Showing papers by "University of Exeter published in 2005"

The genome sequence of the rice blast fungus Magnaporthe grisea

Abstract: Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.

Information and its use by animals in evolutionary ecology

Abstract: Information is a crucial currency for animals from both a behavioural and evolutionary perspective. Adaptive behaviour relies upon accurate estimation of relevant ecological parameters; the better informed an individual, the better it can develop and adjust its behaviour to meet the demands of a variable world. Here, we focus on the burgeoning interest in the impact of ecological uncertainty on adaptation, and the means by which it can be reduced by gathering information, from both 'passive' and 'responsive' sources. Our overview demonstrates the value of adopting an explicitly informational approach, and highlights the components that one needs to develop useful approaches to studying information use by animals. We propose a quantitative framework, based on statistical decision theory, for analysing animal information use in evolutionary ecology. Our purpose is to promote an integrative approach to studying information use by animals, which is itself integral to adaptive animal behaviour and organismal biology.

The Glass Cliff: Evidence that Women are Over‐Represented in Precarious Leadership Positions

Abstract: There has been much research and conjecture concerning the barriers women face in trying to climb the corporate ladder, with evidence suggesting that they typically confront a ‘glass ceiling’ while men are more likely to benefit from a ‘glass escalator’. But what happens when women do achieve leadership roles? And what sorts of positions are they given? This paper argues that while women are now achieving more high profile positions, they are more likely than men to find themselves on a ‘glass cliff’, such that their positions are risky or precarious. This hypothesis was investigated in an archival study examining the performance of FTSE 100 companies before and after the appointment of a male or female board member. The study revealed that during a period of overall stock-market decline those companies who appointed women to their boards were more likely to have experienced consistently bad performance in the preceding five months than those who appointed men. These results expose an additional, largely invisible, hurdle that women need to overcome in the workplace. Implications for the evaluation of women leaders are discussed and directions for future research are outlined.

Experimental Verification of Designer Surface Plasmons

Abstract: We studied the microwave reflectivity of a structured, near perfectly conducting substrate that was designed to verify the existence of a theoretically proposed new class of surface mode. Measurements of the mode's dispersion curve show that it correctly approaches the predicted asymptotic frequency; the curve also agrees well with that derived from a computer simulation. Modeling of the field distribution on resonance provides evidence of strong localization of the electric field at the interface and substantial power flow along the interface, thus verifying the surface plasmon-like nature of the mode.

Interventions for promoting physical activity

Abstract: Background Little is known about the effectiveness of strategies to enable people to achieve and maintain recommended levels of physical activity. Objectives To assess the effectiveness of interventions designed to promote physical activity in adults aged 16 years and older, not living in an institution. Search methods We searched The Cochrane Library (issue 1 2005), MEDLINE, EMBASE, CINAHL, PsycLIT, BIDS ISI, SPORTDISCUS, SIGLE, SCISEARCH (from earliest dates available to December 2004). Reference lists of relevant articles were checked. No language restrictions were applied. Selection criteria Randomised controlled trials that compared different interventions to encourage sedentary adults not living in an institution to become physically active. Studies required a minimum of six months follow up from the start of the intervention to the collection of final data and either used an intention-to-treat analysis or, failing that, had no more than 20% loss to follow up. Data collection and analysis At least two reviewers independently assessed each study quality and extracted data. Study authors were contacted for additional information where necessary. Standardised mean differences and 95% confidence intervals were calculated for continuous measures of self-reported physical activity and cardio-respiratory fitness. For studies with dichotomous outcomes, odds ratios and 95% confidence intervals were calculated. Main results The effect of interventions on self-reported physical activity (19 studies; 7598 participants) was positive and moderate (pooled SMD random effects model 0.28 95% CI 0.15 to 0.41) as was the effect of interventions (11 studies; 2195 participants) on cardio-respiratory fitness (pooled SMD random effects model 0.52 95% CI 0.14 to 0.90). There was significant heterogeneity in the reported effects as well as heterogeneity in characteristics of the interventions. The heterogeneity in reported effects was reduced in higher quality studies, when physical activity was self-directed with some professional guidance and when there was on-going professional support. Authors' conclusions Our review suggests that physical activity interventions have a moderate effect on self-reported physical activity, on achieving a predetermined level of physical activity and cardio-respiratory fitness. Due to the clinical and statistical heterogeneity of the studies, only limited conclusions can be drawn about the effectiveness of individual components of the interventions. Future studies should provide greater detail of the components of interventions.

RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins

Abstract: Motivation: Recent studies have found many proteins containing regions that do not form well-defined three-dimensional structures in their native states. The study and detection of such disordered regions is important both for understanding protein function and for facilitating structural analysis since disordered regions may affect solubility and/or crystallizability. Results: We have developed the regional order neural network (RONN) software as an application of our recently developed 'bio-basis function neural network' pattern recognition algorithm to the detection of natively disordered regions in proteins. The results of blind-testing a panel of nine disorder prediction tools (including RONN) against 80 protein sequences derived from the Protein Data Bank shows that, based on the probability excess measure, RONN performed the best. Availability: RONN is available at http://www.strubi.ox.ac.uk/RONN. Requests for the RONN software and the database of disorder (XML format) can be directed to the corresponding author. Contact: robert@strubi.ox.ac.uk Supplementary information: Details of all predictions made during blind testing, also available at http://www.strubi.ox.ac.uk/RONN3_Supplementary.pdf

Taking the strain: Social identity, social support, and the experience of stress

Abstract: The social identity/self-categorization model of stress suggests that social identity can play a role in protecting group members from adverse reactions to strain because it provides a basis for group members to receive and benefit from social support. To examine this model, two studies were conducted with groups exposed to extreme levels of strain: patients recovering from heart surgery (Study 1), bomb disposal officers and bar staff (Study 2). Consistent with predictions, in both studies there was a strong positive correlation between social identification and both social support and life/job satisfaction and a strong negative correlation between social identification and stress. In both studies path analysis also indicated that social support was a significant mediator of the relationship between (a) social identification and stress and (b) social identification and life/job satisfaction. In addition, Study 2 revealed that group membership plays a significant role in perceptions of how stressful different types of work are. Implications for the conceptualization of stress and social support are discussed.

Social identity and the dynamics of leadership: Leaders and followers as collaborative agents in the transformation of social reality

Abstract: Traditional models see leadership as a form of zero-sum game in which leader agency is achieved at the expense of follower agency and vice versa. Against this view, the present article argues that leadership is a vehicle for social identity-based collective agency in which leaders and followers are partners. Drawing upon evidence from a range of historical sources and from the BBC Prison Study, the present article explores the two sides of this partnership: the way in which a shared sense of identity makes leadership possible and the way in which leaders act as entrepreneurs of identity in order to make particular forms of identity and their own leadership viable. The analysis also focuses (a) on the way in which leaders' identity projects are constrained by social reality, and (b) on the manner in which effective leadership contributes to the transformation of this reality through the initiation of structure that mobilizes and redirects a group's identity-based social power.

Three-month-olds, but not newborns, prefer own-race faces

Abstract: Adults are sensitive to the physical differences that define ethnic groups. However, the age at which we become sensitive to ethnic differences is currently unclear. Our study aimed to clarify this by testing newborns and young infants for sensitivity to ethnicity using a visual preference (VP) paradigm. While newborn infants demonstrated no spontaneous preference for faces from either their own- or other-ethnic groups, 3-month-old infants demonstrated a significant preference for faces from their own-ethnic group. These results suggest that preferential selectivity based on ethnic differences is not present in the first days of life, but is learned within the first 3 months of life. The findings imply that adults’ perceptions of ethnic differences are learned and derived from differences in exposure to own- versus other-race faces during early development.

Strong coupling between surface plasmon-polaritons and organic molecules in subwavelength hole arrays

Abstract: The interaction of a $J$-aggregate and surface plasmon polariton modes of a subwavelength hole array have been studied in detail. By measuring the effects of hole array period, angular dispersion and concentration of the $J$-aggregate on the transmission of the array, the existence of a strong coupling regime is demonstrated with a Rabi splitting of 250 meV. This large splitting is explained not only by the high oscillator strength of the dye but also by the high local field amplitudes generated by surface plasmons of the metallic structure.

Chandra Orion Ultradeep Project: Observations and Source Lists

Abstract: We present a description of the data reduction methods and the derived catalog of more than 1600 X-ray point sources from the exceptionally deep 2003 January Chandra X-Ray Observatory (Chandra) observation of the Orion Nebula Cluster and embedded populations around OMC-1. The observation was obtained with Chandra's Advanced CCD Imaging Spectrometer (ACIS) and has been nicknamed the Chandra Orion Ultradeep Project (COUP). With an 838 ks exposure made over a continuous period of 13.2 days, the COUP observation provides the most uniform and comprehensive data set on the X-ray emission of normal stars ever obtained in the history of X-ray astronomy.

Distinct modes of ruminative self-focus: impact of abstract versus concrete rumination on problem solving in depression.

Abstract: One account for the negative effects of rumination on social problem solving (SPS) is the symptom-focus hypothesis, which proposes that focus on symptoms amplifies the vicious cycle between depressed mood and negative cognition. The authors tested a contrasting account, the reduced concreteness hypothesis, which postulates that the abstract thinking typical of rumination impairs SPS. In 40 depressed patients and 40 never-depressed controls, SPS was assessed before and after versions of symptom-focused rumination known to differentially induce abstract versus concrete self-focus (E. Watkins & J. D. Teasdale, 2001). As predicted by reduced concreteness theory, relative to abstract self-focus, concrete self-focus improved SPS in depressed patients, suggesting that the particular mode of symptom-focus, rather than symptom-focus per se, determines the effects of rumination on problem solving.

Myosin domain evolution and the primary divergence of eukaryotes

Abstract: Eukaryotic cells have two contrasting cytoskeletal and ciliary organizations. The simplest involves a single cilium-bearing centriole, nucleating a cone of individual microtubules (probably ancestral for unikonts: animals, fungi, Choanozoa and Amoebozoa). In contrast, bikonts (plants, chromists and all other protozoa) were ancestrally biciliate with a younger anterior cilium, converted every cell cycle into a dissimilar posterior cilium and multiple ciliary roots of microtubule bands. Here we show by comparative genomic analysis that this fundamental cellular dichotomy also involves different myosin molecular motors. We found 37 different protein domain combinations, often lineage-specific, and many previously unidentified. The sequence phylogeny and taxonomic distribution of myosin domain combinations identified five innovations that strongly support unikont monophyly and the primary bikont/unikont bifurcation. We conclude that the eukaryotic cenancestor (last common ancestor) had a cilium, mitochondria, pseudopodia, and myosins with three contrasting domain combinations and putative functions.

Technical note: Simple and robust removal of sun glint for mapping shallow‐water benthos

Abstract: Specular reflection of solar radiation on non-flat water surfaces is a serious confounding factor for benthic remote sensing in shallow-water environments. This problem was recently overcome by Hochberg et al., who provided an effective method for the removal of 'sun glint' from remotely sensed images by utilization of the brightness in a near-infrared (NIR) band. Application of the technique was shown to give an increase in the accuracy of benthic habitat classification. However, as presented, the method is sensitive to outlier pixels, requires a time-consuming masking of land and cloud, and is not formulated in a manner leading to ease of implementation. We present a revised version of the method, which is more robust, does not require masking and can be implemented very simply. The practical approach described here will hopefully expedite the routine adoption of this effective and simple technique throughout the aquatic remote sensing community.

Social influence in small groups: An interactive model of social identity formation

Abstract: The present paper tries to overcome the dualism of group-level vs. individualistic analysis of small group processes, by presenting a model of social identity formation that incorporates factors at both levels of analysis as well as their interaction. On the basis of prior theorising in the social identity tradition and a programme of research spanning several interactive group research paradigms, we suggest that within small groups a social identity can operate as a contextual given, which shapes the behaviour of individuals within the group, as much as the behaviour of individuals within the group can shape social identity. This proposal is supported by a programme of research into social influence within small interactive groups. This research explores deductive (top-down) processes through which existing identities influence group processes, but also shows a reciprocal influence through which intragroup discussion creates a sense of group identity in the apparent absence of any direct intergroup compa...

The origin of the initial mass function and its dependence on the mean Jeans mass in molecular clouds

Abstract: We investigate the dependence of stellar properties on the mean thermal Jeans mass in molecular clouds. We compare the results from the two largest hydrodynamical simulations of star formation to resolve the fragmentation process down to the opacity limit, the first of which was reported by Bate, Bonnell & Bromm. The initial conditions of the two calculations are identical except for the radii of the clouds, which are chosen so that the mean densities and mean thermal Jeans masses of the clouds differ by factors of 9 and 3, respectively. We find that the denser cloud, with the lower mean thermal Jeans mass, produces a higher proportion of brown dwarfs and has a lower characteristic (median) mass of the stars and brown dwarfs. This dependence of the initial mass function (IMF) on the density of the cloud may explain the observation that the Taurus star-forming region appears to be deficient in brown dwarfs when compared with the Orion Trapezium cluster. The new calculation also produces wide binaries (separations >20 au), one of which is a wide binary brown dwarf system. Based on the hydrodynamical calculations, we develop a simple accretion/ejection model for the origin of the IMF. In the model, all stars and brown dwarfs begin with the same mass (set by the opacity limit for fragmentation) and grow in mass until their accretion is terminated stochastically by their ejection from the cloud through dynamically interactions. The model predicts that the main variation of the IMF in different star-forming environments should be in the location of the peak (due to variations in the mean thermal Jeans mass of the cloud) and in the substellar regime. However, the slope of the IMF at high masses may depend on the dispersion in the accretion rates of protostars. Ke yw ords: accretion, accretion discs ‐ hydrodynamics ‐ binaries: general ‐ stars: formation ‐ stars: low-mass, brown dwarfs ‐ stars: luminosity function, mass function.

A social identity approach to trust: Interpersonal perception, group membership and trusting behaviour

Abstract: Trusting behaviour involves relinquishing control over outcomes valuable to the self. Previous research suggests that interpersonal perceptions of trustworthiness are closely related to this behaviour. The present research suggests that the more proximal determinant of trusting behaviour is the expectation that the other will reciprocate. Based on the Social Identity model of Deindividuation Effects (SIDE) model, reciprocity expectations may be created by interpersonal perceptions of trustworthiness or a shared group membership. To investigate this, group membership and individual identifiability were experimentally manipulated (N = 139): When individuals were not identifiable, trusting behaviour was based on expectations of reciprocity inferred from group membership, not on perceived trustworthiness. In contrast, personal identifiability fostered perceptions of trustworthiness for both in- and out-group members. In this case interpersonal trustworthiness enhanced expectations of reciprocity, which in turn increased trusting behaviour. Copyright © 2005 John Wiley & Sons, Ltd.

Mutations in hepatocyte nuclear factor‐1β and their related phenotypes

Abstract: Background: Hepatocyte nuclear factor-1 beta (HNF-1β) is a widely distributed transcription factor which plays a critical role in embryonic development of the kidney, pancreas, liver, and Mullerian duct. Thirty HNF-1β mutations have been reported in patients with renal cysts and other renal developmental disorders, young-onset diabetes, pancreatic atrophy, abnormal liver function tests, and genital tract abnormalities. Methods: We sequenced the HNF-1β gene in 160 unrelated subjects with renal disease, 40% of whom had a personal/family history of diabetes. Results: Twenty three different heterozygous HNF-1β mutations were identified in 23/160 subjects (14%), including 10 novel mutations (V61G, V110G, S148L, K156E, Q176X, R276Q, S281fsinsC, R295P, H324fsdelCA, Q470X). Seven (30%) cases were proven to be due to de novo mutations. Renal cysts were found in 19/23 (83%) patients (four with glomerulocystic kidney disease, GCKD) and diabetes in 11/23 (48%, while three other families had a family history of diabetes. Only 26% of families met diagnostic criteria for maturity-onset diabetes of the young (MODY) but 39% had renal cysts and diabetes (RCAD). We found no clear genotype/phenotype relationships. Conclusion: We report the largest series to date of HNF-1β mutations and confirm HNF-1β mutations as an important cause of renal disease. Despite the original description of HNF-1β as a MODY gene, a personal/family history of diabetes is often absent and the most common clinical manifestation is renal cysts. Molecular genetic testing for HNF-1β mutations should be considered in patients with unexplained renal cysts (including GCKD), especially when associated with diabetes, early-onset gout, or uterine abnormalities.

Auxetic behaviour from rotating rigid units

Abstract: Auxetic materials exhibit the unexpected feature of becoming fatter when stretched and narrower when compressed, in other words, they exhibit a negative Poisson's ratio. This counter-intuitive behaviour imparts many beneficial effects on the material's macroscopic properties that make auxetics superior to conventional materials in many commercial applications. Recent research suggests that auxetic be-haviour generally results from a cooperative effect between the material's internal structure (geometry setup) and the deformation mechanism it undergoes when submitted to a stress. Auxetic behaviour is also known to be scale-independent, and thus, the same geometry/deformation mechanism may operate at the macro-, micro- and nano- (molecular) level. A considerable amount of research has been focused on the ‘re-entrant honeycomb structure’ which exhibits auxetic behaviour if deformed through hinging at the joints or flexure of the ribs, and it was proposed that this ‘re-entrant’ geometry plays an impor- tant role in generating auxetic behaviour in various forms of materials ranging from nanostructured polymers to foams. This paper discusses an alternative mode of deformation involving ‘rotating rigid units’ which also results in negative Poisson's ratios. In its most ideal form, this mechanism may be construc- ted in two dimensions using ‘rigid polygons’ connected together through hinges at their vertices. On application of uniaxial loads, these ‘rigid polygons’ rotate with respect to each other to form a more open structure hence giving rise to a negative Poisson's ratio. This paper also discusses the role that ‘rotating rigid units’ are thought to have in various classes of materials to give rise to negative Poisson's ratios. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Perceived autonomy support in physical education and leisure-time physical activity : A cross-cultural evaluation of the trans-contextual model

Abstract: This study tested the replicability and cross-cultural invariance of a trans-contextual model of motivation across 4 samples from diverse cultures. The model proposes a motivational sequence in which perceived autonomy support (PAS) in physical education (PE) predicts autonomous motivation, intentions, and behavior in a leisure-time (LT) physical activity context. High-school pupils from Britain, Greece, Poland, and Singapore completed measures of PAS and autonomous motives in a PE context. Goodfitting path-analytic models supported the main hypotheses of the trans-contextual model in the British, Greek, and Singaporean samples. PAS in PE had significant total effects on autonomous motives in LT, except in the Polish sample. The effect of autonomous motives in LT on physical activity intentions and behavior was mediated by theory of planned behavior constructs in all samples. Results supported the main hypotheses of the trans-contextual model across cultures, although the effect of PAS was not pervasive in the Polish sample.

A MOPSO algorithm based exclusively on pareto dominance concepts

Abstract: In extending the Particle Swarm Optimisation methodology to multi-objective problems it is unclear how global guides for particles should be selected. Previous work has relied on metric information in objective space, although this is at variance with the notion of dominance which is used to assess the quality of solutions. Here we propose methods based exclusively on dominance for selecting guides from a non-dominated archive. The methods are evaluated on standard test problems and we find that probabilistic selection favouring archival particles that dominate few particles provides good convergence towards and coverage of the Pareto front. We demonstrate that the scheme is robust to changes in objective scaling. We propose and evaluate methods for confining particles to the feasible region, and find that allowing particles to explore regions close to the constraint boundaries is important to ensure convergence to the Pareto front.

Individuality and social influence in groups : Inductive and deductive routes to group identity

Abstract: A distinction between forms of social identity formation in small interactive groups is investigated. In groups in which a common identity is available or given, norms for individual behavior may be deduced from group properties (deductive identity). In groups in which interpersonal relations are central, a group identity may also be induced from individual group members' contributions, making individuality and individual distinctiveness a defining feature of the group (inductive identity). Two studies examined the prediction that depersonalization produced by anonymity has opposite effects for groups in which social identity has been induced or deduced. Results confirmed the prediction that depersonalization increases social influence in groups whose identity was more deductive. In contrast, depersonalization decreases social influence in inductive identity groups. Implications for the role of social identity in small groups are discussed. ((c) 2005 APA, all rights reserved).

How Do Institutions Affect Corruption and the Shadow Economy

Abstract: This paper analyzes a simple model that captures the relationship between institutional quality, the shadow economy and corruption. It shows that an improvement in institutional quality reduces the shadow economy and affects the corruption market. The exact relationship between corruption and institutional quality is, however, ambiguous and depends on the relative effectiveness of the institutional quality in the shadow and corruption markets. The predictions of the model are empirically tested - by means of Structural Equation Modelling that treats the shadow economy and the corruption market as latent variables - using data from OECD countries. The results show that an improvement in institutional quality reduces the shadow economy directly and corruption both directly and indirectly (through its effect on the shadow market).