PhyreStorm: A Web Server for Fast Structural Searches Against the PDB

AbstractThe identification of structurally similar proteins can provide a range of biological insights, and accordingly, the alignment of a query protein to a database of experimentally determined protein structures is a technique commonly used in the fields of structural and evolutionary biology. The PhyreStorm Web server has been designed to provide comprehensive, up-to-date and rapid structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user interface. It is intended that this facility will enable biologists inexpert in bioinformatics access to a powerful tool for exploring protein structure relationships beyond what can be achieved by sequence analysis alone. By partitioning the PDB into similar structures, PhyreStorm is able to quickly discard the majority of structures that cannot possibly align well to a query protein, reducing the number of alignments required by an order of magnitude. PhyreStorm is capable of finding 93±2% of all highly similar (TM-score>0.7) structures in the PDB for each query structure, usually in less than 60s. PhyreStorm is available at http://www.sbg.bio.ic.ac.uk/phyrestorm/

Climbing depth-bounded adjacent discrepancy search for solving hybrid flow shop scheduling problems with multiprocessor tasks

This paper considers multiprocessor task scheduling in a multistage hybrid flow-shop environment. The problem even in its simplest form is NP-hard in the strong sense. The great deal of interest for this problem, besides its theoretical complexity, is animated by needs of various manufacturing and computing systems. We propose a new approach based on limited discrepancy search to solve the problem. Our method is tested with reference to a proposed lower bound as well as the best-known solutions in literature. Computational results show that the developed approach is efficient in particular for large-size problems

What other's disappointment may do to selfish people: Emotion and social value orientation in a negotiation context

The authors examined whether individual differences in social value orientation moderate responses to other’s expressions of disappointment in negotiation. The literature suggested competing hypotheses: First, prosocials are more responsive to other’s disappointment because they have a greater concern for other; second, proselfs are more responsive because they see other’s disappointment as a threat to their own outcomes. Results of a computer-mediated negotiation in which a simulated opponent expressed disappointment, no emotion, or anger supported the second prediction: Proselfs conceded more to a disappointed opponent than to a neutral or angry one, whereas prosocials were unaffected by the other’s emotion. This effect was mediated by participants’ motivation to satisfy the other’s needs, which disappointment triggered more strongly in proselfs than in prosocials. Implications for theorizing on emotion, social value orientation, and negotiation are discussed

Accessing elite nurses for research: reflections on the theoretical and practical issues of telephone interviewing

Elite groups are interesting as they frequently are powerful (in terms of position, knowledge and influence) and enjoy considerable authority. It is important, therefore, to involve them in research concerned with understanding social contexts and processes. This is particularly pertinent in healthcare, where considerable strategic development and change are features of everyday practice that may be guided or perceived as being guided, by elites. This paper evolved from a study investigating the availability and role of nurses whose remit involved leading nursing research and development within acute NHS Trusts in two health regions in Southern England. The study design included telephone interviews with Directors of Nursing Services during which time the researchers engaged in a reflective analysis of their experiences of conducting research with an `elite' group. Important issues identified were the role of gatekeepers, engagement with elites and the use of the telephone interview method in this context. The paper examines these issues and makes a case for involving executive nurses in further research. The paper also offers strategies to help researchers design and implement telephone interview studies successfully to maximise access to the views and experiences of `hard to reach groups', such as elites, while minimising the associated disruption

Mouse Retinal Development: a Dark Horse Model for Systems Biology Research

The developing retina is an excellent model to study cellular fate determination and differentiation in the context of a complex tissue. Over the last decade, many basic principles and key genes that underlie these processes have been experimentally identified. In this review, we construct network models to summarize known gene interactions that underlie determination and fundamentally affect differentiation of each retinal cell type. These networks can act as a scaffold to assemble subsequent discoveries. In addition, these summary networks provide a rational segue to systems biology approaches necessary to understand the many events leading to appropriate cellular determination and differentiation in the developing retina and other complex tissues

Solving variational inequalities defined on a domain with infinitely many linear constraints

We study a variational inequality problem whose domain is defined by infinitely many linear inequalities. A discretization method and an analytic center based inexact cutting plane method are proposed. Under proper assumptions, the convergence results for both methods are given. We also provide numerical examples to illustrate the proposed method

Ultrasound attenuation in gap-anisotropic systems

Transverse ultrasound attenuation provides a weakly-coupled probe of momentum current correlations in electronic systems. We develop a simple theory for the interpretation of transverse ultrasound attenuation coefficients in systems with nodal gap anisotropy. Applying this theory we show how ultrasound can delineate between extended-s and d-wave scenarios for the cuprate superconductors.Comment: Uuencode file: 4 pages (Revtex), 3 figures. Some references adde

Milagrito: a TeV air-shower array

Milagrito, a large, covered water-Cherenkov detector, was the world's first air-shower-particle detector sensitive to cosmic gamma rays below 1 TeV. It served as a prototype for the Milagro detector and operated from February 1997 to May 1998. This paper gives a description of Milagrito, a summary of the operating experience, and early results that demonstrate the capabilities of this technique.Comment: 38 pages including 24 figure

A shooting algorithm for problems with singular arcs

In this article we propose a shooting algorithm for a class of optimal control problems for which all control variables appear linearly. The shooting system has, in the general case, more equations than unknowns and the Gauss-Newton method is used to compute a zero of the shooting function. This shooting algorithm is locally quadratically convergent if the derivative of the shooting function is one-to-one at the solution. The main result of this paper is to show that the latter holds whenever a sufficient condition for weak optimality is satisfied. We note that this condition is very close to a second order necessary condition. For the case when the shooting system can be reduced to one having the same number of unknowns and equations (square system) we prove that the mentioned sufficient condition guarantees the stability of the optimal solution under small perturbations and the invertibility of the Jacobian matrix of the shooting function associated to the perturbed problem. We present numerical tests that validate our method.Comment: No. RR-7763 (2011); Journal of Optimization, Theory and Applications, published as 'Online first', January 201

Nonlinear Integer Programming

Research efforts of the past fifty years have led to a development of linear integer programming as a mature discipline of mathematical optimization. Such a level of maturity has not been reached when one considers nonlinear systems subject to integrality requirements for the variables. This chapter is dedicated to this topic. The primary goal is a study of a simple version of general nonlinear integer problems, where all constraints are still linear. Our focus is on the computational complexity of the problem, which varies significantly with the type of nonlinear objective function in combination with the underlying combinatorial structure. Numerous boundary cases of complexity emerge, which sometimes surprisingly lead even to polynomial time algorithms. We also cover recent successful approaches for more general classes of problems. Though no positive theoretical efficiency results are available, nor are they likely to ever be available, these seem to be the currently most successful and interesting approaches for solving practical problems. It is our belief that the study of algorithms motivated by theoretical considerations and those motivated by our desire to solve practical instances should and do inform one another. So it is with this viewpoint that we present the subject, and it is in this direction that we hope to spark further research.Comment: 57 pages. To appear in: M. J\"unger, T. Liebling, D. Naddef, G. Nemhauser, W. Pulleyblank, G. Reinelt, G. Rinaldi, and L. Wolsey (eds.), 50 Years of Integer Programming 1958--2008: The Early Years and State-of-the-Art Surveys, Springer-Verlag, 2009, ISBN 354068274