VictorJuiz/thesis huggingface dataset:
Embracing Incompleteness in Schema Mappings
Keywords: Data Integration
Data Exchange
Schema Mappings
Incompleteness
Skolem Functions
UnSkolemization
Vivification

Various forms of information integration have become ubiquitous in current Business Intelligence (BI) technologies. In many cases, the semantic relationship between heterogeneous data sources is specified using high-level declarative rules, called schema mappings. For decades, Skolem functions have been regarded as an important tool in schema mappings as they permit a precise representation of incomplete information. The powerful mapping language of second-order tuple generating dependencies (SO tgds) permits arbitrary Skolem functions and has been proven to be the right class for modeling many integration problems, such as composition and correlation of mappings. This language is strictly more powerful than the languages used in many integration systems, including source-to-target and nested tgds which are both first-order (FO) languages (commonly known as GLAV and nested GLAV mappings). An important class of GLAV mappings are Local-As-View (LAV) tgds, which has found important application in data integration. These FO mapping languages are known to have more desirable programmatic and computational properties. In this thesis, we present a number of techniques for translating some SO tgds into equivalent, more manageable FO schema mappings. Our results rely on understanding and controlling the presence of incompleteness in mappings. We show that the composition of LAV mappings is not only FO, but can always be expressed as a LAV mapping. As a byproduct, we show that the problem of recovery checking for LAV mappings becomes tractable, in contrast to the case of GLAV mappings for which it is known to be undecidable. We introduce two approaches for transforming SO tgds into equivalent nested GLAV mappings. Our approach considers the presence of source constraints, and provides sufficient conditions for when the rich Skolem functions in SO tgds are well-behaved and have an FO semantics. We experimentally show that these conditions are able to handle a very large number of real schema mappings. Last, we propose a first-step for embracing incompleteness in the context of BI applications. Specifically, we present elements of a formal framework for vivifying data with respect to a business model. We view the task of discovering data-to-business interpretations as one of removing incompleteness from these mappings.
The Pleiotropic Roles of FGLamide Allatostatins in the African Migratory Locust, Locusta migratoria
Keywords: Allatostatin
Neuropeptide
Gut physiology
Hormone release
Ion transport
FGLa/AST
muscle contraction
Locusta migratoria

The FGLa/ASTs are one family of allatostatin peptides and share an amidated C-terminal sequence (FGL-amide). The inhibitory effect of FGLa/ASTs on juvenile hormone (JH) biosynthesis in Diploptera punctata led to their discovery, but there is a lack of allatostatic function across most insect species that suggests this function may not be their primary role. Rather, the FGLa/ASTs are implicated as brain/gut peptides, modulating gut physiology. This thesis demonstrates the pleiotropic nature of FGLa/ASTs in Locusta migratoria and emphasizes the role of FGLa/ASTs as brain/gut peptides involved in homeostatic processes. FGLa/AST-like immunoreactivity (FLI) is associated with the corpus cardiacum (CC) and corpus allatum (CA). FGLa/ASTs increase adipokinetic hormone release from the CC and alter JH biosynthesis from the CA, suggesting roles in energy utilization and in growth and metamorphosis. Each region of the gut exhibits FLI. The gut is dually innervated: neurons in the abdominal ganglia of the central nervous system (CNS) innervate the posterior gut and some contain FLI, while neurons within the stomatogastric nervous system (STNS) that innervate the anterior gut do not seem to contain FLI, indicating that source of FLI on the gut are cells within the CNS, which may release FGLa/ASTs at the gut to alter aspects of gut physiology. FGLa/ASTs are involved in peristalsis, neural control of foregut contractions, and ileal K+ transport. In particular, FGLa/ASTs inhibit contractions of each gut region and also modulate the rhythmic motor output of a central pattern generator within the ventricular ganglion of the STNS. FGLa/ASTs also inhibit ileal K+ efflux, suggesting a diuretic action and implicating FGLa/ASTs in fluid and ion homeostasis. This work provides a comprehensive picture of how FGLa/ASTs play an integral role in nutrient processing, energy mobilization, and growth and metamorphosis to contribute to the overall maintenance of homeostasis. This reinforces the role of FGLa/ASTs as brain/gut peptides and emphasizes their involvement in the flexibility of nervous communication and integration of the endocrine system with the CNS to achieve homeostasis.
The Role of Fungal Stress Responses in Regulation of Azole Resistance
Keywords: antifungal
Candida albicans
Hsp90
acetylation

Fungal pathogens are a leading cause of human mortality, at least in part due to their ability to thwart therapeutic regimens by rapidly evolving resistance to antifungal drugs, and as a consequence of the increasing frequency of immunocompromised individuals most vulnerable to fungal infection. Candida albicans, the leading human fungal pathogen, has evolved an elegant repertoire of mechanisms to survive the cellular stress exerted by the azoles, which are the most widely deployed class of antifungals and inhibit ergosterol biosynthesis, inducing cell membrane stress. The evolution and maintenance of diverse resistance phenotypes is contingent upon cellular stress response circuitry, including that regulated by the molecular chaperone Hsp90 and its client protein calcineurin. My doctoral research focuses on three aspects of the role of fungal stress responses in regulation of azole resistance. First, I establish a novel role for nutrients and nutrient signalling in azole resistance of C. albicans and the model yeast Saccharomyces cerevisiae. Compromising a global regulator that couples growth to environmental cues, Tor kinase, provides a powerful strategy to abrogate fungal drug resistance with broad therapeutic potential. Second, I implicate the molecular chaperone Hsp90 as a key regulator of biofilm drug resistance in C. albicans. Compromising Hsp90 function transforms the azoles from ineffective to highly efficacious at eradicating biofilms in vitro and in vivo. Depletion of Hsp90 leads to reduction of client proteins’ calcineurin and Mkc1 in planktonic but not biofilm conditions, suggesting that Hsp90 regulates drug resistance through different mechanisms in these distinct cellular states. Third, I establish that inhibition of lysine deacetylases (KDACs) blocks the emergence and maintenance of Hsp90-dependent azole resistance in C. albicans and S. cerevisiae. S. cerevisiae Hsp90 is acetylated on lysine 27 and 270, and key KDACs for drug resistance are Hda1 and Rpd3. Compromising KDACs alters stability and function of Hsp90 client proteins, including drug resistance regulator calcineurin. Overall, this work provides novel insight into the mechanisms by which cellular stress responses mediate azole resistance, and establishes acetylation as a novel mechanism of post-translational control of Hsp90 function in fungi; ultimately, this unveils numerous targets that could be exploited for therapeutic benefit in the treatment of fungal disease.
Search for New Phenomena with the Mono-jet Signature, and a Direct Measurement of the Z Boson Invisible Width, with the ATLAS Detector at the CERN Large Hadron Collider
Keywords: ATLAS
LHC

A search for new physics in events with an energetic jet and large missing transverse momentum is performed with the ATLAS detector, using 2011 dataset corresponding to 4.7 fb−1 integrated luminosity. A model–independent approach is adopted, making predictions in various kinematic regions sensitive to potentially new physics scenarios. Data–driven background determination methods are developed to obtain robust predictions of the Standard Model expectations of the number of events in each probed kinematic region. No deviation from the Standard Model expectation is observed, and the results are hence interpreted in the context of the ADD scenario of Large Extra Dimensions, and pair production of WIMP dark matter candidates. This results in the world’s tightest constraints on the size of the D-dimensional Planck scale as the fundamental parameter of the ADD theory. The constraints obtained on Dark Matter suppression scale are stronger than those obtained from dedicated direct and indirect dark matter experiments for a large range of WIMP masses. Furthermore, data-driven estimates of various Standard Model processes contributing to the mono-jet final state allows a precise direct measurement of the invisible decay width of the Z boson. This results in a measurement at 5% precision level, comparable to the results of the L3 experiment, and better than all other LEP direct measurements.
Vaporized Perfluorocarbon Droplets as Ultrasound Contrast Agents
Keywords: ultrasound
contrast agents
perfluorocarbon droplets
vaporization
microbubbles
nonlinear imaging
medical imaging

Microbubble contrast agents for ultrasound are widely used in numerous medical applications, both diagnostic and therapeutic. Due to their size, similar to that of red blood cells, microbubbles are able to traverse the entire vascular bed, enabling their utilization for applications such as tumour diagnosis. Vaporizable submicron droplets of liquid perfluoro- carbon potentially represent a new generation of extravascular contrast agents for ultrasound. Droplets of a few hundred nanometers in diameter have the ability to extravasate selectively in regions of tumour growth while staying intravascular in healthy tissues. Upon extravasation, these droplets may be vaporized with ultrasound and converted into gas bubbles. In this thesis we argue that vaporized submicron perfluorocarbon droplets possess the necessary stability and acoustic characteristics to be potentially applicable as a new gener- ation of extravascular ultrasound contrast agents. We examine, separately, the ultrasound conditions necessary for vaporization of the droplets into microbubbles, the size and stability of these bubbles following vaporization, on timescales ranging from nanoseconds to minutes, and the bubbles’ acoustic response to incident diagnostic ultrasound. We show that submicron droplets may be vaporized into bubbles of a few microns in diameter using single ultrasound pulse within the diagnostic range. The efficiency of conversion is shown to be on the order of at least 10% of the exposed droplets converting into stable microbubbles. The bubbles are shown to be stabilized by the original coating material encapsulating the droplet precursors, and be stable for at least minutes following vaporization. Finally, vaporized droplets are shown to be echogenic, with acoustic characteristics comparable to these of the commercially available ultrasound contrast agents. The results presented here show that vaporized droplets possess the necessary stability properties and echogenicity required for successful application as contrast agents, suggesting potential for their future translation into clinical practice.
Computer Vision-based Solution to Monitor Earth Material Loading Activities
Keywords: Construction Management
Computer Vision
Automated Data Collection
Equipment Productivity

Large-scale earthmoving activities make up a costly and air-polluting aspect of many construction projects and mining operations, which depend entirely on the use of heavy construction equipment. The long-term jobsites and manufacturing nature of the mining sector has encouraged the application of automated controlling systems, more specifically GPS, to control the earthmoving fleet. Computer vision-based methods are another potential tool to provide real-time information at low-cost and to reduce human error in surface earthmoving sites as relatively clear views can be selected and the equipment offer recognizable targets. Vision-based methods have some advantages over positioning devices as they are not intrusive, provide detailed data about the behaviour of each piece of equipment, and offer reliable documentation for future reviews. This dissertation explains the development of a vision-based system, named server-customer interaction planner (SCIT), to recognize and estimate earth material loading cycles. The SCIT system consists of three main modules: object recognition, tracking, and action recognition. Different object recognition and tracking algorithms were evaluated and modified, and then the ideal methods were used to develop the object recognition and tracking modules. A novel hybrid tracking framework was developed for the SCIT system to track dump trucks in the challenging views found in the loading zones. The object recognition and tracking engines provide spatiotemporal data about the equipment which are then analyzed by the action recognition module to estimate loading cycles. The entire framework was evaluated using videos taken under varying conditions. The results highlight the promising performance of the SCIT system with the hybrid tracking engine, thereby validating the possibility of its practical application.
Truth, Justification, and Literary Merit
Keywords: aesthetics
philosophy of literature

This thesis develops and defends a new version of an old view known as literary cognitivism, which holds that the merit of a literary work as such sometimes depends on its cognitive merit. The newness of my view lies in the way it recommends we think about the cognitive merits of a literary work as they relate to its literary merits. Whereas some cognitivists identify the cognitive merit of a literary work with the truth of its themes and others with its capacity to provide certain non-propositional forms of knowledge, I propose that the cognitive dimension most relevant to literary value is the extent to which it provides certain forms of justification for its themes. In particular, I emphasize two ways in which a literary work can justify its themes: one, by providing evidence that its themes are the products of an intellectually virtuous mind and, two, by expressing its themes within a richly coherent framework of beliefs. I argue that the literary-evaluative significance of these two forms of justification is implicit, in the first case, in literary critical judgments that refer to a work’s didacticism, and, in the second case, in judgments that refer to a work’s thematic coherence. Insofar as it bears on these sources of justification, I contend, the truth or falsity of some non-thematic propositions can be relevant to literary value, though truth is generally not relevant at the thematic level.
Direct and Indirect Sources of Human Exposure to Perfluorinated Carboxylates: Investigating the Significance of Perfluorinated Carboxylate Reactive Precursor Metabolites
Keywords: Environmental Chemistry
Perfluorinated Carboxylates
Fluorotelomer
Reactivity
Biotransformation
Persistent

Perfluorinated carboxylates (PFCAs) are persistent and ubiquitous in the environment. Humans are exposed to PFCAs through direct and indirect sources, although the relative importance of each is uncertain. Direct sources of PFCAs have been attributed to two primary fluorochemical manufacturing processes: electrochemical fluorination (ECF) and telomerization. A focus of this thesis was to elucidate an additional direct source of PFCAs resulting from the direct fluorination of polyolefin materials. High density polyethylene bottles with varying levels of fluorination were observed to contain significant amounts of PFCAs, particularly those with carbon chain-lengths ≤ C6, marking an unexplored source of PFCA exposure. PFCAs are also produced indirectly from the biotransformation of fluorotelomer-based compounds, such as polyfluoroalkyl phosphate esters (PAPs) and fluorotelomer alcohols (FTOHs). During this transformation process, two predominant classes of metabolic intermediates are formed: the fluorotelomer unsaturated aldehydes (FTUALs) and the fluorotelomer unsaturated carboxylic acids (FTUCAs). Another focus of this thesis was to examine the reactivity of FTUALs and FTUCAs with endogenous nucleophiles such as glutathione (GSH), select amino acids, and model proteins. FTUALs formed adducts with all nucleophiles examined, where those having shorter carbon chain lengths (i.e. 6:2 and 8:2 FTUAL) were more reactive than longer carbon chains (i.e. 10:2 FTUAL). By contrast, FTUCAs had comparably limited reactivity; although FTUCAs showed mild reactivity with GSH, they did not react with any other nucleophiles. In vitro and in vivo experiments were carried out to determine the extent of protein binding formed from the biotransformation of fluorotelomer-based compounds, including the 8:2 FTOH and the 6:2 PAP diester. A significant portion of these biotransformations yielded covalent protein binding at nmol/mg protein concentrations. Protein adducts were observed predominantly in rat liver and also in plasma and kidney. The formation of reactive intermediates may be toxicologically important through protein deactivation. Cellular toxicity of FTUALs was significantly higher compared to PFCAs and the acid metabolic intermediates (i.e. FTUCAs). The EC50 values calculated from dose-response incubations were dependant on chain length and functional group. The work in this thesis examined an unexplored consequence of indirect exposure to PFCAs, potentially impacting the relative importance of PFCA exposure sources.
Towards a Structural and Methodological Improvement of Eutrophication Modelling
Keywords: Eutrophication Modelling
Bayesian

The credibility of the scientific methodology of mathematical models and their adequacy to form the basis of public policy decisions has frequently been challenged. Skeptical views of the scientific value of modelling argue that there is no true model of an ecological system, but rather several adequate descriptions of different conceptual basis and structure. The purpose of this work was to first advance the Bayesian calibration of process-based models for guiding the water quality criteria setting process in Hamilton Harbour, Ontario, Canada. The analysis suggests that the water quality targets for total phosphorus and chlorophyll a concentrations will likely be met, if the recommendation for phosphorus loading at the level of 142 kg day-1 is achieved. My dissertation also examines how the Bayesian approach can effectively support the decision making process by synthesizing the predictions of different models developed for the same system. The model averaging approach consolidates the finding that the existing total phosphorus goal is most likely unattainable. The discrepancy between the chlorophyll a predictions of the two models pinpoints the need to delve into the dynamics of phosphorus in the sediment-water column interface. This work also aims to examine statistical formulations that explicitly accommodate the covariance among the process error terms for various model endpoints. The analysis suggests that the statistical characterization of the model error can be influential to the inference drawn by a modelling exercise. Finally, my dissertation challenges the capacity of the ecological foundation of eutrophication models to predict the role of nutrient regeneration. It shows that the recycled nutrients can be significant drivers in low as well as in high-productivity ecosystems depending on the period of the year examined. My dissertation also discusses several prescriptive guidelines that should be helpful towards a structural and methodological improvement of eutrophication modelling.
Evaluating the Greenhouse Gas Mitigation Potential and Cost-competitiveness of Forest Bioenergy Systems in Ontario
Keywords: renewable energy
bioenergy
greenhouse gas emissions
carbon accounting
life cycle assessment
fossil fuels
natural gas
electricity
harvest operations
supply chain
Ontario
sustainable management
BiOS-Map
CBM-CFS3
GHGenius
cost
coal
climate change
biomass
forest residues
Gordon Cosens Forest
boreal forest

Recent literature has recommended that life cycle assessments (LCA) of forest bioenergy supply chains consider the impact of biomass harvest on ecosystem carbon stocks as well as the net emissions arising from combustion of various forms of biofuels compared with reference fossil fuel systems. The present study evaluated the magnitude and temporal variation of ecosystem C stock changes resulting from harvest of roadside residues and unutilized whole trees for bioenergy. The Carbon Budget Model (CBM-CFS3) was applied to the Gordon Cosens Forest, in northeastern Ontario, along with the Biomass Opportunity Supply Model (BiOS-Map), for cost analysis of different types of biomass comminution. Natural gas (NG) steam and electricity, grid electricity, and coal electricity reference systems were analyzed for a pulp and paper mill. The findings showed that the forested landscape becomes a net sink for carbon following the 20th year of roadside residue harvest, compared to whole-tree harvest, where the forested landscape remained a net source of carbon over the entire 100 year rotation. The cumulative ecosystem carbon loss from whole-tree harvest was 11 times greater compared to roadside residue harvest. BiOS-Map analysis suggested that due to technical and operational limits, between 55%-59% and 16%-24% of aboveground biomass was not recovered under roadside residue and whole-tree harvest respectively. The cost of delivering roadside residues was estimated at $52.32/odt–$57.45/odt, and for whole trees $92.63/odt–$97.44/odt. The Life Cycle Assessment (LCA) analysis showed break-even points of 25, 33 and 6 years for roadside residues displacing NG steam, NG electricity, and coal, respectively. No GHG reduction was achieved when forest biomass was used to displace grid electricity that is generated in Ontario. Whole-tree bioenergy resulted in no GHG reduction for NG displacement, and a break-even point of 70-86 years for coal. A net GHG reduction of 67% and 16% was realized when roadside residues and whole trees were used to displace coal, compared to 45% and 38% when roadside residues were used to displace NG steam and NG electricity, respectively. Therefore, it is recommended that bioenergy deployment strategies focus on the utilization of roadside residues, if the main goal is GHG mitigation.