CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

ABSTRACT Summary: The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. Availability and Implementation: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz

Multivoxel Pattern Analysis Reveals Auditory Motion Information in MT+ of Both Congenitally Blind and Sighted Individuals

Cross-modal plasticity refers to the recruitment of cortical regions involved in the processing of one modality (e.g. vision) for processing other modalities (e.g. audition). The principles determining how and where cross-modal plasticity occurs remain poorly understood. Here, we investigate these principles by testing responses to auditory motion in visual motion area MT+ of congenitally blind and sighted individuals. Replicating previous reports, we find that MT+ as a whole shows a strong and selective responses to auditory motion in congenitally blind but not sighted individuals, suggesting that the emergence of this univariate response depends on experience. Importantly, however, multivoxel pattern analyses showed that MT+ contained information about different auditory motion conditions in both blind and sighted individuals. These results were specific to MT+ and not found in early visual cortex. Basic sensitivity to auditory motion in MT+ is thus experience-independent, which may be a basis for the region's strong cross-modal recruitment in congenital blindness

Cross-Modal Plasticity Preserves Functional Specialization in Posterior Parietal Cortex

In congenitally blind individuals, many regions of the brain that are typically heavily involved in visual processing are recruited for a variety of nonvisual sensory and cognitive tasks (Rauschecker 1995; Pascual-Leone et al. 2005). This phenomenon—cross-modal plasticity—has been widely documented, but the principles that determine where and how cross-modal changes occur remain poorly understood (Bavelier and Neville 2002). Here, we evaluate the hypothesis that cross-modal plasticity respects the type of computations performed by a region, even as it changes the modality of the inputs over which they are carried out (Pascual-Leone and Hamilton 2001). We compared the fMRI signal in sighted and congenitally blind participants during proprioceptively guided reaching. We show that parietooccipital reach-related regions retain their functional role—encoding of the spatial position of the reach target-even as the dominant modality in this region changes from visual to nonvisual inputs. This suggests that the computational role of a region, independently of the processing modality, codetermines its potential cross-modal recruitment. Our findings demonstrate that preservation of functional properties can serve as a guiding principle for cross-modal plasticity even in visuomotor cortical regions, i.e. beyond the early visual cortex and other traditional visual areas.Psycholog

Results of univariate and multivariate analyses.

<p>(a) An axial slice of a brain in the standard Talairach space showing a section through the two 10 mm spherical ROIs corresponding to rMT+ and lMT+. (b) Univariate results showing activity in MT+ for high and low motion conditions in congenitally blind and sighted participants. (c) Multivariate results showing classification performance for the decoding of high versus low motion conditions in congenitally blind and sighted participants. The dashed line represents the chance level for classification. Error bars represent the standard error of the mean.</p

MVPA results.

<p>Factor legend:</p><p>sub_grp  =  subject group.</p><p>hem  =  hemisphere.</p

Univariate results.

<p>Factor legend:</p><p>sub_grp  =  subject group.</p><p>hem  =  hemisphere.</p><p>cond  =  condition.</p