Motivated proteins: a web application for studying small three-dimensional protein motifs

<b>BACKGROUND:</b> Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns.We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. <b>DESCRIPTION:</b> The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. <b>CONCLUSION:</b> Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schem

Rate-Based Transition Systems for Stochastic Process Calculi

A variant of Rate Transition Systems (RTS), proposed by Klin and Sassone, is introduced and used as the basic model for defining stochastic behaviour of processes. The transition relation used in our variant associates to each process, for each action, the set of possible futures paired with a measure indicating their rates. We show how RTS can be used for providing the operational semantics of stochastic extensions of classical formalisms, namely CSP and CCS. We also show that our semantics for stochastic CCS guarantees associativity of parallel composition. Similarly, in contrast with the original definition by Priami, we argue that a semantics for stochastic π-calculus can be provided that guarantees associativity of parallel composition

Positive practices : solution-focused and narrative therapeutic techniques with children with sexually harmful behaviours

This article explores the use of solution-focused and Narrative Therapeutic approaches with a boy who had sexually harmful behaviours. The paper will highlight the practical challenges of working with someone who is 'problem-saturated' through institutionalisation and who is also subjected to powerful discourses claiming the 'truth' about him. The use of solution-focused and Narrative Therapeutic principles and approaches will be demonstrated in the work described, in a way that allows the reader to reflect on how these may differ from modernist understandings and responses to this behaviour

Remarkable change of tunneling conductance in YBCO films in fields up to 32.4T

We studied the tunneling density of states in YBCO films under strong currents flowing along node directions. The currents were induced by fields of up to 32.4T parallel to the film surface and perpendicular to the $CuO_{2}$ planes. We observed a remarkable change in the tunneling conductance at high fields where the gap-like feature shifts discontinuously from 15meV to a lower bias of 11meV, becoming more pronounced as the field increases. The effect takes place in increasing fields around 9T and the transition back to the initial state occurs around 5T in decreasing fields. We argue that this transition is driven by surface currents induced by the applied magnetic field.Comment: 4 pages, 7 figure

On the emergent Semantic Web and overlooked issues

The emergent Semantic Web, despite being in its infancy, has already received a lotof attention from academia and industry. This resulted in an abundance of prototype systems and discussion most of which are centred around the underlying infrastructure. However, when we critically review the work done to date we realise that there is little discussion with respect to the vision of the Semantic Web. In particular, there is an observed dearth of discussion on how to deliver knowledge sharing in an environment such as the Semantic Web in effective and efficient manners. There are a lot of overlooked issues, associated with agents and trust to hidden assumptions made with respect to knowledge representation and robust reasoning in a distributed environment. These issues could potentially hinder further development if not considered at the early stages of designing Semantic Web systems. In this perspectives paper, we aim to help engineers and practitioners of the Semantic Web by raising awareness of these issues

Using local ecological knowledge to assess the status of the Critically Endangered Chinese giant salamander Andrias davidianus in Guizhou Province, China

The Critically Endangered Chinese giant salamander Andrias davidianus, the world's largest amphibian, is severely threatened by unsustainable exploitation of wild individuals. However, field data with which to assess the salamander's status, population trends, or exploitation across its geographical range are limited, and recent field surveys using standard ecological field techniques have typically failed to detect wild individuals. We conducted community-based fieldwork in three national nature reserves (Fanjingshan, Leigongshan and Mayanghe) in Guizhou Province, China, to assess whether local ecological knowledge constitutes a useful tool for salamander conservation. We collected a sample of dated salamander sighting records and associated data from these reserves for comparative assessment of the relative status of salamander populations across the region. Although Fanjingshan and Leigongshan are still priority sites for salamander conservation, few recent sightings were recorded in either reserve, and respondents considered that salamanders had declined locally at both reserves. The species may already be functionally extinct at Mayanghe. Although respondent data on threats to salamanders in Guizhou are more difficult to interpret, overharvesting was the most commonly suggested explanation for salamander declines, and it is likely that the growing salamander farming industry is the primary driver of salamander extraction from Guizhou's reserves. Questionnaire-based surveys can collect novel quantitative data that provide unique insights into the local status of salamander populations, and we advocate wide-scale incorporation of this research approach into future salamander field programmes

Vesicles in solutions of hard rods

The surface free energy of ideal hard rods near curved hard surfaces is determined to second order in curvature for surfaces of general shape. In accordance with previous results for spherical and cylindrical surfaces it is found that this quantity is non-analytical when one of the principal curvatures changes signs. This prohibits writing it in the common Helfrich form. It is shown that the non-analytical terms are the same for any aspect ratio of the rods. These results are used to find the equilibrium shape of vesicles immersed in solutions of rod-like (colloidal) particles. The presence of the particles induces a change in the equilibrium shape and to a shift of the prolate-oblate transition in the vesicle phase diagram, which are calculated within the framework of the spontaneous curvature model. As a consequence of the special form of the energy contribution due to the rods these changes cannot be accounted for by a simple rescaling of the elastic constants of the vesicle as for solutions of spherical colloids or polymers.Comment: 11 pages, 7 figures, submitted to Phys. Rev.

Sigref – A Symbolic Bisimulation Tool Box

We present a uniform signature-based approach to compute the most popular bisimulations. Our approach is implemented symbolically using BDDs, which enables the handling of very large transition systems. Signatures for the bisimulations are built up from a few generic building blocks, which naturally correspond to efficient BDD operations. Thus, the definition of an appropriate signature is the key for a rapid development of algorithms for other types of bisimulation. We provide experimental evidence of the viability of this approach by presenting computational results for many bisimulations on real-world instances. The experiments show cases where our framework can handle state spaces efficiently that are far too large to handle for any tool that requires an explicit state space description. This work was partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS). See www.avacs.org for more information

Cooperative Carbon Dioxide Adsorption in Alcoholamine- and Alkoxyalkylamine-Functionalized Metal-Organic Frameworks.

A series of structurally diverse alcoholamine- and alkoxyalkylamine-functionalized variants of the metal-organic framework Mg2 (dobpdc) are shown to adsorb CO2 selectively via cooperative chain-forming mechanisms. Solid-state NMR spectra and optimized structures obtained from van der Waals-corrected density functional theory calculations indicate that the adsorption profiles can be attributed to the formation of carbamic acid or ammonium carbamate chains that are stabilized by hydrogen bonding interactions within the framework pores. These findings significantly expand the scope of chemical functionalities that can be utilized to design cooperative CO2 adsorbents, providing further means of optimizing these powerful materials for energy-efficient CO2 separations

Interfaces in Diblocks: A Study of Miktoarm Star Copolymers

We study AB$_n$ miktoarm star block copolymers in the strong segregation limit, focussing on the role that the AB interface plays in determining the phase behavior. We develop an extension of the kinked-path approach which allows us to explore the energetic dependence on interfacial shape. We consider a one-parameter family of interfaces to study the columnar to lamellar transition in asymmetric stars. We compare with recent experimental results. We discuss the stability of the A15 lattice of sphere-like micelles in the context of interfacial energy minimization. We corroborate our theory by implementing a numerically exact self-consistent field theory to probe the phase diagram and the shape of the AB interface.Comment: 12 pages, 11 included figure