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     

Voluntarily controlled bi-stable slant perception of real and photographed surfaces

We have quantified voluntarily selected perceived slant of real trapezoidal surfaces (a 'reverse-perspective' scene) and their photographed counterparts (pictorial space). The surfaces were slanted about the vertical axis and observers estimated slant relative to the frontal plane. We were particularly interested in those cases in which binocular disparity and monocular perspective provided conflicting slant information. We varied the monocularly and binocularly specified surface slants independently across stimulus presentations. To eliminate texture and shading cues we used sand-blasted aluminium trapezoidal surfaces illuminated from all directions. When disparity-specified slant and perspective-specified slant were conflicting, observers were able to perceive the surfaces in two ways: they perceived either a trapezoid or a rectangle. Our main finding is twofold. First, when subjects chose to perceive the trapezoid, the slant estimates followed the disparity-predicted slant with only a slight underestimation, as if they selected a pure binocular representation of slant governed only by disparity. Second, when subjects chose to perceive the rectangle their estimates for real surfaces were similar to those for photographed surfaces, as if they selected a representation of slant governed by perspective foreshortening.     

Slant-tilt: The visual encoding of surface orientation

A specific form for the internal representation of local surface orientation is proposed, which is similar to Gibson's (1950) “amount and direction of slant”. Slant amount is usually quantifed by the angle σ between the surface normal and the line of sight (0°≦σ≦90°). Slant direction corresponds to the direction of the gradient of distance from the viewer to the surface, and may be defined by the image direction τ to which the surface normal would project (0°≦τ≦360°). Since the direction of slant is specified by the tilt of the projected surface normal, it is referred to as surface tilt (Stevens, 1979; Marr, 1982). The two degrees of freedom of orientation are therefore quantified by slant, an angle measured perpendicular to the image plane, and tilt, an angle measured in the image plane. The slanttilt form provides several computational advantages relative to some other proposals and is consistent with various psychological phenomena. Slant might be encoded by various means, e.g. by the cosine of the angle, by the tangent, or linearly by the angle itself. Experimental results are reported that suggest that slant is encoded by an internal parameter that varies linearly with slant angle, with resolution of roughly one part in 100. Thus we propose that surface orientation is encoded in human vision by two quantities, one varying linearly with slant angle, the other varying linearly with tilt angle.     

Nucleotide Frequencies in Human Genome and Fibonacci Numbers

This work presents a mathematical model that establishes an interesting connection between nucleotide frequencies in human single-stranded DNA and the famous Fibonacci’s numbers. The model relies on two assumptions. First, Chargaff’s second parity rule should be valid, and second, the nucleotide frequencies should approach limit values when the number of bases is sufficiently large. Under these two hypotheses, it is possible to predict the human nucleotide frequencies with accuracy. This result may be used as evidence to the Fibonacci string model that was proposed to the sequence growth of DNA repetitive sequences. It is noteworthy that the predicted values are solutions of an optimization problem, which is commonplace in many of nature’s phenomena.     

May Rapoport’s Rule Apply to Human Associated Pathogens?

Many debates surround the generalization of Rapoport’s rule (i.e., the presence of a positive correlation between range size and latitude); however, little attention has been devoted to this spatial pattern (1) worldwide and (2) for pathogenic microorganisms. In this study, we analyzed this relationship for 290 human pathogenic species dispersed throughout the world to test whether pathogenic organisms with different ecological niches and strategies will show this trend. The midpoint method was used to calculate the correlation between the geographical range size and the latitude applied to different subsets of pathogens, including taxonomic subdivisions (bacteria, viruses, helminths, protozoans, and fungi) and categories based on transmission mode and host specificity. It is assumed that Rapoport’s spatial pattern may exist for human infectious diseases, whatever hemisphere is considered, for 5 to 7 of 8 of the selected groups, depending on the pathogen species included. This is the first study performed to investigate Rapoport’s pattern at a global scale for various pathogenic organisms. We also discuss how three well-known spatial patterns of diversity, i.e., latitudinal gradient, nested species pattern, and Rapoport’s rule, may vary together to produce the actual large-scale geographical distribution of human pathogenic species observed on Earth. These findings have important messages for understanding the distribution and the diffusion of human pathogenic species; however, further studies are needed to investigate the exact underlying mechanisms responsible for those patterns.     

Modeling organelle transport in branching dendrites with a variable cross-sectional area

The purpose of this paper is to develop a method for calculating organelle transport in dendrites with a non-uniform cross-sectional area that depends on the distance from the neuron soma. The model is based on modified Smith–Simmons equations governing molecular motor-assisted organelle transport. The developed method is then applied to simulating organelle transport in branching dendrites with two particular microtubule (MT) orientations reported from experiments. It is found that the rate of organelle transport toward a dendrite’s growth cone heavily depends on the MT orientation, and since there is experimental evidence that the MT orientation in a particular region of a dendrite may depend on the dendrite’s developmental stage, the obtained results suggest that a rearrangement of the MT structure may depend on the amount of organelles needed at the growth cone.     

Competing political visions and Bolivia’s unfinished revolution

In Bolivia, there is a growing conflict between indigenous peoples and multinational corporations, particularly those in extractive industries. Evo Morales’s government is in the middle of the conflict and that makes the ongoing political situation very confusing. The ambiguity derives from the fact that the popular mobilizations did not go far enough; they were not sufficient to reconstitute a stable, alternative form of political rule.     

The Patient’s View: Issues of Theory and Practice

Almost all the knowledge now produced about psychiatry includes what is called “the patient’s or client’s perspective.” This paper analyzes how this notion has been framed in the discourses on mental health over the last two decades, particularly in mental health research and in anthropology. The very concept of the “patient’s perspective” is a social and historical construct. Despite its remarkable prevalence, the notion remains vague. Mental health research pictures it as a stable attribute of the individual. Anthropologists integrate the contextual nature of the patient view; but they still largely envision the psychiatric patient as a rational actor producing narratives based on common sense. However, in psychiatric practice, the client’s perspective is not something the patient individually produces; it is rather shaped by and in a context. To explore this process, my research investigated interactions between staff and patients in a French community mental health center, and showed that the client’s perspective is the result of a collective process. Further analysis demonstrates that eliciting or producing the patient’s view is sometimes considered a therapeutic goal in itself, since being granted the status of a rational and narrative actor gives access to the most valued model of care, one that is based on partnership. Being an outcome that is negotiated between patients and care providers, the “patient’s view” then becomes a new resource in mental health settings.

The molecular basis of speciation: from patterns to processes,rules to mechanisms

The empirical study of speciation has brought us closer to unlocking the origins of life’s vast diversity. By examining recently formed species, a number of general patterns, or rules, become apparent. Among fixed differences between species, sexual genes and traits are one of the most rapidly evolving and novel functional classes, and premating isolation often develops earlier than postmating isolation. Among interspecific hybrids, sterility evolves faster than inviability, the X-chromosome has a greater effect on incompatibilities than autosomes, and hybrid dysfunction affects the heterogametic sex more frequently than the homogametic sex (Haldane’s rule). Haldane’s rule, in particular, has played a major role in reviving interest in the genetics of speciation. However, the large genetic and reproductive differences between taxa and the multi-factorial nature of each rule have made it difficult to ascribe general mechanisms. Here, we review the extensive progress made since Darwin on understanding the origin of species. We revisit the rules of speciation, regarding them as landmarks as species evolve through time. We contrast these ‘rules’ of speciation to ‘mechanisms’ of speciation representing primary causal factors ranging across various levels of organization—from genic to chromosomal to organismal. To explain the rules, we propose a new ‘hierarchical faster-sex’ theory: the rapid evolution of sex and reproduction-related (SRR) genes (faster-SRR evolution), in combination with the preferential involvement of the X-chromosome (hemizygous X-effects) and sexually selected male traits (faster-male evolution). This unified theory explains a comprehensive set of speciation rules at both the prezyotic and postzygotic levels and also serves as a cohesive alternative to dominance, composite, and recent genomic conflict interpretations of Haldane’s rule.     

Effects of the torso boundary and internal conductivity interfaces in electrocardiography: An evaluation of the ‘Infinite medium’ approximation

The analytic, eccentric spheres model of the torso was used to examine the validity of approximating the ‘infinite medium’ potential by integrating ‘finite medium potentials’ over the torso surface. Although idealized, the analytic model is sophisticated enough for all important torso conductivity and geometry parameters to be preserved in the formulation. The model generates both ‘finite medium’ potentials (for which the torso is surrounded by air) and also ‘infinite medium’ potentials (for which the outermost layer of the torso extends outward to infinity). The finite medium torso potentials were integrated over the torso surface in accordance with the approximation used by many investigators in an effort to make the surface distribution more representative of the primary cardiac sources. The resulting potential distribution was compared with the true infinite medium potential, in which the effects of internal inhomogeneities (secondary sources) were taken into account. The difference between the two representations was found to be significant, and caution should be used when interpreting such data.     

Life cycle assessment in green chemistry

Background, Aims and Scope Using renewable feedstock and introducing biocatalysts in the chemical industry have been suggested as the key strategies to reduce the environmental impact of chemicals. The Swedish interdisciplinary programme ‘Greenchem’, is aiming to develop these strategies. One target group of chemicals for Greenchem are wax esters which can be used in wood surface coatings for wood furniture, etc. The aim of this study was to conduct a life cycle assessment of four different wood surface coatings, two wax-based coatings and two lacquers using ultra violet light for hardening (UV lacquers). One of the two wax-based coatings is based on a renewable wax ester produced with biocatalysts from rapeseed oil, denoted ‘green wax’, while the other is based on fossil feedstock and is denoted ‘fossil wax’. The two UV lacquers consist of one ‘100% UV’ coating and one ‘water-based UV’ coating. The scope was to compare the environmental performance of the new ‘green’ coating with the three coatings which are on the market today. Methods The study has a cradle-to-grave perspective and the functional unit is ‘decoration and protection of 1 m² wood table surface for 20 years’. Extensive data collection and calculations have been performed for the two wax-based coatings, whereas mainly existing LCI data have been used to characterise the production of the two UV lacquers. Results For all impact categories studied, the ‘100% UV’ lacquer is the most environmentally benign alternative. The ‘water-based UV’ is the second best alternative for all impact categories except EP, where the ‘fossil wax’ is slightly better. For GWP the ‘fossil wax’ has the highest contribution followed by the ‘green wax’. For AP and EP it is the ‘green wax’ that makes the highest environmental impact due to the contribution from the cultivation of the rapeseed and the production of the rapeseed oil. For POCP the ‘fossil wax’ makes the highest contribution, slightly higher than the contribution from the ‘green wax’. Also the energy requirements for the ‘100% UV’ lacquer is much lower than for the other coatings. The results from the toxicological evaluation conducted in this study, which was restricted to include only the UV lacquers, are inconclusive, giving different results depending on the model chosen, EDIP97 or USES. Discussion The result in this study shows that the environmental benefits of using revewable feedstock and processes based on biocatalysis in the production of wax esters used in wood surface coatings are rather limited. This is due to the high environmental impact from other steps in the life cycle of the coating. Conclusions Overall the ‘100% UV’ lacquer seems to be the best alternative from an environmental point of view. This study shows that the hot spots of the life cycle of the coatings are the production of the ingredients, but also the application and drying of the coatings. The toxicity assessment shows the need for the development of a new model, a model which finds common ground in order to overcome the current situation of diverging results of toxicity assessments. The results in this study also point to the importance of investigating the environmental performance of a product based on fossil or renewable feedstock from a life cycle perspective. Recommendations and Perspectives The results in this study show that an efficient way to improve the wood coating industry environmentally is to increase the utilization of UV lacquers that are 100% UV-based. These coatings can also be even further improved by introducing biocatalytic processes and producing epoxides and diacrylates from renewable raw material instead of the fossil-based ones produced with conventional chemical methods in use today. In doing this, however, choosing a vegetable oil with good environmental performance is important. An alternative application of the ‘green wax’ analysed in this study may be as an ingredient in health care products, for example, which may result in greater environmental benefits than when the wax is used inwood coating products. The results in this study illustrate the importance of investigating the environmental performance of a product from cradle-to-grave perspective and not consider it ‘green’ because it is based on renewable resources.     

Quantifying uncertainty in predictions of invasiveness, with emphasis on weed risk assessment

Using the Australian Weed Risk Assessment (WRA) model as an example, we applied a combination of bootstrapping and Bayesian techniques as a means of explicitly estimating the posterior probability of weediness as a function of an import risk assessment model screening score. Our approach provides estimates of uncertainty around model predictions, after correcting for verification bias arising from the original training dataset having a higher proportion of weed species than would be the norm, and incorporates uncertainty in current knowledge of the prior (base-rate) probability of weediness. The results confirm the high sensitivity of the posterior probability of weediness to the base-rate probability of weediness of plants proposed for importation, and demonstrate how uncertainty in this base-rate probability manifests itself in uncertainty surrounding predicted probabilities of weediness. This quantitative estimate of the weediness probability posed by taxa classified using the WRA model, including estimates of uncertainty around this probability for a given WRA score, would enable bio-economic modelling to contribute to the decision process, should this avenue be pursued. Regardless of whether or not this avenue is explored, the explicit estimates of uncertainty around weed classifications will enable managers to make better informed decisions regarding risk. When viewed in terms of likelihood of weed introduction, the current WRA model outcomes of ‘accept’, ‘further evaluate’ or ‘reject’, whilst not always accurate in terms of weed classification, appear consistent with a high-expected cost of mistakenly introducing a weed. The methods presented have wider application to the quantitative prediction of invasive species for situations where the base-rate probability of invasiveness is subject to uncertainty, and the accuracy of the screening test imperfect.     

Quantifying Uncertainty in Predictions of Invasiveness

Using the Australian weed risk assessment (WRA) model as an example, we applied a combination of bootstrapping and Bayesian techniques as a means for explicitly estimating the posterior probability of weediness as a function of an import risk assessment model screening score. Our approach provides estimates of uncertainty around model predictions, after correcting for verification bias arising from the original training dataset having a higher proportion of weed species than would be the norm, and incorporates uncertainty in current knowledge of the prior (base-rate) probability of weediness. The results confirm the high sensitivity of the posterior probability of weediness to the base-rate probability of weediness of plants proposed for importation, and demonstrate how uncertainty in this base-rate probability manifests itself in uncertainty surrounding predicted probabilities of weediness. This quantitative estimate of the weediness probability posed by taxa classified using the WRA model, including estimates of uncertainty around this probability for a given WRA score, would enable bio-economic modelling to contribute to the decision process, should this avenue be pursued. Regardless of whether or not this avenue is explored, the explicit estimates of uncertainty around weed classifications will enable managers to make better informed decisions regarding risk. When viewed in terms of likelihood of weed introduction, the current WRA model outcomes of ‘accept’, ‘further evaluate’, or ‘reject’, whilst not always accurate in terms of weed classification, appear consistent with a high expected cost of mistakenly introducing a weed. The methods presented have wider application to the quantitative prediction of invasive species for situations where the base-rate probability of invasiveness is subject to uncertainty, and the accuracy of the screening test imperfect     

Discrete Cilia Modelling with Singularity Distributions: Application to the Embryonic Node and the Airway Surface Liquid

We discuss in detail techniques for modelling flows due to finite and infinite arrays of beating cilia. An efficient technique, based on concepts from previous ‘singularity models’ is described, that is accurate in both near and far-fields. Cilia are modelled as curved slender ellipsoidal bodies by distributing Stokeslet and potential source dipole singularities along their centrelines, leading to an integral equation that can be solved using a simple and efficient discretisation. The computed velocity on the cilium surface is found to compare favourably with the boundary condition. We then present results for two topics of current interest in biology. 1) We present the first theoretical results showing the mechanism by which rotating embryonic nodal cilia produce a leftward flow by a ‘posterior tilt,’ and track particle motion in an array of three simulated nodal cilia. We find that, contrary to recent suggestions, there is no continuous layer of negative fluid transport close to the ciliated boundary. The mean leftward particle transport is found to be just over 1 μm/s, within experimentally measured ranges. We also discuss the accuracy of models that represent the action of cilia by steady rotlet arrays, in particular, confirming the importance of image systems in the boundary in establishing the far-field fluid transport. Future modelling may lead to understanding of the mechanisms by which morphogen gradients or mechanosensing cilia convert a directional flow to asymmetric gene expression. 2) We develop a more complex and detailed model of flow patterns in the periciliary layer of the airway surface liquid. Our results confirm that shear flow of the mucous layer drives a significant volume of periciliary liquid in the direction of mucus transport even during the recovery stroke of the cilia. Finally, we discuss the advantages and disadvantages of the singularity technique and outline future theoretical and experimental developments required to apply this technique to various other biological problems, particularly in the reproductive system.     

Joint evolution of predator body size and prey-size preference

We studied the joint evolution of predator body size and prey-size preference based on dynamic energy budget theory. The predators’ demography and their functional response are based on general eco-physiological principles involving the size of both predator and prey. While our model can account for qualitatively different predator types by adjusting parameter values, we mainly focused on ‘true’ predators that kill their prey. The resulting model explains various empirical observations, such as the triangular distribution of predator–prey size combinations, the island rule, and the difference in predator–prey size ratios between filter feeders and raptorial feeders. The model also reveals key factors for the evolution of predator–prey size ratios. Capture mechanisms turned out to have a large effect on this ratio, while prey-size availability and competition for resources only help explain variation in predator size, not variation in predator–prey size ratio. Predation among predators is identified as an important factor for deviations from the optimal predator–prey size ratio.     

Phase-linking and the perceived motion during off-vertical axis rotation

Human off-vertical axis rotation (OVAR) in the dark typically produces perceived motion about a cone, the amplitude of which changes as a function of frequency. This perception is commonly attributed to the fact that both the OVAR and the conical motion have a gravity vector that rotates about the subject. Little-known, however, is that this rotating-gravity explanation for perceived conical motion is inconsistent with basic observations about self-motion perception: (a) that the perceived vertical moves toward alignment with the gravito-inertial acceleration (GIA) and (b) that perceived translation arises from perceived linear acceleration, as derived from the portion of the GIA not associated with gravity. Mathematically proved in this article is the fact that during OVAR these properties imply mismatched phase of perceived tilt and translation, in contrast to the common perception of matched phases which correspond to conical motion with pivot at the bottom. This result demonstrates that an additional perceptual rule is required to explain perception in OVAR. This study investigates, both analytically and computationally, the phase relationship between tilt and translation at different stimulus rates—slow (45°/s) and fast (180°/s), and the three-dimensional shape of predicted perceived motion, under different sets of hypotheses about self-motion perception. We propose that for human motion perception, there is a phase-linking of tilt and translation movements to construct a perception of one’s overall motion path. Alternative hypotheses to achieve the phase match were tested with three-dimensional computational models, comparing the output with published experimental reports. The best fit with experimental data was the hypothesis that the phase of perceived translation was linked to perceived tilt, while the perceived tilt was determined by the GIA. This hypothesis successfully predicted the bottom-pivot cone commonly reported and a reduced sense of tilt during fast OVAR. Similar considerations apply to the hilltop illusion often reported during horizontal linear oscillation. Known response properties of central neurons are consistent with this ability to phase-link translation with tilt. In addition, the competing “standard” model was mathematically proved to be unable to predict the bottom-pivot cone regardless of the values used for parameters in the model.     

Nonparametric density estimation and regression achieved with topographic maps maximizing the information-theoretic entropy of their outputs

We introduce an unsupervised competitive learning rule, called the extended Maximum Entropy learning Rule (eMER), for topographic map formation. Unlike Kohonen's Self-Organizing Map (SOM) algorithm, the presence of a neighborhood function is not a prerequisite for achieving topology-preserving mappings, but instead it is intended: (1) to speed up the learning process and (2) to perform nonparametric regression. We show that, when the neighborhood function vanishes, the neural weigh t density at convergence approaches a linear function of the input density so that the map can be regarded as a nonparametric model of the input density. We apply eMER to density estimation and compare its performance with that of the SOM algorithm and the variable kernel method. Finally, we apply the ‘batch’ version of eMER to nonparametric projection pursuit regression and compare its performance with that of back-propagation learning, projection pursuit learning, constrained topolog ical mapping, and the Heskes and Kappen approach. Received: 12 August 1996 / Accepted in revised form: 9 April 1997     

Immunocytochemical localization of thrombomodulin in the aqueous humor passage of the rat eye

 This report describes the distribution and localization of thrombomodulin (TM) in the rat eye by light and electron microscopic immunocytochemistry. In addition to the endothelium of the entire vasculature, TM was found on the non-vascular structures lining the cavities of the posterior and anterior chambers and the limbus. TM was localized on the basal, lateral, and apical plasma membranes of the inner and outer ciliary epithelium, and the posterior iris epithelium in which there was no polarized expression of TM. In the anterior chamber, TM was localized on the luminal surface of the corneal endothelium, but was negative on the anterior border layer of the iris, which is composed of a discontinuous layer of fibroblasts and collagen fibers. Thus, TM was present at sites of cell-to-cell contact. TM was also present on the endothelia of the trabecular meshwork and the Schlemm’s canal in the limbus. TM was localized not only on the luminal plasma membrane, but also on the cytoplasmic giant vacuoles in the endothelial cells of the Schlemm’s canal. These findings extend the importance of anticoagulant mechanisms to the systems of secretion, circulation, and drainage of the aqueous humor. Accepted: 18 March 1997     

Angle determination for side views in single particle electron microscopy

In order to build a first model in single particle electron microscopy the relative angular orientation of each image of a protein complex must be determined. These orientations can be described by three Eulerian angles. Images of complexes that present the same view can be aligned in two-dimensions and averaged in order to increase their signal-to-noise ratio. Based on these averaged images, several standard approaches exist for determining Euler angles for randomly oriented projection images. The common lines and angular reconstitution methods work well for particles with symmetry while the random conical tilting and related orthogonal tilt reconstruction methods work in most cases but require the acquisition of tilt pairs of images. For the situation where views of particles can be identified that are rotations about a single axis parallel to the grid, an alternative algorithm to determine the orientations of class averages without the need to acquire tilt pairs can be applied. This type of view of a complex is usually called a side view. This paper describes the detailed workings and characterization of an algorithm, named rotational analysis, which uses real-space fiducial markers derived from the averages themselves to determine the Euler angles for side views. We demonstrate how this algorithm works in practice by applying it to a data set of images of affinity-purified bovine mitochondrial ATP synthase.