VictorJuiz/thesis huggingface dataset:
DescribeX: A Framework for Exploring and Querying XML Web Collections
Keywords: XML
Summaries
Framework
Semistructured
Web
XPath

The nature of semistructured data in web collections is evolving. Even when XML web documents are valid with regard to a schema, the actual structure of such documents exhibits significant variations across collections for several reasons: an XML schema may be very lax (e.g., to accommodate the flexibility needed to represent collections of documents in RSS feeds), a schema may be large and different subsets used for different documents (e.g., this is common in industry standards like UBL), or open content models may allow arbitrary schemas to be mixed (e.g., RSS extensions like those used for podcasting). A schema alone may not provide sufficient information for many data management tasks that require knowledge of the actual structure of the collection. Web applications (such as processing RSS feeds or web service messages) rely on XPath-based data manipulation tools. Web developers need to use XPath queries effectively on increasingly larger web collections containing hundreds of thousands of XML documents. Even when tasks only need to deal with a single document at a time, developers benefit from understanding the behaviour of XPath expressions across multiple documents (e.g., what will a query return when run over the thousands of hourly feeds collected during the last few months?). Dealing with the (highly variable) structure of such web collections poses additional challenges. This thesis introduces DescribeX, a powerful framework that is capable of describing arbitrarily complex XML summaries of web collections, providing support for more efficient evaluation of XPath workloads. DescribeX permits the declarative description of document structure using all axes and language constructs in XPath, and generalizes many of the XML indexing and summarization approaches in the literature. DescribeX supports the construction of heterogenous summaries where different document elements sharing a common structure can be declaratively defined and refined by means of path regular expressions on axes, or axis path regular expression (AxPREs). DescribeX can significantly help in the understanding of both the structure of complex, heterogeneous XML collections and the behaviour of XPath queries evaluated on them. Experimental results demonstrate the scalability of DescribeX summary refinements and stabilizations (the key enablers for tailoring summaries) with multi-gigabyte web collections. A comparative study suggests that using a DescribeX summary created from a given workload can produce query evaluation times orders of magnitude better than using existing summaries. DescribeX’s light-weight approach of combining summaries with a file-at-a-time XPath processor can be a very competitive alternative, in terms of performance, to conventional fully-fledged XML query engines that provide DB-like functionality such as security, transaction processing, and native storage.
Mechanisms of Channel Arrest and Spike Arrest Underlying Metabolic Depression and the Remarkable Anoxia-tolerance of the Freshwater Western Painted Turtle (Chrysemys picta bellii)
Keywords: anoxia
reptile
neuroscience
ischemia
facultative anaerobe
NMDA receptor
AMPA receptor
reactive oxygen species
ischemic preconditioning
mKATP channel
GABA
delta opioid receptor

Anoxia is an environmental stress that few air-breathing vertebrates can tolerate for more than a few minutes before extensive neurodegeneration occurs. Some facultative anaerobes, including the freshwater western painted turtle Chrysemys picta bellii, are able to coordinately reduce ATP demand to match reduced ATP availability during anoxia, and thus tolerate prolonged insults without apparent detriment. To reduce metabolic rate, turtle neurons undergo channel arrest and spike arrest to decrease membrane ion permeability and neuronal electrical excitability, respectively. However, although these adaptations have been documented in turtle brain, the mechanisms underlying channel and spike arrest are poorly understood. The aim of my research was to elucidate the cellular mechanisms that underlie channel and spike arrest and the neuroprotection they confer on the anoxic turtle brain. Using electrophysiological and fluorescent imaging techniques, I demonstrate for the first time that: 1) the α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor (AMPAR) undergoes anoxia-mediated channel arrest; 2) delta opioid receptors (DORs), and 3) mild mitochondrial uncoupling via mitochondrial ATP-sensitive K+ channels result in an increase in cytosolic calcium concentration and subsequent channel arrest of the N-methyl-D-aspartate receptor, preventing excitotoxic calcium entry, and 4) reducing nitric oxide (NO) production; 5) the cellular concentration of reactive oxygen species (ROS) decreases with anoxia and ROS bursts do not occur during reoxygenation; and 6) spike arrest occurs in the anoxic turtle cortex, and that this is regulated by increased neuronal conductance to chloride and potassium ions due to activation of γ–amino-butyric acid receptors (GABAA and GABAB respectively), which create an inhibitory electrical shunt to dampen neuronal excitation during anoxia. These mechanisms are individually critical since blockade of DORs or GABA receptors induce excitotoxic cell death in anoxic turtle neurons. Together, spike and channel arrest significantly reduce neuronal excitability and individually provide key contributions to the turtle’s long-term neuronal survival during anoxia. Since the turtle is the most anoxia-tolerant air-breathing vertebrate identified, these results suggest that multiple mechanisms of metabolic suppression acting in concert are essential to maximizing anoxia-tolerance.
Label-free Detection of Oligonucleotide Microarrays by the Scanning Kelvin Nanoprobe
Keywords: Kelvin probe
DNA
oligonucleotide
microarray

The Kelvin measurement is a sensitive and label-free method based on work function measurements. Work function, the minimum energy required to extract an electron from a metallic material, can be shifted by ionic charges and dipoles present on the surface. The scanning Kelvin nanoprobe (SKN), a probe-based microscopic imaging device, was used in the detection of work function changes induced by surface-immobilized oligonucleotide / DNA microarrays. The scanning Kelvin nanoprobe was able to study DNA microarrays smaller than 100 µm in size, produced with solution concentrations lower than 10 µmol/L. The limit of detection was estimated to be 15 ng DNA. Better than ± 10% relative variation was achieved for replicate spots. It was observed that higher surface densities of immobilized DNA molecules produced greater work function changes than lower surface densities. Surface saturation with increasing solution concentrations was observed as well. Also, longer strands of DNA produced greater work function changes than shorter strands. Statistical analysis of the results confirmed that non-complementary DNA strands could be differentiated from complementary strands by the Kelvin measurement. Single base mismatches on the complementary DNA strands were also detected by the Kelvin measurement. Different substrate materials were tested in the search for reliable and inexpensive sample slides with satisfactory DNA immobilization efficiency. Materials such as silicon wafers, gold-coated glass slides, gold-coated stainless steel slides, and gold compact discs (CD) were tested. A surface property comparison of gold-coated glass slides and compact discs was made by atomic force microscopy (AFM), and revealed very different microscopic features. The effect of cleaning on gold-coated glass slides was examined by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Technical improvements were made to the SKN equipment progressively. Several revisions to the tip holder design have been employed for better electromagnetic shielding, enhanced robustness and easier tip change. An older signal generator was replaced with a professional PC audio card to provide more stable signal and more convenient on-screen fine tuning, also at a reduced cost. The Labview-based controlling program has also been improved through multiple iterations.
MILATRAS: MIcrosimulation Learning-based Approach to TRansit ASsignment
Keywords: Public Transportation
Intelligent Transportation Systems
Microsimulation
Reinforcement Learning
Transit Assignment
Traveller Behaviour

Public transit is considered a cost-effective alternative to mitigate the effects of traffic gridlock through the implementation of innovative service designs, and deploying new smart systems for operations control and traveller information. Public transport planners use transit assignment models to predict passenger loads and levels of service. Existing transit assignment approaches have limitations in evaluating the effects of information technologies, since they are neither sensitive to the types of information that may be provided to travellers nor to the traveller’s response to that information. Moreover, they are not adequate for evaluating the impacts of Intelligent Transportation Systems (ITS) deployments on service reliability, which in turn affect passengers’ behaviour. This dissertation presents an innovative transit assignment framework, namely the MIcrosimulation Learning-based Approach to TRansit ASsignment – MILATRAS. MILATRAS uses learning and adaptation to represent the dynamic feedback of passengers’ trip choices and their adaptation to service performance. Individual passengers adjust their behaviour (i.e. trip choices) according to their experience with the transit system performance. MILATRAS introduces the concept of ‘mental model’ to maintain and distinguish between the individual’s experience with service performance and the information provided about system conditions. A dynamic transit path choice model is developed using concepts of Markovian Decision Process (MDP) and Reinforcement Learning (RL). It addresses the departure time and path choices with and without information provision. A parameter-calibration procedure using a generic optimization technique (Genetic Algorithms) is also proposed. A proof-of-concept prototype has been implemented; it investigates the impact of different traveller information provision scenarios on departure time and path choices, and network performance. A large-scale application, including parameter calibration, is conducted for the Toronto Transit Commission (TTC) network. MILATRAS implements a microsimulation, stochastic (nonequilibrium-based) approach for modelling within-day and day-to-day variations in the transit assignment process, where aggregate travel patterns can be extracted from individual choices. MILATRAS addresses many limitations of existing transit assignment models by exploiting methodologies already established in the areas of traffic assignment and travel behaviour modeling. Such approaches include the microsimulation of transportation systems, learning-based algorithms for modelling travel behaviour, agent-based representation for travellers, and the adoption of Geographical Information Systems (GIS). This thesis presents a significant step towards the advancement of the modelling for the transit assignment problem by providing a detailed operational specification for an integrated dynamic modelling framework – MILATRAS.
3D Finite Element Cosserat Continuum Simulation of Layered Geomaterials
Keywords: Cosserat continuum
finite element
anisotropy
layered geomaterial
micropolar theory
explicit joint
discrete element modelling

The goal of this research is to develop a robust, continuum-based approach for a three-dimensional, Finite Element Method (FEM) simulation of layered geomaterials. There are two main approaches to the numerical modeling of layered geomaterials; discrete or discontinuous techniques and an equivalent continuum concept. In the discontinuous methodology, joints are explicitly simulated. Naturally, discrete techniques provide a more accurate description of discontinuous materials. However, they are complex and necessitate care in modeling of the interface. Also, in many applications, the definition of the input model becomes impractical as the number of joints becomes large. In order to overcome the difficulties associated with discrete techniques, a continuum-based approach has become popular in some application areas. When using a continuum model, a discrete material is replaced by a homogenized continuous material, also known as an 'equivalent continuum'. This leads to a discretization that is independent of both the orientation and spacing of layer boundaries. However, if the layer thickness (i.e., internal length scale of the problem) is large, the classical continuum approach which neglects the effect of internal characteristic length can introduce large errors into the solution. In this research, a full 3D FEM formulation for the elasto-plastic modeling of layered geomaterials is proposed within the framework of Cosserat theory. The effect of the bending stiffness of the layers is incorporated in the matrix of elastic properties. Also, a multi-surface plasticity model, which allows for plastic deformation of both the interfaces between the layers and intact material, is introduced. The model is verified against analytical solutions, discrete numerical models, and experimental data. It is shown that the FEM Cosserat formulation can achieve the same level of accuracy as discontinuous models in predicting the displacements of a layered material with a periodic microstructure. Furthermore, the method is capable of reproducing the strength behaviour of materials with one or more sets of joints. Finally, due to the incorporation of layer thickness into the constitutive model, the FEM Cosserat formulation is capable of capturing complicated failure mechanisms such as the buckling of individual layers of material which occur in stratified media.
An Exploration of the Structural, Electronic, and Anion Binding Properties of 2-Indolylphosphines
Keywords: X-ray crystallography
Phosphines

2-Indolylphosphines are unique ligands which have the capability for further phosphine modification by introducing substituents on an indolyl nitrogen centre. Substituents can vary in electronics, sterics, chirality, and can contain amino or phosphino groups which result in a multidentate (P,N)- or (P,P)-2-indolylphosphine. X-ray crystallography was used predominantly to examine and analyze the structural features of 2-indolyphosphines and their metal complexes. While the cone angles could not be determined crystallographically, the sum of the <CPC bond angles provided some information on the steric crowding around a phosphorus atom in selected 2-indolylphosphines. The symmetric tris-2-(3-methylindolyl)phosphine demonstrated anion binding ability through its three indolyl NH sites. Titrations to a series of selected anions were carried out; it was determined that tris-2-(3-methylindolyl)phosphine binds to these selected anions in a 1 : 1 receptor to anion binding ratio. Crystal structures of the fluoride and acetate complexes confirm the binding stoichiometry, and demonstrate the cooperative interaction of all three indolyl NH sites with the anion guest. Synthetic routes to new anion receptors with three or two indolyl NH donors were explored. The second type yielded a molecular cleft that was used in anion binding studies. The net basicity of a 2-indolylphosphine was determined through formation of a Ni(CO)3L complex. Net basicity can be tuned by changing the substituents on phosphorus or on an indolyl nitrogen centre. The [Cu(tris-2-(3-methylindolyl)phosphine)(phenanthroline)]BF4 complex is a discrete ion pair complex, exhibiting coordination chemistry at the phosphorus centre of the phosphine, while simultaneously hydrogen bonding through the indolyl NH sites to the BF4- anion. Complexes of the type [Pd(L)Cl(mu-Cl)]2 were analyzed by crystallography and the effect of net basicity on Pd-P bond length examined. The solid-state structures of (P,N)- and (P,P)-2-indolylphosphines were evaluated. In general, the sum of the <CPC bond angles increased from the parent unfunctionalized 2-indolylphosphine. The metal complexes of (P,N)- and (P,P)-2-indolylphosphines were assessed by crystallography to find possible trends of trans-influence. Lastly, a tetradentate tripodal ligand was synthesized by furnishing diphenylphosphino substituents on the indolyl nitrogen centres of tris-2-(3-methylindolyl)phosphine. The coordination of the tetradentate tripodal ligand to Pt(II) or Rh(I) resulted in five-coordinate trigonal bipyramidal complexes.
Surface-attached Biomolecules and Cells Studied by Thickness Shear Mode Acoustic Wave Sensor
Keywords: analytical chemistry
chemical sensor
bioanalytical chemistry
acoustic wave biosensor

The thickness shear mode acoustic wave (TSM) sensor, operated in a flow-through format, has been widely used in bioanalytical research. My research is mainly focused on the study of surface-attached biomolecules and cells using the TSM sensor, including lesions in DNA, conformational change of calmodulin, as well as the properties and attachment of rat aortic smooth muscle cells. Aldehydic apurinic or apyrimidinic sites (AP sites) that lack a nucleobase moiety are one of the most common forms of toxic lesions in DNA. In this work, synthesized oligodeoxyribonucleotides containing one, two, or three abasic sites were hybridized to complementary sequences immobilized on the gold electrode of the TSM device by affinity binding. The influence of AP sites on local base stacking energy and geometry caused a dramatic destabilization of the DNA duplex structure, which was detected by the TSM sensor. The signals detected by TSM correlated well with the thermostability of DNA duplexes in solution. The results indicate that both the number of sites and their localization in the double-stranded structure influence the stability of a 19 b.p. duplex. TSM was also used to detect the binding of ions or peptides to surface-attached calmodulin. The interaction between calmodulin and ions induced an increase in resonant frequency and a decrease in motional resistance. In addition, these signal changes were reversible upon washing with buffer. The response was interpreted as a decrease in surface coupling induced by exposure of hydrophobic domains on the protein, and an increase in the length of calmodulin by approximately 3 Å. In addition, the interaction of the protein with peptide together with calcium ions was detected successfully, despite the relatively low molecular mass of the 2-kDa peptide. In addition, the attachment of smooth muscle cells to various surfaces has been monitored by TSM. These surfaces include laminin, fibronectin and bare gold. The results of these experiments in terms of changes of frequency (fs) and resistance (Rm) were analyzed. The responses of the surface-bound cells to the introduction of various ions, depolarisation events and damage subsequent to exposure to hydrogen peroxide were also observed. Morphological changes in the cells, as confirmed by atomic force microscopy and scanning electron microscopy, are correlated with results from the TSM sensor.
Surface Intermediates, Mechanism, and Reactivity of Soot Oxidation
Keywords: soot oxidation
TOFSIMS
particulate matter

Factors that may govern diesel particulate matter (DPM) oxidation at low temperatures (~200°C) were studied using reactivity and TP-ToFSIMS analysis. Best-case scenarios that give maximum gasification rates were determined for DPM impregnated with KOH and non-catalyzed DPM using temperature programmed oxidation and isothermal experiments. Conditions of intimate catalyst-carbon contact (K/C molar ratio=1/50) and high NO2 concentrations (1%) to improve the reactivity of the carbon reactive sites were unable to meet the steady state gasification rate needed for particulate filter regeneration for a modern diesel engine at 200°C. Oxygen-free thermal annealing (>500°C) caused reactivity losses of a maximum of 40% that correspond to changes to surface morphology and/or concentration of oxygen-containing functional groups. TP-ToFSIMS identified surface functional group changes with temperature on non-dosed and NOX pre-dosed (1.5%NO, 1%NO2, 4.5%O2, balance helium) diesel soot and sucrose char. Detailed analysis of the NOX dosed sucrose char spectra using both inspection and principal component analysis techniques revealed that the 1200 ion fragments created could be reduced to five sets of ions that are chemically and kinetically distinct. These sets presumably represent surface functional groups on the carbon. For example, Set IV may represent carboxylic acid, lactone, or carboxylic anhydride functional groups. Based on these results a mechanism for the surface reaction of NO2 with carbon under vacuum conditions was postulated. At temperatures less than 200°C the ion fragments contain primarily carbon-NO2 type ions. As temperature increases between 200 and 400°C the ion fragments are primarily carbon-NO and carbon-N type fragments. At higher temperatures (>500°C) the surface is enriched with nitrogen containing functional groups. A surface reaction mechanism is proposed where NO2 is bonded to an armchair site and with increasing temperatures and molecular rearrangements the N is incorporated into the carbon ring. The initial surface composition of NOx containing functional groups changes within the area of relevance of low temperature soot regeneration (i.e. between 25° and 200°C). Further studies are needed to understand the effect of N-incorporation on carbon reactivity. No rate processes either in reactor studies or based on surface functional groups met the rate criteria for low temperature DPM oxidation.