Biomedical subjects

Jeffrey A Saunders

Publications and source records attributed to Jeffrey A Saunders.

12 recordsLinked to original sources

PubMed2006

The accuracy and reliability of perceived depth from linear perspective as a function of image size.

We investigated the ability to use linear perspective to perceive depth from monocular images. Specifically, we focused on the information provided by convergence of parallel lines in an image due to perspective projection. Our stimuli were trapezoid-shaped projected contours, which appear as rectangles slanted in depth. If converging edges of a contour are assumed to be parallel edges of a 3D object, then it is possible in principle to recover its 3D orientation and relative dimensions. This 3D interpretation depends on projected size; hence, if an image contour were scaled, accurate use of perspective predicts changes in perceived slant and shape. We tested this prediction and measured the accuracy and precision with which observers can judge depth from perspective alone. Observers viewed monocular images of slanted rectangles and judged whether the rectangles appeared longer versus wider than a square. The projected contours had varying widths (7, 14, or 21 deg) and side angles (7 or 25 deg), and heights were varied by a staircase procedure to compute a point of subjective equality and 75% threshold for each condition. Observers were able to reliably judge aspect ratios from the monocular images: Weber fractions were 6-9% for the largest rectangles, increasing to as high as 17% for small rectangles with high simulated slant. Overall, the contours judged to be squares were taller than the projections of actual squares, consistent with perceptual underestimation of depth. Judgments were modulated by image size in the direction expected from perspective geometry, but the effect of size was only about 20-30% of what was predicted. We simulated the performance of a Bayesian ideal observer that integrated perspective information with an a priori bias toward compression of depth and which was able to qualitatively model the pattern of results.

Cues↗

PubMed2006

Perception of surface slant from oriented textures.

When a surface covered with a regular texture is viewed in perspective, the projected texture provides a number of cues to 3D surface orientation. For oriented textures, one cue is perspective convergence: symmetry lines that are parallel along the surface project to lines that vary systematically in orientation. We investigated the contribution of perspective convergence to perception of 3D slant and tested whether slant from convergence depends on oriented spectral components. Subjects judged the sign of slant about a vertical axis of rotation. Textures were composed of filled circles in three spatial arrangements: a hex grid with symmetry lines at 0 and +/-60 deg relative to the tilt direction (aligned condition), a hex grid with symmetry lines at 90 and +/-30 deg (perpendicular condition), and random arrangements with similar average spacing (isotropic condition). The two hex grid textures differed in the amount of spectral energy present in the tilt direction (horizontal) but were otherwise closely matched. Slant discrimination thresholds for monocular stimuli were higher for isotropic textures than for either of the two hex grid textures and were higher for the perpendicular texture than for the aligned texture. In a second experiment, we measured the weight given to texture relative to binocular slant information for cue conflict stimuli (+/-5 deg). Weights were found to agree with individual subjects' monocular thresholds, in accordance with optimal estimation theory. We conclude that the visual system uses perspective convergence to perceive slant and that effective use of convergence requires the presence of spectral components aligned with the tilt direction.

Cues↗

PubMed2005

Demonstration of cue recruitment: change in visual appearance by means of Pavlovian conditioning.

Until half a century ago, associative learning played a fundamental role in theories of perceptual appearance [Berkeley, G. (1709) An Essay Towards a New Theory of Vision (Dublin), 1st Ed.]. But starting in 1955 [Gibson, J. J. & Gibson, E. J. (1955) Psychol. Rev. 62, 32-41], most studies of perceptual learning have not been concerned with association or appearance but rather with improvements in discrimination ability. Here we describe a "cue recruitment" experiment, which is a straightforward adaptation of Pavlov's classical conditioning experiment, that we used to measure changes in visual appearance caused by exposure to novel pairings of signals in visual stimuli. Trainees viewed movies of a rotating wire-frame (Necker) cube. This stimulus is perceptually bistable. On training trials, depth cues (stereo and occlusion) were added to force the perceived direction of rotation. Critically, an additional signal was also added, contingent on rotation direction. Stimuli on test trials contained the new signal but not the depth cues. Over 45 min, two of the three new signals that we tested acquired the ability to bias perceived rotation direction on their own. Results were consistent across the eight trainees in each experiment, and the new cue's effectiveness was long lasting. Whereas most adaptation aftereffects on appearance are opposite in direction to the training stimuli, these effects were positive. An individual new signal can be recruited by the visual system as a cue for the construction of visual appearance. Cue recruitment experiments may prove useful for reexamining of the role of experience in perception.

Conditioning, Classical↗

PubMed2005

Humans use continuous visual feedback from the hand to control both the direction and distance of pointing movements.

Vision of the hand during reaching provides dynamic feedback that can be used to control movement. We investigated the relative contributions of feedback about the direction and distance of the hand relative to a target. Subjects made pointing movements in a 3-D virtual environment, in which a small sphere provided dynamic visual feedback about the position of their unseen fingertip. On a subset of trials, the position of the virtual fingertip was smoothly shifted by 2 cm during movement, either (1) in the direction of movement, which would require adjustments to the distance moved, or (2) orthogonal to the direction of movement, which would require adjustments to the direction moved. Despite not noticing the perturbations, subjects adjusted their movements to compensate for both types of visual shifts. Corrective responses to direction perturbations were observed within 117 ms, and response latencies were invariant to movement speed and perturbation onset time. Initial corrections to distance perturbations were smaller and appeared after longer delays of 130-200 ms, and both the speed and magnitude of responses were reduced for early onset perturbations. Simulations of a feedback control model that optimally integrates visual information over time show that the results can be explained by differences in the sensory noise levels in the visual dimensions relevant for direction and distance control.

Adaptation, Physiological↗

PubMed2005

Integrating visual cues for motor control: a matter of time.

The visual system continuously integrates multiple sensory cues to help plan and control everyday motor tasks. We quantified how subjects integrated monocular cues (contour and texture) and binocular cues (disparity and vergence) about 3D surface orientation throughout an object placement task and found that binocular cues contributed more to online control than planning. A temporal analysis of corrective responses to stimulus perturbations revealed that the visuomotor system processes binocular cues faster than monocular cues. This suggests that binocular cues dominated online control because they were available sooner, thus affecting a larger proportion of the movement. This was consistent with our finding that the relative influence of binocular information was higher for short-duration movements than long-duration movements. A motor control model that optimally integrates cues with different delays accounts for our findings and shows that cue integration for motor control depends in part on the time course of cue processing.

Cues↗

PubMed2004

Visual feedback control of hand movements.

We investigated what visual information contributes to on-line control of hand movements. It has been suggested that motion information predominates early in movements but that position information predominates for endpoint control. We used a perturbation method to determine the relative contributions of motion and position information to feedback control. Subjects reached to touch targets in a dynamic virtual environment in which subjects viewed a moving virtual fingertip in place of their own finger. On some trials, we perturbed the virtual fingertip while it moved behind an occluder. Subjects responded to perturbations that selectively altered either motion or position information, indicating that both contribute to feedback control. Responses to perturbations that changed both motion and position information were consistent with superimposed motion-based and position-based control. Results were well fit by a control model that optimally integrates noisy, delayed sensory feedback about both motion and position to estimate hand state.

Biomechanical Phenomena↗

PubMed2004

A united residue force-field for calcium-protein interactions.

United-residue potentials are derived for interactions of the calcium cation with polypeptide chains in energy-based prediction of protein structure with a united-residue (UNRES) force-field. Specific potentials were derived for the interaction of the calcium cation with the Asp, Glu, Asn, and Gln side chains and the peptide group. The analytical expressions for the interaction energies for each of these amino acids were obtained by averaging the electrostatic interaction energy, expressed by a multipole series over the dihedral angles not considered in the united-residue model, that is, the side-chain dihedral angles chi and the dihedral angles lambda for the rotation of peptide groups about the C(alpha)...C(alpha) virtual-bond axes. For the side-chains that do not interact favorably with calcium, simple excluded-volume potentials were introduced. The parameters of the potentials were obtained from ab initio quantum mechanical calculations of model systems at the Restricted Hartree-Fock (RHF) level with the 6-31G(d,p) basis set. The energy surfaces of pairs consisting of Ca(2+)-acetate, Ca(2+)-propionate, Ca(2+)-acetamide, Ca(2+)-propionamide, and Ca(2+)-N-methylacetamide systems (modeling the Ca(2+)-Asp(-), Ca(2+)-Glu(-), Ca(2+)-Asn, Ca(2+)-Gln, and Ca(2+)-peptide group interactions) at different distances and orientations were calculated. For each pair, the restricted free energy (RFE) surfaces were calculated by numerical integration over the degrees of freedom lost when switching from the all-atom model to the united-residue model. Finally, the analytical expressions for each pair were fitted to the RFE surfaces. This force-field was able to distinguish the EF-hand motif from all potential binding sites in the crystal structures of bovine alpha-lactalbumin, whiting parvalbumin, calbindin D9K, and apo-calbindin D9K.

Animals↗

PubMed2003

Humans use continuous visual feedback from the hand to control fast reaching movements.

How visual feedback contributes to the on-line control of fast reaching movements is still a matter of considerable debate. Whether feedback is used continuously throughout movements or only in the "slow" end-phases of movements remains an open question. In order to resolve this question, we applied a perturbation technique to measure the influence of visual feedback from the hand at different times during reaching movements. Subjects reached to touch targets in a virtual 3D space, with visual feedback provided by a small virtual sphere that moved with a subject's fingertip. Small random perturbations were applied to the position of the virtual fingertip at two different points in the movement, either at 25% or 50% of the total movement extent. Despite the fact that subjects were unaware of the perturbations, their hand trajectories showed smooth and accurate corrections. Detectable responses were observed within an average of 160 ms after perturbations, and as early as 60% of the distance to the target. Response latencies were constant across different perturbation times and movement speed conditions, suggesting that a fixed sensori-motor delay is the limiting factor. The results provide direct evidence that the human brain uses visual feedback from the hand in a continuous fashion to guide fast reaching movements throughout their extent.

Analysis of Variance↗

PubMed2003

Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search.

A hierarchical methodology for ab initio structure prediction is extended to treat oligomeric proteins. Modifications are made to a united-residue (UNRES) force field and a Conformational Space Annealing (CSA) global search method. The computational cost of including additional chains and the increase in speed from symmetry optimizations are evaluated. The native structures of two oligomeric proteins from the CASP3 exercise, the retro-GCN4 leucine zipper and the synthetic domain-swapped dimer, were identified as the lowest-energy families resulting from the search of the proteins when rotational symmetry was imposed. Additional searches in different symmetries and oligomerization states were carried out, and the results indicate some problems in the thoroughness of the search and in the search of packing arrangements if symmetry constraints are not imposed.

Leucine Zippers↗

PubMed2003

Challenges in structure prediction of oligomeric proteins at the united-residue level: searching the multiple-chain energy landscape with CSA and CFMC.

A revised version of the Conformational Space Annealing (CSA) global optimization method is developed, with three separate measures of structural similarity, in order to overcome the inability of a single distance measure to evaluate multiple-chain protein structures adequately. A second search method, Conformational Family Monte Carlo (CFMC), involving genetic-type moves, Monte Carlo-with-minimization perturbations, and explicit clustering of the population into conformational families, is adapted to treat multiple-chain proteins. These two methods are applied to two oligomeric proteins, the retro-GCN4 leucine zipper and the synthetic domain-swapped dimer. CFMC proves superior to CSA in its search for low-energy representatives of its conformational families, but both methods encounter difficulty in finding the native packing arrangements in the absence of native-like symmetry constraints, even when native monomers are present in the population.

Algorithms↗

PubMed2003

Do humans optimally integrate stereo and texture information for judgments of surface slant?

An optimal linear system for integrating visual cues to 3D surface geometry weights cues in inverse proportion to their uncertainty. The problem of integrating texture and stereo information for judgments of planar surface slant provides a strong test of optimality in human perception. Since the accuracy of slant from texture judgments changes by an order of magnitude from low to high slants, optimality predicts corresponding changes in cue weights as a function of surface slant. Furthermore, since humans show significant individual differences in their abilities to use both texture and stereo information for judgments of 3D surface geometry, the problem admits the stronger test that individual differences in subjects' thresholds for discriminating slant from the individual cues should predict individual differences in cue weights. We tested both predictions by measuring slant discrimination thresholds and stereo/texture cue weights as a function of surface slant for multiple subjects. The results bear out both predictions of optimality, with the exception of an apparent slight under-weighting of texture information. This may be accounted for by factors specific to the stimuli used to isolate stereo information in the experiments. Taken together, the results are consistent with the hypothesis that humans optimally combine the two cues to surface slant, with cue weights proportional to the subjective reliability of the cues.

Cues↗

PubMed2003

The effect of texture relief on perception of slant from texture.

Texture can be an effective source of information for perception of slant and curvature. A computational assumption required for some texture cues is that texture must be flat along a surface. There are many textures which violate this assumption, and have some sort of texture relief: variations perpendicular to the surface. Some examples include grass, which has vertical elements, or scattered rocks, which are volumetric elements with 3-D shapes. Previous studies of perception of slant from texture have not addressed the case of textures with relief. The experiments reported here test judgments of slant for textures with various types of relief, including textures composed of bumps, columns, and oriented elements. The presence of texture relief was found to affect judgments, indicating that perception of slant from texture is not robust to violations of the flat-texture assumption. For bumps and oriented elements, slant was underestimated relative to matching flat textures, while for columns textures, which had visible flat top faces, perceived slant was equal or greater than for flat textures. The differences can be explained by the way different types of texture relief affect the amount of optical compression in the projected image, which would be consistent with results from previous experiments using cue conflicts in flat textures. These results provide further evidence that compression contributes to perception of slant from texture.

Analysis of Variance↗