FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

Evaluation of water and energy budgets in regional climate models applied over Europe

This study presents a model intercomparison of four regional climate models (RCMs) and one variable resolution atmospheric general circulation model (AGCM) applied over Europe with special focus on the hydrological cycle and the surface energy budget. The models simulated the 15 years from 1979 to 1993 by using quasi-observed boundary conditions derived from ECMWF re-analyses (ERA). The model intercomparison focuses on two large atchments representing two different climate conditions covering two areas of major research interest within Europe. The first is the Danube catchment which represents a continental climate dominated by advection from the surrounding land areas. It is used to analyse the common model error of a too dry and too warm simulation of the summertime climate of southeastern Europe. This summer warming and drying problem is seen in many RCMs, and to a less extent in GCMs. The second area is the Baltic Sea catchment which represents maritime climate dominated by advection from the ocean and from the Baltic Sea. This catchment is a research area of many studies within Europe and also covered by the BALTEX program. The observed data used are monthly mean surface air temperature, precipitation and river discharge. For all models, these are used to estimate mean monthly biases of all components of the hydrological cycle over land. In addition, the mean monthly deviations of the surface energy fluxes from ERA data are computed. Atmospheric moisture fluxes from ERA are compared with those of one model to provide an independent estimate of the convergence bias derived from the observed data. These help to add weight to some of the inferred estimates and explain some of the discrepancies between them. An evaluation of these biases and deviations suggests possible sources of error in each of the models. For the Danube catchment, systematic errors in the dynamics cause the prominent summer drying problem for three of the RCMs, while for the fourth RCM this is related to deficiencies in the land surface parametrization. The AGCM does not show this drying problem. For the Baltic Sea catchment, all models similarily overestimate the precipitation throughout the year except during the summer. This model deficit is probably caused by the internal model parametrizations, such as the large-scale condensation and the convection schemes.

Frying of potato chips in a blend of canola oil and palm olein: changes in levels of individual fatty acids and tocols

The changes occurring in the levels of nutritionally relevant oil components were assessed during repeated frying of potato chips in a blend of palm olein and canola oil (1:1 w/w). The blend suffered minimal reductions in omega-3 and omega-6 polyunsaturated fatty acids. There was no significant difference between the fatty acid composition of the oil extracted from the product and that of the frying medium, in all three cases. The blend also contained a significant amount of tocols which add a nutritional value to the oil. The concentration of the tocols was satisfactorily retained over the period of oil usage, in contrast to the significant loses observed in the case of the individual oils. The blend also performed well when assessed by changes in total polar compounds, free fatty acids, p-anisidine value. When fried in used oil, the product oil content increased progressively with oil usage time. This study shows that blended frying oils can combine good stability and nutritional quality

An experimental manipulation of responsibility in children: a test of the inflated responsibility model of obsessive-compulsive disorder

The objective of this study was to investigate whether Salkovskis (1985) inflated responsibility model of obsessive-compulsive disorder (OCD) applied to children. In an experimental design, 81 children aged 9– 12 years were randomly allocated to three conditions: an inflated responsibility group, a moderate responsibility group, and a reduced responsibility group. In all groups children were asked to sort sweets according to whether or not they contained nuts. At baseline the groups did not differ on children’s self reported anxiety, depression, obsessive-compulsive symptoms or on inflated responsibility beliefs. The experimental manipulation successfully changed children’s perceptions of responsibility. During the sorting task time taken to complete the task, checking behaviours, hesitations, and anxiety were recorded. There was a significant effect of responsibility level on the behavioural variables of time taken, hesitations and check; as perceived responsibility increased children took longer to complete the task and checked and hesitated more often. There was no between-group difference in children’s self reported state anxiety. The results offer preliminary support for the link between inflated responsibility and increased checking behaviours in children and add to the small but growing literature suggesting that cognitive models of OCD may apply to children.

A matrix iteration for dynamic network summaries

We propose a new algorithm for summarizing properties of large-scale time-evolving networks. This type of data, recording connections that come and go over time, is being generated in many modern applications, including telecommunications and on-line human social behavior. The algorithm computes a dynamic measure of how well pairs of nodes can communicate by taking account of routes through the network that respect the arrow of time. We take the conventional approach of downweighting for length (messages become corrupted as they are passed along) and add the novel feature of downweighting for age (messages go out of date). This allows us to generalize widely used Katz-style centrality measures that have proved popular in network science to the case of dynamic networks sampled at non-uniform points in time. We illustrate the new approach on synthetic and real data.

Construction management research at the individual-level of analysis: current status, gaps and future directions

Individual-level constructs are seldom taken into consideration in construction management research relating to project performance. This is antithetical to the objectives of properly conceptualizing and contextualizing the research we do because many project performance outcomes, such as the extent of cooperation and level of communication or teamwork are influenced and moderated by individuals’ perceptions, values and behaviour. A brief review of the literature in organizational studies centred on culture, identity, empowerment and trust is offered. These constructs are then explored in relation to project performance issues and outcomes, and it is noted that they are predominantly studied at the project and industry levels. We argue that focusing these constructs at the individual unit of analysis has significant implications for project performance and therefore their effects need to be systematically accounted for in explanations of the success and failure of projects. Far from being prescriptive, the aim is to generate interest and awareness for more focused research at the individual level of analysis in order to add new insights and perspectives to critical performance questions in construction management. To this end, a research agenda is outlined, arguing that construction management research integrating individual-level constructs and broader, macro-contextual issues will help define and enhance the legitimacy of the field.

Chercher pour or chercher après: arguing the case for contact-induced linguistic innovation in different varieties of French

This paper provides evidence for the claim made in Baetens Beardsmore (1971) that the grammatical collocation "chercher après" «to look for», which is very frequent in Brussels French, is the result of transfer from the contact language, Brussels Dutch. A detailed quantitative analysis of this construction in different varieties of French which have more or less contact with a Germanic language was made to investigate the likelihood of influence from the Germanic substrate. The differences between the meaning of "chercher" and "chercher après" are also analysed in some depth, to find out whether or not the particle is redundant. According to Trudgill (2004) redundant constructions are more often found in contact situations involving long-term, stable contact and child bilingualism. The particle "après" was found to add a particular shade of meaning to "chercher", and is thus not redundant. Therefore no evidence could be obtained from the current data for Trudgill’s (2004) claim.

Competitive exclusion by Bacillus subtilis spores of Salmonella enterica serotype Enteritidis and Clostridium perfringens in young chickens

Cost effective control of avian diseases and food borne pathogens remains a high priority for all sectors of the poultry industry with cleansing and disinfection, vaccination and competitive exclusion approaches being used widely. Previous studies showed that Bacillus subtilis PY79(hr) was an effective competitive exclusion agent for use in poultry to control avian pathogenic Escherichia coli serotype O78:K80. Here we report experiments that were undertaken to test the efficacy of B. subtilis PY79(hr) in the control of Salmonella enterica serotype Enteritidis and Clostridium perfringens in young chickens. To do this, 1-day-old and 20-day-old specific pathogen free (SPF) chicks were dosed with a suspension of B. subtilis spores prior to challenge with S. Enteritidis (S1400) and C. perfringens, respectively. For both challenge models, a single oral inoculum of 1 x 10(9) spores given 24 h prior to challenge was sufficient to suppress colonisation and persistence of both S. Enteritidis and C perfringens. In particular, the faecal shedding of S. Enteritidis, as measured by a semi-quantitative cloacal swabbing technique, was reduced significantly for the 36 days duration of the experiment. B. subtilis persisted in the intestine although with decreasing numbers over the same period. These data add further evidence that B. subtilis spores may be effective agents in the control of avian diseases and food borne pathogens.

File Transfer Protocol

The discourse surrounding the virtual has moved away from the utopian thinking accompanying the rise of the Internet in the 1990s. The Cyber-gurus of the last decades promised a technotopia removed from materiality and the confines of the flesh and the built environment, a liberation from old institutions and power structures. But since then, the virtual has grown into a distinct yet related sphere of cultural and political production that both parallels and occasionally flows over into the old world of material objects. The strict dichotomy of matter and digital purity has been replaced more recently with a more complex model where both the world of stuff and the world of knowledge support, resist and at the same time contain each other. Online social networks amplify and extend existing ones; other cultural interfaces like youtube have not replaced the communal experience of watching moving images in a semi-public space (the cinema) or the semi-private space (the family living room). Rather the experience of viewing is very much about sharing and communicating, offering interpretations and comments. Many of the web’s strongest entities (Amazon, eBay, Gumtree etc.) sit exactly at this juncture of applying tools taken from the knowledge management industry to organize the chaos of the material world along (post-)Fordist rationality. Since the early 1990s there have been many artistic and curatorial attempts to use the Internet as a platform of producing and exhibiting art, but a lot of these were reluctant to let go of the fantasy of digital freedom. Storage Room collapses the binary opposition of real and virtual space by using online data storage as a conduit for IRL art production. The artworks here will not be available for viewing online in a 'screen' environment but only as part of a downloadable package with the intention that the exhibition could be displayed (in a physical space) by any interested party and realised as ambitiously or minimally as the downloader wishes, based on their means. The artists will therefore also supply a set of instructions for the physical installation of the work alongside the digital files. In response to this curatorial initiative, File Transfer Protocol invites seven UK based artists to produce digital art for a physical environment, addressing the intersection between the virtual and the material. The files range from sound, video, digital prints and net art, blueprints for an action to take place, something to be made, a conceptual text piece, etc. About the works and artists: Polly Fibre is the pseudonym of London-based artist Christine Ellison. Ellison creates live music using domestic devices such as sewing machines, irons and slide projectors. Her costumes and stage sets propose a physical manifestation of the virtual space that is created inside software like Photoshop. For this exhibition, Polly Fibre invites the audience to create a musical composition using a pair of amplified scissors and a turntable. http://www.pollyfibre.com John Russell, a founding member of 1990s art group Bank, is an artist, curator and writer who explores in his work the contemporary political conditions of the work of art. In his digital print, Russell collages together visual representations of abstract philosophical ideas and transforms them into a post apocalyptic landscape that is complex and banal at the same time. www.john-russell.org The work of Bristol based artist Jem Nobel opens up a dialogue between the contemporary and the legacy of 20th century conceptual art around questions of collectivism and participation, authorship and individualism. His print SPACE concretizes the representation of the most common piece of Unicode: the vacant space between words. In this way, the gap itself turns from invisible cipher to sign. www.jemnoble.com Annabel Frearson is rewriting Mary Shelley's Frankenstein using all and only the words from the original text. Frankenstein 2, or the Monster of Main Stream, is read in parts by different performers, embodying the psychotic character of the protagonist, a mongrel hybrid of used language. www.annabelfrearson.com Darren Banks uses fragments of effect laden Holywood films to create an impossible space. The fictitious parts don't add up to a convincing material reality, leaving the viewer with a failed amalgamation of simulations of sophisticated technologies. www.darrenbanks.co.uk FIELDCLUB is collaboration between artist Paul Chaney and researcher Kenna Hernly. Chaney and Hernly developed together a project that critically examines various proposals for the management of sustainable ecological systems. Their FIELDMACHINE invites the public to design an ideal agricultural field. By playing with different types of crops that are found in the south west of England, it is possible for the user, for example, to create a balanced, but protein poor, diet or to simply decide to 'get rid' of half the population. The meeting point of the Platonic field and it physical consequences, generates a geometric abstraction that investigates the relationship between modernist utopianism and contemporary actuality. www.fieldclub.co.uk Pil and Galia Kollectiv, who have also curated the exhibition are London-based artists and run the xero, kline & coma gallery. Here they present a dialogue between two computers. The conversation opens with a simple text book problem in business studies. But gradually the language, mimicking the application of game theory in the business sector, becomes more abstract. The two interlocutors become adversaries trapped forever in a competition without winners. www.kollectiv.co.uk

Evaluation of water and energy budgets in regional climate models applied over Europe

Abstract This study presents a model intercomparison of four regional climate models (RCMs) and one variable resolution atmospheric general circulation model (AGCM) applied over Europe with special focus on the hydrological cycle and the surface energy budget. The models simulated the 15 years from 1979 to 1993 by using quasi-observed boundary conditions derived from ECMWF re-analyses (ERA). The model intercomparison focuses on two large atchments representing two different climate conditions covering two areas of major research interest within Europe. The first is the Danube catchment which represents a continental climate dominated by advection from the surrounding land areas. It is used to analyse the common model error of a too dry and too warm simulation of the summertime climate of southeastern Europe. This summer warming and drying problem is seen in many RCMs, and to a less extent in GCMs. The second area is the Baltic Sea catchment which represents maritime climate dominated by advection from the ocean and from the Baltic Sea. This catchment is a research area of many studies within Europe and also covered by the BALTEX program. The observed data used are monthly mean surface air temperature, precipitation and river discharge. For all models, these are used to estimate mean monthly biases of all components of the hydrological cycle over land. In addition, the mean monthly deviations of the surface energy fluxes from ERA data are computed. Atmospheric moisture fluxes from ERA are compared with those of one model to provide an independent estimate of the convergence bias derived from the observed data. These help to add weight to some of the inferred estimates and explain some of the discrepancies between them. An evaluation of these biases and deviations suggests possible sources of error in each of the models. For the Danube catchment, systematic errors in the dynamics cause the prominent summer drying problem for three of the RCMs, while for the fourth RCM this is related to deficiencies in the land surface parametrization. The AGCM does not show this drying problem. For the Baltic Sea catchment, all models similarily overestimate the precipitation throughout the year except during the summer. This model deficit is probably caused by the internal model parametrizations, such as the large-scale condensation and the convection schemes.

Picture this: how illustrations define dictionaries

Illustrations are an integral part of many dictionaries, but the selection, placing, and sizing of illustrations is often highly conservative, and can appear to reflect the editorial concerns and technological constraints of previous eras. We might start with the question ‘why not illustrate?’, especially when we consider the ability of an illustration to simplify the definition of technical terms. How do illustrations affect the reader’s view of a dictionary as objective, and how illustrations reinforce the pedagogic aims of the dictionary? By their graphic nature, illustrations stand out from the field of text against which they stand, and they can immediately indicate to the reader the level of seriousness or popularity of the book’s approach, or the age-range that it is intended for. And illustrations are expensive to create and can add to printing costs, so it is not surprising that there is much direct and indirect copying from dictionary to dictionary, and simple re-use. This article surveys developments in illustrating dictionaries, considering the difference between distributing individual illustrations through the text of the dictionary and grouping illustrations into larger synoptic illustrations; the graphic style of illustrations; and the role of illustrations in ‘feature-led’ dictionary marketing.

A climate of control: flooding, displacement and planned resettlement in the Lower Zambezi River valley, Mozambique

In recent years, the potential role of planned, internal resettlement as a climate change adaptation measure has been highlighted by national governments and the international policy community. However, in many developing countries, resettlement is a deeply political process that often results in an unequal distribution of costs and benefits amongst relocated persons. This paper examines these tensions in Mozambique, drawing on a case study of flood-affected communities in the Lower Zambezi River valley. It takes a political ecology approach – focusing on discourses of human-environment interaction, as well as the power relationships that are supported by such discourses – to show how a dominant narrative of climate change-induced hazards for small-scale farmers is contributing to their involuntary resettlement to higher-altitude, less fertile areas of land. These forced relocations are buttressed by a series of wider economic and political interests in the Lower Zambezi River region, such dam construction for hydroelectric power generation and the extension of control over rural populations, from which resettled people derive little direct benefit. Rather than engaging with these challenging issues, most international donors present in the country accept the ‘inevitability’ of extreme weather impacts and view resettlement as an unfortunate and, in some cases, necessary step to increase people’s ‘resilience’, thus rationalising the top-down imposition of unpopular social policies. The findings add weight to the argument that a depoliticised interpretation of climate change can deflect attention away from underlying drivers of vulnerability and poverty, as well as obscure the interests of governments that are intent on reordering poor and vulnerable populations.

Enhancement of aged and denatured fingerprints using the cyanoacrylate fuming technique following dusting with amino acid-containing powders

We have carried out experiments to investigate the ageing of latent fingerprints deposited on black PVC over a period of 4-15 weeks. A thumbprint was used in each case and before deposition of the print the donor rubbed their thumb around their nose to add sebaceous deposits. We have studied the effect of heat, light and moisture and we find that moisture is the most significant factor in the degradation of the latent print. We have attempted to enhance these latent prints by dusting with valine powder or powders composed of valine mixed with gold or red fluorescent commercial fingerprint powders. In order to make a direct comparison between “treated” and “untreated” prints, the prints were cut in half with one half being “treated” and one not. Our studies show the best results being obtained when powders of valine and red fluorescent powders are applied prior to cyanoacrylate fuming.

Building from scratch a marketing services giant by acquisition: case study and interview with Sir Martin Sorrell, Chief Executive of WPP

Purpose – Mergers and acquisitions are among the most intensely used strategic decisions. Yet research by both academics and consulting groups suggests that many mergers and acquisitions fail to add value. On the other hand there are many companies that successfully use mergers and acquisition to grow and add shareholder value. One such company is WPP. The aim of this paper is to explore why WPP has been successful in its acquisition strategy while so many other companies fail. Design/methodology/approach – The paper draws on documentary evidence and a semi-structured interview with Sir Martin Sorrell – Chief Executive and founder of WPP. Research limitations/implications – The case study offers a unique insight into thinking of a successful acquirer and sheds light on how mergers and acquisitions are managed by WPP. However, because of its design the findings are not generalisable. Originality/value – This case study sheds light on how mergers and acquisitions can be used to create a £9 billion company from a standing start. Furthermore, very few case studies offer insight into the thinking of entrepreneurial Chief Executives who established the business, grew it to become the largest and most profitable marketing services company in the world and engineered close to 300 acquisitions.

Extra-tropical cyclones in the present and future climate: a review

Based on the availability of hemispheric gridded data sets from observations, analysis and global climate models, objective cyclone identification methods were developed and applied to these data sets. Due to the large amount of investigation methods combined with the variety of different datasets, a multitude of results exist, not only for the recent climate period but also for the next century, assuming anthropogenic changed conditions. Different thresholds, different physical quantities, and considerations of different atmospheric vertical levels add to a picture that is difficult to combine into a common view of cyclones, their variability and trends, in the real world and in GCM studies. Thus, this paper will give a comprehensive review of the actual knowledge on climatologies of mid-latitude cyclones for the Northern and Southern Hemisphere for the present climate and for its possible changes under anthropogenic climate conditions.