Development of a Java-based Unified and Flexible Natural Language Discourse System

This paper outlines the design and development of a Java-based, unified and flexible natural language dialogue system that enables users to interact using natural language, e.g. speech. A number of software development issues are considered with the aim of designing an architecture that enables different discourse components to be readily and flexibly combined in a manner that permits information to be easily shared. Use of XML schemas assists this component interaction. The paper describes how a range of Java language features were employed to support the development of the architecture, providing an illustration of how a modern programming language makes tractable the development of a complex dialogue system.

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background
Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures.

Results
This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies.

Conclusion
The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap

Jigsaw Java: Intelligent, Automated Marking

The popularity of Computing degrees in the UK has been increasing significantly over the past number of years. In Northern Ireland, from 2007 to 2015, there has been a 40% increase in acceptances to Computer Science degrees with England seeing a 60% increase over the same period (UCAS, 2016). However, this is tainted as Computer Science degrees also continue to maintain the highest dropout rates.
In Queen’s University Belfast we currently have a Level 1 intake of over 400 students across a number of computing pathways. Our drive as staff is to empower and motivate the students to fully engage with the course content. All students take a Java programming module the aim of which is to provide an understanding of the basic principles of object-oriented design. In order to assess these skills, we have developed Jigsaw Java as an innovative assessment tool offering intelligent, semi-supervised automated marking of code.
Jigsaw Java allows students to answer programming questions using a drag-and-drop interface to place code fragments into position. Their answer is compared to the sample solution and if it matches, marks are allocated accordingly. However, if a match is not found then the corresponding code is executed using sample data to determine if its logic is acceptable. If it is, the solution is flagged to be checked by staff and if satisfactory is saved as an alternative solution. This means that appropriate marks can be allocated and should another student have submitted the same placement of code fragments this does not need to be executed or checked again. Rather the system now knows how to assess it.
Jigsaw Java is also able to consider partial marks dependent on code placement and will “learn” over time. Given the number of students, Jigsaw Java will improve the consistency and timeliness of marking.

The UMIST database for astrochemistry 1999

We report a new version of the UMIST database for astrochemistry. The previous (1995) version has been updated and its format has been revised. The database contains the rate coefficients, temperature ranges and - where available - the temperature dependence of 4113 gas-phase reactions important in astrophysical environments. The data involve 396 species and 12 elements. We have also tabulated permanent electric dipole moments of the neutral species and heats of formation. A new table lists the photo process cross sections (ionisation, dissociation, fragmentation) for a few species for which these quantities have been measured. Data for Deuterium fractionation are given in a separate table. Finally, a new online Java applet for data extraction has been created and its use is explained in detail. The detailed new datafiles and associated software are available on the World Wide Web at http://www.rate99.co.uk.

Systematic Usage of Embedded Modelling Languages in Automated Model Transformation Chains

Annotation of programs using embedded Domain-Specific Languages (embedded DSLs), such as the program annotation facility for the Java programming language, is a well-known practice in computer science. In this paper we argue for and propose a specialized approach for the usage of embedded Domain-Specific Modelling Languages (embedded DSMLs) in Model-Driven Engineering (MDE) processes that in particular supports automated many-step model transformation chains. It can happen that information defined at some point, using an embedded DSML, is not required in the next immediate transformation step, but in a later one. We propose a new approach of model annotation enabling flexible many-step transformation chains. The approach utilizes a combination of embedded DSMLs, trace models and a megamodel. We demonstrate our approach based on an example MDE process and an industrial case study.

Wrapping Legacy Applications into Grid Services: A Case Study of a Three Services Approach

In this paper, the support for legacy application, which is one of the important advantages of Grid computing, is presented. The ability to reuse existing codes/applications in combination with other Web/Internet technologies, such as Java, makes Grid computing a good choice for developers to wrap existing applications behind Intranet or the Internet. The approach developed can be used for migrating legacy applications into Grid Services, which speeds up the popularization of Grid technology. The approach is illustrated using a case study with detailed description of its implementation step by step. Globus Toolkit is utilized to develop the system.

In vitro modeling of respiratory syncytial virus infection of pediatric bronchial epithelium, the primary target of infection in vivo

Respiratory syncytial virus (RSV) is the major viral cause of severe pulmonary disease in young infants worldwide. However, the mechanisms by which RSV causes disease in humans remain poorly understood. To help bridge this gap, we developed an ex vivo/in vitro model of RSV infection based on well-differentiated primary pediatric bronchial epithelial cells (WD-PBECs), the primary targets of RSV infection in vivo. Our RSV/WD-PBEC model demonstrated remarkable similarities to hallmarks of RSV infection in infant lungs. These hallmarks included restriction of infection to noncontiguous or small clumps of apical ciliated and occasional nonciliated epithelial cells, apoptosis and sloughing of apical epithelial cells, occasional syncytium formation, goblet cell hyperplasia/metaplasia, and mucus hypersecretion. RSV was shed exclusively from the apical surface at titers consistent with those in airway aspirates from hospitalized infants. Furthermore, secretion of proinflammatory chemokines such as CXCL10, CCL5, IL-6, and CXCL8 reflected those chemokines present in airway aspirates. Interestingly, a recent RSV clinical isolate induced more cytopathogenesis than the prototypic A2 strain. Our findings indicate that this RSV/WD-PBEC model provides an authentic surrogate for RSV infection of airway epithelium in vivo. As such, this model may provide insights into RSV pathogenesis in humans that ultimately lead to successful RSV vaccines or therapeutics.

Distinct CCK-2 Receptor Conformations Associated with β-Arrestin-2 Recruitment or Phospholipase-C Activation Revealed by a Biased Antagonist

Seven-transmembrane receptors (7TMRs), also termed G protein-coupled receptors (GPCRs), form the largest class of cell surface membrane receptors, involving several hundred members in the human genome. Near 30% of marketed pharmacological agents target 7TMRs. 7TMRs adopt multiple conformations upon agonist binding. Biased agonists, in contrast to non-biased agonists, are believed to stabilize conformations preferentially activating either G-protein- or ß-arrestin-dependent signalling pathways. However, proof that cognate conformations of receptors display structural differences within their binding site where biased agonism initiates, are still lacking. Here, we show that a non-biased agonist, cholecystokinin (CCK) induces conformational states of the CCK2R activating Gq-protein-dependent pathway (CCK2RG) or recruiting ß-arrestin2 (CCK2Rß) that are pharmacologically and structurally distinct. Two structurally unrelated antagonists competitively inhibited both pathways. A third ligand (GV150,013X), acted as a high affinity competitive antagonist on CCK2RG but was nearly inefficient as inhibitor of CCK2Rß. Several structural elements on both GV150,013X and in CCK2R binding cavity, which hinder binding of GV150,013X only to the CCK2Rß were identified. At last, proximity between two conserved amino acids from transmembrane helices 3 and 7 interacting through sulphur-aromatic interaction was shown to be crucial for selective stabilization of the CCK2Rß state. These data establish structural evidences for distinct conformations of a 7TMR associated with ß-arrestin-2 recruitment or G-protein coupling and validate relevance of the design of biased ligands able to selectively target each functional conformation of 7TMRs.