Dans cette thèse, nous proposons une approche combinatoire novatrice fondée sur les matroïdes orientés pour l'étude quantitative de la forme de structures anatomiques 3D. Nous nous basons sur des points de repère qui ont été préalablement localisés par des experts sur la structure anatomique étudiée. La nouveauté de cette méthode provient de l'utilisation de matroïdes orientés. Ces outils mathématiques nous permettent de coder la position relative des points de repère de façon purement combinatoire, c'est-à-dire sans utiliser de notions d'angles ou de distances, en associant un signe (0, + ou -) à chaque sous-ensemble de (d+1) points de repère où d est la dimension de l'espace (dans notre cas 2 ou 3). Dans une première partie, nous supposons qu'il existe des contraintes d'ordres sur chaque axe de coordonnée pour les points de repère. Nous obtenons alors une caractérisation (en dimension 2 et 3) des sous-ensembles de points de repère dont le signe associé est constant, quelles que soient les valeurs des coordonnées satisfaisant les contraintes d'ordre. Dans une deuxième partie, nous cherchons à classifier un ensemble de modèles 3D, en les codant au préalable par ces listes de signes. Nous analysons d'abord comment s'appliquent les algorithmes de clustering classiques, puis nous décrivons comment caractériser des classes de façon directe, à l'aide des signes associés à quelques sous-ensembles de points de repère. Dans une troisième partie, nous détaillons les algorithmes et l'implémentation en machine de cette nouvelle méthode de morphométrie afin de pouvoir l'appliquer à des données réelles. Dans la dernière partie, nous appliquons la méthode sur trois bases de données composées chacune de plusieurs dizaines de points de repères relevés sur plusieurs dizaines à plusieurs centaines de structures crâniennes pour des applications en anatomie comparée, en orthodontie et sur des cas cliniques d'enfants présentant des déformations cranio-faciales. / In this thesis, we propose an innovative combinatorial method based on oriented matroids for the quantitative study of the shape of 3D anatomical structures. We rely on landmarks which were previously defined by experts on the studied anatomical structure. The novelty of this method results from the use of oriented matroids. These mathematical tools allow us to encode the relative position of landmarks in a purely combinatorial way, that is without using concepts of angles or distances, by associating a sign (0, + or -) for each subset of (d+1) landmarks where d is the dimension of space (in our case 2 or 3). In the first part, we assume that there exist constraints of orders on each coordinate axis for the landmarks. We obtain a characterization (in dimension 2 and 3) of the subsets of landmarks of which the associated sign is constant, regardless of the values of the coordinates satisfying the constraints of order. In a second part, we try to classify a set of 3D models, encoding in advance by these lists of signs. We first analyze how to apply classic clustering algorithms, and then describe how to characterize the classes directly, using signs associated with some subsets of landmarks. In the third part, we explain the algorithms and the implementation of this new morphometry method in order to apply it to real data. In the last part, we apply the method to three databases each consisting of several dozens of points defined on several dozens to several hundreds of cranial structures for applications in comparative anatomy, in orthodontics and on clinical cases of children with craniofacial deformities.

Les cellules souches de glioblastomes (GSC) sont sensibles aux propriétés mécaniques de leur microenvironnement et utilisent la rigidité pour favoriser leur invasion.Dans ce contexte, nous avons développé une matrice 3D fibrillaire artificielle permettant de récapituler in vitro les comportements migratoires observés in vivo. Cette matrice étant hautement plastique, nous avons pu moduler la rigidité, la chimie de surface ou encore l'alignement des fibres.Dans un premier temps nous avons modifié leur chimie de surface grâce à l’ajout de protéines de la matrice extracellulaire (MEC) puis déposé des neurosphères (NS) de GSC sur ce tissu artificiel. L’ajout de laminine nous a permis d’observer le passage d’un comportement migratoire collectif à individuel.Dans un deuxième temps nous avons modulé la rigidité des fibres. Après cinq jours de migration des GSC dans différentes conditions de rigidités, nous avons constaté une augmentation de la vitesse de migration à la rigidité intermédiaire de 166kPa par rapport à la condition plus souple de 3,2 kPa et à la condition plus rigides de 1260kPa. Cette capacité migratoire maximale dans nos conditions est associée à des changements de morphologie des GSC, à une augmentation de l'expression des protéines associée à la transition épithélio-mésenchymateuse (EMT) et à une modification de la régulation des protéines des adhérences focales.La surexpression de Mannoside acetyl glucosaminyltransférase 5 (MGAT5) est associée aux tumeurs malignes et est impliquée dans la formation de regroupement de protéines membranaires grâce à la formation d’un treillis. Elle favorise également la maturation des adhérences focales, la migration cellulaire, l'invasion et l’EMT, entraînant ainsi des avantages fonctionnels pour les cellules tumorales. Au vu des résultats précédents sur l'expression des protéines EMT et des modifications de la régulation des protéines des adhérences focales, nous avons généré des GSC n’exprimant plus la MGAT5 grâce à la technique CRISPR Cas9 et les avons placées en NS sur les matrices 3D présentant différentes rigidité. Nous avons alors observé une diminution de la vitesse de migration à 166kPa par rapport aux GSC contrôles, associée à une diminution de l'EMT et de la maturation des adhérences focales. Par conséquent, cette étude démontre l'implication de la glycosylation et plus particulièrement de la glycosylation médiée par la MGAT5 sur la mécanotransduction des GSC. / Glioblastoma stem cells (CSC) have been reported to be sensitive to the mechanical properties of the surrounding tissue/microenvironment and to use the microenvironment stiffness to enhance invasion.In this context, we developed a 3D artificial fibrillary tissue which can allow in vitro recapitulation of the migration behavior observed in vivo. This 3D matrix is highly plastic which allows for modulation of stiffness, surface chemistry and fibers alignment.On the first hand, we functionalized the fibers with extracellular matrix proteins and then we plated GSCs neurospheres (NS) on the developed 3D artificial tissue. The addition of laminin modulates the migration behaviour from single cell to collective mode.On the second hand we have modified stiffness of the fibers. After five days of GSCs NS migration on 3D electrospun fibers of different stiffnesses, we have seen an increase in migration velocity for an intermediate stiffness of 166kPa in comparison with our softest 3.2 kPa and stiffest stiffnesses (1260 kPa). This maximum migration rate is associated with changes in cell shape, increase of EMT proteins expressions and modifications of focal adhesion proteins regulation.Mannoside acetyl glucosaminyltransferase 5 (MGAT5) overexpression is associated with malignant tumors and it is implicated in the clustering of membrane proteins through lattice formation, focal adhesions, cell migration, invasion, and epithelial-to-mesenchymal transition (EMT), resulting in functional advantages for tumor cells.In light of previous results about of EMT proteins expressions and modifications of focal adhesion proteins regulation, we generated MGAT5 CRISPR Cas9 GSCs and placed it on 3D matrix with different stiffnesses. We observe a decrease in migration velocity at the intermediate stiffness in comparison with GSCs WT associated with a decrease in focal adhesion maturation and EMT. This study demonstrates the implication of glycosylation and more particularly MGAT5-mediated glycosylation on GSCs mechanotransduction.

Despite the growing number of publications relating to three-dimension (3D) and education, the need for this technology, its usability and educational impact are not clear for dental education with the exception of haptics. The first stage of this doctoral research used a mixed method to examine key stakeholders’ views about those areas of dentistry that would benefit from having a 3D learning resource. Two hundred and five dental students, academics and graduates responded to the survey (134 females and 71 males). Results suggested that several areas of dentistry would benefit from 3D animations or simulations. Anatomy of the Temporomandibular joint (TMJ) was the top priority area from the list of the identified items. After identifying the areas of need, the researcher determined principles for e-learning and instructional design; followed by a feasibility study that identified a suitable authoring tool for the construction of a resource capable of containing 3D interactive models. A multidisciplinary team headed by the researcher developed the first iBook addressing the Tooth Morphology of the permanent dentition. The researcher collected feedback from users of the tooth morphology iBook using a mixed method experimental study, which included a questionnaire and a focus group session. Scottish and Chilean participants (n=138), from the University of Dundee and The Andes respectively, indicated that the iBook was well designed and it was a valuable resource where they could interact with the 3D models provided. These results informed the construction of a second iBook addressing the anatomy of the temporomandibular joint (TMJ) and masticatory system. Two versions of the TMJ iBook were created: a 3D version containing interactive models and a 2D version holding images. The researcher designed a comparative study including a pre-test/post-test intervention and a questionnaire to compare results from the two groups (3D and 2D). Twenty-seven first-year and thirty-two third-year dental students from the University of Dundee participated. The results of the intervention revealed statistically significant improvements in the results of first-years students who used the 3D version iBook compared to those who used the 2D one. The third-year cohort results revealed no significant difference between the 2D and 3D groups. The researcher arranged two focus group sessions to gain a deeper insight into the results. From those who took part in the intervention, eleven volunteered for the focus group sessions (six first years and five third-years). Results indicated that the TMJ iBook was a valuable resource for learning. Regardless the year of study, all participants preferred the use of the 3D interactive models as they had the potential to simplify visualisation and orientation, and enhance motivation for learning. Three key findings arose from this doctoral study. The first one indicates that several areas of dentistry would benefit from 3D resources and they would satisfy dental students’ needs. The second conclusion suggests that iBooks are a powerful, straightforward and valuable resource for creating new e-learning interactive material capable of displaying 3D models. The final finding suggests that the use of 3D interactive models have the potential to enhance learning in novice dental students, while they are capable of motivating and aiding visualisation both in junior and experienced students.

A 3D recreation of the interior of the main hall of the Union Station train station in Washington DC.

Estágio realizado na Medmat Innovation, Ld.ª e orientado pelo Eng.º Bruno Sá / Tese de mestrado integrado. Engenharia Metalúrgica e de Materiais. Faculdade de Engenharia. Universidade do Porto. 2009

Tese de Doutoramento. Engenharia Informática. Faculdade de Engenharia. Universidade do Porto. 2010

The goals of this research include developing and identifying software technologies, which facilitate the use of buildings described in Building Information Modeling (BIM) tools in both a simulation and visualization. The study focused on the development of a tool to fulfill the visualization needs of a Visual Energy Use System. To accomplish this, the study identified an open BIM file standard, the Industry Foundation Classes (IFC). The study also identified a video game based 3D virtual environment, the Doom 3 Engine. A tool developed during the study, IFCtoMAP, converts IFC data into the .MAP file format understood by the Doom 3 Engine. Finally, the study identified the IFCtoIDF utility, which translates IFC data into a format understood by the building energy simulation program EnergyPlus. Data from the Building Information Modeling tool Revit Building exports to the .IFC file format, which in turn drives the two conversion utilities IFCtoMAP and IFCtoIDF. The output of the IFCtoIDF tool consists of an .IDF file that EnergyPlus uses to perform an energy simulation. The output of the IFCtoMAP tool consists of a .MAP file, which the Doom 3 game engine uses to display three dimensional first person perspective visualization. The result of the study was the successful creation of an automated tool that converts building geometry found in .IFC files into the .MAP file format understood by Doom 3 game engine. This document details the methods employed by the IFCtoMAP software along with a brief discussion of the IFCtoIDF conversion utility.

Three 3D nonlinear finite-element (FE) models are developed to study the behavior of concrete beams and plates with and without externally reinforcement of fibre reinforced polymer (FRP). Ramtekkar’s mixed layer-wise 3 dimensional (3D) 18-node FE model (108 degrees-of-freedom, DOFs) is modified to accommodate the nonlinear concrete and elasto-plastic steel behaviour. Saenz’s stress-strain equation is used for material nonlinearity of concrete. As in any 3D mixed FE analysis, the run time using the model can be computationally expensive. Two additional layer-wise 18-node FE models: Displacement FE model (54 DOF) and transitional FE model (81 DOF) are developed. The displacement FE model is based on purely displacement field, i.e. only displacement components are enforced throughout the thickness of the structures. The transitional FE model has six DOF (three displacement components in the coordinate axis direction and three transverse stress components - where z is the thickness direction) per node in the upper surface and only three DOF (three displacement components in the coordinate axis direction) per node in the bottom surface.The analysis of reinforced concrete (RC) beam strengthened with FRP and composite plate using these models are verified against the experimental results and the results from the commercial software, ANSYS respectively. Several parametric studies are done on composite RC beam and composite plate. / May 2006

Binocular eye-gaze tracking can be used to estimate the point-of-gaze (POG) of a subject in real-world three-dimensional (3D) space using the vergence of the eyes. In this thesis, a novel non-contact, model-based technique for 3D POG estimation is presented. The non-contact system allows people to select real-world objects in 3D physical space using their eyes, without the need for head-mounted equipment. Using a model-based POG estimation algorithm allows for free head motion and a single stage of calibration. The users were free to naturally move and reorient their heads while operating the system, within an allowable headspace of 3.2 x 9.2 x 14 cm. A rela tively high precision, as measured by the standard deviation of the 3D POG estimates, was measured to be 0.26 cm and was achieved with the use of high speed sampling and digital filtering techniques. When observing points in a 3D volume, large head and eye rotations are far more common than when observing a 2D screen. A novel corneal reflection pattern matching algorithm is presented for increasing image feature tracking reliability in the presence of large eye rotations. It is shown that an average accuracy of 3.93 cm was achieved over seven different subjects and a workspace volume of 30 x 23 x 25 cm (width x height x depth). An example application is presented illustrating the use of the 3D POG as a human computer interface in a 3D game of Tic-Tac-Toe on a 3 x 3 x 3 volumetric display.

With sub-micron silicon processing technology reaching under 30nm, it becomes more difficult for integrated circuits to achieve higher integration through the scaling down of the transistor size. Three-dimensional integrated circuit (3D-IC) technology stacks multiple dies together and connects them using through-silicon vias (TSVs). This is a low cost and highly efficient way to increase integration. TSVs and stacked dies are two major features of the 3D-IC technology. However, the stacked structures using TSV interconnects induce concerns in reliability such as TSV strain effect, heat problem, and TSV coupling at high frequency, etc. The reliability concerns need to be carefully addressed before 3D-IC technologies can be widely adopted by the industry. Many studies have been carried out in this field, but there has not been much significant work done for testing electrical, mechanical and thermal issues of the 3D-IC technology simultaneously on a single test chip. In this work, a test chip including various test structures was designed to study and analyze these issues in a 3D-IC technology. An accurate resistance and capacitance (RC) model of the TSV for low frequency design was developed, high frequency electrical performance of the TSVs was characterized, coupling between TSVs was modeled, and the stress effect and the heat dissipation method were analyzed in the 3D-IC technology. The TSV model could be added to the design kit for future 3D-IC design and other results could be used to improve the reliability of 3D-IC designs and optimize the performance.