Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin

Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.

The role of late medieval English monasteries as expressions of patronal authority : Some case studies

St?ber, Karen. 'The role of late medieval English monasteries as expressions of patronal authority: some case studies', in: 'The Use and Abuse of Sacred Places in Late Medieval Towns, Medievalia Lovaniensia, Series I, Studia XXXVIII', (Leuven: Leuven University Press), pp.189-207, 2006 RAE2008

Participation by place-based community organisations in local development: case studies from East Cork

The past two decades have witnessed concerted efforts by theorists and policy-makers to place civil society at the centre of social, economic and environmental development processes. To this end, policies grounded in a Third Way approach have sought to forge stronger linkages between the state and voluntary community-based organisations. Concepts such as active citizenship, social capital, partnership and sustainability have underpinned this political philosophy, which reflects a movement in development theory and political science away from notions of state-led development and unfettered neo-liberalism. In the Irish context, a series of initiatives have given expression to this new policy agenda, the foremost amongst them the publication of a White Paper in 2000. New local governance structures and development schemes have multiplied since the early 1990s, while the physical planning system has also been modified. All this has taken place against the backdrop of unprecedented economic development and social change precipitated by the ‘Celtic Tiger’.This thesis examines the interaction between community organisations, state institutions and other actors in development processes in East Cork. It focuses upon place-based community organisations, who seek to represent the interests of their particular localities. A case study approach is employed to explore the realpolitik of local development and to gauge the extent to which grassroots community organisations wield influence in determining the development of their communities. The study concludes that the transfer of decision-making power to community organisations has been more illusory than real and that, in practical terms, such groups remain marginal in the circuits of power. However, the situation of community organisations operating in different geographical locales cannot be reduced to an overarching theoretical logic. The case studies show that the modus operandi of community groups varies considerably and can be influenced by specific local geographies, events and personalities.

Integrating mobile and cloud resources management using the cloud personal assistant

The mobile cloud computing model promises to address the resource limitations of mobile devices, but effectively implementing this model is difficult. Previous work on mobile cloud computing has required the user to have a continuous, high-quality connection to the cloud infrastructure. This is undesirable and possibly infeasible, as the energy required on the mobile device to maintain a connection, and transfer sizeable amounts of data is large; the bandwidth tends to be quite variable, and low on cellular networks. The cloud deployment itself needs to efficiently allocate scalable resources to the user as well. In this paper, we formulate the best practices for efficiently managing the resources required for the mobile cloud model, namely energy, bandwidth and cloud computing resources. These practices can be realised with our mobile cloud middleware project, featuring the Cloud Personal Assistant (CPA). We compare this with the other approaches in the area, to highlight the importance of minimising the usage of these resources, and therefore ensure successful adoption of the model by end users. Based on results from experiments performed with mobile devices, we develop a no-overhead decision model for task and data offloading to the CPA of a user, which provides efficient management of mobile cloud resources.

BEYOND THE LIBRETTO: HOW THE COMPOSER GUIDES THE CREATION OF CHARACTER THREE CASE STUDIES

When performing in opera, a singer portrays a character. A libretto is used as the principal resource for the research. Music can also reveal insights into the composer’s ideas regarding characterization. This performance dissertation examines how musical devices such as genre, texture, meter, melody, instrumentation and form can be used to inform choices of characterization. Three roles from diverse operas were examined and performed. The first role, Estelle Oglethorpe in Later the Same Evening (2007) by John Musto (b 1954) was performed November 15, 16, 17, 18 2007. The second role, Dorabella in Così fan tutte (1789) by Wolfgang Amadeus Mozart (1756-1791) was performed April 20, 25, 27, 2008. The third role, Olga in Eugene Onegin (1878) by Pyotr Ilyich Tchaikovsky (1840-1893) was performed on April 19, 2009. All operas were presented by the University of Maryland Opera Studio at the Ina and Jack Kay Theater in the Clarice Smith Performing Arts Center, University of Maryland College Park. DVD recordings of all performances can be found in the University of Maryland library system.

Capturing teachers' experience of learning design through case studies

This article distinguishes three dimensions to learning design: a technological infrastructure, a conceptual framework for practice that focuses on the creation of structured sequences of learning activities, and a way to represent and share practice through the use of mediating artefacts. Focusing initially on the second of these dimensions, the article reports the key findings from an exploratory study, eLIDA CAMEL. This project examined a hitherto under-researched aspect of learning design: what teachers who are new to the domain perceive to be its value as a framework for practice in the design of both flexible and classroom-based learning. Data collection comprised 13 case studies constructed from participants' self-reports. These suggest that providing students with a structured sequence of learning activities was the major value to teachers. The article additionally discusses the potential of such case studies to function as mediating artefacts for practitioners who are considering experimenting with learning design.

Teaching and cognitive outcomes in A-levels and Advanced GNVQ's: Case studies from Science and Business Studies Classrooms

The purpose of the paper is to demonstrate how a research diary methodology, designed to analyse A-level and GNVQ classrooms, can be a powerful tool for examining pedagogy and quality of learning at the level of case study. Two subject areas, science and business studies, are presented as cases. Twelve teachers and thirty-four students were studied over a four-week period in May 1997 and contrasts were drawn between lessons from three A-level physics teachers/three Advanced GNVQ science teachers and two A-level business/economics teachers/four Advanced GNVQ business teachers. Lessons were analysed within a cognitive framework which distinguishes between conceptual and procedural learning and emphasizes the importance of metacognition and epistemological beliefs. Two dimensions of lessons were identified: pedagogical activities (e.g. teacher-led explanation, teacher-led guidance on a task, question/answer sessions, group discussions, working with IT) and cognitive outcomes (e.g. structuring and memorizing facts, understanding concepts and arguments, critical thinking, problem-solving, learning core skills, identifying values). Immediately after each lesson, teachers and students (three per class) completed structured research diaries with respect to the above dimensions. Data from the diaries reveal general and unique features of the lessons. Time-ofyear effects were evident (examinations pending in May), particularly in A-level classrooms. Students in business studies classes reported a wider range of learning activities and greater variety in cognitive outcomes than did students in science classes. Science students self-rating of their ability to manage and direct their own learning was generally low. The phenomenological aspects of the classrooms were consistently linked to teachers' lesson plans and what their teaching objectives were for those particular students at that particular time of the year.