Algorithmic computation of knot polynomials of secondary structure elements of proteins

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure-alpha-helix, antiparallel beta-sheet, and parallel beta-sheet-and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome

Background: Germline mutations or large-scale deletions in the coding region and splice sites of STK11/LKB1 do not account for all cases of Peutz-Jeghers syndrome (PJS). It is conceivable that, on the basis of data from other diseases, inherited variation in promoter elements of STK11/LKB1 may cause PJS.

Exploring Innovative Methodologies in time and place to analyze child protection documents as elements of practice

This paper aims to demonstrate how a derived approach to case file analysis, influenced by the work of Michel Foucault and Dorothy E.Smith, can offer innovative means by which to study the relations between discourse and practices in child welfare. The article explores text-based forms of organization in histories of child protection in Finland and in Northern Ireland. It is focused on case file records in different organizational child protection contexts in two jurisdictions. Building on a previous article (Author 1 & 2: 2011), we attempt to demonstrate the potential of how the relations between practices and discourses –a majorly important theme for understanding child welfare social work – can be effectively analysed using a combination of two approaches This article is based on three different empirical studies from our two jurisdictions Northern Ireland (UK) and Finland; one study used Foucault; the other Smith and the third study sought to combine the methods. This article seeks to report on ongoing work in developing, for child welfare studies, ‘a history that speaks back’ as we have described it.

‘Towards a Green New Deal on the Island of Ireland: from economic crisis to a new political economy of sustainability’

This article begins from the assumption (which may seem controversial to many) that anyone who thinks that our current economic crisis is a temporary blip until ‘normal service’ (i.e. a return to ‘business as usual’) is resumed, profoundly misunderstands the severity and significance of what’s happening to the global economy and its impacts on the future prosperity of the island of Ireland. The economic recession represents nothing short of a re-structuring of the global economy and the creation of a new dispensation between governments, markets and citizens. The full implications of the re-regulation of the market, with the state bailing out and part nationalising the financial sector in both jurisdictions on the island (as in other parts of the world) have yet to be seen, but what we are witnessing is the emergence of a new economic model. Those who think we can, or even ought to, return to the pre-2008 economic model, are gravely mistaken. The current economic downturn marks the end of the ‘neo-liberal’ model and the beginnings of the transition (an inevitable transition, this article will argue) towards a new low carbon, renewable, green and sustainable economy and society.

Developing students’ ability to engage critically with science in the news: identifying elements of the ‘media awareness’ dimension

Worldwide, science education reform movements are stressing the need to promote ‘scienti?c literacy’ among young people. Increasingly, this is taken to include empowering students to engage critically with science-related news reporting. Despite this requirement now featuring in statutory curricula throughout the UK, there has, to date, been a dearth of research-informed advice to assist science teachers as they identify appropriate instructional objectives in this regard and design relevant learning activities through which these might be achieved. In this study, prominent science communication
scholars, science journalists, science educators and media educators were interviewed to determine what knowledge, skills and habits of mind they judged valuable for individuals reading science-related news stories. Teachers of science and of English from nine secondary schools in Northern Ireland addressed the same issue. A striking – and signi?cant – ?nding of the study was the very substantial number of statements of knowledge, skill and disposition o?ered by participants that relate to ‘media awareness’, an issue largely overlooked in the science education literature. The school-focused phase of the research suggests that cross-curricular approaches involving teachers of science collaborating with those of English/media education or media studies may best serve to address this important curricular goal.

Regenerative Medicine and New Labour Life Science Policy: Rhetorics of Success, Narratives of Sustainability and Survival

Advances in stem cell science and tissue engineering are being turned into applications and products through a novel medical paradigm known as regenerative medicine. This paper begins by examining the vulnerabilities and risks encountered by the regenerative medicine industry during a pivotal moment in its scientific infancy: the 2000s. Under the auspices of New Labour, British medical scientists and life science innovation firms associated with regenerative medicine, received demonstrative rhetorical pledges of support, aligned with the publication of a number of government initiated reports presaged by Bioscience 2015: Improving National Health, Increasing National Wealth. The Department of Health and the Department of Trade and Industry (and its successors) held industry consultations to determine the best means by which innovative bioscience cultures might be promoted and sustained in Britain. Bioscience 2015 encapsulates the first chapter of this sustainability narrative. By 2009, the tone of this storyline had changed to one of survivability. In the second part of the paper, we explore the ministerial interpretation of the ‘bioscience discussion cycle’ that embodies this narrative of expectation, using a computer-aided content analysis programme. Our analysis notes that the ministerial interpretation of these reports has continued to place key emphasis upon the distinctive and exceptional characteristics of the life science industries, such as their ability to perpetuate innovations in regenerative medicine and the optimism this portends – even though many of the economic expectations associated with this industry have remained unfulfilled.

Bioaccessibility of trace elements in soils in Northern Ireland

Assessment of elevated concentrations of potentially toxic elements (PTE) in soils and the association with specific soil parent material have been the focus of research for a number of years. Risk-based assessment of potential exposure scenarios to identified elevated PTE concentrations has led to the derivation of site- and contaminant-specific soil guideline values (SGVs), which represent generic assessment criteria (GACs) to identify exceeded levels that may reflect an unacceptable risk to human health. A better understanding of the ‘bioavailable’ or ‘bioaccessible’ contaminant concentrations offers an opportunity to better refine contaminant exposure assessments. Utilizing a comprehensive soil geochemical dataset for Northern Ireland provided by the Tellus Survey (GSNI) in conjunction with supplementary bioaccessibility testing of selected soil samples following the Unified BARGE Method, this paper uses exploratory data analysis and geostatistical analysis to investigate the spatial variability of pseudo-total and bioaccessible concentrations of As, Cd, Co, Cr. Cu, Ni, Pb, U, V and Zn. The paper investigates variations in individual element concentrations as well as cross-element correlations and observed lithological/pedological associations. The analysis of PTE concentrations highlighted exceeded levels of GAC values for V and Cr and exceeded SGV/GAC values for Cd, Cu, Ni, Pb, and Zn. UBM testing showed that for some soil parent materials associated with elevated PTE concentrations e.g. the Antrim Lava Group with high Ni concentrations, the measured oral bioaccessible fraction was relatively low. For other soil parent materials with relatively moderate PTE concentrations, measured oral bioaccessible fraction was relatively high (e.g. the Gala Sandstone Group of the Southern Uplands-Down Longford Terrain). These findings have implications for regional human health risk assessments for specific PTEs.