Perception of shape-from-motion in macaque monkeys and humans

Motion is one of the most efficient cues for shape perception. We conducted behavioral experiments to examine how monkeys perceive shapes defined by motion cues and whether they perceive them as humans do. We trained monkeys to perform a shape discrimination task in which shapes were defined by the motion of random dots. Effects of dot density and dot speed on the shape perception of monkeys were examined. Human subjects were also tested using the same paradigm and the test results were compared with those of monkeys. In both monkeys and humans, correct performance rates declined when density or speed of random dots was reduced. Both of them tended to confuse the same combinations of shapes frequently. These results suggest that monkeys and humans perceive shapes defined by motion cues in a similar manner and probably have common neural mechanisms to perceive them. Electronic Publication     

Cross- and auto-correlation in early vision

Neurons that respond selectively to the orientation of visual stimuli were discovered in V1 more than 50 years ago, but it is still not fully understood how or why this is brought about. We report experiments planned to show whether human observers use cross-correlation or auto-correlation to detect oriented streaks in arrays of randomly positioned dots, expecting that this would help us to understand what David Marr called the 'computational goal' of V1. The streaks were generated by two different methods: either by sinusoidal spatial modulation of the local mean dot density, or by introducing coherent pairs of dots to create moiré patterns, as Leon Glass did. A wide range of dot numbers was used in the randomly positioned arrays, because dot density affects cross- and auto-correlation differently, enabling us to infer which method was used. This difference stems from the fact that the cross-correlation task is limited by random fluctuations in the local mean density of individual dots in the noisy array, whereas the auto-correlation task is limited by fluctuations in the numbers of randomly occurring spurious pairs having the same separation and orientation as the deliberately introduced coherent pairs. After developing a new method using graded dot luminances, we were able to extend the range of dot densities that could be used by a large factor, and convincing results were obtained indicating that the streaks generated by amplitude modulation were discriminated by cross-correlation, while those generated as moiré patterns were discriminated by auto-correlation. Though our current results only apply to orientation selectivity, it is important to know that early vision can do more than simple filtering, for evaluating auto-correlations opens the way to more interesting possibilities, such as the detection of symmetries and suspicious coincidences.     

Using Patterns in Track-Plate Footprints to Identify Individual Fishers

Abstract: If individuals can be identified from patterns in their footprints, noninvasive survey methods can be used to estimate abundance. Track plates capture fine detail in the footprints of fishers (Martes pennanti), recording rows of dots corresponding to tiny papillae on the animal's metacarpal pad. We show that the pattern of these dots can be used to identify individual fishers, similar to human fingerprints. A probabilistic model of uniqueness based on variation in spacing between 1,400 pairs of dots that we measured in prints of 14 different fisher feet suggests the probability of encountering a similar pattern in the print of a different foot by chance alone is ≤ 0.35ⁿ, where n = the number of dot pairs examined. This predicts a 0.00003 probability that a match made using 10 pairs of dots is false. Dot spacing from footprints made by the same foot was remarkably consistent (sN = 0.02 mm, n = 24 dot pairs). Combined, these results suggest dot patterns in fisher footprints were unique to individuals and were consistently reproduced on track plates. Empirical tests of matching accuracy were best with good-quality prints, highlighting the need for experience judging when prints are usable. We applied print matching to fisher detections collected on track plates deployed at 500-m intervals along 10 3.5-km transects in the Adirondack region of New York, USA. Of 62 fisher detections, 85% had ≥ 1 footprint of suitable quality to compare with other high-quality prints. We found that most detections from a transect were from the same individual fisher suggesting nonindependence of detections. Thus, data from traditional track-plate deployments over small time periods cannot be used as a measure of abundance, but new study designs using print matching could obtain robust noninvasive, mark—recapture density estimates.     

The role of visual information in numerosity estimation

Mainstream theory suggests that the approximate number system supports our non-symbolic number abilities (e.g. estimating or comparing different sets of items). It is argued that this system can extract number independently of the visual cues present in the stimulus (diameter, aggregate surface, etc.). However, in a recent report we argue that this might not be the case. We showed that participants combined information from different visual cues to derive their answers. While numerosity comparison requires a rough comparison of two sets of items (smaller versus larger), numerosity estimation requires a more precise mechanism. It could therefore be that numerosity estimation, in contrast to numerosity comparison, might rely on the approximate number system. To test this hypothesis, we conducted a numerosity estimation experiment. We controlled for the visual cues according to current standards: each single visual property was not informative about numerosity. Nevertheless, the results reveal that participants were influenced by the visual properties of the dot arrays. They gave a larger estimate when the dot arrays consisted of dots with, on average, a smaller diameter, aggregate surface or density but a larger convex hull. The reliance on visual cues to estimate numerosity suggests that the existence of an approximate number system that can extract numerosity independently of the visual cues is unlikely. Instead, we propose that humans estimate numerosity by weighing the different visual cues present in the stimuli.     

A self-assembled quantum dot probe for detecting beta-lactamase activity

This communication describes a quantum dot probe that can be activated by a reporter enzyme, beta-lactamase. Our design is based on the principle of fluorescence resonance energy transfer (FRET). A biotinylated beta-lactamase substrate was labeled with a carbocyanine dye, Cy5, and immobilized on the surface of quantum dots through the binding of biotin to streptavidin pre-coated on the quantum dots. In assembling this nanoprobe, we have found that both the distance between substrates and the quantum dot surface, and the density of substrates are important for its function. The fluorescence emission from quantum dots can be efficiently quenched (up to 95%) by Cy5 due to FRET. Our final quantum dot probe, assembled with QD605 and 1:1 mixture of biotin and a Cy5-labeled lactam, can be activated by 32microg/mL of beta-lactamase with 4-fold increase in the fluorescence emission.     

Perceptual Strategies of Pigeons to Detect a Rotational Centre—A Hint for Star Compass Learning?

Birds can rely on a variety of cues for orientation during migration and homing. Celestial rotation provides the key information for the development of a functioning star and/or sun compass. This celestial compass seems to be the primary reference for calibrating the other orientation systems including the magnetic compass. Thus, detection of the celestial rotational axis is crucial for bird orientation. Here, we use operant conditioning to demonstrate that homing pigeons can principally learn to detect a rotational centre in a rotating dot pattern and we examine their behavioural response strategies in a series of experiments. Initially, most pigeons applied a strategy based on local stimulus information such as movement characteristics of single dots. One pigeon seemed to immediately ignore eccentric stationary dots. After special training, all pigeons could shift their attention to more global cues, which implies that pigeons can learn the concept of a rotational axis. In our experiments, the ability to precisely locate the rotational centre was strongly dependent on the rotational velocity of the dot pattern and it crashed at velocities that were still much faster than natural celestial rotation. We therefore suggest that the axis of the very slow, natural, celestial rotation could be perceived by birds through the movement itself, but that a time-delayed pattern comparison should also be considered as a very likely alternative strategy.     

Binocular Depth Judgments on Smoothly Curved Surfaces

Binocular disparity is an important cue to depth, allowing us to make very fine discriminations of the relative depth of objects. In complex scenes, this sensitivity depends on the particular shape and layout of the objects viewed. For example, judgments of the relative depths of points on a smoothly curved surface are less accurate than those for points in empty space. It has been argued that this occurs because depth relationships are represented accurately only within a local spatial area. A consequence of this is that, when judging the relative depths of points separated by depth maxima and minima, information must be integrated across separate local representations. This integration, by adding more stages of processing, might be expected to reduce the accuracy of depth judgements. We tested this idea directly by measuring how accurately human participants could report the relative depths of two dots, presented with different binocular disparities. In the first, Two Dot condition the two dots were presented in front of a square grid. In the second, Three Dot condition, an additional dot was presented midway between the target dots, at a range of depths, both nearer and further than the target dots. In the final, Surface condition, the target dots were placed on a smooth surface defined by binocular disparity cues. In some trials, this contained a depth maximum or minimum between the target dots. In the Three Dot condition, performance was impaired when the central dot was presented with a large disparity, in line with predictions. In the Surface condition, performance was worst when the midpoint of the surface was at a similar distance to the targets, and relatively unaffected when there was a large depth maximum or minimum present. These results are not consistent with the idea that depth order is represented only within a local spatial area.     

Suprathreshold perceptual decisions constrain models of confidence

Perceptual confidence is an important internal signal about the certainty of our decisions and there is a substantial debate on how it is computed. We highlight three confidence metric types from the literature: observers either use 1) the full probability distribution to compute probability correct (Probability metrics), 2) point estimates from the perceptual decision process to estimate uncertainty (Evidence-Strength metrics), or 3) heuristic confidence from stimulus-based cues to uncertainty (Heuristic metrics). These metrics are rarely tested against one another, so we examined models of all three types on a suprathreshold spatial discrimination task. Observers were shown a cloud of dots sampled from a dot generating distribution and judged if the mean of the distribution was left or right of centre. In addition to varying the horizontal position of the mean, there were two sensory uncertainty manipulations: the number of dots sampled and the spread of the generating distribution. After every two perceptual decisions, observers made a confidence forced-choice judgement whether they were more confident in the first or second decision. Model results showed that the majority of observers were best-fit by either: 1) the Heuristic model, which used dot cloud position, spread, and number of dots as cues; or 2) an Evidence-Strength model, which computed the distance between the sensory measurement and discrimination criterion, scaled according to sensory uncertainty. An accidental repetition of some sessions also allowed for the measurement of confidence agreement for identical pairs of stimuli. This N-pass analysis revealed that human observers were more consistent than their best-fitting model would predict, indicating there are still aspects of confidence that are not captured by our modelling. As such, we propose confidence agreement as a useful technique for computational studies of confidence. Taken together, these findings highlight the idiosyncratic nature of confidence computations for complex decision contexts and the need to consider different potential metrics and transformations in the confidence computation.     

Sequential mapping of weighting functions for visual location.

The effect upon perceived location of adding an extra dot offset from the centre of a cluster of pseudorandom dots was investigated using a vernier acuity task. With this technique, weighting functions showing the extent to which the added dot pulls the apparent location of the entire cluster can be defined as a function of distance from the centre of the cluster. When dot density within the cluster is high, the weighting functions approximate to what would be expected on the basis of centroid alignment. With low dot densities, it appears that performance is determined by aligning the outermost dots within each cluster. The peak amplitudes of these weighting functions are proportional to the square root of dot density within the clusters. The results are consistent with the view that each vernier element is localised in an orthoaxial direction prior to discrimination of the vernier offset.     

The effects of dot density and motion coherence on perceptual fading of a target in noise

A peripherally presented target embedded in dynamic texture perceptually disappears (or 'fills-in') after around 10 s of steady fixation. This phenomenon was investigated for a target containing moving dots. The effects of manipulating the coherence of the motion within the target and the density of dots across the whole screen were explored. Coherence thresholds for the detection of a target at different dot densities were recorded for comparison. Fading occurred faster as either motion coherence or dot density was reduced. Coherence thresholds for target detection were unaffected by manipulations of dot density. There appeared to be no relationship between the stimulus exposure time needed for fading and the coherence threshold for detection of a target. The results suggest that the time taken for a target to fade is not a simple function of its motion detection threshold.     

Neurexin/Neuroligin Interaction Kinetics Characterized by Counting Single Cell-Surface Attached Quantum Dots

We report what to our knowledge is a new method to characterize kinetic rates between cell-surface-attached adhesion molecules. Cells expressing specific membrane receptors are surface-labeled with quantum dots coated with their respective ligands. The progressive diminution in the total number of surface-diffusing quantum dots tracked over time collectively reflects intrinsic ligand/receptor interaction kinetics. The probability of quantum dot detachment is modeled using a stochastic analysis of bond formation and dissociation, with a small number of ligand/receptor pairs, resulting in a set of coupled differential equations that are solved numerically. Comparison with the experimental data provides an estimation of the kinetic rates, together with the mean number of ligands per quantum dot, as three adjustable parameters. We validate this approach by studying the calcium-dependent neurexin/neuroligin interaction, which plays an important role in synapse formation. Using primary neurons expressing neuroligin-1 and quantum dots coated with purified neurexin-1β, we determine the kinetic rates between these two binding partners and compare them with data obtained using other techniques. Using specific molecular constructs, we also provide interesting information about the effects of neurexin and neuroligin dimerization on the kinetic rates. As it stands, this simple technique should be applicable to many types of biological ligand/receptor pairs.     

Categorical Biases in Perceiving Spatial Relations

We investigate the effect of spatial categories on visual perception. In three experiments, participants made same/different judgments on pairs of simultaneously presented dot-cross configurations. For different trials, the position of the dot within each cross could differ with respect to either categorical spatial relations (the dots occupied different quadrants) or coordinate spatial relations (the dots occupied different positions within the same quadrant). The dot-cross configurations also varied in how readily the dot position could be lexicalized. In harder-to-name trials, crosses formed a “+” shape such that each quadrant was associated with two discrete lexicalized spatial categories (e.g., “above” and “left”). In easier-to-name trials, both crosses were rotated 45° to form an “×” shape such that quadrants were unambiguously associated with a single lexicalized spatial category (e.g., “above” or “left”). In Experiment 1, participants were more accurate when discriminating categorical information between easier-to-name categories and more accurate at discriminating coordinate spatial information within harder-to-name categories. Subsequent experiments attempted to down-regulate or up-regulate the involvement of language in task performance. Results from Experiment 2 (verbal interference) and Experiment 3 (verbal training) suggest that the observed spatial relation type-by-nameability interaction is resistant to online language manipulations previously shown to affect color and object-based perceptual processing. The results across all three experiments suggest that robust biases in the visual perception of spatial relations correlate with patterns of lexicalization, but do not appear to be modulated by language online.     

Creating self-illuminating quantum dot conjugates

Semiconductor quantum dots are inorganic fluorescent nanocrystals that, because of their unique optical properties compared with those of organic fluorophores, have become popular as fluorescent imaging probes. Although external light excitation is typically required for imaging with quantum dots, a new type of quantum dot conjugate has been reported that can luminesce with no need for external excitation. These self-illuminating quantum dot conjugates can be prepared by coupling of commercially available carboxylate-presenting quantum dots to the light-emitting protein Renilla luciferase. When the conjugates are exposed to the luciferase's substrate coelenterazine, the energy released by substrate catabolism is transferred to the quantum dots through bioluminescence resonance energy transfer, leading to quantum dot light emission. This protocol describes step-by-step procedures for the preparation and characterization of these self-illuminating quantum dot conjugates. The preparation process is relatively simple and can be done in less than 2 hours. The availability of self-illuminating quantum dot conjugates will provide many new possibilities for in vivo imaging and detection, such as monitoring of in vivo cell trafficking, multiplex bioluminescence imaging and new quantum dot-based biosensors.     

The development of quantum dot calibration beads and quantitative multicolor bioassays in flow cytometry and microscopy

The use of fluorescence calibration beads has been the hallmark of quantitative flow cytometry. It has enabled the direct comparison of interlaboratory data as well as quality control in clinical flow cytometry. In this article, we describe a simple method for producing color-generalizable calibration beads based on streptavidin functionalized quantum dots. Based on their broad absorption spectra and relatively narrow emission, which is tunable on the basis of dot size, quantum dot calibration beads can be made for any fluorophore that matches their emission color. In an earlier publication, we characterized the spectroscopic properties of commercial streptavidin functionalized dots (Invitrogen). Here we describe the molecular assembly of these dots on biotinylated beads. The law of mass action is used to readily define the site densities of the dots on the beads. The applicability of these beads is tested against the industry standard, namely commercial fluorescein calibration beads. The utility of the calibration beads is also extended to the characterization surface densities of dot-labeled epidermal growth factor ligands as well as quantitative indicators of the binding of dot-labeled virus particles to cells.     

Nest mate recognition in ants with complex colonies: within- and between-population variation

The ability to recognize kin is widespread, and especially importantin highly social organisms. We studied kin recognition by assessingpatterns of aggression within and between nests of the antLeptothorax longispinosus. Colonies of this species can befractionated into subunits, a condition called polydomy. Theproblem of recognizing relatives is therefore more complexwhen those relatives can live in two or more different places.We hypothesized that spatial subdivision may have resulted ina stronger genetic component to kin recognition than in caseswhere colonies live in a single location. To test our hypothesiswe assessed recognition capabilities for two populations ofthis ant that differ in the complexity of their colonies. Ina New York, USA, population, polydomy is very common, and coloniesalso can have multiple queens. By contrast, a population inWest Virginia, USA, has colonies that typically are monogynousand rarely are polydomous. We conducted introductions of antsbetween different nests collected in the same neighborhood,with self-introductions and alien introductions as controls.Nests from the two populations showed corresponding differencesin their aggression towards intruders. For New York nests, the extent of genetic similarity was the single best predictor ofaggression, whereas for West Virginia nests aggression wasjointly influenced by genetic similarity and spatial distance.In both populations, we found nest pairs for which aggressionwas nonreciprocal; these probably reflect recognition errors by one of the nests. After the ants were maintained in the laboratoryfor 3 months, their aggression scores rose and fewer recognitionerrors were made. Thus nest-mate and colony-mate recognitionin this species are mediated primarily by endogenous cues (geneticsimilarity); the importance of exogenous cues for nest materecognition depends on the population's social system.     

The influence of two-dimensional stimulus properties in a reconstruction task with minimal information stimuli

Effects of viewpoint that are typically found in shape recognition tasks have been interpreted in the past as strong evidence against approaches based on the use of geometric invariants by the human visual system. At first sight, the use of such invariants would indeed predict shape recognition to be viewpoint independent. It has been argued before, however, that the visual estimation of invariants need not itself be invariant. Changes of viewpoint introduce changes in 2D stimulus features. The latter may make the estimation of invariants by the visual system more or less difficult. The present study explores how such 2D features influence estimation distributions in a reconstruction paradigm. Subjects were shown four coplanar dots. They were asked to estimate the position of one of the dots relative to the three others on the basis of a slanted version of the configuration. An estimation distribution was obtained for every position of the dot to be estimated. Biases in these distributions indicated that subjects performed the task by using 2D reference axes that were unambiguously identifiable in both the images of the dot pattern.     

Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis

The potential for processive EcoRI endonuclease hydrolysis has been examined on several DNA substrates containing two EcoRI sites which were embedded in identical sequence environments. With a 388-base pair circular DNA, in which the two recognition sites are separated by 51 base pairs (shorter distance) or 337 base pairs (longer distance), 77 and 34% of all events involved processive hydrolysis at ionic strengths of 0.059 and 0.13, respectively. However, the frequency of processive action on linear substrates, in which the two sites were separated by 51 base pairs, was only 42 and 17% at these ionic strengths, values half those observed with the circular DNA. Processive action was not detectable on circular or linear substrates at an ionic strength of 0.23. These findings indicate that DNA search by the endonuclease occurs by facilitated diffusion, a mechanism in which the protein locates and leaves its recognition sequence by interacting with nonspecific DNA sites. We suggest that processivity on linear substrates is limited to values half that for small circles due to partitioning of the enzyme between the two products generated by cleavage of a linear molecule. Given such topological effects, measured processivity values imply that the endonuclease can diffuse within a DNA domain to locate and recognize an EcoRI site 50 to 300 base pairs distant from an initial binding site, with minimum search efficiencies being 80 and 30% at ionic strengths of 0.059 and 0.13, respectively. The high efficiency of processive action indicates that a positionally correlated mode of search plays a major role in facilitated diffusion in this system under such conditions. Also consistent with this view was the identification of a striking position effect when two closely spaced EcoRI sites were asymmetrically positioned near the end of a linear DNA. The endonuclease displays a substantial preference for the more centrally located recognition sequence. This preference does not reflect differential sensitivity of the two sites to cleavage per se, but can be simply explained by preferential entry of the enzyme via the larger nonspecific target available to the more centrally positioned recognition sequence. These conclusions differ from those of a previous qualitative analysis of endonuclease processivity over short distances (Langowski, J., Alves, J., Pingoud, A., and Maass, G. (1983) Nucleic Acids Res. 11, 501-513).     

Long-term memory of individual identity in ant queens

Remembering individual identities is part of our own everyday social life. Surprisingly, this ability has recently been shown in two social insects. While paper wasps recognize each other individually through their facial markings, the ant, Pachycondyla villosa, uses chemical cues. In both species, individual recognition is adaptive since it facilitates the maintenance of stable dominance hierarchies among individuals, and thus reduces the cost of conflict within these small societies. Here, we investigated individual recognition in Pachycondyla ants by quantifying the level of aggression between pairs of familiar or unfamiliar queens over time. We show that unrelated founding queens of P. villosa and Pachycondyla inversa store information on the individual identity of other queens and can retrieve it from memory after 24h of separation. Thus, we have documented for the first time that long-term memory of individual identity is present and functional in ants. This novel finding represents an advance in our understanding of the mechanism determining the evolution of cooperation among unrelated individuals.     

Moloney murine leukemia virus integration protein produced in yeast binds specifically to viral att sites.

The integration protein (IN) of Moloney murine leukemia virus (MuLV), purified after being produced in yeast cells, has been analyzed for its ability to bind its putative viral substrates, the att sites. An electrophoretic mobility shift assay revealed that the Moloney MuLV IN protein binds synthetic oligonucleotides containing att sequences, with specificity towards its cognate (MuLV) sequences. The terminal 13 base pairs, which are identical at both ends of viral DNA, are sufficient for binding if present at the ends of oligonucleotide duplexes in the same orientation as in linear viral DNA. However, only weak binding was observed when the same sequences were positioned within a substrate in a manner simulating att junctions in circular viral DNA with two long terminal repeats. Binding to att sites in oligonucleotides simulating linear viral DNA was dependent on the presence of the highly conserved CA residues preceding the site for 3' processing (an IN-dependent reaction that removes two nucleotides from the 3' ends of linear viral DNA); mutation of CA to TG abolished binding, and a CA to TA change reduced affinity by at least 20-fold. Removal of either the terminal two base pairs from both ends of the oligonucleotide duplex or the terminal two nucleotides from the 3' ends of each strand did not affect binding. The removal of three 3' terminal nucleotides, however, abolished binding, suggesting an essential role for the A residue immediately upstream of the 3' processing site in the binding reaction. These results help define the sequence requirements for att site recognition by IN, explain the conservation of the subterminal CA dinucleotide, and provide a simple assay for sequence-specific IN activity.     

Sequence-specific interaction of the Salmonella Hin recombinase in both major and minor grooves of DNA.

The Hin recombinase of Salmonella catalyzes a site-specific recombination event which leads to flagellar phase variation. Starting with a fully symmetrical recombination site, hixC, a set of 40 recombination sites which vary by pairs of single base substitutions was constructed. This set was incorporated into the Salmonella-specific bacteriophage P22 based challenge phage selection and used to define the DNA sequence determinants for the binding of Hin to DNA in vivo. The critical sequence-specific contacts between a Hin monomer and a 13 bp hix half-site are at two T:A base pairs in the major groove of the DNA which are separated by one base pair, and two consecutive A:T contacts in the minor groove. The base substitutions in the major groove recognition portion which were defective in binding Hin still retained residual binding capability in vivo, while the base pair substitutions affecting the minor groove recognition region lost all in vivo binding. Using in vitro binding assays, Hin was found to bind to hix symmetrical sites with A:T base pairs or I:C base pairs in the minor groove recognition sequences, but not to G:C base pairs. In separate in vitro binding assays, Hin was equally defective in binding to either a G:C or a I:C contact in a major groove recognition sequence. Results from in vitro binding assays to hix sites in which 3-deazaadenine was substituted for adenine are consistent with Hin making a specific contact to either the N3 of adenine or O2 of thymine in the minor groove within the hix recombination site on each symmetric half-site. These results taken with the results of previous studies on the DNA binding domain of Hin suggest a sequence-specific minor groove DNA binding motif.