Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Random walk”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71Linked to original sources
PubMed2005

Migration of perilesional microglia after focal brain injury and modulation by CC chemokine receptor 5: an in situ time-lapse confocal imaging study.

Microglia rapidly become reactive in response to diverse stimuli and are thought to be prominent participants in the pathophysiology of both acute injury and chronic neurological diseases. However, mature microglial reactions to a focal lesion have not been characterized dynamically in adult vertebrate tissue. Here, we present a detailed analysis of long-distance perilesional microglial migration using time-lapse confocal microscopy in acutely isolated living slices from adult brain-injured mice. Extensive migration of perilesional microglia was apparent by 24 h after injury and peaked at 3 d. Average instantaneous migration speeds of approximately 5 microm/min and peak speeds >10 microm/min were observed. Collective, directed migration toward the lesion edge was not observed as might be expected in the presence of chemoattractive gradients. Rather, migration was autonomous and could be modeled as a random walk. Pharmacological blockade of the cysteine-cysteine chemokine receptor 5 reduced migration velocity and the number of perilesional migratory microglia without affecting directional persistence, suggesting a novel role for chemokines in modulation of discrete migratory parameters. Finally, activated microglia in the denervated hippocampal stratum oriens did not migrate extensively, whereas human immunodeficiency virus-1 tat-activated microglia migrated nearly twice as fast as those at the stab lesion, indicating a nonuniform microglial response to different stimuli. Understanding the characteristics and specific molecular mechanisms underlying microglial migration after neural injury could reveal novel targets for therapeutic strategies for modulating neuroinflammation in human diseases.

Amides↗
PubMed2004

Kinetics of filament bundling with attractive interactions.

We study the kinetics of filament bundling by variable time-step Brownian-dynamics simulations employing a simplified attractive potential based on earlier atomic-level calculations for actin filaments. Our results show that collisions often cluster in time, due to memory in the random walk. The clustering increases the bundling opportunities. Small-angle collisions and collisions with short center-to-center distance are more likely to lead to bundling. Increasing the monomer-monomer attraction decreases the bundling time to a diffusional limit, which is determined by the capture cross-section and diffusion coefficients. The simulations clearly show that the bundling process consists of two sequential phases: rotation, by which two filaments align parallel to each other; and sliding, by which they maximize their contact length. Whether two filaments bundle or not is determined by the competition between rotation to a parallel state and escape. Increasing the rotational diffusion coefficient and attraction enhances rotation; decreasing attraction and increasing the translational diffusion coefficients enhance escape. Because of several competing effects, the filament length only affects the bundling time weakly.

Actin Cytoskeleton↗
PubMed2005

Convergence to the island-model coalescent process in populations with restricted migration.

In this article we apply some graph-theoretic results to the study of coalescence in a structured population with migration. The graph is the pattern of migration among subpopulations, or demes, and we use the theory of random walks on graphs to characterize the ease with which ancestral lineages can traverse the habitat in a series of migration events. We identify conditions under which the coalescent process in populations with restricted migration, such that individuals cannot traverse the habitat freely in a single migration event, nonetheless becomes identical to the coalescent process in the island migration model in the limit as the number of demes tends to infinity. Specifically, we first note that a sequence of symmetric graphs with Diaconis-Stroock constant bounded above has an unstructured Kingman-type coalescent in the limit for a sample of size two from two different demes. We then show that circular and toroidal models with long-range but restricted migration have an upper bound on this constant and so have an unstructured-migration coalescent in the limit. We investigate the rate of convergence to this limit using simulations.

Algorithms↗
PubMed2006

Simultaneous fine mapping of multiple closely linked quantitative trait Loci using combined linkage disequilibrium and linkage with a general pedigree.

Within a small region (e.g., <10 cM), there can be multiple quantitative trait loci (QTL) underlying phenotypes of a trait. Simultaneous fine mapping of closely linked QTL needs an efficient tool to remove confounded shade effects among QTL within such a small region. We propose a variance component method using combined linkage disequilibrium (LD) and linkage information and a reversible jump Markov chain Monte Carlo (MCMC) sampling for model selection. QTL identity-by-descent (IBD) coefficients between individuals are estimated by a hybrid MCMC combining the random walk and the meiosis Gibbs sampler. These coefficients are used in a mixed linear model and an empirical Bayesian procedure combines residual maximum likelihood (REML) to estimate QTL effects and a reversible jump MCMC that samples the number of QTL and the posterior QTL intensities across the tested region. Note that two MCMC processes are used, i.e., an (internal) MCMC for IBD estimation and an (external) MCMC for model selection. In a simulation study, the use of the multiple-QTL model clearly removes the shade effects between three closely linked QTL located at 1.125, 3.875, and 7.875 cM across the region of 10 cM, using 40 markers at 0.25-cM intervals. It is shown that the use of combined LD and linkage information gives much more useful information compared to using linkage information alone for both single- and multiple-QTL analyses. When using a lower marker density (11 markers at 1-cM intervals), the signal of the second QTL can disappear. Extreme values of past effective size (resulting in extreme levels of LD) decrease the mapping accuracy.

Chromosome Mapping↗
PubMedDate not supplied

Behaviors producing photodispersal in Stentor coeruleus.

The ciliate Stentor coeruleus exhibits photodispersal, that is, these cells swim away from light sources and collect in dimly lighted areas. We imaged and reconstructed the tracks of 48 Stentor to determine which swimming behaviors produced their photodispersal. We observed that their photodispersal is not due to a change in their swimming speed but rather to a change in the frequency with which they reorient their swimming direction. Therefore, their photodispersal must be due to either (1) a gradual reorientation of the organism's swimming direction determined by the direction of the light beam (phototaxis) or (2) multiple randomly directed reorientations in swimming direction that occur less frequently when the cell is swimming away from the light source (biased random walk). Sixteen (19%) of the 83 observed forward swimming tracks lasting three or more seconds exhibited a gradual bending away from the light source consistent with a phototaxis. However, most tracks were interrupted repeatedly by abrupt reorientations resulting from ciliary reversals and "smooth turns" that caused cells to reorient through 5.4 times as many degrees as were needed to direct them away from the light source. When cells were swimming away from the light source, their probability of reorienting was reduced and photodispersal resulted.

Animals↗
PubMed2005

Dynamic Monte Carlo study on the probability distribution functions of tail-like polymer chain.

The configurational properties of tail-like polymer chains with one end attached to a flat surface are studied by using dynamic Monte Carlo technique. We find that the probability distribution of the free end in z direction P(R(z)) and the density profile rho(z) can be scaled approximately by a factor beta to be a length independent function for both random walking (RW) and self-avoiding walking (SAW) tail-like chains, where the factor beta is related to the mean square end-to-end distance . The scaled P(R(z)) of the SAW chain roughly overlaps that of the RW chain, but the scaled rho(z) of the SAW chain locates at smaller betaz than that of the RW chain.

Computer Simulation↗
PubMed2001

Life history and spatial distribution of the enchytraeid worm Cognettia sphagnetorum (Oligochaeta) in metal-polluted soil: below-ground sink-source population dynamics?

We studied the life history, metal-avoidance behavior, spatial distribution, and population growth of enchytraeid worms (Cognettia sphagnetorum [Oligochaeta]) originating from two sites: one uncontaminated, and another patchily polluted by heavy metals. Effects of patchy soil contamination on populations were studied in microcosms. In uncontaminated soil, worms from the polluted site had lower viability and reduced growth rate as juveniles but higher growth rate as adults compared to worms from the unpolluted site. They were also smaller in size at fragmentation (reproduction). Worms from the polluted site reached a larger population size than worms from the unpolluted site. Hence, worms from the polluted site seemed to allocate more energy to reproduction, because such a strategy can be highly adaptive when living in a less-polluted patch (the source) in, on average, a highly polluted environment. The C. sphagnetorum actively avoided Cu-contaminated soil, with the response being stronger in individuals from the contaminated site. When an unpolluted patch (the source) was surrounded by a toxic environment (the sink), worms were found in the sink, either because intraspecific competition overrode the avoidance behavior or because of random walk migration. As a result, total population size in these microcosms were as high as those in totally uncontaminated microcosms. Our results indicate that avoidance behavior and increased allocation to reproduction, together with the observed dispersal pattern, can be an adaptive strategy for C. sphagnetorum in the presence of small, less-polluted patches in, on average, a hostile environment. Hence, sink-source population regulation can explain spatial distribution and survival of C. sphagnetorum in patchily polluted field soils. When such population dynamics occur, this pattern should be taken into account when population densities in the field are monitored for ecological risk-assessment procedures concerning toxicants.

Adaptation, Physiological↗
PubMed1997

Weapon carrying among black adolescents: a social network perspective.

OBJECTIVES: This report describes the salience of social networks to the phenomena of adolescent weapon carrying. METHODS: A random-walk network sampling design was used to survey 113 adolescents about topics, including weapon carrying. RESULTS: In a probability sample of 12- to 15-year-olds, 20.9% reported ever carrying a weapon. Carriers were eight times as likely as noncarriers to report weapon carrying by an older associate, and 19 times as likely to report weapon carrying by a peer. A significant dose-response effect was present. CONCLUSIONS: This evidence supports the interpretation that modeling of weapon carrying by personal network members is important for its initiation and maintenance in adolescence.

Adolescent↗
PubMed1989

Threshold tracking for assessment of long-term adaptation and sensitization in pain perception.

To assess temporal variations in the perception of "phasic" heat pain stimuli a psychophysical tracking procedure was developed that enables repeated assessment of the pain threshold at short intervals. This "double-tracking" procedure produces two tracking curves simultaneously, one that approaches the pain threshold gradually from above, the other from below. The threshold for phasic heat pain was measured in 80 tracking trials with stimuli at temperatures near the pain threshold. Concurrently, the threshold for "tonic" heat pain was determined after every 20 tracking trials with a stimulus adjustment procedure. Eleven healthy subjects (age: 26.4 yr. +/- 6.0) participated in 2 sessions each. Phasic stimulation near the pain threshold did not produce any trends in either of the two threshold measures. Hence there was no long-term adaptation or sensitization. However, there were random variations (random walks) in the tracking curves, which we interpret as resulting from a stochastic relationship between stimulus and sensation. In agreement with other reports, discrimination seemed to be better at painful than at nonpainful temperatures.

Adaptation, Physiological↗
PubMedDate not supplied

Estimation of subject-specific normal ranges based on some statistical models of an individual's physiological variations.

Three statistical models of the individual's physiological variations, proposed by Dr Eugene K. Harris, were applied to the long-term series of individual test results in our health control system. It was found from this study that, in most cases, the homeostatic model shows the best fit to the population level from comparing correlation coefficients between the observations and estimations made based on Harris's three models. It was also found that for most cases, the homeostatic model gives the most reliable estimates in individual's level from the comparison of the chi-square values between the observations and estimations made for the individual's successive test results. Further, for a group of members with hyperglycaemia, the proportion of individuals in whom the random-walk model produced the most accurate predictions was increased to the proportion in the normal group. In the age group under 39 years of age, the autoregressive model showed a relatively high degree of predictive success, while the homeostatic model showed a relatively low degree in comparison with the results found in other age groups. From these investigations, it was found that the physiologically normal state shows strict homeostatic stability.

Female↗
PubMed2004

A response time model for judging order relationship between two symbolic stimuli.

The response time to judge the order relationship between two symbolic stimuli is frequently modeled as the time spent in a (constant-rate) accumulative sampling process until a threshold is reached. We will show that empirical descriptions of observed effects in number comparisons suggest an accrual process that reaches the threshold at an exponential rate. The model accrual equations and stopping conditions have an immediate interpretation in terms of a simple quantitative connectionist network. The encoded stimuli and thresholds are inputs to the network. The former are considered to result from the participant's learning history, and the latter modulate the rearrangement of the network parts; each arrangement models a different task. We have found a good correlation between model predictions and other authors' experimental data, both in number comparisons and in experiments in which the ordering of the symbolic stimuli has been artificially induced. Incorrect answers are discussed, and predictions are compared with data. We will explore differences and similarities with other approaches, such as random walk and the symbolic comparison model. In a limit case, our model becomes identical to the discriminability model.

Humans↗
PubMed2001

A comparison of four methods for simulating the diffusion process.

Four methods for the simulation of the Wiener process with constant drift and variance are described. These four methods are (1) approximating the diffusion process by a random walk with very small time steps; (2) drawing directly from the joint density of responses and reaction time by means of a (possibly) repeated application of a rejection algorithm; (3) using a discrete approximation to the stochastic differential equation describing the diffusion process; and (4) a probability integral transform method approximating the inverse of the cumulative distribution function of the diffusion process. The four methods for simulating response probabilities and response times are compared on two criteria: simulation speed and accuracy of the simulation. It is concluded that the rejection-based and probability integral transform method perform best on both criteria, and that the stochastic differential approximation is worst. An important drawback of the rejection method is that it is applicable only to the Wiener process, whereas the probability integral transform method is more general.

Algorithms↗
PubMed2004

Assessing the informational value of parameter estimates in cognitive models.

Mathematical models of cognition often contain unknown parameters whose values are estimated from the data. A question that generally receives little attention is how informative such estimates are. In a maximum likelihood framework, standard errors provide a measure of informativeness. Here, a standard error is interpreted as the standard deviation of the distribution of parameter estimates over multiple samples. A drawback to this interpretation is that the assumptions that are required for the maximum likelihood framework are very difficult to test and are not always met. However, at least in the cognitive science community, it appears to be not well known that standard error calculation also yields interpretable intervals outside the typical maximum likelihood framework. We describe and motivate this procedure and, in combination with graphical methods, apply it to two recent models of categorization: ALCOVE (Kruschke, 1992) and the exemplar-based random walk model (Nosofsky & Palmeri, 1997). The applications reveal aspects of these models that were not hitherto known and bring a mix of bad and good news concerning estimation of these models.

Algorithms↗
PubMed2001

A hybrid model of categorization.

Category learning is often modeled as either an exemplar-based or a rule-based process. This paper shows that both strategies can be combined in a cognitive architecture that was developed to model other task domains. Variations on the exemplar-based random walk (EBRW) model of Nosofsky and Palmeri (1997b) and the rule-plus-exception (RULEX) rule-based model of Nosofsky, Palmeri, and McKinley (1994) were implemented in the ACT-R cognitive architecture. The architecture allows the two strategies to be mixed to produce classification behavior. The combined system reproduces latency, learning, and generalization data from three category-learning experiments--Nosofsky and Palmeri (1997b), Nosofsky et al., and Erickson and Kruschke (1998). It is concluded that EBRW and ACT-R have different but equivalent means of incorporating similarity and practice. In addition, ACT-R brings a theory of strategy selection that enables the exemplar and the rule-based strategies to be mixed.

Cognition↗
PubMed1989

A semantic memory sentence verification model based on relative judgment theory.

A subjective referent model of sentence verification in semantic memory tasks based on the relative judgment theory of Link and Heath (1975), together with the derivation of a discriminability index, are presented in this paper. An attractive feature of the model is its consideration of both error rates and response times (RTs) in the calculation of the discriminability index. The model is also able to account for the frequent finding in semantic memory tasks that error RTs are longer than correct RTs. A partial replication of Experiment 2 of McCloskey and Glucksberg's (1979) sentence verification context effect studies, in which we employed 44 subjects and 28 categories, and controlled for item familiarity, revealed that error RTs were consistently longer than correct RTs--a finding inconsistent with the McCloskey and Glucksberg property comparison model, but in accord with the subjective referent model. An important fortuitous result was the detection of a context effect by the discriminability measure, an effect not detected by the RT data alone. The discriminability measures yielded a near perfect correlation with estimates of the mean step size of the random walk obtained by application of the parameter estimation program FITTRW (Heath, 1983).

Adult↗
PubMed1996

A test of the deadline model for speed-accuracy tradeoffs.

Two experiments were conducted to evaluate the deadline model for speed-accuracy tradeoffs. According to the deadline model, participants in speeded-response tasks terminate stimulus discrimination as soon as it has run to completion or as soon as a predetermined time deadline has arrived, whichever comes first. Speed is traded for accuracy by varying the time deadlines; short deadlines yield fast but sometimes inaccurate responses, whereas long deadlines allow for slow, accurate responses. A new prediction of this model, based on a comparison of reaction time distributions, was derived and tested in experiments involving the joint manipulation of speed stress and stimulus discriminability. Clear violations of this prediction were observed when participants made relative brightness judgments (Experiment 1) and when they made lexical decisions (Experiment 2), rejecting both the deadline model and the fast-guess model. Several alternative models for speed-accuracy tradeoffs, including random-walk and accumulator models, are compatible with the results.

Adolescent↗
PubMed1997

Comparing exemplar-retrieval and decision-bound models of speeded perceptual classification.

The authors compared the exemplar-based random-walk (EBRW) model of Nosofsky and Palmeri (1997) and the decision-bound model (DBM) of Ashby and Maddox (1994; Maddox & Ashby, 1996) on their ability to predict performance in Garner's (1974) speeded classification tasks. A key question was the extent to which the models could predict facilitation in the correlated task and interference in the filtering task, in situations involving integral-dimension stimuli. To obtain rigorous constraints for model evaluation, the goal was to fit the detailed structure of the response time (RT) distribution data associated with each individual stimulus in each task. Both models yielded reasonably good global quantitative fits to the RT distribution and accuracy data. However, the DBM failed to properly characterize the interference effects in the filtering task. Apparently, a fundamental limitation of the DBM is that it predicts that the fastest RTs in the filtering task should be faster than the fastest RTs in the control task, whereas the opposite pattern was observed in our data.

Decision Making↗
PubMed2000

Misconceptions and false expectations in neutral evolution.

Neutral evolution results from random recurrent mutation and genetic drift. A small part of random evolution, that which is related to protein or DNA polymorphisms, is the subject of the Neutral Theory of Evolution. One of the foundations of this theory is the demonstration that the mutation rate (m) is equal to the substitution rate. Since both rates are independent of population size, they are independent of drift, which is dependent upon population size. Neutralists have erroneously equated the substitution rate with the fixation rate, despite the fact that they are antithetical conceptions. The neutralists then applied the random walk stochastic model to justify alleles or bases that were fixated or eliminated. In this model, once the allele or base frequencies reach the monomorphic states (values of 1.0 or 0.0), the absorbing barriers, they can no longer return to the polymorphic state. This operates in a pure mathematical model. If recurrent mutation occurs (as in biotic real systems) fixation and elimination are impossible. A population of bacteria in which m = 10(-8) base mutation (or substitution)/site/generation and the reproduction rate is 1000 cell cycle/year should replace all its genome bases in approximately 100,000 years. The expected situation for all sites is polymorphism for the four bases rather than monomorphism at 1.0 or 0.0 frequencies. If fixation and elimination of a base for more than 500,000 years are impossible, then most of the neutral theory is untenable. A new complete neutral model, which allows for recurrent substitutions, is proposed here based on recurrent mutation or substitution and drift alone. The model fits a binomial or Poisson distribution and not a geometric one, as does neutral theory.

Bacteria↗