Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Combining influence maps and cellular automata for reactive game agents

Agents make up an important part of game worlds, ranging from the characters and monsters that live in the world to the armies that the player controls. Despite their importance, agents in current games rarely display an awareness of their environment or react appropriately, which severely detracts from the believability of the game. Some games have included agents with a basic awareness of other agents, but they are still unaware of important game events or environmental conditions. This paper presents an agent design we have developed, which combines cellular automata for environmental modeling with influence maps for agent decision-making. The agents were implemented into a 3D game environment we have developed, the EmerGEnT system, and tuned through three experiments. The result is simple, flexible game agents that are able to respond to natural phenomena (e.g. rain or fire), while pursuing a goal.

Scripting versus emergence : issues for game developers and players in game environment design

This paper defines and discusses two contrasting approaches to designing game environments. The first, referred to as scripting, requires developers to anticipate, hand-craft and script specific game objects, events and player interactions. The second, known as emergence, involves defining general, global rules that interact to give rise to emergent gameplay. Each of these approaches is defined, discussed and analyzed with respect to the considerations and affects for game developers and game players. Subsequently, various techniques for implementing these design approaches are identified and discussed. It is concluded that scripting and emergence are two extremes of the same continuum, neither of which are ideal for game development. Rather, there needs to be a compromise in which the boundaries of action (such as story and game objectives) can be hardcoded and non-scripted behavior (such as interactions and strategies) are able to emerge within these boundaries.

Toward automated power line corridor monitoring using advanced aircraft control and multisource feature fusion

The conventional manual power line corridor inspection processes that are used by most energy utilities are labor-intensive, time consuming and expensive. Remote sensing technologies represent an attractive and cost-effective alternative approach to these monitoring activities. This paper presents a comprehensive investigation into automated remote sensing based power line corridor monitoring, focusing on recent innovations in the area of increased automation of fixed-wing platforms for aerial data collection, and automated data processing for object recognition using a feature fusion process. Airborne automation is achieved by using a novel approach that provides improved lateral control for tracking corridors and automatic real-time dynamic turning for flying between corridor segments, we call this approach PTAGS. Improved object recognition is achieved by fusing information from multi-sensor (LiDAR and imagery) data and multiple visual feature descriptors (color and texture). The results from our experiments and field survey illustrate the effectiveness of the proposed aircraft control and feature fusion approaches.

Practical improvements to simultaneous computation of multi-view geometry and radial lens distortion

This paper discusses practical issues related to the use of the division model for lens distortion in multi-view geometry computation. A data normalisation strategy is presented, which has been absent from previous discussions on the topic. The convergence properties of the Rectangular Quadric Eigenvalue Problem solution for computing division model distortion are examined. It is shown that the existing method can require more than 1000 iterations when dealing with severe distortion. A method is presented for accelerating convergence to less than 10 iterations for any amount of distortion. The new method is shown to produce equivalent or better results than the existing method with up to two orders of magnitude reduction in iterations. Through detailed simulation it is found that the number of data points used to compute geometry and lens distortion has a strong influence on convergence speed and solution accuracy. It is recommended that more than the minimal number of data points be used when computing geometry using a robust estimator such as RANSAC. Adding two to four extra samples improves the convergence rate and accuracy sufficiently to compensate for the increased number of samples required by the RANSAC process.

Teaching and Learning in Maritime Security: A Literature Review

With the rise in attacks and attempted attacks on marine‐based critical infrastructure, maritime security is an issue of increasing importance worldwide. However, there are three significant shortfalls in the efforts to overcome potential threats to maritime security: the need for greater understanding of whether current standards of best practice are truly successful in combating and reducing the risks of terrorism and other security issues, the absence of a collective maritime security best practice framework and the need for improved access to maritime security specific graduate and postgraduate (long) courses. This paper presents an overview of existing international, regional national standards of best practice and shows that literature concerning the measurement and/ or success of standards is virtually non‐existent. In addition, despite the importance of maritime workers to ensuring the safety of marine based critical infrastructure, a similar review of available Australian education courses shows a considerable lack of availability of maritime security‐specific courses other than short courses that cover only basic security matters. We argue that the absence of an Australian best practice framework informed by evaluation of current policy responses – particularly in the post 9/11 environment – leaves Australia vulnerable to maritime security threats. As this paper shows, the reality is that despite the security measures put in place post 9/11, there is still considerable work to be done to ensure Australia is equipped to overcome the threats posed to maritime security.

Feature-based visual odometry and featureless place recognition for SLAM in 2.5D environments

In this paper we present a novel algorithm for localization during navigation that performs matching over local image sequences. Instead of calculating the single location most likely to correspond to a current visual scene, the approach finds candidate matching locations within every section (subroute) of all learned routes. Through this approach, we reduce the demands upon the image processing front-end, requiring it to only be able to correctly pick the best matching image from within a short local image sequence, rather than globally. We applied this algorithm to a challenging downhill mountain biking visual dataset where there was significant perceptual or environment change between repeated traverses of the environment, and compared performance to applying the feature-based algorithm FAB-MAP. The results demonstrate the potential for localization using visual sequences, even when there are no visual features that can be reliably detected.

Towards lifelong navigation and mapping in an office environment

This paper addresses the challenge of developing robots that map and navigate autonomously in real world, dynamic environments throughout the robot’s entire lifetime – the problem of lifelong navigation. Static mapping algorithms can produce highly accurate maps, but have found few applications in real environments that are in constant flux. Environments change in many ways: both rapidly and gradually, transiently and permanently, geometrically and in appearance. This paper demonstrates a biologically inspired navigation algorithm, RatSLAM, that uses principles found in rodent neural circuits. The algorithm is demonstrated in an office delivery challenge where the robot was required to perform mock deliveries to goal locations in two different buildings. The robot successfully completed 1177 out of 1178 navigation trials over 37 hours of around the clock operation spread over 11 days.

Outdoor simultaneous localisation and mapping using RatSLAM

In this paper an existing method for indoor Simultaneous Localisation and Mapping (SLAM) is extended to operate in large outdoor environments using an omnidirectional camera as its principal external sensor. The method, RatSLAM, is based upon computational models of the area in the rat brain that maintains the rodent’s idea of its position in the world. The system uses the visual appearance of different locations to build hybrid spatial-topological maps of places it has experienced that facilitate relocalisation and path planning. A large dataset was acquired from a dynamic campus environment and used to verify the system’s ability to construct representations of the world and simultaneously use these representations to maintain localisation.

Using strategic movement to calibrate a neural compass : a spiking network for tracking head direction in rats and robots

The head direction (HD) system in mammals contains neurons that fire to represent the direction the animal is facing in its environment. The ability of these cells to reliably track head direction even after the removal of external sensory cues implies that the HD system is calibrated to function effectively using just internal (proprioceptive and vestibular) inputs. Rat pups and other infant mammals display stereotypical warm-up movements prior to locomotion in novel environments, and similar warm-up movements are seen in adult mammals with certain brain lesion-induced motor impairments. In this study we propose that synaptic learning mechanisms, in conjunction with appropriate movement strategies based on warm-up movements, can calibrate the HD system so that it functions effectively even in darkness. To examine the link between physical embodiment and neural control, and to determine that the system is robust to real-world phenomena, we implemented the synaptic mechanisms in a spiking neural network and tested it on a mobile robot platform. Results show that the combination of the synaptic learning mechanisms and warm-up movements are able to reliably calibrate the HD system so that it accurately tracks real-world head direction, and that calibration breaks down in systematic ways if certain movements are omitted. This work confirms that targeted, embodied behaviour can be used to calibrate neural systems, demonstrates that ‘grounding’ of modeled biological processes in the real world can reveal underlying functional principles (supporting the importance of robotics to biology), and proposes a functional role for stereotypical behaviours seen in infant mammals and those animals with certain motor deficits. We conjecture that these calibration principles may extend to the calibration of other neural systems involved in motion tracking and the representation of space, such as grid cells in entorhinal cortex.

Lingodroids : studies in spatial cognition and language

The Lingodroids are a pair of mobile robots that evolve a language for places and relationships between places (based on distance and direction). Each robot in these studies has its own understanding of the layout of the world, based on its unique experiences and exploration of the environment. Despite having different internal representations of the world, the robots are able to develop a common lexicon for places, and then use simple sentences to explain and understand relationships between places even places that they could not physically experience, such as areas behind closed doors. By learning the language, the robots are able to develop representations for places that are inaccessible to them, and later, when the doors are opened, use those representations to perform goal-directed behavior.

Vacuum cleaner emissions as a source of indoor exposure to airborne particles and bacteria

Vacuuming can be a source of indoor exposure to biological and non-biological aerosols, although there is little data that describes the magnitude of emissions from the vacuum cleaner itself. We therefore sought to quantify emission rates of particles and bacteria from a large group of vacuum cleaners and investigate their potential determinants, including temperature, dust bags, exhaust filters, price and age. Emissions of particles between 0.009 and 20 µm and bacteria were measured from 21 vacuums. Ultrafine (<100 nm) particle emission rates ranged from 4.0 × 10^6 to 1.1 × 10^11 particles min-1. Emission of 0.54 to 20 µm particles ranged from 4.0 × 10^4 to 1.2 × 10^9 particles min-1. PM2.5 emissions were between 2.4 × 10-1 and 5.4 × 10^3 µg min-1. Bacteria emissions ranged from 0 to 7.4 × 10^5 bacteria min-1 and were poorly correlated with dust bag bacteria content and particle emissions. Large variability in emission of all parameters was observed across the 21 vacuums we assessed, which was largely not attributable to the range of determinant factors we assessed. Vacuum cleaner emissions contribute to indoor exposure to non-biological and biological aerosols when vacuuming, and this may vary markedly depending on the vacuum used.

A framework for analysing system intelligence of the building control system: a study of the integrated building management system

The lack of satisfactory consensus for characterizing the system intelligence and structured analytical decision models has inhibited the developers and practitioners to understand and configure optimum intelligent building systems in a fully informed manner. So far, little research has been conducted in this aspect. This research is designed to identify the key intelligent indicators, and develop analytical models for computing the system intelligence score of smart building system in the intelligent building. The integrated building management system (IBMS) was used as an illustrative example to present a framework. The models presented in this study applied the system intelligence theory, and the conceptual analytical framework. A total of 16 key intelligent indicators were first identified from a general survey. Then, two multi-criteria decision making (MCDM) approaches, the analytic hierarchy process (AHP) and analytic network process (ANP), were employed to develop the system intelligence analytical models. Top intelligence indicators of IBMS include: self-diagnostic of operation deviations; adaptive limiting control algorithm; and, year-round time schedule performance. The developed conceptual framework was then transformed to the practical model. The effectiveness of the practical model was evaluated by means of expert validation. The main contribution of this research is to promote understanding of the intelligent indicators, and to set the foundation for a systemic framework that provide developers and building stakeholders a consolidated inclusive tool for the system intelligence evaluation of the proposed components design configurations.