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.

A comparison of alternative bankruptcy prediction models

Early models of bankruptcy prediction employed financial ratios drawn from pre-bankruptcy financial statements and performed well both in-sample and out-of-sample. Since then there has been an ongoing effort in the literature to develop models with even greater predictive performance. A significant innovation in the literature was the introduction into bankruptcy prediction models of capital market data such as excess stock returns and stock return volatility, along with the application of the Black–Scholes–Merton option-pricing model. In this note, we test five key bankruptcy models from the literature using an upto- date data set and find that they each contain unique information regarding the probability of bankruptcy but that their performance varies over time. We build a new model comprising key variables from each of the five models and add a new variable that proxies for the degree of diversification within the firm. The degree of diversification is shown to be negatively associated with the risk of bankruptcy. This more general model outperforms the existing models in a variety of in-sample and out-of-sample tests.

Modelling word meaning using efficient tensor representations

Models of word meaning, built from a corpus of text, have demonstrated success in emulating human performance on a number of cognitive tasks. Many of these models use geometric representations of words to store semantic associations between words. Often word order information is not captured in these models. The lack of structural information used by these models has been raised as a weakness when performing cognitive tasks. This paper presents an efficient tensor based approach to modelling word meaning that builds on recent attempts to encode word order information, while providing flexible methods for extracting task specific semantic information.

Prediction of structural integrity, robustness and service life using advanced finite element methods

Corrosion is a common phenomenon and critical aspects of steel structural application. It affects the daily design, inspection and maintenance in structural engineering, especially for the heavy and complex industrial applications, where the steel structures are subjected to hash corrosive environments in combination of high working stress condition and often in open field and/or under high temperature production environments. In the paper, it presents the actual engineering application of advanced finite element methods in the predication of the structural integrity and robustness at a designed service life for the furnaces of alumina production, which was operated in the high temperature, corrosive environments and rotating with high working stress condition.

An investigation of unique challenges in National Historic relics and scenic sites (NHRSSs) in Chinese research literature 1982-2008 using co-word analysis

National Housing Relics and Scenic Sites (NHRSSs) in China are the equivalent of National Parks in the West but have contrasting features and broader roles when compared to their Western counterparts. By reviewing and analysing more than 370 academic sources, this paper identifies 6 major issue clusters and future challenges that will influence the management of NHRSSs over time. It also provides a number of cases to illustrate the particular features of NHRSSs. Identifying the hot issues and important challenges in Chinese NHRSSs will provide valuable insights into priorities now being discussed in highly populated areas of the World.

New percentage body fat prediction equations for Japanese females

Anthropometry is a simple and cost-efficient method for the assessment of body composition. However prediction equations to estimate body composition using anthropometry should be ‘population-specific’. Most popular body composition prediction equations for Japanese females were proposed more than 40 years ago and there is some concern regarding their usefulness in Japanese females living today. The aim of this study was to compare percentage body fat (%BF) estimated from anthropometry and dual energy x-ray absorptiometry (DXA) to examine the applicability of commonly used prediction equations in young Japanese females. Body composition of 139 Japanese females aged between 18 and 27 years of age (BMI range: 15.1–29.1 kg/m2) was measured using whole-body DXA (Lunar DPX-LIQ) scans. From anthropometric measurements %BF was estimated using four equations developed from Japanese females. The results showed that the traditionally employed prediction equations for anthropometry significantly (p<0.01) underestimate %BF of young Japanese females and therefore are not valid for the precise estimation of body composition. New %BF prediction equations were proposed from the DXA and anthropometry results. Application of the proposed equations may assist in more accurate assessment of body fatness in Japanese females living today.

Preliminary study on bridge health prediction using Dynamic Objective Oriented Bayesian Network (DOOBN)

The availability of bridges is crucial to people’s daily life and national economy. Bridge health prediction plays an important role in bridge management because maintenance optimization is implemented based on prediction results of bridge deterioration. Conventional bridge deterioration models can be categorised into two groups, namely condition states models and structural reliability models. Optimal maintenance strategy should be carried out based on both condition states and structural reliability of a bridge. However, none of existing deterioration models considers both condition states and structural reliability. This study thus proposes a Dynamic Objective Oriented Bayesian Network (DOOBN) based method to overcome the limitations of the existing methods. This methodology has the ability to act upon as a flexible unifying tool, which can integrate a variety of approaches and information for better bridge deterioration prediction. Two demonstrative case studies are conducted to preliminarily justify the feasibility of the methodology

Associations between young children's emotion attributions and prediction of outcome in differing social situations

Associations between young children's attributions of emotion at different points in a story, and with regard to their own prediction about the story's outcome, were investigated using two hypothetical scenarios of social and emotional challenge (social entry and negative event). First grade children (N = 250) showed an understanding that emotions are tied to situational cues by varying the emotions they attributed both between and within scenarios. Furthermore, emotions attributed to the main protagonist at the beginning of the scenarios were differentially associated with children's prediction of a positive or negative outcome and with the valence of the emotion attributed at the end of the scenario. Gender differences in responses to some items were also found. © 2010 The British Psychological Society.

A Bayesian‐Markov process for reliability prediction

Accurate reliability prediction for large-scale, long lived engineering is a crucial foundation for effective asset risk management and optimal maintenance decision making. However, a lack of failure data for assets that fail infrequently, and changing operational conditions over long periods of time, make accurate reliability prediction for such assets very challenging. To address this issue, we present a Bayesian-Marko best approach to reliability prediction using prior knowledge and condition monitoring data. In this approach, the Bayesian theory is used to incorporate prior information about failure probabilities and current information about asset health to make statistical inferences, while Markov chains are used to update and predict the health of assets based on condition monitoring data. The prior information can be supplied by domain experts, extracted from previous comparable cases or derived from basic engineering principles. Our approach differs from existing hybrid Bayesian models which are normally used to update the parameter estimation of a given distribution such as the Weibull-Bayesian distribution or the transition probabilities of a Markov chain. Instead, our new approach can be used to update predictions of failure probabilities when failure data are sparse or nonexistent, as is often the case for large-scale long-lived engineering assets.