An automated graphics tool for comparative genomics: the Coulson plot generator.

BACKGROUND: Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. RESULTS: We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. CONCLUSIONS: CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its original purpose, the software can be used to visualize any dataset where entity occupancy is compared between different classes. AVAILABILITY: CPG software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox.com/u/6701906/Web/Sites/Labsite/CPG.html.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins.

BACKGROUND: In membrane trafficking, the mechanisms ensuring vesicle fusion specificity remain to be fully elucidated. Early models proposed that specificity was encoded entirely by SNARE proteins; more recent models include contributions from Rab proteins, Syntaxin-binding (SM) proteins and tethering factors. Most information on membrane trafficking derives from an evolutionarily narrow sampling of model organisms. However, considering factors from a wider diversity of eukaryotes can provide both functional information on core systems and insight into the evolutionary history of the trafficking machinery. For example, the major Qa/syntaxin SNARE families are present in most eukaryotic genomes and likely each evolved via gene duplication from a single ancestral syntaxin before the existing eukaryotic groups diversified. This pattern is also likely for Rabs and various other components of the membrane trafficking machinery. RESULTS: We performed comparative genomic and phylogenetic analyses, when relevant, on the SM proteins and components of the tethering complexes, both thought to contribute to vesicle fusion specificity. Despite evidence suggestive of secondary losses amongst many lineages, the tethering complexes are well represented across the eukaryotes, suggesting an origin predating the radiation of eukaryotic lineages. Further, whilst we detect distant sequence relations between GARP, COG, exocyst and DSL1 components, these similarities most likely reflect convergent evolution of similar secondary structural elements. No similarity is found between the TRAPP and HOPS complexes and the other tethering factors. Overall, our data favour independent origins for the various tethering complexes. The taxa examined possess at least one homologue of each of the four SM protein families; since the four monophyletic families each encompass a wide diversity of eukaryotes, the SM protein families very likely evolved before the last common eukaryotic ancestor (LCEA). CONCLUSION: These data further support a highly complex LCEA and indicate that the basic architecture of the trafficking system is remarkably conserved and ancient, with the SM proteins and tethering factors having originated very early in eukaryotic evolution. However, the independent origin of the tethering complexes suggests a novel pattern for increasing complexity in the membrane trafficking system, in addition to the pattern of paralogous machinery elaboration seen thus far.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

A Statistical Method for Reassociating Human Tali and Calcanei from a Commingled Context.

In a commingled context, assessing that a talus and a calcaneus correspond to the same individual could become a primary step for accurately sorting human remains. For this purpose, the lengths and widths of the trochlea, posterior calcaneal articular surface, and posterior talar articular surface were measured in 197 individuals (105 males, 92 females) from the Athens Collection. A total of 12 highly accurate equations for reassociating tali and calcanei were developed, using simple and multiple linear regression analysis and they were found to be suitable for sorting commingled human remains. Bilateral asymmetry and sex did not have an effect on the accuracy of the method

Experiments on Multidimensional Solitons

This article presents an overview of experimental efforts in recent years related to multidimensional solitons in Bose-Einstein condensates. We discuss the techniques used to generate and observe multidimensional nonlinear waves in Bose-Einstein condensates with repulsive interactions. We further summarize observations of planar soliton fronts undergoing the snake instability, the formation of vortex rings, and the emergence of hybrid structures.Comment: review paper, to appear as Chapter 5b in "Emergent Nonlinear Phenomena in Bose-Einstein Condensates: Theory and Experiment," edited by P. G. Kevrekidis, D. J. Frantzeskakis, and R. Carretero-Gonzalez (Springer-Verlag

Bunge’s Mathematical Structuralism Is Not a Fiction

In this paper, I explore Bunge’s fictionism in philosophy of mathematics. After an overview of Bunge’s views, in particular his mathematical structuralism, I argue that the comparison between mathematical objects and fictions ultimately fails. I then sketch a different ontology for mathematics, based on Thomasson’s metaphysical work. I conclude that mathematics deserves its own ontology, and that, in the end, much work remains to be done to clarify the various forms of dependence that are involved in mathematical knowledge, in particular its dependence on mental/brain states and material objects

How Valid Are Measures of Children’s Self-Concept/ Self-Esteem? Factors and Content Validity in Three Widely Used Scales

Children’s self-esteem/self-concept, a core psychological construct, has been measured in an overwhelming number of studies, and the widespread use of such measures should indicate they have well-established content validity, internal consistency and factor structures. This study, sampling a demographically representative cohort in late childhood/early adolescence in Dublin, Ireland (total n = 651), examined three major self-esteem/self-concept scales designed for late childhood/early adolescence: Piers-Harris Self-Concept Scale for Children 2 (Piers et al. 2002), Self-Description Questionnaire I (Marsh 1992) and Self-Perception Profile for Children (Harter 1985). It also examined findings in light of the salient self factors identified by participants in a linked mixed-methods study. The factor structure of Piers-Harris Self-Concept Scale was not replicated. The Self-Description Questionnaire I and Self-Perception Profile for Children were replicated only in part although in similar ways. In all three scales, a global/ appearance self evaluation factor accounted for the largest variance in factor analyses. Sport/athletic ability, school ability, school enjoyment, maths and reading ability/enjoyment, behaviour, peer popularity, and parent factors were also identified but did not always reflect existing scale structures. Notably, the factors extracted, or items present in these scales, often did not reflect young people’s priorities, such as friendship over popularity, the importance of family and extended family members, and the significance of incremental personal mastery in activities rather than assessing oneself as comparatively good at preferred activities. The findings raise questions about how self-esteem/self-concept scales are used and interpreted in research with children and young people

Prevalence of purging at age 16 and associations with negative outcomes among girls in three community-based cohorts.

The comorbidity of purging behaviours, such as vomiting, inappropriate use of laxatives, diuretics or slimming medications, has been examined in literature. However, most studies do not include adolescents, individuals who purge in the absence of binge eating, or those purging at subclinical frequency. This study examines the prevalence of purging among 16-year-old girls across three countries and their association with substance use and psychological comorbidity

Refining the content and design of an alcohol reduction app, Drink Less, to improve its usability and effectiveness: a mixed methods approach

Background: Digital interventions have the potential to reduce alcohol consumption, although evidence on the effectiveness of apps is lacking. Drink Less is a popular, evidence-informed app with good usability, putting it in a strong position to be improved upon prior to conducting a confirmatory evaluation. This paper describes the process of refining Drink Less to improve its usability and likely effectiveness. // Methods: The refinement consisted of three phases and involved qualitative and quantitative (mixed) methods: i) identifying changes to app content, based on findings from an initial evaluation of Drink Less, an updated review of digital alcohol interventions and a content analysis of user feedback; ii) designing new app modules with public input and a consultation with app developers and researchers; and iii) improving the app’s usability through user testing. Results: As a result of the updated review of digital alcohol interventions and user feedback analysis in Phase 1, three new modules: ‘Behaviour Substitution’, ‘Information about Antecedents’ and ‘Insights’, were added to the app. One existing module – ‘Identity Change’ – was removed based on the initial evaluation of Drink Less. Phases 2 and 3 resulted in changes to existing features, such as improving the navigational structure and onboarding process, and clarifying how to edit drinks and goals. // Conclusions: A mixed methods approach was used to refine the content and design of Drink Less, providing insights into how to improve its usability and likely effectiveness. Drink Less is now ready for a confirmatory evaluation