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.

What it means to become a public relations professional: student perceptions of professional identity through real-world learning

Public relations educators need new solutions to prepare students to become tomorrow's practitioner today. Managers and employers in the new creative workforce (McWilliam, 2008) expect graduates to be problem solvers, critical and creative thinkers, reflective, and self reliant (Barrie, 2008; David, 2004). Enabling students to develop these attributes requires a collaborative and creative approach to pedagogy (Jeffrey & Craft, 2001, 2004). A model for the next generation of public relations education was developed to integrate industry partnerships as a way to bridge pedagogy and professional practice. The model suggests (a) that industry partnerships be embedded in learning activities, (b) that assessment items be considered on a continuum and delivered incrementally across a course of study, and (c) that connections between classroom and workplace activities are clearly signposted for students.

Parametric differences between a real-world distributed denial-of-service attack and a flash event

Distributed Denial-of-Service (DDoS) attacks continue to be one of the most pernicious threats to the delivery of services over the Internet. Not only are DDoS attacks present in many guises, they are also continuously evolving as new vulnerabilities are exploited. Hence accurate detection of these attacks still remains a challenging problem and a necessity for ensuring high-end network security. An intrinsic challenge in addressing this problem is to effectively distinguish these Denial-of-Service attacks from similar looking Flash Events (FEs) created by legitimate clients. A considerable overlap between the general characteristics of FEs and DDoS attacks makes it difficult to precisely separate these two classes of Internet activity. In this paper we propose parameters which can be used to explicitly distinguish FEs from DDoS attacks and analyse two real-world publicly available datasets to validate our proposal. Our analysis shows that even though FEs appear very similar to DDoS attacks, there are several subtle dissimilarities which can be exploited to separate these two classes of events.

Operational performance of low-cost carriers and international airlines : New evidence using a bootstrap truncated regression

Between 2001 and 2005, the US airline industry faced financial turmoil. At the same time, the European airline industry entered a period of substantive deregulation. This period witnessed opportunities for low-cost carriers to become more competitive in the market as a result of these combined events. To help assess airline performance in the aftermath of these events, this paper provides new evidence of technical efficiency for 42 national and international airlines in 2006 using the data envelopment analysis (DEA) bootstrap approach first proposed by Simar and Wilson (J Econ, 136:31-64, 2007). In the first stage, technical efficiency scores are estimated using a bootstrap DEA model. In the second stage, a truncated regression is employed to quantify the economic drivers underlying measured technical efficiency. The results highlight the key role played by non-discretionary inputs in measures of airline technical efficiency.

Developing a curriculum for the real world : a whole of institution approach

Keynote address at University of Surrey, Real World Education Symposium, 29 September 2010. Full-text in audio form only. Link to audio provided in Official URL field.

Reality bytes : technology in real world legal education

The use of technology for purposes such as communication and document management has become essential to legal practice with practitioners and courts increasingly relying on various forms of technology. Accordingly, legal practitioners need to be able to understand, communicate with, and persuade their audience using this technology. Technology skills are therefore an essential and integral part of undergraduate legal education, and given the widening participation agenda in Australia and consequent increasing diversity of law students, it must also be available to all students. To neglect this most crucial part of modern legal education is to fail in a fundamental aspect of a University’s obligation not just to its students, but ultimately to our students’ potential employers and their future clients. This paper will consider how law schools can facilitate the development of technology skills by using technology to facilitate mooting in settings that replicate legal practice. In order to assess the facilities at the disposal of universities, the authors surveyed the law schools in Australia about their equipment in and use of electronic moot court rooms. The authors also conducted and evaluated an internal mooting competition using Elluminate, an online communication platform available to students through Blackboard. Students were able to participate wherever they were located without the need to attend a moot court room. The results of the survey and evaluation of the Elluminate competition will be discussed. The paper will conclude that while it is essential to teach technology skills as part of legal education, it is important that the benefits and importance of using technology be made clear in order for it to be accepted and embraced by the students. Technology must also be available to all students considering the widening participation in higher education and consequent increasing diversity of law students.

Augmenting mobile computing with video game elements to support, motivate and engage young people in educational, real-world events

Video games have shown great potential as tools that both engage and motivate players to achieve tasks and build communities in fantasy worlds. We propose that the application of game elements to real world activities can aid in delivering contextual information in interesting ways and help young people to engage in everyday events. Our research will explore how we can unite utility and fun to enhance information delivery, encourage participation, build communities and engage users with utilitarian events situated in the real world. This research aims to identify key game elements that work effectively to engage young digital natives, and provide guidelines to influence the design of interactions and interfaces for event applications in the future. This research will primarily contribute to areas of user experience and pervasive gaming.

What determines real-world meal size? Evidence for pre-meal planning

The customary approach to the study of meal size suggests that ‘events’ occurring during a meal lead to its termination. Recent research, however, suggests that a number of decisions are made before eating commences that may affect meal size. The present study sought to address three key research questions around meal size: the extent to which plate cleaning occurs; prevalence of pre-meal planning and its influence on meal size; and the effect of within-meal experiences, notably the development of satiation. To address these, a large-cohort internet-based questionnaire was developed. Results showed that plate cleaning occurred at 91% of meals, and was planned from the outset in 92% of these cases. A significant relationship between plate cleaning and meal planning was observed. Pre meal plans were resistant to modification over the course of the meal: only 18% of participants reported consumption that deviated from expected. By contrast, 28% reported continuing eating beyond satiation, and 57% stated that they could have eaten more at the end of the meal. Logistic regression confirmed pre-meal planning as the most important predictor of consumption. Together, our findings demonstrate the importance of meal planning as a key determinant of meal size and energy intake.

Providing a law degree for the 'real world' : perspective of an Australian law school

This paper focuses on the ‘real world’ approach to the degree achieved through the first year program, embedding and scaffolding law graduate capabilities through authentic and valid assessment and work integrated learning to assist graduates with transition into the workplace.

Virtual world process perspective visualization

Product Lifecycle Management has been developed as an approach to providing timely engineering information. However, the number of domain specializations within manufacturing makes such information communication disjointed, inefficient and error-prone. In this paper we propose an immersive 3D visualization of linked domain- specific information views for improving and accelerating communication processes in Product Lifecycle Management. With a common and yet understandable visualization of several domain views, interconnections and dependencies become obvious. The conceptual framework presented here links domain-specific information extracts from Product Lifecycle Management systems with each other and displays them via an integrated 3D representation scheme. We expect that this visualization framework should support holistic tactical decision making processes between domain-experts in operational and tactical manufacturing scenarios.

Knowledge based urban development in classrooms : planning Taipei's knowledge based development

Rapid urbanisation of the global population over the last two centuries has inevitably brought with it a number of challenges and opportunities for economic, environmental and social sustainability of regions. This is arguably a result of rapid globalisation and subsequent growth in knowledge and service based economic markets. This paper reviews the introduction of a specialised teaching structure where the concepts of Knowledge Based Urban Development and Knowledge Cities were taught to various students of the discipline of Urban and Regional Planning at the Queensland University of Technology, through their study tour to the city of Taipei, Taiwan. The concepts were conveyed under the name ‘Taipei Metropolis Knowledge Based Regional Planning Studio’ and its methodology reviewed a series of tasks that was considered to provide a stronger level of understanding of how Knowledge Cities and Knowledge Based Urban Development had been formed in some areas of Taiwan. Findings from this international collaborative planning studio indicate that students have gained a greater level of understanding and insight into planning systems and processes in a trans-cultural context. The students have also been exposed to ideas and knowledge that have challenged conventional perspectives and encouraged global awareness.

The health of women and girls determines the health and well-being of our modern world : a white paper from the International Council on Women's Health Issues

The International Council on Women's Health Issues (ICOWHI) is an international nonprofit association dedicated to the goal of promoting health, health care, and well-being of women and girls throughout the world through participation, empowerment, advocacy, education, and research. We are a multidisciplinary network of women's health providers, planners, and advocates from all over the globe. We constitute an international professional and lay network of those committed to improving women and girl's health and quality of life. This document provides a description of our organization mission, vision, and commitment to improving the health and well-being of women and girls globally.