VictorJuiz/thesis huggingface dataset:
Design of a Shape Optimized Metallic Nano-heater
Keywords: Photothermal
Shape optimization
Metal nanostructure

The absorption of the energy in the form of heat from electromagnetic radiation is strongly dependent on the shape of the surface. Also, the transfer of this generated thermal energy is dependent on the surface area of the object in contact with the surrounding medium. Here in this thesis, we present a structural optimization method for metal nanostructures based on the shape dependency of their electromagnetic heat dissipation and thermodynamic transfer to the surroundings. We have used a parallel genetic algorithm (GA) in conjunction with a coupled electromagnetic (FDTD) and thermodynamic modeling of the metallic nanostructures for the optimization. The optimized nano-structure demonstrates significant improvement in electromagnetic heating in the spectral window of optimization as well as expedited cooling properties. The symmetry of the structures which is inherent in the design procedure makes them independent of the polarization at normal incidence and insensitive to the azimuthal direction of incidence.
Tumor Gene Expression Purification Using Infinite Mixture Topic Models
Keywords: Bayesian methods
Gene expression purficiation
Bayesian Nonparametric
Topic models

There is significant interest in using gene expression measurements to aid in the personalization of medical treatment. The presence of significant normal tissue contamination in tumor samples makes it difficult to use tumor expression measurements to predict clinical variables and treatment response. I present a probabilistic method, TMMpure, to infer the expression profile of the cancerous tissue using a modified topic model that contains a hierarchical Dirichlet process prior on the cancer profiles. I demonstrate that TMMpure is able to infer the expression profile of cancerous tissue and improves the power of predictive models for clinical variables using expression profiles.
Vocal Frequency Estimation and Voicing State Prediction with Surface EMG Pattern Recognition
Keywords: vocal frequency
EMG
voicing state
respiration
prediction

Most electrolarynges do not allow hands-free use or pitch modulation. This study presents the potential of pattern recognition to support electrolarynx use by predicting fundamental frequency (F0) and voicing state (VS) from neck surface EMG and respiratory trace. Respiratory trace and neck surface EMG were collected from 10 normal, adult males (18-60 years old) during different vocal tasks. Time-domain features were extracted from both signals, and a Support Vector Machine (SVM) classifier was employed to model F0 and VS. An average mean-squared-error (MSE) of 8.21 ± 3.5 semitones2 was achieved for the estimation of vocal frequency. An average classification accuracy of 78.05 ± 6.3 % was achieved for the prediction of voicing state from EMG and 65.24 ± 7.8 % from respiratory trace. Our results show that pattern classification of neck-muscle EMG and respiratory trace has merit in the prediction of F0 and VS during vocalization.
Investigating the Use of Hair to Assess Polybrominated Diphenyl Ether (PBDE) Exposure Retrospectively, and in Male Infants with Genitourinary Tract Malformations
Keywords: environmental exposure
hair
polybrominated diphenyl ethers (PBDE)
genitourinary tract malformations
male reproduction
brominated flame retardants

Polybrominated diphenyl ethers (PBDEs) are synthetic chemicals that are added to a variety of consumer products as flame-retardants. The ubiquitous nature and endocrine disrupting properties of PBDEs are a public concern. A pilot study was performed to investigate whether in utero PBDE exposure, as measured in maternal hair, is associated with genitourinary tract malformations in male infants. In addition, we compared PBDE levels in maternal and infant hair and used segmental analysis to investigate how PBDEs varied along the shaft. Preliminary results suggest a trend toward an elevated PBDE body burden in mothers whose infants were born with genitourinary tract malformations; this was significant for some PBDEs. The sum of PBDEs (ΣPBDEs) in maternal hair did not correlate with infant hair levels; children had significantly greater levels. A significant increase in the ΣPBDEs was observed in distal hair suggesting hair PBDEs may be reflective of both internal and external exposure.
Targeting Aberrant STAT3 Signaling as a Therapeutic Strategy for Multiple Myeloma
Keywords: STAT3
Targeted therapeutics
Multiple Myeloma
Small molecule inhibitors

The oncogenic transcription factor STAT3 is aberrantly activated in over 70% of human tumours, including Multiple myeloma (MM). The present studies use both genetic and chemical tools to validate STAT3 as a therapeutic target, and demonstrate the anti-MM activity of a novel small molecule STAT3 inhibitor, BP-4-018. We show that shRNA-mediated STAT3 knockdown induces apoptosis in human myeloma cell lines (HMCLs). We translate these findings to a therapeutically relevant setting by demonstrating the broad anti-MM activity of BP-4-018 against HCMLs and primary patient samples, and demonstrate that BP-4-018 remains active against HMCLs co-cultured with bone marrow stroma. Inhibiting STAT3 via shRNA knockdown and BP-4-018 suppresses STAT3 transcriptional activity and down-regulates anti-apoptotic and proliferative STAT3 target genes. Finally, we show that BP-4-018 has activity in vivo, both alone and combined with subtherapeutic doses of bortezomib, without significant toxicities. Taken together, these data support the utility of STAT3 inhibitors for MM treatment.
Rosie - A Recovery-oriented Security System
Keywords: computer system
dependency analysis
recovery
computer security

Recovery is a time-consuming and computationally expensive operation. If an attacker can affect heavily-shared objects on the machine, then many other processes and files can be compromised from accessing them. This would greatly increase the recovery effort. Since intrusions start with a network connection, we argue that the integrity of heavily-shared objects should be protected from the network, in order to minimize the recovery effort. We discuss our prototype Rosie, which is designed with incident response and post-intrusion recovery in mind. Rosie predicts how heavily-shared each file or process is, based on the previous system activities observed. Rosie enforces appropriate mandatory access control and uses techniques such as sandboxing, in order to protect heavily-shared objects’ integrity. Rosie provides an important recovery guarantee that the maximum number of files need to be recovered is at most equal to the dependency threshold, a value that can be adjusted by a system administrator.
Exploring the Reactivity of S-cis-methylaziridine Aldehyde
Keywords: peptide macrocyclization
Ugi four component condensation

In 2006, an amphoteric molecule containing both an aldehyde and an unprotected amine was reported in the Yudin group by Dr. Ryan Hili. The unprotected aziridine aldehyde exists as homochiral dimers. Furthermore, due to the reversibility of the hemiacetal formation, the free aldehyde is available to undergo a wide array of reactions including an Ugi multicomponent reaction to give the final peptide macrocycle. Thus far, the mechanistic pathway involved in the Ugi reaction between S-trans aziridine aldehyde dimer and L-amino acids in the presence of tert-butyl isocyanide has given high diastereoselectivity whereas low diastereoselectivity is observed if the aziridine dimer is of the opposite stereochemistry. Herein, preliminary results show that a S-cis aziridine aldehyde with either a D or L-secondary amino acid gives high diastereoselectivity showing that the reaction is under Felkin-Ahn control.
Over the Hill and Under the Radar: Participation in Physical Activity of Older People at the St. George Campus of the University of Toronto
Keywords: older adult
physical activity

An examination of data from 21 older members of the University community aged 59 and older, including those who do and those who do not use the campus gyms, and six athletic programming staff from the two facilities to attempt to understand how older adults choose to negotiate their physical activity as they age. The study demonstrates that those respondents most comfortable in the gym spaces in the university setting are those who have occupied those spaces over many years, or those who have been habituated to gym culture through their activities outside the university setting. Using the ’mask of ageing theory’ in combination with Bourdieu’s concepts of habitus, capital and field, this study is an attempt to understand the individual and cultural practices that older adults engage in to manage their physical activities at the University, their other activities outside, as well as the performative aspects of their engagement.
Identification of Molecular and Functional Heterogeneity of Epithelial Progenitor Cells in the Upper Airway
Keywords: airway epithelium
lung progenitor cells

Upper airways are lined with a pseudostratified mucociliary epithelium maintained by basal cells. To investigate functional and phenotypic heterogeneity within the human basal cell compartment, we used a combination of limiting dilution assays and surface marker profiling on primary cultures of basal cells with verified progenitor activity. The limiting dilution assay suggested functional heterogeneity in the ability of basal cells to repopulate a filter and maintain a barrier at ALI. The frequency of cells with this activity varied between patient strains and ranged from 0.08%-1% of basal cells. Validation of large-scale comprehensive surface marker profiling on basal cells led to identification of 74 antigens demarking consistent subpopulations. Preliminary functional analyses suggest differences in differentiation potential of some subpopulations. This work supports the idea that the basal cell compartment may be functionally heterogeneous, and provides new molecular tools for interrogation of human basal cells.
Rspondin-1 Deficiency Enhances Beta Cell Neogenesis in a Murine Model of Diabetes
Keywords: Rspondin-1
beta-cell
neogenesis
apoptosis
diabetes

The cWnt activator, Rspondin-1 (Rspo1), has been identified as a regulator of β-cell growth and function, although its role in pathophysiological conditions such as streptozotocin (STZ)-induced diabetes is unknown. Hence, I hypothesized that Rspo1 deficiency stimulates β-cell neogenesis in STZ-diabetes. There was no difference in oral glucose handling between STZ-induced Rspo1mice, although, Rspo1-/- mice demonstrated increased insulin sensitivity compared to wild-type littermates. Moreover, β-cell mass and the total number of islets did not differ between STZ-induced Rspo1+/+ and Rspo1-/- mice, although mice with Rspo1 deficiency had reduced β-cell apoptosis and significantly enhanced numbers of insulin-positive ductal cells suggestive of β-cell neogenesis. Furthermore, the increased β-cell regeneration observed in knockout animals appeared to be associated with a more differentiated/mature β-cell phenotype in Rspo1-/- versus Rspo1+/+ mice. Collectively, these findings indicate a role for Rspo1 as a negative regulator of in vivo β-cell neogenesis and survival in the face of STZ-induced diabetes.
Organic Matter Biomarker Fingerprinting of Glacial Deposits
Keywords: organic matter biomarkers
glacial deposits
Oak Ridges Moraine
Hudson Bay Lowlands

The goal of this thesis was to test the applicability of biomarker analyses to better understand the glacial stratigraphic record of the Hudson Bay Lowlands and Oak Ridges Moraine. A biomarker analysis conducted on three geologic deposits from the Hudson Bay Lowlands showed that they can be differentiated based on organic matter (OM) inputs and stage of diagenesis, relating to paleoclimate and depositional environments. In the second study, a biomarker analysis was applied to samples from ten deposits in the Oak Ridges Moraine. These deposits were differentiated based on OM inputs relating to paleovegetation. Additionally, reincorporation and post-deposition alteration led to sample heterogeneity confirming the current understanding of glacial depositional processes and environments. This thesis shows that biomarker analyses can effectively differentiate and contextualize geologic deposits based on OM inputs and stage of diagenesis. This in turn will provide a more robust understanding of the stratigraphic record.
Evaluating Psychosocial Variables and their Link to Hypertension Using Mindfulness-based Stress Reduction
Keywords: Hypertension
Perceived stress
Anger
Mindfulness-based stress reduction
Ambulatory blood pressure monitoring

Previous research has reported positive associations between anger, perceived stress and blood pressure. These associations have largely been based on cross-sectional data and a small number of longitudinal works. Using a prospective longitudinal cohort design, this study more directly tested the relationships between anger, perceived stress and blood pressure by using a psychological therapeutic intervention (mindfulness-based stress reduction) to manipulate anger and perceived stress. Anger and perceived stress were in turn evaluated for association with blood pressure. Despite improvements in psychosocial functioning and reductions in blood pressure, findings from this study failed to demonstrate an association between change in anger or perceived stress with change in daytime or 24-hour ambulatory blood pressure. A model where these variables interact indirectly via stress coping mechanisms or health behaviours may be the linking mechanism in this study. Results from this thesis have contributed evidence to a divided field dominated by cross-sectional research.
Measurement of Spine Density in Mouse Models of Hypodopaminergia
Keywords: dopamine
medium spiny neurons
Parkinson's disease

Dopamine (DA) is a key catecholamine neurotransmitter involved in motor control, cognition, and neuroendocrine regulation. Reduced DA transmission is associated with Parkinson’s disease, depression, and anhedonia. An overexpression of the dopamine transporter in mice (DAT-tg) results in a 40% reduction in extracellular DA, and can be classified as a genetic model of hypodopaminergia. Reserpine treatment depletes extracellular DA, and is a pharmacological model of hypodopaminergia. The aim of this study was to determine morphological and proteomic changes to medium spiny neurons (MSNs), which receive dopaminergic input, as a consequence of reduced DA transmission. To achieve this, MSNs were fluorescently labelled using a diolistics method and immunofluorescence. There were no observable changes to morphology or proteomic profile of MSNs in DAT-tg animals. Reserpine treatment resulted in reduced spine density in MSNs. DAT-tg animals may present a level of DA depletion that is below the threshold to induce morphological changes to MSNs.
The Comparative Performance of Micro- and Nano-topographically Complex Endosseous Implant Surfaces in Normoglycemic and Hyperglycemic Subjects
Keywords: Nano Surface
Mechanical Testing
Bone
Bone-bonding
Osteoconduction
Contact osteogenesis
de novo bone formation
Implant design
Titanium
Calcium phosphate
Hyperglycemia
Diabetes
Drill defect
Bone healing
Micro Surface
Surface topography

Endosseous implants have notably high success rates, yet a small percentage of implants still fail for unidentified reasons. Recent literature points to hyperglycemia, resulting from untreated or undiagnosed diabetes, as a possible contraindication in an otherwise apparently healthy population. To investigate the effect of surface design on peri-implant healing in the presence of hyperglycemia, STZ-treated rats were implanted with custom rectangular implants of two surface topographies: grit blasted (GB) and grit-blast with a calcium phosphate nanotopography (GB-DCD). Tensile testing was conducted at 5, 7, and 9 days post-operative. Results demonstrated hyperglycemia to delay early stages of the peri-implant healing. Contact osteogenesis was increased along the GB-DCD surface, even in an environment of uncontrolled hyperglycemia, and the GB-DCD surface outperformed the GB surface in both healthy and hyperglycemic animals, showing peri-implant bone matured more rapidly on nanotopographically complex surfaces, even in the presence of uncontrolled hyperglycemia.
A Holocene Paleolimnological Record from the Turkey Lakes Watershed Long-term Monitoring Site in Central Ontario, Canada
Keywords: paleoclimatology
diatoms
acidification
chrysophytes
climate change
multiple stressors
Algoma region
aquatic ecology

A Holocene lake sediment record spanning 7300 years from Wishart Lake, in the Turkey Lakes Watershed central Ontario, was produced to determine the main drivers of long-term change in the lake ecosystem. The mid-Holocene sediments are dominated by benthic diatoms, around 4000 yrs BP, diatoms in the genera Cyclotella and Tabellaria increase. Comparisons with nearby pollen records show that changes in local vegetation and diatom assemblages occurred synchronously, suggesting a response to nutrient changes caused by vegetation succession. The most recent sediments, dated using activity of 210Pb and the Ambrosia pollen rise, show increases in planktonic Cyclotella spp., particularly around the Ambrosia rise (1880 AD). Thus, the diatom changes in the recent sediments suggest a response to multiple stressors. However, due to some buffering capacity in watershed soil, recent acidification of the lake has not taken place despite nearby industrial air pollution, tracked since 1980 by an on-site monitoring program.
An Exploration of Cell Receptor Labeling via Dark Field Imaging and Quantifying Densely Bound SERS Labels via Raman Signal Strength
Keywords: nanoparticles
SERS
dark field imaging
diagnostic labels
electron beam patterning
plasmonics
Raman scattering
antibody targetting

Two experiments explore the application of plasmonic nanoparticles to cellular pathology. The first devised a platform by which gold-silver nanoparticles act as differentiable labels for cell surface receptors under dark field imaging. By conjugating particles of various constitutions with receptor-targeting antibodies, particles scatter characteristically according to their plasmon peak. The second experiment programmed receptor placement via the patterning of two substrates and used the binding of SERS nanoparticles to explore the quantification of such targets at high-density. On one substrate, anchor pairs established receptors at specified distances in order to define the relationship between scattering intensity and the distance between SERS particles. On the second, anchor regions are filled with increasing densities of receptors and the particle-saturated substrates are probed to relate scattering intensity to particle density. This should discover the density-threshold between linear and non-linear scattering and inform the quantification of particles in the exponential density regime.
Evaluation of the Toronto Palatal Lift Prosthesis for Patients with Hypernasal Resonance Disorders
Keywords: palatal lift
hypernasality
speech aid
velopharyngeal incompetence
velopharyngeal insufficiency
maxillofacial prosthetics
speech disorders
removable dental prosthetics

Statement of the problem. Hypernasality resulting from velopharyngeal insufficiency or incompetency is a resonance disorder that has negative consequences for speech production and intelligibility of afflicted individuals. Purpose. The purpose of this prospective study is to ascertain if a palatal lift prosthesis with a generic silicon velar lamina, termed the Toronto Palatal Lift Prosthesis (TPLP), can assist velopharyngeal valve function to reduce hypernasality in patients. Methods. A prospective study of six patients treated with the TPLP was compared by the outcome measures of nasalance scores, perceptual evaluations, and patient satisfaction to those obtained using a contemporary acrylic palatal lift prosthesis. Results. The six patients had varying degrees of reduction in hypernasality and acceptance of the TPLP. Conclusion. On the basis of this preliminary study on the TPLP it is possible to fabricate a palatal lift prosthesis with a generic silicon velar lamina that reduces hypernasality in select patients.
Aqueous Phase Photo-oxidation of Water Soluble Organic Compounds (WSOC): Kinetics, Mechanisms and Method Characterization
Keywords: atmospheric chemistry
organics
oxidation
aqueous phase
SOA
aerosols
mechanism
kinetics
CI-ToFMS
reagent ions
MBTCA
pinonic acid

The aqueous phase photo-oxidation of water soluble organic compounds (WSOC) extracted from α-pinene ozonolysis secondary organic aerosol (SOA) was investigated using high resolution time-of-flight chemical ionization mass spectrometry (CI-ToFMS). The results have shown that WSOC get more functionalized and fragmented as the reaction proceeds. The capabilities of three reagent ions, were assessed; specifically, (H2O)nH+ ionizes organic compounds with carbon oxidation state (OSC) ≤ 1.3, whereas CH3C(O)O- and I(H2O)n- ionize highly oxygenated organics with OSC up to 4, with I(H2O)n- showing more selectivity. The aqueous phase OH oxidation of cis-pinonic acid and tricarballylic acid (a surrogate for 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA), recognized as a tracer of α-pinene SOA) were also studied. The respective rate constants at 301 K were measured to be 3.4(±0.5)×10^9 M^-1s^-1 at pH=2 and 3.1(±0.3)×10^8 M^-1s^-1 at pH=4.6. This work also illustrates possible aqueous phase mechanism for MBTCA formation from cis-pinonic oxidation.
Analyzing Intact Meiocytes of Wild-type Arabidopsis thaliana and Meiotic Mutants, ahp2 and spo11-2-2, using Confocal Microscopy
Keywords: Arabidopsis
Confocal Microscope
ahp2
spo11

The purpose of this study was to assess the utility of confocal microscopy to examine nuclear organization and chromosome pairing for intact Arabidopsis male meiocytes. The efficiency of the confocal technique was evaluated by analyzing wild-type nuclei throughout meiosis. Early-mid leptotene meiocytes demonstrated the presence of several propidium iodide stained signals within the nucleolus prior to the onset of chromosome pairing in zygotene. Pachytene chromosomes were completely paired and were traced to confirm the Arabidopsis karyotype. Additionally, the confocal technique was employed on meiotic mutants, ahp2 and spo11-2-2, to characterize their meiotic defects. Leptotene ahp2 meiocytes and zygotene meiocytes in both meiotic mutants appeared normal. In contrast, pachytene meiocytes in ahp2 and spo11-2-2 mutants demonstrated a wide-spread lack of paired chromosomes. Despite this general lack of pairing, a small amount of chromosome pairing was detected on the short arms of NOR-bearing chromosomes 2 and 4 in ahp2 and spo11-2-2 mutants.
Functionalization of the Photonic Crystal Slab Biosensors
Keywords: photonic crystals
biosensing
surface chemistry
label-free sensing

This work describes the functionalization and testing of Si3N 4-based photonic crystal slabs (PCS) for label-free biosensing. PCS support optical resonance modes that are sensitive to the local re- fractive index. Knowing that surface binding events change the local RI, analyte binding to the activated sensor can be detected. Various functionalization recipes were tried, and one was preferred for the biosensing experiments due to its higher yield and uniformity. Additionally, thickness of the topmost sensor layer was studied to assess biosensor performance quantified through sensitivity metrics. On the systems level, a reusable clamping system and customized micro uidic channels were designed, fabricated, and implemented on the PCS biosensors to enable device refurbishment. Proof-of-principle biodetection experiments were carried out using the established functionaliza- tion protocol on the in-house fabricated PCS. Conjugation of streptavidin and bovine serum albumin to the sensor surface was observed through wavelength shifts of the resonant modes.