VictorJuiz/thesis huggingface dataset:
Self-assembled Polymeric Nanoparticles for Targeted Delivery of Anticancer Drugs
Keywords: drug delivery
polymeric nanoparticle

Targeted delivery of drugs to specific regions of the body, or even to specific regions of the cell, promises enhanced drug efficacy and reduced systemic toxicity. By covalently coupling targeting ligands, the smart drug delivery systems are capable of targeting specific cell types exclusively through ligand-receptor interactions. The main goal of the project is to create a polymeric nanoparticle drug delivery system from synthesized biodegradable polymers and modify the polymeric nanoparticles using targeting antibodies for targeted delivery of anticancer drugs. A new biodegradable copolymer poly(2-methyl, 2-carboxy trimethylene carbonate-co-D,L-lactide)-graft-poly(ethylene glycol)-furan (poly(TMCC-co-LA)-g-PEG-furan) was synthesized and characterized. The copolymers self-assembled into spherical nanoparticles in aqueous environments with the hydrodynamic diameters controlled over a broad size range. Immuno-polymeric nanoparticles were created by coupling maleimide-modified anti-human epidermal growth factor receptor 2 (anti-HER2) antibodies to the self-assembled nanoparticles through Diels-Alder (DA) chemistry. This new coupling methodology was demonstrated to be relatively rapid, highly efficient and specific under mild conditions. In vitro studies showed that the immuno-nanoparticles bound specifically and efficiently with SKBR3 breast cancer cells that overexpress HER2 receptors. Anticancer drugs were incorporated into the immuno-nanoparticle system and the drug delivery via an antibody-mediated targeting mechanism was investigated in vitro. First, a protein anticancer drug, interleukin-2 (IL-2), was physically encapsulated through polymer-drug association. The IL-2 encapsulated anti-HER2 immuno-nanoparticles exhibited a cell-binding associated IL-2 release in the extracellular space upon binding with HER2-overexpressing SKBR3 breast cancer cells. Second, a small molecule hydrophobic drug, doxorubicin (DOX), was chemically conjugated on the nanoparticle surface after the antibody coupling, using the same DA chemistry. The novel formulation localized DOX in the cell nucleus of HER2-overexpressing SKBR3 breast cancer cells and remained the biological function of conjugated DOX. Compared to the nanoparticles bearing DOX or anti-HER2 antibody alone, the nanoparticles having a combination of DOX and anti-HER2 antibody exhibited the most significant cytotoxicity and specificity against SKBR3 cells relative to healthy HMEC-1 endothelial cells, demonstrating the potential of the DOX-immuno-nanoparticles as a novel platform for intracellular DOX delivery. This work provides a novel means for the delivery of combination immunotherapy/chemotherapy to more effectively treat certain malignancies.
Genetic and Chemical Genetic Analysis of the Cell Cycle
Keywords: cell cycle

Proper progression through the cell cycle is critical for cell growth and survival. Disruption of cell cycle progression can lead to cell cycle arrest and cell death. In addition, uncontrolled cell cycle progression can lead to cancer. Cells have evolved complex mechanisms to regulate each phase of the cell cycle to ensure proper cell cycle progression. In the presence of cellular stress, cells will respond promptly to arrest the cell cycle and allow repair. In order to study this complex process, it is important to identify the complete complement of proteins involved. I took two large-scale approaches to study the cell cycle. First, I down-regulated the majority of essential genes in Saccharomyces cerevisiae, and determined how depletion of individual gene product affected progression through the cell cycle. I determined that over 65% of essential genes I tested are most important at a specific cell cycle phase. In addition, I found that two genes, Smc4 and Cse1, have novel roles in S-phase of the cell cycle. In the second approach, I discovered two anti-proliferative compounds. Both compounds caused cell cycle delay in G1 phase of the cell cycle. Chemical genetic screens in yeast allowed me to determine the pathways most sensitive to each of these two compounds. By studying the response of cells to these compounds, I confirmed that compound 13 causes mitochondrial dysfunction in cells and compound 15 causes nuclear DNA damage. Furthermore, I found that both compounds are toxic in mammalian cells and that the responses that they elicit in mammalian cells are similar to those observed in yeast cells.
Probing Septin Function Through Interaction Screens: Identification of Novel Septins and Possible Regulatory Mechanisms
Keywords: septin, GTP, sperm, annulus, SUMO

Septins are a family of guanine nucleotide-binding proteins that function in eukaryotic cell division, where they form a high-order cortical structure at the site of division, which is essential in most eukaryotes. Expanded roles have evolved for septins in metazoans, where they also have essential functions in terminally-differentiated cell types, such as neurons and spermatozoa. Specific details of septin function are lacking in most roles described, due at least in part to the limited number of characterized binding partners. In this work, yeast two-hybrid screens and pull-downs from tissue homogenate were used to identify novel septin binding partners for subsequent characterization. The neuron-enriched septin, SEPT5, interacted directly with SUMO E3 ligases of the PIAS family. However, I was not able to demonstrate endogenous sumoylation of SEPT5 and SUMO isoforms did not concentrate with the septins during cytokinesis. SEPT5 also interacted with a novel septin, SEPT12, which I further characterized to be testis-specific and localized to the annulus in mature spermatozoa. Further, using SEPT12-specific reagents, I determined that the annulus forms via sequestration and subsequent segregation from the Golgi during spermiogenesis. SEPT9 pull-downs identified another novel testis-specific septin, SEPT14. Reagents specific to SEPT2 and SEPT9 also revealed a septin-rich structure in the seminiferous epithelium in close association with the ectoplasmic specialization. The specific role of septins in this structure awaits further characterization. Several other intriguing candidate septin-interaction partners were identified and the further study of their possible in vivo interaction with septins may provide substantial insight into the mechanisms of septin function in eukaryotes.
The Role of Ligand Induced Stabilization in the Allosteric Mechanism of Tetracycline Repressor
Keywords: TetR
allostery
tetracycline
stabilization

Allosteric regulation of proteins by reversible ligand binding is essential for regulation of fundamental biological processes. The mechanism by which a binding event alters the function of a distant site in a protein is only poorly understood. In this thesis, I use the Tetracycline Repressor (TetR) as a model system to study ligand induced allostery. The transcription of genes encoding the resistance to the antibiotic, tetracycline (Tc), is repressed by TetR, which is a homodimeric alpha-helical protein possessing a small N-terminal DNA binding domain (DNB domain) and a larger C-terminal tetracycline binding and dimerization domain (TBD domain). Based on previous structural and thermodynamic studies, the DNB domains are thought to exist in two stable, distinct conformations. One conformation is able to bind the Tc resistance operator sequence (tetO) with high affinity, while the other, which is induced by Tc binding, binds very weakly. While most previous studies on TetR have focused on the effects of Tc binding on the DNB domain conformation, here I have investigated the role of the DNB domain in modulating Tc binding. By introducing destabilizing mutations into the DNB domain I ascertained that the conformation and stability of the DNB domain plays an important role in determining Tc binding affinity. I also discovered that in the absence of ligand, the DNB domain exists in an unstable and flexible state with respect to the TBD domain. However, Tc binding to the TBD domain stabilizes the DNB domain, causing it to fold cooperatively with the TBD domain. I have discovered that the behavior of previously isolated non-inducible mutants is caused by the inability of Tc to stabilize the DNB domain in these mutants. Furthermore, reverse TetR mutants, which bind DNA better in the presence of Tc have an unfolded DNB domain that is only partially stabilized by Tc binding. My work suggests a new comprehensive, Tc induced stabilization and domain cooperativity model that can describe the mechanism of allostery in TetR and previously unexplainable mutants. A practical outcome of this research is the creation of a Tc induced folding switch that can be exploited to control the in vivo degradation of a protein of interest.
Airfoil Optimization for Unsteady Flows with Application to High-lift Noise Reduction
Keywords: unsteady discrete adjoint
unsteady optimization
hybrid acoustic predictions
computational fluid dynamic
airframe-generated noise
optimal control
gradient-based optimization
Ffowcs Williams and Hawkings equation

The use of steady-state aerodynamic optimization methods in the computational fluid dynamic (CFD) community is fairly well established. In particular, the use of adjoint methods has proven to be very beneficial because their cost is independent of the number of design variables. The application of numerical optimization to airframe-generated noise, however, has not received as much attention, but with the significant quieting of modern engines, airframe noise now competes with engine noise. Optimal control techniques for unsteady flows are needed in order to be able to reduce airframe-generated noise. In this thesis, a general framework is formulated to calculate the gradient of a cost function in a nonlinear unsteady flow environment via the discrete adjoint method. The unsteady optimization algorithm developed in this work utilizes a Newton-Krylov approach since the gradient-based optimizer uses the quasi-Newton method BFGS, Newton's method is applied to the nonlinear flow problem, GMRES is used to solve the resulting linear problem inexactly, and last but not least the linear adjoint problem is solved using Bi-CGSTAB. The flow is governed by the unsteady two-dimensional compressible Navier-Stokes equations in conjunction with a one-equation turbulence model, which are discretized using structured grids and a finite difference approach. The effectiveness of the unsteady optimization algorithm is demonstrated by applying it to several problems of interest including shocktubes, pulses in converging-diverging nozzles, rotating cylinders, transonic buffeting, and an unsteady trailing-edge flow. In order to address radiated far-field noise, an acoustic wave propagation program based on the Ffowcs Williams and Hawkings (FW-H) formulation is implemented and validated. The general framework is then used to derive the adjoint equations for a novel hybrid URANS/FW-H optimization algorithm in order to be able to optimize the shape of airfoils based on their calculated far-field pressure fluctuations. Validation and application results for this novel hybrid URANS/FW-H optimization algorithm show that it is possible to optimize the shape of an airfoil in an unsteady flow environment to minimize its radiated far-field noise while maintaining good aerodynamic performance.
The Public Life of Older People: Neighbourhoods and Networks
Keywords: healthy aging
geographical gerontology
aging in place
social networks

Preserving and improving the health and well-being of older people is a significant public health issue of the 21st century. The increased attention to the promotion of health in old age has given rise to an extensive body of literature on the subject of “healthy aging” – a discourse dedicated to understanding the multidimensional factors associated with aging and health and the application of this knowledge. Adopting a place-based, qualitative approach, this dissertation addresses key gaps in the healthy aging literature. The public life of older people aging in place was examined to understand how neighbourhoods, as important physical and social places of aging, contribute to the well-being and healthy aging of older people. This dissertation employed a critical geographical gerontology research framework and a methodology called ‘friendly visiting’ which combines ethnography, narrative and case study research and utilizes participant observation, visual methods and interview techniques. The qualitative data were analyzed using grounded theory and an adapted coding strategy that integrated the textual, visual, and auditory data. The analysis process highlighted theoretically-informed themes that characterized participant’s perceptions and experiences of their neighbourhoods. Findings reveal neighbourhoods are important places of aging that impact the well-being of older people aging in place. This dissertation provides insight into the micro-territorial functioning of neighbourhoods for older people. Embedded within these environments are key sites for informal public life called third places (e.g., parks, streets and coffee shops). Third places are important material and social places for older populations. Preparing for, journeying to, and engaging in these public sites promotes healthy aging by providing opportunities for engagement in life and facilitating social networks. Results advance healthy aging and aging and place research, contribute to gerontological and geographical methodologies, and have implications for policy and practice in areas such as health promotion and age-friendly community initiatives.
Against Modalities: On the Presumed Coherence and Alleged Indispensability of Some Modal Notions
Keywords: Modalities
Transworld Identity Problem
Natural Kinds
Essentialism

Part I investigates the idea that kinds (as opposed to individuals) have some modal properties. I argue that concerning typical kind-essentialist claims there is a non-trivial question—the transworld identity problem—about what the relevant kind terms are supposed to refer to in non-actual possible worlds. I reject several ideas for solving the problem. The upshot is a worry about the coherence of modal talk concerning kinds. Waiving this worry for the sake of argument, in Part II the target is the use of modal talk in the sciences. I offer a deflationary account of modalities, based on the familiar idea of reducing modalities to logical relationships between non-modal statements and non-modal background theories. I argue that this account is adequate for making sense of modal talk in the sciences. Moreover, I argue that irreducible modal properties of the world, if there are any, cannot be scientifically discovered or inferred. Thus we have a number of arguments against modalities: the threat of incoherence, their epistemic inaccessibility, and the dispensability of modal talk in the sciences.
Belief Internalism
Keywords: Belief
Motivational Internalism
Humean Theory of Motivation
Morality

I defend a version of cognitivist motivational internalism which I call belief internalism. The constitutive claim of any version of cognitivist motivational internalism is that moral belief entails motivation. But, while this internalist thesis captures the practical nature of morality, it is in tension with the dominantly held Humean theory of motivation. The constitutive claim of the Humean thesis is that no belief could entail motivation. In defence of this internalist it is tempting to argue either that the Humean constraint only applies to non-moral beliefs or that moral beliefs only motivate ceteris paribus. But, while succumbing to the first temptation places one under an ultimately insurmountable burden to justify the motivational exceptionality of moral beliefs, succumbing to the second temptation saddles one with a thesis that fails to do justice to the practical nature of morality. I avoid the temptation to defend this thesis in either of these flawed ways by defending a more radical departure from the Humean theory of motivation. I avoid the first temptation by arguing for a motivationally efficacious conception of belief. I start the defence by demonstrating that it is conceptually coherent for belief to entail motivation. I then argue that all beliefs have behavioural dispositional properties that are not predicated on desire; in particular, all beliefs can motivate assent without the assistance of a conceptually independent desire. I then develop a unified and inclusive account of cognitive motivation, according to which unqualified normative cognition—which includes moral cognition—motivates normative actions without the assistance of such a desire. Beliefs of the form ‘I ought to ф’, in other words, motivate the believer to ф. I avoid the second temptation by arguing that moral belief motivates simpliciter as opposed to ceteris paribus. There are, however, both commonsense and scientifically informed counterexamples which prima facie demonstrate that it is possible to both fully believe and fully understand one’s first person cognitive moral judgement and yet not motivated by that judgement. I argue that the commonsense prima facie counterexamples are not decisive; and I argue that the scientifically informed prima facie counterexamples misinterpret the empirical research on salient psychological conditions.
Aristotle's Ethics and the Crafts: A Critique
Keywords: Aristotle
Ethics
Crafts
Techne

This dissertation is a study of the relation between Aristotle’s ethics and the crafts (or technai). My thesis is that Aristotle’s argument is at key points shaped by models proper to the crafts, this shaping being deeper than is generally acknowledged, and philosophically more problematic. Despite this, I conclude that the arguments I examine can, if revised, be upheld. The plan of the dissertation is as follows – Preface: The relation of my study to the extant secondary literature; Introduction: The pre-Platonic concept of technē, as evidenced in Greek philosophical and literary sources, in particular the early Hippocratic corpus; Chapter one: The Platonic concept of technē, followed by an investigation of whether Plato affirms a virtue-technē in the Protagoras and Republic; Chapter two: Aristotle’s concept of technē, followed by scrutiny of his arguments in NE VI.5 against a virtue-technē, and of his analyses of slavery and deliberation; Chapter three: An exposition of Aristotle’s function argument, followed by a dominantist interpretation of it, and an explanation of dominantism as in part a technē-influenced doctrine; Chapter four: An examination of Aristotle’s ethical mean and its problems, with a diagnosis of these in terms of influence by the Philebus, and by paradigms derived from the crafts; Chapter five: Argument that Aristotle’s theory of habituation suffers from two significant opacities, these being a function of influence both by the Republic, and by models of craft-learning; Conclusion: Response to key objection; Aristotle’s ethics revised, defended.
The Effect of a Ketogenic Diet in the Treatment of Succinic Semialdehyde Dehydrogenase Deficiency in Mice
Keywords: ketogenic diet
epilepsy
succinic semialdehyde dehydrogenase
GABA metabolism

Succinic semialdehyde dehydrogenase (ALDH5A1) deficiency (SSADH-d) is an autosomal recessive, inborn error of gamma-aminobutyric acid (GABA) metabolism that results in psychomotor retardation, ataxia and seizures. A mouse model of SSADH-d (the Aldh5a1-/- mouse) was created to study the pathophysiology and treatment of SSADH-d. Aldh5a1-/- mice have psychomotor retardation and a progressive seizure phenotype results in death around P25. The present experiments tested the effects of a ketogenic diet in the treatment of Aldh5a1-/- mice. The KD was found to prolong the lives of Aldh5a1-/- mice by >300% while significantly delaying the onset the ataxia and preventing weight loss that is seen in untreated Aldh5a1-/- mice. Electrophysiological recordings revealed a corresponding decrease in seizures in KD fed mutants, as compared to control diet (CD) fed mutants. We assessed spontaneous miniature postsynaptic currents (mPSC) in CD and KD fed mutants. We found that CD fed mutants had significantly decreased inhibitory mPSC (mIPSC) activity compared to CD fed wildtype controls. mIPSC activity was restored in KD fed Aldh5a1-/- mice. A similar effect was found in [35S]TBPS binding experiments. TBPS binding was significantly reduced in CD fed Aldh5a1-/- mice, but restored in KD fed mutants. Plasma analysis revealed that an elevation of serum beta-hydroxybutyrate may play a role in the KD’s effects. The KD led to a significant elevation in the number of hippocampal mitochondria in mutant mice. Further, the KD was able to normalize the deficiencies in the hippocampal ATP levels seen in the Aldh5a1-/- mice. The present data suggest that the KD is able to significantly improve the Aldh5a1-/- phenotype. The effect of the KD on mIPSC activity is novel and furthers our understanding of how the KD may exert its effects. The mitochondrial studies confirm the findings of others, that the KD elevates the number of mitochondria. The KD also restores ATP deficiencies in Aldh5a1-/- mice, which is a novel finding. Together, these show that the KD may be an effective treatment for SSADH-d in humans. These data also further our understanding of the KD’s mechanisms of action.
H. pylori Infection in Ontario: Prevalence, Risk Factors and Effect on the Bioavailability of Vitamins E and C
Keywords: H. pylori

H. pylori has been classified by World Health Organization as type I carcinogen for its association with gastric cancer. Among its suggested pathological pathways is oxidative stress, which may reduce the bioavailability of dietary antioxidants. The main objectives of this thesis were to estimate the prevalence of H. pylori infection in Ontario and to assess its effect on the bioavailability of two main dietary antioxidants, vitamins E and C. To estimate the prevalence of H. pylori infection, a volume of 10 ul of plasma was aliquoted from stored blood of 1306 adults from Ontario. The blood samples belonged to controls of a population-based study of colorectal cancer. The overall weighted seroprevalence of H. pylori was 23.1% (95% CI: 17.7-29.5) with males having higher infection rates than females. Seroprevalence of the infection increased with age and number of siblings. Being non-white, born outside Canada and immigrating at an age greater than 20 years increased risk for H. pylori infection. An inverse association with seroprevalence was found for education and alcohol consumption. In order to investigate whether H. pylori positive compared to H. pylori negative subjects have lower changes in plasma concentrations of ascorbic acid and alpha tocopherol when supplemented with these vitamins, H. pylori negative (n=32) and H. pylori positive (n=27) volunteers received vitamin C (500 mg) and alpha tocopherol (400 IU) supplementation daily for 28 days. H. pylori infection status was determined by 13C urea breath test. Post supplementation plasma ascorbic acid and alpha tocopherol were significantly higher than pre supplementation concentrations in both groups. The changes in plasma ascorbic acid and alpha tocopherol were not significantly different between H. pylori negative and positive groups (ascorbic acid: 13.97±16.86 vs. 20.87±27.66, p=0.76; alpha tocopherol: 15.52±9.4 vs. 14.47±15.77; p=0.39 for H. pylori negative and positive groups respectively). The weighted seroprevalence of H. pylori infection was 23.1%. Age, sex, ethnicity, place of birth, age at immigration, education and alcohol consumption were factors associated with the infection prevalence in the population studied. In addition, we found no effect of H. pylori infection on the bioavailability of vitamins E and C.