Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.

Integration of a 3D Variational data assimilation scheme with a coastal area morphodynamic model of Morecambe Bay

This paper describes the implementation of a 3D variational (3D-Var) data assimilation scheme for a morphodynamic model applied to Morecambe Bay, UK. A simple decoupled hydrodynamic and sediment transport model is combined with a data assimilation scheme to investigate the ability of such methods to improve the accuracy of the predicted bathymetry. The inverse forecast error covariance matrix is modelled using a Laplacian approximation which is calibrated for the length scale parameter required. Calibration is also performed for the Soulsby-van Rijn sediment transport equations. The data used for assimilation purposes comprises waterlines derived from SAR imagery covering the entire period of the model run, and swath bathymetry data collected by a ship-borne survey for one date towards the end of the model run. A LiDAR survey of the entire bay carried out in November 2005 is used for validation purposes. The comparison of the predictive ability of the model alone with the model-forecast-assimilation system demonstrates that using data assimilation significantly improves the forecast skill. An investigation of the assimilation of the swath bathymetry as well as the waterlines demonstrates that the overall improvement is initially large, but decreases over time as the bathymetry evolves away from that observed by the survey. The result of combining the calibration runs into a pseudo-ensemble provides a higher skill score than for a single optimized model run. A brief comparison of the Optimal Interpolation assimilation method with the 3D-Var method shows that the two schemes give similar results.

Considering user attitude and behaviour in persuasive systems design: the 3D-RAB model

As in any technology systems, analysis and design issues are among the fundamental challenges in persuasive technology. Currently, the Persuasive Systems Development (PSD) framework is considered to be the most comprehensive framework for designing and evaluation of persuasive systems. However, the framework is limited in terms of providing detailed information which can lead to selection of appropriate techniques depending on the variable nature of users or use over time. In light of this, we propose a model which is intended for analysing and implementing behavioural change in persuasive technology called the 3D-RAB model. The 3D-RAB model represents the three dimensional relationships between attitude towards behaviour, attitude towards change or maintaining a change, and current behaviour, and distinguishes variable levels in a user’s cognitive state. As such it provides a framework which could be used to select appropriate techniques for persuasive technology.

Analyzing the persuasion context of the persuasive systems design model with the 3D-RAB model

Research into design methodology is one of the most challenging issues in the field of persuasive technology. However, the introduction of the Persuasive Systems Design model, and the consideration of the 3-Dimensional Re-lationship between Attitude and Behavior, offer to make persuasive technolo-gies more practically viable. In this paper we demonstrate how the 3-Dimensional Relationship between Attitude and Behavior guides the analysis of the persuasion context in the Persuasive System Design model. As a result, we propose a modification of the persuasion context and assert that the technology should be analyzed as part of strategy instead of event.

3D digital elevation model generation

This chapter presents techniques used for the generation of 3D digital elevation models (DEMs) from remotely sensed data. Three methods are explored and discussed—optical stereoscopic imagery, Interferometric Synthetic Aperture Radar (InSAR), and LIght Detection and Ranging (LIDAR). For each approach, the state-of-the-art presented in the literature is reviewed. Techniques involved in DEM generation are presented with accuracy evaluation. Results of DEMs reconstructed from remotely sensed data are illustrated. While the processes of DEM generation from satellite stereoscopic imagery represents a good example of passive, multi-view imaging technology, discussed in Chap. 2 of this book, InSAR and LIDAR use different principles to acquire 3D information. With regard to InSAR and LIDAR, detailed discussions are conducted in order to convey the fundamentals of both technologies.

Using the Technology Acceptance Model to explore community dwelling older adults’ perceptions of a 3D interior design application to facilitate pre-discharge home adaptations

Background In the UK occupational therapy pre-discharge home visits are routinely carried out as a means of facilitating safe transfer from the hospital to home. Whilst they are an integral part of practice, there is little evidence to demonstrate they have a positive outcome on the discharge process. Current issues for patients are around the speed of home visits and the lack of shared decision making in the process, resulting in less than 50 % of the specialist equipment installed actually being used by patients on follow-up. To improve practice there is an urgent need to examine other ways of conducting home visits to facilitate safe discharge. We believe that Computerised 3D Interior Design Applications (CIDAs) could be a means to support more efficient, effective and collaborative practice. A previous study explored practitioners perceptions of using CIDAs; however it is important to ascertain older adult’s views about the usability of technology and to compare findings. This study explores the perceptions of community dwelling older adults with regards to adopting and using CIDAs as an assistive tool for the home adaptations process. Methods Ten community dwelling older adults participated in individual interactive task-focused usability sessions with a customised CIDA, utilising the think-aloud protocol and individual semi-structured interviews. Template analysis was used to carry out both deductive and inductive analysis of the think-aloud and interview data. Initially, a deductive stance was adopted, using the three pre-determined high-level themes of the technology acceptance model (TAM): Perceived Usefulness (PU), Perceived Ease of Use (PEOU), Actual Use (AU). Inductive template analysis was then carried out on the data within these themes, from which a number of sub-thmes emerged. Results Regarding PU, participants believed CIDAs served as a useful visual tool and saw clear potential to facilitate shared understanding and partnership in care delivery. For PEOU, participants were able to create 3D home environments however a number of usability issues must still be addressed. The AU theme revealed the most likely usage scenario would be collaborative involving both patient and practitioner, as many participants did not feel confident or see sufficient value in using the application autonomously. Conclusions This research found that older adults perceived that CIDAs were likely to serve as a valuable tool which facilitates and enhances levels of patient/practitioner collaboration and empowerment. Older adults also suggested a redesign of the interface so that less sophisticated dexterity and motor functions are required. However, older adults were not confident, or did not see sufficient value in using the application autonomously. Future research is needed to further customise the CIDA software, in line with the outcomes of this study, and to explore the potential of collaborative application patient/practitioner-based deployment.

Automatic camera control in virtual environments augmented using multiple sparse videos

Automated virtual camera control has been widely used in animation and interactive virtual environments. We have developed a multiple sparse camera based free view video system prototype that allows users to control the position and orientation of a virtual camera, enabling the observation of a real scene in three dimensions (3D) from any desired viewpoint. Automatic camera control can be activated to follow selected objects by the user. Our method combines a simple geometric model of the scene composed of planes (virtual environment), augmented with visual information from the cameras and pre-computed tracking information of moving targets to generate novel perspective corrected 3D views of the virtual camera and moving objects. To achieve real-time rendering performance, view-dependent textured mapped billboards are used to render the moving objects at their correct locations and foreground masks are used to remove the moving objects from the projected video streams. The current prototype runs on a PC with a common graphics card and can generate virtual 2D views from three cameras of resolution 768 x 576 with several moving objects at about 11 fps. (C)2011 Elsevier Ltd. All rights reserved.

Integration of Ligand- and Target-Based Virtual Screening for the Discovery of Cruzain Inhibitors

A myriad of methods are available for virtual screening of small organic compound databases. In this study we have successfully applied a quantitative model of consensus measurements, using a combination of 3D similarity searches (ROCS and EON), Hologram Quantitative Structure Activity Relationships (HQSAR) and docking (FRED, FlexX, Glide and AutoDock Vina), to retrieve cruzain inhibitors from collected databases. All methods were assessed individually and then combined in a Ligand-Based Virtual Screening (LBVS) and Target-Based Virtual Screening (TBVS) consensus scoring, using Receiving Operating Characteristic (ROC) curves to evaluate their performance. Three consensus strategies were used: scaled-rank-by-number, rank-by-rank and rank-by-vote, with the most thriving the scaled-rank-by-number strategy, considering that the stiff ROC curve appeared to be satisfactory in every way to indicate a higher enrichment power at early retrieval of active compounds from the database. The ligand-based method provided access to a robust and predictive HQSAR model that was developed to show superior discrimination between active and inactive compounds, which was also better than ROCS and EON procedures. Overall, the integration of fast computational techniques based on ligand and target structures resulted in a more efficient retrieval of cruzain inhibitors with desired pharmacological profiles that may be useful to advance the discovery of new trypanocidal agents.

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.

Proposta de biomodelagem virtual utilizando softwares livres

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Sistema avançado de realidade virtual para visualização de estruturas odontológicas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

3D stability orbits close to 433 Eros using an effective polyhedral model method

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A multiple intelligences theory-based 3D virtual lab environment for digital systems teaching.

This paper describes a 3D virtual lab environment that was developed using OpenSim software integrated into Moodle. Virtuald software tool was used to provide pedagogical support to the lab by enabling to create online texts and delivering them to the students. The courses taught in this virtual lab are methodologically in conformity to theory of multiple intelligences. Some results are presented.

O CAD 3D aplicado na validação de protótipos na indústria do vestuário

Pós-graduação em Design - FAAC