Discriminative ability with respect to amino acid types: assessing the performance of knowledge-based potentials without threading

We present a novel method designed to analyze the discriminative ability of knowledge-based potentials with respect to the 20 residue types. The method is based on the preference of amino acids for specific types of protein environment, and uses a virtual mutagenesis experiment to estimate how much information a given potential can provide about environments of each amino acid type. This allows one to test and optimize the performance of real potentials at the level of individual amino acids, using actual data on residue environments from a dataset of known protein structures. We have applied our method to long-range and medium-range pairwise distance-dependent potentials. The results of our study indicate that these potentials are only able to discriminate between a very limited number of residue types, and that discriminative ability is extremely sensitive to the choice of parameters used to construct the potentials, and even to the size of the training dataset. We also show that different types of pairwise distance potentials are dominated by different types of interactions. These dominant interactions strongly depend on the type of approximation used to define residue position. For each potential, our methodology is able to identify a potential-specific amino acid distance matrix and a reduced amino acid alphabet of any specified size, which may have implications for sequence alignment and multibody models.     

Measurement of larval striped bass (Morone saxatilis) net avoidance using evasion radius estimation to improve estimates of abundance and mortality

Net avoidance rate increases as a function of larval striped bass size. This causes under-estimation of abundance and overestimation of mortality rate. We modeled net avoidance by assuming that fish avoid the net by swimming a radial distance at a right angle to the net axis. This distance, the evasion radius, was estimated by comparing the calculated densities of striped bass larvae from a series of paired tows involving a large and a small net. Iteration and solution models were used to estimate the evasion radius for each millimeter size group of fish in order to estimate the actual density in the environment. Avoidance of the nets increased with fish length. The ratio of actual density in the environment to the measured density in the small net was used to adjust abundances measured in our ichthyoplankton surveys. After adjusting for net avoidance, mortality rates of striped bass larvae from the Sacramento-San Joaquin Estuary were reduced by 10% compared to the unadjusted rates.      

Can virtual reality be used to conduct mass prophylaxis clinic training? A pilot program

OBJECTIVE: To create and evaluate a pilot bioterrorism defense training environment using virtual reality technology. METHODS: The present pilot project used Second Life, an internet-based virtual world system, to construct a virtual reality environment to mimic an actual setting that might be used as a Strategic National Stockpile (SNS) distribution site for northern California in the event of a bioterrorist attack. Scripted characters were integrated into the system as mock patients to analyze various clinic workflow scenarios. Users tested the virtual environment over two sessions. RESULTS: Thirteen users who toured the environment were asked to complete an evaluation survey. Respondents reported that the virtual reality system was relevant to their practice and had potential as a method of bioterrorism defense training. CONCLUSIONS: Computer simulations of bioterrorism defense training scenarios are feasible with existing personal computer technology. The use of internet-connected virtual environments holds promise for bioterrorism defense training. Recommendations are made for public health agencies regarding the implementation and benefits of using virtual reality for mass prophylaxis clinic training.     

Size Constancy in Bat Biosonar? Perceptual Interaction of Object Aperture and Distance

Perception and encoding of object size is an important feature of sensory systems. In the visual system object size is encoded by the visual angle (visual aperture) on the retina, but the aperture depends on the distance of the object. As object distance is not unambiguously encoded in the visual system, higher computational mechanisms are needed. This phenomenon is termed “size constancy”. It is assumed to reflect an automatic re-scaling of visual aperture with perceived object distance. Recently, it was found that in echolocating bats, the ‘sonar aperture’, i.e., the range of angles from which sound is reflected from an object back to the bat, is unambiguously perceived and neurally encoded. Moreover, it is well known that object distance is accurately perceived and explicitly encoded in bat sonar. Here, we addressed size constancy in bat biosonar, recruiting virtual-object techniques. Bats of the species Phyllostomus discolor learned to discriminate two simple virtual objects that only differed in sonar aperture. Upon successful discrimination, test trials were randomly interspersed using virtual objects that differed in both aperture and distance. It was tested whether the bats spontaneously assigned absolute width information to these objects by combining distance and aperture. The results showed that while the isolated perceptual cues encoding object width, aperture, and distance were all perceptually well resolved by the bats, the animals did not assign absolute width information to the test objects. This lack of sonar size constancy may result from the bats relying on different modalities to extract size information at different distances. Alternatively, it is conceivable that familiarity with a behaviorally relevant, conspicuous object is required for sonar size constancy, as it has been argued for visual size constancy. Based on the current data, it appears that size constancy is not necessarily an essential feature of sonar perception in bats.     

Welcome to Wonderland: The Influence of the Size and Shape of a Virtual Hand On the Perceived Size and Shape of Virtual Objects

The notion of body-based scaling suggests that our body and its action capabilities are used to scale the spatial layout of the environment. Here we present four studies supporting this perspective by showing that the hand acts as a metric which individuals use to scale the apparent sizes of objects in the environment. However to test this, one must be able to manipulate the size and/or dimensions of the perceiver’s hand which is difficult in the real world due to impliability of hand dimensions. To overcome this limitation, we used virtual reality to manipulate dimensions of participants’ fully-tracked, virtual hands to investigate its influence on the perceived size and shape of virtual objects. In a series of experiments, using several measures, we show that individuals’ estimations of the sizes of virtual objects differ depending on the size of their virtual hand in the direction consistent with the body-based scaling hypothesis. Additionally, we found that these effects were specific to participants’ virtual hands rather than another avatar’s hands or a salient familiar-sized object. While these studies provide support for a body-based approach to the scaling of the spatial layout, they also demonstrate the influence of virtual bodies on perception of virtual environments.     

Perceptual distance and the constancy of size and stereoscopic depth

The relationship between distance and size perception is unclear because of conflicting results of tests investigating the size-distance invariance hypothesis (SDIH), according to which perceived size is proportional to perceived distance. We propose that response bias with regard to measures of perceived distance is at the root of the conflict. Rather than employ the usual method of magnitude estimation, the bias-free two-alternative forced choice (2AFC) method was used to determine the precision (1/sigma) of discriminating depth at different distances. The results led us to define perceptual distance as a bias free power function of physical distance, with an exponent of approximately 0.5. Similar measures involving size differences among stimuli of equal angular size yield the same power function of distance. In addition, size discrimination is noisier than depth discrimination, suggesting that distance information is processed prior to angular size. Size constancy implies that the perceived size is proportional to perceptual distance. Moreover, given a constant relative disparity, depth constancy implies that perceived depth is proportional to the square of perceptual distance. However, the function relating the uncertainties of depth and of size discrimination to distance is the same. Hence, depth and size constancy may be accounted for by the same underlying law.     

Probing depth in monocular images

It is generally expected that depth (distance) is the internal representational primitive that corresponds to much of the perception of 3D. We tested this assumption in monocular surface stimuli that are devoid of distance information (due to orthographic projection and the chosen surface shape, with perspective projection used as a control) and yet are vividly three-dimensional. Slant judgments were found to be in close correspondence with the actual geometric slant of the stimuli; the spatial orientation of the surfaces was perceived accurately. The apparent depth in these stimuli was then tested by superimposing a stereo depth probe over the monocular surface. In both the perspective and orthographic projection the gradient of perceived depth, measured by matching the apparent depth of the stereo probe with that of the monocular surface at a series of locations, was substantial. The experiments demonstrate that in orthographic projection the visual system can compute from local surface orientation a depth quantity that is commensurate with the relative depth derived from stereo disparity. The depth data suggests that, at least in the near field, the zero value for relative depth lies at the same absolute depth as the stereo horopter (locus of zero stereo disparity). Relative to this zero value, the depth-from-slant computation seems to provide an estimate of distance information that is independent of the absolute distance to the surface.Supproted by Office of Naval Research Contract N00014-K-84-0533. We gratefully acknowledge the suggestions of Jacob Beck regarding the experimental design, and the assistance provided by Cathryn Stanford     

The Effect of Perspective on Presence and Space Perception

In this paper we report two experiments in which the effect of perspective projection on presence and space perception was investigated. In Experiment 1, participants were asked to score a presence questionnaire when looking at a virtual classroom. We manipulated the vantage point, the viewing mode (binocular versus monocular viewing), the display device/screen size (projector versus TV) and the center of projection. At the end of each session of Experiment 1, participants were asked to set their preferred center of projection such that the image seemed most natural to them. In Experiment 2, participants were asked to draw a floor plan of the virtual classroom. The results show that field of view, viewing mode, the center of projection and display all significantly affect presence and the perceived layout of the virtual environment. We found a significant linear relationship between presence and perceived layout of the virtual classroom, and between the preferred center of projection and perceived layout. The results indicate that the way in which virtual worlds are presented is critical for the level of experienced presence. The results also suggest that people ignore veridicality and they experience a higher level of presence while viewing elongated virtual environments compared to viewing the original intended shape.     

Emmert's Law and the moon illusion

A cognitive account is offered of puzzling, though well known phenomena, including increased size of afterimages with greater distance (Emmert's Law) and increased size of the moon near the horizon (the Moon Illusion). Various classical distortion illusions are explained by Size Scaling when inappropriate to distance, 'flipping' depth ambiguity being used to separate botton-up and top-down visual scaling. Helmholtz's general Principle is discussed with simpler wording - that retinal images are attributed to objects - for object recognition and spatial vision.     

Understanding 2D projections on mirrors and on windows

Representational art tries to capture a 3D world on a 2D surface, and artists often discuss this in relation to the projected image on window panes and mirrors. But are 2D projections on transparent surfaces useful to learn about projections in general? Most people are unaware of the 2D projected size of objects on the surface of mirrors. They also incorrectly expect that these projections always get smaller with distance of the target object from the mirror, and do not change with distance of the observer (when the target is stationary). In this paper we extend this result about surfaces of mirrors to surfaces of windows, and we confirm that the errors that people make are not specific to Western culture by replicating the study in China. In contrast to their errors about projections, people are more accurate at predicting how field of view will vary depending on distance of the observer from a mirror or window. To explain how this pattern of (false) beliefs can stem from experience we argue that people do not perceive projections on transparent surfaces.     

Perceived motion in complementary afterimages: verification of a neural network theory

Steady fixation of a regular pattern like a bar grating or concentric circles leads to a complementary afterimage at pattern offset. The afterimage has the appearance of shimmering lines that are locally orthogonal to the orientations of the inducing image. Additionally, the afterimage includes motion running parallel to the orientation of the afterimage lines. We argue that this afterimage motion supports the existence of a cue to motion that is based on the spatial organization of oriented responses. This cue was previously proposed after analysis of a neural network model of visual perception. We test predictions of the model on various types of complementary afterimage inducing stimuli. When a contrast or size gradient is included in the inducing image, the afterimage motion moves toward the higher part of the gradient, in agreement with the model. Implications of this cue for computational and neurophysiological theories of motion perception are discussed.     

People favour imperfect catching by assuming a stable world

The visual angle that is projected by an object (e.g. a ball) on the retina depends on the object's size and distance. Without further information, however, the visual angle is ambiguous with respect to size and distance, because equal visual angles can be obtained from a big ball at a longer distance and a smaller one at a correspondingly shorter distance. Failure to recover the true 3D structure of the object (e.g. a ball's physical size) causing the ambiguous retinal image can lead to a timing error when catching the ball. Two opposing views are currently prevailing on how people resolve this ambiguity when estimating time to contact. One explanation challenges any inference about what causes the retinal image (i.e. the necessity to recover this 3D structure), and instead favors a direct analysis of optic flow. In contrast, the second view suggests that action timing could be rather based on obtaining an estimate of the 3D structure of the scene. With the latter, systematic errors will be predicted if our inference of the 3D structure fails to reveal the underlying cause of the retinal image. Here we show that hand closure in catching virtual balls is triggered by visual angle, using an assumption of a constant ball size. As a consequence of this assumption, hand closure starts when the ball is at similar distance across trials. From that distance on, the remaining arrival time, therefore, depends on ball's speed. In order to time the catch successfully, closing time was coupled with ball's speed during the motor phase. This strategy led to an increased precision in catching but at the cost of committing systematic errors.     

A demonstration of 'broken' visual space

It has long been assumed that there is a distorted mapping between real and 'perceived' space, based on demonstrations of systematic errors in judgements of slant, curvature, direction and separation. Here, we have applied a direct test to the notion of a coherent visual space. In an immersive virtual environment, participants judged the relative distance of two squares displayed in separate intervals. On some trials, the virtual scene expanded by a factor of four between intervals although, in line with recent results, participants did not report any noticeable change in the scene. We found that there was no consistent depth ordering of objects that can explain the distance matches participants made in this environment (e.g. A>B>D yet also A相似文献   

Developing a Novel Measure of Body Satisfaction Using Virtual Reality

Body image disturbance (BID), considered a key feature in eating disorders, is a pervasive issue among young women. Accurate assessment of BID is critical, but the field is currently limited to self-report assessment methods. In the present study, we build upon existing research, and explore the utility of virtual reality (VR) to elicit and detect changes in BID across various immersive virtual environments. College-aged women with elevated weight and shape concerns (n = 38) and a non-weight and shape concerned control group (n = 40) were randomly exposed to four distinct virtual environments with high or low levels of body salience and social presence (i.e., presence of virtual others). Participants interacted with avatars of thin, normal weight, and overweight body size (BMI of approximately 18, 22, and 27 respectively) in virtual social settings (i.e., beach, party). We measured state-level body satisfaction (state BD) immediately after exposure to each environment. In addition, we measured participants’ minimum interpersonal distance, visual attention, and approach preference toward avatars of each size. Women with higher baseline BID reported significantly higher state BD in all settings compared to controls. Both groups reported significantly higher state BD in a beach with avatars as compared to other environments. In addition, women with elevated BID approached closer to normal weight avatars and looked longer at thin avatars compared to women in the control group. Our findings indicate that VR may serve as a novel tool for measuring state-level BID, with applications for measuring treatment outcomes. Implications for future research and clinical interventions are discussed.     

Visuomotor Dissociation in Cerebral Scaling of Size

Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in which 16 right-handed subjects copied geometric figures while the result of drawing remained out of sight. Either the size of the example figure varied while maintaining a constant size of drawing (visual incongruity) or the size of the examples remained constant while subjects were instructed to make changes in size (motor incongruity). These incongruent were compared to congruent conditions. Statistical Parametric Mapping (SPM8) revealed brain activations related to size incongruity in the dorsolateral prefrontal and inferior parietal cortex, pre-SMA / anterior cingulate and anterior insula, dominant in the right hemisphere. This pattern represented simultaneous use of a ‘resized’ virtual template and actual picture information requiring spatial working memory, early-stage attention shifting and inhibitory control. Activations were strongest in motor incongruity while right pre-dorsal premotor activation specifically occurred in this condition. Visual incongruity additionally relied on a ventral visual pathway. Left ventral premotor activation occurred in all variably sized drawing while constant visuomotor size, compared to congruent size variation, uniquely activated the lateral occipital cortex additional to superior parietal regions. These results highlight size as a fundamental parameter in both general hand movement and movement guided by objects perceived in the context of surrounding 3D space.     

A Computational Model of Afterimage Rotation in the Peripheral Drift Illusion Based on Retinal ON/OFF Responses

Human observers perceive illusory rotations after the disappearance of circularly repeating patches containing dark-to-light luminance. This afterimage rotation is a very powerful phenomenon, but little is known about the mechanisms underlying it. Here, we use a computational model to show that the afterimage rotation can be explained by a combination of fast light adaptation and the physiological architecture of the early visual system, consisting of ON- and OFF-type visual pathways. In this retinal ON/OFF model, the afterimage rotation appeared as a rotation of focus lines of retinal ON/OFF responses. Focus lines rotated clockwise on a light background, but counterclockwise on a dark background. These findings were consistent with the results of psychophysical experiments, which were also performed by us. Additionally, the velocity of the afterimage rotation was comparable with that observed in our psychophysical experiments. These results suggest that the early visual system (including the retina) is responsible for the generation of the afterimage rotation, and that this illusory rotation may be systematically misinterpreted by our high-level visual system.     

Discrimination and scaling of velocity of stimulus motion across the skin

The capacity of human subjects to discriminate and to scale the velocity of tactile brushing stimuli was assessed. Signal detection and classical psychophysical techniques were employed to estimate the Weber fraction over a wide range of velocities (from 1.5 to 140 cm/sec). In addition, free magnitude estimates of (1) the velocity and (2) the duration of moving tactile stimuli were obtained. It was found that human capacity to discriminate stimuli delivered to a 4 to 6-cm chord of skin on the dorsal forearm and differing in velocity remains grossly constant over the range of velocities tested and is relatively poor (i.e., the Weber fraction = 0.2-0.25). A simple power function (exponent = 0.6) satisfactorily describes the psychophysical relation (1) between the perceived and actual velocity and (2) between the perceived and actual duration of these stimuli. Since a direct proportionality between the reciprocal of a subject's estimate of duration and his or her estimate of velocity was observed, it is suggested that these two sensory attributes may reflect the operation of a neural mechanism sensitive to the duration of stimulation. Moreover, the data are inconsistent with the hypothesis that the subjects computed estimates of mean velocity from the ratio of perceived distance to perceived duration.     

Self versus Environment Motion in Postural Control

To stabilize our position in space we use visual information as well as non-visual physical motion cues. However, visual cues can be ambiguous: visually perceived motion may be caused by self-movement, movement of the environment, or both. The nervous system must combine the ambiguous visual cues with noisy physical motion cues to resolve this ambiguity and control our body posture. Here we have developed a Bayesian model that formalizes how the nervous system could solve this problem. In this model, the nervous system combines the sensory cues to estimate the movement of the body. We analytically demonstrate that, as long as visual stimulation is fast in comparison to the uncertainty in our perception of body movement, the optimal strategy is to weight visually perceived movement velocities proportional to a power law. We find that this model accounts for the nonlinear influence of experimentally induced visual motion on human postural behavior both in our data and in previously published results.     

Effects of spatial autocorrelation,natal philopatry and phenotypic plasticity on the heritability of laying date

We investigated the effect of spatial autocorrelation on heritability (h²) estimates of laying date and clutch size in a population of great tits Parus major. We found that h² of laying date, but not clutch size, declined significantly with increasing distance between the nestbox of mothers and daughters. This decline was caused by a decreasing effect of spatial autocorrelation in laying date, rather than by the existence of genotype–environment interactions (GEI). After correcting for the effect of spatial autocorrelation, h² of laying date was low (0.16 ± 0.07), but significant, and surprisingly consistent with increasing distance between parental and offspring environments. The h² of clutch size was not much affected by spatial autocorrelation. Most previously published estimates of the heritability of laying date include various degrees of common environment effects, which can bias estimates both upwards and downwards. We suggest that using techniques that take spatial autocorrelation into account might be a fruitful approach to estimate h² of traits that show a high degree of plasticity.     

Afterimage-like effects in the motion-sensitive neuron H1

A powerful effect resembling an afterimage is demonstrated on the pathway to the motion-sensitive neuron H1. This effect is independent of the locally generated gain control described in an earlier paper (Maddess & Laughlin 1985, Proc. R. Soc. Lond. B 225, 251). The afterimage, produced across the eye by a stationary pattern, causes the sensitivity to movement to be different according to the local stimulus history, and the effects of low-contrast (0.1) patterns, presented for as little as a few hundred milliseconds, remain for up to 2 s. Moving patterns interact with the afterimage to modulate the spike rate of H1. The afterimage increases with contrast but saturates at contrasts above 0.5. Low spatial frequencies generate afterimages less effectively than moderate ones; this result indicates that the afterimage process could lie at, or after, lateral inhibition between tonic units. This is supported by the fact that the altered sensitivity profiles generated by single bright and dark vertical bars initially resemble Mach bands. However, this character alters as the afterimage decays, and the depression of H1's response to moving bright stimuli, produced by the afterimage of a dark bar, continues to grow for up to 1 s after the adapting bar is removed. A short-lived (0.5 s) reduction of H1's directional selectivity accompanies strong afterimage formation. All these factors, especially the saturation at low contrasts and the spatial frequency tuning, rule out light adaptation by photoreceptors as the afterimage source. Luminances used were also low enough to exclude influence by the pupil mechanism. Lastly, responses to patterns that are occasionally jumped by large or small distances are broadened by stimuli that produce an afterimage. Responses to small displacements have previously been described as 'velocity impulse responses' (Srinivasan 1983, Vision Res. 23, 659; Zaagman et al. 1983, IEEE Trans. SMC 13, 900) and so the response broadening (stimulus blurring) can be taken as a reduction of the fly's temporal resolution of moving objects. Previously reported work shows that afterimages seen in humans and the effect reported here act over the same range of temporal frequencies rather than retinal drift speeds. This may suggest an important role for afterimage-like effects in the processing of the low temporal frequency components of moving images. Certainly, the fly's afterimage system reduces the visibility of moving objects within patches of an image that, have on average, contained slowly varying motion signals.(ABSTRACT TRUNCATED AT 400 WORDS)