Development of user-friendly, high throughput screening for ligands and inhibitors of carbohydrate modifying enzymes

This paper describes the impact of cloud computing and the use of GPUs on the performance of Autodock and Gromacs respectively. Cloud computing was applicable to reducing the ‘‘tail’’ seen in running Autodock on desktop grids and the GPU version of Gromacs showed significant improvement over the CPU version. A large (200,000 compounds) library of small molecules, seven sialic acid analogues of the putative substrate and 8000 sugar molecules were converted into pdbqt format and used to interrogate the Trichomonas vaginalis neuraminidase using Autodock Vina. Good binding energy was noted for some of the small molecules (~-9 kcal/mol), but the sugars bound with affinity of less than -7.6 kcal/mol. The screening of the sugar library resulted in a ‘‘top hit’’ with a-2,3-sialyllacto-N-fucopentaose III, a derivative of the sialyl Lewisx structure and a known substrate of the enzyme. Indeed in the top 100 hits 8 were related to this structure. A comparison of Autodock Vina and Autodock 4.2 was made for the high affinity small molecules and in some cases the results were superimposable whereas in others, the match was less good. The validation of this work will require extensive ‘‘wet lab’’ work to determine the utility of the workflow in the prediction of potential enzyme inhibitors.

Just noticeable differences in perceived image contrast with changes in displayed image size

An evaluation of the change in perceived image contrast with changes in displayed image size was carried out. This was achieved using data from four psychophysical investigations, which employed techniques to match the perceived contrast of displayed images of five different sizes. A total of twenty-four S-shape polynomial functions were created and applied to every original test image to produce images with different contrast levels. The objective contrast related to each function was evaluated from the gradient of the mid-section of the curve (gamma). The manipulation technique took into account published gamma differences that produced a just-noticeable-difference (JND) in perceived contrast. The filters were designed to achieve approximately half a JND, whilst keeping the mean image luminance unaltered. The processed images were then used as test series in a contrast matching experiment. Sixty-four natural scenes, with varying scene content acquired under various illumination conditions, were selected from a larger set captured for the purpose. Results showed that the degree of change in contrast between images of different sizes varied with scene content but was not as important as equivalent perceived changes in sharpness.

A model for information retrieval driven by conceptual spaces

A retrieval model describes the transformation of a query into a set of documents. The question is: what drives this transformation? For semantic information retrieval type of models this transformation is driven by the content and structure of the semantic models. In this case, Knowledge Organization Systems (KOSs) are the semantic models that encode the meaning employed for monolingual and cross-language retrieval. The focus of this research is the relationship between these meanings’ representations and their role and potential in augmenting existing retrieval models effectiveness. The proposed approach is unique in explicitly interpreting a semantic reference as a pointer to a concept in the semantic model that activates all its linked neighboring concepts. It is in fact the formalization of the information retrieval model and the integration of knowledge resources from the Linguistic Linked Open Data cloud that is distinctive from other approaches. The preprocessing of the semantic model using Formal Concept Analysis enables the extraction of conceptual spaces (formal contexts)that are based on sub-graphs from the original structure of the semantic model. The types of conceptual spaces built in this case are limited by the KOSs structural relations relevant to retrieval: exact match, broader, narrower, and related. They capture the definitional and relational aspects of the concepts in the semantic model. Also, each formal context is assigned an operational role in the flow of processes of the retrieval system enabling a clear path towards the implementations of monolingual and cross-lingual systems. By following this model’s theoretical description in constructing a retrieval system, evaluation results have shown statistically significant results in both monolingual and bilingual settings when no methods for query expansion were used. The test suite was run on the Cross-Language Evaluation Forum Domain Specific 2004-2006 collection with additional extensions to match the specifics of this model.

Context-aware Approach for Determining the Threshold Price in Name-Your-Own-Price Channels

Key feature of a context-aware application is the ability to adapt based on the change of context. Two approaches that are widely used in this regard are the context-action pair mapping where developers match an action to execute for a particular context change and the adaptive learning where a context-aware application refines its action over time based on the preceding action’s outcome. Both these approaches have limitation which makes them unsuitable in situations where a context-aware application has to deal with unknown context changes. In this paper we propose a framework where adaptation is carried out via concurrent multi-action evaluation of a dynamically created action space. This dynamic creation of the action space eliminates the need for relying on the developers to create context-action pairs and the concurrent multi-action evaluation reduces the adaptation time as opposed to the iterative approach used by adaptive learning techniques. Using our reference implementation of the framework we show how it could be used to dynamically determine the threshold price in an e-commerce system which uses the name-your-own-price (NYOP) strategy.

Charabancs and Social Class in 1930s Britain

The renowned writer J. B. Priestley suggested in 1934 that the motor-coach had annihilated the old distinction between rich and poor passengers in Britain. This article considers how true this was by examining the relationship between charabancs, motor coaches and class. It shows that this important vehicle of inter-war working class mobility had a complicated relationship with class, identifying three distinct forms of this method of travel. It positions the charabanc alongside historical responses to unwelcome steamer and railway day-trippers, and examines how resorts provided separate class-based entertainment for these holidaymakers. Using the case study of a new charabancwelcoming pub, the Prospect Inn, it proposes that, in the late 1930s, some pubs were beginning to offer charabanc customers facilities that were almost the match of their middle class equivalent. Motor coaches and charabancs contributed to the process of social convergence in inter-war Britain.

Adulteration and Poor Quality of Ginkgo biloba Supplements

Adulteration of Ginkgo products sold as unregistered supplements within the very large market of Ginkgo products (reputedly £650 million annually) through the post-extraction addition of cheaper (e.g. buckwheat derived) rutin is suspected to allow sub-standard products to appear satisfactory to third parties, e.g. secondary buyers along the value chain or any regulatory authorities. This study was therefore carried out to identify products that did not conform to their label specification and may have been actively adulterated to enable access to the global markets. 500 MHz Bruker NMR spectroscopy instrumentation combined with Topspin version 3.2 and a CAMAG HPTLC system (HPTLC Association for the analysis of Ginkgo biloba leaf) were used to generate NMR spectra (focusing on the 6–8 ppm region for analysis) and chromatograms, respectively. Out of the 35 samples of Ginkgo biloba analysed, 33 were found to contain elevated levels of rutin and/or quercetin, or low levels of Ginkgo metabolites when compared with the reference samples. Samples with disproportional levels of rutin or quercetin compared with other gingko metabolites are likely to be adulterated, either by accident or intentionally, and those samples with low or non-existent gingko metabolite content may have been produced using poor extraction techniques. Only two of the investigated samples were found to match with the High-Performance Thin-Layer Chromatography (HPTLC) fingerprint of the selected reference material. All others deviated significantly. One product contained a 5-hydroxytryptophan derivative, which is not a natural constituent of Ginkgo biloba. Overall, these examples either suggest a poor extraction technique or deliberate adulteration along the value chain. Investigating the ratio of different flavonoids e.g. quercetin and kaempferol using NMR spectroscopy and HPTLC will provide further evidence as to the degree and kind of adulteration of Gingko supplements. From a consumer perspective the equivalence in identity and overall quality of the products needs to be guaranteed for supplements too and not only for products produced according to a quality standard or pharmacopoeial monograph.