Text Mining Improves Prediction of Protein Functional Sites

We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions

Ovidian Shakespeare: Wit and the Iconography of the Passions

published or submitted for publicatio

Ovidian Pictures and "The Rules and Compasses" of Criticism

published or submitted for publicatio

Network Centrality and Open Innovation: A Social Network Analysis of an SME Manufacturing Cluster

IEEE Research on open innovation has, in the main, focused on large, high-technology firms and tended to adopt an organization-centric approach in examining external links. In contrast, this article uses social network analysis and network centrality to explore open innovation among a cluster of 33 low-technology small and medium-sized enterprise (SME) manufacturers in Ireland. Adopting a mixed-methods approach this article looks beyond the immediate external links that SMEs form with external organizations and explores the wider network in which such firms are located, their position in these networks and the impact of such positioning on open innovation. This article reports a generally positive relationship between networking activity and innovation performance. Within the context of the low-technology cluster it is apparent that the positioning of a firm within the network may serve to enhance or impede its innovation activity in product development. Despite factors such as fears of appropriation limiting the degree of knowledge and resource exchange within the network, this evidence suggests that those firms occupying central network positions and thus connected to a greater number of other members of the cluster, typically demonstrate greater degrees of innovation activity. Finally, as a means of elucidating the factors that may influence a firm\u27s position the article illustrates that firm size, absorptive capacity, and managerial orientation serve as antecedents of network position

Network Centrality and Open Innovation: A Social Network Analysis of an SME Manufacturing Cluster

IEEE Research on open innovation has, in the main, focused on large, high-technology firms and tended to adopt an organization-centric approach in examining external links. In contrast, this article uses social network analysis and network centrality to explore open innovation among a cluster of 33 low-technology small and medium-sized enterprise (SME) manufacturers in Ireland. Adopting a mixed-methods approach this article looks beyond the immediate external links that SMEs form with external organizations and explores the wider network in which such firms are located, their position in these networks and the impact of such positioning on open innovation. This article reports a generally positive relationship between networking activity and innovation performance. Within the context of the low-technology cluster it is apparent that the positioning of a firm within the network may serve to enhance or impede its innovation activity in product development. Despite factors such as fears of appropriation limiting the degree of knowledge and resource exchange within the network, this evidence suggests that those firms occupying central network positions and thus connected to a greater number of other members of the cluster, typically demonstrate greater degrees of innovation activity. Finally, as a means of elucidating the factors that may influence a firm\u27s position the article illustrates that firm size, absorptive capacity, and managerial orientation serve as antecedents of network position

A partnership enterprise : scenario based learning for diverse nursing students working in a diverse community

The Nursing programme has students from a wide range of backgrounds with approximately half representing minority communities. A proportion of students are allocated placements in a borough where more than forty-five percent of the population is from black and ethnic minorities, and at least fifty-two percent of the staff supporting students also originate from an ethnically diverse background. Research has demonstrated that nursing students can find their practice placement a challenging experience, with anecdotal evidence indicating that students wait to discuss concerns with academic staff in their university rather than to independently address situations as they arise. This proposal outlines some of the findings of a project where students from community and acute nursing placements in a London Borough were immersed in culturally and ethnically diverse communities of practice. Student learning was co-facilitated by link lecturers and practice partners and offered a platform for open discussion and creative problem solving. Project findings emerged from facilitators’ reflections on observation of student interactions, which revealed unique learning and development opportunities

Evaluation of teaching and learning Leadership, Management and Teamwork skills through use of class debate

In order to apply for entry to the NMC register, all student nurses are required to meet Leadership, Management and Team-working (LMT) competency requirements of the Standards for pre-registration nursing education, (NMC, 2010). Increasing size of student cohorts numbers presents challenges for both teachers and students, particularly in the field of LMT where development of self-awareness, questioning attitude and confidence to challenge the status quo are particularly requisite. Classroom debates are recognised as an effective method to encourage development of skills such as critical thinking and communication in other disciplines, but there is limited evidence in support of debates in healthcare education. The aim of this preliminary study was to gain insight into 3rd year nursing students’ perceptions of the effectiveness of class debates as a learning opportunity for development of their LMT competencies. Information derived from systematic data analysis using a framework approach was used to gain understanding of the factors contributing to the effectiveness of class debates as a teaching strategy in LMT nursing education and to inform the design of future teaching interventions. Presentation of findings is followed by a discussion of lessons learned and the author’s reflections about the sustainability of the intervention

Ethnic differences in incidence of stroke: prospective study with stroke register

OBJECTIVE: To identify ethnic differences in the incidence of first ever stroke. DESIGN: A prospective community stroke register (1995-6) with multiple notification sources. Pathological classification of stroke in all cases was based on brain imaging or necropsy data. Rates were standardised to European and world populations and adjusted for age, sex, and social class in multivariate analysis. SETTING: A multi-ethnic population of 234 533 in south London, of whom 21% are black. RESULTS: 612 strokes were registered. The crude annual incidence rate was 1.3 strokes per 1000 population per year (95% confidence interval 1.20 to 1.41) and 1.25 per 1000 population per year (1.15 to 1.35) age adjusted to the standard European population. Incidence rates adjusted for age and sex were significantly higher in black compared with white people (P<0.0001), with an incidence rate ratio of 2.21 (1.77 to 2.76). In multivariable analysis increasing age (P<0.0001), male sex (P<0.003), black ethnic group (P<0.0001), and lower social class (P<0.0001) in people aged 35-64 were independently associated with an increased incidence of stroke. CONCLUSIONS: Incidence rates of stroke are higher in the black population; this is not explained by confounders such as social class, age, and sex. Ethnic differences in genetic, physiological, and behavioural risk factors for stroke require further elucidation to aid development of effective strategies for stroke prevention in multi-ethnic communities