Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

Liquid–Vapor Interface of Formic Acid Solutions in Salt Water: A Comparison of Macroscopic Surface Tension and Microscopic in Situ X-ray Photoelectron Spectroscopy Measurements

The liquid–vapor interface is difficult to access experimentally but is of interest from a theoretical and applied point of view and has particular importance in atmospheric aerosol chemistry. Here we examine the liquid–vapor interface for mixtures of water, sodium chloride, and formic acid, an abundant chemical in the atmosphere. We compare the results of surface tension and X-ray photoelectron spectroscopy (XPS) measurements over a wide range of formic acid concentrations. Surface tension measurements provide a macroscopic characterization of solutions ranging from 0 to 3 M sodium chloride and from 0 to over 0.5 mole fraction formic acid. Sodium chloride was found to be a weak salting out agent for formic acid with surface excess depending only slightly on salt concentration. In situ XPS provides a complementary molecular level description about the liquid–vapor interface. XPS measurements over an experimental probe depth of 51 Å gave the C 1s to O 1s ratio for both total oxygen and oxygen from water. XPS also provides detailed electronic structure information that is inaccessible by surface tension. Density functional theory calculations were performed to understand the observed shift in C 1s binding energies to lower values with increasing formic acid concentration. Part of the experimental −0.2 eV shift can be assigned to the solution composition changing from predominantly monomers of formic acid to a combination of monomers and dimers; however, the lack of an appropriate reference to calibrate the absolute BE scale at high formic acid mole fraction complicates the interpretation. Our data are consistent with surface tension measurements yielding a significantly more surface sensitive measurement than XPS due to the relatively weak propensity of formic acid for the interface. A simple model allowed us to replicate the XPS results under the assumption that the surface excess was contained in the top four angstroms of solution.

Working at the interface : the descriptive relevance of Grunig and Hunt’s theories to public relations practices in south east Queensland schools

This article examines the relevance of James Grunig and Todd Hunt’s (1984) theories to public relations practitioners’ roles in south east Queensland schools. It focuses in particular on the two-way symmetric model in this context. The geographical boundaries of the research mean that this article is intended primarily as an exploratory, descriptive analysis of a specific area rather than an exhaustive treatise on the general topic of public relations in Australian schools. However, it is hoped that it will prove useful in identifying bases for further study and discussion.

Cipher cities : effective user interface design for building a digital social network around location-based gaming

In this paper we explore what is required of a User Interface (UI) design in order to encourage participation around playing and creating Location-Based Games (LBGs). To base our research in practice, we present Cipher Cities, a web based system. Through the design of this system, we investigate how UI design can provide tools for complex content creation to compliment and encourage the use of mobile phones for designing, distributing, and playing LBGs. Furthermore we discuss how UI design can promote and support socialisation around LBGs through the design of functional interface components and services such as groups, user profiles, and player status listings.

Psychological predictors of the propensity to omit short-response items on a high-stakes achievement test

This article presents the findings of a study of the psychological variables that discriminate between high and low omitters on a high-stakes achievement test using a short-response format. Data were obtained from a questionnaire administered to a random sample (N = 1,908) of students prior to sitting the 1997 Queensland Core Skills (QCS) Test (N = 29,273). Fourteen psychological variables were measured including test anxiety (four subscales), emotional stability, achievement motivation, self-esteem, academic self-concept, self-estimate of ability, locus of control (three subscales), and approaches to learning (two subscales). The results were analyzed using descriptive discriminant analysis and suggested that the psychological predictors of the propensity to omit short-response items include test-irrelevant thinking and academic self-concept, with sex of candidate being a mediating variable.

The quality of interface design for educational courseware development in Malaysian educational context

Interactive educational courseware has been adopted in diverse education sectors such as primary, secondary, tertiary education, vocational and professional training. In Malaysian educational context, the ministry of education has implemented Smart School Project that aims to increase high level of academic achievement in primary and secondary schools by using interactive educational courseware. However, many researchers have reported that many coursewares fail to accommodate the learner and teacher needs. In particular, the interface design is not appropriately designed in terms of quality of learning. This paper reviews educational courseware development process in terms of defining quality of interface design and suggests a conceptual model of interface design through the integration of design components and interactive learning experience into the development process. As a result, it defines the concept of interactive learning experience in a more practical approach in order to implement each stage of the development process in a seamless and integrated way.