Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

Two and Three Finger Caging of Polygons and Polyhedra

Multi-finger caging offers a rigorous and robust approach to robot grasping. This thesis provides several novel algorithms for caging polygons and polyhedra in two and three dimensions. Caging refers to a robotic grasp that does not necessarily immobilize an object, but prevents it from escaping to infinity. The first algorithm considers caging a polygon in two dimensions using two point fingers. The second algorithm extends the first to three dimensions. The third algorithm considers caging a convex polygon in two dimensions using three point fingers, and considers robustness of this cage to variations in the relative positions of the fingers.

This thesis describes an algorithm for finding all two-finger cage formations of planar polygonal objects based on a contact-space formulation. It shows that two-finger cages have several useful properties in contact space. First, the critical points of the cage representation in the hand’s configuration space appear as critical points of the inter-finger distance function in contact space. Second, these critical points can be graphically characterized directly on the object’s boundary. Third, contact space admits a natural rectangular decomposition such that all critical points lie on the rectangle boundaries, and the sublevel sets of contact space and free space are topologically equivalent. These properties lead to a caging graph that can be readily constructed in contact space. Starting from a desired immobilizing grasp of a polygonal object, the caging graph is searched for the minimal, intermediate, and maximal caging regions surrounding the immobilizing grasp. An example constructed from real-world data illustrates and validates the method.

A second algorithm is developed for finding caging formations of a 3D polyhedron for two point fingers using a lower dimensional contact-space formulation. Results from the two-dimensional algorithm are extended to three dimension. Critical points of the inter-finger distance function are shown to be identical to the critical points of the cage. A decomposition of contact space into 4D regions having useful properties is demonstrated. A geometric analysis of the critical points of the inter-finger distance function results in a catalog of grasps in which the cages change topology, leading to a simple test to classify critical points. With these properties established, the search algorithm from the two-dimensional case may be applied to the three-dimensional problem. An implemented example demonstrates the method.

This thesis also presents a study of cages of convex polygonal objects using three point fingers. It considers a three-parameter model of the relative position of the fingers, which gives complete generality for three point fingers in the plane. It analyzes robustness of caging grasps to variations in the relative position of the fingers without breaking the cage. Using a simple decomposition of free space around the polygon, we present an algorithm which gives all caging placements of the fingers and a characterization of the robustness of these cages.

Novel hydrogen-bonded three-dimensional networks encapsulating one-dimensional covalent chains: [M(4,4 '-bipy)(H2O)4](4-abs)2 center dot nH(2)O (4,4 '-bipy=4,4 '-Bipyridine; 4-abs=4-aminobenzenesulfonate) (M=Co, n=1; M=Mn, n=2)

Two novel compounds, [Co(4,4'-bipy)(H2O)(4)](4-abS)(2).H2O (1) and [Mn(4,4'-bipy)(H2O)(4)](4-abs)(2).2H(2)O (2) (4,4'-bipy = 4,4'-bipyridine; 4-abs = 4-aminobenzenesulfonate), have been synthesized in aqueous solution and characterized by single-crystal X-ray diffraction, elemental analyses, UV-vis and IR spectra, and TG analysis. X-ray structural analysis revealed that 1 and 2 both possess unusual hydrogen-bonded three-dimensional (3-D) networks encapsulating one-dimensional (1-D) covalently bonded infinite [M(4,4'-bipy)(H2O)(4)](2+) (M = Co, Mn) chains. The 4-abs anions in 1 form 1-D zigzag chains through hydrogen bonds. These chains are further extended through crystallization water molecules into 3-D hydrogen-bonded networks with 1-D channels, in which the [Co(4,4'-bipy)(H2O)(4)](2+) linear covalently bonded chains are located. Crystal data for 1: C22H30CoN4O11S2, monoclinic P2(1), a = 11.380(2) Angstrom, b = 8.0274(16) Angstrom, c = 15.670(3) Angstrom, alpha = gamma = 90degrees, beta = 92.82(3)degrees, Z = 2. Compound 2 contains interesting two-dimensional (2-D) honeycomb-like networks formed by 4-abs anions and lattice water molecules via hydrogen bonding, which are extended through other crystallization water molecules into three dimensions with 1-D hexagonal channels. The [Mn(4,4'-bipy)(H2O)(4)](2+) linear covalent chains exist in these channels. Crystal data for 2: C22H32WN4O12S2, monoclinic P2(1)/c, a = 15.0833(14) Angstrom, b = 8.2887(4) Angstrom, c = 23.2228(15) Angstrom, alpha = gamma = 90degrees, beta = 95.186(3)degrees, Z = 4.

The Three-Dimensional Interpretation of a Class of Simple Line-Drawings

We provide a theory of the three-dimensional interpretation of a class of line-drawings called p-images, which are interpreted by the human vision system as parallelepipeds ("boxes"). Despite their simplicity, p-images raise a number of interesting vision questions: *Why are p-images seen as three-dimensional objects? Why not just as flatimages? *What are the dimensions and pose of the perceived objects? *Why are some p-images interpreted as rectangular boxes, while others are seen as skewed, even though there is no obvious distinction between the images? *When p-images are rotated in three dimensions, why are the image-sequences perceived as distorting objects---even though structure-from-motion would predict that rigid objects would be seen? *Why are some three-dimensional parallelepipeds seen as radically different when viewed from different viewpoints? We show that these and related questions can be answered with the help of a single mathematical result and an associated perceptual principle. An interesting special case arises when there are right angles in the p-image. This case represents a singularity in the equations and is mystifying from the vision point of view. It would seem that (at least in this case) the vision system does not follow the ordinary rules of geometry but operates in accordance with other (and as yet unknown) principles.

QUANTITATIVE THREE DIMENSIONAL ELASTICITY IMAGING

Neoplastic tissue is typically highly vascularized, contains abnormal concentrations of extracellular proteins (e.g. collagen, proteoglycans) and has a high interstitial fluid pres- sure compared to most normal tissues. These changes result in an overall stiffening typical of most solid tumors. Elasticity Imaging (EI) is a technique which uses imaging systems to measure relative tissue deformation and thus noninvasively infer its mechanical stiffness. Stiffness is recovered from measured deformation by using an appropriate mathematical model and solving an inverse problem. The integration of EI with existing imaging modal- ities can improve their diagnostic and research capabilities. The aim of this work is to develop and evaluate techniques to image and quantify the mechanical properties of soft tissues in three dimensions (3D). To that end, this thesis presents and validates a method by which three dimensional ultrasound images can be used to image and quantify the shear modulus distribution of tissue mimicking phantoms. This work is presented to motivate and justify the use of this elasticity imaging technique in a clinical breast cancer screening study. The imaging methodologies discussed are intended to improve the specificity of mammography practices in general. During the development of these techniques, several issues concerning the accuracy and uniqueness of the result were elucidated. Two new algorithms for 3D EI are designed and characterized in this thesis. The first provides three dimensional motion estimates from ultrasound images of the deforming ma- terial. The novel features include finite element interpolation of the displacement field, inclusion of prior information and the ability to enforce physical constraints. The roles of regularization, mesh resolution and an incompressibility constraint on the accuracy of the measured deformation is quantified. The estimated signal to noise ratio of the measured displacement fields are approximately 1800, 21 and 41 for the axial, lateral and eleva- tional components, respectively. The second algorithm recovers the shear elastic modulus distribution of the deforming material by efficiently solving the three dimensional inverse problem as an optimization problem. This method utilizes finite element interpolations, the adjoint method to evaluate the gradient and a quasi-Newton BFGS method for optimiza- tion. Its novel features include the use of the adjoint method and TVD regularization with piece-wise constant interpolation. A source of non-uniqueness in this inverse problem is identified theoretically, demonstrated computationally, explained physically and overcome practically. Both algorithms were test on ultrasound data of independently characterized tissue mimicking phantoms. The recovered elastic modulus was in all cases within 35% of the reference elastic contrast. Finally, the preliminary application of these techniques to tomosynthesis images showed the feasiblity of imaging an elastic inclusion.

Beginning primary teachers’ perspectives on becoming a teacher in the workplace: Contextual, emotional, and temporo-spatial dimensions of identity shaping

The issue, with international and national overtones, of direct relevance to the present study, relates to the shaping of beginning teachers’ identities in the workplace. As the shift from an initial teacher education programme into initial practice in schools is a period of identity change worthy of investigation, this study focuses on the transformative search by nine beginning primary teachers for their teaching identities, throughout the course of their initial year of occupational experience, post-graduation. The nine beginning teacher participants work in a variety of primary school settings, thus strengthening the representativeness of the research cohort. Privileging ‘insider’ perspectives, the research goal is to understand the complexities of lived experience from the viewpoints of the participating informants. The shaping of identity is conceived of in dimensional terms. Accordingly, a framework composed of three dimensions of beginning teacher experience is devised, namely: contextual; emotional; temporo-spatial. Data collection and analysis is informed by principles derived from sociocultural theories; activity theory; figured worlds theory; and, dialogical self theory. Individual, face-to-face semi-structured interviews, and the maintenance of solicited digital diaries, are the principal methods of data collection employed. The use of a dimensional model fragments the integrated learning experiences of beginning teachers into constituent parts for the purpose of analysis. While acknowledging that the actual journey articulated by each participant is a more complex whole than the sum of its parts, key empirically-based claims are presented as per the dimensional framework employed: contextuality; emotionality; temporo-spatiality. As a result of applying the foci of an international literature to an under-researched aspect of Irish education, this study is offered as a context-specific contribution to the knowledge base on beginning teaching. As the developmental needs of beginning teachers constitute an emerging area of intense policy focus in Ireland, this research undertaking is both relevant and timely.

The Supremacy of the Sequence: Key Elements and Dimensions in the Process of Change

How single organizations manage the process of change and why only some of them are able to actually reach radical change are central questions in today’s theoretical debate. The role played by the process of change and its dimensions (namely, pace, sequence and linearity), however, has been poorly investigated. Drawing on archetype theory, this paper explores: (i) whether a specific pace of radical change exists; (ii) whether different outcomes of change are characterized by different sequences of change in key-structures and systems (iii) how the three dimensions of the process of change possibly interact. As an example of organizational change the study takes into consideration processes of accounting change in three departments of two Canadian and two Italian municipalities. The results suggest the supremacy of the sequence of implemented changes over the other two dimensions of the process in order to achieve a radical outcome of change.

The Dimensions of Expatriate Adjustment

A narrow and partial theoretical base has limited current concepts of expatriate adjustment and the research based upon them. This conceptual article explores one of the less theorized aspects of expatriate adjustment: the fact that it has multiple dimensions. We conceive of adjustment as a person-environment relationship that takes place in the three dimensions of cognitions, feelings, and behaviors. Combining these elements takes us one step closer to a comprehensive and more realistic understanding of the nature of expatriate adjustment. We include suggestions for future research that follow from our reconceptualization.

Three-Dimensional Dynamics of Breakout Afterburner Ion Acceleration Using High-Contrast Short-Pulse Laser and Nanoscale Targets

Breakout afterburner (BOA) laser-ion acceleration has been demonstrated for the first time in the laboratory. In the BOA, an initially solid-density target undergoes relativistically induced transparency, initiating a period of enhanced ion acceleration. First-ever kinetic simulations of the BOA in three dimensions show that the ion beam forms lobes in the direction orthogonal to laser polarization and propagation. Analytic theory presented for the electron dynamics in the laser ponderomotive field explains how azimuthal symmetry breaks even for a symmetric laser intensity profile; these results are consistent with recent experiments at the Trident laser facility. © 2011 American Physical Society.

Les déterminants organisationnels et sociaux des trois dimensions de l'épuisement professionnel

Réalisée à partir d’un échantillon de 410 travailleurs civils et policiers du Service de Police de la Ville de Montréal (SPVM) atteint en février 2009, cette recherche vise à approfondir les connaissances relatives à l’influence de l’utilisation des compétences, de l’autorité décisionnelle, du soutien social au travail, de la supervision abusive et du soutien social hors travail sur les trois dimensions du syndrome d’épuisement professionnel (épuisement émotionnel, cynisme, efficacité professionnelle). Cette recherche vise également à déterminer si les relations qui unissent ces facteurs organisationnels et sociaux aux trois dimensions d’épuisement professionnel varient selon que les travailleurs appartiennent à la main-d’œuvre policière ou civile. Les résultats des analyses multivariées témoignent de l’influence distinctive des variables explicatives sur les trois dimensions d’épuisement professionnel et supportent la conceptualisation tridimensionnelle du syndrome d’épuisement professionnel. Les résultats appuient également la distinction des concepts d’utilisation des compétences et d’autorité décisionnelle et permettent d’approfondir les connaissances relatives à l’influence de la supervision abusive, du soutien social hors travail et du rôle modérateur de la profession sur les trois dimensions du syndrome d’épuisement professionnel.

Évaluation de la validité prédictive de la Statique-99R et de ses dimensions

Les objectifs du présent mémoire étaient d’identifier les dimensions présentes dans la Statique-99R, l’échelle actuarielle de prédiction de la récidive sexuelle la plus utilisée, et de tester leur validité prédictive. Une analyse factorielle exploratoire des items de l’instrument en a extrait trois dimensions : la déviance sexuelle, l’orientation antisociale et le détachement émotionnel. Des analyses de régressions de Cox ont révélé que ces facteurs affichaient une validité prédictive différentielle; la déviance sexuelle ne prédisait que la récidive sexuelle, alors que l’orientation antisociale ne prédisait que la récidive violente non sexuelle et la récidive générale. Le détachement émotionnel affichait une validité prédictive incohérente. Des analyses de courbes ROC ont indiqué que la dernière révision de la Statique-99, la Statique-99R, surpassait pratiquement en tout point son prédécesseur. Ces mêmes analyses indiquaient que la validité prédictive de l’échelle était similaire pour les agresseurs sexuels de femmes et d’enfants.

Affectation de composantes basée sur des contraintes énergétiques dans une architecture multiprocesseurs en trois dimensions

La lithographie et la loi de Moore ont permis des avancées extraordinaires dans la fabrication des circuits intégrés. De nos jours, plusieurs systèmes très complexes peuvent être embarqués sur la même puce électronique. Les contraintes de développement de ces systèmes sont tellement grandes qu’une bonne planification dès le début de leur cycle de développement est incontournable. Ainsi, la planification de la gestion énergétique au début du cycle de développement est devenue une phase importante dans la conception de ces systèmes. Pendant plusieurs années, l’idée était de réduire la consommation énergétique en ajoutant un mécanisme physique une fois le circuit créé, comme par exemple un dissipateur de chaleur. La stratégie actuelle est d’intégrer les contraintes énergétiques dès les premières phases de la conception des circuits. Il est donc essentiel de bien connaître la dissipation d’énergie avant l’intégration des composantes dans une architecture d’un système multiprocesseurs de façon à ce que chaque composante puisse fonctionner efficacement dans les limites de ses contraintes thermiques. Lorsqu’une composante fonctionne, elle consomme de l’énergie électrique qui est transformée en dégagement de chaleur. Le but de ce mémoire est de trouver une affectation efficace des composantes dans une architecture de multiprocesseurs en trois dimensions en tenant compte des limites des facteurs thermiques de ce système.

Développement des dimensions du capital culturel dans l'étude des inégalités sociales liées au tabagisme chez les jeunes adultes

La théorie du capital culturel est de plus en plus utilisée en santé publique et pourrait être utile à l’étude des inégalités sociales liées au tabagisme chez les jeunes adultes. Ceux-ci véhiculent une haute prévalence du tabagisme et plusieurs particularités qui font d’eux un groupe cible qui mérite davantage d’attention. Cependant, le développement du capital culturel porte encore peu de consensus quant à sa définition et son opérationnalisation. Nous proposons un nouveau cadre de référence autour de trois dimensions – champs, générations et états – et établissons une application empirique de celui-ci en étudiant l’association entre certains indicateurs du capital culturel et le tabagisme des jeunes adultes. Nous utilisons les données du projet Interdisciplinary Study of Inequalities in Smoking qui a recruté 2 093 jeunes adultes à Montréal, Canada en 2011-2012. Nos variables dépendantes sont le statut tabagique courant et le nombre de cigarettes fumées dans une journée. Nous examinons les corrélations entre les indicateurs de capital culturel et leur association avec le tabagisme au travers de modèles de régression hiérarchique logistique et linéaire. Nous observons de faibles associations entre les indicateurs retenus. Nous observons aussi que les indicateurs du capital culturel liés aux champs de la santé et de l’éducation, chez les participants et leurs parents, étaient tous associés au comportement tabagique. A la lumière de notre cadre de référence, une approche multidimensionnelle à l’utilisation du capital culturel peut nous permettre de mieux comprendre les inégalités sociales liées au tabagisme chez les jeunes adultes.

Trajectoires développementales des dimensions du profil de dysrégulation (CBCL-DE) – agressivité, anxiété et inattention : éléments prédicteurs de diplomation au secondaire chez les garçons.

Ouvrage réalisé sous la supervision du comité de jury composé des membres suivants: Dre Leila Ben Amor, Dre Diane Sauriol, Daniel Fiset, PhD. & Éric Lacourse PhD.

Learning Three-Dimensional Shape Models for Sketch Recognition

Artifacts made by humans, such as items of furniture and houses, exhibit an enormous amount of variability in shape. In this paper, we concentrate on models of the shapes of objects that are made up of fixed collections of sub-parts whose dimensions and spatial arrangement exhibit variation. Our goals are: to learn these models from data and to use them for recognition. Our emphasis is on learning and recognition from three-dimensional data, to test the basic shape-modeling methodology. In this paper we also demonstrate how to use models learned in three dimensions for recognition of two-dimensional sketches of objects.