Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

The hybridization kinetics for a series of designed 25mer probe�target pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution and on the surface, respectively. Kinetic rate constants derived from the resultant data decrease with increasing probe and target secondary structure similarly in both solution and surface environments. Specifically, addition of three intramolecular base pairs in the probe and target structure slow hybridization by a factor of two. For individual strands containing four or more intramolecular base pairs, hybridization cannot be described by a traditional two-state model in solution-phase nor on the surface. Surface hybridization rates are also 20- to 40-fold slower than solution-phase rates for identical sequences and conditions. These quantitative findings may have implications for the design of better biosensors, particularly those using probes with deliberate secondary structure.

Surface Reconstruction from Multiple Views using Rational B-Splines

A method for reconstructing 3D rational B-spline surfaces from multiple views is proposed. The method takes advantage of the projective invariance properties of rational B-splines. Given feature correspondences in multiple views, the 3D surface is reconstructed via a four step framework. First, corresponding features in each view are given an initial surface parameter value (s; t), and a 2D B-spline is fitted in each view. After this initialization, an iterative minimization procedure alternates between updating the 2D B-spline control points and re-estimating each feature's (s; t). Next, a non-linear minimization method is used to upgrade the 2D B-splines to 2D rational B-splines, and obtain a better fit. Finally, a factorization method is used to reconstruct the 3D B-spline surface given 2D B-splines in each view. This surface recovery method can be applied in both the perspective and orthographic case. The orthographic case allows the use of additional constraints in the recovery. Experiments with real and synthetic imagery demonstrate the efficacy of the approach for the orthographic case.

Surface Reconstruction from Multiple Views using Rational B-Splines and Knot Insertion

A method for reconstruction of 3D rational B-spline surfaces from multiple views is proposed. Given corresponding features in multiple views, though not necessarily visible in all views, the surface is reconstructed. First 2D B-spline patches are fitted to each view. The 3D B-splines and projection matricies can then be extracted from the 2D B-splines using factorization methods. The surface fit is then further refined via an iterative procedure. Finally, a hierarchal fitting scheme is proposed to allow modeling of complex surfaces by means of knot insertion. Experiments with real imagery demonstrate the efficacy of the approach.

A Neural Model of Surface Perception: Lightness, Anchoring, and Filling-in

This article develops a neural model of how the visual system processes natural images under variable illumination conditions to generate surface lightness percepts. Previous models have clarified how the brain can compute the relative contrast of images from variably illuminate scenes. How the brain determines an absolute lightness scale that "anchors" percepts of surface lightness to us the full dynamic range of neurons remains an unsolved problem. Lightness anchoring properties include articulation, insulation, configuration, and are effects. The model quantatively simulates these and other lightness data such as discounting the illuminant, the double brilliant illusion, lightness constancy and contrast, Mondrian contrast constancy, and the Craik-O'Brien-Cornsweet illusion. The model also clarifies the functional significance for lightness perception of anatomical and neurophysiological data, including gain control at retinal photoreceptors, and spatioal contrast adaptation at the negative feedback circuit between the inner segment of photoreceptors and interacting horizontal cells. The model retina can hereby adjust its sensitivity to input intensities ranging from dim moonlight to dazzling sunlight. A later model cortical processing stages, boundary representations gate the filling-in of surface lightness via long-range horizontal connections. Variants of this filling-in mechanism run 100-1000 times faster than diffusion mechanisms of previous biological filling-in models, and shows how filling-in can occur at realistic speeds. A new anchoring mechanism called the Blurred-Highest-Luminance-As-White (BHLAW) rule helps simulate how surface lightness becomes sensitive to the spatial scale of objects in a scene. The model is also able to process natural images under variable lighting conditions.

Laminar Cortical Dynamics of 3D Surface Perception: Stratification, transparency, and Neon Color Spreading

How does the laminar organization of cortical circuitry in areas VI and V2 give rise to 3D percepts of stratification, transparency, and neon color spreading in response to 2D pictures and 3D scenes? Psychophysical experiments have shown that such 3D percepts are sensitive to whether contiguous image regions have the same relative contrast polarity (dark-light or lightdark), yet long-range perceptual grouping is known to pool over opposite contrast polarities. The ocularity of contiguous regions is also critical for neon color spreading: Having different ocularity despite the contrast relationship that favors neon spreading blocks the spread. In addition, half visible points in a stereogram can induce near-depth transparency if the contrast relationship favors transparency in the half visible areas. It thus seems critical to have the whole contrast relationship in a monocular configuration, since splitting it between two stereogram images cancels the effect. What adaptive functions of perceptual grouping enable it to both preserve sensitivity to monocular contrast and also to pool over opposite contrasts? Aspects of cortical development, grouping, attention, perceptual learning, stereopsis and 3D planar surface perception have previously been analyzed using a 3D LAMINART model of cortical areas VI, V2, and V4. The present work consistently extends this model to show how like-polarity competition between VI simple cells in layer 4 may be combined with other LAMINART grouping mechanisms, such as cooperative pooling of opposite polarities at layer 2/3 complex cells. The model also explains how the Metelli Rules can lead to transparent percepts, how bistable transparency percepts can arise in which either surface can be perceived as transparent, and how such a transparency reversal can be facilitated by an attention shift. The like-polarity inhibition prediction is consistent with lateral masking experiments in which two f1anking Gabor patches with the same contrast polarity as the target increase the target detection threshold when they approach the target. It is also consistent with LAMINART simulations of cortical development. Other model explanations and testable predictions will also be presented.

A Neuromorphic Model for Achromatic and Chromatic Surface Representation of Natural Images

This study develops a neuromorphic model of human lightness perception that is inspired by how the mammalian visual system is designed for this function. It is known that biological visual representations can adapt to a billion-fold change in luminance. How such a system determines absolute lightness under varying illumination conditions to generate a consistent interpretation of surface lightness remains an unsolved problem. Such a process, called "anchoring" of lightness, has properties including articulation, insulation, configuration, and area effects. The model quantitatively simulates such psychophysical lightness data, as well as other data such as discounting the illuminant, the double brilliant illusion, and lightness constancy and contrast effects. The model retina embodies gain control at retinal photoreceptors, and spatial contrast adaptation at the negative feedback circuit between mechanisms that model the inner segment of photoreceptors and interacting horizontal cells. The model can thereby adjust its sensitivity to input intensities ranging from dim moonlight to dazzling sunlight. A new anchoring mechanism, called the Blurred-Highest-Luminance-As-White (BHLAW) rule, helps simulate how surface lightness becomes sensitive to the spatial scale of objects in a scene. The model is also able to process natural color images under variable lighting conditions, and is compared with the popular RETINEX model.

View-Invariant Object Category Learning, Recognition, and Search: How Spatial and Object Attention Are Coordinated Using Surface-Based Attentional Shrouds

Air Force Office of Scientific Research (F49620-01-1-0397); National Science Foundation (SBE-0354378); Office of Naval Research (N00014-01-1-0624)

Exact Geosedics and Shortest Paths on Polyhedral Surface

We present two algorithms for computing distances along a non-convex polyhedral surface. The first algorithm computes exact minimal-geodesic distances and the second algorithm combines these distances to compute exact shortest-path distances along the surface. Both algorithms have been extended to compute the exact minimalgeodesic paths and shortest paths. These algorithms have been implemented and validated on surfaces for which the correct solutions are known, in order to verify the accuracy and to measure the run-time performance, which is cubic or less for each algorithm. The exact-distance computations carried out by these algorithms are feasible for large-scale surfaces containing tens of thousands of vertices, and are a necessary component of near-isometric surface flattening methods that accurately transform curved manifolds into flat representations.

A Neural Theory of Attentive Visual Search: Interactions of Boundary, Surface, Spatial, and Object Representations

Visual search data are given a unified quantitative explanation by a model of how spatial maps in the parietal cortex and object recognition categories in the inferotemporal cortex deploy attentional resources as they reciprocally interact with visual representations in the prestriate cortex. The model visual representations arc organized into multiple boundary and surface representations. Visual search in the model is initiated by organizing multiple items that lie within a given boundary or surface representation into a candidate search grouping. These items arc compared with object recognition categories to test for matches or mismatches. Mismatches can trigger deeper searches and recursive selection of new groupings until a target object io identified. This search model is algorithmically specified to quantitatively simulate search data using a single set of parameters, as well as to qualitatively explain a still larger data base, including data of Aks and Enns (1992), Bravo and Blake (1990), Chellazzi, Miller, Duncan, and Desimone (1993), Egeth, Viri, and Garbart (1984), Cohen and Ivry (1991), Enno and Rensink (1990), He and Nakayarna (1992), Humphreys, Quinlan, and Riddoch (1989), Mordkoff, Yantis, and Egeth (1990), Nakayama and Silverman (1986), Treisman and Gelade (1980), Treisman and Sato (1990), Wolfe, Cave, and Franzel (1989), and Wolfe and Friedman-Hill (1992). The model hereby provides an alternative to recent variations on the Feature Integration and Guided Search models, and grounds the analysis of visual search in neural models of preattentive vision, attentive object learning and categorization, and attentive spatial localization and orientation.

A Neural Model of 3D Shape-From-Texture: Multiple-Scale Filtering, Boundary Grouping, and Surface Filling-In

A neural model is presented of how cortical areas V1, V2, and V4 interact to convert a textured 2D image into a representation of curved 3D shape. Two basic problems are solved to achieve this: (1) Patterns of spatially discrete 2D texture elements are transformed into a spatially smooth surface representation of 3D shape. (2) Changes in the statistical properties of texture elements across space induce the perceived 3D shape of this surface representation. This is achieved in the model through multiple-scale filtering of a 2D image, followed by a cooperative-competitive grouping network that coherently binds texture elements into boundary webs at the appropriate depths using a scale-to-depth map and a subsequent depth competition stage. These boundary webs then gate filling-in of surface lightness signals in order to form a smooth 3D surface percept. The model quantitatively simulates challenging psychophysical data about perception of prolate ellipsoids (Todd and Akerstrom, 1987, J. Exp. Psych., 13, 242). In particular, the model represents a high degree of 3D curvature for a certain class of images, all of whose texture elements have the same degree of optical compression, in accordance with percepts of human observers. Simulations of 3D percepts of an elliptical cylinder, a slanted plane, and a photo of a golf ball are also presented.

From Stereograms to Surface: How the Brain Sees the World in Depth

When we look at a scene, how do we consciously see surfaces infused with lightness and color at the correct depths? Random Dot Stereograms (RDS) probe how binocular disparity between the two eyes can generate such conscious surface percepts. Dense RDS do so despite the fact that they include multiple false binocular matches. Sparse stereograms do so even across large contrast-free regions with no binocular matches. Stereograms that define occluding and occluded surfaces lead to surface percepts wherein partially occluded textured surfaces are completed behind occluding textured surfaces at a spatial scale much larger than that of the texture elements themselves. Earlier models suggest how the brain detects binocular disparity, but not how RDS generate conscious percepts of 3D surfaces. A neural model predicts how the layered circuits of visual cortex generate these 3D surface percepts using interactions between visual boundary and surface representations that obey complementary computational rules.