Perceptual organization of local elements into global shapes in the human visual cortex

The question of how local image features on the retina are integrated into perceived global shapes is central to our understanding of human visual perception. Psychophysical investigations have suggested that the emergence of a coherent visual percept, or a "good-Gestalt", is mediated by the perceptual organization of local features based on their similarity. However, the neural mechanisms that mediate unified shape perception in the human brain remain largely unknown. Using human fMRI, we demonstrate that not only higher occipitotemporal but also early retinotopic areas are involved in the perceptual organization and detection of global shapes. Specifically, these areas showed stronger fMRI responses to global contours consisting of collinear elements than to patterns of randomly oriented local elements. More importantly, decreased detection performance and fMRI activations were observed when misalignment of the contour elements disturbed the perceptual coherence of the contours. However, grouping of the misaligned contour elements by disparity resulted in increased performance and fMRI activations, suggesting that similar neural mechanisms may underlie grouping of local elements to global shapes by different visual features (orientation or disparity). Thus, these findings provide novel evidence for the role of both early feature integration processes and higher stages of visual analysis in coherent visual perception.     

Analysis of fragmented images perception: local features and global description

Analysis of experimental investigations of the perception of incomplete images is presented. It illustrates two different approaches to work of the brain mechanisms involved: one approach is based on the perception of whole images and another on local informative features. These approaches describe two different mechanisms, which are possibly used by brain systems for incomplete image recognition. Performance on the Gollin test (measuring recognition thresholds for fragmented line drawings of everyday objects and animals) depends upon recognition based on image informational-statistical characteristics. We suggest that recognition thresholds for Gollin stimuli in part reflect the extraction of signal from noise. The brain uses local informative features as an additional source of information about them. We have suggested that fragmented images in the Gollin-test are perceived as whole structures. This structure is compared with a template in memory which is extracted with the help of selective attention mechanism in accordance with a matched filtration model. The Gollin-test is a tool for differential diagnosis of a various forms of cognitive disorders.     

Processing local signals into global patterns

Perceptual organization or grouping is one of the central issues in vision research. Recent reports in the neuroimaging literature suggest that perceptual organization is mediated by distributed visual areas that range from the primary visual cortex (V1) to higher visual areas, depending on the availability of grouping cues and on the weight of contribution of each visual area. Evidence suggests that grouping by proximity and collinearity, and also perhaps filling-in, involve V1, whereas grouping by similarity and symmetry seems to depend on activation of higher visual areas. Further studies should include deliberate controls for confounding factors such as attentional artifacts and radial orientation bias, to clarify how spatiotemporal information in visual areas is integrated to give rise to perceptual organization.     

Interpreting local visual features as a global shape requires awareness

How the brain constructs a coherent representation of the environment from noisy visual input remains poorly understood. Here, we explored whether awareness of the stimulus plays a role in the integration of local features into a representation of global shape. Participants were primed with a shape defined either by position or orientation cues, and performed a shape-discrimination task on a subsequently presented probe shape. Crucially, the probe could either be defined by the same or different cues as the prime, which allowed us to distinguish the effect of priming by local features and global shape. We found a robust priming benefit for visible primes, with response times being faster when the probe and prime were the same shape, regardless of the defining cue. However, rendering the prime invisible uncovered a dissociation: position-defined primes produced behavioural benefit only for probes of the same cue type. Surprisingly, orientation-defined primes afforded an enhancement only for probes of the opposite cue. In further experiments, we showed that the effect of priming was confined to retinotopic coordinates and that there was no priming effect by invisible orientation cues in an orientation-discrimination task. This explains the absence of priming by the same cue in our shape-discrimination task. In summary, our findings show that while in the absence of awareness orientation signals can recruit retinotopic circuits (e.g. intrinsic lateral connections), conscious processing is necessary to interpret local features as global shape.     

Hormonal regulation of root growth: integrating local activities into global behaviour

To date, plant researchers have probed the control of root growth by studying the roles of individual regulatory components or cellular processes. However, recent studies in the Arabidopsis (Arabidopsis thaliana) root have shown that different hormones control organ growth by regulating specific growth processes (cell proliferation, differentiation or expansion) in distinct tissues. We discuss key issues raised by these new insights and hypothesise that novel tissue-to-tissue signals exist to coordinate organ growth. We conclude by describing how multiscale models can help probe the interplay between the different scales at which hormones and their regulatory networks operate in different cells and tissues. Such approaches promise to generate new insights into the mechanisms that control root growth.     

Seeing invisible motion: a human FMRI study

A common view about visual consciousness is that it could arise when and where activity reaches some higher level of processing along the cortical hierarchy. Reports showing that activity in striate cortex can be dissociated from awareness , whereas the latter modulates activity in higher areas , point in this direction. In the specific case of visual motion, a central, "perceptual" role has been assigned to area V5: several human and monkey studies have shown V5 activity to correlate with the motion percept. Here we show that activity in this and other higher cortical areas can be also dissociated from perception and follow the physical stimulus instead. The motion information in a peripheral grating modulated fMRI responses, despite being invisible to human volunteers: under crowding conditions , areas V3A, V5, and parietal cortex still showed increased activity when the grating was moving compared to when it was flickering. We conclude that stimulus-specific activation of higher cortical areas does not necessarily result in awareness of the underlying stimulus.     

Representation of objective similarity among three-dimensional shapes in the monkey

Humans have been recently shown to represent parameterized three-dimensional objects in a manner that preserves relative similarities (as measured by parameter-space distances) among the objects (Cutzu and Edelman 1996). We show that the representation of objects in the monkey visual system is similarly faithful to the parametric variation built into the stimulus set. A monkey (Macaca fuscata) performed a delayed matching-to-sample task with 28 images (4 views 7 objects). Stimuli in each of the two experiments were seven computer-rendered parameterized animal-like shapes, arranged in a low-dimensional configuration (namely, a two-dimensional TRIANGLE) in a common 56-dimensional parameter space. The monkey's task was to match objects (not views). Each experiment lasted for 3–4 weeks after the introduction of the stimulus set to the subject. Error rates were entered into a object confusion matrix and submitted to nonmetric multidimensional scaling (MDS). In both experiment 1 (mean correct rate 69.7%) and experiment 2 (mean correct rate 59.9%), the MDS solutions resembled closely the low-dimensional parameter-space patterns built into the stimuli, in the sense that the point corresponding to the central one in the original pattern was inside the other six points and that the order of the six points in angular positions around the center point was preserved. A simulation study showed that the resemblance could not be due to chance. These results demonstrate the possibility of veridical representation of parametric similarity among complex objects in the monkey. Received: 9 May 1997 / Accepted in revised form: 18 September 1997     

Protein-protein interactions: from global to local analyses

For the increasing number of species with complete genome sequences, the task of elucidating their complete proteomes and interactomes has attracted much recent interest. Although the proteome describes the complete repertoire of proteins expressed, the interactome comprises the pairwise protein-protein interactions that occur, or could occur, within an organism, and forms a large-scale sparse network. Here we discuss the challenges provided by present data, and outline a route from global analysis to more detailed and focused studies of protein-protein interactions. Carefully using protein-interaction data allows us to explore its potential fully alongside the evaluation of mechanistic hypotheses about biological systems.     

Relation of enzyme activity to local/global stability of murine adenosine deaminase: 19F NMR studies

Adenosine deaminase (ADA, EC 3.5.4.4) is a ubiquitous (beta/alpha)8-barrel enzyme crucial for purine metabolism and normal immune competence. In this study, it was observed that loss of enzyme activity of murine ADA (mADA) precedes the global secondary and tertiary structure transition when the protein is exposed to denaturant. The structural mechanism for this phenomenon was probed using site-specific 19F NMR spectroscopy in combination with [6-19F]tryptophan labeling and inhibitor binding. There are four tryptophan residues in mADA and all are located more than 12 A from the catalytic site. The 19F NMR spectra of [6-19F]Trp-labelled mADA show that the urea-induced chemical shift change of 19F resonance of W161, one of the four tryptophan 19F nuclei, correlates with the loss of enzyme activity. The urea-induced chemical shift change of another 19F resonance of W117 correlates with the change of the apparent rate constant for the binding of transition-state analogue inhibitor deoxycoformycin to the enzyme. On the other hand, the chemical environment of the local region around W264 does not change significantly, as a consequence of perturbation by low concentrations of urea or substrate analog. The results indicate that different regions of mADA have different local stability, which controls the activity and stability of the enzyme. The results provide new insights into the relationship between the function of a protein and its conformational flexibility as well as its global stability. This study illustrates the advantage of 19F NMR spectroscopy in probing site-related conformational change information in ligand binding, enzymatic activity and protein folding.     

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.     

Integration of the Serratia marcescens haemolysin into human erythrocyte membranes

The haemolytic activity of Serratia marcescens is determined by two proteins, ShlA and ShlB. ShlA integrates into the erythrocyte membrane and causes osmotic lysis through channel formation. The conformation of ShlA and its interaction with erythrocyte membranes were studied by determining the cleavage of ShlA by added trypsin. Our results suggest that the conformation of inactive ShlA (from an ShlB- strain) differs from the active ShlA, and that in a hydrophobic environment (detergent or membrane) active ShlA assumes a conformation distinct from that in buffer. Only active haemolysin adsorbed to erythrocytes. ShlA was firmly integrated into the erythrocyte membrane since it was only released under conditions which also dissolved the integral erythrocyte membrane proteins. Moreover, ShlA integrated into 'ghosts' remained there and was not haemolytic when incubated with erythrocytes. From the trypsin cleavage pattern obtained with haemolysin and C-terminally truncated, but still active, haemolysin derivatives integrated into erythrocytes, and sealed and unsealed erythrocyte 'ghosts', we conclude that ShlA is preferentially cleaved by trypsin at a few sites but only from the inside of the erythrocyte. Haemolysin in the erythrocyte membrane forms a water-filled channel and is resistant to trypsin and other proteases.     

Micropuncture and microanalytical studies of rhesus monkey and baboon epididymis and the human ductus deferens

Using micropuncture and microanalytical techniques, we studied the microenvironment surrounding the maturing spermatozoa in different regions along the epididymis of the rhesus monkey (Macaca mulatta; 3 animals) and the baboon (Papio cynocephalus; 1 animal) and in the human ductus deferens. In the monkey and baboon, samples of luminal contents (luminal fluid and spermatozoa) of approximately 50 to 300 nanolitres were collected from several epididymal sites and the luminal fluid analyzed for inositol. Similarly, a sample of approximately 0.5 to 1.0 μl of luminal contents was collected from each human ductus deferens and the luminal fluid analyzed for sodium, potassium, chloride, inositol, carnitine, glycerophosphocholine (GPC), phosphocholine and total phosphate. Each analysis required the modification of standard methods to accommodate the very small sample volumes collected. We show that the microenvironment in the monkey, baboon, and human is different from those in other species with respect to the concentration of compounds estimated. In the luminal fluid of the human ductus deferens, the majority of the osmoticallyactive compounds are the inorganic ions which is in direct contrast to the rat, hamster, rabbit, ram and boar. In these species, organic compounds contribute significantly more to the osmolarity of the luminal fluid than do inorganic ions. Although the significance of these findings is unclear, a relationship seems to exist between the appearance of carnitine in the luminal fluid of the proximal caput epididymidis of the rat and the point where spermatozoa develop the potential for motility. These investigations also raise the question of which species most closely reflects the physiology of the reproductive system of man.     

One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies

The mechanistic details of metallonuclease reactions, typically supported by Mg(II), have a long and contentious history. Two-metal ion mechanisms have enjoyed much favor, based largely in the multitude of X-ray crystal structures of these enzymes with more than one metal ion per active site. Most recently, this mechanism has come under challenge. Reviewed herein are the applications of different experimental strategies that collectively support a mechanism in which only one metal ion is necessary for nucleic acid hydrolysis. Based on global kinetic analysis, analysis of reactions in which the nonsupportive Ca(ii) is added, and a number of computational approaches, secondary sites are proposed to either be occupied by activity-modulating metal ions or occupied in turn by a single metal that changes position during the course of the reaction.     

Comparative cognition: comparing human and monkey memory

Humans store a limited number of items in short-term working memory to perform subsequent operations. A newly described assessment of memory in rhesus monkeys suggests qualitative similarities and quantitative dissimilarities to humans.