VictorJuiz/thesis huggingface dataset:
Bayesian networks for pattern classification, data compression, and channel coding

Pattern classification, data compression, and channel coding are tasks that usually must deal with complex but structured natural or artificial systems. Patterns that we wish to classify are a consequence of a causal physical process. Images that we wish to compress are also a consequence of a causal physical process. Noisy outputs from a telephone line are corrupted versions of a signal produced by a structured man-made telephone modem. Not only are these tasks characterized by complex structure, but they also contain random elements. Graphical models such as Bayesian networks provide a way to describe the relationships between random variables in a stochastic system. In this thesis, I use Bayesian networks as an overarching framework to describe and solve problems in the areas of pattern classification, data compression, and channel coding. Results on the classification of handwritten digits show that Bayesian network pattern classifiers outperform other standard methods, such as the k-nearest neighbor method. When Bayesian networks are used as source models for data compression, an exponentially large number of codewords are associated with each input pattern. It turns out that the code can still be used efficiently, if a new technique called "bits-back coding" is used. Several new error-correcting decoding algorithms are instances of "probability propagation" in various Bayesian networks. These new schemes are rapidly closing the gap between the performances of practical channel coding systems and Shannon's 50-year-old channel coding limit. The Bayesian network framework exposes the similarities between these codes and leads the way to a new class of "trellis-constraint codes" which also operate close to Shannon's limit.
Automated motif discovery in protein structure prediction

The protein structure prediction problem (PSP) is one of the central problems in molecular and structural biology. A computational method that could produce a correct detailed three-dimensional structural model for a protein, given its linear sequence of amino acids, would greatly accelerate progress in the biomedical sciences and industries. This thesis presents PSP as a combinatorial optimization problem, the most straightforward formulations of which require search of an exponentially-large conformation space and are known to be NP-Hard. This otherwise intractable search can in practice be reduced or eliminated through the discovery and use of motifs. Motifs are abstractions of observed patterns that encode structurally important relationships among constituent parts of a complex object like a protein tertiary structure. Motif discovery is accomplished by particular combinatorial search and statistical estimation methods. This thesis explores in detail two particular motif discovery subproblems, and discusses how their solutions can be applied to the overall structure prediction problem: (1) For a complex multi-stage prediction task, what makes a good intermediate representation language? We address this question by presenting and analyzing methods for the discovery of protein secondary structure classes that are more predictable from amino acid sequence than the standard classes of $\alpha$-helix, $\beta$-sheet, and "random coil". (2) Given a database of M objects, each characterized by values $a\sb{ij}\in {\cal A}\sb{j}$ for each of N discrete variables $\{c\sb{j}\}\sbsp{j=1}{N},$ return the list of "most interesting" higher-order features $\gamma\sb{l},$ i.e., sets of $k\sb{l}$ variables with highest estimated correlation, for any $2 \le k\sb{l} \le N$. In the PSP context, the problem is the detection of correlations between amino acid residues in an aligned set of evolutionarily-related protein sequences. We present and analyze a fast procedure, based on multinomial sampling and a novel coding scheme, that avoids the exhaustive search, prior limits on the order k, and exponentially large parameter space of other methods. The focus of this thesis is PSP, but the techniques and analysis are also aimed at wider application to other hard, multi-stage prediction problems.
On the physics of perception

A single equation has been discovered governing the flow of information or entropy from a sensory stimulus (such as light or sound) to the organ of sensation (such as a rod or a hair cell) which can account for nearly all experimental results recorded in sensory neurophysiology relating stimulus intensity and stimulus duration to biological response. This equation is capable of handling any time-varying single-stimulus input. The biological response is taken as the frequency of neural discharge. When this equation is extended to the psychophysical level, the theory is capable of unifying many phenomena associated with thresholds. There may be no other sensory theory of comparable generality. The scope and limitations of the theory are discussed.
St. Dymphna, a chamber opera in two acts

This is a chamber opera in two acts for five singer/actors, five instrumentalists, and electro-acoustic segments pre-recorded on a compact disc. The duration of the work is 140 minutes. St. Dymphna (ca. 7th century) is the patron saint of the insane and excessively nervous. Accounts of her life and martyrdom, along with the miracles and healings from mental illness attributed to her were first documented in the 11th century in the Belgian town of Gheel, the site of her martyrdom, and the centre of her cult, which became very popular in the late middle ages. A list of the source materials is included here. The narrative of this opera works on two levels. In act I, the story of St. Dymphna is told along conventional lines, beginning with her childhood, moving through the death of her mother, her father's attempt to seduce and marry her, and her flight with the Jester and Gerebern from her father's Irish kingdom. This linear narrative is interspersed with vignettes of madness and medical doctors. The musical characterizations are less conventional, relying more on cues. In act II the linear and non-linear narrative lines converge. The insane characters from act I begin interacting with the characters of the Dymphna story. The doctors' interventions are broader in scope, and more ruthless in nature, particularly as the King's insanity grows. In the final scene St. Dymphna subdues the doctor while her secure and affirming music draws the fragmented sounds of the mentally ill characters towards it, creating a kind of wounded unity out of disparate material.

Keywords: Operas
Scores
Opéras
Partitions
The meaning of aristocracy in Aristotle's political thought

What is the relationship between Aristotle's concern for the best regime and virtue and his concern for practical political matters? This is one of the most perplexing interpretative questions of the Politics. By investigating the meaning of aristocracy in the Politics, we get a much better understanding of this relationship than currently exists. We learn that there are actually two best regimes in the Politics. There is the regime discussed in books VII and VIII, which Aristotle explicitly presents as the best regime. It is an aristocratic regime and it functions as an aristocratic standard for commonly existing regimes. Aristotle's concern for it and the virtue that defines it is part of his concern for practical political matters. But Aristotle also quietly presents another regime as the best regime in the Politics. It is aristocracy in the strict sense of the term or the simply best regime. Aristotle discusses it in book III of the Politics and it turns out to be the same as the best regime in logos of Plato's Republic, the regime ruled by philosopher-kings. The simply best regime is not any sort of standard for existing regimes. Aristotle's concern for it and the virtue that defines it is not directly related to his concern for practical political matters. The investigation of aristocracy reveals that the concern for the best regime and virtue in the Politics is both part of and separate from the concern for practical political matters. But since Aristotle only quietly presents the teaching on the simply best regime, the investigation also elucidates the peculiar character of his political thought, of how it aims primarily yet not exclusively at practical political matters.
Nuclear Structure Studies in Highly Neutron-Deficient 114,116Xe

Lifetimes of nuclear states in $\sp{114}$Xe and $\sp{116}$Xe were measured for the first time; these nuclei represent the most neutron-deficient isotopes of xenon for which lifetimes have now been measured. The fusion-evaporation reactions $\sp{58}$Ni($\sp{60}$Ni, 2p)$\sp{116}$Xe at 223 MeV beam energy and $\sp{58}$Ni($\sp{58}$Ni, 2p)$\sp{114}$Xe at 215 MeV beam energy were used. Lifetimes were measured using the Recoil Distance Method (RDM) with the 8$\pi$ gamma-ray spectrometer at Chalk River Laboratories. The new measurements of the $B(E2;2\sp{+}\to 0\sp{+})$ strength in these nuclei, coupled with the recent measurements for heavier xenon isotopes, are well described within the framework of the O(6) symmetry limit of the Interacting Boson Approximation. The octupole nature of the negative parity side-band was also studied, and the lifetime measurements indicate a change from a $K\approx 3$ structure in heavier xenon isotopes to a $K\approx 0,\ 1$ structure in $\sp{114}$Xe.
The clearance kinetics and tissue distribution of tumor necrosis factor-Ã in parenterally and enterally fed rats

We have developed an animal model in which the cachexia of chronic and acute disease is reproduced by the provision of a continuous infusion of tumor necrosis factor-$\alpha.$ TNF-infused, orally-fed animals developed anorexia and tissue-wasting, however there was no mortality. The provision of total parenteral nutrition (TPN) to TNF infused animals resulted in a potentiation of the metabolic effects of TNF as well as in significant mortality. Since circulating levels of exogenous TNF were highest in the animals with the most severe metabolic abnormalities, we hypothesized that TPN affects TNF clearance. Our initial study compared the plasma clearance of a bolus of labelled TNF in TPN-fed animals given sufficient nutrients to allow weight-gain (WGR) with those given 50% of the WGR nutrients called weight-losing rats (WLR) and also in orally fed rats (OFR). Data were analyzed using compartmental and linear systems analysis. In a second study, a mammillary model of compartmental analysis was used to compare the tissue distribution and uptake of TNF in rats sacrificed at 4, 10, 20, 60 and 180 minutes post-TNF injection. Plasma data, from both studies, indicated that although metabolic clearance was similar, WGR had a slower fractional clearance rate as well as a larger volume of distribution than WLR or OFR. An increased proportion of the total mass of TNF resided in the plasma-associated compartment in WGR suggesting that TNF is retained in this compartment in these animals. Organ studies suggested impaired uptake of TNF by the tissues of WGR, especially in the kidney, which is thought to be the major organ of TNF clearance. The low affinity for TNF in organs of WGR as well as the expanded volume of distribution suggest that TNF is retained in the plasma by soluble TNF receptors resulting in impaired clearance. Malnutrition and tissue wasting observed in the clinical setting has resulted in the provision of aggressive nutrition support. Our studies suggest that aggressive nutrition support can affect TNF clearance, possibly enhancing the metabolic effects of TNF. Therefore, we suggest that treatment of the underlying cause of cachexia should have priority over the implementation of aggressive nutrition support.
Characterization of a mouse insertional mutation lpd associated with a defect in triglyceride metabolism

A line of transgenic mice Z-14 was generated following microinjection of a 3.9 kb lacZ mini-gene into CD1 zygotes. The resulting homozygous mice are runts and have striking liver pathology characterized by the presence of numerous lipid-containing vacuoles. The plasma triglyceride level is elevated as well. Genetic analysis revealed that Z-14 mice carried a recessive, insertional mutation. The genetic locus for this mutation is designated lpd (lipid defect). To understand the genetic basis of the mutation at the molecular level, both the mutant and wild type lpd locus were cloned. Analysis of the genomic sequences which flank the transgene demonstrated that the integration was accompanied by a DNA duplication of host sequences at the site of integration. Mapping of the lpd locus with a mouse interspecific backcross panel of (C57BL/6J x Mus spretus)F1 x Mus spretus placed the lpd locus to the distal part of chromosome 16. Interestingly, the genomic probes derived from the two flanking sides mapped 1.06 cM apart in the normal genome, implying that the gene rearrangement may be large. Experiments involving quantitative Southern blot analysis revealed that both junctions of the rearranged sequences had been cloned, and a phylogenetically conserved genomic sequence was identified from the 5$\sp\prime$-flanking junction. This conserved sequence will be further investigated to identify the transcript expressed in the region, and to search for the gene which is disrupted by the transgene insertion.
Adolescent Understanding of Communicative Intention in History Texts, a Developmental Analysis

Many studies have shown that while high school students are generally competent in grasping the surface content of historical text, they fail to recognize historical accounts as reconstructions, based on an author's belief, a belief based on either factual evidence or on opinion. This exploratory study assessed developmental changes in (a) adolescents' ability to distinguish between factual and inferential claims made by the author, (b) the relationship between recognition of the stance/attitude/intention of the author and the ability to evaluate the quality of statements presented as evidence and (c) adolescents' ability to denote, by means of cognitive, metarepresentational terms, the author's attitude towards statements used as evidence. These abilities allow students to detect the author's communicative intention in historical text and acknowledge both what the author meant by the text and what message the author wanted the reader to take from the text. Ninety-two (92) subjects, drawn from grade 9 (25), grade 13 (42), and first year college (25), answered written questions about an important Canadian historical event recounted from either a French Canadian or an English Canadian perspective. The data indicated that students appeared to reason differently in dealing with the two accounts. In this Toronto based sample, most students were more inclined to disregard the potential for bias in the account written from the English Canadian perspective. Secondly, students' detection of bias, as shown by their ability to evaluate the quality of the evidence statements, correlated with their recognition of the stance or attitude of the author towards the text. Thirdly, students' ability to denote the attitude of the author towards particular statements, by using appropriate cognitive terms related to their evaluation of evidence. The findings indicated that students' ability to identity the rhetorical properties of text may be an important cognitive component of historical understanding. Recognition of the author "behind the text" seemed to facilitate a more objective evaluation of the acceptability of evidence in both accounts and allowed some students to evaluate evidence presented with less interference from prior belief bias.
Cognitive and emotional aspects of maladaptive interpersonal patterns, a dynamic systems approach

The purpose of this study was to test the utility of a dynamic systems model and methodology for the study of personality, and, more specifically, the mechanisms underlying repetitive maladaptive behaviour. Several streams of thinking within psychoanalytic theory, personality theory, emotional and cognitive theory were reviewed. The basic principles of dynamic systems theory were reviewed, and a specific dynamic systems model for understanding personality organization and the maintenance of maladaptive interpersonal behaviours was advanced (Lewis, 1995; Lewis & Junyk, in press). These behaviours were seen as self-organizing in the moment from cognitive and emotional components, and at times serving a defensive function by protecting the individual from the intense anxiety associated with particular states. The researcher then went on to test this theoretical model with empirical clinical data. The data were gathered from viewing videotaped records of psychotherapy sessions for one subject. The data were subjected to both a qualitative and quantitative analysis. In the qualitative analysis, a dynamic systems model of the subject's personality state space was constructed. In this model, repetitive maladaptive behaviours were described as defensive attractors on the personality state space, and avoided states were described as aversive repellors. A coding system for cognitive and emotional elements was devised and segments of eight sessions were transcribed and coded for the quantitative analysis. In the quantitative analysis the researcher went on to test the assumptions of the model using statistical procedures. The cognitive and emotional components were tested for hypothetical patterns of synchrony. Attractor states were tested for stability, and repellor states were tested for instability. The relationship of the defensive and aversive states with anxiety was tested, as was the relationship between affect and anxiety. Finally, the role of anxiety in facilitating phase shifts from an aversive appraisal to the defensive attractors was explored. The results of the analysis were mixed. Some of the claims of the model were supported, such as the stability of hypothesized attractor states and the instability of the hypothesized repellors. Affect level and anxiety were highly correlated for all states except nondefensive states, as hypothesized. However, no statistical support was found for the synchrony of particular cognitive and emotional components, the relationship between personality state and anxiety, or the role of anxiety as a control parameter. The implications of these results were discussed in reference to repetitive maladaptive behaviour patterns. It was concluded that a dynamic systems framework provided a rich and valuable model for studying repetitive interpersonal behaviours.
Behaviour of metals in MSW incinerator fly ash during roasting with chlorinating agents

A process for removal of heavy metals from municipal solid waste (MSW) incinerator fly ash was studied on a laboratory scale. The process is characterized by the formation of volatile chlorides of heavy metals during thermal treatment at temperatures from 600$\sp\circ$C to 1050$\sp\circ$C. A quartz tube furnace was used for roasting the fly ash sample in an air stream with the presence of a chlorinating agent. Operational parameters, such as roasting temperature, roasting time, and types and quantities of chlorinating agents, were studied. The working conditions for volatilization of Pb, Cu, Zn and Cd, were established. This process not only recovers the valuable heavy metals from the fly ash, but also converts the fly ash from potentially hazardous into non-hazardous material for recycle or its safe disposal in a landfill. Material balances on the fly ash components revealed the metal contaminant distribution between the volatile matter and the ash residue. More acid resistant compounds were formed after the heat treatment. CaCl$\sb2$ was found to be a more selective chlorinating agent compared to Cl$\sb2$ for volatilizing the above heavy metals from a complex matrix such as fly ash. A linear relationship between the efficiencies of volatilization of the partially recovered metals and their standard free-energy changes for the chlorination reactions was indicated. Many of these chlorination reactions were found to be of first order. X-ray powder diffraction was used to identify various chemical compounds to confirm specific reaction mechanisms and to characterize the volatile matter and the heat-treated/untreated fly ash. The reason for the unexpected leachability of Cr and Al from the treated ash residue was investigated and resolved. The applicability of the results to other residues was determined. The techniques developed for the MSW fly ash were applied to a steel dust waste with success for removal of zinc and lead contaminants.
Metaphors of marginalization and silencing of women in Eva Luna and Cuentos de Eva Luna by Isabel Allende

This dissertation is a study of the marginalization and silencing of women in Eva Luna and Cuentos de Eva Luna by Isabel Allende. These two works form a unit since they are intimately linked through a series of intertextual references which include the repetition of the name Eva Luna; references to Scheherezade, the story-teller in A Thousand and One Nights; the preface to the collection of short stories; and the resurfacing in the short stories of characters and places mentioned in the novel. This juxtaposition of the two works implies that the stories in the Cuentos are those told by the story-teller protagonist of the novel. The investigation begins with a theoretical study of the set of binary, hierarchical oppositions that, according to many theorists, have structured Western thought. These place woman on the side of negativity, lack, and emptiness, and in patriarchal society have traditionally led to marginalization and silencing. The present study focuses on Allende's representation of and response to this marginalization and silencing. The focus of the analysis of Eva Luna is on the transformation of the protagonist from a young girl, who is aware of the transforming power of language in oral story-telling, to a woman writer, who decides to influence society through the power of written language. This emphasis on the power of words to overcome silence and marginalization reappears in the Cuentos, not so much in terms of the gradual evolution of one main character (as in the novel) but rather through the story-telling techniques employed by the author. Some of these include the use of ironic language, the creation of parodies of the traditionally accepted roles for men and women, the highlighting of contrasts between male and female characters, and the use of names to convey meanings and connotations. The techniques vary, but the message remains the same: women must gain access to the power of the word in order to subvert, transform, and, eventually, overcome the marginalization and silencing imposed on them by patriarchal society.