VictorJuiz/thesis huggingface dataset:
Quantifying the Spatial Relationship between Landcover Hheterogeneity and Species' Distributions

Although considerable research has been invested in disentangling the factors limiting species’ ranges at local and continental spatial scales, less attention has been granted to the relationship between species’ spatial distributions and landscape attributes at intermediate spatial scales. This research investigates the spatial relationship between avian species’ distributions (Ontario Breeding Bird Atlas [2001-2005] data) and landcover heterogeneity (Ontario Land Cover [1991-1998] data) in terms of their respective boundary locations (i.e., high rates of change in landcover composition and avian species turnover) in a vulnerable transitional zone in southern Ontario. Significant spatial overlap was found between landcover and avian boundaries. Given that land management decisions are most often made at the regional or landscape scales, this positive spatial relationship has important implications for conservation efforts. Future research should focus on assessing the spatial relationship between landcover heterogeneity and avian species’ distributions for different functional and taxonomic groups.

Keywords: boundary analysis
species range
birds
spatial heterogeneity
conservation
Ontario
Advisor: Fortin, Marie-Josee
Automated Microfluidic Sample Preparation for Laser Scanning Cytometry

Laser scanning cytometry (LSC) is a slide-based method that is used clinically for Quantitative Imaging Cytometry (QIC). A “Clatch” slide, named after the inventor, which is used in conjunction with the LSC for immunophenotyping patient cell samples, has several drawbacks. The slide requires time consuming and laborious pipette steps, making the slide prone to handling errors. The Clatch slide also uses a significant amount of cell sample, limiting the number of analyses for fine needle aspirate (FNA) samples. This thesis details an automated microfluidic system, composed of an embedded circuit, a plastic and polymer microfluidic device, and an aluminum frame, which can perform the same immunophenotyping procedures. This new system reduces the labor from 36 pipette steps to 8, it reduces the amount of cell sample from 180 μL to 56 μL, and it shortens the entire procedure from 75 minutes to 42 minutes.

Keywords: microfluidics
laser scanning cytometry
automated
Advisor: Sun, Yu
An Investigation of the Exocyst Complex and its role in Compatible Pollen-pistil Interactions in Arabidopsis

Compatible interactions between male gametophytes (pollen) and the female reproductive organ (pistil) are essential for fertilization in flowering plants. Recognition at a molecular level allows “compatible” pollen grains to adhere/germinate on the stigma while pollen grains from unrelated plant species are largely ignored. The exocyst is a large eight subunit complex that is primarily involved in polarized secretion or regulated exocytosis in eukaryotic cells where it functions to tether vesicles to the plasma membrane. Recent research has implicated one of the Exo70 family members, Exo70A1, in compatible pollen-pistil interactions in Arabidopsis and Brassica. The loss of Exo70A1 in Arabidopsis Col-0 stigmas leads to the rejection of compatible pollen producing a “female sterile” phenotype. Through my research I have demonstrated that, driven by a stigma-specific promoter, an RFP:Exo70A1 fusion protein rescues this defect in exo70A1-1 mutant and Exo70A1 is found to be localized to the plasma membrane at flower opening.

Keywords: Exocyst Complex
Arabidopsis
Molecular signaling
Plant Reproduction
Pollen-Pistil Interactions
Compatibility
Self-Incompatibility
Exo70A1
Vesicle Trafficking
Docking Complexes
Brassica
Stigma
Papillae Cells
Advisor: Goring, Daphne
Effects of Rosiglitazone on Nitrolgycerin-induced Endothelial Dysfunction

Sustained nitroglycerin (GTN) therapy impairs endothelial function in healthy volunteers and patients with cardiovascular disease, caused by an increase in vascular oxidative stress. This study aims to estimate the effect of rosiglitazone on vascular endothelial function in healthy volunteers continuously dosed to transdermal GTN (0.6mg/hr) for 7 days. To assess endothelial function, forearm blood flow was measured by venous occlusion strain-gauge plethysmography in response to intra-brachial infusions of acetylcholine. GTN-treated subjects experienced significant attenuation of endothelium-dependent responses to acetylcholine (p<0.05; compared to placebo), but was reversed with vitamin C (p=ns; compared to placebo). Endothelium-dependent responses to acetylcholine were blunted in groups randomized to rosiglitazone alone (p<0.05; compared to placebo) and rosiglitazone + GTN (p<0.05 compared to placebo). Interestingly, this effect was not modified by vitamin C. In conclusion, rosiglitazone impairs endothelial function and concurrent therapy with rosiglitazone does not attenuate the adverse effects of transdermal GTN on the vasculature.

Keywords: rosiglitazone
endothelial dysfunction
Advisor: Parker, John
Ultrastructural and Histochemical Characterization of the Zebra Mussel Adhesive Apparatus

Since their accidental introduction into the Great Lakes in mid- to late-1980s, the freshwater zebra mussels, Dreissena polymorpha, have colonized most lakes and waterways across eastern North America. Their rapid spread is partly attributed to their ability to tenaciously attach to hard substrates via an adhesive apparatus called the byssus, resulting in serious environmental and economic impacts. A detailed ultrastructural study of the bysuss revealed a 10 nm adhesive layer at the attachment interface. Distributions of the main adhesive amino acid, 3,4-dihydroxyphenylalanine (DOPA), and its oxidizing (cross-linking) enzyme, catechol oxidase, were determined histochemically. It was found that, upon aging, DOPA levels remained high in the portion of the byssus closest to the interface, consistent with an adhesive role. In contrast, reduced levels of DOPA corresponded well with high levels of catechol oxidase in the load-bearing component of the byssus, presumably forming cross-links and increasing the cohesive strength.

Keywords: Zebra Mussel
Dreissena polymorpha
byssus
ultrastructure
bioadhesive
adhesive
3,4-dihydroxyphenylalanine
DOPA
TEM
transmission electron microscopy
bio-adhesive
catechol oxidase
immunogold labeling
histochemistry
histochemical methods
adhesive plaque
cryoultramicrotomy
TEM biological sample preparation
Advisor: Sone, Eli D.
Development of an Enzyme Immunoassay and Cellular Function Assays to Probe the Function of Teneurin C-terminal Associated Peptide (TCAP)

The teneurin C-terminal associated peptides (TCAP) are a family of four predicted peptides that are expressed in all metazoans where the teneurins have been studied to date. Of the four peptides, TCAP-1 has been studied most extensively. In vitro, TCAP-1 increases neuronal proliferation and neurite outgrowth. In vivo, the peptide reduces CRF-induced behavioural responses in rats. Despite the large body of evidence indicating a strong biological role for TCAP-1, little is known about the chemistry and solubility of the peptide, or the signaling pathway(s) mediating these effects. The aim of this research was to appropriately solubilize the peptide and to develop detection assays for its study in greater detail. I have now established an appropriate formulation of TCAP-1 and developed an immunoassay to assess its concentrations in tissues and in circulation. Also, by examining a number of transcriptional response elements, I have found two assays for probing the signal transduction mechanisms of this peptide.

Keywords: ELISA
reporter
TCAP
teneurin
cFos
solubility
solution
immunoassay
peptide
signal transduction
neuron
promoter element
Advisor: Lovejoy, David A.
Transparent Conductive Oxides for Organic Photovoltaics

Organic solar cells and organic light emitting diodes are on the forefront of emerging technologies aimed at harnessing light in ways never thought possible. Largear installations of OLED solid state lighting (SSL), as well as organic photovoltaics(OPVs), will become possible as the efficiencies of these devices continue to rise. All organic solar cells and OLEDs require the use of transparent conductive electrodes.Indium oxide (ITO) is currently the transparent conductor of choice for these applications, due to its unique combination of transparency, high conductivity, durability,and favourable surface properties. Indium, however, is a rare and expensive metal; proposed large-area installations of OPV cells and OLEDs will add further strain to global indium supply. Transparent conductive materials that are abundant, inexpensive, and which enable efficient and robust organic devices must therefore be developed. In the present work, suitable ITO anode replacement materials are demonstrated for OLEDS, small-molecule, polymer, and PbS colloidal quantum dot photovoltaics.

Keywords: organic electronics
transparent conductors
Advisor: Lu, Zhenghong
Optical and Structural Characterization of Amorphous Carbon Films

A fundamental study of the correlations between ion energy, substrate temperature, and plasma density with hydrogen content, percent sp2 bonding, optical gap, and refractive index of hydrogenated amorphous carbon (a-C) films is presented. A strong dependency between the ion energy used during deposition and the film’s microstructure is shown. Moreover, it is revealed that the optical properties of the a-C films are controlled by the concentration and size of sp2 clusters in the film. Through N2 mixing in the source gas, room-temperature nitrogen doped polymeric-like a-C films were demonstrated for the first time. X-ray Photoelectron Spectroscopy revealed an increase in the Fermi level of these films with increased nitrogen content. A proof-of-concept a-C based transparent heat mirror (THM) was demonstrated. It was shown that a-C acts as an oxygen-free protective barrier and anti-reflective coating for Ag films in the THM, increasing the transmission in the visible region by 10-20%.

Keywords: amorphous carbon
optical
Advisor: Kherani, Nazir P.
Zukotynski, Stefan
The Role of Rac1 and Rac2 in Determining Bone Quality in Aged and Osteoporotic Female Mouse Models

The osteoclasts, the bone cells responsible for bone degradation, have a crucial role in the age-related bone loss and post-menopause osteoporosis. Rac1 and Rac2, members of the Rho-family of small GTPases, are known for having a key role in osteoclast formation and activity, which could be translated to bone quality. In this study, we characterize the roles of Rac1 and Rac2 on bone quality using an aged and osteoporotic mouse model. Bones from wild type, Rac1KO and Rac2KO mice were harvested for mechanical tests, bone densitometry, micro-computed tomography and histomorphometric analyses to evaluate bone mineralization and architecture. We observed that the deletion of Rac1 or Rac2 in pre-osteoclasts minimized bone loss in both age-related and post-menopause osteoporosis. These results highlight the importance of the two small GTPases in bone remodeling and identify Rac1 and Rac2 as potential targets for the development of new therapies for the treatment of osteoporosis.

Keywords: Rac GTPases
bone remodeling
osteoclastogenesis
bone quality
Advisor: Glogauer, Michael
Grynpas, Marc D.
Fracture Resistance of Non-metallic Molar Crowns Manufactured with CEREC 3D

Objectives: To compare fracture strength and fatigue resistance of ceramic (ProCAD, Ivoclar-Vivadent)(C) and resin composite (Paradigm MZ100, 3M/ ESPE)(R) crowns made with CEREC-3D. Methods: A prepared ivorine molar tooth was duplicated to produce 40 identical prepared specimens made of epoxy resin (Viade). Twenty (C) crowns and 20 (R) were cemented to their dies using resin cement. Ten of each group were subjected to compressive loading to fracture. The remaining 10 of each group were subjected to mechanical cyclic loading for 500,000 cycles. The survivors were subjected to compressive loading to fracture. Results: No significant difference in mean fracture load was found between the two materials. However, only 30% of the (C) crowns vs. 100% of the (R) crowns survived the cyclic loading test. Conclusions: (R) crowns demonstrated higher fatigue Resistance than (C) crowns in-vitro and might better resist cracking in-vivo.

Keywords: CEREC 3D
Paradigm MZ100 crowns
ProCAD crowns
Composite resin crowns
Advisor: El-Mowafy, Omar
Ubiquitin Specific Protease 34 (USP34), a New Positive Regulator of Canonical Wnt/β-catenin Signalling

The Wnt pathway is a fundamental signalling pathway conserved in all animals, regulating growth, differentiation, embryonic development, and tissue homeostasis in adults. Wnt signalling is kept quiescent by ubiquitin-mediated degradation of the transcription factor β-catenin, orchestrated by a group of proteins called the Destruction Complex. Aberrant Destruction Complex activity is a common theme in many cancers, and is the primary cause of colon cancer. Through mass spectrometry analysis of Axin protein complexes (a key Destruction Complex component) we identified the deubiquitinating enzyme USP34 as an Axin-interacting protein. Functional studies showed USP34 functions to positively regulate Wnt signalling, acting downstream of β-catenin stabilization. While characterizing USP34 we also discovered a new positive regulatory role for Axin in promoting signalling that is dependent on its nuclear localization. Our results suggest that USP34 stabilizes the nuclear pool of Axin through regulating its ubiquitination and offers a potential strategy to target pathological Wnt signalling.

Keywords: wnt
usp34
dub
axin
ubiquitin specific protease
deubiquitinase
Advisor: Angers, Stephane
Measurements on Large-scale Peer-assisted Live Streaming: A Survival Analysis Approach

In large-scale peer-assisted live streaming systems with hundreds of online channels, it becomes critically important to investigate the lifetime pattern of streaming sessions to have a better understanding of peer dynamics. Aiming to improve performance of the P2P streaming systems, the goal of this thesis is twofold: 1) for popular channels, we wish to identify superior peers, that contribute a higher percentage of upload capacities and stay for a longer period of time; 2) for unpopular channels, we seek to explore factors that affect the peer instability. Utilizing more than 130 GB worth of run-time traces from a large-scale real-world live streaming system, UUSee, we conduct a comprehensive and in-depth statistical analysis. Using survival analysis techniques, we discover critical factors that may influence the longevity. Based on the Cox regression models we built, we also discuss several interesting insights from our measurement results.

Keywords: Measurement
Peer-to-Peer
Live Streaming
Survival Analysis
Advisor: Li, Baochun
Identification and Characterization of Interaction Partners of Drosophila cadherin 99C

Drosophila cadherin Cad99C is a critical regulator of follicle cell microvilli during Drosophila oogenesis. I extended the functional analysis of Cad99C by identifying Drosophila Myosin VIIA, and Cad74A and Cad87A, which are homologues of human Myosin VIIA and Cadherin 23, respectively, as components of the Cad99C protein complex and by studying their interactions in follicle cell microvilli. My co-immunoprecipitation data show that the cytoplasmic tail of Cad99C interacts with Myosin VIIA, and the extracellular cadherin repeats of Cad99C interact with Cad87A and Cad74A, independent of the cytoplasmic tail of Cad99C. Genetic studies indicate that 1) Cad99C and Cad74A/Cad87A localize independently to microvilli, although their amount is affected by changes in the ratio of their concentrations. 2) All cadherins affect microvillus morphology when overexpressed although the phenotypes are different. The overexpression effect of Cad74A depends on Cad99C but not vice versa. These data point to complex interactions between the microvillus cadherins.

Keywords: Biology
Development
Advisor: Godt, Dorothea
The Asian Renaissance: Reclaiming Centrality

With Asia’s (inclusive of Southeast Asia) re-emergence on the world stage, its civilization origins have become a subject of intense study. Three main value systems define Asian civilization—Confucianism, Taoism and Buddhism. Asians will derive inspiration from the past for the future, a similar phase the West underwent as it emerged from the medieval ages; hence the word 'renaissance' has been applied to Asia's re-emergence. Rediscovery of these heritages is a crucial part of the Asian renaissance. My thesis will expound the economic resurgence of the Asian nations, the emergence of Asian regional institutions and the emergence of an Asian ideology—Samagri.

Keywords: East Asia
Samagri
Renaissance
Economy
Ideology
Advisor: Falkenheim, Victor
Bridge System with Precast Concrete Double-T Girder and External Unbonded Post-tensioning

This thesis compares the consumption of primary superstructure material in a conventional single span CPCI system with those of double-T alternatives. The CPCI system is currently the preferred bridge type for short and medium spans in Canada, despite its relatively inefficient use of materials due to imperfect live load sharing among multiple parallel girders. The double-T alternatives utilize slender double-T cross-sections, fully precast segments, and post-tensioning in both longitudinal and transverse direction. The economy of the CPCI and double-T systems is compared within the framework of four sample designs. The results indicate that the double-T systems are in general more efficient than the CPCI system and have the potential to achieve better economy.

Keywords: Post-tensioned concrete bridges
External unbonded tendons
Double-T concrete girders
Short/medium-span bridges
Advisor: Gauvreau, Douglas Paul
Flow-based Organization of Perfusable Soft Material in Three Dimensions

This thesis presents a microfluidic strategy for the in-flow definition of a 3D soft material with a tunable and perfusable microstructure. The strategy was enabled by a microfluidic device containing up to fifteen layers that were individually patterned in polydimethylsiloxane (PDMS). Each layer contained an array of ten to thirty equidistantly spaced microchannels. Two miscible fluids (aqueous solutions of alginate and CaCl2) were used as working fluids and were introduced into the device via separate inlets and distributed on chip to form a complex fluid at the exit. The fluid microstructure was tuned by altering the flow rates of the working fluids. Upon solidification of alginate in the presence of calcium chloride, the created microstructure was retained and a soft material with a tunable microstructure was formed. The produced material was subsequently perfused using the same microfluidic architecture. The demonstrated strategy potentially offers applications in materials science and regenerative medicine.

Keywords: microfluidics
multilayer
3D
soft material
vascularized
perfusable
tunable
tissue engineering
Advisor: Guenther, Axel
Long-term Changes in Alveolarization in the Postnatal Rat Following Transient Inhibition of Early "Classical" Alveologenesis

Rationale: Activation of the platelet-derived growth factor receptors-α and -β (PDGF-Rα and -Rβ) is critical in the formation of secondary crests/septa during alveologenesis, and its regulation has been found to be disrupted in rat lung injury models. Objective: To determine whether the process of secondary septation can occur after transient pharmacologic inhibition of PDGF-R action during postnatal days (P)1 – 7 in rats. Hypothesis: The initial process of secondary crest formation is time-limited and, if missed, will result in a permanent loss of alveoli. Methods: Imatinib mesylate, a PDGF-R inhibitor, was injected intraperitoneally from P1 – 7. Pups were sacrificed on P2, 4, 8, 14, 28 and 65 for studies of alveolar development. Main results: The injection of imatinib inhibited PDGF-R action, resulting in a permanent decrease in alveolar number in treated rats. Conclusions: Inhibition of secondary septation during the first 7 days of life resulted in a decrease in alveolar number lasting into early adult life. This is consistent with a critical time window for secondary septation, which, if disrupted, results in long-term adverse effects on lung development.

Keywords: alveolarization
lung development
alveologenesis
secondary crests
septation
imatinib
Advisor: Tanswell, Keith
Interval and Continuous Exercise Elicit Equivalent Post- exercise Hypotension Despite Differences in Baroreflex Sensitivity and Heart Rate Variability

Equi-caloric bouts of interval (INT: 5x 2:2 min at 85 and 40% VO2max) and continuous (21 minutes at 60% VO2max) exercise were performed by 13 older prehypertensive males on separate days, at equivalent times of day, to assess the influence of exercise mode on post-exercise hypotension (PEH). Cardiovascular measures were collected for 30 min pre and 60 min post-exercise. PEH as measured by mean post-exercise systolic blood pressure (SBP) decrease, area under the SBP curve, and minimum SBP achieved, was equivalent after both conditions. SV was significantly reduced and HR was significantly elevated post-exercise after both conditions. No significant reductions in CO or TPR were observed. INT exercise provided a larger perturbation to the autonomic nervous system as measured by Baroreflex sensitivity and Heart Rate Variability. The responses elicited by acute INT exercise, with repeated exposure, may lead to greater improvements in blood pressure regulation than those associated with continuous aerobic training.

Keywords: Exercise
Blood Pressure
Heart Rate Variability
Post Exericse Hypotension
Hypotension
Interval
Intermittent
Baroreflex
Area Under Curve
Pre-Hypertension
Hypertension
Advisor: Thomas, Scott
Phenotypic and Functional Characteristics of the IgM-IgD+ Naive B Cell Population in SLE Patients

The presence of autoantibodies in systemic lupus erythematosus (SLE) suggests a breach of tolerance. Recently, the IgM-IgD+ naïve B cell population has been shown to be enriched for self-reactive cells that are anergic in healthy subjects. Therefore, to determine whether there is altered selection of self-reactive cells in SLE, this population was examined using multiparameter flow cytometry. SLE patients had increased proportions of IgM-IgD+ cells in mature and transitional B cell compartments that were activated as compared to controls. Comparison of mature and transitional IgM-IgD+ B cell proportions suggested altered selection between the transitional to mature stages in SLE. There was no correlation between altered B cell function or genetic polymorphisms in B cell signalling molecules and the expansion or activation of IgM-IgD+ cells. Thus, selection of self-reactive B cells appears to be abnormal in SLE, but this does not appear to result from altered responses to Ig crosslinking.

Keywords: B cell
Systemic Lupus Erythematosus
human
anergy
Advisor: Wither, Joan