VictorJuiz/thesis huggingface dataset:
Design and use of the biomolecular interaction network database (BIND) for storing and analyzing protein-protein interaction data

As genomics and proteomics technologies such as mass spectrometry, yeast two-hybrid, phage display and genetic interaction screens become more sensitive and robust, they are becoming more automated and high-throughput. These experimental systems are currently providing a wealth of data on genetic and molecular interactions and post-translational protein modifications. The Biomolecular Interaction Network Database (BIND - http://bind.ca) has been designed to store details about these molecular and genetic interactions, complexes and pathways and thus captures proteomics data in a computer readable format. Chemical reactions, photochemical activation and conformational changes can be described down to the atomic level of detail. Everything from small molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for full pathway kinetic simulations. Currently, BIND is a web-based system that allows the database to be queried and for records to be entered. A Java applet to visually navigate the database and a BLAST against BIND service are both available via the web. BIND is an open community effort. All BIND records are in the public domain and source code for the project is made freely available under the GNU Public License. The system is designed so that both users and a curation staff can submit interactions described in the literature, which are then vetted. BIND has been used to manage and automatically discover new knowledge residing in large yeast protein-protein and genetic interaction networks in Saccharomyces cerevisiae determined using mass-spectrometry, phase-display, yeast two-hybrid and roboticized synthetic lethal screens. A system, called MCODE (Molecular Complex Detection), for automatically recognizing molecular complexes in large molecular interaction networks, has been devised. MCODE is based on the notion that densely connected regions of a molecular network, or graph, represent molecular complexes. The BIND project illustrates how a structured software development process focusing on the design phase provides a sturdy foundation for the future implementation of bioinformatics tools that solve real biological problems.
Instability detector for quiet standing

Incorporating a measure of stability into a portable sensor has a number of clinically relevant applications. This study investigated the feasibility of developing a real-time assessment tool to monitor balance during quiet standing. Forward and backward perturbations were performed on 16 able-bodied subjects using a pulley system attached to the subjects' waist. A linear relationship was found between the maximum centre of pressure (COP) velocity and the maximum COP position caused by the perturbations. As the maximum COP velocity occurs considerably before the maximum COP position, this model serves as an instability predictor. A sensor that measures COP velocity can use the model to predict a maximum COP position and compare it with an instability threshold. Results show that the proposed model is a viable solution to quantitatively measure stability in real-time.
The influence of the nickel to copper ratio and arsenic on the slow cooling matte separation process

Synthetic mattes of different nickel to copper ratios, containing 20% mass per cent sulfur were slowly cooled from the liquid state to room temperature. The resulting morphology of the matte was examined using optical and scanning electron microscopy. Chemical analysis was performed by use of the electron microprobe. Three phases were observed, Cu2S, Ni 3S2 and a Cu-Ni alloy. The effect of arsenic, up to 1 mass per cent, on the morphology and elemental distribution was studied. It was found that arsenic decreased the size of Cu2S and Cu-Ni gains. Arsenic also contributed towards the formation of cellular morphology and tended to concentrate in the metallic phase. A mechanism is proposed to account for the change in matte morphology when small amounts of arsenic are present in the system.
Aerodynamic flow calculations using finite-differences and multigrid

A multigrid solver is presented based on generalized curvilinear coordinates using explicit Runge-Kutta time-marching and finite-difference spatial discretization in which fast convergence rates are realized by using novel weighted restriction and prolongation operators. The restriction and prolongation operators use variable weighting factors in such a way as to account for the stretching and curvilinear nature of each grid level. The Euler and thin-layer Navier-Stokes equations are solved for various flows over airfoils. Convergence histories are compared to those from an implicit approximately-factored multigrid solver. The results show the implicit approach to be somewhat more efficient in terms of CPU time; however, the explicit algorithm may be more amenable to massively parallel implementation.
Electron diffraction based molecular movies: Sample preparation and theoretical simulations for triiodide photodissociation

Femtosecond electron diffraction (FED) is a novel technique which has recently been employed to study the structures of short-lived transient states connecting initial and final states along a reaction pathway. The photodissociation of triiodide ions represents a simple reaction which one can explore the reaction dynamics through transient structures. The reaction life-time is typically a few hundred fs which is within the time resolution of our FED machine. Therefore, by tracking changes in diffraction patterns during the photodissociation, one can create so-called 'molecular movies' of the reaction dynamics. However, an important practical challenge is to prepare samples which are sufficiently thin (
A goal-oriented instrumentation approach for requirements monitoring

Requirements monitoring is concerned with the deviations of executing a target program from system requirements to assure the correctness of a software system at runtime. A requirements monitoring framework [Wan07] was presented for monitoring and diagnosing requirements. To enrich the instrumentation component of the framework, we present the goal-oriented instrumentation approach for monitoring system goals. Using the techniques of Aspect-Oriented Programming, we have formalized the format of traceability links, and implemented a code generator that transforms goal models to a, monitoring module without changing source code. To reduce overhead, the non-intrusive approach supports dynamically tuning the level of granularity on the monitored goals. The application of this approach is demonstrated in an ATM simulation system.
SapM, an acid phosphatase of pathogenic mycobacteria

SapM is a 28-kDa acid phosphatase specific to the pathogenic mycobacteria. It is secreted and its expression is selectively induced by the mildly acidic phagosomal pH in macrophages. These properties suggest that SapM may play a role in the pathogenesis of Mycobacterium tuberculosis and that it may also serve as a marker in diagnostic assays. This thesis focuses on the development of optimized protein expression and purification methods in order to obtain sufficient amounts of SapM for future functional studies. Factors affecting the expression and purification of SapM such as promoters, host strains, temperature, fusion tags and chaperones were tested and an optimal system has been developed. The construction of a sapM knock-out mutant was also investigated. Homologous recombination approaches to construct sapM mutants proved to be inefficient. Enzyme-Linked Immunosorbent Assay (ELISA) using denatured SapM as antigen revealed that SapM could be potentially used in clinical diagnosis of tuberculosis.
Investigating the relative effects of persons, items, sections, and languages on TOEIC score dependability

This study applied generalizability theory to investigate the contributions of persons, items, sections, and language backgrounds to the score dependability of the Test of English for International Communication (TOEIC). I replicated and extended J.D. Brown's (1998) study of the TOEFL, using data from two language groups: 45,156 Japanese examinees and 46,067 Korean examinees, who took the same form of the TOEIC. Both classical reliability analyses and generalizability analyses found the TOEIC scores of the examinees in question to be highly reliable/generalizable. However, the TOEIC did not distinguish among examinees well, neither within each language group, nor for both language groups combined. The items within a section varied greatly in difficulty. The findings regarding the effect of language backgrounds on TOEIC score dependability were inconclusive, which suggests directions for future research. TOEIC test developers might explore design alternatives with fewer items per section.

Keywords: Test of English for International Communication
English language, Examinations
English language, Study and teaching
Optimal linear transformation of space-time block coding with channel covariance feedback

This thesis develops the optimal linear transformation of orthogonal space-time block coding (STBC) for transmission over correlated flat fading channels. The transformation is developed under the assumption that the channel correlation matrix is available at the transmitter and minimizes the probability of decoding error. We build on recent work that stated the optimization criterion without solving the problem. Specifically, we provide a closed-form solution for the Multi-Input-Single-Output (MISO) system, and present a numerical solution for the Multi-Input-Multi-Output (MIMO) system. Furthermore, several simplified schemes are presented to reduce the complexity. Our results can be considered as waterfilling on the eigenvectors of the transmit correlation matrix. This conclusion is similar to one reached from the capacity-achieving viewpoint.
El papel de la prostitución en la picaresca. (Spanish text, Francisco Delicado, Miguel de Cervantes Saavedra, Francisco Lopez de Ubeda, Alonso Geronimo Salas de Barbadillo)

My study considers the connections between the sex of the protagonist in Spanish picaresque fiction, the disorder that follows when female characters do not behave according to social norms and the response to this disorder that the female picaresque suggests. In its treatment of prostitution, the female picaresque novel not only shows a concern with unrestrained women, but also offers a literary response to a social question that was very controversial in its day. Although officially legal in early modern Spain, prostitution was approved by pragmatists as a "lesser evil" and condemned by moralists as a license to sin. As part of the same discourse, picaresque texts demonstrate that when the picara accomplishes some success by exploiting the masculine values of honor, bravery and loyalty, society at large avenges her deviation by restoring order. By punishing the fictional picara and to a larger extent every woman who behaves like her, the texts not only reaffirm the values of the hegemonic power but also calm the anxieties of their male readers. This strategy allows the reader to see how the picara is finally controlled and reduced by the institutions (matrimony, legal or social punishment) that secure that power. My analysis centers on works conventionally accepted as part of the female picaresque tradition like La picara Justina and La hija de Celestina, as well as the lesser known Vida y costumbres de la madre Andrea. I also focus on La Lozana andaluza as a precursor of the picaresque and on Don Quijote as a commentary on both the genre of the picaresque and the gender of its protagonists. It is my belief that literary texts of the female picaresque, together with moral treatises, manuals of conduct and the laws that limit prostitutes' behavior apply to the condition of women in general. There is an interplay between the fictional discourse of lust, sex, disease, and misogyny and the discourse of legal and moral control in early modern Spain whose main objective is to control women who are out of control.
Investigation of MTBE degradation using advanced oxidation technologies: UV/H2O2, UV/TiO2, and UV/TiO2/H2O2

Methyl tert-butyl ether (MTBE) present in drinking water sources poses a potential threat to human health. In this study, three advanced oxidation processes (AOPs) were investigated for MTBE degradation: UV/H 2O2, UV/TiO2, and UV/TiO2/H2O 2. MTBE degradation was found to follow the pseudo-first-order kinetics in all the three processes, and the rate constant (k) was affected by the concentrations of H2O2 and TiO 2. But higher concentration levels demonstrated a diminishing return on the reaction rate since excessive H2O2 would act as ·OH scavenger and more TiO2 would block the light passage. The addition of H2O2 to the UV/TiO2 system displayed a negative influence on MTBE degradation compared to the UV/TiO 2 system. Increasing light intensity enhanced MTBE degradation in the UV/H2O2 process (k prop; IavgH) and the UV/TiO2 processes (k prop; IavgT). Two mathematical models were proposed to estimate the rate constants with respect to the average light intensity in the solution (I avgH) and H2O2 concentration in the UV/H 2O2 process, and average light intensity in the solution (IavgT) and TiO2 concentration in the UV/TiO2 process.
Planar left-handed transmission-line metamaterials exhibiting a negative refractive index

This thesis proposes a transmission-line approach to the design of left-handed media that exhibit a negative refractive index based on the periodic reactive loading of a host transmission line medium in a dual (high-pass) configuration. A practical two-dimensional implementation of these metamaterials using a microstrip host medium is proposed, and the essential features of the dispersion characteristic are obtained using periodic analysis, including expressions for a negative effective permittivity and permeability. These ideas are then applied to the design of planar structures for microwave circuit and full-wave simulation, and negative refraction and focusing at a planar interface are verified. Experimental results for two experimental prototypes demonstrate focusing and dispersion characteristics in excellent correspondence with theory and simulations. These results represent the first experimental verification of focusing at a planar interface by virtue of a negative refractive index, and depict extremely large bandwidths over which the refractive index remains negative.
The deregulation of complementary and alternative medicine in science-based regulation: merging myths, science and law

This work examines the compatibility of the diagnostic and therapeutic theories of complementary and alternative medicine (CAM) with a science-based regulatory framework. The paper examines the relationship between scientific validation and health care system legitimization, based on the centrality of therapeutic effect to legal regulation, consumers' patronage and health care funding. The paper analyzes two competing theories for CAM regulation—science-based (statutory) regulation and voluntary/ethical regulation through a number of approaches, ranging from medical epidemiology/philosophy to anthropology in the determination of the appropriate regulatory framework for CAM. The central argument is for a broad-based regulatory framework that supports a pluralistic health care system and balances the imperative of quality assurance with the need to ensure access. In establishing legal standards that are correlative to the practice within a particular school of CAM, policy makers would in effect be applying the law to accommodate the present growth of diverse health practices.
Effect of sodium compounds on particle adhesion in lime kiln

One of the problems faced in the operation of a lime kiln in a kraft pulp mill is the particle adhesion on the kiln wall, which may contribute to the formation of a ring. It has long been suspected that sodium compounds makes the particle sticky. Thus, experiments were carried out to investigate the effect of Na compounds on particle adhesion in a laboratory kiln. The results indicate that the presence of Na compounds in lime mud impacts particle adhesion, which greatly depends on the concentration of the Na compounds and the form of compounds in which sodium is present. Adhesion increases when lime mud undergoes calcination. The effect of other impurities were also studied. The result showed that low melting temperature compounds, Na5P3O10 and P2O5, increased the particle adhesion, but higher melting compounds, Al2O3 and MgO, did not show any effect.
"Whither fictitious tales". "Tsukuri Monogatari no Yukue" from "Imakagami": a study and translation

The core of this thesis is an annotated translation of " Tsukuri Monogatari no Yukue" (Whither Fictitious Tales), the last section of Imakagami (The New Mirror), a 12th century text categorized as a historical tale." Whither Fictitious Tales" contains the earliest reference to the belief first circulated in the late Heian period that Murasaki Shikibu was suffering in hell for having written a tale as seductive and full of immoral content as the Tale of Genji. This study examines the social, literary, and ideological context that gave birth to such a belief. It explores the significance of the author's choice of a female narrator for Imakagami as a whole and for this critical piece (Tsukuri Monogatari no Yukue) in which Murasaki Shikibu is defended against these charges. The thesis demonstrates that the defence of Murasaki Shikibu is constructed by recasting in her favour the same Buddhist arguments used in the accusation.
Learning language in cooperatively structured groups in a first-year level university classroom: a case study of Japanese as a foreign language

This study takes the form of action research investigating the feasibility and effectiveness of learning Japanese as a foreign language (JFL) in cooperatively structured groups at the university beginners' level. The evaluation of incorporating cooperatively structured group activities in JFL classes is framed by theoretical and empirical studies in the fields of SLA and cooperative learning. It embraces the idea that a theory of SLA should integrate various aspects of the L2 learning process and that cooperatively structured group work facilitates SLA by providing more input/output and scaffolding among learners and a more constructive affective and social environment for learning. An experimental and a comparison JFL beginner's level classes at a university in Southern Ontario framed the context of this study. I taught both experimental and comparison classes giving a variety of cooperatively structured group activity treatment over a 16 week period in the experimental class while giving comparison class a more teacher-fronted treatment. Results of the vocabulary and kanji quizzes I administered after each vocabulary and kanji learning activity in both experimental and comparison classes were compared quantitatively between the two classes. Data collected from questionnaires, interviews, teacher's journal in the experimental and comparison classes, and audio- and videotapes made in the experimental class were also used to qualitatively evaluate the experimental students' interactional patterns, attitudes towards cooperative group learning, and group cohesiveness, and to compare with the patterns and attitudes observed in the comparison class. The results of vocabulary and kanji quizzes and the post-test indicated that cooperatively structured activities seemed not to have differentially affected the linguistic performances of the students in the experimental class. Further investigation indicated, however, that a significant amount of linguistic input/outputs and scaffolding among students was present in their discourses. The results of questionnaires and interviews suggested that cooperatively structured groups provided the students with a favourable affective and social learning environment. These findings suggest that cooperatively structured group work may be valuable for beginner university level learners of a second language, and that pedagogical merits of second language learning using cooperatively structured groups should be further evaluated at this level.

Keywords: Second language acquisition
Japanese language, Study and teaching (Higher)
Language and languages, Study and teaching
Japanese, Language and languages
In vitro and in vivo investigations into idiosyncratic drug reactions: the role of reactive metabolites produced by the target tissue in terbinafine-induced cholestatic hepatitis and antipsychotic-induced agranulocytosis

Idiosyncratic drug reactions (IDRs), although rare, can be severe and life threatening. Little is known about the mechanisms of these reactions because they are just as idiosyncratic in animals as they are in humans; therefore, testing hypotheses in a clinical or laboratory setting is difficult. It is conventionally assumed that an adaptive immune response against drug-modified protein, the latter of which can arise due to reactive metabolite formation, is responsible for the pathogenesis of IDRs. However this hypothesis, dubbed the Hapten Hypothesis, has been supported by only a few IDRs for which drug-specific antibodies are produced, and moreover, does little to account for their idiosyncratic nature. An alternative hypothesis of adaptive immunity which better accounts for the idiosyncratic nature of these reactions, the Danger Hypothesis, was instead employed in the present studies to test whether or not a drug and/or its reactive metabolites have the necessary characteristics of providing a “danger signal” to the immune system. Previously, we attempted to develop animal models of terbinafine-induced cholestatic hepatitis in rats and DMP 406-induced agranulocytosis in beagle dogs. However, the syndromes were not reproduced in these animals due to their idiosyncratic natures. In the absence of animal models, we tested the abilities of terbinafine and DMP 406 to form reactive metabolites in their target tissues—liver and neutrophils, respectively. Furthermore, using various in vitro and in vivo techniques, biochemical and functional changes imposed by the neutrophil-generated reactive metabolite of DMP 406 were compared to those of its chemical analogues, clozapine and mianserin. Clozapine and mianserin are associated with idiosyncratic agranulocytosis in humans, and their reactive metabolites are believed to be involved in the pathogenesis of of this syndrome. Clozapine was found to have the greatest impact on neutrophil function and life-span. Furthermore, clozapine caused oxidative stress in both the liver and neutrophil precursors in the bone marrow, thus providing a potential “danger signal” to the immune system. Such biochemical changes to the target tissues caused by clozapine may provide insight into the mechanism of some IDRs.
Textual variations of Sei Shonagon's "Makura no soshi": Perception of the text and the narratorial voice

This thesis examines the complex textual history of Sei Shonagon's Makura no soshi, an 11th century text. It describes and compares the four main textual lineages of the work, Noinbon, Sankanbon, Maedakebon and Sakaibon, and summarizes the debates among Japanese scholars concerning the issue of authenticity. This thesis defends the consensus of centuries of readers and modern scholarship that the two textual lines organized in random order, the Noinbon and the Sankanbon, represent the version closest to the original text. Detailed textual analysis is performed on passages that vary between the Sakanbon and Noinbon, focusing particularly on the work's "epilogue." On the basis of that analysis, this thesis proposes that the sense of temporal proximity, intimacy, and spontaneity apparent in the narrative style of the Noinbon make it the best candidate for the most authentic manuscript line.