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Biomedical subjects

M Lappe

Publications and source records attributed to M Lappe.

At least 19 recordsLinked to original sources
PubMed2006

Perception of biological motion from limited-lifetime stimuli.

The visual perception of human movement from sparse point-light walkers is often believed to rely on local motion analysis. We investigated the role of local motion in the perception of human walking, viewed from the side, in different tasks. The motion signal was manipulated by varying point lifetime. We found the task of coherence discrimination, commonly used in biological motion studies, to be inappropriate for testing the role of motion. A task requiring temporal information showed a strong performance drop when fewer points were used or when the image sequence was sampled and displayed at a reduced frame rate. Irrespective of the frame rate, performance did not vary with point lifetime. We concluded that local motion is not required for the perception of tested biological movements, suggesting that the analysis of biological motion does not benefit from examining local motion. The reliance of perception on the number of displayed points and frames supports the idea that biological motion is perceived from a sequence of spatiotemporally sampled forms.

Child↗
PubMed2005

Algorithms for protein interaction networks.

The functional characterization of all genes and their gene products is the main challenge of the postgenomic era. Recent experimental and computational techniques have enabled the study of interactions among all proteins on a large scale. In this paper, approaches will be presented to exploit interaction information for the inference of protein structure, function, signalling pathways and ultimately entire interactomes. Interaction networks can be modelled as graphs, showing the operation of gene function in terms of protein interactions. Since the architecture of biological networks differs distinctly from random networks, these functional maps contain a signal that can be used for predictive purposes. Protein function and structure can be predicted by matching interaction patterns, without the requirement of sequence similarity. Moving on to a higher level definition of protein function, the question arises how to decompose complex networks into meaningful subsets. An algorithm will be demonstrated, which extracts whole signal-transduction pathways from noisy graphs derived from text-mining the biological literature. Finally, an algorithmic strategy is formulated that enables the proteomics community to build a reliable scaffold of the interactome in a fraction of the time compared with uncoordinated efforts.

Algorithms↗
PubMed2005

Local image structures and optic flow estimation.

Different kinds of local image structures (such as homogeneous, edge-like and junction-like patches) can be distinguished by the intrinsic dimensionality of the local signals. Intrinsic dimensionality makes use of variance from a point and a line in spectral representation of the signal in order to classify it as homogeneous, edge-like or junction-like. The concept of intrinsic dimensionality has been mostly exercised using discrete formulations; however, recent work has introduced a continuous definition. The current study analyzes the distribution of local patches in natural images according to this continuous understanding of intrinsic dimensionality. This distribution reveals specific patterns than can be also associated to local image structures established in computer vision and which can be related to orientation and optic flow features. In particular, we link quantitative and qualitative properties of optic-flow error estimates to these patterns. In this way, we also introduce a new tool for better analysis of optic flow algorithms.

Algorithms↗
PubMed2005

Biologically motivated space-variant filtering for robust optic flow processing.

We describe and test a biologically motivated space-variant filtering method for decreasing the noise in optic flow fields. Our filter model adopts certain properties of a particular motion-sensitive area of the brain (area MT), which averages the incoming motion signals over receptive fields, the sizes of which increase with the distance from the center of the projection. We use heading estimation from optic flow as a criterion to evaluate the improvement of the filtered flow field. The tests are conducted on flow fields calculated with a standard flow algorithm from image sequences. We use two different sets of image sequences. The first set is recorded by a camera which is installed in a moving car. The second set is derived from a database containing three dimensional data and reflectance information from natural scenes. The latter set guarantees full control of the camera motion and ground truth about the flow field and the heading. We test the space-variant filtering method by comparing heading estimation results between space-variant filtered flow, flow filtered by averaging over domains of the visual field with constant size (constant filtering) and raw unfiltered flow. Because of noise and the aperture problem the heading estimates obtained from the raw flows are often unreliable. Estimated heading differs widely for different sub-sampled calculations. In contrast, the results obtained from the filtered flows are much less variable and therefore more consistent. Furthermore, we find a significant improvement of the results obtained from the space-variant filtered flow compared to the constant filtered flow. We suggest extensions to the space-variant filtering procedure that take other properties of motion representation in area MT into account.

Algorithms↗
PubMed2002

Perception of biological motion without local image motion.

A vivid perception of the moving form of a human figure can be obtained from a few moving light points on the joints of the body. This is known as biological motion perception. It is commonly believed that the perception of biological motion rests on image motion signals. Curiously, however, some patients with lesions to motion processing areas of the dorsal stream are severely impaired in image motion perception but can easily perceive biological motion. Here we describe a biological motion stimulus based on a limited lifetime technique that tests the perception of a moving human figure in the absence of local image motion. We find that subjects can spontaneously recognize a moving human figure in displays without local image motion. Their performance is very similar to that for classic point-light displays. We also find that tasks involving the discrimination of walking direction or the coherence of a walking figure can be performed in the absence of image motion. Thus, although image motion may generally aid processes such as segmenting figure from background, we propose that it is not the basis for the precept of biological motion. Rather, we suggest biological motion is derived from dynamic form information on body posture evolving over time.

Humans↗
PubMed2002

Measurement of generalization fields for the recognition of biological motion.

The human visual system processes complex biological motion stimuli with high sensitivity and selectivity. The characterization of spatio-temporal generalization in the perception of biological motion is still a largely unresolved problem. We present an experiment that investigates how the visual system responds to motion stimuli that interpolate spatio-temporally between natural biological motion patterns. Inspired by analogous studies in stationary object recognition, we generated stimuli that interpolate between natural perceptual categories by morphing. Spatio-temporal morphs between natural movement patterns were obtained with a technique that allows to calculate linear combinations of spatio-temporal patterns. The weights of such linear combinations define a linear metric space over the set of generated movement patterns, so that the spatio-temporal similarity of the motion patterns can be quantified. In our experiments, we found smooth and continuous variation of the categorization probabilities with the weights of the prototypes in the morphs. For bipedal locomotion patterns we could accurately predict the perceived properties of the morphs by linear combinations of the perceived properties of the prototypes. Such predictions were not possible for morphs between locomotion and very dissimilar movements. We conclude that the visual system shows generalization within classes of motion patterns with similar basic structure, such as bipedal locomotion.

Adult↗
PubMed2001

Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast.

In the postgenomic era, one of the most interesting and important challenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist independently. To study the large-scale patterns and evolution of interactions between protein domains, we view interactions between protein domains in terms of the interactions between structural families of evolutionarily related domains. This allows us to classify 8151 interactions between individual domains in the Protein Data Bank and the yeast Saccharomyces cerevisiae in terms of 664 types of interactions, between protein families. At least 51 interactions do not occur in the Protein Data Bank and can only be derived from the yeast data. The map of interactions between protein families has the form of a scale-free network, meaning that most protein families only interact with one or two other families, while a few families are extremely versatile in their interactions and are connected to many families. We observe that almost half of all known families engage in interactions with domains from their own family. We also see that the repertoires of interactions of domains within and between polypeptide chains overlap mostly for two specific types of protein families: enzymes and same-family interactions. This suggests that different types of protein interaction repertoires exist for structural, functional and regulatory reasons.

Binding Sites↗
PubMed2001

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3.

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families.

Amino Acid Motifs↗
PubMed2001

Neuronal latencies and the position of moving objects.

Neuronal latencies delay the registration of the visual signal from a moving object. By the time the visual input reaches brain structures that encode its position, the object has already moved on. Do we perceive the position of a moving object with a delay because of neuronal latencies? Or is there a brain mechanism that compensates for latencies such that we perceive the true position of a moving object in real time? This question has been intensely debated in the context of the flash-lag illusion: a moving object and an object flashed in alignment with it appear to occupy different positions. The moving object is seen ahead of the flash. Does this show that the visual system extrapolates the position of moving objects into the future to compensate for neuronal latencies? Alternative accounts propose that it simply shows that moving and flashed objects are processed with different delays, or that it reflects temporal integration in brain areas that encode position and motion. The flash-lag illusion and the hypotheses put forward to explain it lead to interesting questions about the encoding of position in the brain. Where is the 'where' pathway and how does it work?

Animals↗
PubMed2001

Generating protein interaction maps from incomplete data: application to fold assignment.

MOTIVATION: We present a framework to generate comprehensive overviews of protein-protein interactions. In the post-genomic view of cellular function, each biological entity is seen in the context of a complex network of interactions. Accordingly, we model functional space by representing protein-protein-interaction data as undirected graphs. We suggest a general approach to generate interaction maps of cellular networks in the presence of huge amounts of fragmented and incomplete data, and to derive representations of large networks which hide clutter while keeping the essential architecture of the interaction space. This is achieved by contracting the graphs according to domain-specific hierarchical classifications. The key concept here is the notion of induced interaction, which allows the integration, comparison and analysis of interaction data from different sources and different organisms at a given level of abstraction. RESULTS: We apply this approach to compute the overlap between the DIP compendium of interaction data and a dataset of yeast two-hybrid experiments. The architecture of this network is scale-free, as frequently seen in biological networks, and this property persists through many levels of abstraction. Connections in the network can be projected downwards from higher levels of abstraction down to the level of individual proteins. As an example, we describe an algorithm for fold assignment by network context. This method currently predicts protein folds at 30% accuracy without any requirement of detectable sequence similarity of the query protein to a protein of known structure. We used this algorithm to compile a list of structural assignments for previously unassigned genes from yeast. Finally we discuss ways forward to use interaction networks for the prediction of novel protein-protein interactions. AVAILABILITY: http://www.ebi.ac.uk/~lappe/FoldPred/.

Algorithms↗
PubMed2000

Postsaccadic visual references generate presaccadic compression of space.

With every rapid gaze shift (saccade), our eyes experience a different view of the world. Stable perception of visual space requires that points in the new image are associated with corresponding points in the previous image. The brain may use an extraretinal eye position signal to compensate for gaze changes, or, alternatively, exploit the image contents to determine associated locations. Support for a uniform extraretinal signal comes from findings that the apparent position of objects briefly flashed around the time of a saccade is often shifted in the direction of the saccade. This view is challenged, however, by observations that the magnitude and direction of the displacement varies across the visual field. Led by the observation that non-uniform displacements typically occurred in studies conducted in slightly illuminated rooms, here we determine the dependence of perisaccadic mislocalization on the availability of visual spatial references at various times around a saccade. We find that presaccadic compression occurs only if visual references are available immediately after, rather than before or during, the saccade. Our findings indicate that the visual processes of transsaccadic spatial localization use mainly postsaccadic visual information.

Fixation, Ocular↗
PubMed2000

Perception of two-dimensional, simulated ego-motion trajectories from optic flow.

A veridical percept of ego-motion is normally derived from a combination of visual, vestibular, and proprioceptive signals. A previous study showed that blindfolded subjects can accurately perceive passively travelled straight or curved trajectories provided that the orientation of the head remained constant along the trajectory. When they were turned (whole-body, head-fixed) relative to the trajectory, errors occurred. We ask whether vision allows for better path perception in that situation, to correct or complement vestibular perception. Seated, stationary subjects wore a head mounted display showing optic flow stimuli which simulated linear or curvilinear 2D trajectories over a horizontal ground plane. The observer's orientation was either fixed in space, fixed relative to the path, or changed relative to both. After presentation, subjects reproduced the perceived movement with a model vehicle, of which position and orientation were recorded. They tended to correctly perceive ego-rotation (yaw), but they perceive orientation as fixed relative to trajectory or (unlike in the vestibular study) to space. This caused trajectory misperception when body rotation was wrongly attributed to a rotation of the path. Visual perception was very similar to vestibular perception.

Head Movements↗
PubMed2000

A model of the perceived relative positions of moving objects based upon a slow averaging process.

We extend the local energy model of position detection to cope with temporally varying position signals and the perception of relative position. The extension entails two main components. First, a form of persistence for the position signal based on the temporal impulse response function of the visual system. Secondly, we hypothesise that the perceived relative position of two objects is determined by a slow average of the difference of the objects' position signals. The model explains why briefly flashed static dots are perceived to lag behind continuously visible moving dots, without the need for a motion extrapolation process [Nijhawan, R. (1994). Nature, 370, 256-257]. The dependence of this illusion on parameters such as the velocity, duration, frequency and number of flashes of the motion trajectories is accurately captured by the model. Furthermore, the model makes two predictions. First, briefly flashed dots on a staircase trajectory should lead dots with a long duration. Secondly, it should be possible to abolish the lag-effect between continuously visible and stroboscopically moving objects by halting the continuously visible dots during the interflash interval of the stroboscopic dots. Both predictions are corroborated in experiments.

Computer Simulation↗
PubMed2000

Responses to continuously changing optic flow in area MST.

We studied the temporal behavior and tuning properties of medial superior temporal (MST) neurons in response to constant flow-field stimulation and continuously changing flow-field stimulation (transitions), which were obtained by morphing one flow field into another. During transitions, the flow fields resembled the motion pattern seen by an observer during changing ego-motion. Our aim was to explore the behavior of MST cells in response to changes in the flow-field pattern and to establish whether the responses of MST cells are temporally independent or if they are affected by contextual information from preceding stimulation. We first tested whether the responses obtained during transitions were linear with respect to the two stimuli defining the transition. In over half of the transitions, the cell response was nonlinear: the response during the transition could not be predicted by the linear interpolation between the stimulus before and after the transition. Nonlinearities in the responses could arise from a dependence on temporal context or from nonlinearities in the tuning to flow-field patterns. To distinguish between these two hypotheses, we fit the responses during transitions and during continuous stimuli to the predictions of a temporally independent model (temporal-independence test) and we compared the responses during transitions to the responses elicited by inverse transitions (temporal-symmetry test). The effect of temporal context was significant in only 7.2% and 5.5% of cells in the temporal-independence test and in the temporal-symmetry test, respectively. Most of the nonlinearities in the cell responses could be accounted for by nonlinearities in the tuning to flow-field stimuli (i.e., the responses to a restricted set of flow fields did not predict the responses to other flow fields). Tuning nonlinearities indicate that a complete characterization of the tuning properties of MST neurons cannot be obtained by testing only a small number of flow fields. Because the cells' responses do not depend on temporal context, continuously changing stimulation can be used to characterize the receptive field properties of cells more efficiently than constant stimulation. Temporal independence in the responses to transitions indicates that MST cells do not code for second-order temporal properties of flow-field stimuli, i.e., for changes in the flow field through time that can be construed as paths through the environment. Information about ego-motion three-dimensional paths through the environment may either be processed at the population level in MST or in other cortical areas.

Action Potentials↗
PubMed1999

Linear vestibular self-motion signals in monkey medial superior temporal area.

The present study was aimed at investigating the sensitivity to linear vestibular stimulation of neurons in the medial superior temporal area (MST) of the macaque monkey. Two monkeys were moved on a parallel swing while single-unit activity was recorded. About one-half of the cells (28/51) responded in the dark either to forward motion (n = 10), or to backward motion (n = 11), or to both (n = 7). Twenty cells responding to vestibular stimulation in darkness were also tested for their responses to optic flow stimulation simulating forward and backward self-motion. Forty-five percent (9/20) of them preferred the same self-motion directions, that is, combined visual and vestibular signals in a synergistic manner. Thirty percent (6/20) of the cells were not responsive to visual stimulation alone. The remaining 25% (5/20) preferred directions that were antialigned. Our results provide strong evidence that neurons in the MST area are at least in part involved in the processing of self-motion.

Animals↗