Computer-aided biotechnology:from immuno-informatics to reverse vaccinology

Genome sequences from many organisms, including humans, have been completed, and high-throughput analyses have produced burgeoning volumes of 'omics' data. Bioinformatics is crucial for the management and analysis of such data and is increasingly used to accelerate progress in a wide variety of large-scale and object-specific functional analyses. Refined algorithms enable biotechnologists to follow 'computer-aided strategies' based on experiments driven by high-confidence predictions. In order to address compound problems, current efforts in immuno-informatics and reverse vaccinology are aimed at developing and tuning integrative approaches and user-friendly, automated bioinformatics environments. This will herald a move to 'computer-aided biotechnology': smart projects in which time-consuming and expensive large-scale experimental approaches are progressively replaced by prediction-driven investigations.

A systematic exploration of perceptual and semantic differences in category-specific object-processing using magnetoencephalography

In a series of experiments, we tested category-specific activation in normal parti¬cipants using magnetoencephalography (MEG). Our experiments explored the temporal processing of objects, as MEG characterises neural activity on the order of milliseconds. Our experiments explored object-processing, including assessing the time-course of ob¬ject naming, early differences in processing living compared with nonliving objects and processing objects at the basic compared with the domain level, and late differences in processing living compared with nonliving objects and processing objects at the basic compared with the domain level. In addition to studies using normal participants, we also utilised MEG to explore category-specific processing in a patient with a deficit for living objects. Our findings support the cascade model of object naming (Humphreys et al., 1988). In addition, our findings using normal participants demonstrate early, category-specific perceptual differences. These findings are corroborated by our patient study. In our assessment of the time-course of category-specific effects as well as a separate analysis designed to measure semantic differences between living and nonliving objects, we found support for the sensory/motor model of object naming (Martin, 1998), in addition to support for the cascade model of object naming. Thus, object processing in normal participants appears to be served by a distributed network in the brain, and there are both perceptual and semantic differences between living and nonliving objects. A separate study assessing the influence of the level at which you are asked to identify an object on processing in the brain found evidence supporting the convergence zone hypothesis (Damasio, 1989). Taken together, these findings indicate the utility of MEG in exploring the time-course of object processing, isolating early perceptual and later semantic effects within the brain.

The role of oscillatory brain activity in object processing and figure-ground segmentation in human vision

The perception of an object as a single entity within a visual scene requires that its features are bound together and segregated from the background and/or other objects. Here, we used magnetoencephalography (MEG) to assess the hypothesis that coherent percepts may arise from the synchronized high frequency (gamma) activity between neurons that code features of the same object. We also assessed the role of low frequency (alpha, beta) activity in object processing. The target stimulus (i.e. object) was a small patch of a concentric grating of 3c/°, viewed eccentrically. The background stimulus was either a blank field or a concentric grating of 3c/° periodicity, viewed centrally. With patterned backgrounds, the target stimulus emerged--through rotation about its own centre--as a circular subsection of the background. Data were acquired using a 275-channel whole-head MEG system and analyzed using Synthetic Aperture Magnetometry (SAM), which allows one to generate images of task-related cortical oscillatory power changes within specific frequency bands. Significant oscillatory activity across a broad range of frequencies was evident at the V1/V2 border, and subsequent analyses were based on a virtual electrode at this location. When the target was presented in isolation, we observed that: (i) contralateral stimulation yielded a sustained power increase in gamma activity; and (ii) both contra- and ipsilateral stimulation yielded near identical transient power changes in alpha (and beta) activity. When the target was presented against a patterned background, we observed that: (i) contralateral stimulation yielded an increase in high-gamma (>55 Hz) power together with a decrease in low-gamma (40-55 Hz) power; and (ii) both contra- and ipsilateral stimulation yielded a transient decrease in alpha (and beta) activity, though the reduction tended to be greatest for contralateral stimulation. The opposing power changes across different regions of the gamma spectrum with 'figure/ground' stimulation suggest a possible dual role for gamma rhythms in visual object coding, and provide general support of the binding-by-synchronization hypothesis. As the power changes in alpha and beta activity were largely independent of the spatial location of the target, however, we conclude that their role in object processing may relate principally to changes in visual attention.

The spatial distribution and temporal dynamics of brain regions activated during the perception of object and non-object patterns

Both animal and human studies suggest that the efficiency with which we are able to grasp objects is attributable to a repertoire of motor signals derived directly from vision. This is in general agreement with the long-held belief that the automatic generation of motor signals by the perception of objects is based on the actions they afford. In this study, we used magnetoencephalography (MEG) to determine the spatial distribution and temporal dynamics of brain regions activated during passive viewing of object and non-object targets that varied in the extent to which they afforded a grasping action. Synthetic Aperture Magnetometry (SAM) was used to localize task-related oscillatory power changes within specific frequency bands, and the time course of activity within given regions-of-interest was determined by calculating time-frequency plots using a Morlet wavelet transform. Both single subject and group-averaged data on the spatial distribution of brain activity are presented. We show that: (i) significant reductions in 10-25 Hz activity within extrastriate cortex, occipito-temporal cortex, sensori-motor cortex and cerebellum were evident with passive viewing of both objects and non-objects; and (ii) reductions in oscillatory activity within the posterior part of the superior parietal cortex (area Ba7) were only evident with the perception of objects. Assuming that focal reductions in low-frequency oscillations (< 30 Hz) reflect areas of heightened neural activity, we conclude that: (i) activity within a network of brain areas, including the sensori-motor cortex, is not critically dependent on stimulus type and may reflect general changes in visual attention; and (ii) the posterior part of the superior parietal cortex, area Ba7, is activated preferentially by objects and may play a role in computations related to grasping. © 2006 Elsevier Inc. All rights reserved.

Developmental trajectories of part-based and configural object recognition in adolescence.

Three experiments assessed the development of children's part and configural (part-relational) processing in object recognition during adolescence. In total, 312 school children aged 7-16 years and 80 adults were tested in 3-alternative forced choice (3-AFC) tasks. They judged the correct appearance of upright and inverted presented familiar animals, artifacts, and newly learned multipart objects, which had been manipulated either in terms of individual parts or part relations. Manipulation of part relations was constrained to either metric (animals, artifacts, and multipart objects) or categorical (multipart objects only) changes. For animals and artifacts, even the youngest children were close to adult levels for the correct recognition of an individual part change. By contrast, it was not until 11-12 years of age that they achieved similar levels of performance with regard to altered metric part relations. For the newly learned multipart objects, performance was equivalent throughout the tested age range for upright presented stimuli in the case of categorical part-specific and part-relational changes. In the case of metric manipulations, the results confirmed the data pattern observed for animals and artifacts. Together, the results provide converging evidence, with studies of face recognition, for a surprisingly late consolidation of configural-metric relative to part-based object recognition.

Observation of a finger or an object movement primes imitative responses differentially

Behavioural advantages for imitation of human movements over movements instructed by other visual stimuli are attributed to an ‘action observation-execution matching’ (AOEM) mechanism. Here, we demonstrate that priming/exogenous cueing with a videotaped finger movement stimulus (S1) produces specific congruency effects in reaction times (RTs) of imitative responses to a target movement (S2) at defined stimulus onset asynchronies (SOAs). When contrasted with a moving object at an SOA of 533 ms, only a human movement is capable of inducing an effect reminiscent of ‘inhibition of return’ (IOR), i.e. a significant advantage for imitation of a subsequent incongruent as compared to a congruent movement. When responses are primed by a finger movement at SOAs of 533 and 1,200 ms, inhibition of congruent or facilitation of incongruent responses, respectively, is stronger as compared to priming by a moving object. This pattern does not depend on whether S2 presents a finger movement or a moving object, thus effects cannot be attributed to visual similarity between S1 and S2. We propose that, whereas both priming by a finger movement and a moving object induces processes of spatial orienting, solely observation of a human movement activates AOEM. Thus, S1 immediately elicits an imitative response tendency. As an overt imitation of S1 is inadequate in the present setting, the response is inhibited which, in turn, modulates congruency effects.

Teallach - a flexible user - interface development environment for object database applications

The Teallach project has adapted model-based user-interface development techniques to the systematic creation of user-interfaces for object-oriented database applications. Model-based approaches aim to provide designers with a more principled approach to user-interface development using a variety of underlying models, and tools which manipulate these models. Here we present the results of the Teallach project, describing the tools developed and the flexible design method supported. Distinctive features of the Teallach system include provision of database-specific constructs, comprehensive facilities for relating the different models, and support for a flexible design method in which models can be constructed and related by designers in different orders and in different ways, to suit their particular design rationales. The system then creates the desired user-interface as an independent, fully functional Java application, with automatically generated help facilities.

Retrieval of implicit inhibitory processes:the impact of visual field, object-identity, and memory dynamics

After exogenously cueing attention to a peripheral location, the return of attention and response to the location can be inhibited. We demonstrate that these inhibitory mechanisms of attention can be associated with objects and can be automatically and implicitly retrieved over relatively long periods. Furthermore, we also show that when face stimuli are associated with inhibition, the effect is more robust for faces presented in the left visual field. This effect can be even more spatially specific, where most robust inhibition is obtained for faces presented in the upper as compared to the lower visual field. Finally, it is revealed that the inhibition is associated with an object’s identity, as inhibition moves with an object to a new location; and that the retrieved inhibition is only transiently present after retrieval.

Imagery in multi-modal object learning

Spatial objects may not only be perceived visually but also by touch. We report recent experiments investigating to what extent prior object knowledge acquired in either the haptic or visual sensory modality transfers to a subsequent visual learning task. Results indicate that even mental object representations learnt in one sensory modality may attain a multi-modal quality. These findings seem incompatible with picture-based reasoning schemas but leave open the possibility of modality-specific reasoning mechanisms.

An international round-robin calibration protocol for nanoindentation measurements

Nanoindentation has become a common technique for measuring the hardness and elastic-plastic properties of materials, including coatings and thin films. In recent years, different nanoindenter instruments have been commercialised and used for this purpose. Each instrument is equipped with its own analysis software for the derivation of the hardness and reduced Young's modulus from the raw data. These data are mostly analysed through the Oliver and Pharr method. In all cases, the calibration of compliance and area function is mandatory. The present work illustrates and describes a calibration procedure and an approach to raw data analysis carried out for six different nanoindentation instruments through several round-robin experiments. Three different indenters were used, Berkovich, cube corner, spherical, and three standardised reference samples were chosen, hard fused quartz, soft polycarbonate, and sapphire. It was clearly shown that the use of these common procedures consistently limited the hardness and reduced the Young's modulus data spread compared to the same measurements performed using instrument-specific procedures. The following recommendations for nanoindentation calibration must be followed: (a) use only sharp indenters, (b) set an upper cut-off value for the penetration depth below which measurements must be considered unreliable, (c) perform nanoindentation measurements with limited thermal drift, (d) ensure that the load-displacement curves are as smooth as possible, (e) perform stiffness measurements specific to each instrument/indenter couple, (f) use Fq and Sa as calibration reference samples for stiffness and area function determination, (g) use a function, rather than a single value, for the stiffness and (h) adopt a unique protocol and software for raw data analysis in order to limit the data spread related to the instruments (i.e. the level of drift or noise, defects of a given probe) and to make the H and E r data intercomparable. © 2011 Elsevier Ltd.

Effectiveness of the interventions in preventing the progression of pre-frailty and frailty in older adults:a systematic review protocol

REVIEW QUESTION / OBJECTIVE : The objective of this review is to identify the effectiveness of the interventions in preventing progression of pre-frailty and frailty in older adults. More specifically, the review questions are: - What is the effectiveness of interventions in preventing or reducing frailty in older adults? - How does effectiveness vary with degree of frailty? - Are there factors that influence the effectiveness of interventions? - What is the economic feasibility of interventions for pre-frailty and frailty? INCLUSION CRITERIA : Types of participants This review will consider studies that include older adults (female and male) aged 65 years and over, explicitly identified as pre-frail or frail by the researchers or associated medical professionals according to a pre-specified scale or index, and who have received health care and support services in any type of setting (primary care, nursing homes, hospitals). This review will exclude studies that: - Include participants who have been selected because they have one specific illness - Consider people with a terminal diagnosis only. - Types of intervention(s)/phenomena of interest: The clinical/medical component of the review will consider studies that evaluate any type of interventions to prevent the progression of pre-frailty and frailty in older adults. These interventions will include, but will not be limited to, physical activity, multifactorial intervention, psychosocial intervention, health and social care provision, and cognitive, nutrition or medication/medical maintenance and adherence focused interventions. The economic component of the review will consider studies that have performed any type of health economic analysis of ...