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1
Akkoyun, Emrah. "Parallelization Of Functional Flow To Predict Protein Functions." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12612932/index.pdf.
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Protein-protein interaction networks provide important information about what the biological function of proteins whose roles are unknown might be in a cell. These interaction networks were analyzed by a variety of approaches by running them on a single computer and the roles of the proteins identified were used to predict the function of the proteins unidentified. The functional flow is an approach that takes the network connectivity, distance effect, topology of the network with local and global views into account. With these advantages, that the functional flow produces more accurate results on the prediction of protein functions was presented by the previos conducted researches. However, the application implemented for this approach could not be practically applied on the large and complex network produced for the complex species because of memory limitation. The purpose of this thesis is to provide a new application be implemented on the high computing performance where the application can be scaled on the large data sets. Therefore, Hadoop, one of the open source map/reduce environments, was installed on 18 hosts each of which has eight cores.
Methodthe first map/reduce job distributes the protein interaction network as a format which allows parallel distributed computing to all the worker nodes, the other map/reduce job generates flows for each known protein function and the role of the proteins unidentified are predicted by accumulating all of these generated flows. It has been observed in the experiments we performed that the application requiring high performance computing can be decomposed into worker nodes efficiently and the application can provide better performance as the resources increase.
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Lee, Jungkwan. "Alignment between genetic and physical map, and pheromone functions in Gibberella zeae." Diss., Manhattan, Kan. : Kansas State University, 2007. http://hdl.handle.net/2097/562.
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Rizzardo, Caitlan A. "Multipurpose Map Designs for GPS Surface-Vehicle Navigation: Spatial Knowledge and Advisory Functions." Wright State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=wright1316635259.
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Muir, Autumn M. "The Psalter Mappaemundi: Medieval Maps Enabling Ascension of the Soul within Christian Devotional Practices." Bowling Green State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1300733958.
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Meneghini, Marc D. "A MAP kinase-related pathway functions with the Wnt pathway to regulate anterior-posterior polarity in C. elegans /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9977911.
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Thesis (Ph. D.)--University of Oregon, 2000.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 76-79). Also available for download via the World Wide Web; free to University of Oregon users.
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Labrande, Hugo. "Explicit computation of the Abel-Jacobi map and its inverse." Thesis, Université de Lorraine, 2016. http://www.theses.fr/2016LORR0142/document.
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L'application d'Abel-Jacobi fait le lien entre la forme de Weierstrass d'une courbe elliptique définie sur C et le tore complexe qui lui est associé. Il est possible de la calculer en un nombre d'opérations quasi-linéaire en la précision voulue, c'est à dire en temps O(M(P) log P). Son inverse est donné par la fonction p de Weierstrass, qui s'exprime en fonction de thêta, une fonction importante en théorie des nombres. L'algorithme naturel d'évaluation de thêta nécessite O(M(P) sqrt(P)) opérations, mais certaines valeurs (les thêta-constantes) peuvent être calculées en O(M(P) log P) opérations en exploitant les liens avec la moyenne arithmético-géométrique (AGM). Dans ce manuscrit, nous généralisons cet algorithme afin de calculer thêta en O(M(P) log P). Nous exhibons une fonction F qui a des propriétés similaires à l'AGM. D'une façon similaire à l'algorithme pour les thêta-constantes, nous pouvons alors utiliser la méthode de Newton pour calculer la valeur de thêta. Nous avons implanté cet algorithme, qui est plus rapide que la méthode naïve pour des précisions supérieures à 300 000 chiffres décimaux. Nous montrons comment généraliser cet algorithme en genre supérieur, et en particulier comment généraliser la fonction F. En genre 2, nous sommes parvenus à prouver que la même méthode mène à un algorithme qui évalue thêta en O(M(P) log P) opérations ; la même complexité s'applique aussi à l'application d'Abel-Jacobi. Cet algorithme est plus rapide que la méthode naïve pour des précisions plus faibles qu'en genre 1, de l'ordre de 3 000 chiffres décimaux. Nous esquissons également des pistes pour obtenir la même complexité en genre quelconque. Enfin, nous exhibons un nouvel algorithme permettant de calculer une isogénie de courbes elliptiques de noyau donné. Cet algorithme utilise l'application d'Abel-Jacobi, car il est facile d'évaluer l'isogénie sur le tore ; il est sans doute possible de le généraliser au genre supérieurThe Abel-Jacobi map links the short Weierstrass form of a complex elliptic curve to the complex torus associated to it. One can compute it with a number of operations which is quasi-linear in the target precision, i.e. in time O(M(P) log P). Its inverse is given by Weierstrass's p-function, which can be written as a function of theta, an important function in number theory. The natural algorithm for evaluating theta requires O(M(P) sqrt(P)) operations, but some values (the theta-constants) can be computed in O(M(P) log P) operations by exploiting the links with the arithmetico-geometric mean (AGM). In this manuscript, we generalize this algorithm in order to compute theta in O(M(P) log P). We give a function F which has similar properties to the AGM. As with the algorithm for theta-constants, we can then use Newton's method to compute the value of theta. We implemented this algorithm, which is faster than the naive method for precisions larger than 300,000 decimal digits. We then study the generalization of this algorithm in higher genus, and in particular how to generalize the F function. In genus 2, we managed to prove that the same method leads to a O(M(P) log P) algorithm for theta; the same complexity applies to the Abel-Jacobi map. This algorithm is faster than the naive method for precisions smaller than in genus 1, of about 3,000 decimal digits. We also outline a way one could reach the same complexity in any genus. Finally, we study a new algorithm which computes an isogeny of elliptic curves with given kernel. This algorithm uses the Abel-Jacobi map because it is easy to evaluate the isogeny on the complex torus; this algorithm may be generalizable to higher genera
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Kulkarni, Praveen P. "Functional MRI Data Analysis Techniques and Strategies to Map the Olfactory System of a Rat Brain." Digital WPI, 2006. https://digitalcommons.wpi.edu/etd-dissertations/37.
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Understanding mysteries of a brain represents one of the great challenges for modern science. Functional magnetic resonance imaging (fMRI) has two features that make it unique amongst other imaging modalities used in behavioral neuroscience. First, it can be entirely non-invasive and second, fMRI has the spatial and temporal resolution to resolve patterns of neuronal activity across the entire brain in less than a minute. fMRI indirectly detects neural activity in different parts of the brain by comparing contrast in MR signal intensity prior to and following stimulation. Areas of the brain with increased synaptic and neuronal activity require increased levels of oxygen to sustain this activity. Enhanced brain activity is accompanied by an increase in metabolism followed by increases in blood flow and blood volume. The enhanced blood flow usually exceeds the metabolic demand exposing the active brain area to high level of oxygenated hemoglobin. Oxygenated hemoglobin increases the MR signal intensity that can be detected in MR scanner. This relatively straight forward scenario is, unfortunately, oversimplified. The fMRI signal change to noise ratio is extremely small. In this work a quantitative analysis strategy to analyze fMRI data was successfully developed, implemented and optimized for the rat brain. Therein, each subject is registered or aligned to a complete volume-segmented rat atlas. The matrices that transformed the subject's anatomy to the atlas space are used to embed each slice within the atlas. All transformed pixel locations of the anatomy images are tagged with the segmented atlas major and minor regions creating a fully segmented representation of each subject. This task required the development of a full 3D surface atlas based upon 2D non-uniformly spaced 2D slices from an existing atlas. A multiple materials marching cube (M3C) algorithm was used to generate these 1277 subvolumes. After this process, they were coalesced into a dozen major zones of the brain (amygdaloid complex, cerebrum, cerebellum, hypothalamus, etc.). Each major brain category was subdivided into approximately 10 sub-major zones. Many scientists are interested in behavior and reactions to pain, pleasure, smell, for example. Consequently, the 3D volume atlas was segmented into functional zones as well as the anatomical regions. A utility (program) called Tree Browser was developed to interactively display and choose different anatomical and/or functional areas. Statistical t-tests are performed to determine activation on each subject within their original coordinate system. Due to the multiple t-test analyses performed, a false-positive detection controlling mechanism was introduced. A statistical composite of five components was created for each group. The individual analyses were summed within groups. The strategy developed in this work is unique as it registers segments and analyzes multiple subjects and presents a composite response of the whole group. This strategy is robust, incredibly fast and statistically powerful. The power of this system was demonstrated by mapping the olfactory system of a rat brain. Synchronized changes in neuronal activity across multiple subjects and brain areas can be viewed as functional neuro-anatomical circuits coordinating the thoughts, memories and emotions for particular behaviors using this fMRI module.
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Lkhamsuren, Altangerel. "A duality approach to gap functions for variational inequalities and equilibrium problems." Doctoral thesis, Universitätsbibliothek Chemnitz, 2006. http://nbn-resolving.de/urn:nbn:de:swb:ch1-200601214.
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This work aims to investigate some applications of the
conjugate duality for scalar and vector optimization problems to
the construction of gap functions for variational inequalities and
equilibrium problems. The basic idea of the approach is to
reformulate variational inequalities and equilibrium problems into
optimization problems depending on a fixed variable, which allows
us to apply duality results from optimization problems.
Based on some perturbations, first we consider the conjugate
duality for scalar optimization. As applications, duality
investigations for the convex partially separable optimization
problem are discussed.
Afterwards, we concentrate our attention on some applications of
conjugate duality for convex optimization problems in finite and
infinite-dimensional spaces to the construction of a gap function
for variational inequalities and equilibrium problems. To verify
the properties in the definition of a gap function weak and strong
duality are used.
The remainder of this thesis deals with the extension of this
approach to vector variational inequalities and vector equilibrium
problems. By using the perturbation functions in analogy to the
scalar case, different dual problems for vector optimization and
duality assertions for these problems are derived. This study
allows us to propose some set-valued gap functions for the vector
variational inequality. Finally, by applying the Fenchel duality
on the basis of weak orderings, some variational principles for
vector equilibrium problems are investigated.
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Kurdej, Marek. "Exploitation of map data for the perception of intelligent vehicles." Thesis, Compiègne, 2015. http://www.theses.fr/2015COMP2174/document.
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La plupart des logiciels contrôlant les véhicules intelligents traite de la compréhension de la scène. De nombreuses méthodes existent actuellement pour percevoir les obstacles de façon automatique. La majorité d’entre elles emploie ainsi les capteurs extéroceptifs comme des caméras ou des lidars. Cette thèse porte sur les domaines de la robotique et de la fusion d’information et s’intéresse aux systèmes d’information géographique. Nous étudions ainsi l’utilité d’ajouter des cartes numériques, qui cartographient le milieu urbain dans lequel évolue le véhicule, en tant que capteur virtuel améliorant les résultats de perception. Les cartes contiennent en effet une quantité phénoménale d’information sur l’environnement : sa géométrie, sa topologie ainsi que d’autres informations contextuelles. Dans nos travaux, nous avons extrait la géométrie des routes et des modèles de bâtiments afin de déduire le contexte et les caractéristiques de chaque objet détecté. Notre méthode se base sur une extension de grilles d’occupations : les grilles de perception crédibilistes. Elle permet de modéliser explicitement les incertitudes liées aux données de cartes et de capteurs. Elle présente également l’avantage de représenter de façon uniforme les données provenant de différentes sources : lidar, caméra ou cartes. Les cartes sont traitées de la même façon que les capteurs physiques. Cette démarche permet d’ajouter les informations géographiques sans pour autant leur donner trop d’importance, ce qui est essentiel en présence d’erreurs. Dans notre approche, le résultat de la fusion d’information contenu dans une grille de perception est utilisé pour prédire l’état de l’environnement à l’instant suivant. Le fait d’estimer les caractéristiques des éléments dynamiques ne satisfait donc plus l’hypothèse du monde statique. Par conséquent, il est nécessaire d’ajuster le niveau de certitude attribué à ces informations. Nous y parvenons en appliquant l’affaiblissement temporel. Étant donné que les méthodes existantes n’étaient pas adaptées à cette application, nous proposons une famille d’opérateurs d’affaiblissement prenant en compte le type d’information traitée. Les algorithmes étudiés ont été validés par des tests sur des données réelles. Nous avons donc développé des prototypes en Matlab et des logiciels en C++ basés sur la plate-forme Pacpus. Grâce à eux nous présentons les résultats des expériences effectués en conditions réellesThis thesis is situated in the domains of robotics and data fusion, and concerns geographic information systems. We study the utility of adding digital maps, which model the urban environment in which the vehicle evolves, as a virtual sensor improving the perception results. Indeed, the maps contain a phenomenal quantity of information about the environment : its geometry, topology and additional contextual information. In this work, we extract road surface geometry and building models in order to deduce the context and the characteristics of each detected object. Our method is based on an extension of occupancy grids : the evidential perception grids. It permits to model explicitly the uncertainty related to the map and sensor data. By this means, the approach presents also the advantage of representing homogeneously the data originating from various sources : lidar, camera or maps. The maps are handled on equal terms with the physical sensors. This approach allows us to add geographic information without imputing unduly importance to it, which is essential in presence of errors. In our approach, the information fusion result, stored in a perception grid, is used to predict the stateof environment on the next instant. The fact of estimating the characteristics of dynamic elements does not satisfy the hypothesis of static world. Therefore, it is necessary to adjust the level of certainty attributed to these pieces of information. We do so by applying the temporal discounting. Due to the fact that existing methods are not well suited for this application, we propose a family of discoun toperators that take into account the type of handled information. The studied algorithms have been validated through tests on real data. We have thus developed the prototypes in Matlab and the C++ software based on Pacpus framework. Thanks to them, we present the results of experiments performed in real conditions
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Голованова, В. С., and V. S. Golovanova. "Проект электронной литературной карты : магистерская диссертация." Master's thesis, б. и, 2020. http://hdl.handle.net/10995/94028.
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Диссертационная работа посвящена исследованию феномена литературных карт с точки зрения литературоведческого и издательского аспекта. Исследование имеет практический характер: теоретическое освоение материала, посвященного литературным картам, позволило достичь цель исследования ‒ реализовать проект «Электронная интерактивная литературная карта по роману Е. Сосновского “Апокриф Аглаи”».The thesis is devoted to the study of the phenomenon of literary maps from the point of view of literary and publishing aspects. The research is of a practical nature: the theoretical development of the material devoted to literary maps allowed us to achieve the goal of the research ‒ to implement the project "Electronic interactive literary map based on the novel by E. Sosnovsky "Apocryph of Aglaia"".
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Belova, Anna. "Computational dynamics – real and complex." Doctoral thesis, Uppsala universitet, Matematiska institutionen, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-332280.
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The PhD thesis considers four topics in dynamical systems and is based on one paper and three manuscripts. In Paper I we apply methods of interval analysis in order to compute the rigorous enclosure of rotation number. The described algorithm is supplemented with a method of proving the existence of periodic points which is used to check rationality of the rotation number. In Manuscript II we provide a numerical algorithm for computing critical points of the multiplier map for the quadratic family (i.e., points where the derivative of the multiplier with respect to the complex parameter vanishes). Manuscript III concerns continued fractions of quadratic irrationals. We show that the generating function corresponding to the sequence of denominators of the best rational approximants of a quadratic irrational is a rational function with integer coefficients. As a corollary we can compute the Lévy constant of any quadratic irrational explicitly in terms of its partial quotients. Finally, in Manuscript IV we develop a method for finding rigorous enclosures of all odd periodic solutions of the stationary Kuramoto-Sivashinsky equation. The problem is reduced to a bounded, finite-dimensional constraint satisfaction problem whose solution gives the desired information about the original problem. Developed approach allows us to exclude the regions in L2, where no solution can exist.
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Rodrigo-Peiris, Thushani. "Unraveling the Functions of Plant Ran GTPase-Activating Protein (RanGAP) by T-DNA Mutant Analysis and Investigation of Molecular Interactions of Tandem Zinc Finger 1 (TZF1) in Arabidopsis thaliana." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1343796551.
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VILLELA, Andr? Luis Oliveira. "Mapeamento digital de solos da Forma??o Solim?es sob Floresta Tropical Amaz?nica." Universidade Federal Rural do Rio de Janeiro, 2013. https://tede.ufrrj.br/jspui/handle/jspui/1985.
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The Brazilian territory region covered by the Amazon rainforest, due to its continental dimensions and difficulty of access and various interests in extractive activities, has great demand for information to provide support for the occupation, exploitation, and systematic recuperation thus keeping environmental safeguards. The regional soil information available is scarce and in scales inconsistent with the current demands, and the investments in new areas of research in the region is still insufficient. With technological developments, especially in the area of informatics that enables the storage and analysis of large banks of pedological data, the soil mapping techniques improved considerably. Pedometric techniques have been used to store and to explore large databases, thus enabling the improvement of existing soil databases and allowing manufacture of new products in larger scale and mapped areas, with low investment required. The hypothesis of this study is that the technique of reference area may allow the systematic digital mapping of soils from the Solim?es Formation, in the Amazon State. The general objective was to develop and compare methods for mapping soils in the Oil Province Uruc? (AM), using relief covariates. A conventional pedological survey of an area of 8.000 hectares, at the detail level, was executed to be used as a reference area (RA), in the augmentation of the map using digital soil mapping (MDS) techniques for an area of 73.000 hectares after downscaling and grouping of the legend. The numerical modeling of the terrain (MDT) was used (11 covariates derived from MDT) for further application of this soil formation factor as a predictor of the map units, in discriminant functions (DF), and in an expert system based on a tree model classification (AC). Four MDS models were developed, where two were trained using the studied region conceptual model of the pedologist, and the other two were trained with models based on a statistical analysis of the reference area information. The techniques were effective for predicting the mapping units (MU) in the study region, with overall accuracy (EG) ranging from 74.62 % to 88.81 %, and the kappa index was between 0.68 and 0.85. The MDS based in the expert system and AC showed significantly better results in terms of the kappa index, general EG, and the EG for 3 of the 4 mapping units in the area. Although the FD had not the highest accuracy levels, they showed a great potential for use in MDS, especially for preliminary mapping for the pedological survey of new regions, using knowledge of AR neighboring areas. The limitations were observed in the use of FD for mapping unities with small territorial expression, and it is recommended to increase the number of training observations in a way inversely proportional to the frequency of observation of these MUs. The major contribution of this work to scientific community was the establishment of bases and techniques of MDS, using AR and the soil relief relationship, for systematic mapping of new soils form Solim?es Formation.
A regi?o do territ?rio brasileiro coberta por floresta tropical amaz?nica, por suas dimens?es continentais e dificuldade de acesso e interesses diversos em atividades extrativistas, apresenta forte demanda por informa??es gerais que possam servir como subs?dio para a ocupa??o, explora??o e recupera??o ordenada e ambientalmente equilibrada. As informa??es pedol?gicas dispon?veis sobre a ?rea s?o escassas e em escalas incompat?veis com as demandas atuais, e os investimentos em novas frentes de pesquisa na regi?o ainda s?o insuficientes. Com a evolu??o tecnol?gica, sobretudo na ?rea da inform?tica que possibilita o armazenamento e an?lises de extensos bancos de dados pedol?gicos, as t?cnicas de mapeamento pedol?gico v?m se aperfei?oando consideravelmente. T?cnicas de pedometria t?m sido utilizadas para armazenar e explorar grandes bancos de dados e t?m possibilitado o aperfei?oamento das bases pedol?gicas existentes e permitido a confec??o de novos produtos em escala e ?reas mapeadas maiores, com menores investimentos exigidos. A hip?tese deste trabalho ? de que a t?cnica de ?rea de refer?ncia permite o mapeamento digital sistem?tico dos solos da regi?o da forma??o Solim?es, e o objetivo geral foi desenvolver e comparar m?todos de mapeamento de solos da Forma??o Solim?es, na Prov?ncia Petrol?fera de Urucu, AM, utilizando covari?veis do relevo. Foi executado um levantamento pedol?gico convencional de uma regi?o com 8.000 ha, em n?vel de detalhe para ser utilizado como ?rea de refer?ncia (AR) para a amplia??o do mapa, com t?cnicas de mapeamento digital de solos (MDS) para uma ?rea de 73.000 ha com redu??o de escala e agrupamento de legenda. Foi ent?o elaborada modelagem num?rica do terreno (MDT) (11 covari?veis derivadas do MDT) para posterior utiliza??o deste fator de forma??o do solo, como preditor das unidades de mapeamento, em fun??es discriminantes (FD) e um sistema especialista baseado em modelo de ?rvores de classifica??o (AC). Foram desenvolvidas 4 cartas MDS, sendo duas treinadas por modelos baseados no modelo conceitual do ped?logo sobre a regi?o em estudo, e duas treinadas por modelos baseados em an?lise estat?stica de informa??es sobre a ?rea de referencia. As t?cnicas mostraram-se eficientes para predi??o de unidades de mapeamento (UM) na regi?o de estudo, com exatid?o global (EG) variando entre 74,62% a 88,81% e ?ndice kappa entre 0,68 e 0,85. O MDS baseado em sistema especialista e AC apresentou resultados sensivelmente melhores em termos de ?ndice kappa, EG geral e EG para 3 das 4 UM da ?rea. Embora as FD n?o tenham apresentado os maiores ?ndices de acur?cia, estas tem grande potencial de uso em MDS, sobretudo para a confec??o de mapas preliminares para o levantamento pedol?gico de novas regi?es, utilizando-se do conhecimento de AR de ?reas vizinhas. Foram observadas limita??es no emprego de FD para o mapeamento de UM?s com pequena express?o territorial, sendo recomend?vel o aumento do n?mero de observa??es de treinamento inversamente proporcional ? frequ?ncia de observa??o destas UM?s. A maior contribui??o deste trabalho para a comunidade cient?fica foi o estabelecimento de bases e t?cnicas de MDS, utilizando AR e rela??o solo-relevo para o mapeamento sistem?tico de novas ?reas da forma??o Solim?es.
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Gumos, Aleksander Karol. "Modelling the Cross-Country Trafficability with Geographical Information Systems." Thesis, Linköping University, Department of Computer and Information Science, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-313.
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The main objectives of this work were to investigate Geographical Information Systems techniques for modelling a cross-country trafficability. To accomplished stated tasks, reciprocal relationships between the soil deposits, local hydrology, geology and geomorphology were studied in relation to the study area in South-Eastern Sweden.
Growing awareness of nowadays users of GIS in general is being concentrated on understanding an importance of soil conditions changed after cross-country trafficability. Therefore, in this thesis, constructing of the Soil Knowledge Database introduced to the genuine geological soil textural classes a new, modified geotechnical division with desirable for off-road ground reasoning measurable factors, like soil permeability, capillarity or Atterberg’s consistency limits.
Digital Elevation Model, the driving force for landscape studies in the thesis, was carefully examined together with the complementary datasets of the investigated area. Testing of the elevation data was done in association to the hydrological modelling, which resulted with the Wetness Index map. The three distinguishable soil wetness conditions: dry, moist and wet, were obtained, and used consequently for creation of the static ground conditions map, a visible medium of soils susceptibility to for example machine compaction.
The work resulted with a conceptual scheme for cross-country trafficability modelling, which was put into effect while modeling in GIS. As a final outcome, by combining all processed data together, derivatives were incorporated and draped over the rendered 3D animating scene. A visually aided simulation enabled to concretized theoretical, hypothetical and experimental outcomes into one coherent model of apprised under Multicriterial Evaluation techniques standardized factor maps for ground vehicle maneuverability. Also further steps of research were proposed.
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Genot, Baptiste. "Functional characterization of the stress-activated Arabidopsis MAP Kinase MPK3 using gain-of-function mutations." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLE010.
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Les plantes détectent les pathogènes dans leur environnement et s’y adaptent pour survivre. Le groupe Stress Signalling de l’IPS2 cherche à décrire les mécanismes cellulaires mis alors en jeu et à proposer des stratégies permettant de développer des cultures plus résistantes aux stress. Les modules Mitogen-Activated Protein Kinases (MAPKs) semblent être des acteurs clés de la transduction du signal: ils sont en effet très rapidement activés par de nombreux stress et notamment par les Pathogen-Associated Molecular Patterns (PAMPs). Des approches de génétique, utilisant des mutants perte-de-fonction, ont montré que ces modules MAPKs régulaient de nombreux aspects de l’adaptation des plantes à leur environnement.Dans notre laboratoire, nous avons précédemment identifié des mutations capables de rendre les MAPKs de la plante modèle Arabidopsis thaliana constitutivement actives (CA). L’objectif de mon projet était de clarifier les rôles spécifiques des MAPKs activées par le PAMP flg22 à l’aide de ce nouvel outil. Pour cela, j’ai créé des plantes exprimant des CA MAPKs et j’ai caractérisé leur phénotype en conditions normales de croissance ou lors d’interactions avec des pathogènes. Je me suis particulièrement intéressé à la MAPK MPK3. J’ai montré que des plantes exprimant une version CA de MPK3 avaient un phénotype d’auto-immunité caractérisé par un nanisme associé à la mort cellulaire spontanée et à une accumulation de formes activées de l’oxygène. Des études métabolomiques, transcriptomiques et de génétique ont permis de préciser les réponses régulées par cette MAPK. J’ai en particulier montré que le phénotype des plantes CA-MPK3 était dépendant de la protéine EDS1 (Enhanced Disease Susceptibility 1), un régulateur primordial des réponses aux pathogènes, et partiellement dépendant de l’acide salicylique. J’ai également créé et caractérisé des plantes exprimant des formes CA de MPK6 et MPK11.En conclusion, mon travail tirant partie des mutations CA a permis de proposer de nouveaux rôles spécifiques pour certaines MAPKs activées par le stress. Mes résultats préliminaires suggèrent également que les plantes exprimant des CA MAPK peuvent présenter une meilleure résistance aux pathogènesPlants can detect pathogens in their environment and adapt to survive it. The Stress Signalling group in IPS2 aims to decipher cellular mechanisms occurring after pathogens detection and to propose strategies to develop stress-resistant crops. Mitogen-Activated Protein Kinases (MAPKs) modules define key actors of signal transduction. MAPKs are indeed quickly activated in response to various stresses including pathogens-associated molecular patterns (PAMPs). Genetic approaches using loss-of-function mutants showed that MAPK modules regulate many aspects of plant adaptation to their environment.In our laboratory, we previously identified mutations which render MAPKs constitutively active (CA) in the plant model Arabidopsis thaliana.The main objective of my thesis was to clarify the specific roles of MAPKs activated by the PAMP flg22 using this new tool. For this, I created plants expressing CA MAPKs and characterized them in normal growth conditions or after pathogen infections. I mainly focused my project on the MAPK MPK3. I showed that plants expressing a CA version of MPK3 had an auto-immune phenotype characterized by a severe dwarfism, spontaneous cell death and accumulation of reactive oxygen species. Transcriptomic, metabolomic and genetic studies were performed to understand which pathways are regulated by this MAPK. This work demonstrates that MPK3 is a positive regulator of plant immunity, whose function depends on EDS1 (Enhanced Disease Susceptibility 1), a key regulator of pathogens responses, and partially depends on the phytohormone salicylic acid. I also created and characterized plants expressing constitutively active MPK6 and MPK11. In conclusion, CA mutations allowed us to reveal new specific roles for several stress-activated MAPKs. My preliminary results also suggest that plants expressing CA MAPK may have a better resistance to pathogens
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Pachev, Ivan. "GPUMap: A Transparently GPU-Accelerated Map Function." DigitalCommons@CalPoly, 2017. https://digitalcommons.calpoly.edu/theses/1704.
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As GPGPU computing becomes more popular, it will be used to tackle a wider range of problems. However, due to the current state of GPGPU programming, programmers are typically required to be familiar with the architecture of the GPU in order to effectively program it. Fortunately, there are software packages that attempt to simplify GPGPU programming in higher-level languages such as Java and Python. However, these software packages do not attempt to abstract the GPU-acceleration process completely. Instead, they require programmers to be somewhat familiar with the traditional GPGPU programming model which involves some understanding of GPU threads and kernels. In addition, prior to using these software packages, programmers are required to transform the data they would like to operate on into arrays of primitive data. Typically, such software packages restrict the use of object-oriented programming when implementing the code to operate on this data. This thesis presents GPUMap, which is a proof-of-concept GPU-accelerated map function for Python. GPUMap aims to hide all the details of the GPU from the programmer, and allows the programmer to accelerate programs written in normal Python code that operate on arbitrarily nested objects using a majority of Python syntax. Using GPUMap, certain types of Python programs are able to be accelerated up to 100 times over normal Python code.
There are also software packages that provide simplified GPU acceleration to distributed computing frameworks such as MapReduce and Spark. Unfortunately, these packages do not provide a completely abstracted GPU programming experience, which conflicts with the purpose of the distributed computing frameworks: to abstract the underlying distributed system. This thesis also presents GPU-accelerated RDD (GPURDD), which is a type of Spark Resilient Distributed Dataset (RDD) which incorporates GPUMap into its map, filter, and foreach methods in order to allow Spark applicatons to make use of the abstracted GPU acceleration provided by GPUMap.
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Nováková, Marie. "Mapování pohybových artefaktů ve fMRI." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2013. http://www.nusl.cz/ntk/nusl-220039.
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This thesis summarizes a theory of magnetic resonance and the method of functional magnetic resonance. It is focused on the influence of motion artifacts and image preprocessing methods, especially realign. It deals with the possibility of using movement parameters obtained in the process of alignment of functional scans to create maps that show the expression of motion artifacts. In this thesis, three different methods were designed, implemented a tested. These methods lead to the creation of probability, power and statistical group maps showing areas typically affected by movement artifacts.
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Ang, Jason. "Offset Surface Light Fields." Thesis, University of Waterloo, 2003. http://hdl.handle.net/10012/1100.
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For producing realistic images, reflection is an important visual effect. Reflections of the environment are important not only for highly reflective objects, such as mirrors, but also for more common objects such as brushed metals and glossy plastics. Generating these reflections accurately at real-time rates for interactive applications, however, is a difficult problem. Previous works in this area have made assumptions that sacrifice accuracy in order to preserve interactivity.
I will present an algorithm that tries to handle reflection accurately in the general case for real-time rendering. The algorithm uses a database of prerendered environment maps to render both the original object itself and an additional bidirectional reflection distribution function (BRDF). The algorithm performs image-based rendering in reflection space in order to achieve accurate results. It also uses graphics processing unit (GPU) features to accelerate rendering.
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Eger, Glenda. "Regulation and Function of MAP Kinases in PDGF Signaling." Doctoral thesis, Uppsala universitet, Ludwiginstitutet för cancerforskning, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-301057.
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Platelet-derived growth factor (PDGF) is a family of signaling molecules that stimulates cell growth, survival and migration. PDGF is recognized by specific transmembrane proteins, the PDGF receptors, which relay the signals to the cell activating the Mitogen-activated protein (MAP) kinases and other signaling pathways. Aberrant activation of these pathways is frequently detected in cancer. Hence, the study of these processes is essential for identifying potential drug targets or diagnostic markers. In paper I, we identified Receptor Subfamily 4 Group A Member 1 NR4A1 to be regulated by PDGF via MAP kinases, clarifying the role of Extracellular signal–regulated kinases (Erk) 1/2, Erk5 and Nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) in its regulation. NR4A1 was found to be important for the tumorigenic potential, measured as anchorage-independent growth, of glioblastoma cells. Since the cellular responses elicited by PDGF result from the balance between phosphorylation and dephosphorylation events, we investigated the role of the dual specificity phosphatases DUSP4/MKP-2 and DUSP6/MKP-3. In paper II, we describe the crucial role of Erk1/2 and p53 in the expression of DUSP4/MKP2. Moreover, we observed that DUSP4/MKP-2 downregulation decreases Erk5 activation and accelerates PDGFRβ internalization and downregulation resulting in a specific inhibition of Signal transducers and activators of transcription (Stat) 3, Src and protein kinase C (PKC), and partially of p38, Stat1/5 and Phoshoplipase Cγ (PLCγ). In paper III, we report that DUSP6/MKP-3 creates a negative cross-talk between Erk1/2 and Erk5 and an auto-inhibitory feedback loop on the PI3-kinase/Akt pathway. In paper IV, we identify a new regulative mechanism of the PDGF pathway. PDGF induces Erk5 expression and activation that modulates the PDGFRβ activity. After Erk5 downregulation, the receptor undergoes to a faster and stronger activation that results in a faster internalization and degradation. In conclusion, we present a mechanism through which the PDGF/MAP kinases support tumor growth, and elucidate different regulatory pathways involved in PDGF signaling.
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Da, Silva Carla Cristina 1978. "Construction of a functional map for rubber tree (Hevea brasiliensis) = Construção de um mapa funcional em seringueira (Hevea brasiliensis)." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316470.
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Orientador: Anete Pereira de Souza.Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A seringueira (Hevea brasiliensis), espécie nativa da Amazônia, é a maior fonte de borracha natural do mundo. Programas de melhoramento genético da seringueira têm sido cruciais para a obtenção de caracteres desejáveis. Entretanto, o ciclo de melhoramento da seringueira é muito longo (cerca de 30 anos), tornando-se essencial o desenvolvimento de novas técnicas de avaliação precoce. As bibliotecas de cDNA e Expressed Sequence Tags (ESTs) são ferramentas muito importantes em biologia molecular: possibilitam identificar genes preferencialmente expressos em tecidos ou tipos celulares e também são valiosas fontes de marcadores polimórficos, instrumentos poderosos para genotipagem e mapeamento molecular. O uso de marcadores derivados de ESTs permite construir mapas funcionais, nos quais são posicionados genes transcritos ou regiões próximas aos genes. Este tipo de mapeamento é importante para estudos de associação gene-característica, e identificação de genes candidatos. Este trabalho objetivou a construção de bibliotecas de cDNA de diferentes tecidos (painel, látex e folha) e tratamentos (exposição ao frio e infecção controlada por Microcyclus ulei) de seringueira para desenvolver sequências EST e marcadores moleculares gene-direcionados a partir destas sequências, para aumentar a saturação de um mapa integrado baseado em microssatélites, no qual identificaram 18 quantitative trait loci (QTLs) para características de crescimento, construído previamente em nosso laboratório. Foram sequenciados 10.464 clones, gerando 8.551 ESTs de alta qualidade que agrupadas formaram 5.211 unigenes. Destes, 3.582 (68,7%) apresentam similaridade com uma proteína hipotética ou expressa. Foram desenvolvidos 173 marcadores EST-SSR e 43 marcadores SNP para H. brasiliensis. 150 EST-SSRs (87%) podem estar associados a genes funcionais, e 98,8% foram transferidos para outras espécies de Hevea, sugerindo que o gênero seja um complexo formado pelas diferentes espécies. Os SNPs foram identificados em 13 ESTs similares a proteínas de resposta a estresse, desenvolvimento e síntese de látex. Seis sequências foram abundantes nas bibliotecas de exposição ao frio e análises de expressão demonstraram que a expressão de cinco sequências aumentou durante o experimento, principalmente a expressão de duas sequências que foi aumentada mais de 70 vezes. Dos EST-SSRs desenvolvidos, 46 foram genotipados na população segregante F1 com 270 indivíduos, e estes marcadores foram adicionados ao mapa genético de seringueira, totalizando 330 marcadores. O programa OneMap foi usado para a construção do mapa que possui 3.068,9 cM de extensão e 22 grupos de ligação (LGs). Cinco locos foram mapeados em regiões QTL, e os transcritos de três são similares a proteínas de resposta a estresse e desenvolvimento. Estes locos podem ser genes candidatos para estudos relacionados a características de crescimento em seringueira. Até o momento, este é o primeiro trabalho em seringueira que combina análises de ESTs de diferentes tecidos e tratamentos, e análises sobre a exposição a baixas temperaturas, em vários genótipos de seringueira. Os novos marcadores adicionados ao mapa poderão auxiliar na identificação de genes de interesse e de QTLs para outras características de importância agronômica. Os vários marcadores gene-direcionados desenvolvidos serão utilizados para mapeamento e posicionamento de possíveis genes em outras populações de mapeamento que estão sendo avaliadas no Laboratório de Análise Genética e Molecular
Abstract: Rubber tree (Hevea brasiliensis), native species of the Amazon, is world¿s major source of natural rubber. Rubber tree breeding programs have been fundamental for the selection of desirable traits. However, the breeding cycle is time consuming (around 30 years), which makes the development of new techniques for early evaluation a necessity. cDNA libraries and Expressed Sequence Tags (ESTs) are very important tools in molecular biology: they enable the identification of genes preferentially expressed in tissues or cellular types and are also a valuable resource of polymorphic markers, powerful instruments for genotyping and molecular mapping. The use of EST-derived markers allows the construction of functional maps, wherein expressed genes or regions near genes are positioned. This type of mapping is important for gene-trait association studies and candidate genes identification. The present study aimed at the construction of cDNA libraries from different tissues (panel, latex and leave) and treatments (cold exposure and Microcyclus ulei controlled infection) of rubber tree for the development of EST sequences and gene-targeted molecular markers, to raise the saturation of a microsatellite-based integrated genetic map previously constructed in our laboratory, in which 18 quantitative trait loci (QTLs) related to growth traits were identified. Sequencing of 10.464 clones generated 8,551 high quality ESTs that were clustered into 5,211 unigenes. Among these, 3,582 (68.7%) showed similarity to a hypothetical or expressed protein. A total of 173 EST-SSR and 43 SNP markers were developed for H. brasiliensis. 150 SSRs (87%) could be associated with functional genes, and 98.8% were transferred to other Hevea species, suggesting that the genus is a complex formed by different species. The SNP markers were identified in 13 ESTs that showed similarity to stress response, development and latex biosynthesis proteins. Six sequences were highly abundant in the cold exposure libraries and expression analyses demonstrated that five sequences were up-regulated during the exposure, with emphasis to two sequences with more than 70-fold increase in expression. From the developed EST-SSRs, 46 were genotyped in the segregating F1 population comprised of 270 plants. These markers were added to the genetic map, which know contains a total of 330 markers. The OneMap software was used for the map construction that now has 3,068.9 cM and 22 linkage groups. Five loci were mapped into QTLs, and transcripts of three of them present similarity to proteins involved in stress response and developmental processes. These loci may be candidate genes for studies related to rubber tree growth traits. To our knowledge, this is the first work in rubber tree that combines analyses of ESTs from different tissues and treatments, and to analyze sequences under cold stress, in several H. brasiliensis genotypes. The new positioned markers may help in the identification of genes of interest and QTLs for other agronomic important traits. The several gene-targeted markers developed here will be used in the mapping and positioning of possible genes in other mapping populations that are now being evaluated at Genetics and Molecular Analysis Laboratory
Doutorado
Genetica Vegetal e Melhoramento
Doutora em Genética e Biologia Molecular
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Edalat, Maryam. "Multiple Functions of Glutathione Transferases : A Study on Enzymatic Function, Regulatory Role and Distribution in Mouse and Man." Doctoral thesis, Uppsala University, Department of Biochemistry, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2152.
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To cope with various endogenous toxin and xenobiotics nature has equipped the organisms with a proper protection system. Glutathione transferases (GSTs) are important components of the cellular defense against oxidative stress. These proteins appear to be suited for different tasks.
Based on catalytic activity of GSTs with monochlorobimane (MCB), a screening method was developed for identification of active GSTs in bacterial colonies and for characterization of combinatorial GST libraries.
Solvent viscosity effects on kcat and kcat/Km on wild-type human GST A1-1 and phenylalanine-220 mutants indicate a physical step being the rate-limiting step in the catalytic mechanism.
Three residues that were under evolutionary selection pressure were identified in Mu class GSTs. By changing these residues in human GSTM2-2, a 1000-fold change of catalytic activity towards GSTM1-1 was accomplished.
Using peptide phage display, a peptide sequence was found that acts as non-substrate ligand for human GST M2-2. The peptide sequence was shown to be highly similar to the C-terminal region of c-Jun N-terminal kinase (JNK). JNK is a kinase linked to activating protein-1 (AP-1) transcriptional activity, which is part of the regulation of cell proliferation and apoptosis in response to cellular stress. Reporter gene assays in cell lines showed that human GST M2-2 coactivates the transcriptional activity of AP-1.
GSTs as part of the cellular defense against oxidative stress could be important in inflammatory processes. The distribution of GSTs in the intestine of both mice and human in abnormal inflammatory state was investigated immunohistochemically. Using an experimental mouse model, it was shown that mouse GST A4-4 is markedly induced while, the expression of Mu and Pi class GSTs is reduced in the colon of conventional and germ-free mice with extensive colitis. Moreover, the expression of mouse GST A4-4 was elevated with time when germ-free mice were exposed to normal bacteria flora. In contrast, Mu and Pi class GSTs showed decreased expression in the colon of germ-free mice associated with commensal flora. The Alpha, Mu and Pi class GST levels in mouse colon were increased when germ-free mice received Lactobacillus strain GG.
The distribution of Alpha, Mu and Pi class GST in the intestinal tissues of patients with Crohn’s disease was investigated using immunohistochemistry. All the three classes were consistently expressed in the intestinal epithelium as well as in macrophage-like cells and smooth muscle tissue. The mucus secreting goblet cells, however, did not express Alpha class GST.
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Berriri, Souha. "Identification of constitutively active forms of Arabidopsis MAP Kinases : brings more evidence on MPK4 function in plant immunity." Thesis, Evry-Val d'Essonne, 2012. http://www.theses.fr/2011EVRY0024.
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La phosphorylation/déphosphorylation des protéines est un mécanisme de signalisation intracellulaire commun. Parmi les kinases végétales, les Mitogen-Activated Protein Kinases (MAPKs) sont impliquées dans de nombreux processus biologiques importants, comme la réponse aux stress biotiques et abiotiques, le développement et la dynamique du cytosquelette. Chez Arabidopsis thaliana et ce malgré de nombreux efforts, les fonctions des kinases impliquées dans les cascades MAPK restent peu inconnues. L'activation des kinases en utilisant des mutations mimant la phosphorylation des sites normalement phosphorylés est une approchequi a fait ses preuves dans le cas de MAP2Ks et a largement contribué à élucider leurs fonctions. Cette stratégie s’est révélée impossible dans le cas des MAPKs, puisque les résidus à muter restent encore à identifier. Pour contourner ce problème, nous avons adapté un crible basé sur la complémentation fonctionnelle d’un mutant MAPK de levure avec des formes aléatoirement mutées de MPK6d’Arabidopsis dans le but d'identifier des mutants présentant une activité constitutive. Nous en avons identifiés plusieurs et avons montré que ces formes constitutivement actives (CA) de MPK6 sont actives sans phosphorylation par les MAP2Ks. Par ailleurs, les mutations des résidus équivalents dans d'autres MAPKs les rendent également hyperactives, ce qui indique que cette stratégie peut être utilisée comme approche générale pour activer les MAPKs afin d’en comprendre les fonctions. L’étude des interactions protéine-protéine et l’analyse des profils dephosphorylation indiquent que les MAPKs CA conservent leur spécificité envers leurs substrats et interacteurs. Comme preuve de concept, nous avons généré des formes actives du MPK4. La MPK4 CA exprimée sous son propre promoteur a parfaitement complémenté le mutant mpk4. La caractérisation des lignées exprimant MPK4 CA confirme le rôle négatif de cette kinase dans les réponses de défense aux pathogènes des plantes que ce soit dans la PTI (PAMP Triggered Immunity) ou dans la ETI (Effector Triggered Immunity). Globalement, ce travail permettra de fournir des informations directes sur les cibles des MAPKs et devrait contribuer à la compréhension globale de la transduction du signal chez les plantesProtein phosphorylations and dephosphorylations are common events occurring duringintracellular signaling processes. Among plant kinases, Mitogen-Activated Protein Kinases (MAPKs) are involved in signaling of many important biological processes, including biotic and abiotic stresses, development and cytoskeleton organization. Despite an abundant literature on MAPKs, the exact roles and direct targets of many Arabidopsis thaliana MAPKs are not clear yet. The activation of kinases using phospho-mimicking mutations of the phosphorylated residues was a successful approach in the case of MAP2Ks, helping to elucidate their functions. This strategy failed in the case of MAPKs since the necessary residues to mutate remain unclear. To bypass this problem, we adapted a screen based on the functional complementation of a MAPK yeast mutant with randomly mutated Arabidopsis MPK6 in order to identify the ones mutants showing constitutive activity. We identified several clones and showed that these constitutively active (CA) of MPK6 candidates are indeed active without phosphorylation by MAP2Ks. Interestingly, mutations of the equivalent residues in other MAPKs triggered constitutive activity as well, indicating that this strategy may be used as a general approach to activate MAPKs and identify their functions. Interaction and phosphorylation assays indicatedthat CA MAPKs retain their substrate and interactor specificity. As proof-of-concept, we generated active versions of MPK4. CA MPK4 expressed under itsown promoter successfully complements mpk4 mutant plants. Characterization of CA MPK4 lines further confirmed the negative role of MPK4 in plant pathogen defense responses and its implication in both PTI (PAMP Triggered Immunity) and ETI (Effector Triggered Immunity). Overall, the work will help to provide direct information on all MAPK targets and should be an important contribution to the overall understanding of signal transduction in plants
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Torrance, Emma. "MAP kinase phosphatase-2 in vascular smooth cell muscle function." Thesis, University of Strathclyde, 2013. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=23297.
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The progression of major cardiovascular disorders are a consequence of a pathophysiological modification within the blood vessel; a process often driven by vascular smooth muscle cell hyperproliferation. A major mechanism by which smooth muscle cell proliferation occurs involves ligand-induced activation of MAP kinase signalling (Schad et al., 2011). MAP kinases have been noteworthy but troublesome targets in cardiovascular therapeutics; thus exploration of targeting endogenous regulatory dual specificity proteins namely MAP kinase phosphatases has been advancing in recent years. Mitogen-activated protein kinase phosphatase-2 (MKP-2) is a type 1 nuclear phosphatase with the ability to dephosphorylate and ultimately inactivate MAP kinases ERK and JNK in vitro (Lawan et al., 2012). Therefore, by the use of a novel MKP-2-/- mouse, we assess a role for MKP-2 in smooth muscle proliferation as a potential future therapeutic target in cardiovascular disease. Contrary to current literature, mouse aortic smooth muscle cells cultured from a novel Dusp4 knockout mouse exhibit no significant difference in MAP kinase signalling profiles when compared with wild-type. Interestingly however, a significant reduction in proliferation rate corresponded with MKP-2 knockout cells and further cell cycle investigation elucidated a significant accumulation of MKP-2-/- cells in G2/M phase of the cell cycle. With levels of p-cdc-2 comparable between MKP-2 wild-type and knockout cells, mitotic entry was unaffected by MKP-2 deficiency which therefore diverted our study downstream to cytokinesis. Utilising time-lapse microscopy, smooth muscle cells lacking in MKP-2 exhibited a delay in cytokinesis and failure in abscission, resulting in the dividing cells connected by an intercellular bridge. The molecular mechanism of cytokinesis requires phosphorylation of the mitotic kinase aurora B for successful division of two daughter cells. However nocodazole-arrest studies reveal MKP-2 is required for aurora B phosphorylation and its downstream target histone H3, thus identifying MKP-2 as essential in the effective completion of cytokinesis. Within this thesis, an early investigation into the possible use of Adv.WT-MKP-2 as a vascular therapeutic in human aortic smooth muscle cells (HASMCs) was conducted. The over-expression of MKP-2 negated ERK signalling and consequently resulted in a reduction in cellular proliferation. Furthermore, the reduction in cellular proliferation was shown to be caused by a G1/S accumulation in the cell cycle. Collectively, these data suggest a novel role for MKP-2 in mouse aortic smooth muscle cell proliferation, providing new insights into the understanding of MKP-2 in the completion of cytokinesis. Furthermore, MKP-2 kinase binding domain is required for successful completion of cytokinesis but may not involve the inactivation of ERK or JNK. Therefore, modification of MKP-2 expression or function may represent a new approach in reducing SMC hyperproliferation in vascular disease states.
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Huggins, Mark C. (Mark Christopher). "A Continuous, Nowhere-Differentiable Function with a Dense Set of Proper Local Extrema." Thesis, University of North Texas, 1993. https://digital.library.unt.edu/ark:/67531/metadc500353/.
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In this paper, we use the following scheme to construct a continuous, nowhere-differentiable function 𝑓 which is the uniform limit of a sequence of sawtooth functions 𝑓ₙ : [0, 1] → [0, 1] with increasingly sharp teeth. Let 𝑋 = [0, 1] x [0, 1] and 𝐹(𝑋) be the Hausdorff metric space determined by 𝑋. We define contraction maps 𝑤₁ , 𝑤₂ , 𝑤₃ on 𝑋. These maps define a contraction map 𝑤 on 𝐹(𝑋) via 𝑤(𝐴) = 𝑤₁(𝐴) ⋃ 𝑤₂(𝐴) ⋃ 𝑤₃(𝐴). The iteration under 𝑤 of the diagonal in 𝑋 defines a sequence of graphs of continuous functions 𝑓ₙ. Since 𝑤 is a contraction map in the compact metric space 𝐹(𝑋), 𝑤 has a unique fixed point. Hence, these iterations converge to the fixed point-which turns out to be the graph of our continuous, nowhere-differentiable function 𝑓. Chapter 2 contains the background we will need to engage our task. Chapter 3 includes two results from the Baire Category Theorem. The first is the well known fact that the set of continuous, nowhere-differentiable functions on [0,1] is a residual set in 𝐶[0,1]. The second fact is that the set of continuous functions on [0,1] which have a dense set of proper local extrema is residual in 𝐶[0,1]. In the fourth and last chapter we actually construct our function and prove it is continuous, nowhere-differentiable and has a dense set of proper local extrema. Lastly we iterate the set {(0,0), (1,1)} under 𝑤 and plot its points. Any terms not defined in Chapters 2 through 4 may be found in [2,4]. The same applies to the basic properties of metric spaces which have not been explicitly stated. Throughout, we will let 𝒩 and 𝕽 denote the natural numbers and the real numbers, respectively.
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Nicholson, Hannele Buffy Marie. "Disfluency in dialogue : attention, structure and function." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/1763.
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Spontaneous speech is replete with disfluencies: pauses, hesitations, restarts, and less than ideal deliveries of information. Disfluency is a topic of interdisciplinary research with insights from psycholinguistics, phonetics and speech technology. Researchers have tried to determine: When does disfluency occur?, Can disfluency be reliably predicted to occur?, and ultimately, Why does disfluency occur? The focus of my thesis will be to address the question of why disfluency occurs by reporting the results of analyses of disfluency frequency and the relationship between disfluency and eye gaze in a collaborative dialogue. Psycholinguistic studies of disfluency and collaborative dialogue differ on their answers to why disfluency occurs and its role in dialogue. One hypothesis, which I will refer to as Strategic Modelling, suggests that disfluencies are designed by the speaker. According to the alternative view, which I will call the Cognitive Burden View, disfluency is the result of an overburdened language production system. Throughout this thesis, I will contrast these two theories for an ultimate answer to why disfluency occurs. Each hypothesis attaches a functional role to a structural definition of disfluency and therefore in order to determine why disfluency occurs, I will contrast the structural and functional characteristics of disfluency. I will attempt to do this by analysing the dialogue behaviour in terms of speech goals and eye gaze behaviour a speaker is engaged in when they make certain types of disfluencies. A multi-modal Map Task paradigm was used in this thesis, in which speakers were asked to describe the route on a cartoon map to a distant confederate listener who provided either visual or verbal feedback. Speakers were eye-tracked during the dialogue and a record was kept of when the speaker attended to the listener’s visual feedback. Experiment 1 tested the visual feedback paradigm to establish its validity as a baseline condition. Speakers were found to make more disfluencies when they could interact with the visual feedback, suggesting disfluency is more common in interactive circumstances. Experiment 2 added verbal feedback to the experimental paradigm to test whether listeners react differently to the two modalities of feedback. Speakers made more disfluencies when the feedback was more complicated. Structural disfluency types were also observed to fulfil different functions. Finally, Experiment 3 manipulated the motivation of the speaker and found that Motivated speakers gazed more often and were more disfluent per opportunity than Control speakers suggesting that highly motivated subjects are more willing to engage in difficult tasks.
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Geiger, Stephanie. "Untersuchungen zur Struktur und Funktion taktiler kartographischer Medien und ihren Wechselwirkungen." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1213600928558-29559.
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Es wird heute weltweit versucht, Konzepte für vielfältige taktile kartographische Medien zu entwickeln, die vorrangig der allgemeinen Orientierung und Mobilität, aber auch verstärkt dem Wissenserwerb, z.B. im Geographieunterricht an Schulen für Blinde und Sehbehinderte, dienen sollen. Diese Konzepte müssen von denen der "visuellen Kartographie"1 zwangsläufig mehr oder weniger abweichen und auf weitgehend anderen Methoden, Regeln und Techniken beruhen. Wesentliche und durch die Praxis verifizierte Erkenntnisse der visuellen Kartographie sind der taktilen Kartographie zugänglich zu machen bzw. in/an diese zu adaptieren. Trotzdem dürfen grundlegende Theorien und Erfahrungen der Kartengestaltung und Kartennutzung für Sehende nicht völlig negiert werden.
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Galli, Daniele. "The Selberg Zeta Function: A golden thread through hyperbolic geometry, dynamics and number theory." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amslaurea.unibo.it/18781/.
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This thesis deals with the profound relationship that exists between the dynamics on surfaces of negative curvature, some spectral aspects of hyperbolic geometry, and the ergodic properties of continued fractions. One of the most elegant results to reveal the connections between the geodesic flow on a surface of constant negative curvature and the spectrum of the Laplace-Beltrami operator is the celebrated trace formula of Selberg. From a standpoint which is not that of this thesis, one could say that any such trace formula represents one of the most direct connections between observations of classical dynamics and observations of quantum dynamics. At any rate, the main mathematical tool behind the original trace formula is the Selberg zeta function. The purpose of the thesis is to review certain papers of D. H. Mayer, and more recently of C.Bonanno and S. Isola, on certain representations of the Selberg zeta function for surfaces of constant negative curvature based on families of transfer operators for the Gauss and Farey maps, which are the dynamical systems associated to the continued-fraction expansion of real numbers. In particular, we extend some results of Bonanno and Isola to subgroups of the full modular group PSL(2;Z);
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Nyarko-Adomfeh, Charles. "Cardiovascular function in normal man." Thesis, University of Nottingham, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317595.
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Rhodes, John Richard. "On the kernel of the symbol map for multiple polylogarithms." Thesis, Durham University, 2012. http://etheses.dur.ac.uk/3905/.
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The symbol map (of Goncharov) takes multiple polylogarithms to a tensor product space where calculations are easier, but where important differential and combinatorial properties of the multiple polylogarithm are retained. Finding linear combinations of multiple polylogarithms in the kernel of the symbol map is an effective way to attempt finding functional equations. We present and utilise methods for finding new linear combinations of multiple polylogarithms (and specifically harmonic polylogarithms) that lie in the kernel of the symbol map. During this process we introduce a new pictorial construction for calculating the symbol, namely the hook-arrow tree, which can be used to easier encode symbol calculations onto a computer. We also show how the hook-arrow tree can simplify symbol calculations where the depth of a multiple polylogarithm is lower than its weight and give explicit expressions for the symbol of depth 2 and 3 multiple polylogarithms of any weight. Using this we give the full symbol for I_{2,2,2}(x,y,z). Through similar methods we also give the full symbol of coloured multiple zeta values. We provide introductory material including the binary tree (of Goncharov) and the polygon dissection (of Gangl, Goncharov and Levin) methods of finding the symbol of a multiple polylogarithm, and give bijections between (adapted forms of) these methods and the hook-arrow tree.
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Huguet, Romain. "Comparative functional proteomics of MAP kinase signalling in Magnaporthe oryzae." Thesis, University of Exeter, 2010. http://hdl.handle.net/10036/118007.
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Rice blast disease is caused by the heterothallic ascomycete fungus Magnaporthe oryzae and is one of the most severe diseases of cultivated rice throughout the world. The PMK1 (Pathogenicity Mitogen-activated protein Kinase) gene in M. oryzae has been identified to play diverse roles during pathogenesis-related development. PMK1 regulates appressorium formation and infectious hyphal growth. PMK1 is functionally related to Saccharomyces cerevisiae FUS3 and KSS1 MAPK genes which regulate the transcription factor Ste12. The STE12 homologue in M. oryzae, MST12, has also been identified and is known to be essential for appressorium mediated penetration and infectious growth. These observations imply that Pmk1 regulates a diverse set of targets important in both the initiation of appressorium development and the subsequent stages of invasive growth. In addition, the Mst12 transcription factor may function downstream of Pmk1 to regulate genes involved in appressorial penetration and infectious hyphal growth. We have used a comparative proteomic study between Guy11 (isogenic wild type), ∆mst12 and ∆pmk1 mutants to understand which genes are induced during appressorium formation and may be regulated by Mst12 and Pmk1. We carried out two-dimensional gel electrophoresis with proteins extracted from conidia that had germinated on a hydrophobic surface after 6h, 12h, 16h and 24h of incubation. M. oryzae underwent major changes in protein abundance and expression during the first 6 hours of spore germination in Guy11 which suggested that much of protein synthesis associated with appressorium morphogenesis and virulence occurs precociously during conidium germination on rice leaf surface. More than 394 differentially expressed proteins during conidium germination and appressorium formation have been identified by mass spectrometry. We confirmed many proteins already known as determinants of pathogenicity in M. oryzae such as enzymes involved in melanin biosynthesis or fatty acid β-oxidation. However, we also identified proteins absent or lowly induced in the Δpmk1 and Δmst12 mutants involved in cell wall reorganisation, secondary metabolism, lipid metabolism, photomorphogenesis or found as proteins of unknown functions. We generated 28 targeted gene deletion mutants to test the putative function of proteins predicted by proteomics analysis to be associated with appressorium development. We obtained 7 mutants showing a significant reduction in virulence and confirmed importance of regulated proteolysis during appressorium development but also elucidated new processes involved in infection such as the phosphoinositide pathway and three proteins of unknown function.
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Blokhina, Olga. "Anoxia and oxidative stress : lipid peroxidation, mitochondrial functions in plants antioxidant status and mitochondrial functions in plants." Helsinki : University of Helsinki, 2000. http://ethesis.helsinki.fi/julkaisut/mat/bioti/vk/blokhina/.
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Giacomantone, Javier Oscar. "Ressonância magnética funcional com filtragem pela difusão anisotrópica robusta." Universidade de São Paulo, 2005. http://www.teses.usp.br/teses/disponiveis/3/3142/tde-01112005-200330/.
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Esta dissertação apresenta os principais métodos estatísticos para analisar as séries temporais de fMRI com o objetivo de detectar regiões ativadas e caracterizar o erro envolvido nessa decisão. Na análise de imagens funcionais, devido à baixa razão sinal-ruído, torna-se necessário o uso de técnicas elaboradas de processamento. O resultado da aplicação de técnicas estatísticas sobre as séries temporais obtidas da imagem de fMRI, é um mapa estatístico paramétrico, (Statistical Parametric Map), (SPM), uma imagem 3-D que permite determinar o estado do voxel, ativado ou não ativado, e a significância estatística do resultado. Propomos um novo método baseado na Difusão Anisotrópica Robusta, (Robust Anisotropic Diffusion), (RAD), que explora uma característica fundamental da imagem funcional, a correlação espacial das regiões ativadas do cérebro humano. O método proposto permite obter mapas estatísticos que melhoram a determinação das áreas ativadas a partir de dados fMRI ruidosos. Os novos mapas estatísticos paramétricos, baseados na correlação espacial da imagem fMRI, reduzem os erros do processo de classificação dos voxels, melhorando assim o mapeamento das regiões ativadas no cérebro. Aplicamos a técnica proposta em dados gerados artificialmente, simulando ruído e sinal, e avaliamos o novo método proposto e um método clássico de processamento de fMRI. Apresentamos resultados comparativos entre um método clássico, o método de correlação e o novo método. Calculamos os erros envolvidos e apresentamos a curvas características de operação de um receptor, (Receiver Operating Characteristics), (ROC), para ambos métodos, comparando os parâmetros mais importantes. Também avaliamos o novo método em dados reais de fMRI de um experimento em blocos com estímulo visual.This dissertation presents the main statistical methods to analyse fMRI temporal series to detect activated regions and to characterise the error involved in this decision. Due to low signal to noise ratio, elaborate processing techniques are necessary to analyse functional images. Statistical techniques are usually applied on the temporal series obtained from fMRI, resulting in a Statistical Parametric Map (SPM), a 3-D image that makes it possible to determine the state of a voxel, as activated or not activated, and the statistical significance of the result. We proposed a new, simple an elegant method based on Robust Anisotropic Diffusion (RAD) to exploit the spatial correlation of activated regions of the human brain. The new method, named Robust Anisotropic Diffusion of Statistical Parametric Maps (RADSPM), allows one to obtain statistical maps that improve the determination of activated areas from noisy fMRI data. The new parametric statistical maps, based on the voxel spatial correlation of the fMRI image, reduce the classification error thus improving the significance of the results. We have tested the new technique in both simulated and real fMRI, obtaining sharp and noiseless SPMs with increased statistical significance. We compare results of the new RADSPM method with those of a classic method, the conventional correlation method. We calculate the involved errors and we present Receiver Operating Characteristics (ROC) curves for both methods, comparing the most important parameters for simulated fMRI data. We also evaluate the new method on real data of a visual fMRI experiment.
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Čáchová, Barbora. "Aplikace procesního řízení v podniku." Master's thesis, Vysoké učení technické v Brně. Fakulta podnikatelská, 2013. http://www.nusl.cz/ntk/nusl-224031.
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The master thesis is focused on the application of process management in the company PROFI am BAU CM, Ltd. The theoretical part deals with the explanation of the process approach in business management and defines the basic concepts used, as well as analysis of the current situation in the company. Based on the acquired knowledge are described and analyzed the main business processes and proposed optimization steps.
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Lawan, Ahmed. "The role of map kinase phosphatase-2 (MKP-2) in cardiac function." Thesis, University of Strathclyde, 2010. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=14506.
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Benjamin, Wayne. "Design for placement of modified optodes to non-invasively map cerebral function." FIU Digital Commons, 2003. http://digitalcommons.fiu.edu/etd/1607.
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By using near infrared spectroscopy (NIRS) and by modifying the current Somanetics® optodes being used with the INVOS oximeter, the modified optodes are made to be fairly functional not only across the forehead, but across the hairy regions of the scalp as well. A major problem arises in the positioning of these optodes on the patients scalp and holding them in place while recording data. Another problem arises in the inconsistent repeatability of the trends displayed in the recorded data. A method was developed to facilitate the easy placement of these optodes on the patients scalp keeping in mind thepatient's comfort. The sensitivity of the optodes, too, was improved by incorporating better refined techniques for manufacturing the fiber optic brushes and fixing the same to the optode transmitting and receiving windows. The modified and improved optodes, in the single as well as in the multiplexed modes, were subjected to various tests on different areas of the brain to determine their efficiency and functionality.
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Canavan, A. G. M. "Functions of basal ganglia in man and monkey." Thesis, University of Oxford, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376889.
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Reffitt, David Michael. "The metabolism and functions of silicon in man." Thesis, King's College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.405750.
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Kilgore, Kevin Lloyd. "Optimization and automation of stimulus map synthesis for upper extremity FNS." Case Western Reserve University School of Graduate Studies / OhioLINK, 1991. http://rave.ohiolink.edu/etdc/view?acc_num=case1059576993.
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Wilson, Aimee A. "Holding hands with Virginia Woolf a map of Orlando's functional subversion /." View electronic thesis, 2008. http://dl.uncw.edu/etd/2008-1/wilsona/aimeewilson.pdf.
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McMahon, Mary Newman. "A study of selfobject functions among heterosexual couples." Click here for text online. The Institute of Clinical Social Work Dissertations website, 1991. http://www.icsw.edu/_dissertations/mcmahon_1991.pdf.
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Dissertation (Ph.D.) -- The Institute for Clinical Social Work, 1991.A dissertation submitted to the faculty of the Institute of Clinical Social Work in partial fulfillment for the degree of Doctor of Philosophy.
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Vestlund, Jimmy. "Streamlining tool design and manufacturing process for blancing and function test equipment to a propeller hub assembly." Thesis, Karlstads universitet, Institutionen för ingenjörsvetenskap och fysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-35176.
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Rolls-Royce AB in Kristinehamn, Sweden, part of Rolls-Royce Marine, is a leading developer and supplier of water jet and propeller based propulsion equipment. Its low volume production series and wide product variety offered to its customers along with an increasingly competitive market has entailed an increased demand on both delivery time and cost reductions. The on-site manufacturing engineering department is responsible for developing all tools and fixtures, and programming required to maintain the on-site production, assembling and quality testing. As part of the departments streamlining efforts this study aimed on evaluating streamlining possibilities related to the existing tool design used for static balancing and function testing controllable pitch propeller assemblies before packaging and shipping, along with the related tool development and manufacturing processes has been conducted.The process evaluation started from the point when a hub assembly design was finalized until when a manufactured tool was delivered for use in production. Work focused on locating inefficient activities and product properties, with respect to tool cost and lead time, followed by setting up an amendment proposal, implementing it and producing an alternate tool design of which the effects on tool cost and manufacturing lead time would be evaluated. Post evaluating the current state of the process and product a set based front loaded product development methodology known as Modular Function Deployment was chosen to be the applied method. This application resulted in a modular tool design that avoided the determined most inefficient manufacturing operation combination of welding and annealing. Modularity increased manufacturing flexibility, enabling more concurrent manufacturing, to reduce the lead time. The tool design also applied integral properties by identifying the common components and features between tool sizes. This led to reducing manufacturing and material costs. Possible lead time reduction for manufacturing was determined to be 35-45%, 3-4weeks, in comparison with the original tool design due to increased parallel manufacturing and avoiding inefficient manufacturing methods. The estimated cost reduction for combined development and manufacturing was determined to be 105K SEK the initial year followed by 175K SEK the second year assuming the current tool manufacturing rate. The combined effects of reduced cost and lead time would be beneficial to Rolls-Royce AB by contributing to an increase in delivery reliability and competitive prices on the market
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Giboudot, Yoel. "Study of beam dynamics in NS-FFAG EMMA with dynamical map." Thesis, Brunel University, 2011. http://bura.brunel.ac.uk/handle/2438/5947.
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Dynamical maps for magnetic components are fundamental to studies of beam dynamics in accelerators. However, it is usually not possible to write down maps in closed form for anything other than simplified models of standard accelerator magnets. In the work presented here, the magnetic field is expressed in analytical form obtained from fitting Fourier series to a 3D numerical solution of Maxwell’s equations. Dynamical maps are computed for a particle moving through this field by applying a second order (with the paraxial approximation) explicit symplectic integrator. These techniques are used to study the beam dynamics in the first non-scaling FFAG ever built, EMMA, especially challenging regarding the validity of the paraxial approximation for the large excursion of particle trajectories. The EMMA lattice has four degrees of freedom (strength and transverse position of each of the two quadrupoles in each periodic cell). Dynamical maps, computed for a set of lattice configurations, may be efficiently used to predict the dynamics in any lattice configuration. We interpolate the coefficients of the generating function for the given configuration, ensuring the symplecticity of the solution. An optimisation routine uses this tool to look for a lattice defined by four constraints on the time of flight at different beam energies. This provides a way to determine the tuning of the lattice required to produce a desired variation of time of flight with energy, which is one of the key characteristics for beam acceleration in EMMA. These tools are then benchmarked against data from the recent EMMA commissioning.
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Wang, Yupeng. "Regulation and function of BDNF-activated ERK5 and ERK1/2 MAP kinases in CNS neurons /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/8455.
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Hayward, Gail. "Aspects of cingulate cortex function in man." Thesis, University of Oxford, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.401084.
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Can, Sermet. "Dissecting domain-specific functions of the IGF2/M6P receptor." Thesis, University of Oxford, 2016. http://ora.ox.ac.uk/objects/uuid:63ee7b6a-a619-4d42-973e-e888dc427378.
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The P-type lectin Mannose 6-phosphate/Insulin-like growth factor 2 receptor (M6P/IGF2R) is a type I trans-membrane protein with 15 homologous extracellular domains that bind several ligands. While domains 3, 5 and 9 bind to Mannose 6-Phosphate (M6P), domain 11 binds to IGF2 (Insulin-like growth factor 2). In mice, igf2r expression is monoallelic and full knock-out of the receptor maternal allele (Igf2r-m/+p) results in developmental abnormalities and neonatal lethality, marking the significance of the receptor in organogenesis and postnatal viability. What remains unknown is the contribution of each of these domains into M6P/IGF2R's roles in development. My aims are dissecting M6P and IGF2 binding domains' functions in the context of full length receptor in vitro and investigating Domain 11 loss-of-function in vivo. In this thesis, SPR analysis of full-length M6P/IG2R mutants showed that M6P binding domains function independent of each other, and domain 3 is the dominant M6P binding domain at physiological pH. Introducing gain-of-function mutations to domain 11 binding site revealed presence of inter-loop interactions and inhibitory residues in CD and FG loop in the context of the full-length receptor. I1572A results in domain 11 loss of-function mutation with preserved binding of other ligands, suggesting that I1572A (or its homolog mutations in other mammals) could be utilized in in vivo studies to dissect domain 11 functions. In mice, maternal transmission of Domain 11 loss-of-binding function mutation (I1565A, mouse homolog of I1572A) resulted in increased birth weight and substantially reduced postnatal survival (~30%). The disproportional cardiomegaly and disorganised myocardium in Igf2rI1565Am/+p neonates suggest that postnatal lethality is due to cardiac insufficiency. Furthermore, placental and embryonic oedema in Igf2rI1565Am/+p mice is indicative of the presence of prenatal congestive cardiac failure, beginning as early as at embryonic day 14.5. In addition, surviving females developed uterine distension due to vaginal atresia. Overall, these results show that domain 11 loss-of-function, on its own, is the primary reason for the most of abnormalities that is previously reported in the full knock out mice. Thus, domain 11 is the primary domain for M6P/IGF2R's roles in development.
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Chapman, Samuel D. "Applying Evolutionary Computation and Ensemble Approaches to Protein Contact Map and Protein Function Determination." Thesis, North Carolina Agricultural and Technical State University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10191042.
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Proteins are important biological molecules that perform many different functions in an organism. They are composed of sequences of amino acids that play a large part in determining both their structure and function. In turn, the structures of proteins are related to their functions. Using computational methods for protein study is a popular approach, offering the possibility of being faster and cheaper than experimental methods. These software-based methods are able to take information such as the protein sequence and other empirical data and output predictions such as protein structure or function.
In this work, we have developed a set of computational methods that are used in the application of protein structure prediction and protein function prediction. For protein structure prediction, we use the evolution of logic circuits to produce logic circuit classifiers that predict the protein contact map of a protein based on high-dimensional feature data. The diversity of the evolved logic circuits allows for the creation of ensembles of classifiers, and the answers from these ensembles are combined to produce more-accurate answers. We also apply a number of ensemble algorithms to our results.
Our protein function prediction work is based on the use of six existing computational protein function prediction methods, of which four were optimized for use on a benchmark dataset, along with two others developed by collaborators. We used a similar ensemble framework, combining the answers from the six methods into an ensemble using an algorithm, CONS, that we helped develop.
Our contact map prediction study demonstrated that it was possible to evolve logic circuits for this purpose, and that ensembles of the classifiers improved performance. The results fell short of state-of-the-art methods, and additional ensemble algorithms failed to improve the performance. However, the method was also able to work as a feature detector, discovering salient features from the high-dimensional input data, a computationally-intractable problem. In our protein function prediction work, the combination of methods similarly led to a robust ensemble. The CONS ensemble, while not performing as well as the best individual classifier in absolute terms, was nevertheless very close in terms of performance. More intriguingly, there were many specific cases where it performed better than any single method, indicating that this ensemble provided valuable information not captured by any single methods.
To our knowledge, this is the first time the evolution of logic circuits has been used in any Bioinformatics problem, and it is expected that as the method becomes more developed, results will improve. It is also expected that the feature-detection aspect of this method can be used in other studies. The function prediction study also marks, to our knowledge, the most-comprehensive ensemble classification for protein function prediction. Finally, we expect that the ensemble classification methods used and developed in our protein structure and function work here will pave the way towards stronger ensemble predictors in the future.
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Cheng, Jia. "Functional analysis of MAPK phosphatase AtMKP2." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/7297.
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Plants have evolved complex signal transduction pathways to sense and respond to the fast-changing environment. Among several crucial signaling pathways, MAPK pathways are known to be involved in regulating many biological processes, including development, cytokinesis, biotic and abiotic stress signaling and hormone signaling. As negative regulators of MAP kinases (MPKs), MAPK phosphatases (AtMKPs) can reverse the activation status of AtMPKs by dephosphorylating the activation sites of AtMPKs. There are 5 putative AtMKPs in the Arabidopsis genome and previous research has shown they play an important role in MAP kinase control. AtMKP2 has been shown to be a novel regulator for ozone stress responses, but how it might be involved in other biological aspects of Arabidopsis development and growth remains unknown. In this study, I examined the biological functions of AtMKP2 in trichome development. Phenotype analysis showed that in AtMKP2-RNAi mutants, trichome density as well as trichome branching number were affected. Both proAtMKP2: GUS signal and proAtMKP2:YFP signal showed that AtMKP2 was expressed in all development stages of developing trichomes. RT-PCR showed that the expression levels of several known trichome development regulators were affected in AtMKP2-RNAi plants. Genetic analysis of AtMKP2 RNAi x try and AtMKP2 RNAi x cpc double mutants showed phenotype consistent with the involvement of AtMKP2 in trichome development. To characterize the biological processes in which AtMKP2 plays a role, I also employed microarray approaches to examine the short-term transcriptional events in AtMKP2 LOF and GOF mutants. I was able to validate the microarray data of AtMKP2 LOF mutants using qRT-PCR. However, the gene expression patterns in AtMKP2 GOF mutants were not verified. This might result from the different overexpression levels of AtMKP2 in different biological replicates. Several defense-related genes showed transcriptional changes in both AtMKP2 LOF and GOF mutants, suggesting AtMKP2 might function in response to pathogen attack. In all, I studied the biological function of AtMKP2 in Arabidopsis trichome development and placed AtMKP2 within the network of known trichome development regulators. My microarray experiments provided some useful clues suggesting other biological functions of AtMKP2.
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Kuusinen, Arja. "Structure-function relations in AMPA receptors." Helsinki : University of Helsinki, 2000. http://ethesis.helsinki.fi/julkaisut/mat/bioti/vk/kuusinen/.
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Suopanki, Jaana. "Studies on palmitoyl-protein thioesterase 1 : implications for synaptic functions." Helsinki : University of Helsinki, 2002. http://ethesis.helsinki.fi/julkaisut/mat/bioti/vk/suopanki/.
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Wilkinson, Marc George. "Functional analysis of the STY1 stress-activated map kinase pathway of fission yeast." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286786.
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