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PubMed1998

No turning, a mouse mutation causing left-right and axial patterning defects.

Patterning along the left/right axes helps establish the orientation of visceral organ asymmetries, a process which is of fundamental importance to the viability of an organism. A linkage between left/right and axial patterning is indicated by the finding that a number of genes involved in left/right patterning also play a role in anteroposterior and dorsoventral patterning. We have recovered a spontaneous mouse mutation causing left/right patterning defects together with defects in anteroposterior and dorsoventral patterning. This mutation is recessive lethal and was named no turning (nt) because the mutant embryos fail to undergo embryonic turning. nt embryos exhibit cranial neural tube closure defects and malformed somites and are caudally truncated. Development of the heart arrests at the looped heart tube stage, with cardiovascular defects indicated by ballooning of the pericardial sac and the pooling of blood in various regions of the embryo. Interestingly, in nt embryos, the direction of heart looping was randomized. Nodal and lefty, two genes that are normally expressed only in the left lateral plate mesoderm, show expression in the right and left lateral plate mesoderm. Lefty, which is normally also expressed in the floorplate, is not found in the prospective floor plate of nt embryos. This suggests the possibility of notochordal defects. This was confirmed by histological analysis and the examination of sonic hedgehog, Brachyury, and HNF-3 beta gene expression. These studies showed that the notochord is present in the early nt embryo, but degenerates as development progresses. Overall, these findings support the hypothesis that the notochord plays an active role in left/right patterning. Our results suggest that nt may participate in this process by modulating the notochordal expression of HNF-3 beta.

Animals↗
PubMed2000

Conformational analysis of long spacers in PROSITE patterns.

To determine if variable sequences (spacers) between conserved positions in a sequence motif or pattern share a consensus structure, three-dimensional structures containing PROSITE patterns with spacers of fixed length greater than three residues were analyzed. Structural similarities of a given pattern were evaluated by computing the backbone phi, psi and side-chain chi1 dihedral order parameters. The exact bias information in analyzing the conformational variability of the patterns was taken into account by introducing a new parameter, the bias coefficient, which describes the number and distribution of residue types found at each position of a pattern in the structures. The results of the analyses show that backbone conformational heterogeneity at a given position in a sequence motif does not necessarily correlate with the residue-type variability at that position, and the long spacer region can adopt a well-defined backbone conformation, in addition to the conserved residues. Furthermore, a PROSITE pattern may be redefined to yield two or more "refined" regular expressions, each corresponding to a distinct backbone conformation. A way in which the observed structural consensus in a pattern may be employed to improve the accuracy of function prediction from sequence is suggested.

Amino Acid Motifs↗
PubMed1991

The intrasession repeatability of pattern electroretinograms and the effects of digital filtering.

Transient pattern electroretinograms were recorded in 12 normal young volunteers with the use of 12' and 30' checkerboard stimuli and 1 c/deg and 2.5 c/deg vertical gratings. The intrasession repeatability of pattern electroretinograms was determined by employing alternative statistics to the frequently used correlation coefficients. Comparisons were made with the repeatability of cone electroretinograms elicited by ganzfeld stimulation. The coefficient of repeatability was substantially lower (better) for pattern electroretinogram b-wave implicit times than for a-wave implicit times and b-wave amplitudes, the latter having high coefficients of repeatability. Cone electroretinograms had better repeatability with respect to all three parameters. Digital filtering using a bandpass of 1-40 Hz was applied to the original pattern electroretinograms recorded with a bandpass of 1-250 Hz. Although peak definition was generally enhanced, repeatability did not show marked improvement. Differences between broadband analogue-filtered pattern electroretinograms and the same responses with high-frequency noise removed by digital filtering need to be taken into account. The coefficient of repeatability statistic appears to facilitate the assessment of pattern electroretinograms and permits the comparison of the repeatability of both implicit time and amplitude parameters irrespective of absolute values. The implications of the relatively poor repeatability of pattern electroretinogram b-wave amplitudes for clinical applications need to be considered.

Adult↗
PubMed1981

Analysis of pattern recognition by man using detection experiments.

This paper addresses the problem of analyzing biological pattern recognition systems. As no complete analysis is possible due to limited observability, the theoretical part of the paper examines some principles of construction for recognition systems. The relations between measurable and characteristic variables of these systems are described. The results of the study are: 1. Human recognition systems can always be described by a model consisting of an analyzer (FA) and a linear classifier. 2. The linearity of the classifier places no limits on the universal validity of the model. The principle of organization of such a system may be put into effect in many different ways. 3. The analyzer function FA determines the transformation of external patterns into their internal representations. For the experiments described in this paper, FA can be approximated by a filtering operation and a transformation of features (contour line filter). 4. Narrow band filtering (comb filter) in the space frequency domain is inadequate for pattern recognition because noise of different bandwidths and mean frequencies affects sinusoidal gratings differently. This excludes the use of a Fourier analyzer. 5. The relations between the measurable variables, which are the probabilities of detection (PD curves), and the characteristic variables of the recognition system are established analytically. 6. The probability of detection not only depends on signal energy but also on signal structure. This would not be the case in a simple matched filter system. 7. The differing probabilities of error in multiple detection experiments show that the interference is pattern specific and the bandwidth (steepness of the PD curves) is different for the different sets of patterns. 8. The distance between the reference vectors in feature space can be determined from the internal representation of the patterns defined by the model. Through multiple detection experiments it is possible to determine not only the relative distances between the patterns but also their absolute position in feature space.

Cognition↗
PubMed1987

A model of neural network for spatiotemporal pattern recognition.

A model of neural network to recognize spatiotemporal patterns is presented. The network consists of two kinds of neural cells: P-cells and B-cells. A P-cell generates an impulse responding to more than one impulse and embodies two special functions: short term storage (STS) and heterosynaptic facilitation (HSF). A B-cell generates several impulses with high frequency as soon as it receives an impulse. In recognizing process, an impulse generated by a P-cell represents a recognition of stimulus pattern, and triggers the generation of impulses of a B-cell. Inhibitory impulses with high frequency generated by a B-cell reset the activities of all P-cells in the network. Two examples of spatiotemporal pattern recognition are presented. They are achieved by giving different values to the parameters of the network. In one example, the network recognizes both directional and non-directional patterns. The selectivities to directional and non-directional patterns are realized by only adjusting excitatory synaptic weights of P-cells. In the other example, the network recognizes time series of spatial patterns, where the lengths of the series are not necessarily the same and the transitional speeds of spatial patterns are not always the same. In both examples, the HSF signal controls the total activity of the network, which contributes to exact recognition and error recovery. In the latter example, it plays a role to trigger and execute the recognizing process. Finally, we discuss the correspondence between the model and physiological findings.

Brain↗
PubMed1980

Further consideration on pattern separability in a random neural net with inhibitory connections.

A two-layer random neural net with inhibitory connections composing of threshold elements has been regarded as a model of the cerebellar cortex. Many properties of pattern separation with the model have been disclosed through consideration on the degree of pattern separation. However, we have not shown yet that the degree of pattern separation is given by some different functions which are decided by the relation between the firing rates of input patterns. The present study is intended to reveal that the functions of the degree of pattern separation are synthesized with some different partial functions, and they are differently given on the relation between the firing rates of input patterns. Simultaneously, it is proved that the number of the functions also depend on the number of connections between two layers in the model. We also disclose the properties of the degree of pattern separation, and give some suggestions on the sizes of the firing rates of mossy fibers and granule cells under the knowledge about them.

Cerebellar Cortex↗
PubMed1994

Differences between pattern-evoked electroretinograms obtained by a scanning laser ophthalmoscope and by a mechanical mirror system.

Pattern electroretinograms were studied in response to stripe patterns of different spatial frequencies and intensities in the pattern-onset and reversal mode by means of a scanning laser ophthalmoscope and a mechanical mirror system (maxwellian view). The stimulus conditions in both procedures were as close as possible: 31 degrees square field, 633-nm wavelength and the same equipment for recording. The remaining differences between the two methods were the line and pixel structure in the scanning laser ophthalmoscope and the buildup speed (40 ms in the scanning laser ophthalmoscope and less than 1 ms in the mirror system). This difference was reflected in the response peak times of the pattern electroretinogram, which were up to 10 ms in the scanning laser ophthalmoscope measurement. The pattern-related onset response was smaller with the scanning laser ophthalmoscope, indicating a strong sensitivity to the slow build-up speed, while the offset and reversal responses showed no differences in amplitudes. All differences were found only with the use of high luminances. The results suggest that responses evoked with patterns displayed on a television screen could be faster and larger if stimulators faster than the conventional television standard were used. Because of the smallness of onset amplitudes, the pattern-reversal mode might be better for stimulation in a clinical study when the scanning laser ophthalmoscope is used.

Adult↗
PubMed1995

Pattern electroretinogram, visual evoked potential and psychophysical functions in maculopathy.

To compare pattern electroretinograms and visual evoked potentials with psychophysical examinations, such as visual acuity, static (automated) perimetry and color vision in unilateral maculopathies of various origins, 20 patients with unilateral retinal diseases within the macula and the posterior pole were tested. Pattern electroretinography, visual evoked potential testing and static perimetry (Octopus program M1) were performed with three different test field sizes (20 degrees x 20 degrees, 10 degrees x 10 degrees and 6 degrees x 6 degrees). The best correlation in all three test field sizes was found between visual acuity, static perimetry and visual evoked potential. This result is surprising, since central area defined functions (visual evoked potentials, visual acuity) correlated well with a total area integrating function (mean defect in static perimetry. The pattern electroretinogram, which seems to reflect an area-related function as well, showed a correlation to static perimetry only in the smaller 10 degrees x 10 degrees and 6 degrees x 6 degrees fields and not a significant correlation in the 20 degrees x 20 degrees field. Smaller stimulation fields may therefore produce sharper results in pattern electroretinographic testing. There was no correlation between pattern electroretinograms and visual evoked potentials or visual acuity. The pattern electroretinogram was recorded under monocular and binocular viewing conditions. In 60% of the patients, the amplitude of the affected eye was more reduced in the monocular than the binocular viewing condition; the healthy fellow eye controlled stable fixation of the affected eye more readily during binocular pattern electroretinogram registration. The degree of the color vision disturbance (C-index, desaturated panel D-15 test) did not correlate to any of the other examinations.

Adolescent↗
PubMed1993

Pattern electroretinogram and visual evoked potential amplitudes are influenced by different stimulus field sizes and scotomata.

The pattern electroretinogram and the visual evoked potential were recorded simultaneously with various stimulus fields and artificial scotomata of increasing sizes. In contrast to an earlier study, a smaller check size (20') and two stimulus field sizes (20 degrees x 20 degrees and 10 degrees x 10 degrees) for the scotomata were used. With a concentric decreasing stimulus field, a reduction of both the pattern electroretinogram and visual evoked potential was found. Both showed a simultaneous reduction of amplitudes, but, compared with the amplitude in the full field, the reduction was more extensive for the pattern electroretinogram at each test field size. This implies a greater contribution to the pattern electroretinogram from more eccentric retinal parts. An artificial central scotoma of increasing size in the 20 degrees x 20 degrees field had less influence on the pattern electroretinogram than on the visual evoked potential. The percentage amplitude loss of the visual evoked potential was more pronounced. The visual evoked potential was eventually abolished by a scotoma size from 10 degrees x 10 degrees upward, while the pattern electroretinogram was still registrable. When scotomata of similar size were introduced in a smaller (10 degrees x 10 degrees) field, percentage pattern electroretinogram and visual evoked potential amplitude losses were less separated than in a larger (20 degrees x 20 degrees) test field.

Adult↗
PubMed1989

Bottom-up approach to the ECG pattern-recognition problem.

A bottom-up approach to the recognition problem in ECG waveforms is presented in the paper. This approach is based on the assumption that ECG waveforms are composite entities that can be decomposed into other simpler entities, these into other simpler ones etc., until peak patterns and segment patterns are obtained. The peak patterns and the segment patterns are considered primitive (nondecomposable) patterns. The recognition is achieved by first recognising the primitive patterns and then recognising the (higher) ECG patterns using a bottom-up procedure.

Algorithms↗
PubMed2002

Mode-doubling and tripling in reaction-diffusion patterns on growing domains: a piecewise linear model.

Reaction-diffusion equations are ubiquitous as models of biological pattern formation. In a recent paper we have shown that incorporation of domain growth in a reaction-diffusion model generates a sequence of quasi-steady patterns and can provide a mechanism for increased reliability of pattern selection. In this paper we analyse the model to examine the transitions between patterns in the sequence. Introducing a piecewise linear approximation we find closed form approximate solutions for steady-state patterns by exploiting a small parameter, the ratio of diffusivities, in a singular perturbation expansion. We consider the existence of these steady-state solutions as a parameter related to the domain length is varied and predict the point at which the solution ceases to exist, which we identify with the onset of transition between patterns for the sequence generated on the growing domain. Applying these results to the model in one spatial dimension we are able to predict the mechanism and timing of transitions between quasi-steady patterns in the sequence. We also highlight a novel sequence behaviour, mode-tripling, which is a consequence of a symmetry in the reaction term of the reaction-diffusion system.

Animals↗
PubMed2006

Interactions between pattern formation and domain growth.

In this paper we develop a theoretical framework for investigating pattern formation in biological systems for which the tissue on which the spatial pattern resides is growing at a rate which is itself regulated by the diffusible chemicals that establish the spatial pattern. We present numerical simulations for two cases of interest, namely exponential domain growth and chemically controlled growth. Our analysis reveals that for domains undergoing rapid exponential growth dilution effects associated with domain growth influence both the spatial patterns that emerge and the concentration of chemicals present in the domain. In the latter case, there is complex interplay between the effects of the chemicals on the domain size and the influence of the domain size on the formation of patterns. The nature of these interactions is revealed by a weakly nonlinear analysis of the full system. This yields a pair of nonlinear equations for the amplitude of the spatial pattern and the domain size. The domain is found to grow (or shrink) at a rate that depends quadratically on the pattern amplitude, the particular functional forms used to model the local tissue growth rate and the kinetics of the two diffusible species dictating the resulting behaviour.

Body Patterning↗
PubMed1981

Evoked potentials in albinos: efficacy of pattern stimuli in detecting misrouted optic fibers.

Misrouting of retinogeniculostriate projections associated with retinal hypopigmentation has been found to be a general phenomenon in mammals, including humans. Anomalous optic pathway projections of albinos may be detected by recording visually evoked potentials (VEPs). To determine the efficacy of various stimulus conditions for detecting misrouted optic fibers, we compared flash, modulated light, pattern reversal and pattern onset/offset (appearance/disappearance) stimuli. Pattern onset/offset were found superior in detecting anomalies of misrouting of retinogeniculostriate projections. As a group, humans with retinal hypopigmentation have poor evoked potentials to offset and pattern reversal stimuli. Nystagmus seems to be most symptomatic of poor pattern reversal responses. In general onset/offset pattern stimuli are more versatile for detection of abnormalities in the visual system than pattern reversal stimuli.

Adolescent↗
PubMed1983

The effect of background illumination on pattern onset visual evoked potentials.

The early part (first 200 msec) of pattern onset VEPs elicited by a dartboard pattern was studied in conditions of varying level of background illumination. The effect of pattern adaptation and pattern blurr was also studied. The observed complex behaviour of the main negativity within this part of the VEP can be best described in terms of a composite of two independent negative peaks labelled N100 and N130. In high luminance conditions peak N100 was dominant and the presence of N130 was indicated only by a 'notch' on the rising slope of the negativity. As luminance decreased the situation was reversed and N130 became a dominant feature of the negative wave. This finding did not depend on the particular choice of reference site. For checkerboard stimulation the same features were present, but variability of the VEP wave form was greater than in the case of dartboard stimulation. Present results relate the well-known pattern specific properties of the negativity in onset VEPs to N100 only, whereas N130 is not pattern specific. Lower and upper half-field stimulation produced peaks of opposite polarity at 100 msec but no change was observed in polarity of N130. These findings support the suggestion that these two parts of the negativity in pattern onset VEPs may have different cortical sources.

Adaptation, Physiological↗
PubMed1983

Linear systems analysis of infant visual pattern preferences.

Karmel's check-pattern preference data for 13-week-old infants were reanalyzed using linear systems analysis. The two-dimensional Fourier amplitude spectrum was calculated for each of his eight checkerboard and random check patterns. The mean contrast sensitivity data for 3-month-old infants of Banks and Salapatek and the spatial frequency amplitudes of the patterns were used to derive three metrics to predict the looking times observed by Karmel. One was based on the sensitivity of the visual system to the single pattern component highest above threshold (maximum amplitude), the second was based on the total amount of pattern energy above threshold (total summation), and the third was based on the maximum amplitude with summation over nearby spatial frequency components (limited summation). The predictive power of the maximum amplitude and the total summation metrics depended on whether the pattern type was checkerboard or random check. The limited summation metric predicted looking times well for both pattern types. A linear function of the logarithm of the limited summation metric accounted for 91% of the total variance in looking time.

Fixation, Ocular↗
PubMed1985

Pattern electroretinogram: use of noncorneal skin electrodes.

Pattern electroretinograms (ERGs) were recorded in three adults by a noncorneal electrode technique: silver-silver chloride skin electrodes attached to the inferior orbit of the left eye while the subject monocularly viewed a high contrast checker-board that reversed in contrast at a rate of 10 Hz. Recordings revealed pattern ERGs with an average amplitude of 1.5 microV. In addition, pattern ERGs were recorded as a function of spatial frequency and contrast of a square-wave grating. The results showed that an increase in spatial frequency or contrast yielded an increase in the amplitude of the pattern ERG. The results demonstrate that the pattern ERG can be recorded with a noncorneal electrode technique and that the noncorneal electrode technique is sensitive to changes in retinal function. Finally, it is demonstrated that the pattern ERG can transfer between the eyes such that the pattern ERG from a viewing eye can be recorded from an electrode placed below an occluded eye.

Adult↗
PubMed1988

Human velocity and direction discrimination measured with random dot patterns.

In the present experiments three different motion discrimination tasks were studied using a random dot pattern as stimulus: velocity discrimination, direction discrimination and discrimination of opposite directions. The analysis of the motion of random dot patterns is based on motion sensitive mechanisms without the confounding interference of position sensitive mechanisms (Nakayama and Tyler, 1981). Furthermore, since isotropic random dot patterns contain no dominant orientation, a change in the direction of motion does not parallel a change in orientation. Hence the use of a random dot pattern as stimulus allows velocity and direction discrimination to be compared. Human velocity discrimination displays a U-shaped dependence on the stimulus velocity: the JNDs, expressed as Weber-fractions, are minimal for velocities ranging from 4 to 64 deg.sec-1. The Weber-fractions in velocity, determined with a staircase procedure tracking a 84% correct response level, were about 7% at the optimal speeds. The velocity discrimination curve obtained with the random dot pattern is similar to that obtained with light bars. Human direction discrimination, defined as the smallest difference in direction which can be resolved, also displays a U-shaped dependence on the stimulus velocity. Direction discrimination thresholds decrease up to a velocity of 4 deg.sec-1, they then stay at a constant level up to 128 deg.sec-1. Beyond this velocity the thresholds increase again. The mean direction discrimination threshold was 1.8 deg at optimal speeds. Discrimination of opposite directions, determined for the same conditions as those for which velocity and direction discrimination thresholds were determined, was better than the 90% response level at all speeds. However at low contrast, opposite directions are reliably discriminated only at intermediate speeds. Perceiving a coherent moving random dot pattern is supposed to be based on a cooperation between a large number of local motion detectors. In order to evaluate the importance of detector output pooling, the influence of the size of the pattern and of the presentation time on the three discrimination tasks was measured. The results indicate that the pooling requirements are task dependent. A somewhat larger pooling is required for velocity discrimination than for direction discrimination, whereas for discrimination of opposite directions only a few local motion detectors are involved.

Differential Threshold↗
PubMed1995

A labeled lines explanation of the perceived spatial frequency of moderate-, near-threshold- and zero-contrast spatial patterns.

We tested the predictions of a multiple-channels model about the appearance of spatial patterns. Specifically we tested how encoding the perceived spatial frequency of a near-threshold pattern compared with encoding of a zero-contrast or moderate-contrast pattern. For example, the model predicts that the mean perceived spatial frequency of a near-threshold pattern is a weighted average of the response to the stimulus and the noise. Six subjects used the method of adjustment procedure to match a peripherally viewed test stimulus (or a blank) with a foveally viewed grating. For near-threshold patterns we found a smooth perceived spatial-frequency function, with a smaller range of perceived spatial frequencies than obtained for 0.16 contrast patterns. These results are consistent with the predictions of the model: noise can affect the appearance of near-threshold and zero-contrast patterns.

Contrast Sensitivity↗