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.

Evaluating multivariate volatility forecasts : how effective are statistical and economic loss functions?

Multivariate volatility forecasts are an important input in many financial applications, in particular portfolio optimisation problems. Given the number of models available and the range of loss functions to discriminate between them, it is obvious that selecting the optimal forecasting model is challenging. The aim of this thesis is to thoroughly investigate how effective many commonly used statistical (MSE and QLIKE) and economic (portfolio variance and portfolio utility) loss functions are at discriminating between competing multivariate volatility forecasts. An analytical investigation of the loss functions is performed to determine whether they identify the correct forecast as the best forecast. This is followed by an extensive simulation study examines the ability of the loss functions to consistently rank forecasts, and their statistical power within tests of predictive ability. For the tests of predictive ability, the model confidence set (MCS) approach of Hansen, Lunde and Nason (2003, 2011) is employed. As well, an empirical study investigates whether simulation findings hold in a realistic setting. In light of these earlier studies, a major empirical study seeks to identify the set of superior multivariate volatility forecasting models from 43 models that use either daily squared returns or realised volatility to generate forecasts. This study also assesses how the choice of volatility proxy affects the ability of the statistical loss functions to discriminate between forecasts. Analysis of the loss functions shows that QLIKE, MSE and portfolio variance can discriminate between multivariate volatility forecasts, while portfolio utility cannot. An examination of the effective loss functions shows that they all can identify the correct forecast at a point in time, however, their ability to discriminate between competing forecasts does vary. That is, QLIKE is identified as the most effective loss function, followed by portfolio variance which is then followed by MSE. The major empirical analysis reports that the optimal set of multivariate volatility forecasting models includes forecasts generated from daily squared returns and realised volatility. Furthermore, it finds that the volatility proxy affects the statistical loss functions’ ability to discriminate between forecasts in tests of predictive ability. These findings deepen our understanding of how to choose between competing multivariate volatility forecasts.

Higher-Order spectra of nonlinear polynomial models for Chua's circuit

Polynomial models are shown to simulate accurately the quadratic and cubic nonlinear interactions (e.g. higher-order spectra) of time series of voltages measured in Chua's circuit. For circuit parameters resulting in a spiral attractor, bispectra and trispectra of the polynomial model are similar to those from the measured time series, suggesting that the individual interactions between triads and quartets of Fourier components that govern the process dynamics are modeled accurately. For parameters that produce the double-scroll attractor, both measured and modeled time series have small bispectra, but nonzero trispectra, consistent with higher-than-second order nonlinearities dominating the chaos.

Event-related brain potentials dissociate the developmental time-course of automatic numerical magnitude analysis and cognitive control functions during the first three years of primary school

In this study we set out to dissociate the developmental time course of automatic symbolic number processing and cognitive control functions in grade 1-3 British primary school children. Event-related potential (ERP) and behavioral data were collected in a physical size discrimination numerical Stroop task. Task-irrelevant numerical information was processed automatically already in grade 1. Weakening interference and strengthening facilitation indicated the parallel development of general cognitive control and automatic number processing. Relationships among ERP and behavioral effects suggest that control functions play a larger role in younger children and that automaticity of number processing increases from grade 1 to 3.

Structural damage detection using frequency response functions and neural networks

This paper illustrates the damage identification and condition assessment of a three story bookshelf structure using a new frequency response functions (FRFs) based damage index and Artificial Neural Networks (ANNs). A major obstacle of using measured frequency response function data is a large size input variables to ANNs. This problem is overcome by applying a data reduction technique called principal component analysis (PCA). In the proposed procedure, ANNs with their powerful pattern recognition and classification ability were used to extract damage information such as damage locations and severities from measured FRFs. Therefore, simple neural network models are developed, trained by Back Propagation (BP), to associate the FRFs with the damage or undamaged locations and severity of the damage of the structure. Finally, the effectiveness of the proposed method is illustrated and validated by using the real data provided by the Los Alamos National Laboratory, USA. The illustrated results show that the PCA based artificial Neural Network method is suitable and effective for damage identification and condition assessment of building structures. In addition, it is clearly demonstrated that the accuracy of proposed damage detection method can also be improved by increasing number of baseline datasets and number of principal components of the baseline dataset.

Structural damage identification with noise polluted Frequency Response Functions (FRFs)

Damage detection in structures has become increasingly important in recent years. While a number of damage detection and localization methods have been proposed, very few attempts have been made to explore the structure damage with noise polluted data which is unavoidable effect in real world. The measurement data are contaminated by noise because of test environment as well as electronic devices and this noise tend to give error results with structural damage identification methods. Therefore it is important to investigate a method which can perform better with noise polluted data. This paper introduces a new damage index using principal component analysis (PCA) for damage detection of building structures being able to accept noise polluted frequency response functions (FRFs) as input. The FRF data are obtained from the function datagen of MATLAB program which is available on the web site of the IASC-ASCE (International Association for Structural Control– American Society of Civil Engineers) Structural Health Monitoring (SHM) Task Group. The proposed method involves a five-stage process: calculation of FRFs, calculation of damage index values using proposed algorithm, development of the artificial neural networks and introducing damage indices as input parameters and damage detection of the structure. This paper briefly describes the methodology and the results obtained in detecting damage in all six cases of the benchmark study with different noise levels. The proposed method is applied to a benchmark problem sponsored by the IASC-ASCE Task Group on Structural Health Monitoring, which was developed in order to facilitate the comparison of various damage identification methods. The illustrated results show that the PCA-based algorithm is effective for structural health monitoring with noise polluted FRFs which is of common occurrence when dealing with industrial structures.

The impact of penalty increases on speeding behaviour in Queensland and a characterisation of speeding offenders

This project examined the effects of speeding penalty changes that occurred in Queensland in 2003 on the behaviour of speeding offenders. These penalty changes included increasing the number of offence categories, and in turn narrowing the range of speeds associated with the offence categories; increasing the monetary fines for all offences, with the largest increases observed for high-range offences; and introducing automatic licence suspension and an eight demerit point penalty for the highest offence category. To explore the impact of the penalty changes, offence data collected for two cohorts of motorists in Queensland who were caught speeding prior to and subsequent to the penalty changes (N = 84,456) were compared. The first cohort consisted of individuals (operators of all vehicles including motorcycles) who committed a speeding offence in May 2001 (two years prior to the speeding penalty change); and individuals who committed a speeding offence in May 2003 (one month after the introduction of the penalty change). Four measures of recidivism were devised and used to assess the effects of the new penalties with regard to deterring the speeding behaviour of offenders. Additionally, the project investigated the relationship between speeding offences, other risky driving behaviours, crash involvement, and criminal behaviour.

A comparison of safety climate and safety outcomes between construction and resource functions in a large case study organisation

The research described in this paper forms part of an in-depth investigation of safety culture in one of Australia’s largest construction companies. The research builds on a previous qualitative study with organisational safety leaders and further investigates how safety culture is perceived and experienced by organisational members, as well as how this relates to their safety behaviour and related outcomes at work. Participants were 2273 employees of the case study organisation, with 689 from the Construction function and 1584 from the Resources function. The results of several analyses revealed some interesting organisational variance on key measures. Specifically, the Construction function scored significantly higher on all key measures: safety climate, safety motivation, safety compliance, and safety participation. The results are discussed in terms of relevance in an applied research context.

Planar difference functions

In 1980 Alltop produced a family of cubic phase sequences that nearly meet the Welch bound for maximum non-peak correlation magnitude. This family of sequences were shown by Wooters and Fields to be useful for quantum state tomography. Alltop’s construction used a function that is not planar, but whose difference function is planar. In this paper we show that Alltop type functions cannot exist in fields of characteristic 3 and that for a known class of planar functions, x^3 is the only Alltop type function.

Principles of motor learning in ecological dynamics : a comment on functions of learning and the acquisition of motor skills (with reference to sport)

This paper provides a commentary on the contribution by Dr Chow who questioned whether the functions of learning are general across all categories of tasks or whether there are some task-particular aspects to the functions of learning in relation to task type. Specifically, they queried whether principles and practice for the acquisition of sport skills are different than what they are for musical, industrial, military and human factors skills. In this commentary we argue that ecological dynamics contains general principles of motor learning that can be instantiated in specific performance contexts to underpin learning design. In this proposal, we highlight the importance of conducting skill acquisition research in sport, rather than relying on empirical outcomes of research from a variety of different performance contexts. Here we discuss how task constraints of different performance contexts (sport, industry, military, music) provide different specific information sources that individuals use to couple their actions when performing and acquiring skills. We conclude by suggesting that his relationship between performance task constraints and learning processes might help explain the traditional emphasis on performance curves and performance outcomes to infer motor learning.

Exploring the validity and predictive power of an extended volunteer functions inventory within the context of episodic skilled volunteering by retirees

The current study examined the structure of the volunteer functions inventory within a sample of older individuals (N = 187). The career items were replaced with items examining the concept of continuity of work, a potentially more useful and relevant concept for this population. Factor analysis supported a four factor solution, with values, social and continuity emerging as single factors and enhancement and protective items loading together on a single factor. Understanding items did not load highly on any factor. The values and continuity functions were the only dimensions to emerge as predictors of intention to volunteer. This research has important implications for understanding the motivation of older adults to engage in contemporary volunteering settings.

Instructional constraints on movement and performance of players in the penalty kick

The influence of different instructional constraints on movement organisation and performance outcomes of the penalty kick (PK) was investigated according to participant age. Sixty penalty takers and twelve goalkeepers from two age groups (under 15 and under 17) performed 300 PKs under five different task conditions, including: no explicit instructional constraints provided (Control); instructional constraints on immobility (IMMOBILE) and mobility (MOBILE) of goalkeepers; and, use of keeper-dependent (DEP) and independent (INDEP) strategies by penalty takers. Every trial was video recorded and digitised using motion analysis techniques. Dependent variables (DVs) were: movement speed of penalty takers and the angles between the goalkeeper's position and the goal line (i.e., diving angle), and between the penalty taker and a line crossing the penalty spot and the centre of the goal (i.e., run up angle). Instructions significantly influenced the way that goalkeepers (higher values in MOBILE relative to Control) and penalty takers (higher values in Control than in DEP) used movement speed during performance, as well as the goalkeepers' movements and diving angle (less pronounced dives in the MOBILE condition compared with INDEP). Results showed how different instructions constrained participant movements during performance, although players' performance efficacy remained constant, reflecting their adaptive variability.

Pleading - self-incrimination and penalty privileges

In Anderson v Australian Securities and Investments Commission [2012] QCA 301 the Queensland Court of Appeal allowed an appeal from the decision of the primary judge (ASIC v Managed Investments Ltd No 3 [2012] QSC 74. The Court of Appeal was satisfied that the defendants’ non-compliance with the pleading rules in the Uniform Civil Procedure Rules 1999 (Qld) was justified by the claims to privilege against self-incrimination or exposure to a penalty.