The perception of a dotted line in noise: a model of good continuation and some experimental results

A formal model is proposed, describing how the perceptual interpretation of dot figures is guided by the Gestalt rule of good continuation. The algorithm will be restricted to figures with a collinear dot array (line) embedded in a background of randomly placed dots. The model, CODE-2, is an elaboration of the model, CODE-1, of grouping dots on the basis of the Gestalt rule of (relative) proximity, and consists of the introduction of non-circular symmetric gaussian distribution functions for the representation of the orientation dependent strength of interaction between collinear dots. Supra-threshold contours of the function, resulting from a superposition on each dot of the gaussian functions, are assumed to predict the perceptual grouping of the dots. A quantitative measure for the perceptual salience of dotted lines was defined as the contrast between the internal coherence of the line dots, and their interference with the noise dots. For 20 stimuli the CODE-2 grouping of the dots is reported, together with the results of a line-in-noise latency experiment. There was a significant correlation between the predicted saliences and the experimental results. The results support the usefulness of representing good continuation between collinear dots by non-circular symmetric gaussian distribution functions.     

Spatio-temporally averaged positions of moving objects

This study investigated the case where a spatial offset was periodically and momentarily introduced between two vernier components during their excursion, to determine how such an offset affects the relative localization of the components. If the object in motion is perceived at a position averaged over a limited spatio-temporal range, spatial offsets in a moving vernier should be perceived accordingly. This prediction was confirmed by the outcome of the first experiment. A second experiment was performed to inquire into the relationship between vernier threshold and the averaging of spatial offset, and also the spatio-temporal limit of the integrative process. The upper temporal limit of the averaging was estimated to be about 50 ms, and the spatial extent of positional modulation was shown to have a significant effect on the detection of vernier offset. It was found that the larger the extent over which the vernier positions were distributed, the smaller the offset detected between them. It is suggested that spatial offset can be detected directly, perhaps by some mechanism sensitive to the phase relationship of the components of visual patterns.     

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.     

A model for the perception of curves in dot figures: The role of local salience of “virtual lines”

In many models of visual information processing the notion of a virtual line or dipole is introduced in order to represent the configurational information, notably length and relative orientation, between identical figure elements in figures with discrete elements. Virtual lines have proven to be very useful in predicting perceptual phenomena (Julesz et al. 1973; Stevens 1978). In the present study, virtual lines are utilized in a model which aims to predict the perception of (dotted) curves in dot figures. Clearly many possible curves, formed by adjacent virtual lines, can be constructed within a set of dots. It is proposed that already at the local level of the virtual lines each line has a perceptual salience which results from the function induced by the global dot figure. It is this local line salience or connectivity that directs further processing and determines the curves to be seen in a dot figure. The model presented is an information processing model with a clear modular design. It entails three successive levels of representation. First image functions are derived through a convolution of the input with gaussian distribution functions. Next, a discrete internal representation is extracted from the image function consisting of two primitives; blobs, representing the dots, and virtual lines, representing pairwise relations between blobs. The attributes of the blobs are their positions in the image plane, while those of the virtual lines are length, relative orientation and connectivity. At the third level, the discrete internal representation is used to predict the perceived curves. It is shown that the model has advantages over other approaches, e.g. autocorrelation and network models.     

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.     

The Silent Period of Evidence Integration in Fast Decision Making

In a typical experiment on decision making, one out of two possible stimuli is displayed and observers decide which one was presented. Recently, Stanford and colleagues (2010) introduced a new variant of this classical one-stimulus presentation paradigm to investigate the speed of decision making. They found evidence for “perceptual decision making in less than 30 ms”. Here, we extended this one-stimulus compelled-response paradigm to a two-stimulus compelled-response paradigm in which a vernier was followed immediately by a second vernier with opposite offset direction. The two verniers and their offsets fuse. Only one vernier is perceived. When observers are asked to indicate the offset direction of the fused vernier, the offset of the second vernier dominates perception. Even for long vernier durations, the second vernier dominates decisions indicating that decision making can take substantial time. In accordance with previous studies, we suggest that our results are best explained with a two-stage model of decision making where a leaky evidence integration stage precedes a race-to-threshold process.     

Basis for large differences in the cooperativity of the formation of antiparallel β-sheets and clusters of interacting α-helices in isolated chains

Configuration partition functions that describe the intramolecular formation of antiparallel β-sheets and clusters of antiparallel interacting α-helices are very nearly of the same form. They can be interconverted by a simple change in notation and the addition of one weighting factor for each cluster of interacting α-helices. This extra weighting factor is the Zimm–Bragg σ which must be less than one. When it is assigned a reasonable numerical value, it plays an important role in the determination of the nature of the transition from the disordered chain to the ordered structure. It causes the formation of clusters of interacting α-helices to be more cooperative than the formation of antiparallel β-sheets in isolated chains.     

Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods

Calculations of charge interactions complement analysis of a characterised active site, rationalising pH-dependence of activity and transition state stabilisation. Prediction of active site location through large DeltapK(a)s or electrostatic strain is relevant for structural genomics. We report a study of ionisable groups in a set of 20 enzymes, finding that false positives obscure predictive potential. In a larger set of 156 enzymes, peaks in solvent-space electrostatic properties are calculated. Both electric field and potential match well to active site location. The best correlation is found with electrostatic potential calculated from uniform charge density over enzyme volume, rather than from assignment of a standard atom-specific charge set. Studying a shell around each molecule, for 77% of enzymes the potential peak is within that 5% of the shell closest to the active site centre, and 86% within 10%. Active site identification by largest cleft, also with projection onto a shell, gives 58% of enzymes for which the centre of the largest cleft lies within 5% of the active site, and 70% within 10%. Dielectric boundary conditions emphasise clefts in the uniform charge density method, which is suited to recognition of binding pockets embedded within larger clefts. The variation of peak potential with distance from active site, and comparison between enzyme and non-enzyme sets, gives an optimal threshold distinguishing enzyme from non-enzyme. We find that 87% of the enzyme set exceeds the threshold as compared to 29% of the non-enzyme set. Enzyme/non-enzyme homologues, "structural genomics" annotated proteins and catalytic/non-catalytic RNAs are studied in this context.     

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.     

The role of attention in ambiguous reversals of structure-from-motion

Multiple dots moving independently back and forth on a flat screen induce a compelling illusion of a sphere rotating in depth (structure-from-motion). If all dots simultaneously reverse their direction of motion, two perceptual outcomes are possible: either the illusory rotation reverses as well (and the illusory depth of each dot is maintained), or the illusory rotation is maintained (but the illusory depth of each dot reverses). We investigated the role of attention in these ambiguous reversals. Greater availability of attention--as manipulated with a concurrent task or inferred from eye movement statistics--shifted the balance in favor of reversing illusory rotation (rather than depth). On the other hand, volitional control over illusory reversals was limited and did not depend on tracking individual dots during the direction reversal. Finally, display properties strongly influenced ambiguous reversals. Any asymmetries between 'front' and 'back' surfaces--created either on purpose by coloring or accidentally by random dot placement--also shifted the balance in favor of reversing illusory rotation (rather than depth). We conclude that the outcome of ambiguous reversals depends on attention, specifically on attention to the illusory sphere and its surface irregularities, but not on attentive tracking of individual surface dots.     

Form from motion parallax and form from luminance contrast: vernier discrimination

Some objects are perfectly camouflaged when stationary, but are clearly visible when moving; the boundaries of such an object are defined entirely by motion parallax. Little is known about the eye's ability to make spatial discriminations between motion-defined objects. In this study, subjects viewed a pseudo-random pattern of dots within which a camouflaged bar was made visible by relative motion of dots. Vernier acuity for the motion-defined bar was 27-45 sec arc for three subjects, much less than the interdot separation of 360 sec arc, much less than the 2 deg receptive field size for motion, and comparable with the foveal intercone separation of 30 sec arc. It is proposed that an opponent-orientation process and an opponent-position process can both contribute to vernier judgements for motion-defined objects. Real-world motion contrast commonly confounds the following cues for figure-ground segregation: (1) different texture velocities on either side of the figure's boundary; (2) in any given time interval, texture in figure and ground moves different distances; and (3) texture continually appears and disappears along the figure's boundary. When cues (2) and (3) were eliminated, thus ensuring figure-ground segregation was achieved entirely by motion-sensitive neural elements, vernier acuity was 44 +/- 5 sec arc compared with 36 +/- 8 sec arc for a dotted bar defined by luminance contrast. Conclusion: Vernier acuity for a dotted bar whose boundary was defined entirely by motion-sensitive neural elements was similar to vernier acuity for a dotted bar whose boundary was defined by luminance contrast.     

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.     

Identification of a novel nuclear domain

For most known nuclear domains (ND), specific functions have been identified. In this report we used murine mAbs and human autoantibodies to investigate precisely circumscribed structures 0.2-0.3 micron in diameter which appear as "nuclear dots" distributed throughout the nucleoplasm. Nuclear dots are metabolically stable and resistant to nuclease digestion and salt extraction. The localization of nuclear dots is separate from kinetochores, centromeres, sites of mRNA processing and tRNA synthesis, nuclear bodies, and chromosomes. The nuclear dots, therefore, represent a novel ND. Nuclear dots break down as cells enter metaphase and reassemble at telophase. In interphase cells, nuclear dots are frequently "paired," and some are visible as "doublets" when stained with one particular antiserum. The number of dot doublets increased when quiescent cells were stimulated with serum although the total number of dots did not change substantially. One of the antigens was identified as a protein with a molecular mass of approximately 55 kD showing three charge isomers in the pI range of 7.4 to 7.7. Autoantibodies affinity purified from this nuclear dot protein (NDP-55) show nuclear dots exclusively. Nuclear dot-negative rat liver parenchymal cells became positive after chemical hepatectomy, suggesting involvement of the NDP-55 in the proliferative state of cells.     

Tilt aftereffects generated by symmetrical dot patterns with two or four axes of symmetry

This paper follows from studies by Joung, van der Zwan and Latimer (2000) in which symmetrical dot patterns with one axis of symmetry were used to produce tilt aftereffects (TAEs). The present paper investigates TAE functions produced by symmetrical dot patterns with multiple axes of symmetry. In Experiments 1 and 2, TAE functions produced by dot patterns with two axes of symmetry were compared with TAE functions produced by line stimuli arranged in the same orientation and location as the axes of symmetry in the dot patterns. Similar functions were found. In Experiments 3 and 4, functions produced by dot patterns with four axes of symmetry were compared with functions produced by line stimuli arranged in the same orientation and location as the four axes of symmetry. Again, similar functions were found. These experiments demonstrate that line stimuli and dot stimuli produce similar TAE functions. The implications of these results are discussed.     

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.     

Identification of repertoires of surface antigens on leukemias using an antibody microarray

We have previously described a microarray of cluster of differentiation (CD) antibodies that enables concurrent determination of more than 60 CD antigens on leukocytes. This procedure does not require protein purification or labeling, or a secondary detection system. Whole cells are captured by a microarray of 10 nL antibody dots immobilized on a nitrocellulose film on a microscope slide. Distinct patterns of cell binding are observed for different leukemias or lymphomas. These haematological malignancies arise from precursor cells of T- or B-lymphocytic, or myeloid lineages of hematopoiesis. The dot patterns obtained from patients are distinct from those of peripheral blood leukocytes from normal subjects. This microarray technology has recently undergone a number of refinements. The microarray now contains more CD antibodies, and a scanner for imaging dot patterns and software for data analysis provide an extensive immunophenotype sufficient for diagnosis of common leukemias. The technology is being evaluated for diagnosis of leukemias with parallel use of conventional diagnostic criteria.     

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.     

Retinal encoding of ultrabrief shape recognition cues

Shape encoding mechanisms can be probed by the sequential brief display of dots that mark the boundary of the shape, and delays of less that a millisecond between successive dots can impair recognition. It is not entirely clear whether this is accomplished by preserving stimulus timing in the signal being sent to the brain, or calls for a retinal binding mechanism. Two experiments manipulated the degree of simultaneity among and within dot pairs, requiring also that the pair members be in the same half of the visual field or on opposite halves, i.e., across the midline from one another. Recognition performance was impaired the same for these two conditions. The results make it likely that simultaneity of cues is being registered within the retina. A potential mechanism is suggested, calling for linkage of stimulated sites through activation of PA1 cells. A third experiment confirmed a prior finding that the overall level of recognition deficit is partly a function of display-set size, and affirmed submillisecond resolution in binding dot pairs into effective shape-recognition cues.