An optimized TOPS+ comparison method for enhanced TOPS models

This article has been made available through the Brunel Open Access Publishing Fund.Background Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+. Results We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method. Conclusions Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun

Rarity of monodominance in hyperdiverse Amazonian forests.

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors

"Give me some space" : exploring youth to parent aggression and violence

A small scale qualitative project, undertaken by an interdisciplinary domestic violence research group involving academic researchers and research assistants, with colleagues from Independent Domestic Abuse Services (IDAS), investigated youth aggression and violence against parents. Following the literature review, data was generated through several research conversations with young people (n = 2), through semi-structured interviews with mothers (n = 3) and practitioners (n = 5), and through a practitioner focus group (n = 8). Thematic analysis and triangulation of the data from parents, practitioners and young people, elicited interconnected and complex overarching themes. Young people could be both victim and perpetrator. The witnessing or experiencing of domestic aggression and violence raised the concept of ‘bystander children’. The impact of young people experiencing familial violence was underestimated by parents. For practitioners, the effects of working with domestic violence was shown to be significant - both positively and negatively

Material reutilization cycles across industries and production lines

The concept of Industrial Symbiosis aims at organizing industrial activity like a living ecosystem where the by-product outputs of one process are used as valuable raw material input for another process. A significant method for the systematic planning of Industrial Symbiosis is found in input–output matching, which is aimed at collecting material input and output data from companies, and using the results to establish links across industries. The collection and classification of data is crucial to the development of synergies in Industrial Symbiosis. Public and private institutions involved in the planning and development of Industrial Symbiosis rely however on manual interpretation of information in the course of creating synergies. Yet, the evaluation and analysis of these data sources on Industrial Symbiosis topics is a tall order. Within this chapter a method is presented which describes value creation activities according to the Value Creation Module (VCM). They are assessed before they are integrated in Value Creation Networks (VCNs), where alternative uses for by-products are proposed by means of iterative input-output matching of selected value creation factors

Mapping the disease-specific LupusQoL to the SF-6D

Purpose To derive a mapping algorithm to predict SF-6D utility scores from the non-preference-based LupusQoL and test the performance of the developed algorithm on a separate independent validation data set. Method LupusQoL and SF-6D data were collected from 320 patients with systemic lupus erythematosus (SLE) attending routine rheumatology outpatient appointments at seven centres in the UK. Ordinary least squares (OLS) regression was used to estimate models of increasing complexity in order to predict individuals’ SF-6D utility scores from their responses to the LupusQoL questionnaire. Model performance was judged on predictive ability through the size and pattern of prediction errors generated. The performance of the selected model was externally validated on an independent data set containing 113 female SLE patients who had again completed both the LupusQoL and SF-36 questionnaires. Results Four of the eight LupusQoL domains (physical health, pain, emotional health, and fatigue) were selected as dependent variables in the final model. Overall model fit was good, with R2 0.7219, MAE 0.0557, and RMSE 0.0706 when applied to the estimation data set, and R2 0.7431, MAE 0.0528, and RMSE 0.0663 when applied to the validation sample. Conclusion This study provides a method by which health state utility values can be estimated from patient responses to the non-preference-based LupusQoL, generalisable beyond the data set upon which it was estimated. Despite concerns over the use of OLS to develop mapping algorithms, we find this method to be suitable in this case due to the normality of the SF-6D data

X-Ray Spectroscopy of Stars

(abridged) Non-degenerate stars of essentially all spectral classes are soft X-ray sources. Low-mass stars on the cooler part of the main sequence and their pre-main sequence predecessors define the dominant stellar population in the galaxy by number. Their X-ray spectra are reminiscent, in the broadest sense, of X-ray spectra from the solar corona. X-ray emission from cool stars is indeed ascribed to magnetically trapped hot gas analogous to the solar coronal plasma. Coronal structure, its thermal stratification and geometric extent can be interpreted based on various spectral diagnostics. New features have been identified in pre-main sequence stars; some of these may be related to accretion shocks on the stellar surface, fluorescence on circumstellar disks due to X-ray irradiation, or shock heating in stellar outflows. Massive, hot stars clearly dominate the interaction with the galactic interstellar medium: they are the main sources of ionizing radiation, mechanical energy and chemical enrichment in galaxies. High-energy emission permits to probe some of the most important processes at work in these stars, and put constraints on their most peculiar feature: the stellar wind. Here, we review recent advances in our understanding of cool and hot stars through the study of X-ray spectra, in particular high-resolution spectra now available from XMM-Newton and Chandra. We address issues related to coronal structure, flares, the composition of coronal plasma, X-ray production in accretion streams and outflows, X-rays from single OB-type stars, massive binaries, magnetic hot objects and evolved WR stars.Comment: accepted for Astron. Astrophys. Rev., 98 journal pages, 30 figures (partly multiple); some corrections made after proof stag

Epítome de la crónica del Rey Don Iván el Segundo de Castilla

Sign. : [calderón]\p6\s, A-Z\p6\s, Aa-Hh\p6\s.Desde p.308 a 342 "Libro quinto. Claros varones que florecieron en España... reducido a un breve catálogo por el noble caballero Fernán Pérez de Guzmán, corregido y adicionado por el Doctor Lorenço Galindez de Carvajal..."Esc. del editor Gabriel de LeónAntep.Texto a dos col.Port. a dos tintas.Copia digital. Valladolid : Junta de Castilla y León. Consejería de Cultura y Turismo, 2009-201

Linking Ethnic Identification to Organisational Solidarity

This paper investigates the process through which ethnic identification (EI) influences employees’ sense of organisational solidarity (OS). A survey of 1525 employees working in different ministries of a state government in Nigeria was collected and analysed by means of a regression to investigate EI-OS relationships. As expected, EI was a significant determinant of OS with co-worker social support explaining the rationale for EI-OS relationship. The conceptualisation of OS as a composite construct that manifest in employees’ self-efficacy, organisational self-identity and employee voice behaviours is novel. The study provides evidence from an under researched area to further generalise existing debates

Asteroseismology and Interferometry

Asteroseismology provides us with a unique opportunity to improve our understanding of stellar structure and evolution. Recent developments, including the first systematic studies of solar-like pulsators, have boosted the impact of this field of research within Astrophysics and have led to a significant increase in the size of the research community. In the present paper we start by reviewing the basic observational and theoretical properties of classical and solar-like pulsators and present results from some of the most recent and outstanding studies of these stars. We centre our review on those classes of pulsators for which interferometric studies are expected to provide a significant input. We discuss current limitations to asteroseismic studies, including difficulties in mode identification and in the accurate determination of global parameters of pulsating stars, and, after a brief review of those aspects of interferometry that are most relevant in this context, anticipate how interferometric observations may contribute to overcome these limitations. Moreover, we present results of recent pilot studies of pulsating stars involving both asteroseismic and interferometric constraints and look into the future, summarizing ongoing efforts concerning the development of future instruments and satellite missions which are expected to have an impact in this field of research.Comment: Version as published in The Astronomy and Astrophysics Review, Volume 14, Issue 3-4, pp. 217-36

Activity and Habitat Use of Chimpanzees (Pan troglodytes verus) in the Anthropogenic Landscape of Bossou, Guinea, West Africa

Many primate populations inhabit anthropogenic landscapes. Understanding their long-term ability to persist in such environments and associated real and perceived risks for both primates and people is essential for effective conservation planning. Primates in forest–agricultural mosaics often consume cultivars to supplement their diet, leading to potentially negative encounters with farmers. When crossing roads, primates also face the risk of encounters with people and collision with vehicles. Chimpanzees (Pan troglodytes verus) in Bossou, Guinea, West Africa, face such risks regularly. In this study, we aimed to examine their activity budget across habitat types and the influence of anthropogenic risks associated with cultivated fields, roads, and paths on their foraging behavior in noncultivated habitat. We conducted 6-h morning or afternoon follows daily from April 2012 to March 2013. Chimpanzees preferentially used forest habitat types for traveling and resting and highly disturbed habitat types for socializing. Wild fruit and crop availability influenced seasonal habitat use for foraging. Overall, chimpanzees preferred mature forest for all activities. They showed a significant preference for foraging at >200 m from cultivated fields compared to 0–100 m and 101–200 m, with no effect of habitat type or season, suggesting an influence of associated risk. Nevertheless, the chimpanzees did not actively avoid foraging close to roads and paths. Our study reveals chimpanzee reliance on different habitat types and the influence of human-induced pressures on their activities. Such information is critical for the establishment of effective land use management strategies in anthropogenic landscapes