how South Africa and Zimbabwe have addressed marital rape. I will examine the benefits and limitations of criminal law in addressing marital rape. I will argue that an examination of the wrongful gender stereotypes of married women is essential to create effective and holistic remedies; that wrongful gender stereotypes of married women violate their rights to equality and non-discrimination and the right to be free from violence.
Oral Health-related Quality of Life in an Aging Canadian Population
Keywords: oral health-related quality of life
elderly
aging
seniors

The purpose of the study is to describe the impact of oral health-related quality of life (OHRQoL) on the lives of pre-seniors and seniors living in Nova Scotia, Canada. This cross-sectional study involved 1461 participants, grouped by age (pre-seniors [45-64] and seniors [65+]) and residential status (long-term care facility [LTC] or community). OHRQoL was measured using the 14-item Oral Health Impact Profile questionnaire. Approximately one in four pre-seniors and seniors reported at least one OHRQoL impact ‘fairly/very often’. Of those residing in the community, pre-seniors (28.8%) reported significantly more impacts than seniors (22.0%). Logistic regression revealed that for the community dwelling sample, those who were dissatisfied with their teeth or dentures were 5.16 times more likely to report an impact ‘fairly/very often’, which was the strongest indicator. Among the LTC sample, those who have poor perceived mouth health were 9.87 times more likely to report an impact.