Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Can audio-visual speech recognition outperform acoustically enhanced speech recognition in automotive environment?

The use of visual features in the form of lip movements to improve the performance of acoustic speech recognition has been shown to work well, particularly in noisy acoustic conditions. However, whether this technique can outperform speech recognition incorporating well-known acoustic enhancement techniques, such as spectral subtraction, or multi-channel beamforming is not known. This is an important question to be answered especially in an automotive environment, for the design of an efficient human-vehicle computer interface. We perform a variety of speech recognition experiments on a challenging automotive speech dataset and results show that synchronous HMM-based audio-visual fusion can outperform traditional single as well as multi-channel acoustic speech enhancement techniques. We also show that further improvement in recognition performance can be obtained by fusing speech-enhanced audio with the visual modality, demonstrating the complementary nature of the two robust speech recognition approaches.

Achieving supply chain sustainability : the role of relationship management, culture and procurement form

In this research we examined, by means of case studies, the mechanisms by which relationships can be managed and by which communication and cooperation can be enhanced in developing sustainable supply chains. The research was predicated on the contention that the development of a sustainable supply chain depends, in part, on the transfer of knowledge and capabilities from the larger players in the supply chain. A sustainable supply chain requires proactive relationship management and the development of an appropriate organisational culture, and trust. By legitimising individuals’ expectations of the type of culture which is appropriate to their company and empowering employees to address mismatches that may occur, a situation can be created whereby the collaborating organisations develop their competences symbiotically and so facilitate a sustainable supply chain. Effective supply chain management enhances organisation performance and competitiveness through the management of operations across organisational boundaries. Relational contracting approaches facilitate the exchange of information and knowledge and build capacity in the supply chain, thus enhancing its sustainability. Relationship management also provides the conditions necessary for the development of collaborative and cooperative relationships However, often subcontractors and suppliers are not empowered to attend project meetings or to have direct communication with project based staff. With this being a common phenomenon in the construction industry, one might ask: what are the barriers to implementation of relationship management through the supply chain? In other words, the problem addressed in this research is the engagement of the supply chain through relationship management.

3D ellipsoid fitting for multi-view gait recognition

Gait recognition approaches continue to struggle with challenges including view-invariance, low-resolution data, robustness to unconstrained environments, and fluctuating gait patterns due to subjects carrying goods or wearing different clothes. Although computationally expensive, model based techniques offer promise over appearance based techniques for these challenges as they gather gait features and interpret gait dynamics in skeleton form. In this paper, we propose a fast 3D ellipsoidal-based gait recognition algorithm using a 3D voxel model derived from multi-view silhouette images. This approach directly solves the limitations of view dependency and self-occlusion in existing ellipse fitting model-based approaches. Voxel models are segmented into four components (left and right legs, above and below the knee), and ellipsoids are fitted to each region using eigenvalue decomposition. Features derived from the ellipsoid parameters are modeled using a Fourier representation to retain the temporal dynamic pattern for classification. We demonstrate the proposed approach using the CMU MoBo database and show that an improvement of 15-20% can be achieved over a 2D ellipse fitting baseline.

Gait energy volumes and frontal gait recognition using depth images

Gait energy images (GEIs) and its variants form the basis of many recent appearance-based gait recognition systems. The GEI combines good recognition performance with a simple implementation, though it suffers problems inherent to appearance-based approaches, such as being highly view dependent. In this paper, we extend the concept of the GEI to 3D, to create what we call the gait energy volume, or GEV. A basic GEV implementation is tested on the CMU MoBo database, showing improvements over both the GEI baseline and a fused multi-view GEI approach. We also demonstrate the efficacy of this approach on partial volume reconstructions created from frontal depth images, which can be more practically acquired, for example, in biometric portals implemented with stereo cameras, or other depth acquisition systems. Experiments on frontal depth images are evaluated on an in-house developed database captured using the Microsoft Kinect, and demonstrate the validity of the proposed approach.

Implementation of a survey form marking system using image processing techniques on an Imputer

This paper describes the feasibility of the application of an Imputer in a multiple choice answer sheet marking system based on image processing techniques.

An enriched radial point interpolation method based on weak-form and strong-form

In this article, an enriched radial point interpolation method (e-RPIM) is developed for computational mechanics. The conventional radial basis function (RBF) interpolation is novelly augmented by the suitable basis functions to reflect the natural properties of deformation. The performance of the enriched meshless RBF shape functions is first investigated using the surface fitting. The surface fitting results have proven that, compared with the conventional RBF, the enriched RBF interpolation has a much better accuracy to fit a complex surface than the conventional RBF interpolation. It has proven that the enriched RBF shape function will not only possess all advantages of the conventional RBF interpolation, but also can accurately reflect the deformation properties of problems. The system of equations for two-dimensional solids is then derived based on the enriched RBF shape function and both of the meshless strong-form and weak-form. A numerical example of a bar is presented to study the effectiveness and efficiency of e-RPIM. As an important application, the newly developed e-RPIM, which is augmented by selected trigonometric basis functions, is applied to crack problems. It has been demonstrated that the present e-RPIM is very accurate and stable for fracture mechanics problems.

The safety risk management of unmanned aircraft systems

The safety risk management process describes the systematic application of management policies, procedures and practices to the activities of communicating, consulting, establishing the context, and identifying, analysing, evaluating, treating, monitoring and reviewing risk. This process is undertaken to provide assurances that the risks of a particular unmanned aircraft system activity have been managed to an acceptable level. The safety risk management process and its outcomes form part of the documented safety case necessary to obtain approvals for unmanned aircraft system operations. It also guides the development of an organisation’s operations manual and is a primary component of an organisation’s safety management system. The aim of this chapter is to provide existing risk practitioners with a high level introduction to some of the unique issues and challenges in the application of the safety risk management process to unmanned aircraft systems. The scope is limited to safety risks associated with the operation of unmanned aircraft in the civil airspace system and over inhabited areas. The structure of the chapter is based on the safety risk management process as defined by the international risk management standard ISO 31000:2009 and draws on aviation safety resources provided by International Civil Aviation Organization, the Federal Aviation Administration and U.S. Department of Defense. References to relevant aviation safety regulations, programs of research and fielded systems are also provided.

Service delivery in one-stop government portals : observations based on a market research study in Queensland

New government service delivery models based on a “franchise” metaphor are being proposed recently to allow more citizen-centric service delivery by decoupling the government’s internal departmental structure from the way services are presented and delivered to citizens. In order to evaluate the approach from an online channel perspective, the Queensland Government commissioned a market research study to compare their websites with the online presences of the UK Government and the South Australian Government, who both have adopted the “franchise” approach. The study aimed to inform an understanding of citizens’ preferred model for interacting in the online channel and to identify the relative strengths and weaknesses of the existing websites. In this paper, we will a) report on the findings of this third party usability study and b) position the study, in the form of a critical reflection, against the background of a more comprehensive “Transformational Government” approach using a “franchise marketplace”. The critical reflection points towards limitations of the study with regard to this bigger picture and discusses the potential benefits of service bundling that remained unconsidered in the study.