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PubMed2002

Pattern-motion responses in human visual cortex.

Physiological models of visual motion processing posit that 'pattern-motion cells' represent the direction of moving objects independent of their particular spatial pattern. We performed fMRI experiments to identify neuronal activity in the human brain selective for pattern motion. A protocol using adaptation to moving 'plaid' stimuli allowed us to separate pattern-motion responses from other types of motion-related activity within the same brain structures, and revealed strong pattern-motion selectivity in human visual area MT+. Reducing the perceptual coherence of the plaids yielded a corresponding decrease in pattern-motion responsivity, providing evidence that percepts of coherent motion are closely linked to the activity of pattern-motion cells in human MT+.

Adult↗
PubMed2002

Perceiving patterns in random series: dynamic processing of sequence in prefrontal cortex.

We demonstrate that regions within human prefrontal cortex develop moment-to-moment models for patterns of events occurring in the sensory environment. Subjects viewed a random binary sequence of images, each presented singly and each requiring a different button press response. Patterns occurred by chance within the presented series of images. Using functional magnetic resonance imaging (fMRI), we identified activity evoked by viewing a stimulus that interrupted a pattern. Prefrontal activation was evoked by violations of both repeating and alternating patterns, and the amplitude of this activation increased with increasing pattern length. Violations of repeating patterns, but not of alternating patterns, activated the basal ganglia.

Adolescent↗
PubMed2002

Propulsion patterns and pushrim biomechanics in manual wheelchair propulsion.

OBJECTIVES: To classify stroke patterns of manual wheelchair users and to determine if different patterns of propulsion lead to different biomechanics. DESIGN: Case series. SETTING: Biomechanics laboratory. PARTICIPANTS: Thirty-eight individuals with paraplegia who use manual wheelchairs for mobility. INTERVENTION: Subjects propelled their own wheelchair on a dynamometer at 2 different steady state speeds. Bilateral biomechanical data were obtained by using a force and moment sensing pushrim and a motion analysis system. MAIN OUTCOME MEASURES: The propulsive stroke of each participant for each speed and side was classified as following 1 of 4 patterns. These 4 patterns were then compared by using a mixed-model analysis of variance. The biomechanical variables that were compared were cadence, peak and rate of rise of the resultant force, mechanical effective force, push angle, and ratio of time spent pushing to time in recovery. RESULTS: The most common propulsive stroke involved the user lifting the hand over the pushrim during the recovery phase. The stroke pattern was independent of axle position and varied from side to side and between speeds. After controlling for subject characteristics, significant differences were observed between stroke patterns in cadence and ratio of time spent pushing to time in recovery. A stroke pattern that involves using a semicircular motion with the hand below the pushrim during the recovery phase of the propulsion stroke was associated with a lower cadence and more time spent in the push phase relative to the recovery phase. CONCLUSION: The semicircular motion of propulsion displayed characteristics consistent with reduced repetition and more efficient propulsion. Use of this propulsion style may reduce trauma to the upper extremities. Clinicians should consider training individuals in this propulsion style.

Adult↗
PubMed1984

Pattern and orientation effects on afterimage duration.

Patterns composed of a pair of lines: vertical + horizontal, vertical + oblique, horizontal + oblique, and oblique + oblique, either centrally-aligned or edge-aligned, were shown at two positions of rotation. After a 1-s exposure to the pattern observers timed the duration of afterimages consisting of individual lines (fragmentary state) and the pattern as a whole (unitary state) for the ensuring 60 s. Summing unitary and fragmentary afterimage durations yielded the total afterimage duration for each pattern. Three hypotheses were confirmed by the results: (i) total afterimage duration is constant for all patterns when integrated spatiotemporal luminances are equal; (ii) unitary afterimage duration is also constant; (iii) fragmentary afterimages of vertically oriented lines have longer durations than either their horizontal or oblique pair members, regardless of alignment and, with one exception, rotation. For all patterns, the durations of the unitary and the fragmentary state represent a fixed portion of the total afterimage duration. The difference between afterimage duration for differently oriented lines in patterns which include a vertical is discussed in relation to the vertical-horizontal illusion, the function and structure of cortical orientation processes, and perceptual development.

Adult↗
PubMed2005

Auditory orientation in crickets: pattern recognition controls reactive steering.

Many groups of insects are specialists in exploiting sensory cues to locate food resources or conspecifics. To achieve orientation, bees and ants analyze the polarization pattern of the sky, male moths orient along the females' odor plume, and cicadas, grasshoppers, and crickets use acoustic signals to locate singing conspecifics. In comparison with olfactory and visual orientation, where learning is involved, auditory processing underlying orientation in insects appears to be more hardwired and genetically determined. In each of these examples, however, orientation requires a recognition process identifying the crucial sensory pattern to interact with a localization process directing the animal's locomotor activity. Here, we characterize this interaction. Using a sensitive trackball system, we show that, during cricket auditory behavior, the recognition process that is tuned toward the species-specific song pattern controls the amplitude of auditory evoked steering responses. Females perform small reactive steering movements toward any sound patterns. Hearing the male's calling song increases the gain of auditory steering within 2-5 s, and the animals even steer toward nonattractive sound patterns inserted into the species-specific pattern. This gain control mechanism in the auditory-to-motor pathway allows crickets to pursue species-specific sound patterns temporarily corrupted by environmental factors and may reflect the organization of recognition and localization networks in insects.

Acoustic Stimulation↗
PubMed1979

Memorizing and copying visual patterns: a Piagetian interpretation.

Six-, 8-, 10-, and 12-year-old children (10 boys and 10 girls) reconstructed two visual patterns from immediate memory, while other 5- and 6-year-old children (10 boys and 10 girls) reconstructed the identical patterns by direct copying. Patterns were simple and composed entirely of circles or squares as component items. Four results were emphasized: (a) Numerous errors mady by the copying groups led to the conclusion that memory loss is often overestimated in young children. Since an independent estimate of perceptual encoding errors is rarely carried out, encoding mistakes are often included among forgetting errors. (b) One pattern was both copied and remembered more poorly than the other in accord with a Piagetian interpretation of a conceptual conflict inherent in the pattern design between spatial and numerical correspondence of component pattern items. (c) A memory strategy emphasizing configuration preservation was suggested for the 6-year-olds who made slightly fewer memory than copying errors for two configural scoring categories. (d) Performance in an unrelated planning-for-memory task significantly differentiated between better and worse performers on the visual pattern memory task.

Age Factors↗
PubMed1998

Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.

MOTIVATION: The discovery of motifs in biological sequences is an important problem. RESULTS: This paper presents a new algorithm for the discovery of rigid patterns (motifs) in biological sequences. Our method is combinatorial in nature and able to produce all patterns that appear in at least a (user-defined) minimum number of sequences, yet it manages to be very efficient by avoiding the enumeration of the entire pattern space. Furthermore, the reported patterns are maximal: any reported pattern cannot be made more specific and still keep on appearing at the exact same positions within the input sequences. The effectiveness of the proposed approach is showcased on a number of test cases which aim to: (i) validate the approach through the discovery of previously reported patterns; (ii) demonstrate the capability to identify automatically highly selective patterns particular to the sequences under consideration. Finally, experimental analysis indicates that the algorithm is output sensitive, i.e. its running time is quasi-linear to the size of the generated output.

Algorithms↗
PubMed2004

Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.

MOTIVATION: Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of feature selection inherent to large, high-dimensional gene expression datasets. New flexible data analysis approaches capable of searching relevant subgroups of genes and experiments are needed to understand multivariate associations of gene expression patterns with observed phenotypes. RESULTS: We present in detail a deterministic algorithm to discover patterns of multivariate gene associations in gene expression data. The patterns discovered are differential with respect to a control dataset. The algorithm is exhaustive and efficient, reporting all existent patterns that fit a given input parameter set while avoiding enumeration of the entire pattern space. The value of the pattern discovery approach is demonstrated by finding a set of genes that differentiate between two types of lymphoma. Moreover, these genes are found to behave consistently in an independent dataset produced in a different laboratory using different arrays, thus validating the genes selected using our algorithm. We show that the genes deemed significant in terms of their multivariate statistics will be missed using other methods. AVAILABILITY: Our set of pattern discovery algorithms including a user interface is distributed as a package called Genes@Work. This package is freely available to non-commercial users and can be downloaded from our website (http://www.research.ibm.com/FunGen).

Algorithms↗
PubMed2005

Shifting and scaling patterns from gene expression data.

MOTIVATION: During the last years, the discovering of biclusters in data is becoming more and more popular. Biclustering aims at extracting a set of clusters, each of which might use a different subset of attributes. Therefore, it is clear that the usefulness of biclustering techniques is beyond the traditional clustering techniques, especially when datasets present high or very high dimensionality. Also, biclustering considers overlapping, which is an interesting aspect, algorithmically and from the point of view of the result interpretation. Since the Cheng and Church's works, the mean squared residue has turned into one of the most popular measures to search for biclusters, which ideally should discover shifting and scaling patterns. RESULTS: In this work, we identify both types of patterns (shifting and scaling) and demonstrate that the mean squared residue is very useful to search for shifting patterns, but it is not appropriate to find scaling patterns because even when we find a perfect scaling pattern the mean squared residue is not zero. In addition, we provide an interesting result: the mean squared residue is highly dependent on the variance of the scaling factor, which makes possible that any algorithm based on this measure might not find these patterns in data when the variance of gene values is high. The main contribution of this paper is to prove that the mean squared residue is not precise enough from the mathematical point of view in order to discover shifting and scaling patterns at the same time. CONTACT: aguilar@lsi.us.es.

Algorithms↗
PubMed2006

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.

The mechanism of protein folding remains largely a mystery in molecular biology, despite the enormous effort from many groups in the past decades. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates such as the fraction of native contacts, the radius of gyration and so on. In this paper, we present an integrated approach towards understanding the folding process via visual analysis of patterns of these reaction coordinates. The three disparate processes (1) protein folding simulation, (2) pattern elicitation and (3) visualization of patterns, work in tandem. Thus as the protein folds, the changing landscape in the pattern space can be viewed via the visualization tool, PROTERAN, a program we developed for this purpose. We first present an incremental (on-line) trie-based pattern discovery algorithm to elicit the patterns and then describe the terrain metaphor based visualization tool. Using two example small proteins, a beta-hairpin and a designed protein Trp-cage, we next demonstrate that this combined pattern discovery and visualization approach extracts crucial information about protein folding intermediates and mechanism.

Algorithms↗
PubMed2004

The importance of pattern similarity between Müllerian mimics in predator avoidance learning.

Müllerian mimicry, where unpalatable prey share common warning patterns, has long fascinated evolutionary biologists. It is commonly assumed that Müllerian mimics benefit by sharing the costs of predator education, thus reducing per capita mortality, although there has been no direct test of this assumption. Here, we specifically measure the selection pressure exerted by avian predators on unpalatable prey with different degrees of visual similarity in their warning patterns. Using wild-caught birds foraging on novel patterned prey in the laboratory, we unexpectedly found that pattern similarity did not increase the speed of avoidance learning, and even dissimilar mimics shared the education of naive predators. This was a consistent finding across two different densities of unpalatable prey, although mortalities were lower at the higher density as expected. Interestingly, the mortalities of Müllerian mimics were affected by pattern similarity in the predicted way by the end of our experiment, although the result was not quite significant. This suggests that the benefits to Müllerian mimics may emerge only later in the learning process, and that predator experience of the patterns may affect the degree to which pattern similarity is important. This highlights the need to measure the behaviour of real predators if we are to understand fully the evolution of mimicry systems.

Adaptation, Physiological↗
PubMed2004

A computational model for periodic pattern perception based on frieze and wallpaper groups.

We present a computational model for periodic pattern perception based on the mathematical theory of crystallographic groups. In each N-dimensional Euclidean space, a finite number of symmetry groups can characterize the structures of an infinite variety of periodic patterns. In 2D space, there are seven frieze groups describing monochrome patterns that repeat along one direction and 17 wallpaper groups for patterns that repeat along two linearly independent directions to tile the plane. We develop a set of computer algorithms that "understand" a given periodic pattern by automatically finding its underlying lattice, identifying its symmetry group, and extracting its representative motifs. We also extend this computational model for near-periodic patterns using geometric AIC. Applications of such a computational model include pattern indexing, texture synthesis, image compression, and gait analysis.

Algorithms↗
PubMed2005

Clustering and re-clustering for pattern discovery in gene expression data.

The combined interpretation of gene expression data and gene sequences is important for the investigation of the intricate relationships of gene expression at the transcription level. The expression data produced by microarray hybridization experiments can lead to the identification of clusters of co-expressed genes that are likely co-regulated by the same regulatory mechanisms. By analyzing the promoter regions of co-expressed genes, the common regulatory patterns characterized by transcription factor binding sites can be revealed. Many clustering algorithms have been used to uncover inherent clusters in gene expression data. In this paper, based on experiments using simulated and real data, we show that the performance of these algorithms could be further improved. For the clustering of expression data typically characterized by a lot of noise, we propose to use a two-phase clustering algorithm consisting of an initial clustering phase and a second re-clustering phase. The proposed algorithm has several desirable features: (i) it utilizes both local and global information by computing both a "local" pairwise distance between two gene expression profiles in Phase 1 and a "global" probabilistic measure of interestingness of cluster patterns in Phase 2, (ii) it distinguishes between relevant and irrelevant expression values when performing re-clustering, and (iii) it makes explicit the patterns discovered in each cluster for possible interpretations. Experimental results show that the proposed algorithm can be an effective algorithm for discovering clusters in the presence of very noisy data. The patterns that are discovered in each cluster are found to be meaningful and statistically significant, and cannot otherwise be easily discovered. Based on these discovered patterns, genes co-expressed under the same experimental conditions and range of expression levels have been identified and evaluated. When identifying regulatory patterns at the promoter regions of the co-expressed genes, we also discovered well-known transcription factor binding sites in them. These binding sites can provide explanations for the co-expressed patterns.

Algorithms↗
PubMed1976

Effect of pulvinar lesions on visual pattern discrimination in monkeys.

This study compares the performance (percent correct responses and reaction times) of three unoperated control monkeys with the postoperative performance of eight monkeys with pulvinar lesions, either inferior pulvinar or medial and lateral pulvinar, on a tachistoscopically presented visual pattern-discrimination task highly demanding of attention. To further emphasize and assess the attentional factor in visual pattern discrimination, all monkeys who attained criterion performance (90% correct response on three consecutive sessions of 100 trials each) were tested for the effects of visually distracting interference stimuli added to the original discriminative stimuli. In addition, retention of postoperatively learned discriminations was tested after a 6-wk interval withou training and compared with the performance of control monkeys. Four monkeys with only inferior pulvinar lesions and one monkey with inferior pulvinar plus medial and lateral pulvinar lesions were markedly impaired in the postoperative learning of a visual pattern discrimination. Three of these monkeys failed to acquire criterion perfromance in 9,000 or more training trials, while two learned to ceiterion level only after prolonged training (7,400 and 6,900 trials). In contrast, monkeys with medial and lateral pulvinar lesions showed no deficit in learning ability compared to unoperated control monkeys. Furthermore, the performance of the two monkeys with inferior pulvinar lesions, who attained the criterion level of learning only with difficulty, was further impaired by the addition of distracting interference stimuli, where the performance of monkeys with medial and lateral pulvinar lesions as well as the control monkeys was only temporarily disrupted by this procedure. None of the monkeys with pulvinar lesions, who were tested for retention of the postoperatively learned discrimination, showed appreciable deficits in comparison to control monkeys. All monkeys, including controls and those uith pulvinar lesions who were able to learn the visual pattern discrimination, showed a common pattern of reaction time (RT) change during the course of the learning; that is, RT was low during change-level performance, increased during learning, and decreased once criterion performance was achieved. Reaction times of monkeys with inferior pulvinar lesions tended to be longer than for controls or for those with medial and lateral pulvinar lesions. These results provide the first behavior evidence that the inferior pulvinar of monkeys is involved in visual pattern discrimination and add further support to the concept of a second visual system in which the inferior pulvinar plays a role. The attentional aspects of the visual pattern-discrimination task employed in this study and the additional effects obtained with distracting stimuli suggest that the impairments arising from inferior pulvinar lesions may be dependent in part on visual attentional factors.

Acoustic Stimulation↗
PubMed1985

Selective internal operations in the recognition of locally and globally point-inverted patterns.

Performance in discriminating rotated 'same' patterns from 'different' patterns may decrease with rotation angle up to about 90 degrees and then increase with angle up to 180 degrees. This anomalously improved performance under 180 degrees pattern rotation or point-inversion can be explained by assuming that patterns are internally represented in terms of local features and their spatial-order relations ('left of', 'above', etc.), and that, in pattern comparison, an efficient internal sense-reversal operation occurs (transforming 'left of' to 'right of', etc.). Previous experiments suggested that local features and spatial relations could not be efficiently separated in some pattern-comparison tasks. This hypothesis was tested by measuring 'same-different' discrimination performance under four transformation: point-inversion 1 of the whole pattern, point-inversion 1F of local features alone, point-inversion 1P of local-feature positions alone, and identity transformation Id. The results suggested that internal sense-reversal operations could be applied selectively and efficiently, provided that local features were well separated. Under this condition performances for 1F and 1 were about the same whereas performance for 1P was significantly worse, the latter performance resulting possibly from an attempt to apply internal global and local sense-reversal operations serially.

Adult↗
PubMed2005

Global competition dictates local suppression in pattern rivalry.

Certain pairs of visual patterns, when superimposed as if transparent, elicit a wavering percept in which one or the other pattern can enjoy temporary periods of exclusive visibility. This multistable perceptual phenomenon is called monocular rivalry or pattern rivalry (PR) and is most pronounced when the component patterns are faint and devoid of detail. The principal mechanisms that give rise to PR continue to be a topic of speculation. In the present study, we examine the determinants of exclusive dominance during PR using a novel stimulus in which a central portion is free of conflict. By observing the properties of suppression in this so-called rivalry-free region, we demonstrate that perception is driven largely by the global and holistic interpretation of the patterns, rather than by the need to resolve local spatial conflict. The suppression of this central region was often complete and varied as a function of the parameters of the global stimulus, including the size of the surround region, its ocular configuration, and stereoscopic depth ordering. Suppression also varied as a function of pattern continuity across the central region as well as with the temporal offset of the overlapping components. These findings demonstrate that the visibility or invisibility of a pattern is not fundamentally a product of local processing, but is instead shaped by the brain's global interpretive assumptions regarding the composition of the stimulus.

Adolescent↗
PubMed1981

A technique for the objective assessment of routine analytical methods in clinical laboratories using pattern recognition.

A technique is presented to assess objectively the reliability of analytical methods used routinely in clinical laboratories. From the Netherlands National Coupled External/Internal Quality Control Programme information can be gathered about the performance of routine analytical methods. The performance of a method in a trial is described by four 'features': the accuracy of a method; its day to-day precision; its susceptibility to give erroneous results (eg, extreme bias, drift, extreme week-to-week variations); and its susceptibility to give systematic errors for different laboratories. These four features obtained in a trial for a given analytical method determine the position of a 'pattern' in the four-dimensional space. The results of six trials discussed in this paper provided six 'patterns' per analytical method. Using pattern recognition techniques, clusters of patterns were detected in the four-dimensional space. A weighting procedure revealed the relative importance of the various features for discrimination between the detected clusters. For various blood components, different features are of importance for this discrimination. Patterns belonging to the same clusters appeared to be patterns of the same (or comparable) analytical methods; thus analytical methods could be distinguished from each other. The means of the feature values of the patterns in a cluster determine the quality of that cluster. Thus the quality of an analytical method can be objectively assessed. Some tentative conclusions on the validity of analytical methods are given.

Blood Glucose↗
PubMed2006

PhyloPat: phylogenetic pattern analysis of eukaryotic genes.

BACKGROUND: Phylogenetic patterns show the presence or absence of certain genes or proteins in a set of species. They can also be used to determine sets of genes or proteins that occur only in certain evolutionary branches. Phylogenetic patterns analysis has routinely been applied to protein databases such as COG and OrthoMCL, but not upon gene databases. Here we present a tool named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. DESCRIPTION: PhyloPat is an easy-to-use webserver, which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. We found in total 446,825 genes and 3,164,088 orthologous relationships within the EnsMart v40 database. We used a single linkage clustering algorithm to create 147,922 phylogenetic lineages, using every one of the orthologies provided by Ensembl. PhyloPat provides the possibility of querying with either binary phylogenetic patterns (created by checkboxes) or regular expressions. Specific branches of a phylogenetic tree of the 21 included species can be selected to create a branch-specific phylogenetic pattern. Users can also input a list of Ensembl or EMBL IDs to check which phylogenetic lineage any gene belongs to. The output can be saved in HTML, Excel or plain text format for further analysis. A link to the FatiGO web interface has been incorporated in the HTML output, creating easy access to functional information. Finally, lists of omnipresent, polypresent and oligopresent genes have been included. CONCLUSION: PhyloPat is the first tool to combine complete genome information with phylogenetic pattern querying. Since we used the orthologies generated by the accurate pipeline of Ensembl, the obtained phylogenetic lineages are reliable. The completeness and reliability of these phylogenetic lineages will further increase with the addition of newly found orthologous relationships within each new Ensembl release.

Algorithms↗