Vertical disparity, egocentric distance and stereoscopic depth constancy: a new interpretation

There has long been a problem concerning the presence in the visual cortex of binocularly activated cells that are selective for vertical stimulus disparities because it is generally believed that only horizontal disparities contribute to stereoscopic depth perception. The accepted view is that stereoscopic depth estimates are only relative to the fixation point and that independent information from an extraretinal source is needed to scale for absolute or egocentric distance. Recently, however, theoretical computations have shown that egocentric distance can be estimated directly from vertical disparities without recourse to extraretinal sources. There has been little impetus to follow up these computations with experimental observations, because the vertical disparities that normally occur between the images in the two eyes have always been regarded as being too small to be of significance for visual perception and because experiments have consistently shown that our conscious appreciation of egocentric distance is rather crude and unreliable. Nevertheless, the veridicality of stereoscopic depth constancy indicates that accurate distance information is available to the visual system and that the information about egocentric distance and horizontal disparity are processed together so as to continually recalibrate the horizontal disparity values for different absolute distances. Computations show that the recalibration can be based directly on vertical disparities without the need for any intervening estimates of absolute distance. This may partly explain the relative crudity of our conscious appreciation of egocentric distance. From published data it has been possible to calculate the magnitude of the vertical disparities that the human visual system must be able to discriminate in order for depth constancy to have the observed level of veridicality. From published data on the induced effect it has also been possible to calculate the threshold values for the detection of vertical disparities by the visual system. These threshold values are smaller than those needed to provide for the recalibration of the horizontal disparities in the interests of veridical depth constancy. An outline is given of the known properties of the binocularly activated cells in the striate cortex that are able to discriminate and assess the vertical disparities. Experiments are proposed that should validate, or otherwise, the concepts put forward in this paper.     

Spatial phase and frequency in motion capture of random-dot patterns

A square matrix of spots (A) was presented in rapid alternation with an uncorrelated matrix (B). If the square arrays are superimposed spatially one sees random incoherent motion. However, incoherent motion was seen only if the outer edges were exactly aligned. If the outline of matrix A is shifted horizontally by 1 degree in relation to B, then the edges are seen to oscillate to and fro. Surprisingly, all the dots in the matrix were seen to 'adhere' to the edges and to move horizontally (Ramachandran, 1981). We then aligned the edges again to produce incoherent motion and superimposed a sine-wave grating on the pattern. If the grating was moved horizontally then all the spots 'adhered' to it and moved horizontally as well. This illusion ('motion capture') was optimal (a) at a 90 degrees spatial phase shift of the grating; (b) at low spatial frequencies (less than 0.5 cycles); and (c) when the grating was alternated in step with the dot patterns. Density modulated gratings were just as effective. We conclude that the unambiguous motion signal derived from the grating is applied spontaneously to the dots as well.     

Stabilized structure from motion without disparity induces disparity adaptation

3D structures can be perceived based on the patterns of 2D motion signals. With orthographic projection of a 3D stimulus onto a 2D plane, the kinetic information can give a vivid impression of depth, but the depth order is intrinsically ambiguous, resulting in bistable or even multistable interpretations. For example, an orthographic projection of dots on the surface of a rotating cylinder is perceived as a rotating cylinder with ambiguous direction of rotation. We show that the bistable rotation can be stabilized by adding information, not to the dots themselves, but to their spatial context. More interestingly, the stabilized bistable motion can generate consistent rotation aftereffects. The rotation aftereffect can only be observed when the adapting and test stimuli are presented at the same stereo depth and the same retinal location, and it is not due to attentional tracking. The observed rotation aftereffect is likely due to direction-contingent disparity adaptation, implying that stimuli with kinetic depth may have activated neurons sensitive to different disparities, even though the stimuli have zero relative disparity. Stereo depth and kinetic depth may be supported by a common neural mechanism at an early stage in the visual system.     

Use of random-dot displays in the study of biomolecular conformation

The perception of random-dot interference patterns is potentially useful in the global characterization of conformational changes occurring in biomolecules. The proposed method can be applied whenever both the structure of the initial and final state of a molecule are known, and an equivalent axis of rotation relating the two forms is desired.     

Allele-specific disparity in breast cancer

Background

Molecular alterations critical to development of cancer include mutations, copy number alterations (amplifications and deletions) as well as genomic rearrangements resulting in gene fusions. Massively parallel next generation sequencing, which enables the discovery of such changes, uses considerable quantities of genomic DNA (> 5 ug), a serious limitation in ever smaller clinical samples. However, a commonly available microarray platforms such as array comparative genomic hybridization (array CGH) allows the characterization of gene copy number at a single gene resolution using much smaller amounts of genomic DNA. In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities.

Methods

We performed array CGH on whole genome amplified and not amplified genomic DNA from MCF-7 breast cancer cells, using 244 K and 1 M Agilent arrays. The ADM-2 algorithm was used to identify micro-copy number alterations that measured less than 1 Mb in genomic length.

Results

DNA from MCF-7 breast cancer cells was analyzed for micro-copy number alterations, defined as measuring less than 1 Mb in genomic length. The 4-fold extra resolution of the 1 M array platform relative to the less dense 244 K array platform, led to the improved detection of copy number variations (CNVs) and micro-CNAs. The identification of intra-genic breakpoints in areas of DNA copy number gain signaled the possible presence of gene fusion events. However, the ultra-dense platforms, especially the densest 1 M array, detect artifacts inherent to whole genome amplification and should be used only with non-amplified DNA samples.

Conclusions

This is a first report using 1 M array CGH for the discovery of cancer genes and biomarkers. We show the remarkable capacity of this technology to discover CNVs, micro-copy number alterations and even gene fusions. However, these platforms require excellent genomic DNA quality and do not tolerate relatively small imperfections related to the whole genome amplification.     

Allometric disparity in rodent evolution

In this study, allometric trajectories for 51 rodent species, comprising equal representatives from each of the major clades (Ctenohystrica, Muroidea, Sciuridae), are compared in a multivariate morphospace (=allometric space) to quantify magnitudes of disparity in cranial growth. Variability in allometric trajectory patterns was compared to measures of adult disparity in each clade, and dietary habit among the examined species, which together encapsulated an ecomorphological breadth. Results indicate that the evolution of allometric trajectories in rodents is characterized by different features in sciurids compared with muroids and Ctenohystrica. Sciuridae was found to have a reduced magnitude of inter‐trajectory change and growth patterns with less variation in allometric coefficient values among members. In contrast, a greater magnitude of difference between trajectories and an increased variation in allometric coefficient values was evident for both Ctenohystrica and muroids. Ctenohystrica and muroids achieved considerably higher adult disparities than sciurids, suggesting that conservatism in allometric trajectory modification may constrain morphological diversity in rodents. The results provide support for a role of ecology (dietary habit) in the evolution of allometric trajectories in rodents.     

Psychophysical and computational studies of random-dot Moire patterns

Random-dot Moire dot patterns epitomize the local/global gap, the problem of perceiving global structures when only physical local information is available to the perceptual system. At present, no single theory appears to be able to account for all the phenomena these physically simple patterns generate.     

Stereopsis measured by random-dot patterns--a new clinical test.

Comparative measures are presented of stereo-acuity by random-dot stereograms using a phase difference haploscope and a Titmus stereogram. Using two groups of fifteen subjects each, one with full binocular vision and the other of small-angle strabismic amblyopes, greater discrimination between subject groups was found with the random-dot stereograms. It is concluded that random-dot stereograms produced by crossed Polaroid would be a more effective clinical means of determining stereo-acuity.     

Method for calculating 3-D coordinates from molecular stereograms

The three-dimensional coordinates for the -carbon atoms of crambin and basic pancreatic trypsin inhibitor (BPTI) were determined from the respective -carbon trace stereograms using an improved Simplex algorithm. This algorithm was used in a two-step process to estimate thez-coordinate values. In one approach, an average interatomic distance value, an approximate viewing angle, and a table of digitized values forx _left,y _left andx _right,y _right are provided in the first step. In the second step, thez-coordinate values are derived by varyingz to minimize the bond distance error (Rossmann and Argos, 1980). In another approach, only a reference bond distance table is provided along with the table ofx _left,y _left andx _right,y _right digitized values. In the first step, the viewing angle (), a combined scale and viewing distance parameter (q), a rotational angular distortion from digitizing and/or photocopying (z), and translational distortion factors (x _err andy _err) are calculated. In the second step, thez-coordinate values are varied to minimize the bond distance error. RMS difference values of less than 1.5 Å were obtained for both crambin and BPTI -carbon atoms.     

Cooperative and non-cooperative processes of apparent movement of random-dot cinematograms

In this study, we investigated the cooperative and non-cooperative models of stereopsis on apparent movement of the short-range process using spatial frequency filtered random-dot cinematograms. Our results showed that when spatial frequencies were below 4 cycles/degree, maximum displacement (dmax) was decreasing (linearly) with increasing mean frequencies, but at 4 cycles/degree and above dmax stayed constant. For low frequencies, non-cooperative models such as Marr and Poggio's could explain these findings, but not for frequencies above 4 cycles/degree. However, in a previous study we found that the average cooperative neighbourhood for apparent movement of the short-range process is 15 arc min. This fortuitous agreement on 4 cycles/degree could suggest that dmax being constant at frequencies above 4 cycles is related to a cooperative process.     

Allometric space and allometric disparity: a developmental perspective in the macroevolutionary analysis of morphological disparity

Here, we advance novel uses of allometric spaces--multidimensional spaces specifically defined by allometric coefficients--with the goal of investigating the focal role of development in shaping the evolution of morphological disparity. From their examination, operational measures of allometric disparity can be derived, complementing standard signals of morphological disparity through an intuitive and process-oriented refinement of established analytical protocols used in disparity studies. Allometric spaces thereby become a promising context to reveal different patterns of evolutionary developmental changes and to assess their relative prevalence and importance. Such spaces offer a novel domain of investigation of phenotypic variation and should help in detecting large-scale trends, thus placing various macroevolutionary phenomena in an explicitly developmental context. Ammonoidea (Cephalopoda) at the Lower-Middle Jurassic transition were chosen as a case study to illustrate this methodological approach. We constructed two phenotypic spaces: a static, adult one (adult morphospace) and a dynamic, developmental one (allometric space). Comparative disparity analyses show a strikingly stable occupation in both spaces, despite extensive change in taxonomic composition. In contrast, disparity analyses of subclades reveal clearly distinct morphological and allometric disparity dynamics. Allometric approaches allow developmental insights into morphological diversification otherwise intractable from the analysis of adult morphospace alone.     

Limb disparity and wing shape in pterosaurs

The limb proportions of the extinct flying pterosaurs were clearly distinct from their living counterparts, birds and bats. Within pterosaurs, however, we show that further differences in limb proportions exist between the two main groups: the clade of short-tailed Pterodactyloidea and the paraphyletic clades of long-tailed rhamphorhynchoids. The hindlimb to forelimb ratios of rhamphorhynchoid pterosaurs are similar to that seen in bats, whereas those of pterodactyloids are much higher. Such a clear difference in limb ratios indicates that the extent of the wing membrane in rhamphorhynchoids and pterodactyloids may also have differed; this is borne out by simple ternary analyses. Further, analyses also indicate that the limbs of Sordes pilosus, a well-preserved small taxon used as key evidence for inferring the extent and shape of the wing membrane in all pterosaurs, are not typical even of its closest relatives, other rhamphorhynchoids. Thus, a bat-like extensive hindlimb flight membrane, integrated with the feet and tail may be applicable only to a small subset of pterosaur diversity. The range of flight morphologies seen in these extinct reptiles may prove much broader than previously thought.     

Low ecological disparity in Early Cretaceous birds

Ecological divergence is thought to be coupled with evolutionary radiations, yet the strength of this coupling is unclear. When birds diversified ecologically has received much less attention than their hotly debated crown divergence time. Here, we quantify how accurately skeletal morphology can predict ecology in living and extinct birds, and show that the earliest known assemblage of birds (= pygostylians) from the Jehol Biota (≈ 125 Ma) was substantially impoverished ecologically. The Jehol avifauna has few representatives of highly preservable ecomorphs (e.g. aquatic forms) and a notable lack of ecomorphological overlap with the pterosaur assemblage (e.g. no large or aerially foraging pygostylians). Comparisons of the Jehol functional diversity with modern and subfossil avian assemblages show that taphonomic bias alone cannot explain the ecomorphological impoverishment. However, evolutionary simulations suggest that the constrained ecological diversity of the Early Cretaceous pygostylians is consistent with what is expected from a relatively young radiation. Regardless of the proximate biological explanation, the anomalously low functional diversity of the Jehol birds is evidence both for ecological vacancies in Cretaceous ecosystems, which were subsequently filled by the radiation of crown Aves, and for discordance between taxonomic richness and ecological diversity in the best-known Mesozoic ecosystem.     

Reading text increases binocular disparity in dyslexic children

Children with developmental dyslexia show reading impairment compared to their peers, despite being matched on IQ, socio-economic background, and educational opportunities. The neurological and cognitive basis of dyslexia remains a highly debated topic. Proponents of the magnocellular theory, which postulates abnormalities in the M-stream of the visual pathway cause developmental dyslexia, claim that children with dyslexia have deficient binocular coordination, and this is the underlying cause of developmental dyslexia. We measured binocular coordination during reading and a non-linguistic scanning task in three participant groups: adults, typically developing children, and children with dyslexia. A significant increase in fixation disparity was observed for dyslexic children solely when reading. Our study casts serious doubts on the claims of the magnocellular theory. The exclusivity of increased fixation disparity in dyslexics during reading might be a result of the allocation of inadequate attentional and/or cognitive resources to the reading process, or suboptimal linguistic processing per se.     

Immunologic disparity in the hypopituitary dwarf mouse.

The Snell-Bagg hypopituitary dwarf mouse has been shown to be deficient in growth hormone, thyroxine, and prolactin. There are reports indicating that in addition to these neuroendocrine abnormalities, development of immune competence is also severely impaired in these animals. However, other studies indicate that the immunologic potential of these mice does not differ from their heterozygous littermate controls. Our data show that dwarf mice weaned at 21 days of age and killed at that time, or 7 days later, have reduced numbers of cells in both the spleen and thymus and the mitogen responsiveness of these cells is impaired. However, if mice weaned on day 21 are analyzed at 32 days of age or the mice are weaned at day 30 and analyzed 7 days later the ability to respond to mitogenic stimulation does not differ from controls. Further experiments show that dwarf mice weaned at 30 days of age have a normal complement of V-beta TCR as evidenced by immunofluorescence analysis as well as a primary antibody response to SRBC equivalent to that observed in normal littermates. Immunofluorescence analysis of CD4 and CD8 expression on thymocytes obtained from dwarf mice shows a distinct pattern dependent on the time of weaning and time of analysis. Initial analysis of thymocytes from dwarf mice weaned and killed at 21 days of age do not differ from controls. However, cells from dwarf mice weaned on day 21 and killed on day 28 are markedly different with a loss of immature CD4+/CD8+ cells and a corresponding increase in CD4+ and CD8+ mature thymocytes. In contrast, the phenotype of thymocytes obtained from dwarf mice weaned at 30 days of age and killed on day 37 did not differ from normal littermates. Collectively these studies indicate that hypopituitary dwarf mice lag behind their heterozygous littermates with respect to development of immunocompetence but normal immune responsiveness does develop by 32 days of age when the mice are weaned on day 21.     

Global disparity in the resilience of coral reefs

The great sensitivity of coral reefs to climate change has raised concern over their resilience. An emerging body of resilience theory stems largely from research carried out in a single biogeographic region; the Caribbean. Such geographic bias raises the question of transferability of concepts among regions. In this article, we identify factors that might predispose the Caribbean to its low resilience, including faster rates of macroalgal growth, higher rates of algal recruitment, basin-wide iron-enrichment of algal growth from aeolian dust, a lack of acroporid corals, lower herbivore biomass and missing groups of herbivores. Although mechanisms of resilience are likely to be ubiquitous, our analysis suggests that Indo-Pacific reefs would have to be heavily degraded to exhibit bistability or undergo coral-macroalgal phase shifts.     

Fixation disparity and learning disabilities.

This study was conducted at the Massachusetts College of Optometry in 1974 to determine if there is a relationship between binocularity and learning disabilities. A fixation disparity test was administered to 53 learning disabled and 61 normal children in a blind study. The results indicated no statistically significant differences in binocularity between the two groups as measured by the fixation disparity technique.     

Inferring the accumulation of morphological disparity in epiphyllous liverworts

Phylogenetic studies of lineages growing in extreme environments have frequently recovered evidence not only of high level of homoplasy but also of discordance of morphological disparity and species diversity. It has been suggested that this divergence may be caused by developmental constraints and/or natural selection. Here we explored these hypotheses by inferring the phenotypic evolution of the derived liverwort genus Cololejeunea. These liverworts occur preferentially on the surface of leaves or other aerial parts of vascular plants growing in wet forests. The evolution of 12 morphological characters was studied using a phylogenetic framework comprising 70 species of Cololejeunea. The phylogeny was reconstructed using DNA sequences of one nuclear and two plastid regions and enabled the inference of the evolution of the studied morphological characters by determining the frequency of homoplasy. Mantel tests were used to test for correlations of morphological disparity?×?species diversity and morphological disparity?×?epiphytism. The phylogenetic informativeness of each binary character was estimated by the D metric of the Fritz and Purvis test, and the relationship between each character and epiphytism was inferred by Pearson’s coefficient. We evaluated the morphospace occupation using principal coordinate analyses. Our results not only recovered high levels of homoplasy but also weak correlations of morphological disparity and species diversity. Morphological disparity was not linked to epiphytism, although positive or negative relationships between some characters and epiphytism were found. The Brownian model of character evolution was not rejected for the studied morphological disparity in Cololejeunea with the exception of asexual propagules. The observations support the prediction that iterative evolution in a well-defined morphospace may result in rampant homoplasy and the observed divergence of disparity and diversity.     

A map for horizontal disparity in monkey V2

The perception of visual depth is determined by integration of spatial disparities of inputs from the two eyes. Single cells in visual cortex of monkeys are known to respond to specific binocular disparities; however, little is known about their functional organization. We now show, using intrinsic signal optical imaging and single-unit physiology, that, in the thick stripe compartments of the second visual area (V2), there is a clustered organization of Near cells and Far cells, and moreover, there are topographic maps for Near to Far disparities within V2. Our findings suggest that maps for visual disparity are calculated in V2, and demonstrate parallels in functional organization between the thin, pale, and thick stripes of V2.