CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.

Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cross-Phenotype Analysis of GWAS) to look for similarities between 700 traits, build trees with informative clusters, and highlight underlying pathways. Clusters are consistent with pre-defined groups and literature-based validation but also reveal novel connections. We report similarity between plasma palmitoleic acid and Crohn's disease and find that specific fatty acids exacerbate enterocolitis in zebrafish. CPAG will become increasingly powerful as more genetic variants are uncovered, leading to a deeper understanding of complex traits. CPAG is freely available at www.sourceforge.net/projects/CPAG/.

Witnessing Crisis in Contemporary and Golden Age Spain

In this volume, experts on the Spanish Golden Age from the United Kingdom, Ireland, and the United States offer analyses of contemporary works that have been influenced by the classics from the sixteenth and seventeenth centuries.

Spatio-temporal Bayesian network models with latent variables for revealing trophic dynamics and functional networks in fisheries ecology

Ecosystems consist of complex dynamic interactions among species and the environment, the understanding of which has implications for predicting the environmental response to changes in climate and biodiversity. However, with the recent adoption of more explorative tools, like Bayesian networks, in predictive ecology, few assumptions can be made about the data and complex, spatially varying interactions can be recovered from collected field data. In this study, we compare Bayesian network modelling approaches accounting for latent effects to reveal species dynamics for 7 geographically and temporally varied areas within the North Sea. We also apply structure learning techniques to identify functional relationships such as prey–predator between trophic groups of species that vary across space and time. We examine if the use of a general hidden variable can reflect overall changes in the trophic dynamics of each spatial system and whether the inclusion of a specific hidden variable can model unmeasured group of species. The general hidden variable appears to capture changes in the variance of different groups of species biomass. Models that include both general and specific hidden variables resulted in identifying similarity with the underlying food web dynamics and modelling spatial unmeasured effect. We predict the biomass of the trophic groups and find that predictive accuracy varies with the models' features and across the different spatial areas thus proposing a model that allows for spatial autocorrelation and two hidden variables. Our proposed model was able to produce novel insights on this ecosystem's dynamics and ecological interactions mainly because we account for the heterogeneous nature of the driving factors within each area and their changes over time. Our findings demonstrate that accounting for additional sources of variation, by combining structure learning from data and experts' knowledge in the model architecture, has the potential for gaining deeper insights into the structure and stability of ecosystems. Finally, we were able to discover meaningful functional networks that were spatially and temporally differentiated with the particular mechanisms varying from trophic associations through interactions with climate and commercial fisheries.

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.

Microbial analysis of soil and groundwater from a gasworks site and comparison to a sequenced biological reactive barrier remediation process (SEREBAR)

Aims: To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater. Methods and Results: Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal. Conclusion: The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident. Significance and Impact of the Study: This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.

Troubled Geographies: A Spatial History of Religion and Society in Ireland

Ireland’s landscape is marked by fault lines of religious, ethnic, and political identity that have shaped its troubled history. Troubled Geographies maps this history by detailing the patterns of change in Ireland from 16th century attempts to “plant” areas of Ireland with loyal English Protestants to defend against threats posed by indigenous Catholics, through the violence of the latter part of the 20th century and the rise of the “Celtic Tiger.” The book is concerned with how a geography laid down in the 16th and 17th centuries led to an amalgam based on religious belief, ethnic/national identity, and political conviction that continues to shape the geographies of modern Ireland. Troubled Geographies shows how changes in religious affiliation, identity, and territoriality have impacted Irish society during this period. It explores the response of society in general and religion in particular to major cultural shocks such as the Famine and to long term processes such as urbanization.

The impact of the summer 2007 forest fires in Greece: Recent environmental mobilizations, cyber-activism and electoral performance

This report circumambulates around the environmental issue, examining mobilizations in favour of public access to the seafront and protest events against the recent devastating forest fires. By framing this discussion within existing scholarly contributions on related dimensions of the environmental issue (environmental consciousness, grassroots environmental contestation) in Southern Europe in general and Greece in particular, it suggests that the environmental mobilization dynamic in Greece has been infused with a new, global, mobilizing resource that offers new avenues to evaluate the potency of Greek civil society. Finally, the article discusses the results of the 2007 national elections and ponders the chances of political ecology becoming a permanent feature of Greek parliamentary politics.

Is shyness context specific? Relation between shyness and online self-disclosure with and without a live webcam in young adults

The Internet provides a new tool to investigate old questions in experimental social psychology regarding Person x Context interaction. We examined the interaction of self-reported shyness and context on computer-mediated communication measures. Sixty female undergraduates unfamiliar were paired in dyads and engaged in a 10 min free chat conversation on the Internet with and without a live webcam. Free chat conversations were archived, transcripts were objectively coded for communication variables, and a linear mixed model used for data analysis of dyadic interaction was performed on each communication measure. As predicted, increases in self-reported shyness were significantly related to decreases in the number of prompted self-disclosures (after controlling for the number of opportunities to self-disclose) only in the webcam condition. Self-reported shyness was not related to the number of prompted self-disclosures in the no webcam condition, suggesting that shyness was context dependent. The present study appears to be the first to objectively code measures of Internet behaviour in relation to the study of personality in general and shyness in particular. Theoretical and clinical implications for understanding the contextual nature of shyness are discussed. (C) 2006 Elsevier Inc. All rights reserved.

Teaching stylistics: analysing cohesion and narrative structure in a short story by Ernest Hemingway

The main aim of this article is to propose an exercise in stylistic analysis which can be employed in the teaching of English language. It details the design and results of a workshop activity on narrative carried out with undergraduates in a university department of English. The methods proposed are intended to enable students to obtain insights into aspects of cohesion and narrative structure; insights, it is suggested, which are not as readily obtainable through more traditional techniques of stylistic analysis. The text chosen for analysis is a short story by Ernest Hemingway comprising only 11 sentences. A jumbled version of this story is presented to students who are asked to assemble a cohesive and well-formed version of the story. Their (re)constructions are then compared with the original Hemingway version. Much interest, it is argued, lies in the ways in which the students justify their own versions in terms of their expectations about well-formedness in narrative. The activity is also intended to encourage students to see literary texts as a valuable means of providing insights into the subtleties of linguistic form and function.

Detecting Ca2+ sparks on stationary and varying baselines.

Studies concerning the physiological significance of Ca2+ sparks often depend on the detection and measurement of large populations of events in noisy microscopy images. Automated detection methods have been developed to quickly and objectively distinguish potential sparks from noise artifacts. However, previously described algorithms are not suited to the reliable detection of sparks in images where the local baseline fluorescence and noise properties can vary significantly, and risk introducing additional bias when applied to such data sets. Here, we describe a new, conceptually straightforward approach to spark detection in linescans that addresses this issue by combining variance stabilization with local baseline subtraction. We also show that in addition to greatly increasing the range of images in which sparks can be automatically detected, the use of a more accurate noise model enables our algorithm to achieve similar detection sensitivities with fewer false positives than previous approaches when applied both to synthetic and experimental data sets. We propose, therefore, that it might be a useful tool for improving the reliability and objectivity of spark analysis in general, and describe how it might be further optimized for specific applications.

Beyond the Sign. Henri Meschonnic's Poetics of Rhythm and Continuum. Towards an Anthropological Theory of Language

Basing the conception of language on the sign represents also an obstacle to the awareness of certain elements of human life, especially to a full understanding of what language or art do, Henri Meschonnic’s poetics of the continuum and of rhythm criticizes the sign based on Benveniste’s terms of rhythm and discourse, developing an anthropology of language. Rhythm, for Meschonnic, is no formal metrical but a semantic principle, each time unique and unforeseeable. As for Humboldt, his starting point is not the word but the ensemble of speech; language is not ergon but energeia. The poem then is not a literary form but a process of transformation that Meschonnic defines as the invention of a form of life by a form of language and vice versa. Thus a poem is a way of thinking and rhythm is form in movement. The particular subject of art and literature is consequently not the author but a process of subjectivation – this is the contrary of the conception of the sign. By demonstrating the limits of the sign, Meschonnic’s poetics attempts to thematize the intelligibility of presence. Art and literature raise our awareness of this element of human life we cannot grasp conceptually. This poetical thinking is a necessary counterforce against all institutionalization.