The PSIPRED protein structure prediction server

The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition 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.

Characterizing typographic expertise: do we process typefaces like faces?

Studies of face recognition and discrimination provide a rich source of data and debate on the nature of their processing, in particular through using inverted faces. This study draws parallels between the features of typefaces and faces, as letters share a basic configuration, regardless of typeface, that could be seen as similar to faces. Typeface discrimination is compared using paragraphs of upright letters and inverted letters at three viewing durations. Based on previously reported effects of expertise, the prediction that designers would be less accurate when letters are inverted, whereas nondesigners would have similar performance in both orientations, was confirmed. A proposal is made as to which spatial relations between typeface components constitute holistic and configural processing, posited as the basis for better discrimination of the typefaces of upright letters. Such processing may characterize designers’ perceptual abilities, acquired through training.

The ModFOLD4 server for the quality assessment of 3D protein models

Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine readable and graphical output, providing users with intuitive visual reports on the quality of predicted protein tertiary structures. The ModFOLD4 server is freely available to all at: http://www.reading.ac.uk/bioinf/ModFOLD/.

The FunFOLD2 server for the prediction of protein-ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.

Autistic traits modulate frontostriatal connectivity during processing of rewarding faces

Deficits in facial mimicry have been widely reported in autism. Some studies have suggested that these deficits are restricted to spontaneous mimicry and do not extend to volitional mimicry. We bridge these apparently inconsistent observations, by testing the impact of reward value on neural indices of mimicry, and how autistic traits modulate this impact. Neutral faces were conditioned with high and low reward. Subsequently, functional connectivity between the ventral striatum (VS) and inferior frontal gyrus (IFG) was measured whilst neurotypical adults (n = 30) watched happy expressions made by these conditioned faces. We found greater VS-IFG connectivity in response to high-reward vs. low-reward happy faces. This difference was negatively proportional to autistic traits, suggesting that reduced spontaneous mimicry of social stimuli seen in autism, maybe related to a failure in the modulation of the mirror system by the reward system rather than a circumscribed deficit in the mirror system.

Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

Neural responses to emotional faces in women recovered from anorexia nervosa

Impairments in emotional processing have been associated with anorexia nervosa. However, it is unknown whether neural and behavioural differences in the processing of emotional stimuli persist following recovery. The aim of this study was to investigate the neural processing of emotional faces in individuals recovered from anorexia nervosa compared with healthy controls. Thirty-two participants (16 recovered anorexia nervosa, 16 healthy controls) underwent a functional magnetic resonance imaging (fMRI) scan. Participants viewed fearful and happy emotional faces and indicated the gender of the face presented. Whole brain analysis revealed no significant differences between the groups to the contrasts of fear versus happy and vice versa. Region of interest analysis demonstrated no significant differences in the neural response to happy or fearful stimuli between the groups in the amygdala or fusiform gyrus. These results suggest that processing of emotional faces may not be aberrant after recovery from anorexia nervosa.

A model intervenes: the many faces of moral hazard

This article builds on advances in social ontology to develop a new understanding of how mainstream economic modelling affects reality. We propose a new framework for analysing and describing how models intervene in the social sphere. This framework allows us to identify and articulate three key epistemic features of models as interventions: specificity, portability and formal precision. The second part of the article uses our framework to demonstrate how specificity, portability and formal precision explain the use of moral hazard models in a variety of different policy contexts, including worker compensation schemes, bank regulation and the euro-sovereign debt crisis.

The influence of anxiety on the initial selection of emotional faces presented in binocular rivalry

Neurocognitive theories of anxiety predict that threat-related information can be evaluated before attentional selection, and can influence behaviour differentially in high anxious compared to low anxious individuals. We investigate this further by presenting emotional and neutral faces in an adapted binocular rivalry paradigm. We show that the initial selection of emotional faces presented in binocular rivalry is highly influenced by self-reported state and trait anxiety-level. Heightened anxiety was correlated with increased perception of angry and fearful faces, and decreased perception of happy expressions. These results are consistent with recent evidence of involuntary selection of threat in anxiety.

On the 'special' status of emotional faces... Comment on Yang, Hong, and Blake (2010)

A wealth of literature suggests that emotional faces are given special status as visual objects: Cognitive models suggest that emotional stimuli, particularly threat-relevant facial expressions such as fear and anger, are prioritized in visual processing and may be identified by a subcortical “quick and dirty” pathway in the absence of awareness (Tamietto & de Gelder, 2010). Both neuroimaging studies (Williams, Morris, McGlone, Abbott, & Mattingley, 2004) and backward masking studies (Whalen, Rauch, Etcoff, McInerney, & Lee, 1998) have supported the notion of emotion processing without awareness. Recently, our own group (Adams, Gray, Garner, & Graf, 2010) showed adaptation to emotional faces that were rendered invisible using a variant of binocular rivalry: continual flash suppression (CFS, Tsuchiya & Koch, 2005). Here we (i) respond to Yang, Hong, and Blake's (2010) criticisms of our adaptation paper and (ii) provide a unified account of adaptation to facial expression, identity, and gender, under conditions of unawareness

Faces and awareness: low-level, not emotional factors determine perceptual dominance

Threat-relevant stimuli such as fear faces are prioritized by the human visual system. Recent research suggests that this prioritization begins during unconscious processing: A specialized (possibly subcortical) pathway evaluates the threat relevance of visual input, resulting in preferential access to awareness for threat stimuli. Our data challenge this claim. We used a continuous flash suppression (CFS) paradigm to present emotional face stimuli outside of awareness. It has been shown using CFS that salient (e.g., high contrast) and recognizable stimuli (faces, words) become visible more quickly than less salient or less recognizable stimuli. We found that although fearful faces emerge from suppression faster than other faces, this was wholly explained by their low-level visual properties, rather than their emotional content. We conclude that, in the competition for visual awareness, the visual system prefers and promotes unconscious stimuli that are more “face-like,” but the emotional content of a face has no effect on stimulus salience.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Paddy Hartley: of faces and facades

Paddy Hartley's work is primarily concerned with the ways in which the human face can be repaired, manipulated and recontextualised, and the questions these processes raise about our concepts of beauty and disfigurement. Incorporating surgical and pharmaceutical equipment as well as steel, scrap metal, digital embroidery and textiles, Hartley sets out a critique of how we think about the face today. Taking as a starting point records of facially injured servicemen of the First World War and the pioneering surgery they underwent, Project Facade examines the impact of disfigurement on the human psyche, as well as tracing the development of early facial reconstructive surgery. His Face Corsets, meanwhile, examines attitudes towards cosmetic surgery and the beauty industry, providing a non-surgical means to brutally mimic the results of cosmetic procedures and beyond. The series gained notoriety and success in a wide variety of popular publications both nationally and internationally, and continue to feature in contemporary textiles and fashion publications. Paddy Hartley: Of Faces and Facades brings together these works in book form for the first time, presenting previously unpublished texts from David Houston Jones and Marjorie Gehrhardt, as well as drawings and photographs which document a remarkable creative process and a history that is still insufficiently explored.