We analyse the effect of chemical neuro-modulation on collective processes in Ising spin neural n... more We analyse the effect of chemical neuro-modulation on collective processes in Ising spin neural networks with separable Hebbian type synaptic interactions. Neuro-modulation is taken into account in the most simple way: a modulator-specific subset of neurons is prevented from transmitting signals. However, the presence of neuro-modulators is taken into account also during the learning stage, which leads to non-symmetric interaction matrices. We derive (in the limit of an infinite system size) the macroscopic laws that determine the system’s evolution in time on the level of order parameters. These laws are very transparant and show that, within the proposed framework, one can understand the functioning of neuro-modulators as follows: their role is to choose from the repertoire of learned behaviour a particular mode of operation. By considering specific examples of learning stages we indicate how neuro-modulation might be used by the brain as an extra degree of freedom for (a) performing selective pattern reconstruction, (b) controlling the reproduction speed of stored pattern sequences or (c) for choosing a particular path from a set of partially overlapping stored trajectories through state space (at points where the trajectories separate).
Early stages of visual motion processing are modelled by two networks, each consisting of velocit... more Early stages of visual motion processing are modelled by two networks, each consisting of velocity-tuned cells. One network extracts the (possibly multi-valued) velocity-field, while the other extracts the patterns which move. The ‘channel-coded’ output from the velocity-net selects those co-local units in the pattern-net which are tuned to the local velocity, so preventing motion-smear and allowing compensation of target positions for unavoidable processing delays. Under special conditions, however, the model creates some artefacts which correspond well with known visual illusions.
The masses of daughter ions resulting from metastable transitions in the first field free region ... more The masses of daughter ions resulting from metastable transitions in the first field free region of a "reversed geometry" mass spectrometer can be accurately determined through a mass analysed ion kinetic energy scan at the apparent mass at which these daughter ions travel through the magnetic sector. A combination of these mass analysed ion kinetic scans with scanning the magnetic flux allows the resolution of overlapping metastable diffuse peaks.
Proceedings of The Royal Society B: Biological Sciences, Oct 7, 1998
A theoretical model is studied to investigate the possibility of sympatric speciation driven by s... more A theoretical model is studied to investigate the possibility of sympatric speciation driven by sexual selection and ecological diversi¢cation. In particular, we focus on the rock-dwelling haplochromine cichlid species in Lake Victoria. The high speciation rate in these cichlids has been explained by their apparent ability to specialize rapidly to a large diversity of feeding niches. Seehausen and colleagues, however, demonstrated the importance of sexual selection in maintaining reproductive barriers between species. Our individual-orientated model integrates both niche di¡erentiation and a Fisherian runaway process, which is limited by visibility constraints. The model shows rapid sympatric speciation or extinction of species, depending on the strength of sexual selection.
We studied distributions of perceptual rivalry reversals, as defined by the two fitted parameters... more We studied distributions of perceptual rivalry reversals, as defined by the two fitted parameters of the Gamma distribution. We did so for a variety of bi-stable stimuli and voluntary control exertion tasks. Subjects' distributions differed from one another for a particular stimulus and control task in a systematic way that reflects a constraint on the describing parameters. We found a variety of two-parameter effects, the most important one being that distributions of subjects differ from one another in the same systematic way across different stimuli and control tasks (i.e., a fast switcher remains fast across all conditions in a parameter-specified way). The cardinal component of subject-dependent variation was not the conventionally used mean reversal rate, but a component that was oriented-for all stimuli and tasks-roughly perpendicular to the mean rate. For the Necker cube, we performed additional experiments employing specific variations in control exertion, suggesting that subjects have to a considerable extent independent control over the reversal rate of either of the two competing percepts.
Proceedings of The Royal Society B: Biological Sciences, Mar 22, 2004
Naive T cells respond to peptides from foreign proteins and remain tolerant to self peptides from... more Naive T cells respond to peptides from foreign proteins and remain tolerant to self peptides from endogenous proteins. It has been suggested that self tolerance comes about by a 'tuning' mechanism, i.e. by increasing the T-cell activation threshold upon interaction with self peptides. Here, we explore how such an adaptive mechanism of T-cell tolerance would influence the reactivity of the T-cell repertoire to foreign peptides. We develop a computer simulation model in which T cells are tolerized by increasing their activation-threshold dependent on the affinity with which they see self peptides presented in the thymus. Thus, different T cells acquire different activation thresholds (i.e. different cross-reactivities). In previous mathematical models, T-cell tolerance was deletional and based on a fixed cross-reactivity parameter, which was assumed to have evolved to an optimal value. Comparing these two different toleranceinduction mechanisms, we found that the tuning model performs somewhat better than an optimized deletion model in terms of the reactivity to foreign antigens. Thus, evolutionary optimization of clonal cross-reactivity is not required. A straightforward extension of the tuning model is to delete T-cell clones that obtain a too high activation threshold, and to replace these by new clones. The reactivity of the immune repertoires of such a replacement model is enchanced compared with the basic tuning model. These results demonstrate that activation-threshold tuning is a functional mechanism for self tolerance induction.
ABSTRACT Introduction. ‘Bistable perception is the phenomenon that when faced with ambiguous visu... more ABSTRACT Introduction. ‘Bistable perception is the phenomenon that when faced with ambiguous visual input, one experiences a percept alternating between two interpretations.’ Sentences like this form the starting point of myriad papers on the subject, but bistable perception as a two-state process is a simplification: between dominance phases of percept A and B there are phases during which neither prevails. This has been noted before1 but is routinely ignored. We try to clarify how this is possible and study the features of the transition stage in a binocular grating paradigm. Methods. Due to the transition stage’s short duration we cannot rely on subjects’ key presses to report it, but use a novel method based on synchronisation and cueing. Synchronisation means that we force the onset at t0 of a dominance phase, using the flash suppression effect. Then after a chosen time lag, by replacing the gratings by a mask, we cue subjects to report what they saw the instant before mask appearance. By repeating this at various lags, we get probability distributions of percepts as a function of time after t0. Subjects were tested twice: first we instructed them to report the percept to be either A or B; the second time we added the option of reporting a transition percept. Results. Subjects easily executed the two-alternative choice experiment. Still, with the option of reporting a third phase, its mean duration was 300-1100 ms: 0.2-0.7 times that of a dominance phase (the duration of an entire cycle was unaffected). Concluding, reports of putative bistable perception do not prove the absence of a transition percept; merely that subjects were not asked to report it. Instead, the transition stage is a substantial part of the alternation cycle, that models of bistable perception should incorporate. We are presently studying its characteristics, e.g. its duration distribution, its dependence on stimulus features and associated detection thresholds. 1: Mueller & Blake, Biol. Cybern. 61, 1989.
Perceptual dissociation of moving plaid patterns into independently moving bar gratings occurs mo... more Perceptual dissociation of moving plaid patterns into independently moving bar gratings occurs most readily when the grating signals are combined as if the bars were semi-transparent objects (
The number of different major histocompatibility (MHC) molecules expressed per individual is wide... more The number of different major histocompatibility (MHC) molecules expressed per individual is widely believed to represent a trade-off between maximizing the detection of foreign antigens, and minimizing the loss of T cell clones due to self-tolerance induction. Using a mathematical model we here show that this argument fails to explain why individuals typically express of the order of 10-20 different MHC molecules. Expression of extra MHC types decreases the number of clones surviving negative selection, but increases the number of positively selected clones. Based on experimental parameter estimates, we show that the number of clones in the functional T cell repertoire would in fact increase if the MHC diversity within an individual were to exceed its normal value, until more than one hundred different MHC molecules would be expressed. Since additional MHC types also increase the number of presented pathogen peptides, resistance against pathogens only decreases at unrealistically high MHC diversities exceeding 1,500 different MHC molecules per individual.
The immune system contains many types of B-cells, which can activate each other if the shapes and... more The immune system contains many types of B-cells, which can activate each other if the shapes and surface properties of their receptors (or antibodies) match well. The dynamics of the resulting network is analysed using a recently derived B-cell activation function which captures the effects of the binding and crosslinking of B-cell receptors. All receptor/antibody shapes are parametrised by a continuous 'shape-space', such that matching pairs of shapes interact locally. The model produces a variety of activation patterns across shape-space for a wide range of parameters. The spatio-temporal structures differ qualitatively from those seen with a previously used type of activation function. In either case, the pattern formation can largely be understood analytically, by first solving exactly for the various uniform fixed solutions, and then computing the evolution of spatially modulated perturbations. For the more realistic activation function, the following scenario is found. Most (random) initial conditions first lead to the formation of coarse domains, of three possible types: the 'virgin'-(V) state, the 'immune/suppressed' (I/S)-state, and its reverse (S/I). V-domains are stable, but the other two types are unstable to spatial perturbations with a wavelength which is of the order of the interaction range. In the second stage, this instability causes big I/S-and S/I-domains to split up into arrays of small 'dots' which preserve the I/S-asyn~netry of their parent domain. These dots are stable, even in isolation, which allows them to act as a 'memory' for previously encountered antigens. No stable dots are obtained when the model is made to emulate the simpler activation function which has been used widely in earlier models. With this less realistic choice, unstable waves propagate from the boundaries of coarse I/S-domains, eventually filling up most of shape-space. This instability was previously described as 'percolation'.
We sketch an integrated approach to achieve near-optimal target detection as well as resolution o... more We sketch an integrated approach to achieve near-optimal target detection as well as resolution of range/doppler ambiguities. The functional structure respects statistical principles, and allows a clear understanding and analysis of its performance.
Humans do not confound the motion of shadows cast upon a surface with the motion of the surface i... more Humans do not confound the motion of shadows cast upon a surface with the motion of the surface itself, although schemes that propose recombination of orientation-selective motion signals into a rigid motion percept of two-dimensional patterns would predict that they should do so. We propose a simple scheme that avoids recombination and instead attributes perception of two-dimensional pattern motion to the activation of orientation-selective end-stopped units that operate on the logarithm of the luminance. The proposed units respond to the change of contrast along a line, which typically occurs at an intersection. They are not active, however, when a shadow border intersects the edge of an object, because contrast does not change along either of these edges. Thus, end-stopped units signal the motion of transparent intersections weakly or not at all, and the independent motions of the shadow border and the object prevail. We tested two implications of this scheme, using plaids with variable intersection luminance. First, when the intersection luminance was such that it kept the contrast along the intersecting lines nearly constant, the sensitivity for the rigid plaid's direction of motion was minimal, and the sliding motion of the components prevailed. This occurred for light bars on dark backgrounds and for dark bars on light backgrounds. Thus, the effect of the intersection's luminance on the balance between the percepts of rigid-plaid motion and the motion of sliding components was independent of contrast inversion of bar and background. Secondly, when thin lines with the same luminance as the bars covered the borders of the intersection, the intersection's luminance did not affect the rigid-plaid motion percept very much, even when it corresponded to a transparent intersection. This indicates that, when the edges of the intersection and those of the bars were not collinear, the nulling of the end-stopped units did not occur. This result is in line with physiological studies, which showed that the response of an end-stopped cell to a line is only partially inhibited when a similar line is presented non-collinearly with the first in the inhibitory end-zone of its receptive field. Our results are consistent with a scheme in which a second stage of motion detectors combines signals of orientation-selective end-free and orientation-selective end-stopped units for perception of the rigid motion of two-dimensional patterns.
We analyse the effect of chemical neuro-modulation on collective processes in Ising spin neural n... more We analyse the effect of chemical neuro-modulation on collective processes in Ising spin neural networks with separable Hebbian type synaptic interactions. Neuro-modulation is taken into account in the most simple way: a modulator-specific subset of neurons is prevented from transmitting signals. However, the presence of neuro-modulators is taken into account also during the learning stage, which leads to non-symmetric interaction matrices. We derive (in the limit of an infinite system size) the macroscopic laws that determine the system’s evolution in time on the level of order parameters. These laws are very transparant and show that, within the proposed framework, one can understand the functioning of neuro-modulators as follows: their role is to choose from the repertoire of learned behaviour a particular mode of operation. By considering specific examples of learning stages we indicate how neuro-modulation might be used by the brain as an extra degree of freedom for (a) performing selective pattern reconstruction, (b) controlling the reproduction speed of stored pattern sequences or (c) for choosing a particular path from a set of partially overlapping stored trajectories through state space (at points where the trajectories separate).
Early stages of visual motion processing are modelled by two networks, each consisting of velocit... more Early stages of visual motion processing are modelled by two networks, each consisting of velocity-tuned cells. One network extracts the (possibly multi-valued) velocity-field, while the other extracts the patterns which move. The ‘channel-coded’ output from the velocity-net selects those co-local units in the pattern-net which are tuned to the local velocity, so preventing motion-smear and allowing compensation of target positions for unavoidable processing delays. Under special conditions, however, the model creates some artefacts which correspond well with known visual illusions.
The masses of daughter ions resulting from metastable transitions in the first field free region ... more The masses of daughter ions resulting from metastable transitions in the first field free region of a "reversed geometry" mass spectrometer can be accurately determined through a mass analysed ion kinetic energy scan at the apparent mass at which these daughter ions travel through the magnetic sector. A combination of these mass analysed ion kinetic scans with scanning the magnetic flux allows the resolution of overlapping metastable diffuse peaks.
Proceedings of The Royal Society B: Biological Sciences, Oct 7, 1998
A theoretical model is studied to investigate the possibility of sympatric speciation driven by s... more A theoretical model is studied to investigate the possibility of sympatric speciation driven by sexual selection and ecological diversi¢cation. In particular, we focus on the rock-dwelling haplochromine cichlid species in Lake Victoria. The high speciation rate in these cichlids has been explained by their apparent ability to specialize rapidly to a large diversity of feeding niches. Seehausen and colleagues, however, demonstrated the importance of sexual selection in maintaining reproductive barriers between species. Our individual-orientated model integrates both niche di¡erentiation and a Fisherian runaway process, which is limited by visibility constraints. The model shows rapid sympatric speciation or extinction of species, depending on the strength of sexual selection.
We studied distributions of perceptual rivalry reversals, as defined by the two fitted parameters... more We studied distributions of perceptual rivalry reversals, as defined by the two fitted parameters of the Gamma distribution. We did so for a variety of bi-stable stimuli and voluntary control exertion tasks. Subjects' distributions differed from one another for a particular stimulus and control task in a systematic way that reflects a constraint on the describing parameters. We found a variety of two-parameter effects, the most important one being that distributions of subjects differ from one another in the same systematic way across different stimuli and control tasks (i.e., a fast switcher remains fast across all conditions in a parameter-specified way). The cardinal component of subject-dependent variation was not the conventionally used mean reversal rate, but a component that was oriented-for all stimuli and tasks-roughly perpendicular to the mean rate. For the Necker cube, we performed additional experiments employing specific variations in control exertion, suggesting that subjects have to a considerable extent independent control over the reversal rate of either of the two competing percepts.
Proceedings of The Royal Society B: Biological Sciences, Mar 22, 2004
Naive T cells respond to peptides from foreign proteins and remain tolerant to self peptides from... more Naive T cells respond to peptides from foreign proteins and remain tolerant to self peptides from endogenous proteins. It has been suggested that self tolerance comes about by a 'tuning' mechanism, i.e. by increasing the T-cell activation threshold upon interaction with self peptides. Here, we explore how such an adaptive mechanism of T-cell tolerance would influence the reactivity of the T-cell repertoire to foreign peptides. We develop a computer simulation model in which T cells are tolerized by increasing their activation-threshold dependent on the affinity with which they see self peptides presented in the thymus. Thus, different T cells acquire different activation thresholds (i.e. different cross-reactivities). In previous mathematical models, T-cell tolerance was deletional and based on a fixed cross-reactivity parameter, which was assumed to have evolved to an optimal value. Comparing these two different toleranceinduction mechanisms, we found that the tuning model performs somewhat better than an optimized deletion model in terms of the reactivity to foreign antigens. Thus, evolutionary optimization of clonal cross-reactivity is not required. A straightforward extension of the tuning model is to delete T-cell clones that obtain a too high activation threshold, and to replace these by new clones. The reactivity of the immune repertoires of such a replacement model is enchanced compared with the basic tuning model. These results demonstrate that activation-threshold tuning is a functional mechanism for self tolerance induction.
ABSTRACT Introduction. ‘Bistable perception is the phenomenon that when faced with ambiguous visu... more ABSTRACT Introduction. ‘Bistable perception is the phenomenon that when faced with ambiguous visual input, one experiences a percept alternating between two interpretations.’ Sentences like this form the starting point of myriad papers on the subject, but bistable perception as a two-state process is a simplification: between dominance phases of percept A and B there are phases during which neither prevails. This has been noted before1 but is routinely ignored. We try to clarify how this is possible and study the features of the transition stage in a binocular grating paradigm. Methods. Due to the transition stage’s short duration we cannot rely on subjects’ key presses to report it, but use a novel method based on synchronisation and cueing. Synchronisation means that we force the onset at t0 of a dominance phase, using the flash suppression effect. Then after a chosen time lag, by replacing the gratings by a mask, we cue subjects to report what they saw the instant before mask appearance. By repeating this at various lags, we get probability distributions of percepts as a function of time after t0. Subjects were tested twice: first we instructed them to report the percept to be either A or B; the second time we added the option of reporting a transition percept. Results. Subjects easily executed the two-alternative choice experiment. Still, with the option of reporting a third phase, its mean duration was 300-1100 ms: 0.2-0.7 times that of a dominance phase (the duration of an entire cycle was unaffected). Concluding, reports of putative bistable perception do not prove the absence of a transition percept; merely that subjects were not asked to report it. Instead, the transition stage is a substantial part of the alternation cycle, that models of bistable perception should incorporate. We are presently studying its characteristics, e.g. its duration distribution, its dependence on stimulus features and associated detection thresholds. 1: Mueller & Blake, Biol. Cybern. 61, 1989.
Perceptual dissociation of moving plaid patterns into independently moving bar gratings occurs mo... more Perceptual dissociation of moving plaid patterns into independently moving bar gratings occurs most readily when the grating signals are combined as if the bars were semi-transparent objects (
The number of different major histocompatibility (MHC) molecules expressed per individual is wide... more The number of different major histocompatibility (MHC) molecules expressed per individual is widely believed to represent a trade-off between maximizing the detection of foreign antigens, and minimizing the loss of T cell clones due to self-tolerance induction. Using a mathematical model we here show that this argument fails to explain why individuals typically express of the order of 10-20 different MHC molecules. Expression of extra MHC types decreases the number of clones surviving negative selection, but increases the number of positively selected clones. Based on experimental parameter estimates, we show that the number of clones in the functional T cell repertoire would in fact increase if the MHC diversity within an individual were to exceed its normal value, until more than one hundred different MHC molecules would be expressed. Since additional MHC types also increase the number of presented pathogen peptides, resistance against pathogens only decreases at unrealistically high MHC diversities exceeding 1,500 different MHC molecules per individual.
The immune system contains many types of B-cells, which can activate each other if the shapes and... more The immune system contains many types of B-cells, which can activate each other if the shapes and surface properties of their receptors (or antibodies) match well. The dynamics of the resulting network is analysed using a recently derived B-cell activation function which captures the effects of the binding and crosslinking of B-cell receptors. All receptor/antibody shapes are parametrised by a continuous 'shape-space', such that matching pairs of shapes interact locally. The model produces a variety of activation patterns across shape-space for a wide range of parameters. The spatio-temporal structures differ qualitatively from those seen with a previously used type of activation function. In either case, the pattern formation can largely be understood analytically, by first solving exactly for the various uniform fixed solutions, and then computing the evolution of spatially modulated perturbations. For the more realistic activation function, the following scenario is found. Most (random) initial conditions first lead to the formation of coarse domains, of three possible types: the 'virgin'-(V) state, the 'immune/suppressed' (I/S)-state, and its reverse (S/I). V-domains are stable, but the other two types are unstable to spatial perturbations with a wavelength which is of the order of the interaction range. In the second stage, this instability causes big I/S-and S/I-domains to split up into arrays of small 'dots' which preserve the I/S-asyn~netry of their parent domain. These dots are stable, even in isolation, which allows them to act as a 'memory' for previously encountered antigens. No stable dots are obtained when the model is made to emulate the simpler activation function which has been used widely in earlier models. With this less realistic choice, unstable waves propagate from the boundaries of coarse I/S-domains, eventually filling up most of shape-space. This instability was previously described as 'percolation'.
We sketch an integrated approach to achieve near-optimal target detection as well as resolution o... more We sketch an integrated approach to achieve near-optimal target detection as well as resolution of range/doppler ambiguities. The functional structure respects statistical principles, and allows a clear understanding and analysis of its performance.
Humans do not confound the motion of shadows cast upon a surface with the motion of the surface i... more Humans do not confound the motion of shadows cast upon a surface with the motion of the surface itself, although schemes that propose recombination of orientation-selective motion signals into a rigid motion percept of two-dimensional patterns would predict that they should do so. We propose a simple scheme that avoids recombination and instead attributes perception of two-dimensional pattern motion to the activation of orientation-selective end-stopped units that operate on the logarithm of the luminance. The proposed units respond to the change of contrast along a line, which typically occurs at an intersection. They are not active, however, when a shadow border intersects the edge of an object, because contrast does not change along either of these edges. Thus, end-stopped units signal the motion of transparent intersections weakly or not at all, and the independent motions of the shadow border and the object prevail. We tested two implications of this scheme, using plaids with variable intersection luminance. First, when the intersection luminance was such that it kept the contrast along the intersecting lines nearly constant, the sensitivity for the rigid plaid's direction of motion was minimal, and the sliding motion of the components prevailed. This occurred for light bars on dark backgrounds and for dark bars on light backgrounds. Thus, the effect of the intersection's luminance on the balance between the percepts of rigid-plaid motion and the motion of sliding components was independent of contrast inversion of bar and background. Secondly, when thin lines with the same luminance as the bars covered the borders of the intersection, the intersection's luminance did not affect the rigid-plaid motion percept very much, even when it corresponded to a transparent intersection. This indicates that, when the edges of the intersection and those of the bars were not collinear, the nulling of the end-stopped units did not occur. This result is in line with physiological studies, which showed that the response of an end-stopped cell to a line is only partially inhibited when a similar line is presented non-collinearly with the first in the inhibitory end-zone of its receptive field. Our results are consistent with a scheme in which a second stage of motion detectors combines signals of orientation-selective end-free and orientation-selective end-stopped units for perception of the rigid motion of two-dimensional patterns.
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Papers by Andre J Noest