Phonon spectra and temperature variation of thermodynamic properties of fcc metals via Finnis-Sinclair type many body potentials: Sutton-Chen and improved Sutton-Chen models

Volume(density)-independent pair-potentials cannot describe metallic cohesion adequately as the presence of the free electron gas renders the total energy strongly dependent on the electron density. The embedded atom method (EAM) addresses this issue by replacing part of the total energy with an explicitly density-dependent term called the embedding function. Finnis and Sinclair proposed a model where the embedding function is taken to be proportional to the square root of the electron density. Models of this type are known as Finnis-Sinclair many body potentials. In this work we study a particular parametrization of the Finnis-Sinclair type potential, called the "Sutton-Chen" model, and a later version, called the "Quantum Sutton-Chen" model, to study the phonon spectra and the temperature variation thermodynamic properties of fcc metals. Both models give poor results for thermal expansion, which can be traced to rapid softening of transverse phonon frequencies with increasing lattice parameter. We identify the power law decay of the electron density with distance assumed by the model as the main cause of this behaviour and show that an exponentially decaying form of charge density improves the results significantly. Results for Sutton-Chen and our improved version of Sutton-Chen models are compared for four fcc metals: Cu, Ag, Au and Pt. The calculated properties are the phonon spectra, thermal expansion coefficient, isobaric heat capacity, adiabatic and isothermal bulk moduli, atomic root-mean-square displacement and Gr\"{u}neisen parameter. For the sake of comparison we have also considered two other models where the distance-dependence of the charge density is an exponential multiplied by polynomials. None of these models exhibits the instability against thermal expansion (premature melting) as shown by the Sutton-Chen model. We also present results obtained via pure pair potential models, in order to identify advantages and disadvantages of methods used to obtain the parameters of these potentials.

Object-Oriented Genetic Programming for the Automatic Inference of Graph Models for Complex Networks

Complex networks are systems of entities that are interconnected through meaningful relationships. The result of the relations between entities forms a structure that has a statistical complexity that is not formed by random chance. In the study of complex networks, many graph models have been proposed to model the behaviours observed. However, constructing graph models manually is tedious and problematic. Many of the models proposed in the literature have been cited as having inaccuracies with respect to the complex networks they represent. However, recently, an approach that automates the inference of graph models was proposed by Bailey [10] The proposed methodology employs genetic programming (GP) to produce graph models that approximate various properties of an exemplary graph of a targeted complex network. However, there is a great deal already known about complex networks, in general, and often specific knowledge is held about the network being modelled. The knowledge, albeit incomplete, is important in constructing a graph model. However it is difficult to incorporate such knowledge using existing GP techniques. Thus, this thesis proposes a novel GP system which can incorporate incomplete expert knowledge that assists in the evolution of a graph model. Inspired by existing graph models, an abstract graph model was developed to serve as an embryo for inferring graph models of some complex networks. The GP system and abstract model were used to reproduce well-known graph models. The results indicated that the system was able to evolve models that produced networks that had structural similarities to the networks generated by the respective target models.

Identification and characterization of retinoic acid-induced morphological and electrophysiological changes in an invertebrate nervous system

The vitamin A metabolite, retinoic acid (RA) is known to play an important role in the development, patterning and regeneration of nervous tissue, both in the embryo and in the adult. Classically, RA is known to mediate the transcription of target genes through the binding and activation ofits nuclear receptors: the retinoic acid receptors (RARs) and retinoid X receptors (RXRs). Recently, mounting evidence from many animal models has implicated a number of RA-mediated effects operating independently of gene transcription, and thus highlights nove~ nongenornic actions of RA. For example, recent work utilizing cultured neurons from the pond snaa Lymnaea stagnalis, has shown that RA can elicit a regenerative response, growth cone turning, independently of "classical" transcriptional activation While this work illustrates a novel regeneration-inducing effect in culture, it is currently -unknown whether RA also induces regeneration in situ. This study has sought to determine RA's regenerative effucts at the morphological and molecular levels by utilizing an in situ approach focusing on a single identified dopaminergic neuron which possesses a known "mapped" morphology within the CNS. These studies show, for the first time in an invertebrate, that RA can increase neurite outgrowth of dopaminergic cells that have undergone a nerve-crush injury. Utilizing Western blot analysis, it was shown that this effect appears to be independent of any changes in whole CNS expression levels of either the RAR or RXR. Additionally, utilizing immunohistochemistry, to examine protein localization, there does not appear to be any obvious changes in the RXR expression level at the crush site. Changes in cell morphology such as neurity extension are known to be modulated by changes in neuronal firing activity. It has been previously shown that exposure to RA over many days can lead to changes in the electrophysiological properties of cultured Lymnaea neurons; however, no studies have investigated whether short-term exposure to RA can elicit electrophysiological changes and/or changes in firing pattern of neurons in Lymnaea or any other species. The studies performed here show, for the first time in any species, that short-tenn treatment with RA can elicit significant changes in the firing properties of both identified dopaminergic neurons and peptidergic neurons. This effect appears to be independent of protein synthesis, activation of protein kinase A or phospholipase C, and calcium influx but is both dose-dependent and isomer-dependent. These studies provide evidence that the RXR, but not RAR, may be involved, and that intracellular calcium concentrations decrease upon RAexposure with a time course, dose-dependency and isomer-dependency that coincide with the RA-induced electrophysiological changes. Taken together, these studies provide important evidence highlighting RA as a multifunctional molecule, inducing morphological, molecular and electrophysiological changes within the CNS, and highlight the many pathways through which RA may operate to elicit its effects.

The last resort : spa therapy and the docile body in Victorian St. Catharines /

By relying on existing cultural models, the Victorian spa promoted health and wellness. Advertising, together with other forms of promotion, strengthened the legitimacy of its claims to cure a variety of health problems. By the use of some links to science and a mystical folk belief about the efficacy of the local mineral waters, three spas emerged in St.Catharines: the Stephenson House, the WeIland House, and the Springbank. As the twentieth century approached, the spa movement declined and institutionalized medicine struggled to establish a monopoly on health care. This thesis argues that the health spas in St. Catharines occupied that transitional space in nineteenth century medicine between home remedy and hospital. The interplay between scientific discovery and business enterprise produced a climate in which the Victorian health resort flourished. This phenomenon, combined with the various maladies brought on by industrialization, nineteenth-century lifestyle, and the absence of medical options, created a surge in the popularity of health spas and mineral spring therapies. By the tum of the twentieth century, interest in mineral water treatments had declined. The health resorts that had blossomed between 1850 and 1899 began to experience a serious decrease in business. This popular movement became outmoded in the face of emerging medical and scientific knowledge. In St. Catharines, the last resort to remain standing, the WeIland House, finished out the city's spa era as a hospital.

Evolutionary synthesis of stochastic gene network models using feature-based search spaces

A feature-based fitness function is applied in a genetic programming system to synthesize stochastic gene regulatory network models whose behaviour is defined by a time course of protein expression levels. Typically, when targeting time series data, the fitness function is based on a sum-of-errors involving the values of the fluctuating signal. While this approach is successful in many instances, its performance can deteriorate in the presence of noise. This thesis explores a fitness measure determined from a set of statistical features characterizing the time series' sequence of values, rather than the actual values themselves. Through a series of experiments involving symbolic regression with added noise and gene regulatory network models based on the stochastic 'if-calculus, it is shown to successfully target oscillating and non-oscillating signals. This practical and versatile fitness function offers an alternate approach, worthy of consideration for use in algorithms that evaluate noisy or stochastic behaviour.

The relationship between body mass index and breast cancer recurrence/progression and breast cancer-specific death

The aim of this study was to describe the nonlinear association between body mass index (BMI) and breast cancer outcomes and to determine whether BMI improves prediction of outcomes. A cohort of906 breast cancer patients diagnosed at Henry Ford Health System, Detroit (1985-1990) were studied. The median follow-up was 10 years. Multivariate logistic regression was used to model breast cancer recurrence/progression and breast cancer-specific death. Restricted cubic splines were used to model nonlinear effects. Receiver operator characteristic areas under the curves (ROC AUC) were used to evaluate prediction. BMI was nonlinearly associated with recurrence/progression and death (p= 0.0230 and 0.0101). Probability of outcomes increased with increase or decrease ofBMI away from 25. BMI splines were suggestive of improved prediction of death. The ROC AUCs for nested models with and without BMI were 0.8424 and 0.8331 (p= 0.08). I f causally associated, modifying patients BMI towards 25 may improve outcomes.

(A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides

(A) Solid phase synthesis of oligonucleotides are well documented and are extensively studied as the demands continue to rise with the development of antisense, anti-gene, RNA interference, and aptamers. Although synthesis of RNA sequences faces many challenges, most notably the choice of the 2' -hydroxy protecting group, modified 2' -O-Cpep protected ribonucleotides were synthesized as alternitive building blocks. Altering phosphitylation procedures to incorporate 3' -N,N-diethyl phosphoramidites enhanced the overall reactivity, thus, increased the coupling efficiency without loss of integrety. Furthermore, technical optimizations of solid phase synthesis cycles were carried out to allow for successful synthesis of a homo UIO sequences with a stepwise coupling efficiency reaching 99% and a final yield of 91 %. (B) Over the past few decades, dipyrrometheneboron difluoride (BODIPY) has gained recognition as one of the most versatile fluorophores. Currently, BODIPY labeling of oligonucleotides are carried out post-synthetically and to date, there lacks a method that allows for direct incorporation of BODIPY into oligonucleotides during solid phase synthesis. Therefore, synthesis of BODIPY derived phosphoramidites will provide an alternative method in obtaining fluorescently labelled oligonucleotides. A method for the synthesis and incorporation of the BODIPY analogues into oligonucleotides by phosphoramidite chemistry-based solid phase DNA synthesis is reported here. Using this approach, BODIPY-labeled TlO homopolymer and ISIS 5132 were successfully synthesized.

The Effects of Body Posture on Emotion Perception: A Developmental and Theoretical Analysis

Previously, studies investigating emotional face perception - regardless of whether they involved adults or children - presented participants with static photos of faces in isolation. In the natural world, faces are rarely encountered in isolation. In the few studies that have presented faces in context, the perception of emotional facial expressions is altered when paired with an incongruent context. For both adults and 8- year-old children, reaction times increase and accuracy decreases when facial expressions are presented in an incongruent context depicting a similar emotion (e.g., sad face on a fear body) compared to when presented in a congruent context (e.g., sad face on a sad body; Meeren, van Heijnsbergen, & de Gelder, 2005; Mondloch, 2012). This effect is called a congruency effect and does not exist for dissimilar emotions (e.g., happy and sad; Mondloch, 2012). Two models characterize similarity between emotional expressions differently; the emotional seed model bases similarity on physical features, whereas the dimensional model bases similarity on underlying dimensions of valence an . arousal. Study 1 investigated the emergence of an adult-like pattern of congruency effects in pre-school aged children. Using a child-friendly sorting task, we identified the youngest age at which children could accurately sort isolated facial expressions and body postures and then measured whether an incongruent context disrupted the perception of emotional facial expressions. Six-year-old children showed congruency effects for sad/fear but 4-year-old children did not for sad/happy. This pattern of congruency effects is consistent with both models and indicates that an adult-like pattern exists at the youngest age children can reliably sort emotional expressions in isolation. In Study 2, we compared the two models to determine their predictive abilities. The two models make different predictions about the size of congruency effects for three emotions: sad, anger, and fear. The emotional seed model predicts larger congruency effects when sad is paired with either anger or fear compared to when anger and fear are paired with each other. The dimensional model predicts larger congruency effects when anger and fear are paired together compared to when either is paired with sad. In both a speeded and unspeeded task the results failed to support either model, but the pattern of results indicated fearful bodies have a special effect. Fearful bodies reduced accuracy, increased reaction times more than any other posture, and shifted the pattern of errors. To determine whether the results were specific to bodies, we ran the reverse task to determine if faces could disrupt the perception of body postures. This experiment did not produce congruency effects, meaning faces do not influence the perception of body postures. In the final experiment, participants performed a flanker task to determine whether the effect of fearful bodies was specific to faces or whether fearful bodies would also produce a larger effect in an unrelated task in which faces were absent. Reaction times did not differ across trials, meaning fearful bodies' large effect is specific to situations with faces. Collectively, these studies provide novel insights, both developmentally and theoretically, into how emotional faces are perceived in context.

Asymmetries of Influence: Differential Effects of Body Postures on Perceptions of Emotional Facial Expressions

The accuracy and speed with which emotional facial expressions are identified is influenced by body postures. Two influential models predict that these congruency effects will be largest when the emotion displayed in the face is similar to that displayed in the body: the emotional seed model and the dimensional model. These models differ in whether similarity is based on physical characteristics or underlying dimensions of valence and arousal. Using a 3- alternative forced-choice task in which stimuli were presented briefly (Exp 1a) or for an unlimited time (Exp 1b) we provide evidence that congruency effects are more complex than either model predicts; the effects are asymmetrical and cannot be accounted for by similarity alone. Fearful postures are especially influential when paired with facial expressions, but not when presented in a flanker task (Exp 2). We suggest refinements to each model that may account for our results and suggest that additional studies be conducted prior to drawing strong theoretical conclusions.