Benchmarking secondary structure prediction for fold recognition

If secondary structure predictions are to be incorporated into fold recognition methods, an assessment of the effect of specific types of errors in predicted secondary structures on the sensitivity of fold recognition should be carried out. Here, we present a systematic comparison of different secondary structure prediction methods by measuring frequencies of specific types of error. We carry out an evaluation of the effect of specific types of error on secondary structure element alignment (SSEA), a baseline fold recognition method. The results of this evaluation indicate that missing out whole helix or strand elements, or predicting the wrong type of element, is more detrimental than predicting the wrong lengths of elements or overpredicting helix or strand. We also suggest that SSEA scoring is an effective method for assessing accuracy of secondary structure prediction and perhaps may also provide a more appropriate assessment of the “usefulness” and quality of predicted secondary structure, if secondary structure alignments are to be used in fold recognition.

What are the baselines for protein fold recognition?

What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein—ranging from the length of the sequence to a knowledge of its secondary structure—to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications?

A multinomial model of applying recognition to judge between multiple alternatives

Proponents of the “fast and frugal” approach to decision-making suggest that inferential judgments are best made on the basis of limited information. For example, if only one of two cities is recognized and the task is to judge which city has the larger population, the recognition heuristic states that the recognized city should be selected. In preference choices with >2 options, it is also standard to assume that a “consideration set”, based upon some simple criterion, is established to reduce the options available. A multinomial processing tree model is outlined which provides the basis for estimating the extent to which recognition is used as a criterion in establishing a consideration set for inferential judgments.

Spectrally invariant approximation within atmospheric radiative transfer

Certain algebraic combinations of single scattering albedo and solar radiation reflected from, or transmitted through, vegetation canopies do not vary with wavelength. These ‘‘spectrally invariant relationships’’ are the consequence of wavelength independence of the extinction coefficient and scattering phase function in veg- etation. In general, this wavelength independence does not hold in the atmosphere, but in cloud-dominated atmospheres the total extinction and total scattering phase function vary only weakly with wavelength. This paper identifies the atmospheric conditions under which the spectrally invariant approximation can accu- rately describe the extinction and scattering properties of cloudy atmospheres. The validity of the as- sumptions and the accuracy of the approximation are tested with 1D radiative transfer calculations using publicly available radiative transfer models: Discrete Ordinate Radiative Transfer (DISORT) and Santa Barbara DISORT Atmospheric Radiative Transfer (SBDART). It is shown for cloudy atmospheres with cloud optical depth above 3, and for spectral intervals that exclude strong water vapor absorption, that the spectrally invariant relationships found in vegetation canopy radiative transfer are valid to better than 5%. The physics behind this phenomenon, its mathematical basis, and possible applications to remote sensing and climate are discussed.

Does high-frequency repetitive transcranial magnetic stimulation produce residual and/or cumulative effects within an experimental session?

A common procedure for studying the effects on cognition of repetitive transcranial magnetic stimulation (rTMS) is to deliver rTMS concurrent with task performance, and to compare task performance on these trials versus on trials without rTMS. Recent evidence that TMS can have effects on neural activity that persist longer than the experimental session itself, however, raise questions about the assumption of the transient nature of rTMS that underlies many concurrent (or "online") rTMS designs. To our knowledge, there have been no studies in the cognitive domain examining whether the application of brief trains of rTMS during specific epochs of a complex task may have effects that spill over into subsequent task epochs, and perhaps into subsequent trials. We looked for possible immediate spill-over and longer-term cumulative effects of rTMS in data from two studies of visual short-term delayed recognition. In 54 subjects, 10-Hz rTMS trains were applied to five different brain regions during the 3-s delay period of a spatial task, and in a second group of 15 subjects, electroencephalography (EEG) was recorded while 10-Hz rTMS was applied to two brain areas during the 3-s delay period of both spatial and object tasks. No evidence for immediate effects was found in the comparison of the memory probe-evoked response on trials that were vs. were not preceded by delay-period rTMS. No evidence for cumulative effects was found in analyses of behavioral performance, and of EEG signal, as a function of task block. The implications of these findings, and their relation to the broader literature on acute vs. long-lasting effects of rTMS, are considered.

Keeping the world at hand: rapid visuomotor processing for hand-object interactions

The existence of hand-centred visual processing has long been established in the macaque premotor cortex. These hand-centred mechanisms have been thought to play some general role in the sensory guidance of movements towards objects, or, more recently, in the sensory guidance of object avoidance movements. We suggest that these hand-centred mechanisms play a specific and prominent role in the rapid selection and control of manual actions following sudden changes in the properties of the objects relevant for hand-object interactions. We discuss recent anatomical and physiological evidence from human and non-human primates, which indicates the existence of rapid processing of visual information for hand-object interactions. This new evidence demonstrates how several stages of the hierarchical visual processing system may be bypassed, feeding the motor system with hand-related visual inputs within just 70 ms following a sudden event. This time window is early enough, and this processing rapid enough, to allow the generation and control of rapid hand-centred avoidance and acquisitive actions, for aversive and desired objects, respectively

Empathy and emotion recognition in people with autism, first-degree relatives, and controls

Empathy is the lens through which we view others' emotion expressions, and respond to them. In this study, empathy and facial emotion recognition were investigated in adults with autism spectrum conditions (ASC; N=314), parents of a child with ASC (N=297) and IQ-matched controls (N=184). Participants completed a self-report measure of empathy (the Empathy Quotient [EQ]) and a modified version of the Karolinska Directed Emotional Faces Task (KDEF) using an online test interface. Results showed that mean scores on the EQ were significantly lower in fathers (p<0.05) but not mothers (p>0.05) of children with ASC compared to controls, whilst both males and females with ASC obtained significantly lower EQ scores (p<0.001) than controls. On the KDEF, statistical analyses revealed poorer overall performance by adults with ASC (p<0.001) compared to the control group. When the 6 distinct basic emotions were analysed separately, the ASC group showed impaired performance across five out of six expressions (happy, sad, angry, afraid and disgusted). Parents of a child with ASC were not significantly worse than controls at recognising any of the basic emotions, after controlling for age and non-verbal IQ (all p>0.05). Finally, results indicated significant differences between males and females with ASC for emotion recognition performance (p<0.05) but not for self-reported empathy (p>0.05). These findings suggest that self-reported empathy deficits in fathers of autistic probands are part of the 'broader autism phenotype'. This study also reports new findings of sex differences amongst people with ASC in emotion recognition, as well as replicating previous work demonstrating empathy difficulties in adults with ASC. The use of empathy measures as quantitative endophenotypes for ASC is discussed.

Inferring the biggest and best: a measurement model for applying recognition to evoke consideration sets and judge between multiple alternatives

It has long been supposed that preference judgments between sets of to-be-considered possibilities are made by means of initially winnowing down the most promising-looking alternatives to form smaller “consideration sets” (Howard, 1963; Wright & Barbour, 1977). In preference choices with >2 options, it is standard to assume that a “consideration set”, based upon some simple criterion, is established to reduce the options available. Inferential judgments, in contrast, have more frequently been investigated in situations in which only two possibilities need to be considered (e.g., which of these two cities is the larger?) Proponents of the “fast and frugal” approach to decision-making suggest that such judgments are also made on the basis of limited, simple criteria. For example, if only one of two cities is recognized and the task is to judge which city has the larger population, the recognition heuristic states that the recognized city should be selected. A multinomial processing tree model is outlined which provides the basis for estimating the extent to which recognition is used as a criterion in establishing a consideration set for inferential judgments between three possible options.

Recognition of "difference" in Shari'a: a feminist scrutiny through the lens of substantive equality

The paper looks at the works of notable Islamic feminists to examine whether Islam can be reconciled with a substantive approach to gender equality. Located within contemporary feminist debates related to gender equality, it considers the Qur’anic verses related to two controversial areas of Shari’a law, namely, duty of obedience and polygamy, to explore how Islamic scriptures perceive ‘difference’ and its implications for substantive equality-based legal reforms in a Muslim society.

On Hamiltonian balanced dynamics and the slowest invariant manifold

The concept of a slowest invariant manifold is investigated for the five-component model of Lorenz under conservative dynamics. It is shown that Lorenz's model is a two-degree-of-freedom canonical Hamiltonian system, consisting of a nonlinear vorticity-triad oscillator coupled to a linear gravity wave oscillator, whose solutions consist of regular and chaotic orbits. When either the Rossby number or the rotational Froude number is small, there is a formal separation of timescales, and one can speak of fast and slow motion. In the same regime, the coupling is weak, and the Kolmogorov–Arnold-Moser theorem is shown to apply. The chaotic orbits are inherently unbalanced and are confined to regions sandwiched between invariant tori consisting of quasi-periodic regular orbits. The regular orbits generally contain free fast motion, but a slowest invariant manifold may be geometrically defined as the set of all slow cores of invariant tori (defined by zero fast action) that are smoothly related to such cores in the uncoupled system. This slowest invariant manifold is not global; in fact, its structure is fractal; but it is of nearly full measure in the limit of weak coupling. It is also nonlinearly stable. As the coupling increases, the slowest invariant manifold shrinks until it disappears altogether. The results clarify previous definitions of a slowest invariant manifold and highlight the ambiguity in the definition of “slowness.” An asymptotic procedure, analogous to standard initialization techniques, is found to yield nonzero free fast motion even when the core solutions contain none. A hierarchy of Hamiltonian balanced models preserving the symmetries in the original low-order model is formulated; these models are compared with classic balanced models, asymptotically initialized solutions of the full system and the slowest invariant manifold defined by the core solutions. The analysis suggests that for sufficiently small Rossby or rotational Froude numbers, a stable slowest invariant manifold can be defined for this system, which has zero free gravity wave activity, but it cannot be defined everywhere. The implications of the results for more complex systems are discussed.

A time-invariant visco-elastic windkessel model relating blood flow and blood volume

The difference between the rate of change of cerebral blood volume (CBV) and cerebral blood flow (CBF) following stimulation is thought to be due to circumferential stress relaxation in veins (Mandeville, J.B., Marota, J.J.A., Ayata, C., Zaharchuk, G., Moskowitz, M.A., Rosen, B.R., Weisskoff, R.M., 1999. Evidence of a cerebrovascular postarteriole windkessel with delayed compliance. J. Cereb. Blood Flow Metab. 19, 679–689). In this paper we explore the visco-elastic properties of blood vessels, and present a dynamic model relating changes in CBF to changes in CBV. We refer to this model as the visco-elastic windkessel (VW) model. A novel feature of this model is that the parameter characterising the pressure–volume relationship of blood vessels is treated as a state variable dependent on the rate of change of CBV, producing hysteresis in the pressure–volume space during vessel dilation and contraction. The VW model is nonlinear time-invariant, and is able to predict the observed differences between the time series of CBV and that of CBF measurements following changes in neural activity. Like the windkessel model derived by Mandeville, J.B., Marota, J.J.A., Ayata, C., Zaharchuk, G., Moskowitz, M.A., Rosen, B.R., Weisskoff, R.M., 1999. Evidence of a cerebrovascular postarteriole windkessel with delayed compliance. J. Cereb. Blood Flow Metab. 19, 679–689, the VW model is primarily a model of haemodynamic changes in the venous compartment. The VW model is demonstrated to have the following characteristics typical of visco-elastic materials: (1) hysteresis, (2) creep, and (3) stress relaxation, hence it provides a unified model of the visco-elastic properties of the vasculature. The model will not only contribute to the interpretation of the Blood Oxygen Level Dependent (BOLD) signals from functional Magnetic Resonance Imaging (fMRI) experiments, but also find applications in the study and modelling of the brain vasculature and the haemodynamics of circulatory and cardiovascular systems.

Dissociating between object affordances and spatial compatibility effects using early response components

Perception and action are tightly linked: objects may be perceived not only in terms of visual features, but also in terms of possibilities for action. Previous studies showed that when a centrally located object has a salient graspable feature (e.g., a handle), it facilitates motor responses corresponding with the feature's position. However, such so-called affordance effects have been criticized as resulting from spatial compatibility effects, due to the visual asymmetry created by the graspable feature, irrespective of any affordances. In order to dissociate between affordance and spatial compatibility effects, we asked participants to perform a simple reaction-time task to typically graspable and non-graspable objects with similar visual features (e.g., lollipop and stop sign). Responses were measured using either electromyography (EMG) on proximal arm muscles during reaching-like movements, or with finger key-presses. In both EMG and button press measurements, participants responded faster when the object was either presented in the same location as the responding hand, or was affordable, resulting in significant and independent spatial compatibility and affordance effects, but no interaction. Furthermore, while the spatial compatibility effect was present from the earliest stages of movement preparation and throughout the different stages of movement execution, the affordance effect was restricted to the early stages of movement execution. Finally, we tested a small group of unilateral arm amputees using EMG, and found residual spatial compatibility but no affordance, suggesting that spatial compatibility effects do not necessarily rely on individuals’ available affordances. Our results show dissociation between affordance and spatial compatibility effects, and suggest that rather than evoking the specific motor action most suitable for interaction with the viewed object, graspable objects prompt the motor system in a general, body-part independent fashion

Unconscious effects of grammatical gender during object categorisation

Does language modulate perception and categorisation of everyday objects? Here, we approach this question from the perspective of grammatical gender in bilinguals. We tested Spanish–English bilinguals and control native speakers of English in a semantic categorisation task on triplets of pictures in an all-in-English context while measuring event-related brain potentials (ERPs). Participants were asked to press a button when the third picture of a triplet belonged to the same semantic category as the first two, and another button when it belonged to a different category. Unbeknownst to them, in half of the trials, the gender of the third picture name in Spanish had the same gender as that of the first two, and the opposite gender in the other half. We found no priming in behavioural results of either semantic relatedness or gender consistency. In contrast, ERPs revealed not only the expected semantic priming effect in both groups, but also a negative modulation by gender inconsistency in Spanish–English bilinguals, exclusively. These results provide evidence for spontaneous and unconscious access to grammatical gender in participants functioning in a context requiring no access to such information, thereby providing support for linguistic relativity effects in the grammatical domain.

Molecular recognition between functionalized gold nanoparticles and healable, supramolecular polymer blends – a route to property enhancement

A new, healable, supramolecular nanocomposite material has been developed and evaluated. The material comprises a blend of three components: a pyrene-functionalized polyamide, a polydiimide and pyrenefunctionalized gold nanoparticles (P-AuNPs). The polymeric components interact by forming well-defined p–p stacked complexes between p-electron rich pyrenyl residues and p-electron deficient polydiimide residues. Solution studies in the mixed solvent chloroform–hexafluoroisopropanol (6 : 1, v/v) show that mixing the three components (each of which is soluble in isolation), results in the precipitation of a supramolecular, polymer nanocomposite network. The precipitate thus formed can be re-dissolved on heating, with the thermoreversible dissolution/precipitation procedure repeatable over at least 5 cycles. Robust, self-supporting composite films containing up to 15 wt% P-AuNPs could be cast from 2,2,2- trichloroethanol. Addition of as little as 1.25 wt% P-AuNPs resulted in significantly enhanced mechanical properties compared to the supramolecular blend without nanoparticles. The nanocomposites showed a linear increase in both tensile moduli and ultimate tensile strength with increasing P-AuNP content. All compositions up to 10 wt% P-AuNPs exhibited essentially quantitative healing efficiencies. Control experiments on an analogous nanocomposite material containing dodecylamine-functionalized AuNPs (5 wt%) exhibited a tensile modulus approximately half that of the corresponding nanocomposite that incorporated 5 wt% pyrene functionalized-AuNPs, clearly demonstrating the importance of the designed interactions between the gold filler and the supramolecular polymer matrix.