On the computational architecture of the neocortex

This paper is a sequel to an earlier paper which proposed an active role for the thalamus, integrating multiple hypotheses formed in the cortex via the thalamo-cortical loop. In this paper, I put forward a hypothesis on the role of the reciprocal, topographic pathways between two cortical areas, one often a higher area dealing with more abstract information about the world, the other lower, dealing with more concrete data. The higher area attempts to fit its abstractions to the data it receives from lower areas by sending back to them from its deep pyramidal cells a template reconstruction best fitting the lower level view. The lower area attempts to reconcile the reconstruction of its view that it receives from higher areas with what it knows, sending back from its superficial pyramidal cells the features in its data which are not predicted by the higher area. The whole calculation is done with all areas working simultaneously, but with order imposed by synchronous activity in the various top-down, bottom-up loops. Evidence for this theory is reviewed and experimental tests are proposed. A third part of this paper will deal with extensions of these ideas to the frontal lobe.     

A computational model for the primate neocortex based on its functional architecture

Experimental evidence has shown that the primate neocortex consists in the main of a set of cortical regions which form a perception hierarchy, an action hierarchy and connections between them. By using a computer science analysis, we develop a computational architecture for the brain in which each cortical region is represented by a computational module with processing and storage abilities. Modules are interconnected according to the connectivity of the corresponding cortical regions. We develop computational principles for designing such a hierarchical and parallel computing system. We demonstrate this approach by proposing a causal functioning model of the brain. We report on results obtained with an implementation of this model. We conclude with a brief discussion of some consequences and predictions of our work.     

A neuron-inspired computational architecture for spatiotemporal visual processing

In this article, we present a neurologically motivated computational architecture for visual information processing. The computational architecture’s focus lies in multiple strategies: hierarchical processing, parallel and concurrent processing, and modularity. The architecture is modular and expandable in both hardware and software, so that it can also cope with multisensory integrations – making it an ideal tool for validating and applying computational neuroscience models in real time under real-world conditions. We apply our architecture in real time to validate a long-standing biologically inspired visual object recognition model, HMAX. In this context, the overall aim is to supply a humanoid robot with the ability to perceive and understand its environment with a focus on the active aspect of real-time spatiotemporal visual processing. We show that our approach is capable of simulating information processing in the visual cortex in real time and that our entropy-adaptive modification of HMAX has a higher efficiency and classification performance than the standard model (up to \(\sim \!+6\,\% \) ).     

On the architecture of cell regulation networks

Background  

With the rapid development of high-throughput experiments, detecting functional modules has become increasingly important in analyzing biological networks. However, the growing size and complexity of these networks preclude structural breaking in terms of simplest units. We propose a novel graph theoretic decomposition scheme combined with dynamics consideration for probing the architecture of complex biological networks.     

On the molecular architecture of myelinated fibers

Schwann cells and oligodendrocytes make the myelin sheaths of the PNS and CNS, respectively. Their myelin sheaths are structurally similar, consisting of multiple layers of specialized cell membrane that spiral around axons, but there are several differences. (1) CNS myelin has a ”radial component” composed of a tight junction protein, claudin-11/oligodendrocyte-specific protein. (2) Schwann cells have a basal lamina and microvilli. (3) Although both CNS and PNS myelin sheaths have incisures, those in the CNS lack the structural as well as the molecular components of ”reflexive” adherens junctions and gap junctions. In spite of their structural differences, the axonal membranes of the PNS and CNS are similarly organized. The nodal axolemma contains high concentrations of voltage-dependent sodium channels that are linked to the axonal cytoskeleton by ankyrin_G. The paranodal membrane contains Caspr/paranodin, which may participate in the formation of axoglial junctions. The juxtaparanodal axonal membrane contains the potassium channels Kv1.1 and Kv1.2, their associated β2 subunit, as well as Caspr2, which is closely related to Caspr. The myelin sheath probably organizes these axonal membrane-related proteins via trans interactions. Accepted: 25 November 1999     

Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs

Modular architecture is a hallmark of RNA structures, implying structural, and possibly functional, similarity among existing RNAs. To systematically delineate the existence of smaller topologies within larger structures, we develop and apply an efficient RNA secondary structure comparison algorithm using a newly developed two-dimensional RNA graphical representation. Our survey of similarity among 14 pseudoknots and subtopologies within ribosomal RNAs (rRNAs) uncovers eight pairs of structurally related pseudoknots with non-random sequence matches and reveals modular units in rRNAs. Significantly, three structurally related pseudoknot pairs have functional similarities not previously known: one pair involves the 3′ end of brome mosaic virus genomic RNA (PKB134) and the alternative hammerhead ribozyme pseudoknot (PKB173), both of which are replicase templates for viral RNA replication; the second pair involves structural elements for translation initiation and ribosome recruitment found in the viral internal ribosome entry site (PKB223) and the V4 domain of 18S rRNA (PKB205); the third pair involves 18S rRNA (PKB205) and viral tRNA-like pseudoknot (PKB134), which probably recruits ribosomes via structural mimicry and base complementarity. Additionally, we quantify the modularity of 16S and 23S rRNAs by showing that RNA motifs can be constructed from at least 210 building blocks. Interestingly, we find that the 5S rRNA and two tree modules within 16S and 23S rRNAs have similar topologies and tertiary shapes. These modules can be applied to design novel RNA motifs via build-up-like procedures for constructing sequences and folds.     

A computational remodeling approach to predict the physiological architecture of the collagen fibril network in corneo-scleral shells

Organized collagen fibrils form complex networks that introduce strong anisotropic and highly nonlinear attributes into the constitutive response of human eye tissues. Physiological adaptation of the collagen network and the mechanical condition within biological tissues are complex and mutually dependent phenomena. In this contribution, a computational model is presented to investigate the interaction between the collagen fibril architecture and mechanical loading conditions in the corneo-scleral shell. The biomechanical properties of eye tissues are derived from the single crimped fibril at the micro-scale via the collagen network of distributed fibrils at the meso-scale to the incompressible and anisotropic soft tissue at the macro-scale. Biomechanically induced remodeling of the collagen network is captured on the meso-scale by allowing for a continuous re-orientation of preferred fibril orientations and a continuous adaptation of the fibril dispersion. The presented approach is applied to a numerical human eye model considering the cornea and sclera. The predicted fibril morphology correlates well with experimental observations from X-ray scattering data.     

On the architecture of the gram-negative bacterial murein sacculus

The peptidoglycan network of the murein sacculus must be porous so that nutrients, waste products, and secreted proteins can pass through. Using Escherichia coli and Pseudomonas aeruginosa as a baseline for gram-negative sacculi, the hole size distribution in the peptidoglycan network has been modeled by computer simulation to deduce the network's properties. By requiring that the distribution of glycan chain lengths predicted by the model be in accord with the distribution observed, we conclude that the holes are slits running essentially perpendicular to the local axis of the glycan chains (i. e., the slits run along the long axis of the cell). This result is in accord with previous permeability measurements of Beveridge and Jack and Demchik and Koch. We outline possible advantages that might accrue to the bacterium via this architecture and suggest ways in which such defect structures might be detected. Certainly, large molecules do penetrate the peptidoglycan layer of gram-negative bacteria, and the small slits that we suggest might be made larger by the bacterium.     

On the origin of the functional architecture of the cortex

The basic structure of receptive fields and functional maps in primary visual cortex is established without exposure to normal sensory experience and before the onset of the critical period. How the brain wires these circuits in the early stages of development remains unknown. Possible explanations include activity-dependent mechanisms driven by spontaneous activity in the retina and thalamus, and molecular guidance orchestrating thalamo-cortical connections on a fine spatial scale. Here I propose an alternative hypothesis: the blueprint for receptive fields, feature maps, and their inter-relationships may reside in the layout of the retinal ganglion cell mosaics along with a simple statistical connectivity scheme dictating the wiring between thalamus and cortex. The model is shown to account for a number of experimental findings, including the relationship between retinotopy, orientation maps, spatial frequency maps and cytochrome oxidase patches. The theory's simplicity, explanatory and predictive power makes it a serious candidate for the origin of the functional architecture of primary visual cortex.     

The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking

CopA uses ATP to pump Cu(+) across cell membranes. X-ray crystallography has defined atomic structures of several related P-type ATPases. We have determined a structure of CopA at 10?? resolution by cryo-electron microscopy of a new crystal form and used computational molecular docking to study the interactions between the N-terminal metal-binding domain (NMBD) and other elements of the molecule. We found that the shorter-chain lipids used to produce these crystals are associated with movements of the cytoplasmic domains, with a novel dimer interface and with disordering of the NMBD, thus offering evidence for the transience of its interaction with the other cytoplasmic domains. Docking identified a binding site that matched the location of the NMBD in our previous structure by cryo-electron microscopy, allowing a more detailed view of its binding configuration and further support for its role in autoinhibition.     

The collagen fibril architecture in the lamina cribrosa and peripapillary sclera predicted by a computational remodeling approach

The biomechanics of the optic nerve head is assumed to play an important role in ganglion cell loss in glaucoma. Organized collagen fibrils form complex networks that introduce strong anisotropic and nonlinear attributes into the constitutive response of the peripapillary sclera (PPS) and lamina cribrosa (LC) dominating the biomechanics of the optic nerve head. The recently presented computational remodeling approach (Grytz and Meschke in Biomech Model Mechanobiol 9:225–235, 2010) was used to predict the micro-architecture in the LC and PPS, and to investigate its impact on intraocular pressure–related deformations. The mechanical properties of the LC and PPS were derived from a microstructure-oriented constitutive model that included the stretch-dependent stiffening and the statistically distributed orientations of the collagen fibrils. Biomechanically induced adaptation of the local micro-architecture was captured by allowing collagen fibrils to be reoriented in response to the intraocular pressure–related loading conditions. In agreement with experimental observations, the remodeling algorithm predicted the existence of an annulus of fibrils around the scleral canal in the PPS, and a predominant radial orientation of fibrils in the periphery of the LC. The peripapillary annulus significantly reduced the intraocular pressure–related expansion of the scleral canal and shielded the LC from high tensile stresses. The radial oriented fibrils in the LC periphery reinforced the LC against transversal shear stresses and reduced LC bending deformations. The numerical approach presents a novel and reasonable biomechanical explanation of the spatial orientation of fibrillar collagen in the optic nerve head.     

On Wolff's law of trabecular architecture.

Several studies suggest that the yield strain in cancellous bone may be uniformly distributed and isotropic. Yield strain was reported to be independent of textural anisotropy in bovine cancellous bone [Turner, J. biomech. Engng 111, 1-5 (1989)] and it is plausible that yield strain is isotropic in human cancellous bone as well. In this paper, it is hypothesized that uniform, isotropic strain represents a goal of cancellous bone adaptation, i.e. cancellous bone alters its structure to maintain uniform, isotropic peak strains. Therefore, textural anisotropy must exactly cancel the anisotropy of the peak principal stresses imposed upon cancellous bone. When evaluating the relationships between mechanical properties of cancellous bone and trabecular architecture, it was found that over 90% of the variance of yield strength can be explained by one term--rho 2H3 (where rho is apparent density and H is the normalized anisotropy (fabric) constant). Furthermore, this single term explains 70-78% of the variance in Young's modulus of cancellous bone. Based upon these findings, it was postulated that fabric adaptation goes as Hi/Hj = [ sigma i/sigma j[, where Hi and Hj are fabric eigenvalues in the i- and the j-direction and sigma i and sigma j are peak principal stresses.     

On the complexity of fundamental computational problems in pedigree analysis.

Pedigree analysis is a central component of many current efforts to locate genes that contribute to diseases or to valuable traits. The analysis usually involves solving one of two very computation-intense problems. We analyze the complexity of these two problems. Surprisingly, we show that both problems are NP-hard even for pedigrees that contain no inbreeding loops.     

Conditioned reflex-related plasticity in the neocortex

The spike activity of neurons of the sensorimotor cortex was analyzed in cats before, during, and after iontophoretic application of substances influencing synaptic transmission. It was shown that, in addition to glutamate ionotropic receptors, glutamate metabotropic receptors, as well as adrenergic and dopaminergic receptor systems, are involved in plastic rearrangements of synaptic connections among neocortical neurons. The pattern of aftereffects allows us to suppose that potentiation of synaptic events during conditioned reflex-related learning can be maintained for 10 to 20 min, an interval sufficient for consolidation of a memory track.