Colour image of the thorax and abdomen

This is an image taken from Anatomy tv, an interactive resource for teaching and learning in anatomy and physiology which the University Library subscribes to. This image may not be changed, but you may take a copy and present it with other materials and resources you are using so long as they are password protected for access by members of the University only. "All products and all images within the products are protected by copyright. The products and images can only be used for private educational purposes, unless a specific license is purchased for any other usage. For any commercial usage of the images, please contact Primal Pictures Limited. The products allow members of the University of Southampton to ‘copy and paste’ all of the text as well as the images in the 3D-model window and all of the slides. These can then be pasted into nearly any other word-processing or graphics program, including Powerpoint. These resources can be made available to members of the University of Southampton via a password-protected service. This again is designed solely as a service for private educational uses. Like any publisher, Primal Pictures protects itself against copyright infringement. Please do contact Debra Morris in the University Library before using these resources to ensure that conditions are respected. ©Primal Pictures Limited 2007

Human heart

A colour image of the human heart. This is an image taken from Anatomy tv, an interactive resource for teaching and learning in anatomy and physiology which the University Library subscribes to. This image may not be changed, but you may take a copy and present it with other materials and resources you are using so long as they are password protected for access by members of the University only. All products and all images within the products are protected by copyright. The products and images can only be used for private educational purposes, unless a specific license is purchased for any other usage. For any commercial usage of the images, please contact Primal Pictures Limited. The products allow members of the University of Southampton to ‘copy and paste’ all of the text as well as the images in the 3D-model window and all of the slides. These can then be pasted into nearly any other word-processing or graphics program, including Powerpoint. These resources can be made available to members of the University of Southampton via a password-protected service. This again is designed solely as a service for private educational uses. Like any publisher, Primal Pictures protects itself against copyright infringement. Please do contact Debra Morris in the University Library before using these resources to ensure that conditions are respected. ©Primal Pictures Limited 2007

An Integrated Traffic and Pedestrian Model_based Vision System

The paper describes a novel integrated vision system in which two autonomous visual modules are combined to interpret a dynamic scene. The first module employs a 3D model-based scheme to track rigid objects such as vehicles. The second module uses a 2D deformable model to track non-rigid objects such as people. The principal contribution is a novel method for handling occlusion between objects within the context of this hybrid tracking system. The practical aim of the work is to derive a scene description that is sufficiently rich to be used in a range of surveillance tasks. The paper describes each of the modules in outline before detailing the method of integration and the handling of occlusion in particular. Experimental results are presented to illustrate the performance of the system in a dynamic outdoor scene involving cars and people.

Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase

It is known that germin, which is a marker of the onset of growth in germinating wheat, is an oxalate oxidase, and also that germins possess sequence similarity with legumin and vicilin seed storage proteins. These two pieces of information have been combined in order to generate a 3D model of germin based on the structure of vicilin and to examine the model with regard to a potential oxalate oxidase active site. A cluster of three histidine residues has been located within the conserved beta-barrel structure. While there is a relatively low level of overall sequence similarity between the model and the vicilin structures, the conservation of amino acids important in maintaining the scaffold of the beta-barrel lends confidence to the juxtaposition of the histidine residues. The cluster is similar structurally to those found in copper amine oxidase and other proteins, leading to the suggestion that it defines a metal-binding location within the oxalate oxidase active site. It is also proposed that the structural elements involved in intermolecular interactions in vicilins may play a role in oligomer formation in germin/oxalate oxidase.

Towards a holistic modelling framework for embodied carbon and waste in the building lifecycle

As the building industry proceeds in the direction of low impact buildings, research attention is being drawn towards the reduction of carbon dioxide emission and waste. Starting from design and construction to operation and demolition, various building materials are used throughout the whole building lifecycle involving significant energy consumption and waste generation. Building Information Modelling (BIM) is emerging as a tool that can support holistic design-decision making for reducing embodied carbon and waste production in the building lifecycle. This study aims to establish a framework for assessing embodied carbon and waste underpinned by BIM technology. On the basis of current research review, the framework is considered to include functional modules for embodied carbon computation. There are a module for waste estimation, a knowledge-base of construction and demolition methods, a repository of building components information, and an inventory of construction materials’ energy and carbon. Through both static 3D model visualisation and dynamic modelling supported by the framework, embodied energy (carbon), waste and associated costs can be analysed in the boundary of cradle-to-gate, construction, operation, and demolition. The proposed holistic modelling framework provides a possibility to analyse embodied carbon and waste from different building lifecycle perspectives including associated costs. It brings together existing segmented embodied carbon and waste estimation into a unified model, so that interactions between various parameters through the different building lifecycle phases can be better understood. Thus, it can improve design-decision support for optimal low impact building development. The applicability of this framework is anticipated being developed and tested on industrial projects in the near future.

Experimental measurement and numerical simulation of horizontal-coupled slinky ground source heat exchangers

Results from both experimental measurements and 3D numerical simulations of Ground Source Heat Pump systems (GSHP) at a UK climate are presented. Experimental measurements of a horizontal-coupled slinky GSHP were undertaken in Talbot Cottage at Drayton St Leonard site, Oxfordshire, UK. The measured thermophysical properties of in situ soil were used in the CFD model. The thermal performance of slinky heat exchangers for the horizontal-coupled GSHP system for different coil diameters and slinky interval distances was investigated using a validated 3D model. Results from a two month period of monitoring the performance of the GSHP system showed that the COP decreased with the running time. The average COP of the horizontal-coupled GSHP was 2.5. The numerical prediction showed that there was no significant difference in the specific heat extraction of the slinky heat exchanger at different coil diameters. However, the larger the diameter of coil, the higher the heat extraction per meter length of soil. The specific heat extraction also increased, but the heat extraction per meter length of soil decreased with the increase of coil central interval distance.

Exploring the land–ocean contrast in convective vigor using islands

Moist convection is well known to be generally more intense over continental than maritime regions, with larger updraft velocities, graupel, and lightning production. This study explores the transition from maritime to continental convection by comparing the trends in Tropical Rainfall Measuring Mission (TRMM) radar and microwave (37 and 85 GHz) observations over islands of increasing size to those simulated by a cloud-resolving model. The observed storms were essentially maritime over islands of <100 km2 and continental over islands >10 000 km2, with a gradual transition in between. Equivalent radar and microwave quantities were simulated from cloud-resolving runs of the Weather Research and Forecasting model via offline radiation codes. The model configuration was idealized, with islands represented by regions of uniform surface heat flux without orography, using a range of initial sounding conditions without strong horizontal winds or aerosols. Simulated storm strength varied with initial sounding, as expected, but also increased sharply with island size in a manner similar to observations. Stronger simulated storms were associated with higher concentrations of large hydrometeors. Although biases varied with different ice microphysical schemes, the trend was similar for all three schemes tested and was also seen in 2D and 3D model configurations. The successful reproduction of the trend with such idealized forcing supports previous suggestions that mesoscale variation in surface heating—rather than any difference in humidity, aerosol, or other aspects of the atmospheric state—is the main reason that convection is more intense over continents and large islands than over oceans. Some dynamical storm aspects, notably the peak rainfall and minimum surface pressure low, were more sensitive to surface forcing than to the atmospheric sounding or ice scheme. Large hydrometeor concentrations and simulated microwave and radar signatures, however, were at least as sensitive to initial humidity levels as to surface forcing and were more sensitive to the ice scheme. Issues with running the TRMM simulator on 2D simulations are discussed, but they appear to be less serious than sensitivities to model microphysics, which were similar in 2D and 3D. This supports the further use of 2D simulations to economically explore modeling uncertainties.

ATD: a multiplatform for semiautomatic 3-D detection of kidneys and their pathology in real time

This research presents a novel multi-functional system for medical Imaging-enabled Assistive Diagnosis (IAD). Although the IAD demonstrator has focused on abdominal images and supports the clinical diagnosis of kidneys using CT/MRI imaging, it can be adapted to work on image delineation, annotation and 3D real-size volumetric modelling of other organ structures such as the brain, spine, etc. The IAD provides advanced real-time 3D visualisation and measurements with fully automated functionalities as developed in two stages. In the first stage, via the clinically driven user interface, specialist clinicians use CT/MRI imaging datasets to accurately delineate and annotate the kidneys and their possible abnormalities, thus creating “3D Golden Standard Models”. Based on these models, in the second stage, clinical support staff i.e. medical technicians interactively define model-based rules and parameters for the integrated “Automatic Recognition Framework” to achieve results which are closest to that of the clinicians. These specific rules and parameters are stored in “Templates” and can later be used by any clinician to automatically identify organ structures i.e. kidneys and their possible abnormalities. The system also supports the transmission of these “Templates” to another expert for a second opinion. A 3D model of the body, the organs and their possible pathology with real metrics is also integrated. The automatic functionality was tested on eleven MRI datasets (comprising of 286 images) and the 3D models were validated by comparing them with the metrics from the corresponding “3D Golden Standard Models”. The system provides metrics for the evaluation of the results, in terms of Accuracy, Precision, Sensitivity, Specificity and Dice Similarity Coefficient (DSC) so as to enable benchmarking of its performance. The first IAD prototype has produced promising results as its performance accuracy based on the most widely deployed evaluation metric, DSC, yields 97% for the recognition of kidneys and 96% for their abnormalities; whilst across all the above evaluation metrics its performance ranges between 96% and 100%. Further development of the IAD system is in progress to extend and evaluate its clinical diagnostic support capability through development and integration of additional algorithms to offer fully computer-aided identification of other organs and their abnormalities based on CT/MRI/Ultra-sound Imaging.

Developing a mobile visualization environment for construction applications

There is a renewed interest in immersive visualization to navigate digital data-sets associated with large building and infrastructure projects. Following work with a fully immersive visualization facility at the University, this paper details the development of a complementary mobile visualization environment. It articulates progress on the requirements for this facility; the overall design of hardware and software; and the laboratory testing and planning for user pilots in construction applications. Like our fixed facility, this new light-weight mobile solution enables a group of users to navigate a 3D model at a 1:1 scale and to work collaboratively with structured asset information. However it offers greater flexibility as two users can assemble and start using it at a new location within an hour. The solution has been developed and tested in a laboratory and will be piloted in engineering design review and stakeholder engagement applications on a major construction project.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Avaliação de técnicas de interação egocêntricas em ambientes virtuais

Navegação, seleção e manipulação de objetos em ambientes virtuais são baseadas em métodos (técnicas de interação) associados a dispositivos convencionais ou especiais. Existem várias técnicas e dispositivos à disposição dos que desenvolvem aplicações com tais ambientes, sendo a escolha da técnica mais adequada uma tarefa difícil. Neste trabalho, são apresentadas diversas técnicas de interação existentes, suas metáforas e taxonomias, para realizar tarefas de seleção e manipulação de objetos e navegação do usuário pelo AV. A metodologia adotada nos experimentos realizados, visando a avaliar técnicas de interação em AVs imersivos foi composta por critérios de avaliação de interfaces de IHC (interface humano-computador), com critérios utilizados por Bowman, Mine e Poupyrev em seus experimentos com interfaces 3D. Também são apresentados alguns experimentos realizados, tendo vista avaliarem-se técnicas de interação na realização de tarefas de navegação, seleção e manipulação de objetos em ambientes virtuais imersivos. O objetivo deste trabalho foi a realização de experimentos para avaliar técnicas de interação para operações de seleção, manipulação e navegação em ambientes virtuais. Foram realizadas duas experiências: a primeira é uma avaliação de técnicas de seleção e manipulação em um ambiente semi-imersivo similar a um jogo de xadrez. As técnicas avaliadas são a mão virtual, associada a um mouse comum e a uma luva; e a ray-casting, associada à luva. Observou-se que o desempenho dos sujeitos é superior, quando a técnica utilizada é a mão virtual associada ao mouse comum. A segunda experiência apresenta uma avaliação experimental de dispositivos de RV em tarefas de navegação. Foi criado um ambiente, contendo um edifício com um elevador panorâmico e corredores de entrada e saída. Os testes foram realizados num ambiente imersivo, com capacete e luva, e, também em um ambiente semi-imersivo, com mouse comum e óculos com lentes de cristal líquido. Nesse segundo experimento, a preferência dos usuários pelos equipamentos utilizados foram o capacete e a luva. Observou-se que a existência ou não de objetos familiares no trajeto percorrido pelo usuário, não afeta a quantidade de colisões do sujeito com as mesmas.

Construção de modelos de interação in silico e in vitro do inibidor do tipo Kunitz de Adenanthera pavonina L. para as enzimas cisteínicas e serínicas

Serines proteinases inhibitors (PIs) are widely distributed in nature and are able to inhibit both in vitro and in vivo enzymatic activites. Seed PIs in than leguminous are classified in seven families, Bowman-Birk and Kunitz type families that most studied representing an important role in the first line of defense toward insects pests. Some Kunitz type inhibitors possess activities serine and cysteine for proteinases named bifunctional inhibitor, as ApTKI the inhibitor isolate from seed of Adenanthera pavonina. The A. pavonina inhibitor presenting the uncommon property and was used for interaction studies between proteinases serine (trypsin) and cysteine (papain). In order to determinate the in vitro interaction of ApTKI against enzymes inhibitor purification was carried cut by using chromatographic techniques and inhibition assays. The 3D model of the bifunctional inhibitor ApTKI was constructed SWISS-MODEL program by homology modeling using soybean trypsin inhibitor (STI, pdb:1ba7), as template which presented 40% of identity to A. pavonina inhibitor. Model quality was evaluated by PROCHECK program. Moreover in silico analyzes of formed complex between the enzymes and ApTKI was evaluated by HEX 4.5 program. In vitro results confirmed the inhibitory assays, where the inhibitor presented the ability to simultaneously inhibit trypsin and papain. The residues encountered in the inhibitor model of folder structural three-dimensional that make contact to enzymes target coud explain the specificity pattern against serine and cysteine proteinases

Desenvolvimento de um núcleo versátil e integrado de ferramentas CAD/CAE para a modelagem e simulação de peças mecânicas

Currently there is still a high demand for quality control in manufacturing processes of mechanical parts. This keeps alive the need for the inspection activity of final products ranging from dimensional analysis to chemical composition of products. Usually this task may be done through various nondestructive and destructive methods that ensure the integrity of the parts. The result generated by these modern inspection tools ends up not being able to geometrically define the real damage and, therefore, cannot be properly displayed on a computing environment screen. Virtual 3D visualization may help identify damage that would hardly be detected by any other methods. One may find some commercial softwares that seek to address the stages of a design and simulation of mechanical parts in order to predict possible damages trying to diminish potential undesirable events. However, the challenge of developing softwares capable of integrating the various design activities, product inspection, results of non-destructive testing as well as the simulation of damage still needs the attention of researchers. This was the motivation to conduct a methodological study for implementation of a versatile CAD/CAE computer kernel capable of helping programmers in developing softwares applied to the activities of design and simulation of mechanics parts under stress. In this research it is presented interesting results obtained from the use of the developed kernel showing that it was successfully applied to case studies of design including parts presenting specific geometries, namely: mechanical prostheses, heat exchangers and piping of oil and gas. Finally, the conclusions regarding the experience of merging CAD and CAE theories to develop the kernel, so as to result in a tool adaptable to various applications of the metalworking industry are presented

Computations of the flow past a still sphere at moderate reynolds numbers using an immersed boundary method

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)