VictorJuiz/thesis huggingface dataset:
The Influence of Human Disturbance on Avian Frugivory and Seed Dispersal in a Neotropical Rainforest

Habitat loss and disturbance due to human activity are major causes of global biodiversity decline. Beyond outright species loss, one potential outcome is modification of species interactions that are integral to ecosystem functioning. To investigate this possibility, I asked whether human activity influences avian frugivory and seed dispersal, bird-fruit interactions that facilitate plant reproduction. On Tobago (West Indies), I compared patterns of frugivory in three adjacent rainforest habitats along a gradient of increasing disturbance: primary forest in a reserve, unprotected intermediate forest outside the reserve, and nearby forest that was moderately disturbed by subsistence resource use. I assessed plant and bird community composition, seedling species, fruit removal, and bird fecal samples, to estimate human effects on seed dispersal and plant recruitment in this ecosystem. Disturbed forest had different species assemblages than primary forest, characterized by more light-demanding plants, more birds, and a shift in the relative abundance of avian feeding guilds: insectivores and frugivores declined, while nectarivores and omnivores increased. Canopy cover declined with disturbance; along with plant abundance, this explained much of the variation in bird species composition. The rate of avian fruit consumption in removal experiments varied considerably but tended to be highest in primary forest. Fecal samples showed that fruit composition of avian diets also varied with disturbance; birds captured in disturbed forest consumed more seeds from light-demanding plants. Seeds in the samples provided evidence of some seed transfer between habitats—from disturbed forest into the reserve and vice versa. Seedling composition was consistent with plant species fruiting in the same study plots, and illustrated some successful recruitment of light-demanding plants in primary forest and shade-tolerant plants in disturbed forest. Notably, the plant community of intermediate forest was more similar to disturbed than primary forest. This suggests that habitat adjacent to areas of human activity can be susceptible to ecological change, even though it does not experience the same direct disturbance. In summary, the unprotected portion of Tobago’s rainforest has a markedly different plant and bird community than the forest reserve, and my results indicate that avian frugivory and seed dispersal can be influenced by moderate human activity.

Keywords: Ecology
Tropical Biology
Conservation Biology
Advisor: Rodd, F. Helen
Diversity of Pseudomonas aeruginosa Type IV Pilins and Identification of a Novel D-arabinofuranose Post-translational Modification

The opportunistic bacterial pathogen Pseudomonas aeruginosa uses type IV pili (T4P) for adherence to, and rapid colonization of, surfaces via twitching motility. T4P are formed from thousands of pilin (PilA) subunits. Two groups of P. aeruginosa pilins were described previously (I and II), distinguished by protein length and sequence. PilA_I was glycosylated with an O-antigen subunit through the action of PilO/TfpO, encoded downstream of pilA_I. To determine if additional pilin variants existed, analysis of the pilin locus of >300 P. aeruginosa strains from a variety of environments was conducted. Three additional pilin alleles were discovered, each of which was invariantly associated with a unique, previously unidentified, downstream gene(s): pilA_III+tfpY, pilAIV+tfpW+tfpX, pilA_V+tfpZ. This survey also revealed that strains with group I T4P were more commonly associated with respiratory infections than strains with other pilins, suggesting that glycosylated T4P may confer a colonization advantage in this environment. The newly identified group IV pilin, represented by strain Pa5196, migrated aberrantly through SDS-PA gels, suggesting it was also glycosylated, a hypothesis confirmed by periodic acid-Schiff staining and mass spectrometry (MS) analyses. Disruption of Pa5196 O-antigen biosynthesis did not prevent the production of glycosylated pilins, demonstrating that these pilins were modified in a novel manner, unlike group I pilins. Using MS, nuclear magnetic resonance spectroscopy and site-directed mutagenesis, the Pa5196 pilins were shown to be uniquely modified with homo-oligosaccharides of mycobacterial-like α-1,5-D-arabinofuranose at multiple locations. Residues Thr64 and Thr66, located on the αβ-loop region of the protein, appear to be the preferred, but not exclusive sites of modification, each being modified with up to four D-Araf sugars. This region of the pilin is partially surface-exposed in the pilus, therefore modification of these sites may influence the surface chemistry of the fibre. Residues Ser81, Ser82, Ser85 and Ser89, located in the β-strand region, were also modified, mainly with mono- and disaccharides. Bioinformatic analyses and mutagenesis of TfpW suggest that this novel protein is an arabinosyltransferase necessary for PilA_IV modification. This research has increased our understanding of the complexity of this virulence factor, and may aid in development of new therapeutics for P. aeruginosa and mycobacterial infections.

Keywords: Pseudomonas aeruginosa
type IV pili
adhesion
bacterial protein glycosylation
arabinose
Mycobacteria
cystic fibrosis
diversity
mass spectrometry
TfpW
Advisor: Burrows, Lori
Cvitkovitch, Dennis
Design Guidelines for Reducing Redundancy in Relational and XML Data

In this dissertation, we propose new design guidelines to reduce the amount of redundancy that databases carry. We use techniques from information theory to define a measure that evaluates a database design based on the worst possible redundancy carried in the instances. We then continue by revisiting the design problem of relational data with functional dependencies, and measure the lowest price, in terms of redundancy, that has to be paid to guarantee a dependency-preserving normalization for all schemas. We provide a formal justification for the Third Normal Form (3NF) by showing that we can achieve this lowest price by doing a good 3NF normalization. We then study the design problem for XML documents that are views of relational data. We show that we can design a redundancy-free XML representation for some relational schemas while preserving all data dependencies. We present an algorithm for converting a relational schema to such an XML design. We finally study the design problem for XML documents that are stored in relational databases. We look for XML design criteria that ensure a relational storage with low redundancy. First, we characterize XML designs that have a redundancy-free relational storage. Then we propose a restrictive condition for XML functional dependencies that guarantees a low redundancy for data values in the relational storage.

Keywords: Databases
Design
Relational Databases
XML
Redundancy
Normalization
Advisor: Libkin, Leonid
Household Food Insecurity in Canada: An Examination of Nutrition Implications and Factors Associated with Vulnerability

Household food insecurity, defined as "the inability to acquire or consume an adequate diet quality or sufficient quantity of food in socially acceptable ways, or the uncertainty that one will be able to do so”, affected almost one in ten Canadian households in 2004. Responses have been dominated by community-based food initiatives with little attention paid to potential policy directions to alleviate this problem. The lack of impetus for policy responses may stem from the paucity of evidence documenting the nutrition implications of household food insecurity. Further, the development of policy interventions is hindered by a lack of understanding of the factors that influence vulnerability to food insecurity. This thesis comprises three studies aimed at providing stimulus and directions for policy responses to household food insecurity in Canada. The first study, an analysis of data from the 2004 Canadian Community Health Survey, documents poorer dietary intakes and heightened risk of nutrient inadequacies among adults and adolescents in food-insecure households, providing evidence of the public health implications and public policy relevance of household food insecurity. The second and third studies are examinations of household-level factors associated with vulnerability to household food insecurity. Analysis of data from the 2001 Survey of Household Spending demonstrates the relevance of housing costs to household food access. Among lower-income households, as the proportion of income allocated to housing costs increased, the adequacy of household food spending declined significantly. Receipt of a housing subsidy was associated with an improvement in food spending but mean food spending adequacy fell below the cost of a basic nutritious diet even among subsidized households. The final study comprises a cross-sectional survey of 464 low-income Toronto families, two-thirds of whom were food insecure over the preceding 12 months. Analysis of predictors of severe food insecurity highlights the centrality of income and housing costs and raises serious questions about current definitions of housing affordability and the adequacy of current housing subsidy levels. This work provides a public health imperative for action and points to the urgent need for social policy reform to ameliorate problems of household food insecurity in Canada.

Keywords: food security
nutrition
poverty
housing
Advisor: Tarasuk, Valerie
Exercise Training Attenuates Pancreatic β-cell Decompensation and Hepatic Inflammation in the Male Zucker Diabetic Fatty Rat

We hypothesized that with exercise training and the subsequent attenuation of hyperglycemia, β-cell adaptation to worsening insulin resistance would be maintained. Also, because classical stress-activated systems and oxidative stress are involved in hepatic insulin resistance we examined if exercise would be associated with improvements in hepatic markers of oxidative stress and inflammation. Exercise maintained fasted hyperinsulinemia and preserved normoglycemia in male Zucker diabetic fatty (ZDF) rats. β-cell function calculations indicate prolonged β-cell adaptation in exercised animals. Such improved β-cell function was associated with increased β-cell mass. Hypertrophy and replication contributed to expansion of β-cell mass; exercised animals had increased β-cell size and bromodeoxyuridine (BrdU) incorporation rates versus controls. Furthermore, we observed augmented β-cell-specific immunohistochemical staining of GLUT2 and Akt/PKB in exercised versus sedentary controls. We also observed large cytoplasmic ubiquitinated structures which form in response to oxidative stress in pancreatic tissue samples from hyperglycemic ZDF rats. In the exercised groups such aggregate numbers were reduced to numbers compared to those seen in younger non-diabetic basal ZDF animals and age-matched lean Zucker rats. With respect to the liver we investigated whether exercise alters kinases such as c-Jun NH2-terminal kinase (JNK) and IKKβ (as evidenced by IκBα levels) and related insulin receptor substrate-1 (IRS-1) serine phosphorylation which are associated with hepatic insulin resistance in obesity. On average, exercised animals ran 5250m/day which improved insulin sensitivity based on the homeostasis model assessment for insulin resistance (HOMA-IR) calculations, and maintained fed and fasted glucoregulation and glucose tolerance. Ten weeks of running decreased whole-body markers of inflammation and oxidative stress in the blood and in the liver. Exercise lowered circulating interleukin-6 (IL-6), haptoglobin, malondialdehyde (MDA) levels, and protein oxidation in the liver. Exercise reduced phosphorylated JNK (pJNK) indicating decreased JNK activity; in accordance serine phosphorylated IRS-1 was reduced in exercised rats. In conclusion, improvements in glucoregulation were associated with increased β-cell compensation at least in part due to a reduction in oxidative stress. Furthermore, we show exercise attenuates development of hyperglycemia in ZDF rats in association with decreases in plasma and hepatic markers of inflammation, oxidative stress, JNK activation, and serine phosphorylation of IRS-1.

Keywords: Diabetes
ZDF
Inflammation
JNK
Beta-Cells
Pancreas
Hepatic
Oxidative Stress
Advisor: Vranic, Mladen
Matthews, Stephen
Supervisory Hybrid Control of a Wind Energy Conversion and Battery Storage System

This thesis presents a supervisory hybrid controller for the automatic operation and control of a wind energy conversion and battery storage system. The supervisory hybrid control scheme is based on a radically different approach of modeling and control design, proposed for the subject wind energy conversion and battery storage system. The wind energy conversion unit is composed of a 360kW horizontal axis wind turbine mechanically coupled to an induction generator through a gearbox. The assembly is electrically interfaced to the dc bus through a thyristor-controlled rectifier to enable variable speed operation of the unit. Static capacitor banks have been used to meet reactive power requirements of the unit. A battery storage device is connected to the dc bus through a dc-dc converter to support operation of the wind energy conversion unit during islanded conditions. Islanding is assumed to occur when the tiebreaker to the utility feeder is in open position. The wind energy conversion unit and battery storage system is interfaced to the utility grid at the point of common coupling through a 25km long, 13.8kV feeder using a voltage-sourced converter unit. A bank of static (constant impedance) and dynamic (induction motor) loads is connected to the point of common coupling through a step down transformer. A finite hybrid-automata based model of the wind energy conversion and storage system has been proposed that captures the different operating regimes of the system during grid-connected and in islanded operating modes. The hybrid model of the subject system defines allowable operating states and predefines the transition paths between these operating states. A modular control design approach has been adapted in which the wind energy conversion and storage system has been partitioned along the dc bus into three independent system modules. Traditional control schemes using linear proportional-plus-integral compensators have been used for each system module with suitable modifications where necessary in order to achieve the required steady state and transient performance objectives. A supervisory control layer has been used to combine and configure control schemes of the three system modules to suite the requirements of system operation during any one operating state depicted by the hybrid model of the system. Transition management strategies have been devised and implemented through the supervisory control layer to ensure smooth inter-state transitions and bumpless switching among controllers. It has been concluded based on frequency domain linear analysis and time domain electromagnetic transient simulations that the proposed supervisory hybrid controller is capable of operating the wind energy conversion and storage system in both grid-connected and in islanded modes under changing operating conditions including temporary faults on the utility grid.

Keywords: hybrid control
wind energy
supervisory control
linear control
micro grid
battery storage
induction generator
wind turbine
finite hybrid automata
microgrid
Advisor: Iravani, Mohammad Reza
Something to Talk About: Applying the Unwritten Principle of Democracy to Secure a Constitutional Right to Access Government Information in Canada

Something to Talk About: Applying the Unwritten Principle of Democracy to Secure a Constitutional Right to Access Government Information in Canada by Vincent Clayton Kazmierski A thesis submitted in conformity with the requirements for the degree of Doctor of Juridical Science Faculty of Law University of Toronto 2008 ABSTRACT In this thesis, I argue that the unwritten constitutional principle of democracy provides a foundation for the recognition of a constitutional right to access government information in Canada. More specifically, I argue that the principle of democracy can be used to fill the “access gap” in the written provisions of the Constitution. I begin by synthesizing the Supreme Court of Canada’s jurisprudence and the work of a number of academics to outline guidelines for the recognition of unwritten constitutional principles. I also attempt to construct a coherent account of the content and effect of the constitutional principle of democracy. I proceed to argue that recognition of a right of access to government information as part of the principle of democracy fits within the guidelines I identify as it is supported by “strong” pragmatic, historical and structural evidence. I then demonstrate how the constitutional right of access to government information may be applied to protect access to information in at least three different ways: through statutory interpretation, through the regulation of administrative discretion, and, in exceptional circumstances, through the invalidation of legislation. I rely on the work of a number of British scholars and on aspects of David Dyzenhaus’s conception of law as a culture of justification to help bridge the divide between the Supreme Court of Canada’s approach to the application of unwritten constitutional principles and the concerns raised by critics of that approach. I argue that the application of the principle of democracy respects the primary role of democratically elected representatives of the public, while establishing that the judiciary also has an important role to play in the identification and enforcement of fundamental values. I suggest that this judicial role can be effectively constrained through the guidelines sketched by the Supreme Court and more fully articulated in this thesis. Finally, I argue that the application of the principle of democracy to invalidate legislation can also be justified in exceptional circumstances where the legislation imposes substantial impediments on fundamental aspects of the democratic process. In such cases, the principle of parliamentary supremacy is properly counterbalanced by the principle of democracy.

Keywords: constitutional law
access to information
unwritten
judicial review
principles
information
Canada
constitution
constitutional interpretation
democracy
parliamentary supremacy
Advisor: Weinrib, Lorraine
Preferential Allelic Expression of Genetic Information on Human Chromosome 7

Genes are typically expressed in equal amounts from both parentally inherited chromosomes. However, recent studies have demonstrated that genes can be preferentially transcribed from a locus. Non-random preferential expression of alleles can occur in a parent-of-origin pattern, known as imprinting, where epigenetic factors regulate their transcription. Alternatively, it can occur in a haplotype-specific pattern, where cis-acting polymorphisms in regulatory regions are thought to underlie the phenomenon. Both forms of unequal allelic expression have been associated with human disease. Consequently, it is important to identify genes subject to unequal allelic expression and characterize mechanisms that regulate differential transcription. This thesis presents the results of a screen for unequal allelic expression where approximately 50 murine transcripts homologous to genes on human chromosome 7 were analyzed. Human chromosome 7 was selected due to its association with several human disorders that show parent-of-origin effects. The screen identified non-imprinted preferential allelic expression in numerous transcripts and demonstrated that such patterns can occur in tissue specific patterns. Paraoxonase-1 (Pon1), a gene implicated in arthrosclerosis, was identified as having a dynamic pattern of allelic expression which varies throughout embryonic development. This finding represents the first report of a developmentally regulated pattern of allelic variance. Carboxypeptidase-A4 (Cpa4) was identified as having a tissue-specific imprinted pattern of expression, where the maternal allele was preferentially expressed in all embryonic tissues, with the exception of the brain. The Krüppel-like factor 14 gene (Klf14), a novel imprinted transcript, was found to have ubiquitous maternal expression in all human and murine tissues analyzed. A differentially methylated region, generally associated with imprinted transcripts, was not found in the gene’s CpG island, nor was a differential pattern of histone modifications identified. However, it was determined that maternal methylation regulates the transcript. The data in this thesis contribute to our understanding of the numerous patterns of allelic expression that exist in nature and the diverse mechanisms that regulate them. Ultimately, quantitative analyses of allelic expression patterns and the identification of their underlying genomic DNA sequences will become standard protocol in all biomedical studies.

Keywords: Gene Expression
Preferential Allelic Expression
Advisor: Scherer, Stephen W.
Toward More Efficient Motion Planning with Differential Constraints

Agents with differential constraints, although common in the real world, pose a particular difficulty for motion planning algorithms. Methods for solving such problems are still relatively slow and inefficient. In particular, current motion planners generally can neither "see" the world around them, nor generalize from experience. That is, their reliance on collision tests as the only means of sensing the environment yields a tactile, myopic perception of the world. Such short-sightedness greatly limits any potential for detection, learning, or reasoning about frequently encountered situations. In result these methods solve each problem in exactly the same way, whether the first or the hundredth time they attempt it, each time none the wiser. The key component of this thesis proposes a general approach for motion planning in which local sensory information, in conjunction with prior accumulated experience, are exploited to improve planner performance. The approach relies on learning viability models for the agent's "perceptual space", and the use thereof to direct planning effort. In addition, a method is presented for improving runtimes of the RRT motion planning algorithm in heavily constrained search-spaces, a common feature for agents with differential constraints. Finally, the thesis explores the use of viability models for maintaing safe operation of user-controlled agents, a related application which could be harnessed to yield additional, more "natural" experience data for further improving motion planning.

Keywords: motion planning
viability
safety enforcement
Advisor: Panne, Michiel van de