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.

Crisis communication under transformative change : the emergent context and roles of primary and secondary organisations

In an era of complex challenges that draw sustained media attention and entangle multiple organisational actors, this thesis addresses the gap between current trends in society and business, and existing scholarship in public relations and crisis communication. By responding to calls from crisis communication researchers to develop theory (Coombs, 2006a), to examine the interdependencies of crises (Seeger, Sellnow, & Ulmer, 1998), and to consider variation in crisis response (Seeger, 2002), this thesis contributes to theory development in crisis communication and public relations. Through transformative change, this thesis extends existing scholarship built on a preservation or conservation logic where public relations is used to maintain stability by incrementally responding to changes in an organisation‘s environment (Cutlip, Center, & Broom, 2006; Everett, 2001; Grunig, 2000; Spicer, 1997). Based on the opportunity to contribute to ongoing theoretical development in the literature, the overall research problem guiding this thesis asks: How does transformative change during crisis influence corporate actors’ communication? This thesis adopts punctuated equilibrium theory, which describes change as alternating between long periods of stability and short periods of revolutionary or transformative change (Gersick, 1991; Romanelli & Tushman, 1994; Siggelkow, 2002; Tushman, Newman, & Romanelli, 1986; Tushman & Romanelli, 1985). As a theory for change, punctuated equilibrium provides an opportunity to examine public relations and transformative change, building on scholarship that is based primarily on incremental change. Further, existing scholarship in public relations and crisis communication focuses on the actions of single organisations in situational or short-term crisis events. Punctuated equilibrium theory enables the study of multiple crises and multiple organisational responses during transformative change. In doing so, punctuated equilibrium theory provides a framework to explain both the context for transformative change and actions or strategies enacted by organisations during transformative change (Tushman, Newman, & Romanelli, 1986; Tushman & Romanelli, 1985; Tushman, Virany, & Romanelli, 1986). The connections between context and action inform the research questions that guide this thesis: RQ1: What symbolic and substantive strategies persist and change as crises develop from situational events to transformative and multiple linked events? RQ2: What features of the crisis context influence changes in symbolic and substantive strategies? To shed light on these research questions, the thesis adopts a qualitative approach guided by process theory and methods to explicate the events, sequences and activities that were essential to change (Pettigrew, 1992; Van de Ven, 1992). Specifically, the thesis draws on an alternative template strategy (Langley, 1999) that provides several alternative interpretations of the same events (Allison, 1971; Allison & Zelikow, 1999). Following Allison (1971) and Allison and Zelikow (1999), this thesis uses three alternative templates of crisis or strategic response typologies to construct three narratives using media articles and organisational documents. The narratives are compared to identify and draw out different patterns of crisis communication strategies that operate within different crisis contexts. The thesis is based on the crisis events that affected three organisations within the pharmaceutical industry for four years. The primary organisation is Merck, as its product recall crisis triggered transformative change affecting, in different ways, the secondary organisations of Pfizer and Novartis. Three narratives are presented based on the crisis or strategic response typologies of Coombs (2006b), Allen and Caillouet (1994), and Oliver (1991). The findings of this thesis reveal different stories about crisis communication under transformative change. By zooming in to a micro perspective (Nicolini, 2009) to focus on the crisis communication and actions of a single organisation and zooming out to a macro perspective (Nicolini, 2009) to consider multiple organisations, new insights about crisis communication, change and the relationships among multiple organisations are revealed at context and action levels. At the context level, each subsequent narrative demonstrates greater connections among multiple corporate actors. By zooming out from Coombs‘ (2006b) focus on single organisations to consider Allen and Caillouet‘s (1994) integration of the web of corporate actors, the thesis demonstrates how corporate actors add accountability pressures to the primary organisation. Next, by zooming further out to the macro perspective by considering Oliver‘s (1991) strategic responses to institutional processes, the thesis reveals a greater range of corporate actors that are caught up in the process of transformative change and accounts for their varying levels of agency over their environment. By zooming in to a micro perspective and out to a macro perspective (Nicolini, 2009) across alternative templates, the thesis sheds light on sequences, events, and actions of primary and secondary organisations. Although the primary organisation remains the focus of sustained media attention across the four-year time frame, the secondary organisations, even when one faced a similar starting situation to the primary organisation, were buffered by the process of transformative change. This understanding of crisis contexts in transforming environments builds on existing knowledge in crisis communication. At the action level, the thesis also reveals different interpretations from each alternative template. Coombs‘ (2006b) narrative shows persistence in the primary organisation‘s crisis or strategic responses over the four-year time frame of the thesis. That is, the primary organisation consistently applies a diminish crisis response. At times, the primary organisation drew on denial responses when corporate actors questioned its legitimacy or actions. To close the crisis, the primary organisation uses a rebuild crisis posture (Coombs, 2006). These finding are replicated in Allen and Caillouet‘s (1994) narrative, noting this template‘s limitation to communication messages only. Oliver‘s (1991) narrative is consistent with Coombs‘ (2006b) but also demonstrated a shift from a strategic response that signals conformity to the environment to one that signals more active resistance to the environment over time. Specifically, the primary organisation‘s initial response demonstrates conformity but these same messages were used some three years later to set new expectations in the environment in order to shape criteria and build acceptance for future organisational decisions. In summary, the findings demonstrate the power of crisis or strategic responses when considered over time and in the context of transformative change. The conclusions of this research contribute to scholarship in the public relations and management literatures. Based on the significance of organisational theory, the primary contribution of the theory relates to the role of interorganisational linkages or legitimacy buffers that form during the punctuation of equilibrium. The network of linkages among the corporate actors are significant also to the crisis communication literature as they form part of the process model of crisis communication under punctuated equilibrium. This model extends existing research that focuses on crisis communication of single organisations to consider the emergent context that incorporates secondary organisations as well as the localised contests of legitimacy and buffers from regulatory authorities. The thesis also provides an empirical base for punctuated equilibrium in public relations and crisis communication, extending Murphy‘s (2000) introduction of the theory to the public relations literature. In doing this, punctuated equilibrium theory reinvigorates theoretical development in crisis communication by extending existing scholarship around incrementalist approaches and demonstrating how public relations works in the context of transformative change. Further research in this area could consider using alternative templates to study transformative change caused by a range of crisis types from natural disasters to product tampering, and to add further insight into the dynamics between primary and secondary organisations. This thesis contributes to practice by providing guidelines for crisis response strategy selection and indicators related to the emergent context for crises under transformative change that will help primary and secondary organisations‘ responses to crises.

(Re)focusing the Lens to Make Diversity and Difference Visible : Teaching for Quality and Equity

Despite the evidence that Australia’s children are learning literacy, there is also significant evidence that the poorest and most disadvantaged children are being left behind. To date our understanding of the place of transitions in this has been limited, although there has been work on the fourth grade slump (Gee, 2000, 2008), the transition from primary years to secondary years (e.g. Bahr & Pendergast, 2007; Pendergast & Bahr, 2005, 2010), and transitions when changing schools (Henderson, 2008). In this chapter, we consider the notion of transitioning, as we unpack issues related to recognising and valuing student diversity and difference. We want to highlight ways of providing high quality and high equity literacy pedagogy and literacy outcomes for middle years students. We will also discuss the importance of recognising that students transit to schools and school learning from other significant contexts, each with their own combinations of literacy practices, rituals and values.

From classroom resistance to school reform

In the project described in this chapter, a group of educationally disengaged high school students investigated their peers' perspectives of factors related to low aspiration for and access to university. On the basis of their findings, they created an informative DVD to address the student needs.

Successes and stresses : A case study on relations between international higher degree students in Australia and their universities.

The paper examines the situation of postgraduate international students studying in Australia, mostly at doctoral level; a group widely seen as sought-after by Australian universities and employers, though also exposed to difficulties in aspects like learning culture, language and temporary employment. The investigation follows a novel path, as an exercise in practice-led research on issues involved in Higher Degree supervision. It is in fact an exercise within an advanced program of professional development for HD research supervisors. It begins by deploying a journalistic method, to obtain and present information. This has entailed the publishing of two feature articles about the lives of scholars for Subtropic, a campus based online magazine in Brisbane, www.subtropic.com.au. The next step is a review of a set of supervisions, citing issues raised in individual cases. Parallels can be seen between the two information-getting and analytical processes, with scope for contradictions. An exegetical statement deals with supervisory issues that have been exposed, and implications for learning, with recommendations for developing the quality of the experience of these students.

Bouncing back : the role of design in facilitating students to understand and deal with adversity

After state-wide flooding and a category-5 tropical cyclone, three-quarters of the state of Queensland was declared a disaster zone in early 2011. This deluge of adversity had a significant impact on university students, a few weeks prior to the start of the academic semester. The purpose of this paper is to examine the role that design plays in facilitating students to understand and respond to, adversity. The participants of this study were second and fourth year architectural design students at a large Australian University, in Queensland. As a part of their core architectural design studies, students were required to provide architectural responses to the recent catastrophic events in Queensland. Qualitative data was obtained through student surveys, work design work submitted by students and a survey of guests who attending an exhibition of the student work. The results of this research showed that the students produced more than just the required set of architectural drawings, process journals and models, but also recognition of the important role that the affective dimension of the flooding event and the design process played in helping them to both understand and respond to, adversity. They held the ‘real world’ experience and practical aspect of the assessment in higher regard than their typical focus on aesthetics and the making of iconic design. Perhaps most importantly, the students recognised that this process allowed them to have a voice, and a means to respond to adversity through the powerful language of design.

Butterpaper, sweat & tears : the affective dimension of engaging students during the architectural critique

Considering how dominant a feature of architectural education the critique has been, and continues to be, little has been written about the affective dimension of engaging students during this key final stage of the design or documentation process. For most students, the critique is unlike any previous educational or life experience that they have ever confronted, and the abrupt change in the instructor’s role, from tutor to judge, can be disconcerting at a time when the student is feeling their most vulnerable. The fact that the period immediately leading up to the critique habitually entails not only a focused and sustained effort, but also sleepless nights of intensive work, further exacerbates this. The purpose of this paper is to recognise the affective phenomena influencing student engagement, during the critique. The participants of this research were second to fourth year architecture students at a major Australian university. Following the implementation of trials in alternative modes of critique in architectural design and technology studios, qualitative data was obtained from students, through questionnaires and interviews. Six indicators of engagement were investigated through this research: motivation and agency, transactional engagement with staff, transactional engagement with students, institutional support, active citizenship, and non-institutional support. This research confirms that affective phenomena play a significant role in the events of the critique; the relationship between instructor and student influences student engagement, as does the choreography and spatial planning of the critique environment; and these factors ultimately have an impact on the depth of student learning.

Assessing students in senior science: an analysis of questions in contextualised chemistry exams

This study explores the development of a coding system for analysing test questions in two context-based chemistry exams. We describe our unique analytical procedures before contrasting the data from both tests. Our findings indicate that when a new curriculum is developed such as a context-based curriculum, teachers are required to combine the previously separate domains of context and concept to develop contextualised assessment. We argue that constructing contextualised assessment items requires teachers to view concepts and context as interconnected rather than as separate entities that may polarise scientific endeavour. Implications for practice, curriculum and assessment-development in context-based courses are proposed.

Interactive peer-based learning in a comparative case study : what do students gain?

As English increasingly becomes one of the most commonly spoken languages in the world today for a variety of economic, social and cultural reasons, education is impacted by globalisation, the internationalisation of universities and the diversity of learners in classrooms. The challenge for educators is to find more effective ways of teaching English language so that students are better able to create meaning and communicate in the target language as well as to transform knowledge and understanding into relevant skills for a rapidly changing world. This research focuses broadly on English language education underpinned by social constructivist principles informing communicative language teaching and in particular, interactive peer learning approaches. An intervention of interactive peer-based learning in two case study contexts of English as Foreign Language (EFL) undergraduates in a Turkish university and English as Second Language (ESL) undergraduates in an Australian university investigates what students gain from the intervention. Methodology utilising qualitative data gathered from student reflective logs, focus group interviews and researcher field notes emphasises student voice. The cross case comparative study indicates that interactive peer-based learning enhances a range of learning outcomes for both cohorts including engagement, communicative competence, diagnostic feedback as well as assisting development of inclusive social relationships, civic skills, confidence and self efficacy. The learning outcomes facilitate better adaptation to a new learning environment and culture. An iterative instructional matrix tool is a useful product of the research for first year university experiences, teacher training, raising awareness of diversity, building learning communities, and differentiating the curriculum. The study demonstrates that English language learners can experience positive impact through peer-based learning and thus holds an influential key for Australian universities and higher education.

Perceptions of online learning in an Australian university : Malaysian students' perspectives

Several researchers have reported that cultural and language differences can affect online interactions and communications between students from different cultural backgrounds. Other researchers have asserted that online learning is a tool that can improve teaching and learning skills, but, its effectiveness depends on how the tool is used. Therefore, this study aims to investigate the kinds of challenges encountered by the international students and how they actually cope with online learning. To date little research exists on the perceptions of online learning environments by international Asian students, in particular Malaysian students who study in Australian Universities; hence this study aims to fill this gap. A mixed-method approach was used to collect quantitative and qualitative data using a modified Online Learning Environment Survey (OLES) instrument and focus group interviews. The sample comprised 76 international students from a university in Brisbane. Thirty-five domestic Australian students were included for comparison. Contrary to assumptions from previous research, the findings revealed that there were few differences between the international Asian students from Malaysia and Australian students with regard to their perceptions of online learning. Another cogent finding that emerged was that online learning was most effective when included within blended learning environments. The students clearly indicated that when learning in a blended environment, it was imperative that appropriate features are blended in and customised to suit the particular needs of international students. The study results indicated that the university could improve the quality of the blended online learning environment by: 1) establishing and maintaining a sense of learning community; 2) enhancing the self motivation of students; and 3) professional development of lecturers/tutors, unit coordinators and learning support personnel. Feedback from focus group interviews, highlighted the students‘ frustration with a lack of cooperative learning, strategies and skills which were expected of them by their lecturers/tutors in order to work productively in groups. They indicated a strong desire for lecturers/tutors to provide them prior training in these strategies and skills. The students identified four ways to optimise learning opportunities in cross-cultural spaces. These were: 1) providing preparatory and ongoing workshops focusing on the dispositions and roles of students within student-centred online learning environments; 2) providing preparatory and ongoing workshops on collaborative group learning strategies and skills; 3) providing workshops familiarising students with Australian culture and language; and 4) providing workshops on strategies for addressing technical problems. Students also indicated a strong desire for professional development of lecturers/tutors focused on: 1) teacher attributes, 2) ways to culturally sensitive curricula, and 3) collaborative learning and cooperative working strategies and skills, and 4) designing flexible program structures. Recommendations from this study will be useful to Australian universities where Asian international students from Malaysia study in blended learning environments. An induction program (online skills, collaborative and teamwork skills, study expectations plus familiarisation with Australian culture) for overseas students at the commencement of their studies; a cultural awareness program for lecturers (cultural sensitivity, ways to communicate and a better understanding of Asian educational systems), upskilling of lecturers‘ ability to structure their teaching online and to apply strong theoretical underpinnings when designing learning activities such as discussion forums, and consistency with regards to how content is located and displayed in a learning management system like Blackboard. Through addressing the research questions in this study, the researcher hopes to contribute to and advance the domain of knowledge related to online learning, and to better understand how international Malaysian students‘ perceive online learning environments. These findings have theoretical and pragmatic significance.

Connecting online with external students : do we really know how to?

Students are often time poor and find it difficult to manage their time in relation to study and other external factors including work. Online study is no exception to this and in many cases where the student is studying in an online only environment, they are also working in full time employment. Higher Education institutions are now offering an abundance of courses online to attract more under-graduate and post-graduate students. It is in this sense that there is an ever-increasing need to understand the student of today and find ways to connect with them and support them in their studies. This paper will report on a small-scale case study of an undergraduate online-only group of first year education students and their associated online experiences in developing a sense of community whilst interacting with a learning management system and its associated tools. Further the paper will explore the mis-conceptions that are widely held by course designers and lecturers involved with online courses.