Effects of Microstimulation in the Anterior Intraparietal Area during Three-Dimensional Shape Categorization

The anterior intraparietal area (AIP) of rhesus monkeys is part of the dorsal visual stream and contains neurons whose visual response properties are commensurate with a role in three-dimensional (3D) shape perception. Neuronal responses in AIP signal the depth structure of disparity-defined 3D shapes, reflect the choices of monkeys while they categorize 3D shapes, and mirror the behavioral variability across different stimulus conditions during 3D-shape categorization. However, direct evidence for a role of AIP in 3D-shape perception has been lacking. We trained rhesus monkeys to categorize disparity-defined 3D shapes and examined AIP''s contribution to 3D-shape categorization by microstimulating in clusters of 3D-shape selective AIP neurons during task performance. We find that microstimulation effects on choices (monkey M1) and reaction times (monkey M1 and M2) depend on the 3D-shape preference of the stimulated site. Moreover, electrical stimulation of the same cells, during either the 3D-shape-categorization task or a saccade task, could affect behavior differently. Interestingly, in one monkey we observed a strong correlation between the strength of choice-related AIP activity (choice probabilities) and the influence of microstimulation on 3D-shape-categorization behavior (choices and reaction time). These findings propose AIP as part of the network responsible for 3D-shape perception. The results also show that the anterior intraparietal cortex contains cells with different tuning properties, i.e. 3D-shape- or saccade-related, that can be dynamically read out depending on the requirements of the task at hand.     

The inferior temporal cortex: Architecture, computation, and representation

Neurons in the inferior temporal cortex (IT), an area crucially involved in visual object recognition in monkeys, show the visual response properties and anatomical/chemical nature which are distinct from those in the cortical areas that feed visual inputs to the IT. Earlier physiological studies showed that IT neurons have large receptive fields covering the center and contralateral (often bilateral) visual fields, stimulus selectivity for images of complex objects or shapes, and translation invariance of the stimulus selectivity. Recent studies have revealed new aspects of their properties such as invariant selectivity for shapes despite drastic changes in various physical attributes of stimuli, latent excitatory inputs masked by stimulus-specific GABAergic inhibition, selectivity for binocular disparity and 3-dimensional surface structures, profound effects of learning on the stimulus selectivity, and columnar clustering of neurons with similarstimulus selectivity for shapes and other object features. Another line of research using histological techniques have revealed that pyramidal neurons in the IT are larger in the size of dendritic arbors, in the number of dendritic branches and spines, and in the size and distribution of horizontal axonal arbors than those in the earlier areas, allowing them to integrate a larger population of afferents and process more diverse inputs. The concentration of several neurochemicals including those related to synaptic transmission or plasticity changes systematically towards the IT along the occipitotemporal pathway. Many of the characteristics of IT neurons parallel or explain certain aspects of visual object perception, although the behavioral relevance has yet to be addressed experimentally.     

ContPro: A web tool for calculating amino acid contact distances in protein from 3D -structures at different distance threshold

To investigate the functional sites on a protein and the prediction of binding sites (residues)in proteins, it is often required to identify the binding site residues at different distance threshold from protein three dimensional (3D)structures. For the study of a particular protein chain and its interaction with the ligand in complex form, researchers have to parse the output of different available tools or databases for finding binding-site residues. Here we have developed a tool for calculating amino acid contact distances in proteins at different distance threshold from the 3D-structure of the protein. For an input of protein 3D-structure, ContPro can quickly find all binding-site residues in the protein by calculating distances and also allows researchers to select the different distance threshold, protein chain and ligand of interest. Additionally, it can also parse the protein model (in case of multi model protein coordinate file)and the sequence of selected protein chain in Fasta format from the input 3D-structure. The developed tool will be useful for the identification and analysis of binding sites of proteins from 3D-structure at different distance thresholds. AVAILABILITY: IT CAN BE ACCESSED AT: http://procarb.org/contpro/     

Sensory neuroscience: from skin to object in the somatosensory cortex

Humans can perceive the shape of objects by touch alone, by extracting geometric features such as edges. Recently recorded responses of single neurons in the secondary somatosensory cortex of monkeys suggest how the brain integrates tactile shape information across different regions of skin and builds up a representation of tactile objects.     

Anterior regions of monkey parietal cortex process visual 3D shape

The intraparietal cortex is involved in the control of visually guided actions, like reach-to-grasp movements, which require extracting the 3D shape and position of objects from 2D retinal images. Using fMRI in behaving monkeys, we investigated the role of the intraparietal cortex in processing stereoscopic information for recovering the depth structure and the position in depth of objects. We found that while several areas (CIP, LIP, and AIP on the lateral bank; PIP and MIP on the medial bank) are activated by stereoscopic stimuli, AIP and an adjoining portion of LIP are sensitive only to depth structure. Furthermore, only these two regions are sensitive to both the depth structure and the 2D shape of small objects. These results indicate that extracting 3D spatial information from stereo involves several intraparietal areas, among which AIP and anterior LIP are more specifically engaged in extracting the 3D shape of objects.     

Long-Term Stability of Visual Pattern Selective Responses of Monkey Temporal Lobe Neurons

Many neurons in primate inferotemporal (IT) cortex respond selectively to complex, often meaningful, stimuli such as faces and objects. An important unanswered question is whether such response selectivity, which is thought to arise from experience-dependent plasticity, is maintained from day to day, or whether the roles of individual cells are continually reassigned based on the diet of natural vision. We addressed this question using microwire electrodes that were chronically implanted in the temporal lobe of two monkeys, often allowing us to monitor activity of individual neurons across days. We found that neurons maintained their selectivity in both response magnitude and patterns of spike timing across a large set of visual images throughout periods of stable signal isolation from the same cell that sometimes exceeded two weeks. These results indicate that stimulus-selectivity of responses in IT is stable across days and weeks of visual experience.     

Active maintenance of associative mnemonic signal in monkey inferior temporal cortex

We investigated the contribution of the inferior temporal (IT) cortical neurons to the active maintenance of internal representations. The activity of single neurons in the IT cortex was recorded while the monkeys performed a sequential-type associative memory task in which distractor stimuli interrupted the delay epoch between the cue and target (paired-associate) stimuli. For each neuron, information about each stimulus conveyed by the delay activity was estimated as a coefficient of multiple regression analysis. We found that target information derived from long-term memory (LTM) persisted despite the distractors. By contrast, cue information derived from the visual system was attenuated and frequently replaced by distractor information. These results suggest that LTM-derived information required for upcoming behavior is actively maintained in the IT neurons, whereas visually derived information tends to be updated irrespective of behavioral relevance.     

MMDB: Entrez’s 3D-structure database

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure.     

Fragment-based learning of visual object categories in non-human primates

When we perceive a visual object, we implicitly or explicitly associate it with an object category we know. Recent research has shown that the visual system can use local, informative image fragments of a given object, rather than the whole object, to classify it into a familiar category. We have previously reported, using human psychophysical studies, that when subjects learn new object categories using whole objects, they incidentally learn informative fragments, even when not required to do so. However, the neuronal mechanisms by which we acquire and use informative fragments, as well as category knowledge itself, have remained unclear. Here we describe the methods by which we adapted the relevant human psychophysical methods to awake, behaving monkeys and replicated key previous psychophysical results. This establishes awake, behaving monkeys as a useful system for future neurophysiological studies not only of informative fragments in particular, but also of object categorization and category learning in general.     

Deep Supervised,but Not Unsupervised,Models May Explain IT Cortical Representation

Inferior temporal (IT) cortex in human and nonhuman primates serves visual object recognition. Computational object-vision models, although continually improving, do not yet reach human performance. It is unclear to what extent the internal representations of computational models can explain the IT representation. Here we investigate a wide range of computational model representations (37 in total), testing their categorization performance and their ability to account for the IT representational geometry. The models include well-known neuroscientific object-recognition models (e.g. HMAX, VisNet) along with several models from computer vision (e.g. SIFT, GIST, self-similarity features, and a deep convolutional neural network). We compared the representational dissimilarity matrices (RDMs) of the model representations with the RDMs obtained from human IT (measured with fMRI) and monkey IT (measured with cell recording) for the same set of stimuli (not used in training the models). Better performing models were more similar to IT in that they showed greater clustering of representational patterns by category. In addition, better performing models also more strongly resembled IT in terms of their within-category representational dissimilarities. Representational geometries were significantly correlated between IT and many of the models. However, the categorical clustering observed in IT was largely unexplained by the unsupervised models. The deep convolutional network, which was trained by supervision with over a million category-labeled images, reached the highest categorization performance and also best explained IT, although it did not fully explain the IT data. Combining the features of this model with appropriate weights and adding linear combinations that maximize the margin between animate and inanimate objects and between faces and other objects yielded a representation that fully explained our IT data. Overall, our results suggest that explaining IT requires computational features trained through supervised learning to emphasize the behaviorally important categorical divisions prominently reflected in IT.     

Neural coding of 3D features of objects for hand action in the parietal cortex of the monkey.

In our previous studies of hand manipulation task-related neurons, we found many neurons of the parietal association cortex which responded to the sight of three-dimensional (3D) objects. Most of the task-related neurons in the AIP area (the lateral bank of the anterior intraparietal sulcus) were visually responsive and half of them responded to objects for manipulation. Most of these neurons were selective for the 3D features of the objects. More recently, we have found binocular visual neurons in the lateral bank of the caudal intraparietal sulcus (c-IPS area) that preferentially respond to a luminous bar or place at a particular orientation in space. We studied the responses of axis-orientation selective (AOS) neurons and surface-orientation selective (SOS) neurons in this area with stimuli presented on a 3D computer graphics display. The AOS neurons showed a stronger response to elongated stimuli and showed tuning to the orientation of the longitudinal axis. Many of them preferred a tilted stimulus in depth and appeared to be sensitive to orientation disparity and/or width disparity. The SOS neurons showed a stronger response to a flat than to an elongated stimulus and showed tuning to the 3D orientation of the surface. Their responses increased with the width or length of the stimulus. A considerable number of SOS neurons responded to a square in a random dot stereogram and were tuned to orientation in depth, suggesting their sensitivity to the gradient of disparity. We also found several SOS neurons that responded to a square with tilted or slanted contours, suggesting their sensitivity to orientation disparity and/or width disparity. Area c-IPS is likely to send visual signals of the 3D features of an object to area AIP for the visual guidance of hand actions.     

Representation of visual stimuli in inferior temporal cortex.

In primates, inferior temporal (IT) cortex is crucial for the processing and storage of visual information about form and colour. This article reviews the properties of IT neurons and considers how these properties may underlie the perceptual and mnemonic functions of IT cortex. The available evidence suggests that the processing of the facial image by IT cortex is similar to its processing of other visual patterns. Faces and other complex visual stimuli appear to be represented by the pattern of responses over a population of IT neurons rather than by the responses of specific 'feature detectors' or 'grandmother' cells. IT neurons with adult-like stimulus properties are present in monkeys as young as six weeks old.     

Neural Representation of Ambiguous Visual Objects in the Inferior Temporal Cortex

Inferior temporal (IT) cortex as the final stage of the ventral visual pathway is involved in visual object recognition. In our everyday life we need to recognize visual objects that are degraded by noise. Psychophysical studies have shown that the accuracy and speed of the object recognition decreases as the amount of visual noise increases. However, the neural representation of ambiguous visual objects and the underlying neural mechanisms of such changes in the behavior are not known. Here, by recording the neuronal spiking activity of macaque monkeys’ IT we explored the relationship between stimulus ambiguity and the IT neural activity. We found smaller amplitude, later onset, earlier offset and shorter duration of the response as visual ambiguity increased. All of these modulations were gradual and correlated with the level of stimulus ambiguity. We found that while category selectivity of IT neurons decreased with noise, it was preserved for a large extent of visual ambiguity. This noise tolerance for category selectivity in IT was lost at 60% noise level. Interestingly, while the response of the IT neurons to visual stimuli at 60% noise level was significantly larger than their baseline activity and full (100%) noise, it was not category selective anymore. The latter finding shows a neural representation that signals the presence of visual stimulus without signaling what it is. In general these findings, in the context of a drift diffusion model, explain the neural mechanisms of perceptual accuracy and speed changes in the process of recognizing ambiguous objects.     

Figure and ground in the visual cortex: v2 combines stereoscopic cues with gestalt rules

Figure-ground organization is a process by which the visual system identifies some image regions as foreground and others as background, inferring 3D layout from 2D displays. A recent study reported that edge responses of neurons in area V2 are selective for side-of-figure, suggesting that figure-ground organization is encoded in the contour signals (border ownership coding). Here, we show that area V2 combines two strategies of computation, one that exploits binocular stereoscopic information for the definition of local depth order, and another that exploits the global configuration of contours (Gestalt factors). These are combined in single neurons so that the "near" side of the preferred 3D edge generally coincides with the preferred side-of-figure in 2D displays. Thus, area V2 represents the borders of 2D figures as edges of surfaces, as if the figures were objects in 3D space. Even in 3D displays, Gestalt factors influence the responses and can enhance or null the stereoscopic depth information.     

Neuronal Categorization and Discrimination of Social Behaviors in Primate Prefrontal Cortex

It has been implied that primates have an ability to categorize social behaviors between other individuals for the execution of adequate social-interactions. Since the lateral prefrontal cortex (LPFC) is involved in both the categorization and the processing of social information, the primate LPFC may be involved in the categorization of social behaviors. To test this hypothesis, we examined neuronal activity in the LPFC of monkeys during presentations of two types of movies of social behaviors (grooming, mounting) and movies of plural monkeys without any eye- or body-contacts between them (no-contacts movies). Although the monkeys were not required to categorize and discriminate the movies in this task, a subset of neurons sampled from the LPFC showed a significantly different activity during the presentation of a specific type of social behaviors in comparison with the others. These neurons categorized social behaviors at the population level and, at the individual neuron level, the majority of the neurons discriminated each movie within the same category of social behaviors. Our findings suggest that a fraction of LPFC neurons process categorical and discriminative information of social behaviors, thereby contributing to the adaptation to social environments.     

Novel approach to computer modeling of seven-helical transmembrane proteins: current progress in the test case of bacteriorhodopsin.

G-protein coupled receptors (GPCRs) are thought to be proteins with 7-membered transmembrane helical bundles (7TM proteins). Recently, the X-ray structures have been solved for two such proteins, namely for bacteriorhodopsin (BR) and rhodopsin (Rh), the latter being a GPCR. Despite similarities, the structures are different enough to suggest that 3D models for different GPCRs cannot be obtained directly employing 3D structures of BR or Rh as a unique template. The approach to computer modeling of 7TM proteins developed in this work was capable of reproducing the experimental X-ray structure of BR with great accuracy. A combination of helical packing and low-energy conformers for loops most close to the X-ray structure possesses the r.m.s.d. value of 3.13 A. Such a level of accuracy for the 3D-structure prediction for a 216-residue protein has not been achieved, so far, by any available ab initio procedure of protein folding. The approach may produce also other energetically consistent combinations of helical bundles and loop conformers, creating a variety of possible templates for 3D structures of 7TM proteins, including GPCRs. These templates may provide experimentalists with various plausible options for 3D structure of a given GPCR; in our view, only experiments will determine the final choice of the most reasonable 3D template.     

MMDB: Entrez's 3D structure database.

The three dimensional structures for representatives of nearly half of all protein families are now available in public databases. Thus, no matter which protein one investigates, it is increasingly likely that the 3D structure of a homolog will be known and may reveal unsuspected structure-function relationships. The goal of Entrez's 3D-structure database is to make this information accessible and usable by molecular biologists (http://www.ncbi.nlm.nih.gov/Entrez). To this end Entrez provides two major analysis tools, a search engine based on sequence and structure 'neighboring' and an integrated visualization system for sequence and structure alignments. From a protein's sequence 'neighbors' one may rapidly identify other members of a protein family, including those where 3D structure is known. By comparing aligned sequences and/or structures in detail, using the visualization system, one may identify conserved features and perhaps infer functional properties. Here we describe how these analysis tools may be used to investigate the structure and function of newly discovered proteins, using the PTEN gene product as an example.     

MMDB: Entrez's 3D-structure database

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html.     

Phase locking of single neuron activity to theta oscillations during working memory in monkey extrastriate visual cortex

Working memory has been linked to elevated single neuron discharge in monkeys and to oscillatory changes in the human EEG, but the relation between these effects has remained largely unexplored. We addressed this question by measuring local field potentials and single unit activity simultaneously from multiple electrodes placed in extrastriate visual cortex while monkeys were performing a working memory task. We describe a significant enhancement in theta band energy during the delay period. Theta oscillations had a systematic effect on single neuron activity, with neurons emitting more action potentials near their preferred angle of each theta cycle. Sample-selective delay activity was enhanced if only action potentials emitted near the preferred theta angle were considered. Our results suggest that extrastriate visual cortex is involved in short-term maintenance of information and that theta oscillations provide a mechanism for structuring the recurrent interaction between neurons in different brain regions that underlie working memory.     

Responses of neurons in primary and inferior temporal visual cortices to natural scenes.

The primary visual cortex (V1) is the first cortical area to receive visual input, and inferior temporal (IT) areas are among the last along the ventral visual pathway. We recorded, in area V1 of anaesthetized cats and area IT of awake macaque monkeys, responses of neurons to videos of natural scenes. Responses were analysed to test various hypotheses concerning the nature of neural coding in these two regions. A variety of spike-train statistics were measured including spike-count distributions, interspike interval distributions, coefficients of variation, power spectra, Fano factors and different sparseness measures. All statistics showed non-Poisson characteristics and several revealed self-similarity of the spike trains. Spike-count distributions were approximately exponential in both visual areas for eight different videos and for counting windows ranging from 50 ms to 5 seconds. The results suggest that the neurons maximize their information carrying capacity while maintaining a fixed long-term-average firing rate, or equivalently, minimize their average firing rate for a fixed information carrying capacity.