VictorJuiz/thesis huggingface dataset:
Doxa versus epistêmê: a study in aristotle's epistemology and scientific thought

Despite the common view, and despite several passages from which it might have seemed to follow, Aristotle has not inherited Plato's epistemological position from the central books of the Republic regarding two fundamental differences between knowledge (epistêmê ) and opinion (doxa). According to Plato (1) whatever can be known cannot be opined and whatever can be opined cannot be known, and (2) only epistêmê can account for why things are so and so, whereas doxa can only state that they are so and so. The common view (that Aristotle shares both claims) is deeply rooted at least partly because in some central passages Aristotle shares Plato's position regarding the vagueness and instability of doxai concerning sensible particulars. However, when we examine carefully the passages in which Aristotle actually compares and contrasts ‘knowing’ with ‘opining’, we realize that he explicitly allows the possibility of opining necessary truths and says that doxa too should be explanatory. Aristotle's rejection of the Platonic position has a far-reaching philosophical significance. For Aristotle doxa, in the primary sense of this term, does not constitute a cognition of sensible particulars. It is a scientific, or rather a pre-scientific, view or doctrine concerning universal issues. Aristotle considers doxa a kind of incomplete knowledge that, even though imperfect, is often an indispensable scientific tool. This is why he examines on a regular basis the scientific views of his predecessors, whereas Plato hardly discusses them at all. Aristotle's conception of hypolêpsis is the result of his rejection of Plato's dichotomous position. In its generic meaning hypolêpsis is the faculty of which epistêmê, doxa, and phronêsis are the species. Thus, hypolêpsis, a term he may have invented himself, is Aristotle's answer to Plato's claim for incompatibility between knowing and opining. A historical review shows that this fundamental generic connotation of hypolêpsis has been overlooked, or dismissed at best, due to the fact that too often its meaning has been mistakenly identified as synonymous with doxa .
Constrained coding for long-haul fiber-optic systems

Current state-of-the-art long-haul lightwave communication systems operating at channel rates of 40 Gb/s or more are mostly limited by fiber nonlinearity. Nonlinear effects result in peculiar pattern-dependent interactions between optical pulses used for information transmission. Although pulses may interact in a different manner depending on the system design, this intersymbol interference cannot be overcome by simply increasing the signal power. On the contrary, it would only enhance the nonlinear effects and degrade the system performance even further. The method is applied to several channel models, both theoretical and practical. The most important of them are dispersion-managed soliton links and systems operating in the pseudolinear regime. The former are limited by pulse-to-pulse interactions, while the latter suffer from intrachannel four-wave mixing. In each case, a reasonable benchmark system is created first, and various related design aspects are discussed. It has been noticed that shorter optical pulses are generally less susceptible to intersymbol interference so a low duty cycle is preferable. Systems designed in such a way may have a lot of "white space" and are less attractive from the spectral efficiency point of view. For the constrained system, an ideal channel model is developed, and its connection with a physical fiber is established. Four particular runlength-limited coding schemes are constructed, and their performance is analyzed and compared against one another. Based on physical intuition and/or simulation results, specific properties that good codes must satisfy are pointed out. Most importantly, a potential improvement in channel capacity of up to 50% is demonstrated. In this work, it is shown that both problems can be solved by the application of constrained coding, an approach originally employed in magnetic recording systems. More specifically, certain constraints are imposed on transmitted sequences to increase the minimum pulse separation and mitigate the nonlinear interactions. Somewhat surprisingly, the data rate can be improved at the same time!An extension of this approach to multichannel long-haul systems is also considered in a separate chapter, and similar benefits are demonstrated with the help of numerical simulations.
Peer dialogue: cognitive and affective processes and outcomes in an adult EAP classroom

This study examined the nature of peer dialogue as students engaged in a self/peer transcribing task. Linguistic and socio-affective processes and outcomes including metatalk, were of particular interest. The participants were an ethnically mixed group of 14 adult ESL/EFL learners enrolled in an English for Academic Purposes program at a large Canadian university. Data included: audio-recorded pair interaction; jointly constructed transcripts; pre- and post-test scores; pre-and post-task interviews as well as a post-task questionnaire. As the instructor and the researcher of the study, I analyzed the quantitative and qualitative benefits of a collaborative transcribing task. The findings suggested that links can be made between learners' perceptions of pair work and the nature of their interactions as analyzed through language related episodes. Furthermore, peer dialogue, including metatalk, can create the conditions for learners to engage in cognitive processes involved in language learning.
Membranes and membrane proteins: Structure, function, and evolutionary insights

The crystal structure of the CorA Mg2+ transporter homologue from Thermotoga maritima has been solved in complex with 12 calcium ions. CorA reveals a pentameric assembly with a large cytoplasmic funnel domain and a smaller C-terminal transmembrane (TM) domain. An alpha/beta core structure is connected to the pore-lining helices; and these pore-lining helices are flanked by five additional TM helices. One metal is found near the universally conserved GMN motif, apparently stabilized within the TM region. Structural and biochemical data suggest that CorA may achieve specificity by requiring the sequential dehydration of substrates along the length of its sim;55 A long pore. Ten metal sites were identified within the funnel domain and are linked to long extensions of the pore helices. These sites have been characterized as an allosteric Mg2+-specific homeostatic molecular switch. A proteolytic protection assay, biophysical data, and comparison to a funnel domain structure from Archaeoglobus fulgidus has revealed the potential reaction coordinate for this diverse family of transport proteins. The rational and design of a semi-high throughput (HTP) procedure to screen for the expression, purification, and crystallization of prokaryotic integral membrane proteins (MPs) is presented. Upon implementation in a standard laboratory setting, two potential targets for structural analysis were immediately identified (i.e. crystallized). Crystal structures of the citrate and sn-glycerol-1-phosphate (G1P) complexes of (S)-3-O-geranylgeranylglyceryl phosphate synthase (GGGPS) from A. fulgidus have also been determined. GGGPS is a cytosolic protein that performs the committed-step in archaeal lipid biosynthesis, and it presents the first triose isomerase (TIM)-barrel structure with a prenyltransferase function. A novel modification to the canonical TIM-barrel fold suggests a model of enzyme adaptation that may involve a "greasy slide" and a "swinging door". Overall, these structures provide great insight into the catalytic mechanism and stereoselectivity of GGGPS. Functions for the homologous PcrB proteins, which are generally only found within pathogenic Gram-positive bacteria, can also be proposed. Sequence, structural, and functional comparisons with other TIM-barrel proteins indicates an early evolutionary history for GGGPS. As such, this work will highlight a central role for GGGPS in the emergence of Archaea from the last universal ancestor (LUA).
Phylogenetic relationships of shorebirds (Aves: Charadriiformes): Evidence from sequences of nuclear and mitochondrial genes

The shorebirds (Aves: Charadriiformes) are a large and diverse group of non-passerine birds, whose phylogenetic relationships have been difficult to recover because previous studies have used characters that are limited in their resolution power. Here, I examine the utility of DNA sequences from both the mitochondrial and nuclear genomes to infer phylogeny at the family and generic levels in shorebirds. Both types of sequence data recover three subordinal clades of shorebirds: Scolopaci (sandpipers and allies), Lari (gulls and alcids) and Charadrii (plovers and oystercatchers), and highly-supported, congruent topologies. The Charadrii is found to be sister to a (Scolopaci + Lari) clade, which is different than all previous hypotheses of shorebird phylogeny based on morphological and biochemical data. Patterns of evolution in a 3 kb nuclear exon (RAG-1) reveal a homogeneous nucleotide composition and rate of substitution among lineages, making this gene useful for resolving and estimating the timing of deep divergences in this clade. The 14 mitochondrial genes examined are variable in rate, and therefore are useful to construct phylogeny at many different taxonomic levels. However, complex models of substitution are required to accurately estimate distances among taxa that are divergent. This approach confirms the historically recognized division of Paleognath and Neognath birds, when shorebird mitochondrial DNA is analyzed with other published avian mitochondria) genomes. The mitochondrial gene order of shorebirds was also found to be variable around the control region, and is associated with a tandom duplication of these sequences. In addition to contributions to avian systematics, the mitochondrial genomes of shorebirds will also advance understanding of patterns of evolution at the genomic level.
Behaviour of FRP-to-FRP and FRP-to-concrete bond

Local de-bonding is one of the major causes of concern in FRP rehabilitated structures. For practical purposes, a critical bond length for which the bond between FRP-to-FRP and FRP-to-concrete is fully developed has to be determined, which would prevent premature de-bonding failures. This research seeks to determine the bond strength and the critical bond length for Carbon and Glass FRP systems. Eighty FRP single lap bonded specimens and fifty FRP-bonded concrete prisms were designed, built and tested for this purpose. The shear stress-slip characteristics along the bond were evaluated. The results from the test give the critical bond length and bond stiffness. The results also helped evaluate the strain distribution and shear stress distribution along the bond length. The use of the parameter (Gbond), in a simple model that predicts the shear stress distributions in the FRP-to-FRP bond is suggested to improve the accuracy of the predictions.
Chemical genomics in yeast: linking biologically active compounds to their intracellular targets

Target specific chemical inhibitors are highly valuable as both research tools and therapeutic leads, but it is often difficult to identify their mechanism of action or cellular target. Here I have studied genome-wide chemical-genetic interaction profiles in the budding yeast Saccharomyces cerevisiae, by testing the complete set of viable deletion mutants for hypersensitivity to inhibitory compounds. Integration of chemical-genetic and genetic interaction data reveals information about the mode of action of bioactive compounds. First, in a series of proof-of-concept experiments I showed that because a loss-of-function mutation in a gene encoding the target of an inhibitory compound models the primary effect of the compound, crossing such a mutation into the set of viable mutants and scoring the resultant double mutants for reduced fitness generates a genetic interaction profile for the target gene resembling the chemical-genetic interaction profile of its inhibitory compound. Therefore, clustering the compound-specific profiles with a compendium of large-scale genetic interaction profiles enables the identification of target pathways or proteins and thus provides a powerful means for inferring mechanism of action. In the second phase of this project, I expanded our matrix of chemical-genetic interactions by profiling 85 diverse compounds and natural product extracts, including a number of human therapeutics, using parallel fitness tests and a microarray-based readout. Hierarchical clustering of the dataset associates compounds of similar mode of action and reveals insight into the cellular pathways affected by the compounds. In particular, my analysis establishes a cell membrane target for papuamide B, a high molecular weight cyclic lipopeptide with potent anti-fungal and anti-HIV activity.
Internal determinants of change readiness: implications for the continuing education of health professionals

Continuing professional education events do not often result in behaviour change in the learner, even when satisfaction with the event is high and evidence of knowledge acquisition in the learner is present. One important variable that might help explain the relationship between continuing health educational and subsequent change is the degree to which the learner feels ready to change his or her behaviour. While much is known about how physicians learn and change, the cognitive and affective determinants of readiness to change have not been extensively researched in the applied health professions. This study used a mixed methodology, one-group retrospective pre-test, post-test design to investigate the value of readiness to change in predicting behaviour change and to determine if the value of an educational event is dependent on the state of learner "readiness." A readiness to change questionnaire was administered to 84 health professionals registered in the University of Toronto's International Interdisciplinary Wound Care Course in May, 2005. Responses were scored and summed to arrive at a numerical indicator of the degree of readiness to change both at the beginning and at the end of the course. Three regression analyses were conducted to examine the significance of a model in which the three internal determinants predicted learner readiness before, during, and after the course. To examine how the educational event influenced learner readiness, 20 semi-structured interviews were conducted 3 months after the course. Interpretation of quantitative and qualitative data supported that change readiness is a fluid cognitive state comprised of determinants that vary depending upon the temporal proximity to behaviour change. Data further supported a relationship between change readiness and subsequent behaviour change that discriminates across wound care skills. However, behaviour change might be best predicted by a comprehensive examination of factors both internal and external to the individual. Furthermore, the educational event did appear to influence the state of learner readiness. These findings supported the measurement of change readiness both during the program development phase and as an indicator of program success.
Characterization of the ionizing radiation-inducible gene O6-methylguanine DNA methyltransferase and its role in radiation responses

O6-methylguanine DNA methyltransferase (MGMT) is a critical cellular resistance factor against the mutagenic and cytotoxic effects of O6-methylguanine (O6meG) DNA lesions, and via their repair, confers resistance to alkylating agents including several chemotherapeutic drugs. This study investigates the regulation of MGMT by ionizing radiation (IR) and its potential functional role in radiation responses. The present work indicates that the role of MGMT in radiation responses does not involve its classic O6meG repair function. Expression and enzymatic activity analyses show that MGMT is up-regulated by IR over a range of 0.5 to 20 Gy with delayed and long-lasting kinetics in several cell lines in vitro, and in all normal and malignant tissues examined in vivo. This has implications for cancer patients receiving combination modality treatment, where the induction of MGMT by initial radiation therapy could result in altered sensitivity of the tumour or normal surrounding tissues to subsequent chemotherapy.
Facilitating inquiry-based learning as a complex adaptive system

I argue that educators have a responsibility to engage with theirs and their student's immediate daily world. This engagement requires cultivating awareness of how our local immediate relationships in the world are at centre of the educational process. This thesis explores how embodying this engagement is brought about through the practices of complexity thinking and mindfulness. Using my experience of developing this thesis and an autoethnography of facilitating an inquiry-based learning course with undergraduate health sciences students, I outline an approach for how Complexity Science frames facilitating inquiry as a complex adaptive system. I describe how engaging the intrinsic dynamics of learners and working with self-organization enables facilitators to educate for capability and an understanding of complex systems. I undertake an exploratory critique and reflection of my work to examine the ethics of facilitating with complexity and the importance of mindfulness as a practice for engaging lived experience.
Data reduction in data warehouses

Much research has been devoted to the efficient computation of relational aggregations. In this paper we consider the inverse problem, that of deriving (approximately) the original data from the aggregates. We motivate this problem in the context of two specific application areas, approximate query answering and data analysis. We propose a framework based on the notion of information entropy that enables us to estimate the original values in a data set, given only aggregated information about it. We then show how approximate queries on the data from which the aggregates were derived can be performed using our framework. We also describe an alternate use of the proposed framework that enables us to identify values that deviate from the underlying data distribution, suitable for data ruining purposes. We present a detailed performance study of the algorithms using both real and synthetic data, highlighting the benefits of our approach as well as the efficiency of the proposed solutions. Subsequently, we consider the above problem in a space constrained environment, where only a subset of the required aggregates can be stored. More specifically, we wish to select a set of aggregates of interest, subject to a constraint on the total space occupied by these aggregates. The objective is to maximize the total benefit, which is a function of the number and importance of the queries that we can estimate given the selected aggregates. For this problem, which as we show is NP-hard, there are no known polynomial approximation schemes, and we propose several algorithms for solving it. We explore the use of greedy and randomized techniques as well as clustering based approaches. The solutions presented herein are generic and can be applied to other problem domains as well. We explore the properties and special characteristics of the above techniques with an experimental evaluation. Our results illustrate the behavior of the algorithms under different settings, and highlight the benefits of each approach. Based on our analysis, we present worst case scenarios for the algorithms. This offers insight into the operation of the algorithms, and provides a practical guide for selecting among the proposed techniques.
Theoretical and numerical investigation of thermodiffusion (Soret effect) and thermosolutal convection

Thermodiffusion is a mass diffusion phenomenon induced by a temperature gradient and has attracted increasing interests from theorists and experimentalists. In this work, the modelling of thermodiffusion in fluids is theoretically treated in the framework of non-equilibrium thermodynamics. The method developed in this work for thermodiffusion calculation have been incorporated into a computational fluid dynamics program to study the influence of the thermosolutal convection caused by residual gravity and g-jitter. The results have shown that the influence of microgravity environment would become stronger with an increase in the acceleration level, while at the same acceleration level, the effect would decrease at higher frequencies. For an isopropanol-water mixture under a typical microgravity condition for thermodiffusion measurement, the effect of residual gravity lower than 10--5G or the g-jitter components with an acceleration level of 10--4 G and frequencies higher than 0.0005 Hz may be negligible. The analysis in this work has indicated that under the expected microgravity environment on the International Space Station, the influence of g-jitter on the thermodiffusion measurement may be negligibly small for frequencies lower than 1 Hz. Based on four postulates in non-equilibrium thermodynamics, a non-equilibrium thermodynamic approach has been developed for thermodiffusion in associating fluid mixtures. Using the thermodynamic properties provided by the PC-SAFT Equation of State, this approach was used to evaluate the thermal diffusion factor alphaT in aqueous alkanol solutions, including methanol-water, ethanol-water and isopropanol-water mixtures. Using two adjustable parameters calculated from experimental data, the approach has shown a successful estimation of the sign change in the thermodiffusion factor for these mixtures, which was an unresolved problem in thermodiffusion research. In addition to the new model for thermodiffusion in associating mixtures, the current approaches for thermal diffusion estimation in multicomponent hydrocarbon mixtures have been evaluated by comparisons with recent experimental data. Three equations of state, including Peng-Robinson, volume translated Peng-Robinson and PC-SAFT were used in the calculation. The Firoozabadi model combined with vtPR or PC-SAFT was shown to be applicable to thermal diffusion estimation for hydrocarbon mixtures, while PC-SAFT combined with the Firoozabadi model would be a promising choice for mixtures other than hydrocarbons due to the wide applicability of PC-SAFT.