Automatic prediction of functional site regions in low-resolution protein structures

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.

How reward modulates mimicry: EMG evidence of greater automatic facial mimicry of more rewarding faces

Spontaneous mimicry is a marker of empathy. Conditions characterized by reduced spontaneous mimicry (e.g., autism) also display deficits in sensitivity to social rewards. We tested if spontaneous mimicry of socially rewarding stimuli (happy faces) depends on the reward value of stimuli in 32 typical participants. An evaluative conditioning paradigm was used to associate different reward values with neutral target faces. Subsequently, electromyographic activity over the Zygomaticus Major was measured whilst participants watched video clips of the faces making happy expressions. Higher Zygomaticus Major activity was found in response to happy faces conditioned with high reward versus low reward. Moreover, autistic traits in the general population modulated the extent of spontaneous mimicry of happy faces. This suggests a link between reward and spontaneous mimicry and provides a possible underlying mechanism for the reduced response to social rewards seen in autism.

Automatic keyphrase extraction: a comparison of methods

There are many published methods available for creating keyphrases for documents. Previous work in the field has shown that in a significant proportion of cases author selected keyphrases are not appropriate for the document they accompany. This requires the use of such automated methods to improve the use of keyphrases. Often the keyphrases are not updated when the focus of a paper changes or include keyphrases that are more classificatory than explanatory. The published methods are all evaluated using different corpora, typically one relevant to their field of study. This not only makes it difficult to incorporate the useful elements of algorithms in future work but also makes comparing the results of each method inefficient and ineffective. This paper describes the work undertaken to compare five methods across a common baseline of six corpora. The methods chosen were term frequency, inverse document frequency, the C-Value, the NC-Value, and a synonym based approach. These methods were compared to evaluate performance and quality of results, and to provide a future benchmark. It is shown that, with the comparison metric used for this study Term Frequency and Inverse Document Frequency were the best algorithms, with the synonym based approach following them. Further work in the area is required to determine an appropriate (or more appropriate) comparison metric.

Between writing and type: the stencil letter

An exhibition of stencil letters from the 18th century to the present day. Co-curated by Eric Kindel and Fred Smeijers, the exhibition featured a wide selection of stencil letters in the context of historical artefacts, documents and ephemera, including stencil plates and stencilling devices, specimens and catalogues and patent inventions. The exhibition also introduced a series of new stencil fonts designed by Maurice Göldner, Pierre Pané-Farré and Fred Smeijers. The design of each font made reference to and was informed by the historical material.

Automatic near real-time selection of flood water levels from high resolution Synthetic Aperture Radar images for assimilation into hydraulic models: a case study

Flood extents caused by fluvial floods in urban and rural areas may be predicted by hydraulic models. Assimilation may be used to correct the model state and improve the estimates of the model parameters or external forcing. One common observation assimilated is the water level at various points along the modelled reach. Distributed water levels may be estimated indirectly along the flood extents in Synthetic Aperture Radar (SAR) images by intersecting the extents with the floodplain topography. It is necessary to select a subset of levels for assimilation because adjacent levels along the flood extent will be strongly correlated. A method for selecting such a subset automatically and in near real-time is described, which would allow the SAR water levels to be used in a forecasting model. The method first selects candidate waterline points in flooded rural areas having low slope. The waterline levels and positions are corrected for the effects of double reflections between the water surface and emergent vegetation at the flood edge. Waterline points are also selected in flooded urban areas away from radar shadow and layover caused by buildings, with levels similar to those in adjacent rural areas. The resulting points are thinned to reduce spatial autocorrelation using a top-down clustering approach. The method was developed using a TerraSAR-X image from a particular case study involving urban and rural flooding. The waterline points extracted proved to be spatially uncorrelated, with levels reasonably similar to those determined manually from aerial photographs, and in good agreement with those of nearby gauges.

Piety and sociability in early modern women's devotional writing

The letters of early modern women demonstrate that their experience of religion was essentially social, contrary to the impression created by much modern work on diaries or meditations. The stereotypical melancholic, pious lady is far from the ideal offered by spiritual advisors, women and men, in their correspondence. Letters demonstrate how women created networks of spiritual support within and beyond their families. Letters also testify to the agency exercised by early modern women in religious matters, particularly in their assumption of the role of religious advisor and in their engagement with ecclesiastical politics. While this is far from showing that religion empowered all early modern women, it does offer a corrective to the unduly gloomy view of the role of religion in such women's lives. Letters provide indispensable testimony to the social nature of women's responses to the changing religious culture and politics of the eighteenth century.

Writing, death and absence in 'Tim' by H.O. Sturgis

There has been a considerable critical interest in the representation of death in Children's Literature, with an increasingly prevalent move to read it as granting the child the status of object. Thus, for example, Judith Plotz takes it to 'increase [the] presence' of the child. Through a detailed reading of one late C19th school story, I suggest that such readings proceed through a resistance to textuality. This essay offers a reading of death as bound up with the play of the text, deferred, shifting and retrospectively constructed rather than a state of simple, recoverable objecthood.