Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

Hovercraft telemanipulation virtual models and interface design

A control system was designed to allow humans to manually drive an, usually automatic, two wheeled hovercraft. The size, the mass and the way of driving this vehicle proves to be an issue for the everyday, untrained person to achieve. During this thesis several control layouts were designed with the objective of creating an intuitive and easy way of driving such a vehicle. At the end two where usertested using a simulation (also developed during this thesis) of the said hovercraft set against obstacles similar to those expected to be encountered on its real environment. The two layouts are just slightly apart in performance but numerous issues were found that can be used to redesign a better control layout. This means that no definitive winner was found but a foundation for a better design was indeed found.

Building 3D City Models: Testing and Comparing Laser Scanning and Low-Cost UAV Data Using FOSS Technologies

Contém resumo

Virtual Model Control of a Hexapod Walking Robot

Since robots are typically designed with an individual actuator at each joint, the control of these systems is often difficult and non-intuitive. This thesis explains a more intuitive control scheme called Virtual Model Control. This thesis also demonstrates the simplicity and ease of this control method by using it to control a simulated walking hexapod. Virtual Model Control uses imagined mechanical components to create virtual forces, which are applied through the joint torques of real actuators. This method produces a straightforward means of controlling joint torques to produce a desired robot behavior. Due to the intuitive nature of this control scheme, the design of a virtual model controller is similar to the design of a controller with basic mechanical components. The ease of this control scheme facilitates the use of a high level control system which can be used above the low level virtual model controllers to modulate the parameters of the imaginary mechanical components. In order to apply Virtual Model Control to parallel mechanisms, a solution to the force distribution problem is required. This thesis uses an extension of Gardner`s Partitioned Force Control method which allows for the specification of constrained degrees of freedom. This virtual model control technique was applied to a simulated hexapod robot. Although the hexapod is a highly non-linear, parallel mechanism, the virtual models allowed text-book control solutions to be used while the robot was walking. Using a simple linear control law, the robot walked while simultaneously balancing a pendulum and tracking an object.

Generating virtual environments to allow increased access to the built environment

The problems encountered by individuals with disabilities when accessing large public buildings is described and a solution based on the generation of virtual models of the built environment is proposed. These models are superimposed on a control network infrastructure, currently utilised in intelligent building applications such as lighting, heating and access control. The use of control network architectures facilitates the creation of distributed models that closely mirror both the physical and control properties of the environment. The model of the environment is kept local to the installation which allows the virtual representation of a large building to be decomposed into an interconnecting series of smaller models. This paper describes two methods of interacting with the virtual model, firstly a two dimensional aural representation that can be used as the basis of a portable navigational device. Secondly an augmented reality called DAMOCLES that overlays additional information on a user’s normal field of view. The provision of virtual environments offers new possibilities in the man-machine interface so that intuitive access to network based services and control functions can be given to a user.

3D semantic models for dental education

This paper explores the benefits of using immersive and interactive virtual reality environments to teach Dentistry. We present a tool for educators to manipulate and edit virtual models. One of the main contributions is that multimedia information can be semantically associated with parts of the model, through an ontology, enriching the experience; for example, videos can be linked to each tooth demonstrating how to extract them. The use of semantic information gives a greater flexibility to the models, since filters can be applied to create temporary models that show subsets of the original data in a human friendly way. We also explain how the software was written to run in arbitrary multi-projection environments. © 2011 Springer-Verlag.

Design and evaluation of an advanced virtual reality system for visualization of dentistry structures

This paper presents the development of an application created to assist the teaching of dental structures, generate rich content information and different manners of interaction. An ontology was created to provide semantics informations for virtual models. We also used two devices gesture-based interaction: Kinect and Wii Remote. It was developed a system which use intuitive interaction, and it is able to generate three dimensional images, making the experience of teaching / learning motivating. The projection environment used by the system was called Mini CAVE. © 2012 IEEE.

Sistema avançado de realidade virtual para visualização de estruturas odontológicas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A palaeobiologist's guide to 'virtual' micro-CT preparation

This paper provides a brief but comprehensive guide to creating, preparing and dissecting a 'virtual' fossil, using a worked example to demonstrate some standard data processing techniques. Computed tomography (CT) is a 3D imaging modality for producing 'virtual' models of an object on a computer. In the last decade, CT technology has greatly improved, allowing bigger and denser objects to be scanned increasingly rapidly. The technique has now reached a stage where systems can facilitate large-scale, non-destructive comparative studies of extinct fossils and their living relatives. Consequently the main limiting factor in CT-based analyses is no longer scanning, but the hurdles of data processing (see disclaimer). The latter comprises the techniques required to convert a 3D CT volume (stack of digital slices) into a virtual image of the fossil that can be prepared (separated) from the matrix and 'dissected' into its anatomical parts. This technique can be applied to specimens or part of specimens embedded in the rock matrix that until now have been otherwise impossible to visualise. This paper presents a suggested workflow explaining the steps required, using as example a fossil tooth of Sphenacanthus hybodoides (Egerton), a shark from the Late Carboniferous of England. The original NHMUK copyrighted CT slice stack can be downloaded for practice of the described techniques, which include segmentation, rendering, movie animation, stereo-anaglyphy, data storage and dissemination. Fragile, rare specimens and type materials in university and museum collections can therefore be virtually processed for a variety of purposes, including virtual loans, website illustrations, publications and digital collections. Micro-CT and other 3D imaging techniques are increasingly utilized to facilitate data sharing among scientists and on education and outreach projects. Hence there is the potential to usher in a new era of global scientific collaboration and public communication using specimens in museum collections.

Systematic literature review of digital three-dimensional superimposition techniques to create virtual dental patients

PURPOSE Digital developments have led to the opportunity to compose simulated patient models based on three-dimensional (3D) skeletal, facial, and dental imaging. The aim of this systematic review is to provide an update on the current knowledge, to report on the technical progress in the field of 3D virtual patient science, and to identify further research needs to accomplish clinical translation. MATERIALS AND METHODS Searches were performed electronically (MEDLINE and OVID) and manually up to March 2014 for studies of 3D fusion imaging to create a virtual dental patient. Inclusion criteria were limited to human studies reporting on the technical protocol for superimposition of at least two different 3D data sets and medical field of interest. RESULTS Of the 403 titles originally retrieved, 51 abstracts and, subsequently, 21 full texts were selected for review. Of the 21 full texts, 18 studies were included in the systematic review. Most of the investigations were designed as feasibility studies. Three different types of 3D data were identified for simulation: facial skeleton, extraoral soft tissue, and dentition. A total of 112 patients were investigated in the development of 3D virtual models. CONCLUSION Superimposition of data on the facial skeleton, soft tissue, and/or dentition is a feasible technique to create a virtual patient under static conditions. Three-dimensional image fusion is of interest and importance in all fields of dental medicine. Future research should focus on the real-time replication of a human head, including dynamic movements, capturing data in a single step.

A Performance Evaluation of Surface Normals-Based Descriptors for Recognition of Objects using CAD-Models

This paper describes a study and analysis of surface normal-base descriptors for 3D object recognition. Specifically, we evaluate the behaviour of descriptors in the recognition process using virtual models of objects created from CAD software. Later, we test them in real scenes using synthetic objects created with a 3D printer from the virtual models. In both cases, the same virtual models are used on the matching process to find similarity. The difference between both experiments is in the type of views used in the tests. Our analysis evaluates three subjects: the effectiveness of 3D descriptors depending on the viewpoint of camera, the geometry complexity of the model and the runtime used to do the recognition process and the success rate to recognize a view of object among the models saved in the database.

When the virtual influences reality. The conservation project of the toledo gate in ciudad real (Spain)

The Toledo Gate of Ciudad Real, Spain, constructed between the late 13th and early 14th centuries, is the last remaining portion of a once complete medieval city wall. It represents the long history of the city and constitutes its main heritage symbol, dividing the historic city centre from the later 19th and 20th century expansions. In October 2012, the Town Hall and the Montemadrid Foundation started the conservation works to preserve this important monument. The preliminary phase of this project included an in-depth series of scientific studies which were carried out by a multidisciplinary team focusing on archival research, historic investigations, archaeological excavations as well as material composition analysis and main treatment application tests. As a result of these studies a series of virtual 3D models were created to inform, discuss and study the monument. A first digital model permitted visualization of the gate in the 19th century and how the main entrance to the city was integrated as a fundamental part of the city walls. This virtual reconstruction also became an important part of the campaign to raise awareness among the citizens towards a monument that had remained in the shadows for the last century, isolated in a roundabout after the systematic demolition of the city walls in the late 19th century. Over the last three years and as a result of these archaeological and historic investigations and subsequent virtual models, surprisingly new and interesting data were brought to light thus permitting the establishment and corroboration of a new and updated hypothesis of the Toledo Gate that goes beyond the previous ideas. As a result of these studies a new architectural typology with construction techniques of has been suggested. This paper describes how the results of this continuous and interdisciplinary documentation process have benefitted from a computer graphic reconstruction of the gate. It highlights how virtual reconstruction can be a powerful tool for conservation decision making and awareness raising. Furthermore, the interesting results of the final reconstruction hypothesis convinced the technical team responsible for the conservation to alter some aspects of the final project physical interventions in order to focus on some of the features and conclusions discovered through the virtual model study.

Desenvolvimento de recursos educativos em dispositivos móveis - RealHiBook

Nos últimos anos têm existido bastantes pesquisas e um grande investimento quer na área da educação à distância quer ao nível das tecnologias móveis. A dada altura percebeu-se que cada vez mais poderiam ser utilizados dispositivos móveis no contexto da educação e de que estes já seriam capazes de responder às exigências necessárias para que fosse possível criar ou melhorar cenários com recursos educativos. Este trabalho tem como objetivo propor um modelo que facilite a aprendizagem em dispositivos móveis. Nesse sentido, decidiu-se que seria uma mais-valia adicionar a este projeto, a utilização da Realidade Aumentada como potenciador de melhorias no processo de aprendizagem. A Realidade Aumentada, a par do que acontece com a educação à distância e com as tecnologias móveis, é uma área alvo de constantes investigações e inovação. Apresenta como principal capacidade a interação do utilizador com vários modelos virtuais incluídos numa cena real. Esta capacidade proporciona experiências que podem contribuir para o aumento da motivação e da perceção por parte dos alunos. A forma como o utilizador interage com as aplicações móveis é vista com extrema importância, principalmente na área da educação. Aliar uma boa interação à utilização da Realidade Aumentada, é parte integrante deste trabalho. Foram estudados exemplos de interações e formas como o utilizador vive a experiência durante a utilização de aplicações que partilham o mesmo tipo de tecnologias utilizadas neste projeto. O objetivo final foca-se na criação de uma aplicação, capaz de fornecer uma experiência enriquecedora no âmbito do ensino, ligado ao tema história e que consiga fundamentar a criação de um modelo que facilite a aprendizagem utilizando plataformas móveis. Os objetivos são corroborados por um conjunto de testes efetuados à aplicação e pelos resultados obtidos através de um questionário feito a um grupo de pessoas que testaram o protótipo.

MixAR mobile prototype: visualizing virtually reconstructed ancient structures in situ

Archeology and related areas have a special interest on cultural heritage sites since they provide valuable information about past civilizations. However, the ancient buildings present in these sites are commonly found in an advanced state of degradation which difficult the professional/expert analysis. Virtual reconstructions of such buildings aim to provide a digital insight of how these historical places could have been in ancient times. Moreover, the visualization of such models has been explored by some Augmented Reality (AR) systems capable of providing support to experts. Their compelling and appealing environments have also been applied to promote the social and cultural participation of general public. The existing AR solutions regarding this thematic rarely explore the potential of realism, due to the following lacks: the exploration of mixed environments is usually only supported for indoors or outdoors, not both in the same system; the adaptation of the illumination conditions to the reconstructed structures is rarely addressed causing a decrease of credibility. MixAR [1] is a system concerned with those challenges, aiming to provide the visualization of virtual buildings augmented upon real ruins, allowing soft transitions among its interiors and exteriors and using relighting techniques for a faithful interior illumination, while the user freely moves in a given cultural heritage site, carrying a mobile unit. Regarding the focus of this paper, we intend to report the current state of MixAR mobile unit prototype, which allows visualizing virtual buildings – properly aligned with real-world structures – based on user's location, during outdoor navigation. In order to evaluate the prototype performance, a set of tests were made using virtual models with different complexities.

Implementação de metodologias BIM na Direção de Engenharia de Barragens da EDP: casos de estudo de projeto de estruturas em obras hidroelétricas

Dissertação de mestrado integrado em Engenharia Civil