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.

Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.

Where, when and why brain activation differs for bilinguals and monolinguals during picture naming and reading aloud

Using functional magnetic resonance imaging, we found that when bilinguals named pictures or read words aloud, in their native or nonnative language, activation was higher relative to monolinguals in 5 left hemisphere regions: dorsal precentral gyrus, pars triangularis, pars opercularis, superior temporal gyrus, and planum temporale. We further demonstrate that these areas are sensitive to increasing demands on speech production in monolinguals. This suggests that the advantage of being bilingual comes at the expense of increased work in brain areas that support monolingual word processing. By comparing the effect of bilingualism across a range of tasks, we argue that activation is higher in bilinguals compared with monolinguals because word retrieval is more demanding; articulation of each word is less rehearsed; and speech output needs careful monitoring to avoid errors when competition for word selection occurs between, as well as within,language.

The child and imperial return: the mystery of Edwin Drood

The Mystery of Edwin Drood has often been read as an Imperial text, just as Dickens's work has repeatedly been considered in relation to its construction of childhood. Despite this, 'the child' has either been avoided in criticism of Dickens's last novel, or has actively been read as absent. In this essay, I return the ‘repressed’ child to a reading of Drood, and through this disrupt appeals to a hard-impacted Imperial structure I understand to be made within criticism of it.

The role of efficacy and well-being in guiding the use of education and training services by young homeless mothers

This paper builds on previous work applying the concept of well-being to the field of housing. It uses the concepts of self-esteem, efficacy and social identity to explore the situations of a group of young homeless mothers. In particular, it focuses on the impact of well-being factors, among others, in understanding the uptake of education and training services. The paper concludes by arguing that well-being issues are crucial for housing agencies and others who want to engage with young homeless people.

Speech-like and non-speech lip kinematics and coordination in aphasia

Background and aims: In addition to the well-known linguistic processing impairments in aphasia, oro-motor skills and articulatory implementation of speech segments are reported to be compromised to some degree in most types of aphasia. This study aimed to identify differences in the characteristics and coordination of lip movements in the production of a bilabial closure gesture between speech-like and nonspeech tasks in individuals with aphasia and healthy control subjects. Method and procedure: Upper and lower lip movement data were collected for a speech-like and a nonspeech task using an AG 100 EMMA system from five individuals with aphasia and five age and gender matched control subjects. Each task was produced at two rate conditions (normal and fast), and in a familiar and a less-familiar manner. Single articulator kinematic parameters (peak velocity, amplitude, duration, and cyclic spatio-temporal index) and multi-articulator coordination indices (average relative phase and variability of relative phase) were measured to characterize lip movements. Outcome and results: The results showed that when the two lips had similar task goals (bilabial closure) in speech-like versus nonspeech task, kinematic and coordination characteristics were not found to be different. However, when changes in rate were imposed on the bilabial gesture, only speech-like task showed functional adaptations, indicated by a greater decrease in amplitude and duration at fast rates. In terms of group differences, individuals with aphasia showed smaller amplitudes and longer movement durations for upper lip, higher spatio-temporal variability for both lips, and higher variability in lip coordination than the control speakers. Rate was an important factor in distinguishing the two groups, and individuals with aphasia were limited in implementing the rate changes. Conclusion and implications: The findings support the notion of subtle but robust differences in motor control characteristics between individuals with aphasia and the control participants, even in the context of producing bilabial closing gestures for a relatively simple speech-like task. The findings also highlight the functional differences between speech-like and nonspeech tasks, despite a common movement coordination goal for bilabial closure.

A paradoxical presidency: Nicolas Sarkozy, 2007-2012

The Sarkozy presidency is shot through with paradox and contrast: between a well-elected president swiftly loathed by most voters; a ‘hyper-president’ who probably weakened the office; a talented party leader who lost effective control of his party; a right-wing president who was readily compared to Tony Blair; and an ambitious reformer who promised a clean break with the indecision of his two predecessors but whose record was more timid than his rhetoric. This article interprets Sarkozy’s record in the context of the presidential office, the specific circumstances of his presidency, and of the president’s own personality, skills and shortcomings.

Where theory meets practice: a critical comparison of research into identifying letters and craft knowledge of type design

This paper introduces scientific research findings and accounts of skilled design judgement to: (i) develop an interdisciplinary account of what affects our identification of letters when reading; (ii) analyse the relationship between the approaches of psychologists and designers to explaining how we identify letters; (iii) propose ways in which collaboration may work to make psychological research more relevant to typographic practice. The topics reviewed are addressed within each discipline and cover the contribution of letters and words to reading; letter features; essential or structural forms; uniformity within font design; and letter spacing. Analysis of the literature identifies possible means of reconciling different perspectives, points out some anomalies in interpretation of findings, and proposes how designers may contribute to research planning and dissemination.

The kinetics of the gas-phase reactions of selected monoterpenes and cyclo-alkenes with ozone and the NO3 radical

The relative rate method has been used to measure the room-temperature rate constants for the gasphase reactions of ozone and NO3 with selected monoterpenes and cyclo-alkenes with structural similarities to monoterpenes. Measurements were carried out at 298 ! 2 K and 760 ! 10 Torr. The following rate constants (in units of 10"18 cm3 molecule"1 s"1) were obtained for the reaction with ozone: methyl cyclohexene (132 ! 17), terpinolene (1290 ! 360), ethylidene cyclohexane (223 ! 57), norbornene (860 ! 240), t-butyl isopropylidene cyclohexane (1500 ! 460), cyclopentene (543 ! 94), cyclohexene (81 ! 18), cyclooctene (451 ! 66), dicyclopentadiene (1460 ! 170) and a-pinene (107 ! 13). For the reaction with NO3 the rate constants obtained (in units of 10"12 cm3 molecule"1 s"1) were: methyl cyclohexene (7.92 ! 0.95), terpinolene (47.9 ! 4.0), ethylidene cyclohexane (4.30 ! 0.24), norbornene (0.266 ! 0.029), cyclohexene (0.540 ! 0.017), cyclooctene (0.513 ! 0.029), dicyclopentadiene (1.20 ! 0.10) and a-pinene (5.17 ! 0.62). Errors are quoted as the root mean square of the statistical error (95% con!dence) and the quoted error in the rate constant for the reference compound. Combining these results with previous studies, new recommendations for the rate constants are presented. Molecular orbital energies were calculated for each alkene and the kinetic data are discussed in terms of the deviation from the structureeactivity relationship obtained from the rate constants for a series of simple alkenes. Lifetimes with respect to key initiators of atmospheric oxidation have been calculated suggesting that the studied reactions play dominant roles in the night-time removal of these compounds from the atmosphere.

Ergonomics as authoritarian or libertarian: reflections on Ward’s politics of design

Ergonomics is intrinsically connected to political debates about the good society, about how we should live. This article follows the ideas of Colin Ward by setting the practices of ergonomics and design along a spectrum between more libertarian approaches and more authoritarian. Within Anglo-American ergonomics, more authoritarian approaches tend to prevail, often against the wishes of designers who have had to fight with their employers for best possible design outcomes. The article draws on debates about the design and manufacturing of schoolchildren’s furniture. Ergonomics would benefit from embracing these issues to stimulate a broader discourse amongst its practitioners about how to be open to new disciplines, particularly those in the social sciences.

Molecular and phenotypic characterization of a mouse model of oculopharyngeal muscular dystrophy reveals severe muscular atrophy restricted to fast glycolytic fibres

Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by ptosis, dysphagia and proximal limb weakness. Autosomal-dominant OPMD is caused by a short (GCG)8–13 expansions within the first exon of the poly(A)-binding protein nuclear 1 gene (PABPN1), leading to an expanded polyalanine tract in the mutated protein. Expanded PABPN1 forms insoluble aggregates in the nuclei of skeletal muscle fibres. In order to gain insight into the different physiological processes affected in OPMD muscles, we have used a transgenic mouse model of OPMD (A17.1) and performed transcriptomic studies combined with a detailed phenotypic characterization of this model at three time points. The transcriptomic analysis revealed a massive gene deregulation in the A17.1 mice, among which we identified a significant deregulation of pathways associated with muscle atrophy. Using a mathematical model for progression, we have identified that one-third of the progressive genes were also associated with muscle atrophy. Functional and histological analysis of the skeletal muscle of this mouse model confirmed a severe and progressive muscular atrophy associated with a reduction in muscle strength. Moreover, muscle atrophy in the A17.1 mice was restricted to fast glycolytic fibres, containing a large number of intranuclear inclusions (INIs). The soleus muscle and, in particular, oxidative fibres were spared, even though they contained INIs albeit to a lesser degree. These results demonstrate a fibre-type specificity of muscle atrophy in this OPMD model. This study improves our understanding of the biological pathways modified in OPMD to identify potential biomarkers and new therapeutic targets.

Direct evidence for attention-dependent influences of the frontal eye-fields on feature-responsive visual cortex

Voluntary selective attention can prioritize different features in a visual scene. The frontal eye-fields (FEF) are one potential source of such feature-specific top-down signals, but causal evidence for influences on visual cortex (as was shown for "spatial" attention) has remained elusive. Here, we show that transcranial magnetic stimulation (TMS) applied to right FEF increased the blood oxygen level-dependent (BOLD) signals in visual areas processing "target feature" but not in "distracter feature"-processing regions. TMS-induced BOLD signals increase in motion-responsive visual cortex (MT+) when motion was attended in a display with moving dots superimposed on face stimuli, but in face-responsive fusiform area (FFA) when faces were attended to. These TMS effects on BOLD signal in both regions were negatively related to performance (on the motion task), supporting the behavioral relevance of this pathway. Our findings provide new causal evidence for the human FEF in the control of nonspatial "feature"-based attention, mediated by dynamic influences on feature-specific visual cortex that vary with the currently attended property.

Solution-free sets for sums of binary forms

In this paper, we obtain quantitative estimates for the asymptotic density of subsets of the integer lattice Z2 that contain only trivial solutions to an additive equation involving binary forms. In the process we develop an analogue of Vinogradov’s mean value theorem applicable to binary forms.

The resting-state neurovascular coupling relationship: rapid changes in spontaneous neural activity in the somatosensory cortex are associated with haemodynamic fluctuations that resemble stimulus-evoked haemodynamics

Although promise exists for patterns of resting-state blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) brain connectivity to be used as biomarkers of early brain pathology, a full understanding of the nature of the relationship between neural activity and spontaneous fMRI BOLD fluctuations is required before such data can be correctly interpreted. To investigate this issue, we combined electrophysiological recordings of rapid changes in multi-laminar local field potentials from the somatosensory cortex of anaesthetized rats with concurrent two-dimensional optical imaging spectroscopy measurements of resting-state haemodynamics that underlie fluctuations in the BOLD fMRI signal. After neural ‘events’ were identified, their time points served to indicate the start of an epoch in the accompanying haemodynamic fluctuations. Multiple epochs for both neural ‘events’ and the accompanying haemodynamic fluctuations were averaged. We found that the averaged epochs of resting-state haemodynamic fluctuations taken after neural ‘events’ closely resembled the temporal profile of stimulus-evoked cortical haemodynamics. Furthermore, we were able to demonstrate that averaged epochs of resting-state haemodynamic fluctuations resembling the temporal profile of stimulus-evoked haemodynamics could also be found after peaks in neural activity filtered into specific electroencephalographic frequency bands (theta, alpha, beta, and gamma). This technique allows investigation of resting-state neurovascular coupling using methodologies that are directly comparable to that developed for investigating stimulus-evoked neurovascular responses.