Stimulus size and the magnitude of the visual illusion of extent

Psychophysical experiments have been performed to study the dependence of the magnitude of the illusion of extent on the size of the referential part of the stimulus for different lengths of the imaginary wings of a modified Brentano figure. The experimental data are explained in terms of a model based on the concept of biases of the centroids of excitatory patterns evoked by stimulus terminating elements. A good fit of experimental data to calculated values confirms the model’s assumption that the areas of perceptual influence increase depend on their eccentricity in the visual field. An estimation of the model’s parameters also confirms the assumption that distortion of perceived information on the relative positioning of the centers of masses of the stimulus terminators is one of the main factors determining the magnitude of the illusion of extent and supports the hypothesis on the relationship of the phenomenon of this illusion with characteristics of the mechanism responsible for the perception of three-dimensional coordinates of visual objects.     

Planning versus online control: dynamic illusion effects in grasping?

The planning/control model of action assumes that grasping is sensitive to the context of an object only in early stages of the movement (planning), but not in later stages (control). In consequence, the effects of context-induced illusions (such as the Ebbinghaus/Titchener illusion) should decrease during a grasping movement. Here, we tested this claim by reanalysing a large data set (N = 26) on grasping in the Ebbinghaus illusion. Contrary to the predictions of the planning/control model, we found that the effects of the illusion did not decrease over time. Instead, the illusion effects stayed remarkably constant.     

Perception of Body Ownership Is Driven by Bayesian Sensory Inference

Recent studies have shown that human perception of body ownership is highly malleable. A well-known example is the rubber hand illusion (RHI) wherein ownership over a dummy hand is experienced, and is generally believed to require synchronized stroking of real and dummy hands. Our goal was to elucidate the computational principles governing this phenomenon. We adopted the Bayesian causal inference model of multisensory perception and applied it to visual, proprioceptive, and tactile stimuli. The model reproduced the RHI, predicted that it can occur without tactile stimulation, and that synchronous stroking would enhance it. Various measures of ownership across two experiments confirmed the predictions: a large percentage of individuals experienced the illusion in the absence of any tactile stimulation, and synchronous stroking strengthened the illusion. Altogether, these findings suggest that perception of body ownership is governed by Bayesian causal inference—i.e., the same rule that appears to govern the perception of outside world.     

Experimental-neuromodeling framework for understanding auditory object processing: integrating data across multiple scales.

In this article, we review a combined experimental-neuromodeling framework for understanding brain function with a specific application to auditory object processing. Within this framework, a model is constructed using the best available experimental data and is used to make predictions. The predictions are verified by conducting specific or directed experiments and the resulting data are matched with the simulated data. The model is refined or tested on new data and generates new predictions. The predictions in turn lead to better-focused experiments. The auditory object processing model was constructed using available neurophysiological and neuroanatomical data from mammalian studies of auditory object processing in the cortex. Auditory objects are brief sounds such as syllables, words, melodic fragments, etc. The model can simultaneously simulate neuronal activity at a columnar level and neuroimaging activity at a systems level while processing frequency-modulated tones in a delayed-match-to-sample task. The simulated neuroimaging activity was quantitatively matched with neuroimaging data obtained from experiments; both the simulations and the experiments used similar tasks, sounds, and other experimental parameters. We then used the model to investigate the neural bases of the auditory continuity illusion, a type of perceptual grouping phenomenon, without changing any of its parameters. Perceptual grouping enables the auditory system to integrate brief, disparate sounds into cohesive perceptual units. The neural mechanisms underlying auditory continuity illusion have not been studied extensively with conventional neuroimaging or electrophysiological techniques. Our modeling results agree with behavioral studies in humans and an electrophysiological study in cats. The results predict a particular set of bottom-up cortical processing mechanisms that implement perceptual grouping, and also attest to the robustness of our model.     

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble

Prediction of RNA secondary structure by free energy minimization has been the standard for over two decades. Here we describe a novel method that forsakes this paradigm for predictions based on Boltzmann-weighted structure ensemble. We introduce the notion of a centroid structure as a representative for a set of structures and describe a procedure for its identification. In comparison with the minimum free energy (MFE) structure using diverse types of structural RNAs, the centroid of the ensemble makes 30.0% fewer prediction errors as measured by the positive predictive value (PPV) with marginally improved sensitivity. The Boltzmann ensemble can be separated into a small number (3.2 on average) of clusters. Among the centroids of these clusters, the "best cluster centroid" as determined by comparison to the known structure simultaneously improves PPV by 46.5% and sensitivity by 21.7%. For 58% of the studied sequences for which the MFE structure is outside the cluster containing the best centroid, the improvements by the best centroid are 62.5% for PPV and 31.4% for sensitivity. These results suggest that the energy well containing the MFE structure under the current incomplete energy model is often different from the one for the unavailable complete model that presumably contains the unique native structure. Centroids are available on the Sfold server at http://sfold.wadsworth.org.     

Stochastic sampling of the RNA structural alignment space

A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the ‘structural alignment’ space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The ‘best’ centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.     

The Wagon Wheel Illusions and models of orientation selection

We present an analysis of the Wagon Wheel Illusions—classic psychophysical phenomena—in the context of a neural network model of orientation selectivity in the visual system. We find that both the continuous Wagon Wheel Illusion (c-WWI) and the standard, stroboscopic Wagon Wheel Illusion (WWI) can be explained by a recurrent model in which the cortex provides both excitatory and inhibitory feedback to a weakly tuned input from the lateral geniculate nucleus. Comparison of data from recent psychophysics experiments with theoretical predictions derived from the network dynamics leads to excellent agreement. Conversely, this agreement confirms the validity of the model and highlights the fact that the Wagon Wheel Illusion can serve as a useful probe of the human striate cortex. We find that the WWI results from phase-locking in the visual system and that a circle map determines the dynamics of the illusion. Furthermore, our results suggest that the c-WWI is a consequence of continuous processing and cannot be used to support claims of discrete processing by the visual system.     

Milky spots in the greater omentum are predominant sites of local tumour cell proliferation and accumulation in the peritoneal cavity

The role that milky spots in the greater omentum play in tumour cell spread in the peritoneal cavity is presently not fully understood. To study whether intraperitoneally injected tumour cells appear preferentially in milky spots of the greater omentum and to study the changes in the greater omentum, and especially in the cell population of milky spots after tumour cell infiltration, the following study was performed. A detailed temporal sequences of changes in morphology and cellular composition in milky spots of the greater omentum of Wag/Rij rats 5, 15, 30, 60 min, 2, 4, 8, 16, 24 h, 2, 4, 8 days and 2 and 4 weeks after intraperitoneal administration of 2.0 × 10⁶ CC 531 tumour cells was investigated by light microscopy and electron microscopy (pre-embedding labelling). Our data showed that the milky spots in the greater omentum were the sites to which tumour cells migrated preferentially from the peritoneal cavity. The tumour cells infiltrated the milky spots and formed clusters within. The cellular population in milky spots reacted by a very rapid influx of young macrophages during the first hour and an increase of the total number of cells (P < 0.01). After 4 h tumour cells were also located on the greater omentum outside the area of the milky spots. Around these tumour cell deposits, new milky spots are formed, which increased the total number of milky spots. The cells present in milky spots are not capable of reversing the growth of tumours and finally a solid omental cake of tumour cells is formed. Received: 30 June 1998 / Accepted: 3 September 1998     

The body beyond the body: expectation of a sensory event is enough to induce ownership over a fake hand

More than 100 papers have been published on the rubber hand illusion since its discovery 14 years ago. The illusion has been proposed as a demonstration that the body is distinguished from other objects by its participation in specific forms of intermodal perceptual correlation. Here, we radically challenge this view by claiming that perceptual correlation is not necessary to produce the experience of this body as mine. Each of 15 participants was seated with his/her right arm resting upon a table just below another smaller table. Thus, the real hand was hidden from the participant''s view and a life-sized rubber model of a right hand was placed on the small table in front of the participant. The participant observed the experimenter''s hand while approaching—without touching—the rubber hand. Phenomenology of the illusion was measured by means of skin conductance response and questionnaire. Both measures indicated that participants experienced the illusion that the experimenter''s hand was about to touch their hidden hand rather than the rubber hand, as if the latter replaced their own hand. This did not occur when the rubber hand was rotated by 180° or replaced by a piece of wood. This illusion indicates that our brain does not build a sense of self in a merely reactive way, via perceptual correlations; rather it generates predictions on what may or may not belong to itself.     

Nucleation and mobility model of Ag<Subscript>n</Subscript> clusters adsorbed on perfect and oxygen vacancy MgO surfaces

The structures and energy properties for Ag_n (n = 1-8) metal clusters adsorbed on the perfect and oxygen vacancy MgO surfaces have been studied by using the DFT/UB3LYP method with an embedded cluster model. The nucleation and mobility model for the Ag_n (n = 1-8) clusters on the perfect and oxygen vacancy MgO(100) surfaces was investigated. The results show that the Ag atoms locate initially at the surface oxygen vacancy sites; then, with the growth of Ag cluster sizes, the large Ag clusters move possibly out of the vacancy sites by a rolling model, and diffuse on the MgO surface under a certain temperature condition. The relative energies needed for moving out of the oxygen vacancy region for the adsorbed Ag_n clusters with the rolling model have been predicted. The even-odd oscillation behaviors for the cohesive energies, nucleation energies, first ionization potentials and HOMO-LUMO gaps of the adsorbed Ag_n clusters with the variation of cluster sizes have also been discussed.     

Distortions of length perception

A combined influence of stimulus orientation and structure on the judgement of length was tested in psychophysiological experiments. The subjects adjusted the test part of a stimulus to be equal in length to the reference part. The orientation of the parts of the stimulus varied in the experiments. The stimuli (three dots or the Oppel-Kundt figure, which had ten dots within the filled part) were generated on the monitor. In the Oppel-Kundt figure, the filled part was considered as a reference and the empty part as a test. In sessions of the experiments, values of errors were measured as functions of the size and orientation of the stimulus. The reference part length varied within 14–150 min arc range, and the orientation was fixed in 0°, 90°, 180° or 270° positions. The orientation of the test part varied from 0° to 360° in 7° steps. We assume, that the experiments with the three-dot stimuli yielded pure characteristics of visual field anisotropy, while those with the Oppel-Kundt figure showed the combined effect of both the components (anisotropy and spatial filtering). The data demonstrated independence of the two factors from each other in a simultaneous manifestation. The characteristics of a pure Oppel-Kundt illusion have been found to be in close correspondence with the predictions of the model of spatial filtering. Received: 1 July 1998 / Accepted in revised form: 4 November 1998     

Iron–sulfur protein folds,iron–sulfur chemistry,and evolution

An inventory of unique local protein folds around Fe–S clusters has been derived from the analysis of protein structure databases. Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe–2S]^2+,+ or [4Fe–4S]^2+,+ clusters. In contrast, high-potential Fe–S clusters, notwithstanding their structural diversity, occur in only three different protein folds. These observations suggest that the extant population of Fe–S protein folds has to a large extent been shaped in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing biosphere, in conditions where iron and sulfide had become poorly available, Fe–S clusters were less stable, and in addition faced competition from heme iron and copper active sites. Among the low-potential Fe–S active sites, protein folds hosting [4Fe–4S]^2+,+ clusters outnumber those with [2Fe–2S]^2+,+ ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe–S sites are evolving within proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the polypeptide chain. The discovery rate of novel Fe–S-containing protein folds underwent a sharp increase around 1995, and has remained stable to this day. The current trend suggests that the mapping of the Fe–S fold space is not near completion, in agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that the extant structural landscape of Fe–S proteins has been shaped to a large extent by primeval geochemical conditions on one hand, and iron–sulfur chemistry on the other.     

A novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles

Colocalisation, the overlap of subcellular structures labelled with different colours, is a key step to characterise cellular phenotypes. We have developed a novel bioimage informatics approach for quantifying colocalisation of round, blob-like structures in two-colour, highly resolved, three-dimensional fluorescence microscopy datasets. First, the algorithm identifies isotropic fluorescent particles, of relative brightness compared to their immediate neighbourhood, in three dimensions and for each colour. The centroids of these spots are then determined, and each object in one location of a colour image is checked for a corresponding object in the other colour image. Three-dimensional distance maps between the centroids of differently coloured spots then display where and how closely they colocalise, while histograms allow to analyse all colocalisation distances. We use the method to reveal sparse colocalisation of different human leukocyte antigen receptors in choriocarcinoma cells. It can also be applied to other isotropic subcellular structures such as vesicles, aggresomes and chloroplasts. The simple, robust and fast approach yields superresolved, object-based colocalisation maps and provides a first indication of protein–protein interactions of fluorescent, isotropic particles.     

When Passive Feels Active - Delusion-Proneness Alters Self-Recognition in the Moving Rubber Hand Illusion

Psychotic patients have problems with bodily self-recognition such as the experience of self-produced actions (sense of agency) and the perception of the body as their own (sense of ownership). While it has been shown that such impairments in psychotic patients can be explained by hypersalient processing of external sensory input it has also been suggested that they lack normal efference copy in voluntary action. However, it is not known how problems with motor predictions like efference copy contribute to impaired sense of agency and ownership in psychosis or psychosis-related states. We used a rubber hand illusion based on finger movements and measured sense of agency and ownership to compute a bodily self-recognition score in delusion-proneness (indexed by Peters’ Delusion Inventory - PDI). A group of healthy subjects (n=71) experienced active movements (involving motor predictions) or passive movements (lacking motor predictions). We observed a highly significant correlation between delusion-proneness and self-recognition in the passive conditions, while no such effect was observed in the active conditions. This was seen for both ownership and agency scores. The result suggests that delusion-proneness is associated with hypersalient external input in passive conditions, resulting in an abnormal experience of the illusion. We hypothesize that this effect is not present in the active condition because deficient motor predictions counteract hypersalience in psychosis proneness.     

Stationary multiple spots for reaction–diffusion systems

In this paper, we review analytical methods for a rigorous study of the existence and stability of stationary, multiple spots for reaction–diffusion systems. We will consider two classes of reaction–diffusion systems: activator–inhibitor systems (such as the Gierer–Meinhardt system) and activator–substrate systems (such as the Gray–Scott system or the Schnakenberg model). The main ideas are presented in the context of the Schnakenberg model, and these results are new to the literature. We will consider the systems in a two-dimensional, bounded and smooth domain for small diffusion constant of the activator. Existence of multi-spots is proved using tools from nonlinear functional analysis such as Liapunov–Schmidt reduction and fixed-point theorems. The amplitudes and positions of spots follow from this analysis. Stability is shown in two parts, for eigenvalues of order one and eigenvalues converging to zero, respectively. Eigenvalues of order one are studied by deriving their leading-order asymptotic behavior and reducing the eigenvalue problem to a nonlocal eigenvalue problem (NLEP). A study of the NLEP reveals a condition for the maximal number of stable spots. Eigenvalues converging to zero are investigated using a projection similar to Liapunov–Schmidt reduction and conditions on the positions for stable spots are derived. The Green’s function of the Laplacian plays a central role in the analysis. The results are interpreted in the biological, chemical and ecological contexts. They are confirmed by numerical simulations.      

A performance based consensus approach for predicting spatial extent of the Chinese windmill palm (Trachycarpus fortunei) in New Zealand under climate change

The predicted distribution of the Chinese Windmill Palm (Trachycarpus fortunei) was modelled using several algorithms with inputs consisting of occurrence information and bioclimatic datasets. A global species distribution model was developed and projected into New Zealand to provide a visualization of suitability for the species in current and future conditions. To ensure model robustness, occurrence data was checked for redundancy, spatial auto-correlation and the environmental variables checked for cross-correlation and collinearity. The final maps predicting suitability resulted from ensembling the predictions of all the algorithms. The resulting ensembled maps were weighted based on the evaluation parameters AUC, Kappa and TSS. When reclassified into low, medium and high suitability categories, results show an expansion of high suitability areas accompanied by a reduction of low suitability areas for the species. The centroids of the high suitability areas also exhibit a general movement towards the Southwest under future climate conditions. The range expansion was proportional with the representative values of emission trajectories RCPs (2.5, 4.5, 6.0 and 8.5) used in projecting into future conditions. The movement magnitude and direction of predicted high suitability area centroids for the palm supports the use of the plant as an indicator of climate change.     

Magnetic pulse affects a putative magnetoreceptor mechanism

Clusters of superparamagnetic (SP) magnetite crystals have recently been identified in free nerve endings in the upper-beak skin of homing pigeons and are interpreted as being part of a putative magnetoreceptor system. Motivated by these findings, we developed a physical model that accurately predicts the dynamics of interacting SP clusters in a magnetic field. The main predictions are: 1), under a magnetic field, a group of SP clusters self-assembles into a chain-like structure that behaves like a compass needle under slowly rotating fields; 2), in a frequently changing field as encountered by a moving bird, a stacked chain is a structurally more stable configuration than a single chain; 3), chain-like structures of SP clusters disrupt under strong fields applied at oblique angles; and 4), reassemble on a timescale of hours to days (assuming a viscosity of the cell plasma eta approximately 1 P). Our results offer a novel mechanism for magnetic field perception and are in agreement with the response of birds observed after magnetic-pulse treatments, which have been conducted in the past to specifically test if ferrimagnetic material is involved in magnetoreception, but which have defied explanation so far. Our theoretical results are supported by experiments on a technical SP model system using a high-speed camera. We also offer new predictions that can be tested experimentally.     

Deceptive color signaling in the night: a nocturnal predator attracts prey with visual lures

The role color signaling plays in the nocturnal condition ofthe terrestrial ecosystem is currently poorly understood. Ingeneral, arthropods active in the night are inconspicuouslycolored. However, in addition to inconspicuously colored dorsum,several genera of nocturnal orb spiders also have conspicuousventrum spots. In this study, we tested whether the inconspicuouslycolored dorsum functioned to reduce spiders‘ visibilityto diurnal predators while the spiders were perching on barkwith ventrum spots well concealed. We also evaluated when spiderssit on webs with conspicuous ventrum spots fully exposed, wouldthey serve as deceptive color signals to lure visually orientatednocturnal prey. We first quantified how diurnal hymenopteranpredators viewed the dorsum and nocturnal lepidopteran preyviewed the ventrum spots of nocturnal orb spiders Neoscona punctigeraby calculating color contrasts. The diurnal color contrast ofspiders’ dorsum when viewed by hymenopteran insects againstbark was lower than the discrimination threshold. However, thenocturnal color contrasts of spiders‘ ventrum spots whenviewed by moths were high. In the field, webs with N. punctigeraintercepted significantly more insects than those without. Whenthe color signal of ventrum spots was altered by paint, webs’prey interception rates decreased significantly. These resultsdemonstrate that even in the nocturnal condition certain terrestrialorganisms exhibit visual lures to attract prey.     

Responses to worm-like-wriggling models by the praying mantis: effects of amount of motion on prey recognition

Adult females of the mantis, Tenodera angustipennis, were presented with a wriggling model, consisting of six circular spots positioned in a row horizontally and adjacently. During presentation, this model wriggled like a worm by moving some spots. When the motion of the model was small (the number of moving spots ≤2), the mantis sometimes stalked the model with peering movements but seldom struck it. When the motion was large (the number of moving spots ≥3), the mantis frequently fixated, rapidly approached, and struck the model. These results suggest that the mantis changes its approach behavior depending on the amount of prey motion. Disappearance of some terminal spots at the stationary end hardly affected the rates of fixation, peering, and strike. The model that wriggled at each end elicited lower rates of fixation and strike than the model that wriggled at one end. These results suggest that the mantis responds to only the fastest moving part of the wriggling model when the motion of the model is large. Electronic Publication