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.

Executive coaching : investigating effects of leader-empowering behaviours and psychological empowerment

Executive coaching is a rapidly expanding approach to leadership development which has grown at a rate that warrants extensive examination of its effects (Wasylyshyn, 2003). This thesis has therefore examined both behavioural and psychological effects based on a nine month executive coaching intervention within a large not-for-profit organisation. The intervention was a part of a larger ongoing integrated organisational strategy to create an organisational coaching culture. In order to examine the effectiveness of the nine month executive coaching intervention two studies were conducted. A quantitative study used a pre and post questionnaire to examine leaders and their team members‘ responses before and after the coaching intervention. The research examined leader-empowering behaviours, psychological empowerment, job satisfaction and affective commitment. Significant results were demonstrated from leaders‘ self-reports on leader-empowering behaviours and their team members‘ self-reports revealed a significant flow on effect of psychological empowerment. The second part of the investigation involved a qualitative study which explored the developmental nature of psychological empowerment through executive coaching. The examination dissected psychological empowerment into its widely accepted four facets of meaning, impact, competency and self-determination and investigated, through semi-structured interviews, leaders‘ perspectives of the effect of executive coaching upon them (Spreitzer, 1992). It was discovered that a number of the common practices within executive coaching, including goal-setting, accountability and action-reflection, contributed to the production of outcomes that developed higher levels of psychological empowerment. Careful attention was also given to organisational context and its influence upon the outcomes.

A new approach to teaching signal processing at undergraduate level

This paper describes the design and implementation of a unique undergraduate program in signal processing at the Queensland University of Technology (QUT). The criteria that influenced the choice of the subjects and the laboratories developed to support them are presented. A recently established Signal Processing Research Centre (SPRC) has played an important role in the development of the signal processing teaching program. The SPRC also provides training opportunities for postgraduate studies and research.

The development of a new signal processing program at the Queensland University of Technology

The School of Electrical and Electronic Systems Engineering at Queensland University of Technology, Brisbane, Australia (QUT), offers three bachelor degree courses in electrical and computer engineering. In all its courses there is a strong emphasis on signal processing. A newly established Signal Processing Research Centre (SPRC) has played an important role in the development of the signal processing units in these courses. This paper describes the unique design of the undergraduate program in signal processing at QUT, the laboratories developed to support it, and the criteria that influenced the design.

The design and development of an undergraduate signal processing laboratory

The School of Electrical and Electronic Systems Engineering of Queensland University of Technology (like many other universities around the world) has recognised the importance of complementing the teaching of signal processing with computer based experiments. A laboratory has been developed to provide a "hands-on" approach to the teaching of signal processing techniques. The motivation for the development of this laboratory was the cliche "What I hear I remember but what I do I understand." The laboratory has been named as the "Signal Computing and Real-time DSP Laboratory" and provides practical training to approximately 150 final year undergraduate students each year. The paper describes the novel features of the laboratory, techniques used in the laboratory based teaching, interesting aspects of the experiments that have been developed and student evaluation of the teaching techniques

Super-resolved faces for improved face recognition from surveillance video advances in biometrics

Characteristics of surveillance video generally include low resolution and poor quality due to environmental, storage and processing limitations. It is extremely difficult for computers and human operators to identify individuals from these videos. To overcome this problem, super-resolution can be used in conjunction with an automated face recognition system to enhance the spatial resolution of video frames containing the subject and narrow down the number of manual verifications performed by the human operator by presenting a list of most likely candidates from the database. As the super-resolution reconstruction process is ill-posed, visual artifacts are often generated as a result. These artifacts can be visually distracting to humans and/or affect machine recognition algorithms. While it is intuitive that higher resolution should lead to improved recognition accuracy, the effects of super-resolution and such artifacts on face recognition performance have not been systematically studied. This paper aims to address this gap while illustrating that super-resolution allows more accurate identification of individuals from low-resolution surveillance footage. The proposed optical flow-based super-resolution method is benchmarked against Baker et al.’s hallucination and Schultz et al.’s super-resolution techniques on images from the Terrascope and XM2VTS databases. Ground truth and interpolated images were also tested to provide a baseline for comparison. Results show that a suitable super-resolution system can improve the discriminability of surveillance video and enhance face recognition accuracy. The experiments also show that Schultz et al.’s method fails when dealing surveillance footage due to its assumption of rigid objects in the scene. The hallucination and optical flow-based methods performed comparably, with the optical flow-based method producing less visually distracting artifacts that interfered with human recognition.

An examination of monotony and hypovigilance, independent of fatigue : relevance to road safety

Driving is a vigilance task, requiring sustained attention to maintain performance and avoid crashes. Hypovigilance (i.e., marked reduction in vigilance) while driving manifests as poor driving performance and is commonly attributed to fatigue (Dinges, 1995). However, poor driving performance has been found to be more frequent when driving in monotonous road environments, suggesting that monotony plays a role in generating hypovigilance (Thiffault & Bergeron, 2003b). Research to date has tended to conceptualise monotony as a uni-dimensional task characteristic, typically used over a prolonged period of time to facilitate other factors under investigation, most notably fatigue. However, more often than not, more than one exogenous factor relating to the task or operating environment is manipulated to vary or generate monotony (Mascord & Heath, 1992). Here we aimed to explore whether monotony is a multi-dimensional construct that is determined by characteristics of both the task proper and the task environment. The general assumption that monotony is a task characteristic used solely to elicit hypovigilance or poor performance related to fatigue appears to have led to there being little rigorous investigation into the exact nature of the relationship. While the two concepts are undoubtedly linked, the independent effect of monotony on hypovigilance remains largely ignored. Notwithstanding, there is evidence that monotony effects can emerge very early in vigilance tasks and are not necessarily accompanied by fatigue (see Meuter, Rakotonirainy, Johns, & Wagner, 2005). This phenomenon raises a largely untested, empirical question explored in two studies: Can hypovigilance emerge as a consequence of task and/or environmental monotony, independent of time on task and fatigue? In Study 1, using a short computerised vigilance task requiring responses to be withheld to infrequent targets, we explored the differential impacts of stimuli and task demand manipulations on the development of a monotonous context and the associated effects on vigilance performance (as indexed by respone errors and response times), independent of fatigue and time on task. The role of individual differences (sensation seeking, extroversion and cognitive failures) in moderating monotony effects was also considered. The results indicate that monotony affects sustained attention, with hypovigilance and associated performance worse in monotonous than in non-monotonous contexts. Critically, performance decrements emerged early in the task (within 4.3 minutes) and remained consistent over the course of the experiment (21.5 minutes), suggesting that monotony effects can operate independent of time on task and fatigue. A combination of low task demands and low stimulus variability form a monotonous context characterised by hypovigilance and poor task performance. Variations to task demand and stimulus variability were also found to independently affect performance, suggesting that monotony is a multi-dimensional construct relating to both task monotony (associated with the task itself) and environmental monotony (related to characteristics of the stimulus). Consequently, it can be concluded that monotony is multi-dimensional and is characterised by low variability in stimuli and/or task demands. The proposition that individual differences emerge under conditions of varying monotony with high sensation seekers and/or extroverts performing worse in monotonous contexts was only partially supported. Using a driving simulator, the findings of Study 1 were extended to a driving context to identify the behavioural and psychophysiological indices of monotony-related hypovigilance associated with variations to road design and road side scenery (Study 2). Supporting the proposition that monotony is a multi-dimensional construct, road design variability emerged as a key moderating characteristic of environmental monotony, resulting in poor driving performance indexed by decrements in steering wheel measures (mean lateral position). Sensation seeking also emerged as a moderating factor, where participants high in sensation seeking tendencies displayed worse driving behaviour in monotonous conditions. Importantly, impaired driving performance was observed within 8 minutes of commencing the driving task characterised by environmental monotony (low variability in road design) and was not accompanied by a decline in psychophysiological arousal. In addition, no subjective declines in alertness were reported. With fatigue effects associated with prolonged driving (van der Hulst, Meijman, & Rothengatter, 2001) and indexed by drowsiness, this pattern of results indicates that monotony can affect driver vigilance, independent of time on task and fatigue. Perceptual load theory (Lavie, 1995, 2005) and mindlessness theory (Robertson, Manly, Andrade, Baddley, & Yiend, 1997) provide useful theoretical frameworks for explaining and predicting monotony effects by positing that the low load (of task and/or stimuli) associated with a monotonous task results in spare attentional capacity which spills over involuntarily, resulting in the processing of task-irrelevant stimuli or task unrelated thoughts. That is, individuals – even when not fatigued - become easily distracted when performing a highly monotonous task, resulting in hypovigilance and impaired performance. The implications for road safety, including the likely effectiveness of fatigue countermeasures to mitigate monotony-related driver hypovigilance are discussed.

Evaluating effects of eco-driving at traffic intersections based on traffic micro-simulation

Eco-driving is an initiative driving behavior which aims to reduce fuel consumption and emissions from automobiles. Recently, it has attracted increasing interests and has been adopted by many drivers in Australia. Although many of the studies have revealed considerable benefits in terms of fuel consumption and emissions after utilising eco-driving, most of the literature investigated eco-driving effects on individual driver but not traffic flow. The driving behavior of eco-drivers will potentially affect other drivers and thereby affects the entire traffic flow. To comprehensively assess and understand how effectively eco-driving can perform, therefore, measurement on traffic flow is necessary. In this paper, we proposed and demonstrated an evaluation method based on a microscopic traffic simulator (Aimsun). We focus on one particular eco-driving style which involves moderate and smooth acceleration. We evaluated both traffic performance (travel time) and environmental performance (fuel consumption and CO2 emission) at traffic intersection level in a simple simulation model. The before-and-after comparisons indicated potentially negative impacts when using eco-driving, which highlighted the necessity to carefully evaluate and improve eco-driving before wide promotion and implementation.

Size effects on tensile and fatigue behaviour of polycrystalline metal foils at the micrometer scale

Tensile and fatigue properties of as-rolled and annealed polycrystalline Cu foils with different thicknesses at the micrometer scale were investigated. Uniaxial tensile testing results showed that with decreasing foil thickness the uniform elongation decreases for both as-rolled and annealed foils, whereas the yield strength and ultimate tensile strength increase for as-rolled foils, but decrease for the annealed foils. For both the as-rolled or annealed foils, bending fatigue resistance decreases with decreasing the foil thickness. Deformation and fatigue damage behaviour of the free-standing foils were characterised as a function of foil thickness. In addition, the fatigue strength of various small-scale Cu foils was compared to understand they physical mechanisms of size effects on mechanical properties of the metallic material at micrometer scales.