Dissertations / Theses on the topic 'Graph X'

In graph theory graphs are mathematical objects that can be used to model networks, data structures, process scheduling, computations and a variety of other systems where the relations between the objects in the system play a dominant role.We will now consider graphs as mathematically self-contained units with rich structure and comprehensive theory; as models for many phenomena, particularly those arising in computer systems; and as structures which can be processed by a variety of sophisticated and interesting algorithms.For graph theory presentation, we need a very good graphical user interface(GUI) to approach the goal. X Window system is ideally suited for such a purpose. This package program is based on X Window system environment. With this package, we can manipulate graphs by special functions which can put nodes, put edges, delete nodes, delete edges, change the whole graph size, move graph location, and modify edge weights.<br>Department of Computer Science

In New Zealand, a formal tree improvement and breeding programme for Pinus radiata (D.Don) commenced in 1952. A countrywide series of progeny trials was progressively established on over seventy sites, and is managed by the Radiata Pine Breeding Company (RPBC). Diameter at breast height data from the series were used to investigate genotype x environment interaction with a view to establishing the need for partitioning breeding and deployment efforts for P. radiata. Nearly 300,000 measurements made this study one of the largest for genotype x environment interaction ever done. Bivariate analyses were conducted between all pairs of sites to determine genetic correlations between sites. Genetic correlations were used to construct a proximity matrix by subtracting each correlation from unity. The process of constructing the matrix highlighted issues of low connectivity between sites; whereby meaningful correlations between sites were established with just 5 % of the pairs. However, nearly two-thirds of these genetic correlations were between -1.0 and 0.6, indicating the presence of strong genotype x environment interactions. A technique known as multiple regression on resemblance matrices was carried out by regressing a number of environmental correlation matrices on the diameter at breast height correlation matrix. Genotype x environment interactions were found to be driven by extreme maximum temperatures (t-statistic of 2.03 against critical t-value of 1.96 at 95 % confidence level). When tested on its own, altitude was significant with genetic correlations between sites at the 90 % confidence level (t-statistic of 1.92 against critical t-value of 1.645). In addition, a method from Graph Theory using proximity thresholds was utilised as a form of clustering. However, this study highlighted the existence of high internal cohesion within trial series, and high external isolation between trial series. That is, grouping of sites (in terms of diameter) was observed to be a reflection of the series of trials for which each site was established. This characteristic is particularly unhelpful for partitioning sites into regions of similar propensity to genotype x environment interaction, as the genotype x environment effect is effectively over-ridden by the genotype effect. Better cohesion between past, present and future trial series, and more accurate bioclimatic data should allow more useful groupings of sites to be extracted from the data. Given this, however, it is clear that there are a large number of interactive families contained in the RPBC dataset. It is concluded that partitioning of New Zealand’s P. radiata breeding programme cannot be ruled out as an advantageous option.

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No. of bitstreams: 1 chrishebertdejesusfranco.pdf: 4880715 bytes, checksum: 5acf9659d9521fbd8fff7e658b785953 (MD5) Previous issue date: 2014-07-18<br>CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>Este trabalho de dissertação de mestrado versou a síntese e a caracterização estrutural e topológica de quatro novos polímeros de coordenação denominados como Zn-psb, Mn-psb, Cu-psb e Ni-btc com os metais da primeira série de transição (Zn+2, Mn+2, Cu+2 e Ni+2) contendo os ligantes sal ácido 4-sulfobenzoato de monopotássio (H-psb) e ácido 1,2,4-benzenotricarboxilico (4-btc). Além de dois outros compostos poliméricos (Co-btc e Cu-pza) já descritos na literatura. Os compostos foram caracterizados por técnicas espectroscópicas (Infravermelho e Raman) e análise elementar (CHN). A espectroscopia vibracional foi utilizada para apreender sobre os modos de coordenação dos grupos carboxilatos nos compostos com o ligante 4-btc por meio do cálculo do Δѵ [ ѵα(COO) – ѵs(COO) ], em que um estudo da simetria por meio da análise de coordenada normal permitiu uma atribuição mais rigorosa para os modos de coordenação para os grupos SO3 nos compostos derivados do ligante (H-psb). Uma adaptação da técnica de cristalização em gel foi utilizada. Os resultados da análise de CHN evidenciaram que a utilização do agente de cristalização cloridrato de etambutol levou a formação de impurezas na superfície dos compostos Zn-psb e Mn-psb que foram eliminadas durante o processo de cristalização. Os dados de análise térmica (TG/DTA) foram utilizados como dado complementar para caracterização estrutural do composto Ni-btc. As estruturas dos quatro compostos foram determinadas por difração de raios X por monocristal, onde foi possível verificar que a estrutura cristalina do composto Cu-psb encontra-se com uma desordem posicional com fração 54:46 para o anel e oΔѵ grupo SO3, enquanto o monocristal do composto Ni-btc apresenta se geminado com fração 49:51 para os domínios. A solução da estrutura geminada foi dificultada devido à contribuição similar dos domínios formados. Através da difração de raios X por policristais foi possível refinar o modelo estrutural proposto para o composto Ni-btc por meio do método de Rietveld. A descrição topológica desses compostos foi feita utilizando teoria gráfica, sendo que algumas definições e termos foram apresentados. Apesar da semelhança estrutural, o composto Zn-psb apresentou uma rede do tipo tfz-d enquanto o composto Mn-psb apresentou uma rede do tipo pcu.<br>This work shows the synthesis, structural and topological characterization of four new coordination polymers described as Zn-psb , Mn-psb, Cu-psb and Ni-btc with metals of the first row transition metal ions (Zn+2, Mn+2, Cu+2 and Ni+2) and 4-sulphobenzoate monopotassium (Hpsb), 1,2,4- benzenetricarboxylic acid (4-btc) as ligands. And another two polimeric componds (Co-btc and Cu-pza) described in the literature. The compounds were characterized by spectroscopic techniques (infrared and Raman) and elemental analysis (CHN) where thermal analysis (TG/DTA) were only used for structural characterization of the compound Ni-btc. The vibrational spectroscopy was used to understand the coordination modes of the carboxylate groups in the compounds with 4-btc ligand by analyze of Δѵ values [ ѵα(COO) – ѵs(COO) ]. A study of symmetry by analysis of normal coordinates allowed a rigorous assignment to coordination modes for SO3 groups in the compounds derived H-psb ligand. An adaptation of the technique of crystallization in gel was used. The results of CHN showed that the use of ethambutol hydrochloride as a crystallization agent led to formation of impurities on the surface of the Zn-psb and Mn-psb compounds that was eliminated during the crystallization process. The structures of the four compounds were determined for X-ray diffraction by single crystal, where it was observed that the crystal structure of the compound Cu-psb displays a positional disorder with a fraction of 54:46 for the ring and SO3 group, while the single crystal of the compound Ni-btc was twinned with a fraction of 49:51 for the each domain. The solution of structure was complicated due a similar contribution from domains formed. X-ray diffraction by polycrystals was used like a tool for give a support to refine the structural model proposed for the compound Ni-btc by the Rietveld method. The topological description of these compounds was performed using graph theory where some definitions and terms were presented. Despite the structural similarity, the compound Zn-psb displayed a network of type tfz-d while Mn-psb compound showed a net of type pcu.

Les travaux de cette thèse s’inscrivent dans le cadre du planning de traitements minimalement invasifs des lésions des artères coronaires. Le cardiologue réalise un examen coronarographique, puis dans la continuité, une angioplastie transluminale. L’angiographie rotationnelle à rayons X permet de visualiser sous différentes incidences 2D la lumière des artères coronaires sur plusieurs cycles cardiaques et aussi d’obtenir une reconstruction 3D+T des arbres coronaires. A partir de cette séquence, notre objectif est de déterminer automatiquement une incidence optimale 2D du segment sténosé compatible avec les angles du C-arm afin d’aider le cardiologue lors de l’intervention.Différentes étapes sont considérées pour calculer la position angulaire optimale du C-arm. Afin de suivre la zone de lésion durant le cycle cardiaque, une première méthode est proposée pour mettre en correspondance tous les arbres de la séquence 3D+T. Tout d’abord, un appariement deux à deux des arbres successifs est réalisé afin de construire un arbre d’union. Ces derniers sont ensuite fusionnés afin d’obtenir un arbre mosaïque représentant l’arbre le plus complet de la séquence. L’utilisation de mesures de similarités géométriques et hiérarchiques ainsi que l’insertion de nœuds artificiels permet de prendre en compte les différents mouvements non-rigides des artères coronaires subits au cours du cycle cardiaque et les variations topologiques dû à leurs extractions. Cet appariement nous permet de proposer une deuxième méthode afin d’obtenir une vue angiographique 2D optimale de la zone de lésion tout le long du cycle cardiaque. Cette incidence est proposée spécifiquement pour trois types de région d’intérêt (segment unique, segment multiple ou bifurcation) et est calculée à partir de quatre critères (raccourcissement, chevauchement interne et externe ou angle d’ouverture de bifurcation). Une vue 2D déployée du segment projeté avec le moins de superposition avec les structures vasculaires avoisinantes est obtenue. Nous donnons également la possibilité au cardiologue d’avoir une incidence optimale privilégiant soit le déploiement du stent ou soit le guidage d’outils de la racine de l’arbre à la zone sténosée. Nos différents algorithmes ont été évalués sur une séquence réelle de 10 phases segmentées à partir d’un CT et de 41 séquences simulées<br>The thesis work deals with the planning of minimally invasive surgery of coronary artery lesions. The physician performs a coronarography following by a percutaneous transluminal angioplasty. The X-ray rotational angiography permits to visualize the lumen artery under different projection angles in several cardiac cycles. From these 2D projections, a 3D+T reconstruction of coronary arteries can be obtained. Our goal is to determine automatically from this 3D+T sequence, the optimal angiographic viewing angle of the stenotic segment. Several steps are proposed to compute the optimal angular position of the C-arm. Firstly, a mosaic-based tree matching algorithm of the 3D+T sequence is proposed to follow the stenotic lesion in the whole cardiac cycle. A pair-wise inexact tree matching is performed to build a tree union between successive trees. Next, these union trees are merged to obtain the mosaic tree which represents the most complete tree of the sequence. To take into account the non-rigid movement of coronary arteries during the cardiac cycle and their topology variations due to the 3D reconstruction or segmentation, similarity measures based on hierarchical and geometrical features are used. Artificial nodes are also inserted. With this global tree sequence matching, we propose secondly a new method to determine the optimal viewing angle of the stenotic lesion throughout the cardiac cycle. This 2D angiographic view which is proposed for three regions of interest (single segment, multiple segment or bifurcation) is computed from four criteria: the foreshortening, the external and internal overlap and the bifurcation opening angle rates. The optimal view shows the segment in its most extended and unobstructed dimension. This 2D view can be optimal either for the deployment of the stent or for the catheter guidance (from the root to the lesion). Our different algorithms are evaluated on real sequence (CT segmentation) and 41 simulated sequences

L’opération morphologique de squelettisation transforme chaque objet d’une image en une forme linéique qui préserve la topologie de ce dernier (propriété d’homotopie). Elle est largement utilisée en biométrie mais aussi dans la reconnaissance des caractères ainsi que pour l’extraction de la microarchitecture osseuse. L’objectif de cette thèse est de développer une méthode de squelettisation appliquée directement sur les niveaux de gris de l’image, ce qui a pour large avantage de s’affranchir de prétraitement comme la binarisation. Une revue des méthodes de squelettisation en niveaux de gris permet de constater que l’amincissement est l’une des approches les plus usitées de par sa propriété d’homotopie. Cependant, cette approche est sensible au bruit de l’image et produit des squelettes sur-connectés. Un premier paramétrage de l’amincissement a été proposé dans la littérature afin d’abaisser des configurations de pixels liées au bruit. La première contribution de ce travail est de proposer un ajustement de ce paramètre basé sur une décision statistique. Il s’agit d’identifier les tests d’hypothèses correspondants aux différentes configurations d’abaissement en vue de fixer ce paramètre de façon locale. Ceci conduit à la mise en place d’une squelettisation appelée Self Contrast Controlled Thinning (SCCT) puisque robuste au bruit tout en s’adaptant automatiquement au contraste de l’image. La squelettisation SCCT est rendue accessible aux domaines d’application grâce à son implantation optimisée basée sur les files d’attente hiérarchiques. Ayant noté le peu d’efforts consacrés à l’évaluation de la squelettisation en niveaux de gris, la deuxième contribution de ce travail est de proposer un protocole visant à évaluer l’opération de squelettisation sur la base des propriétés requises à savoir la préservation de la topologie et de la géométrie. Ce protocole est déroulé sur une base d’images synthétiques et nous permet de comparer notre approche à celles de la littérature. La troisième contribution est de proposer une structuration du squelette en graphe donnant accès aux descripteurs structurels et morphométriques des objets étudiés en vue d’une exploitation du squelette par les experts des domaines d’applications. Dans le cadre du projet Voxelo coordonné par le laboratoire B2OA de l’Université Paris Diderot, cette structuration est exploitée pour extraire les descripteurs de la qualité de la microarchitecture osseuse à partir d’images RX haute résolution<br>Skeletonization is an image transformation that aims to represent objects by their medial axis while preserving their topological characteristics (homotopy). It is widely used in biometrics, character recognition and also in the extraction of bone microarchitecture. The objective of this thesis is to develop a skeletonization method applied directly on image gray levels. This has the large advantage of freeing the operation from preprocessing techniques such as binarization. A review of grayscale skeletonization methods shows that the morphological thinning is one of the most used approaches for its topology preservation property. However, this approach is sensitive to image noise and produces inexploitable skeletons. A first parameterization of the thinning process has been proposed in the literature to reduce noise-related information. The first contribution of this work is to propose an adjustment of this parameter based on a statistical decision. To this end, a hypothesis test is identified for each lowering criterion in order to set the thinning parameter locally. This leads us to propose the Self Contrast Controlled Thinning method SCCT that is robust to noise and is automatically adjusted to image contrast. The SCCT is made available to application domains through its optimized implementation based on hierarchical queues. Noticing the lack of efforts to assess grayscale skeletonization, the second contribution of this work is to propose a quantitative evaluation protocol assessing skeletonization with regard to its fundamental properties that are namely the preservation of topology and geometry. This protocol is conducted over a synthetic images database and allows us to compare SCCT to approaches from the literature. The third contribution consists in structuring the skeleton into a graph that gives access to objects structural and morphometric descriptors and enables the exploitation of the skeleton by experts from various fields of application. This structuring is applied in the context of Voxelo project which is coordinated by B2OA laboratory of the University Paris Diderot. In this context, descriptors of bone microarchitecture quality are extracted from X-ray high resolution images

Maximum Subarray Problem (MSP) is to find the consecutive array portion that maximizes the sum of array elements in it. The goal is to locate the most useful and informative array segment that associates two parameters involved in data in a 2D array. It's an efficient data mining method which gives us an accurate pattern or trend of data with respect to some associated parameters. Distance Matrix Multiplication (DMM) is at the core of MSP. Also DMM and MSP have the worst-case complexity of the same order. So if we improve the algorithm for DMM that would also trigger the improvement of MSP. The complexity of Conventional DMM is O(n³). In the average case, All Pairs Shortest Path (APSP) Problem can be modified as a fast engine for DMM and can be solved in O(n² log n) expected time. Using this result, MSP can be solved in O(n² log² n) expected time. MSP can be extended to K-MSP. To incorporate DMM into K-MSP, DMM needs to be extended to K-DMM as well. In this research we show how DMM can be extended to K-DMM using K-Tuple Approach to solve K-MSP in O(Kn² log² n log K) time complexity when K ≤ n/log n. We also present Tournament Approach which solves K-MSP in O(n² log² n + Kn²) time complexity and outperforms the K-Tuple

Phenolics derived from grape are essential components of wine quality, contributing to its taste, aroma, color, bitterness, and mouth feel properties. Anthocyanins are responsible for the color of red wine, various interactions occur among the three flavonoid classes in wine resulting in a complex matrix of pigmented polymers. Proanthocyanidins (PAs) or condensed tannins are composed of flavan-3-ol subunits, and are primarily responsible for the astringency of wine and contribute to its bitterness. They possess a high antioxidant capacity and contribute to protection against cardiovascular diseases and cancer (reviewed by Lin and Weng, 2006) when consumed as part of a Mediterranean diet. Berry growth follows a double sigmoid habit that can be divided into two growth phases (Stage I and III) separated by a lag phase (Stage II) (Coombe 1976). The transition from Stage II to Stage III is named veraison and is considered to be the onset of ripening, as at this time sugars and anthocyanins begin to accumulate in red grapes. Tannins are synthesized before veraison, while anthocyanins are synthesized after veraison. The genotype is primary factor to the content of phenolic compounds. Concentration changes due to seasonal weather conditions are far less than those due to genotype. Then the cultivars variations prevail than those due to vintage. There are many environments and field practices factors reputed to affect flavonoid biosynthesis in plants. For example, vine vigor has also been reported to impact upon the tannin content and composition of grape skins in Pinot noir. In the berry skin, proanthocyanidins were higher in low-vigor vines, with an increase in the proportion of epigallocatechin subunits in proanthocyanidin polymers and an increase in the average size of polymers observed with decreasing vine vigor (Cortell et al. 2005). It is uncertain whether this change is due to the difference in vine vigor or is an indirect effect of changes in canopy architecture resulting in differential bunch exposure effects. Some researches suggest that while excessive water application decreased tannin content (Kennedy et al. 2000), water deficit had little or no effect on tannin or anthocyanin accumulation in the grape berry. Rather, the primary effect of water deficit was to decrease berry size and thus change the ratio of skin weight to total berry weight and therefore anthocyanin and tannin concentration in the berry. In a three-year study published by Cohen (2012) was showed that total PA content per berry varied only in one year, when PA content was highest in heated berries (1.46 mg berry) and lowest in cooled berries (0.97 mg berry). In two years, cooling berries resulted in a significant increase in the proportion of (–)-epigallocatechin as an extension subunit. In the third year, rates of berry development, PA accumulation, and the expression levels of several genes involved in flavonoid biosynthesis were assessed. Heating and cooling berries altered the initial rates of PA accumulation, which was correlated strongly with the expression of core genes in the flavonoid pathway. However, the study examined proanthocyanidins content and composition throughout berry development in both shaded and exposed fruit, revealing significant differences in both content and composition throughout the intermediate stages of berry development, with shaded fruit reaching a much lower maximum in proanthocyanidin content than exposed fruit. The peak in proanthocyanidin accumulation in winegrapes occurred around time of veraison and then decreased toward harvest in what is generally considered to be a decrease in tannin extractability rather than degradation or turnover. This decrease in tannin extractability was observed in both shaded and exposed fruit; however, the decrease was greater in exposed fruit such that the levels were virtually the same in shaded and exposed fruit at harvest. The effects of shading on tannin accumulation in grape berries have only been examined in Shiraz, although this is an active area of research in the Australian wine industry (Downey et al. 2006). Goal of this research is the study of some Sicilian native cultivars grown in different areas of Sicily to assess the evolution of proanthocyanidins during ripening. Cultivars considered in this study are Nero d’Avola (biotype A, B and C) and Frappato (biotype A and B). Experimental fields are located in Marsala (TP) and Sambuca (AG). In these vineyards, various agronomic aspects were considered: meteorological data, leaf relative water content (Marchesi, 2004) and pruning wood weight. Experimental grapes samples were analyzed in the laboratory of the Viticulture and Enology Research Center of the Sicilian Region Extension Service located in Marsala (Sicily). Sampling were carried out in pre-veraison, mid-ripening and harvesting. Skins extract were subjected to analysis proanthocyanidins index (PI), flavans reactive to vanillin (FRV) and HPLC analysis (by phloroglucinolysis). The wines were analyzed in the Viticulture and Oenology Department of Fresno State University (California), for the study of proanthocyanidins, through the use of various chromatographic techniques: phloroglucinolysis, molecular mass, and hydrophobic interactions Observed results have confirmed that proanthocyanidins were been synthesized before the veraison; while during ripening they have decreased, in the degree of polymerization they have increased. Environment conditions of Sambuca site have led to increased synthesis of proanthocyanidins, a more severe decreased than Marsala site during ripening. At harvest time, the greater degree of polymerization was found in the grapes of Sambuca site. This result was also confirmed by the analysis results made on wines. At the biotype level, observing the information acquired, to Nero d'Avola, the biotype B presents more and more proanthocyanidins polymerization than other biotype in both sites. For what concerns Frappato, in both sites, no significant differences were found between the two biotypes, both at the level of accumulation of proanthocyanidins both at the level of polymerization.

In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)<br/><br/>Montserrat Vaqué Marquès <br/>En aquesta tesis es pretén aplicar metodologies computacionals (generació de farmacòfors i docking proteïna lligand) en l'àmbit de la nutigenòmica (ciència que pretén entendre, a nivell molecular, com els nutrients afecten la salut). S'aplicaran metodologies in silico per entendre a nivell molecular com productes naturals com els compostos fenòlics presents en la nostra dieta, poden modular la funció d'una diana comportant un efect en la salut. Aquest efecte es creu que podria ser degut a la seva interacció directa amb proteïnes de vies de senyalització molecular o bé a la modificació indirecta de l'expressió gènica. Donat que el coneixement de l'estructura del complex lligand-receptor és bàsic per entendre el mecanisme d'acció d'aquests lligands s'aplica la metodologia docking per predir l'estructura tridimensional del complex. En aquest sentit, un dels programes de docking és AutoGrid/AutoDock (un dels més citats). No obstant, l'automatització d'AutoGrid/AutoDock no és trivial tan per (a) la cerca virtual en una llibreria de lligands contra un grup de possibles receptors, (b) l'ús de flexibilitat, i (c) realitzar un docking a cegues utilitzant tota la superfície del receptor. Per aquest motiu, es dissenya una interfície gràfica de fàcil ús per utilitzar AutoGrid/AutoDock. Blind Docking Tester (BDT) és una aplicació gràfica que s'executa sobre quatre programes escrits en Fortran i que controla les condicions de les execucions d'AutoGrid i AutoDock. BDT pot ser utilitzat per equips d'investigadors en el camp de la química i de ciències de la vida interessats en dur a terme aquest tipus d'experiments però que no tenen suficient habilitats en programació. <br/><br/>En la modulació del metabolisme de la glucosa, treballs in vivio i in vitro en el nostre grup de recerca s'han atribuït els efectes beneficiosos de l'extracte de pinyol de raïm en induir captació de glucosa (punt crític pel manteniment de l'homeostasis de la glucosa). No obstant alguns compostos fenòlics no tenen efecte en la captació de la glucosa, d'altres l'inhibeixen reversiblement. En alguns casos aquesta inhibició és el resultat de la competició dels compostos fenòlics amb ATP pel lloc d'unió de l'ATP de la subunitat catalítica de la fosfatidil inositol 3-kinasa (PI3K). Estudis recents amb inhibidors específics d'isoforma han identificat la p110&#945; (la subunitat catalítica de PI3K&#945;) com la isoforma crucial per la captació de glucosa estimulada per insulina en algunes línies cel·lulars. Els programes computacionals han estat aplicats per tal de correlacionar l'activitat biològica dels compostos fenòlics amb informació estructural per obtenir una relació quantitativa estructura-activitat (3D-QSAR) i obtenir informació dels requeriments estructura-lligand per augmentar l'afinitat i/o selectivitat amb la diana (proteïna). Tot hi haver-se demostrat que l'adició d'extractes de compostos fenòlics en l'aliment pot tenir en general un benefici per la salut, s'ha de tenir en compte que l'estudi 3D-QSAR (construït a partir d'inhibidors sintètics de p110&#945;) prediu que algunes d'aquestes molècules poden agreujar la resistència a la insulina en individus susceptibles dificultant la capatació de glucosa en múscul i teixit adipós i, per tant, produir un efecte secundari indesitjat. <br/><br/>Resultats en el nostre grup de recerca han demostrat que compostos fenòlics presents en extractes de llavor de raïm incrementen l'activitat del receptor "farnesoid x receptor" (FXR) de manera dosi depenent quan el lligand natural de FXR (CDCA) és present. Les metodologies in silico, docking i 3D-QSAR, han estat aplicades juntament amb dades biològiques d'agonistes no esteroidals de FXR que s'uneixen a un lloc d'unió proper però diferent al lligand esteroidal 6CDCA. Els resultats han mostrat que els compostos fenòlics no són capaços d'activar FXR per ells mateixos però poden afegir noves interaccions que estabilitzarien la conformació activa de FXR en presència del lligand natural CDCA. Els compostos fenòlics podrien induir canvis conformacionals específics que augmentarien l'activitat de FXR. <br/><br/><br/><br/>In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)<br/><br/>Montserrat Vaqué Marquès <br/>This thesis was written with the aim of applying computational methods that have already been developed for molecular design and simulation (i.e. pharmacophore generation and protein-ligand docking) to nutrigenomics. So, in silico tools that are routinely used by the pharmaceutical industry to develop drugs have been used to understand, at the molecular level, how natural products such as phenolic compounds (i.e. molecules that are commonly found in fruits and vegetables) can improve health and prevent diseases. Therefore, we first focused on predicting the structure of protein-ligand complexes. The docking algorithms can use the individual structures from receptor and ligand to predict (1) whether they can form a complex and (2) if so, the structure of the resulting complex. This prediction can be made, for instance, with AutoGrid/AutoDock, the most cited docking software in the literature. The automation of AutoGrid/AutoDock is not trivial for tasks such as (1) the virtual screening of a library of ligands against a set of possible receptors; (2) the use of receptor flexibility and (3) making a blind-docking experiment with the whole receptor surface. Therefore, in order to circumvent these limitations, we have designed BDT (i.e. blind-docking tester; http://www.quimica.urv.cat/~pujadas/BDT), an easy-to-use graphic interface for using AutoGrid/AutoDock. BDT is a Tcl/Tk graphic front-end application that runs on top of four Fortran programs and which controls the conditions of the AutoGrid and AutoDock runs. <br/><br/>As far as the modulation of the glucose metabolism is concerned, several in vivo and in vitro results obtained by our group have shown that grape seed procyanidin extracts (GSPE) stimulate glucose uptake in 3T3-L1 adipocytes and thus help to maintain their glucose homeostasis. In contrast, it is also well known that although some phenolic compounds do not affect glucose uptake, others reversibly inhibit it in several cell lines. Moreover, for at least some of these phenolic compounds, this inhibition is the result of their competition with ATP for the ATP-binding site in p110&#945; (i.e. the &#945; isoform of the catalytic subunit of phosphoinositide 3-kinase or PI3K&#945;). Furthermore, recent studies with isoform-specific inhibitors have identified p110&#945; as the crucial isoform for insulin-stimulated glucose-uptake in some cell lines. Therefore, although it has been proved that the addition of phenolic compound extracts to food can have an overall benefit on health, it should be taken into account that some of these molecules may exacerbate insulin resistance in susceptible individuals via impaired glucose uptake in muscle and adipose tissues and, therefore, produce an undesirable side effect. In this context, we have applied computational approaches (i.e. protein-ligand docking and 3D-QSAR) to predict the IC50 (i.e. the concentration that reduces the p110&#945; activity to 50%). Our results agree with previous experimental results and predict that some compounds are potential inhibitors of this enzyme. <br/><br/>Recent results in our research group have demonstrated that the phenolic compounds in GSPE increase the activity of the farnesoid X receptor (i.e. FXR) in a dose-dependent way when the natural ligand of FXR (i.e. CDCA) is also present. The phenolic compounds might induce specific conformational changes that increase FXR activity and then contribute to cardioprotection through mechanisms that are independent of their intrinsic antioxidant capacities but that involve direct interaction with FXR to modulate gene expression. Taking into account this hypothesis a 3D-QSAR analysis was made in an attempt to understand how phenolic compounds activate FXR. So, our results explain why phenolic compounds cannot activate FXR by themselves and how they can add new interactions to stabilize the active conformation of FXR when its natural ligand (i.e. CDCA) is present. Therefore, we proposed a mechanism of FXR activation by dietary phenolic compounds in which they may enhance bile acid-bound FXR activity.

O processo de cultivo da uva e elaboração do vinho tinto varietal Marselan foi parcialmente acompanhado junto a uma vinícola do Vale dos Vinhedos (RS, Brasil), com o objetivo de verificar, com técnicas analíticas baseadas em feixes iônicos, como PIXE, alterações elementares no vinho devido ao seu processamento. Amostras de solo, folhas e galhos das videiras, uvas, mosto e vinhos foram coletadas nas etapas mais importantes do ciclo de cultivo da uva e de produção do vinho. Os alvos foram preparados de acordo com as características de cada material e exigências da técnica e, então, irradiados no sistema de PIXE do Laboratório de Implantação Iônica (IFUFRGS). Os resultados, de acordo com as análises estatísticas realizadas com teste t, ANOVA FATOR ÚNICO e Tukey, mostraram que a composição elementar do solo é constituída por Mg, Al, P, K, Ti, Mn, Fe, As, Rb e Zr. Além disso, foi verificada contaminação superficial devido, principalmente, ao Ca e Cu. Quanto ao cultivo, folhas e galhos revelaram a influência das aplicações de produtos químicos pelo acúmulo de alguns elementos no período de latência. A concentração elementar das uvas variou em função do crescimento e amadurecimento dos bagos. Em geral, durante o processo de vinificação e, em especial durante a fermentação, a concentração de vários elementos aumentou. Este foi o caso de elementos como o Mg, K, Rb e Sr. Por outro lado, alguns elementos tiveram um decréscimo na concentração devido a precipitação, como o Ca e o Cu.<br>The study of the Marselan grape cultivation and winemaking process was partially carried out in a winery located in Vale dos Vinhedos (RS, Brazil). The main goal was to employ ion-based techniques like PIXE in order to obtain elemental variations throughout the production chain of wine. Soil, vine leaves and branches, grapes, must and wine samples were collected at every important step of the production chain. Samples were prepared according to the peculiarities of each material and technique requirements. All PIXE measurements were carried at the Ionic Implantation Laboratory (IF-UFRGS). The data were analyzed with t test, ANOVA ONE WAY and Tukey. The elemental composition of soil comprises Mg, Al, P, K, Ti, Mn, Fe, As, Rb and Zr. Other elements like Cu and Ca were present over superficial layers and might be related to contaminants. With respect to the cultivation process, leaves and branches suffered from the influence of chemicals accumulated during the latency period. The elemental concentration of grapes changed during the berry growth and ripening. In general, later steps including fermentation tended to increase the concentrations of several elements like Mg, K, Rb and Sr. On the other hand, other elemental concentrations decreased due to precipitation, like Ca and Cu.

碩士<br>國立臺灣師範大學<br>科學教育研究所<br>100<br>The purpose of this study is to explore the comprehension students hold for rectilinear motion via the transformation between x-t graph and text. The study included two domain – quality &; quantity strategy. The subjects included 34 junior high school students who have learned the concept of rectilinear motion in Ping-Tung County, to collect the traits of x-t graph subjects sketch, and find the correlation of science knowledge and sketching x-t graph ability with quantity strategy. Researcher selected another gread-9 class to find the relation of reading x-t graph abilities and sketching x-t graph ability, and to know the comprehension students have while they transform text to x-t graph with quality strategy. Based on their response, the major finding as following: 1. There is high correlation between sketch ability and science score(r=.85p< .01) 2. There is difference of sketching x-t graph ability between subjects who have the reading x-t graph abilities that knows the motion direction x-t graph represent or not. (p= .03< .05) 3. There are six error types in sketching x-t graph: (1) Forget to label “0” at the intersection point of axis; (2) Deem the intersection point of axis as the origin of position; (3) Exchange the positions of physical quantities x and t; (4) Confused with physical quantities, like position and velocity; (5) Unable to sketch scales of x-t graph involving negative concepts; (6) Subjects are confused with the negative concepts of physical quantities. 4. Most subjects know x represent position, and less deem x is distance to the origin. 5. Most subjects know the same meaning of direction of motion and velocity, and less know the direction of motion is irrelevant to position. 6. Most Subjects accepting help of sketching graph know “the moving direction” and “the scale of velocity” that x-t graph represent. We can conclude some suggestions from this study: (1)Integrating independent variable-(t, time) and dependent variable-(x, position) into curriculum, (2)Sketching x-t graph involving negative x more often, (3)Clarifying the difference of direction of position and velocity.

碩士<br>國立臺灣師範大學<br>科學教育研究所<br>99<br>Junior high school student’s basic concepts in “linear motion” is vague. They are confused about the meaning of displacement, velocity and acceleration. The reason that causes students hard to learn is because that when students leran those phasics,especially in transformation of displacement, speed, acceleration, students need lots of working memory to do mental activities such as storation or transformation of those concepts. In recent years, several e-learning studies have shown that dynamic presentation helps students to reduce cognitive load. Researchers believe that if we present displacement, velocity, acceleration and other related physical in a dynamic method, it is possible to reduce the cognitive load and prmote effectiveness.The target of this study is that useing mental effort rating-scale and mental load rating-scale to measure learners’ mental status when they learn X-t and V-t material by using dynamic or static presentation , and we also compared their achievements. I hope the results help students learn X-t graphics and V-t graphics more effectively. This research found that(1) dynamic graphics improved learners’ performances, students in dynamic graphics group performed better than students in static graphics groups significantly with respect to academic performance （F(1,153)＝8.911，p＝.003，f＝0.24）. If we divided student in three groups according to their prior knowledge, we found that dynamic graphics have the best effect on high prior knowledge learners (d＝0.44), medium effect on low prior knowledge learners (d＝0.26), and less effect on medium prior knowledge learners (d＝0.10). (2) The presenting methods have low effect on learners（t(1,153)＝-1.93， p＝.055，d＝0.31）. (3) Dynamic graphics can reduce the learners’ mental loadt(1,153)＝-7.75， p＝.000，d＝1.25）, and (4) the learner's mental effort （t(1,153)＝-2.82， p＝.006，d＝0.45）. It is shown that students can use less mental effort and resource to achieve the same or better achievements. Finally, we used regression analysis to find that learners learnd by using dynamic or static graphics were different in achievement. When learners used dynamic and static graphics, the two groups lof earners’ achievement equation were shown as : Static graphs group: Achievement ＝ 0.526 × prior knowledge －0.374 ×mental load +0.221 ×mental effort Dynamic graphs group: Achievement ＝ 0.594 × prior knowledge －0.192 ×mental effort The equation revealed that the achievements of static group learners required more prior knowledge, less mental load and more mental effort, which is consistent with our expectations.When learners learned with dynamic graphics, more prior knowledge and less mental effect are needed, it is shown that mental load isn’t the key factor to effect learners’ achievements, it is also shown that learners just took less mental effort.

Molecular recognition between proteins and their associated ligands constitutes ligand-induced protein rewiring thereby enabling the formation of a stable protein-ligand complex. The studies presented in this thesis address the conformational plasticity inherent to proteins by virtue of which they adapt to diverse ligands and orchestrate complex biological processes like signal transduction, transcription and protein-protein interaction. Adopting network theory based formalisms for understanding protein-ligand associations involve deconstructing the three-dimensional structure of a protein in terms of nodes and edges. With this view, Protein Structure Networks (PSNs) of ligand-bound complexes are studied by considering their side-chain non-covalent interactions. Agonist and antagonist-bound G-Protein Coupled Receptors (GPCRs) are investigated to gain mechanistic insights into allostery and its role in signal transduction. The degree of similarity between PSNs of these complexes is quantified by means of Network Similarity Score (NSS). The physical nature of these networks is inspected by subjecting them to perturbations and major players in maintaining the stability of such networks are identified. Residue-wise groupings (at backbone and side-chain level) are obtained by applying graph spectral methods. All-atom Molecular Dynamics (MD) simulations are carried out to gain a better understanding of protein-ligand binding by analysing conformational ensembles of these complexes. In this scenario, two members from a highly versatile ligand-inducible transcription factor superfamily, i.e., Nuclear Receptors (NR) are studied, that are known to exhibit extremes of ligand binding behavior ranging from promiscuity to specificity. Diverse ligands are known to bind to proteins and the overall nature of their binding site is investigated. In particular, similarities among binding sites of diverse proteins are analysed by using PocketMatch. Percolation of these similarities to regions surrounding the binding site is reported and examples depicting this extended similarity are discussed. Overall, studies presented in this thesis provide a structural perspective into the adaptability of proteins for recognizing diverse ligands and undergoing local or global re-organizations in their framework to regulate complex biological processes.

碩士<br>國立臺灣大學<br>園藝學研究所<br>102<br>This study consisted of two experiments. Experiment one compared the difference in growth among 1202, 5C, 420A, and ‘Kyoho’ grape cuttings. Experiment two investigated the effect of mentioned root stocks on berry quality of Sakurai Kyoho. In the first experiment, budburst, root, aboveground part, cutting wood, canopy and shoot, leaf area, and number of leaves and internodes of the three rootstocks and ‘Kyoho’ cuttings were periodically sampled and measured on 29 May (90 days after cutting), 26 June (118 days after cutting), 18 September (202 days after cutting) 2009, and 29 January 2010 (336 days after cutting). The result showed that fresh weight of cutting woods of 1202 was greater than the others on the first measurement but not different from the others later. Fresh weight of root was significantly different between 1202 and 5C cuttings on 29 May but was not different on the other measuring dates. Fresh weight of shoot of 5C was greatest on all sampling dates. Lengths of shoots were significantly different between 5C and ‘Kyoho’ cuttings on all sampling dates. 5C cuttings had the earliest budburst followed by 120c, 420A, and Kyoho. Fresh weight of aboveground part was greatest in 5C. Overall, 5C had the best growth while Kyoho had the poorest growth. The result was similar to the performance of mature ‘Kyoho’ vines on the mentioned root system. Nevertheless, optimal growth and yield can be managed in mature own-rooted ‘Kyoho’ vines regardless of the short longevity, weak disease resistance, and relative low cropload. In the second experiment, fruit clusters of own-rooted ‘Sakurai Kyoho’ and grafted vines on 1202, 5C, and 420A rootstocks were harvest and berry quality, i.e. number of berries per cluster, weight of fruit cluster and berries, total soluble solids content, berry skin coloration, and berry shedding, at harvest and after cold storage was periodically measured. The result showed that berries from own-rooted vines and vines on 420A rootstock had the best overall quality. These information will help growers on the choice of rootstocks in Taiwan.

碩士<br>國立臺灣大學<br>園藝暨景觀學系<br>104<br>Timing for root growth and root activity is important for orchard management, affecting timing of fertilization application and uptake as well as allocation of carbohydrate and nutrient in plants. Taiwan is located on subtropical region with year round warm climate, allowing a double cropping system that is distinctive from the normal system in the temperate region. Neverthless, fruit load is an important key for the double cropping system. However, root growth and activity in double cropping system has yet to be fully documented. The objective of this theiss was to assess fruiting effect on root growth of ‘Kyoho’ grape. In this study, 9-year-old self-rooted ‘Kyoho’ grapevines were planted in polypropylene containers with root observation windows. Vines were trained to a double-shoot canopy structure. Fruiting or not be treatments and investigating new root growth and development. In the summer cropping cycle, new roots growth in fruiting vines mainly occurred from bloom to verasion, and those in non- fruiting vine delayed until period from verasion to fruit harvest correlating to the phenology of fruit vines. New root remaining white, root survival, or total new roots growth index were not affected by fruiting.In the winter cropping cycle, a peak of new roots growth occurred from bloom to verasion regardless of fruiting. New root remaining white, root survival, or total new roots growth index were also not affected by fruiting. Effective root index / new root growth index and root lifespan were significantly greater in the winter croppying cycle than in the summer cropping. In conclusion, in the double cropping system, root growth patterns were different between summer and winter cropping cycle. Overall, a major root growth peak occurred the summer.